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28 results on '"Mila, Borja"'

3. Genomic variation across the Yellow-rumped Warbler species complex

Author

Toews, David PL, Brelsford, Alan, Grossen, Christine, Mila, Borja, and Irwin, Darren E

Subjects
evolutionary genomics, hybridization, gene flow, genotyping-by-sequencing, speciation, natural selection, Genetics, Biotechnology, Human Genome, Ornithology, Zoology
Published
2016

16. Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones

Author

Fuller, Trevon L., Thomassen, Henri A., Peralvo, Manuel, Buermann, Wolfgang, Milá, Borja, Kieswetter, Charles M., Jarrín-V, Pablo, Devitt, Susan E. Cameron, Mason, Eliza, Schweizer, Rena M., Schlunegger, Jasmin, Chan, Janice, Wang, Ophelia, Schneider, Christopher J., Pollinger, John P., Saatchi, Sassan, Graham, Catherine H., Wayne, Robert K., and Smith, Thomas B.

Published
2013
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23. Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes

Author

Arida, Evy, Ashari, Hidayat, Dahruddin, Hadi, Fitriana, Yuli Sulistya, Hamidy, Amir, Irham, Mohammad, Kadarusman, Riyanto, Awal, Wiantoro, Sigit, Zein, Moch Syamsul Arifin, Hadiaty, Renny K., Apandi, Krey, Frengky, Kurnianingsih, Melmambessy, Edy H.p., Mulyadi, Ohee, Henderite L., Saidin, Salamuk, Ayub, Sauri, Sopian, Suparno, Supriatna, Nanang, Suruwaky, Amir M., Laksono, Wahyudi Tri, Warikar, Evie L., Wikanta, Hadi, Yohanita, Aksamina M., Slembrouck, Jacques, Legendre, Marc, Gaucher, Philippe, Cochet, Christophe, Delrieu‐trottin, Erwan, Thébaud, Christophe, Mila, Borja, Fouquet, Antoine, Borisenko, Alex, Steinke, Dirk, Hocdé, Régis, Semiadi, Gono, Pouyaud, Laurent, Hubert, Nicolas, Arida, Evy, Ashari, Hidayat, Dahruddin, Hadi, Fitriana, Yuli Sulistya, Hamidy, Amir, Irham, Mohammad, Kadarusman, Riyanto, Awal, Wiantoro, Sigit, Zein, Moch Syamsul Arifin, Hadiaty, Renny K., Apandi, Krey, Frengky, Kurnianingsih, Melmambessy, Edy H.p., Mulyadi, Ohee, Henderite L., Saidin, Salamuk, Ayub, Sauri, Sopian, Suparno, Supriatna, Nanang, Suruwaky, Amir M., Laksono, Wahyudi Tri, Warikar, Evie L., Wikanta, Hadi, Yohanita, Aksamina M., Slembrouck, Jacques, Legendre, Marc, Gaucher, Philippe, Cochet, Christophe, Delrieu‐trottin, Erwan, Thébaud, Christophe, Mila, Borja, Fouquet, Antoine, Borisenko, Alex, Steinke, Dirk, Hocdé, Régis, Semiadi, Gono, Pouyaud, Laurent, and Hubert, Nicolas

Abstract

Biodiversity knowledge is widely heterogeneous across the Earth’s biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA‐based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multi‐disciplinary expedition to the Bird’s Head Peninsula (West Papua, Indonesia) conducted between October 17th and November 20th 2014. This expedition resulted in the assembly of 1,005 vertebrate DNA barcodes. Based on the use of multiple species‐delimitation methods (GMYC, PTP, RESL, ABGD), 264 Molecular Operational Taxonomic Units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird’s Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

Published
2021
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24. Evolution of long-distance migration in and historical biogeography of Catharus thrushes: a molecular phylogenetic approach

Author

Outlaw, Diana C., Voelker, Gary, Mila, Borja, and Girman, Derek J.

Subjects
Thrushes -- Research, Thrushes -- Natural history, Biological sciences
Abstract

We addressed the evolution of long-distance migration in and the historical biogeography of Catharus thrushes within a phylogenetic framework. Catharus thrushes are a Nearctic-Neotropical genus consisting of five migrant and seven resident species. We reconstructed a molecular phylogeny using a combined analysis of cytochrome-b and ND2 genes. Phylogenetic reconstructions indicate the nonmonophyly of migratory Catharus species. The Neotropics are the most likely ancestral geographic area for the entire lineage, and migratory species are sister to resident taxa whose ranges are restricted to Central America, Mexico, or both. Resident behavior may be ancestral within the lineage, with migratory behavior evolving three times, although confidence in those reconstructions is equivocal in many cases. However, uncertainty in ancestral character states presents an interesting scenario including potential drop-offs of resident species from migratory ancestors. Received 3 January 2002, accepted 2 February 2003.

Published
2003

25. 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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26. Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species

Author

Caminer, Marcel A., Mila, Borja, Jansen, Martin, Fouquet, Antoine, Venegas, Pablo J., Chavez, German, Lougheed, Stephen C., Ron, Santiago R., Caminer, Marcel A., Mila, Borja, Jansen, Martin, Fouquet, Antoine, Venegas, Pablo J., Chavez, German, Lougheed, Stephen C., and Ron, Santiago R.

Abstract

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relationships and species boundaries of two Amazonian species of the Dendropsophus leucophyllatus species group: D. leucophyllatus and D. triangulum. Our results uncovered the existence of five confirmed and four unconfirmed candidate species. Among the confirmed candidate species, three have available names: Dendropsophus leucophyllatus, Dendropsophus triangulum, and Dendropsophus reticulatus, this last being removed from the synonymy of D. triangulum. A neotype of D. leucophyllatus is designated. We describe the remaining two confirmed candidate species, one from Bolivia and another from Peru. All confirmed candidate species are morphologically distinct and have much smaller geographic ranges than those previously reported for D. leucophyllatus and D. triangulum sensu lato. Dendropsophus leucophyllatus sensu stricto occurs in the Guianan region. Dendropsophus reticulatus comb. nov. corresponds to populations in the Amazon basin of Brazil, Ecuador, and Peru previously referred to as D. triangulum. Dendropsophus triangulum sensu stricto is the most widely distributed species; it occurs in Amazonian Ecuador, Peru and Brazil, reaching the state of Para A. We provide accounts for all described species including an assessment of their conservation status.

Published
2017
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27. A bird’s white-eye view on avian sex chromosome evolution

Author

Leroy, Thibault, Anselmetti, Yoann, Tilak, Marie-Ka, Bérard, Sèverine, Csukonyi, Laura, Gabrielli, Maëva, Scornavacca, Céline, Milá, Borja, Thébaud, Christophe, and Nabholz, Benoit

Subjects
Archaeology, CC1-960, Science
Abstract

Chromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms (N/S) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.

Published
2021
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28. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes.

Author

Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, and Hubert N

Subjects
Animals, Birds genetics, DNA, Indonesia, Phylogeny, Vertebrates genetics, Biodiversity, DNA Barcoding, Taxonomic
Abstract

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed., (© 2021 John Wiley & Sons Ltd.)

Published
2021
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