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33 results on '"Brumfield, Robb T"'

1. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

Author: Salter, Jessie F., Hosner, Peter A., Tsai, Whitney L. E., McCormack, John E., Braun, Edward L., Kimball, Rebecca T., Brumfield, Robb T., Faircloth, Brant C., Salter, Jessie F., Hosner, Peter A., Tsai, Whitney L. E., McCormack, John E., Braun, Edward L., Kimball, Rebecca T., Brumfield, Robb T., and Faircloth, Brant C.
Abstract: As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncerta
Published: 2022

2. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

Author: Salter, Jessie F., Hosner, Peter A., Tsai, Whitney L. E., McCormack, John E., Braun, Edward L., Kimball, Rebecca T., Brumfield, Robb T., Faircloth, Brant C., Salter, Jessie F., Hosner, Peter A., Tsai, Whitney L. E., McCormack, John E., Braun, Edward L., Kimball, Rebecca T., Brumfield, Robb T., and Faircloth, Brant C.
Abstract: As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncerta
Published: 2022

3. Author Correction: Dense sampling of bird diversity increases power of comparative genomics.

Author: Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, Krone, Oliver, Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver
Abstract: In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.
Published: 2021

4. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Author: Leite, Rafael N., Kimball, Rebecca T., Braun, Edward L., Derryberry, Elizabeth P., Hosner, Peter A., Derryberry, Graham E., Anciaes, Marina, McKay, Jessica S., Aleixo, Alexandre, Ribas, Camila C., Brumfield, Robb T., Cracraft, Joel, Leite, Rafael N., Kimball, Rebecca T., Braun, Edward L., Derryberry, Elizabeth P., Hosner, Peter A., Derryberry, Graham E., Anciaes, Marina, McKay, Jessica S., Aleixo, Alexandre, Ribas, Camila C., Brumfield, Robb T., and Cracraft, Joel
Abstract: Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia Glade was an exception to the generally high support we observed; the topology of this Glade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite
Published: 2021

5. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Author: Leite, Rafael N., Kimball, Rebecca T., Braun, Edward L., Derryberry, Elizabeth P., Hosner, Peter A., Derryberry, Graham E., Anciaes, Marina, McKay, Jessica S., Aleixo, Alexandre, Ribas, Camila C., Brumfield, Robb T., Cracraft, Joel, Leite, Rafael N., Kimball, Rebecca T., Braun, Edward L., Derryberry, Elizabeth P., Hosner, Peter A., Derryberry, Graham E., Anciaes, Marina, McKay, Jessica S., Aleixo, Alexandre, Ribas, Camila C., Brumfield, Robb T., and Cracraft, Joel
Abstract: Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia Glade was an exception to the generally high support we observed; the topology of this Glade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite
Published: 2021

6. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
Published: 2020
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7. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
Published: 2020
Full Text: View/download PDF

8. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
Published: 2020
Full Text: View/download PDF

9. Dense sampling of bird diversity increases power of comparative genomics.

Author: Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, Krone, Oliver, Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
Published: 2020

10. Dense sampling of bird diversity increases power of comparative genomics.

Author: Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, Krone, Oliver, Feng, Shaohong, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C, Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S, Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M, Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A, Brumfield, Robb T, Christidis, Les, Bertelsen, Mads F, Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C, Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J, Cowen, Saul J, Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A, Fuchs, Jérôme, Bunce, Michael, Burt, David W, Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J, Ryan, Peter G, Jønsson, Knud Andreas, Jamieson, Ian G, da Fonseca, Rute R, Braun, Edward L, Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B, van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N, Clark, Andrew G, Fitzpatrick, John W, Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B, Edwards, Scott V, Foote, Dustin J, Shakya, Subir B, Sheldon, Frederick H, Vignal, Alain, Soares, André ER, Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O, Székely, Tamás, Liu, Yang, Campana, Michael G, Corvelo, André, Fleischer, Robert C, Rutherford, Kim M, Gemmell, Neil J, Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P, and Krone, Oliver
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
Published: 2020

11. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
Published: 2020
Full Text: View/download PDF

12. Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

Author: Cadena, Carlos Daniel, Cuervo, Andrés M., Céspedes, Laura N., Bravo, Gustavo A., Krabbe, Niels, Schulenberg, Thomas S., Derryberry, Graham E., Silveira, Luis Fabio, Derryberry, Elizabeth P., Brumfield, Robb T., Fjeldså, Jon, Cadena, Carlos Daniel, Cuervo, Andrés M., Céspedes, Laura N., Bravo, Gustavo A., Krabbe, Niels, Schulenberg, Thomas S., Derryberry, Graham E., Silveira, Luis Fabio, Derryberry, Elizabeth P., Brumfield, Robb T., and Fjeldså, Jon
Abstract: We studied the phylogeny, biogeography, and diversification of suboscine passerines in the genus Scytalopus (Rhinocryptidae), a widespread, species-rich, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla and consists of 3 main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and eastern Brazil are sister to each other. Despite their confusing uniformity in plumage coloration, body shape, and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared with those of other birds, suggesting rapid non-adaptive diversification in the group. We attribute this to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to clarify their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.
Published: 2020

13. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Hart Reeve, Andrew, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., Dacosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Hart Reeve, Andrew, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sánchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Ângela M., Eckhart, Leopold, Fjeldså, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jérôme, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jønsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, André E. R., Shapiro, Beth, González-Solís, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalén, Love, Urrutia, Araxi O., Székely, Tamás, Liu, Yang, Campana, Michael G., Corvelo, André, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Milá, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Ángela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., Dacosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Published: 2020

14. Extensive paraphyly in the typical owl family (Strigidae)

Author: Salter, Jessie F., Oliveros, Carl H., Hosner, Peter A., Manthey, Joseph D., Robbins, Mark B., Moyle, Robert G., Brumfield, Robb T., Faircloth, Brant C., Salter, Jessie F., Oliveros, Carl H., Hosner, Peter A., Manthey, Joseph D., Robbins, Mark B., Moyle, Robert G., Brumfield, Robb T., and Faircloth, Brant C.
Abstract: The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.
Published: 2020

15. Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

Author: Cadena, Carlos Daniel, Cuervo, Andrés M., Céspedes, Laura N., Bravo, Gustavo A., Krabbe, Niels, Schulenberg, Thomas S., Derryberry, Graham E., Silveira, Luis Fabio, Derryberry, Elizabeth P., Brumfield, Robb T., Fjeldså, Jon, Cadena, Carlos Daniel, Cuervo, Andrés M., Céspedes, Laura N., Bravo, Gustavo A., Krabbe, Niels, Schulenberg, Thomas S., Derryberry, Graham E., Silveira, Luis Fabio, Derryberry, Elizabeth P., Brumfield, Robb T., and Fjeldså, Jon
Abstract: We studied the phylogeny, biogeography, and diversification of suboscine passerines in the genus Scytalopus (Rhinocryptidae), a widespread, species-rich, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla and consists of 3 main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and eastern Brazil are sister to each other. Despite their confusing uniformity in plumage coloration, body shape, and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared with those of other birds, suggesting rapid non-adaptive diversification in the group. We attribute this to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to clarify their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade.
Published: 2020

16. Dense sampling of bird diversity increases power of comparative genomics

Author: Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, Zhang, Guojie, Feng, Shaohong, Stiller, Josefin, Deng, Yuan, Armstrong, Joel, Fang, Qi, Reeve, Andrew Hart, Xie, Duo, Chen, Guangji, Guo, Chunxue, Faircloth, Brant C., Petersen, Bent, Wang, Zongji, Zhou, Qi, Diekhans, Mark, Chen, Wanjun, Andreu-Sanchez, Sergio, Margaryan, Ashot, Howard, Jason Travis, Parent, Carole, Pacheco, George, Sinding, Mikkel-Holger S., Puetz, Lara, Cavill, Emily, Ribeiro, Angela M., Eckhart, Leopold, Fjeldsa, Jon, Hosner, Peter A., Brumfield, Robb T., Christidis, Les, Bertelsen, Mads F., Sicheritz-Ponten, Thomas, Tietze, Dieter Thomas, Robertson, Bruce C., Song, Gang, Borgia, Gerald, Claramunt, Santiago, Lovette, Irby J., Cowen, Saul J., Njoroge, Peter, Dumbacher, John Philip, Ryder, Oliver A., Fuchs, Jerome, Bunce, Michael, Burt, David W., Cracraft, Joel, Meng, Guanliang, Hackett, Shannon J., Ryan, Peter G., Jonsson, Knud Andreas, Jamieson, Ian G., da Fonseca, Rute R., Braun, Edward L., Houde, Peter, Mirarab, Siavash, Suh, Alexander, Hansson, Bengt, Ponnikas, Suvi, Sigeman, Hanna, Stervander, Martin, Frandsen, Paul B., van der Zwan, Henriette, van der Sluis, Rencia, Visser, Carina, Balakrishnan, Christopher N., Clark, Andrew G., Fitzpatrick, John W., Bowman, Reed, Chen, Nancy, Cloutier, Alison, Sackton, Timothy B., Edwards, Scott V., Foote, Dustin J., Shakya, Subir B., Sheldon, Frederick H., Vignal, Alain, Soares, Andre E. R., Shapiro, Beth, Gonzalez-Solis, Jacob, Ferrer-Obiol, Joan, Rozas, Julio, Riutort, Marta, Tigano, Anna, Friesen, Vicki, Dalen, Love, Urrutia, Araxi O., Szekely, Tamas, Liu, Yang, Campana, Michael G., Corvelo, Andre, Fleischer, Robert C., Rutherford, Kim M., Gemmell, Neil J., Dussex, Nicolas, Mouritsen, Henrik, Thiele, Nadine, Delmore, Kira, Liedvogel, Miriam, Franke, Andre, Hoeppner, Marc P., Krone, Oliver, Fudickar, Adam M., Mila, Borja, Ketterson, Ellen D., Fidler, Andrew Eric, Friis, Guillermo, Parody-Merino, Angela M., Battley, Phil F., Cox, Murray P., Lima, Nicholas Costa Barroso, Prosdocimi, Francisco, Parchman, Thomas Lee, Schlinger, Barney A., Loiselle, Bette A., Blake, John G., Lim, Haw Chuan, Day, Lainy B., Fuxjager, Matthew J., Baldwin, Maude W., Braun, Michael J., Wirthlin, Morgan, Dikow, Rebecca B., Ryder, T. Brandt, Camenisch, Glauco, Keller, Lukas F., DaCosta, Jeffrey M., Hauber, Mark E., Louder, Matthew I. M., Witt, Christopher C., McGuire, Jimmy A., Mudge, Joann, Megna, Libby C., Carling, Matthew D., Wang, Biao, Taylor, Scott A., Del-Rio, Glaucia, Aleixo, Alexandre, Vasconcelos, Ana Tereza Ribeiro, Mello, Claudio V., Weir, Jason T., Haussler, David, Li, Qiye, Yang, Huanming, Wang, Jian, Lei, Fumin, Rahbek, Carsten, Gilbert, M. Thomas P., Graves, Gary R., Jarvis, Erich D., Paten, Benedict, and Zhang, Guojie
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
Published: 2020
Full Text: View/download PDF

17. Extensive paraphyly in the typical owl family (Strigidae)

Author: Salter, Jessie F., Oliveros, Carl H., Hosner, Peter A., Manthey, Joseph D., Robbins, Mark B., Moyle, Robert G., Brumfield, Robb T., Faircloth, Brant C., Salter, Jessie F., Oliveros, Carl H., Hosner, Peter A., Manthey, Joseph D., Robbins, Mark B., Moyle, Robert G., Brumfield, Robb T., and Faircloth, Brant C.
Abstract: The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.
Published: 2020

18. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019
Full Text: View/download PDF

19. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019
Full Text: View/download PDF

20. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019
Full Text: View/download PDF

21. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019
Full Text: View/download PDF

22. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andres M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luis Fabio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyper-diverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019
Full Text: View/download PDF

23. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Keith Barker, F., Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Terry Chesser, R., Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Townsend Peterson, A., Robbins, Mark B., Sheldon, Frederick H., Silveira, Luís Fábio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Keith Barker, F., Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Terry Chesser, R., Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Townsend Peterson, A., Robbins, Mark B., Sheldon, Frederick H., Silveira, Luís Fábio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019

24. Earth history and the passerine superradiation

Author: Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Keith Barker, F., Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Terry Chesser, R., Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Townsend Peterson, A., Robbins, Mark B., Sheldon, Frederick H., Silveira, Luís Fábio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., Faircloth, Brant C., Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Keith Barker, F., Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Terry Chesser, R., Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Townsend Peterson, A., Robbins, Mark B., Sheldon, Frederick H., Silveira, Luís Fábio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.
Abstract: Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Published: 2019

25. Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

Author: Harvey, Michael G., Judy, Caroline Duffie, Seeholzer, Glenn F., Maley, James M., Graves, Gary R., Brumfield, Robb T., Harvey, Michael G., Judy, Caroline Duffie, Seeholzer, Glenn F., Maley, James M., Graves, Gary R., and Brumfield, Robb T.
Published: 2015

26. Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

Author: Harvey, Michael G., Judy, Caroline Duffie, Seeholzer, Glenn F., Maley, James M., Graves, Gary R., Brumfield, Robb T., Harvey, Michael G., Judy, Caroline Duffie, Seeholzer, Glenn F., Maley, James M., Graves, Gary R., and Brumfield, Robb T.
Published: 2015

27. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author: Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y. W., Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., da Fonseca, Rute R., Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md. Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldon, Toni, Capella-Gutierrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Cruz Schneider, Maria Paula, Prosdocimi, Francisco, Samaniego, Jose Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Nunez, Alonzo, Campos, Paula F., Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F. Keith, Jonsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alstrom, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Jun, Wang, Gilbert, M. Thomas P., Zhang, Guojie, Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y. W., Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., da Fonseca, Rute R., Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md. Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldon, Toni, Capella-Gutierrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Cruz Schneider, Maria Paula, Prosdocimi, Francisco, Samaniego, Jose Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Nunez, Alonzo, Campos, Paula F., Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F. Keith, Jonsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alstrom, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Jun, Wang, Gilbert, M. Thomas P., and Zhang, Guojie
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014
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28. Whole-genome analyses resolve early branches in the tree of life of modern birds.

Author: Jarvis, Erich D, Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, Mindell, David P, Jarvis, Erich D, Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, and Mindell, David P
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014

29. Whole-genome analyses resolve early branches in the tree of life of modern birds.

Author: Jarvis, Erich D, Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, Mindell, David P, Jarvis, Erich D, Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, and Mindell, David P
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014

30. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author: Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y W, Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., Rodrigues da Fonseca, Rute Andreia, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Terkelsen, Kasper Munch, Schierup, Mikkel Heide, Lindow, Bent Erik Kramer, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego Castruita, Jose Alfredo, Velazquez, Amhed Missael Vargas, Alfaro Nuñez, Luis Alonso, Campos, Paula, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldså, Jon, Orlando, Ludovic Antoine Alexandre, Barker, F. Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Wang, Jun, Gilbert, M Thomas P, Zhang, Guojie, Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y W, Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., Rodrigues da Fonseca, Rute Andreia, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Terkelsen, Kasper Munch, Schierup, Mikkel Heide, Lindow, Bent Erik Kramer, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego Castruita, Jose Alfredo, Velazquez, Amhed Missael Vargas, Alfaro Nuñez, Luis Alonso, Campos, Paula, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldså, Jon, Orlando, Ludovic Antoine Alexandre, Barker, F. Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Wang, Jun, Gilbert, M Thomas P, and Zhang, Guojie
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data.We recovered a highly resolved tree that confirms previously controversial sister or close relationships.We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014

31. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author: Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y W, Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., Rodrigues da Fonseca, Rute Andreia, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Terkelsen, Kasper Munch, Schierup, Mikkel Heide, Lindow, Bent Erik Kramer, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego Castruita, Jose Alfredo, Velazquez, Amhed Missael Vargas, Alfaro Nuñez, Luis Alonso, Campos, Paula, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldså, Jon, Orlando, Ludovic Antoine Alexandre, Barker, F. Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Wang, Jun, Gilbert, M Thomas P, Zhang, Guojie, Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y W, Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., Rodrigues da Fonseca, Rute Andreia, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Terkelsen, Kasper Munch, Schierup, Mikkel Heide, Lindow, Bent Erik Kramer, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego Castruita, Jose Alfredo, Velazquez, Amhed Missael Vargas, Alfaro Nuñez, Luis Alonso, Campos, Paula, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldså, Jon, Orlando, Ludovic Antoine Alexandre, Barker, F. Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Wang, Jun, Gilbert, M Thomas P, and Zhang, Guojie
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data.We recovered a highly resolved tree that confirms previously controversial sister or close relationships.We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Published: 2014

32. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

Author: McCormack, John E., Maley, James M., Hird, Sarah M., Derryberry, Elizabeth P., Graves, Gary R., Brumfield, Robb T., McCormack, John E., Maley, James M., Hird, Sarah M., Derryberry, Elizabeth P., Graves, Gary R., and Brumfield, Robb T.
Abstract: Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography. This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at low cost. We explore cases of recent divergence in four phylogenetically diverse avian systems using a method for quick and cost-effective generation of primary DNA sequence data using pyrosequencing. NGS data were processed using an analytical pipeline that reduces many reads into two called alleles per locus per individual. Using single nucleotide polymorphisms (SNPs) mined from the loci, we detected population differentiation in each of the four bird systems, including: a case of ecological speciation in rails (Rallus); a rapid postglacial radiation in the genus Junco; recent in situ speciation among hummingbirds (Trochilus) in Jamaica; and subspecies of white-crowned sparrows (Zonotrichia leucophrys) along the Pacific coast. The number of recovered loci aligning closely to chromosomal locations on the zebra finch (Taeniopygia guttata) genome was highly correlated to the size of the chromosome, suggesting that loci are randomly distributed throughout the genome. Using eight loci found in Zonotrichia and Junco lineages, we were also able to generate a species tree of these sparrow sister genera, demonstrating the potential of this method for generating data amenable to coalescent-based analysis. We discuss improvements that should enhance the method’s utility for primary data generation.
Published: 2012

33. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

Author: McCormack, John E., Maley, James M., Hird, Sarah M., Derryberry, Elizabeth P., Graves, Gary R., Brumfield, Robb T., McCormack, John E., Maley, James M., Hird, Sarah M., Derryberry, Elizabeth P., Graves, Gary R., and Brumfield, Robb T.
Abstract: Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography. This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at low cost. We explore cases of recent divergence in four phylogenetically diverse avian systems using a method for quick and cost-effective generation of primary DNA sequence data using pyrosequencing. NGS data were processed using an analytical pipeline that reduces many reads into two called alleles per locus per individual. Using single nucleotide polymorphisms (SNPs) mined from the loci, we detected population differentiation in each of the four bird systems, including: a case of ecological speciation in rails (Rallus); a rapid postglacial radiation in the genus Junco; recent in situ speciation among hummingbirds (Trochilus) in Jamaica; and subspecies of white-crowned sparrows (Zonotrichia leucophrys) along the Pacific coast. The number of recovered loci aligning closely to chromosomal locations on the zebra finch (Taeniopygia guttata) genome was highly correlated to the size of the chromosome, suggesting that loci are randomly distributed throughout the genome. Using eight loci found in Zonotrichia and Junco lineages, we were also able to generate a species tree of these sparrow sister genera, demonstrating the potential of this method for generating data amenable to coalescent-based analysis. We discuss improvements that should enhance the method’s utility for primary data generation.
Published: 2012

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33 results on '"Brumfield, Robb T"'

1. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

2. Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

3. Author Correction: Dense sampling of bird diversity increases power of comparative genomics.

4. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

5. Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

6. Dense sampling of bird diversity increases power of comparative genomics

7. Dense sampling of bird diversity increases power of comparative genomics

8. Dense sampling of bird diversity increases power of comparative genomics

9. Dense sampling of bird diversity increases power of comparative genomics.

10. Dense sampling of bird diversity increases power of comparative genomics.

11. Dense sampling of bird diversity increases power of comparative genomics

12. Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

13. Dense sampling of bird diversity increases power of comparative genomics

14. Extensive paraphyly in the typical owl family (Strigidae)

15. Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

16. Dense sampling of bird diversity increases power of comparative genomics

17. Extensive paraphyly in the typical owl family (Strigidae)

18. Earth history and the passerine superradiation

19. Earth history and the passerine superradiation

20. Earth history and the passerine superradiation

21. Earth history and the passerine superradiation

22. Earth history and the passerine superradiation

23. Earth history and the passerine superradiation

24. Earth history and the passerine superradiation

25. Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

26. Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

27. Whole-genome analyses resolve early branches in the tree of life of modern birds

28. Whole-genome analyses resolve early branches in the tree of life of modern birds.

29. Whole-genome analyses resolve early branches in the tree of life of modern birds.

30. Whole-genome analyses resolve early branches in the tree of life of modern birds

31. Whole-genome analyses resolve early branches in the tree of life of modern birds

32. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

33. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

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33 results on '"Brumfield, Robb T"'

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