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5. Genomic architecture and introgression shape a butterfly radiation

Author

Edelman, Nathaniel B., Frandsen, Paul B., Miyagi, Michael, Clavijo, Bernardo, Davey, John, Dikow, Rebecca B., García-Accinelli, Gonzalo, Van Belleghem, Steven M., Patterson, Nick, Neafsey, Daniel E., Challis, Richard, Kumar, Sujai, Moreira, Gilson R. P., Salazar, Camilo, Chouteau, Mathieu, Counterman, Brian A., Papa, Riccardo, Blaxter, Mark, Reed, Robert D., Dasmahapatra, Kanchon K., Kronforst, Marcus, Joron, Mathieu, Jiggins, Chris D., McMillan, W. Owen, Di Palma, Federica, Blumberg, Andrew J., Wakeley, John, Jaffe, David, and Mallet, James

Published
2019

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-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
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8. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

Author

Mandel, Jennifer R, Dikow, Rebecca B, Funk, Vicki A, Masalia, Rishi R, Staton, S Evan, Kozik, Alex, Michelmore, Richard W, Rieseberg, Loren H, and Burke, John M

Subjects
base tree, conserved, exon capture, next-generation sequencing, orthologs, phylogenomics, Crop and Pasture Production
Abstract

UnlabelledPremise of the studyThe Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. •Methods and resultsWe designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. •ConclusionsThese methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

Published
2014

13. Author Correction: 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-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
2021
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14. The impact of sequencing depth and relatedness of the reference genome in population genomic studies: A case study with two caddisfly species (Trichoptera, Rhyacophilidae, Himalopsyche)

Author

Deng, Xi‐Ling, primary, Frandsen, Paul B., additional, Dikow, Rebecca B., additional, Favre, Adrien, additional, Shah, Deep Narayan, additional, Shah, Ram Devi Tachamo, additional, Schneider, Julio V., additional, Heckenhauer, Jacqueline, additional, and Pauls, Steffen U., additional

Published
2022
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15. Developing responsible AI practices at the Smithsonian Institution.

Author

Dikow, Rebecca B., DiPietro, Corey, Trizna, Michael G., BredenbeckCorp, Hanna, Bursell, Madeline G., Ekwealor, Jenna T. B., Hodel, Richard G. J., Lopez, Nilda, Mattingly, William J. B., Munro, Jeremy, Naples, Richard M., Oubre, Candace, Robarge, Drew, Snyder, Sara, Spillane, Jennifer L., Tomerlin, Melinda Jane, Villanueva, Luis J., and White, Alexander E.

Subjects
ARTIFICIAL intelligence, MACHINE learning, CLIMATE change, CHATGPT, NATURAL language processing
Abstract

Applications of artificial intelligence (AI) and machine learning (ML) have become pervasive in our everyday lives. These applications range from the mundane (asking ChatGPT to write a thank you note) to high-end science (predicting future weather patterns in the face of climate change), but, because they rely on human-generated or mediated data, they also have the potential to perpetuate systemic oppression and racism. For museums and other cultural heritage institutions, there is great interest in automating the kinds of applications at which AI and ML can excel, for example, tasks in computer vision including image segmentation, object recognition (labelling or identifying objects in an image) and natural language processing (e.g. named-entity recognition, topic modelling, generation of word and sentence embeddings) in order to make digital collections and archives discoverable, searchable and appropriately tagged. A coalition of staff, Fellows and interns working in digital spaces at the Smithsonian Institution, who are either engaged with research using AI or ML tools or working closely with digital data in other ways, came together to discuss the promise and potential perils of applying AI and ML at scale and this work results from those conversations. Here, we present the process that has led to the development of an AI Values Statement and an implementation plan, including the release of datasets with accompanying documentation to enable these data to be used with improved context and reproducibility (dataset cards). We plan to continue releasing dataset cards and for AI and ML applications, model cards, in order to enable informed usage of Smithsonian data and research products. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Let the Records Show: Attribution of Scientific Credit in Natural History Collections.

Author

Dikow, Rebecca B., Ekwealor, Jenna T. B., Mattingly, William J. B., Trizna, Michael G., Harmon, Elizabeth, Dikow, Torsten, Arias, Carlos F., Hodel, Richard G. J., Spillane, Jennifer, Tsuchiya, Mirian T. N., Villanueva, Luis, White, Alexander E., Bursell, Madeline G., Curry, Tiana, Inema, Christelle, and Geronimo-Anctil, Kayla

Subjects
*NATURAL history, *WOMEN in science, *CLIMATE research, *ACCOUNT books, *DIGITAL preservation, *COLLECTIONS, *CORPORATION reports
Abstract

Premise of research. Natural history collections are essential resources for taxonomy, systematics, and ecological and climate change research. Mass digitization of these collections provides the opportunity to study broad biological patterns among specimens and their associated metadata at a scale that was previously impossible. The specimen metadata can also be used to study the contributions of the people that collected and identified these specimens. A proper accounting of these contributions impacts our understanding of the history of these collections and who played a role in their growth. Methodology. Here, we provide an assessment of the scientific contributions of past women in science at the Smithsonian Institution, focusing on their specimen collections and identifications. We evaluate natural history specimen collections records available from the Global Biodiversity Information Facility and Smithsonian annual reports, volumes dating to the founding of the Smithsonian in 1846. Pivotal results. We identify 40 women with specimen collections or identifications, with a total of more than 120,000 total specimens attributed to them. In cases where specimens are not yet digitized, we are able to learn more about the women's contributions using annual reports, which provide a richer picture of their work at the Smithsonian. This work relies on collaboration as well as deep institutional knowledge. We also release a semantic search application, which allows users to search the Smithsonian annual reports. Conclusions. Collections records are a rich resource, but there are significant barriers to accurate specimen attribution, which disproportionately affect women collectors and determiners. We propose ways that we might document these problems at scale and remedy cases of misattribution in digital repositories of record. [ABSTRACT FROM AUTHOR]

Published
2023
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18. Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes

Author

Kawahara, Akito Y., primary, Storer, Caroline G., additional, Markee, Amanda, additional, Heckenhauer, Jacqueline, additional, Powell, Ashlyn, additional, Plotkin, David, additional, Hotaling, Scott, additional, Cleland, Timothy P., additional, Dikow, Rebecca B., additional, Dikow, Torsten, additional, Kuranishi, Ryoichi B., additional, Messcher, Rebeccah, additional, Pauls, Steffen U., additional, Stewart, Russell J., additional, Tojo, Koji, additional, and Frandsen, Paul B., additional

Published
2022
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21. First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing

Author

Li, Xuankun, primary, Ellis, Emily, additional, Plotkin, David, additional, Imada, Yume, additional, Yago, Masaya, additional, Heckenhauer, Jacqueline, additional, Cleland, Timothy P, additional, Dikow, Rebecca B, additional, Dikow, Torsten, additional, Storer, Caroline G, additional, Kawahara, Akito Y, additional, and Frandsen, Paul B, additional

Published
2021
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23. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Author

Czech Science Foundation, National Science Foundation (US), W. Harry Feinstone Center for Genomic Research, Freie Universität Berlin, Ministerio de Economía y Competitividad (España), Jones, Katy E. [0000-0003-3728-0408], Fér, Tomáš [0000-0002-0126-3684], Schmickl, Roswitha E. [0000-0002-0632-5143], Dikow, Rebecca B. [0000-0001-9668-3683], Funk, Vicki A. [0000-0002-7975-1450], Herrando Moraira, Sonia [0000-0002-0488-5112], Kilian, Norbert [0000-0003-0890-4373], Siniscalchi, Carolina M. [0000-0003-3349-5081], Susanna de la Serna, Alfonso [0000-0003-4717-9063], Slovák, Marek [0000-0001-9917-3099], Watson, Linda [0000-0001-6098-779X], Mandel, Jennifer R. [0000-0003-3539-2991], Jones, Katy E., Fér, Tomáš, Schmickl, Roswitha E., Dikow, Rebecca B., Funk, Vicki A., Herrando Moraira, Sonia, Kilian, Norbert, Siniscalchi, Carolina M., Susanna de la Serna, Alfonso, Slovák, Marek, Thapa, Ramhari, Watson, Linda, Mandel, Jennifer R., Czech Science Foundation, National Science Foundation (US), W. Harry Feinstone Center for Genomic Research, Freie Universität Berlin, Ministerio de Economía y Competitividad (España), Jones, Katy E. [0000-0003-3728-0408], Fér, Tomáš [0000-0002-0126-3684], Schmickl, Roswitha E. [0000-0002-0632-5143], Dikow, Rebecca B. [0000-0001-9668-3683], Funk, Vicki A. [0000-0002-7975-1450], Herrando Moraira, Sonia [0000-0002-0488-5112], Kilian, Norbert [0000-0003-0890-4373], Siniscalchi, Carolina M. [0000-0003-3349-5081], Susanna de la Serna, Alfonso [0000-0003-4717-9063], Slovák, Marek [0000-0001-9917-3099], Watson, Linda [0000-0001-6098-779X], Mandel, Jennifer R. [0000-0003-3539-2991], Jones, Katy E., Fér, Tomáš, Schmickl, Roswitha E., Dikow, Rebecca B., Funk, Vicki A., Herrando Moraira, Sonia, Kilian, Norbert, Siniscalchi, Carolina M., Susanna de la Serna, Alfonso, Slovák, Marek, Thapa, Ramhari, Watson, Linda, and Mandel, Jennifer R.

Abstract

[Premise] Hybrid capture with high‐throughput sequencing (Hyb‐Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family‐specific Hyb‐Seq probe set and the outcomes of different phylogenetic analyses are investigated here.[ [Methods] Hyb‐Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non‐paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. [Results] Alignments of the Asteraceae family‐wide Hyb‐Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. [Discussion] The approach used to build a Hyb‐Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb‐Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage‐specific.

Published
2019

24. Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera)

Author

Olsen, Lindsey K, primary, Heckenhauer, Jacqueline, additional, Sproul, John S, additional, Dikow, Rebecca B, additional, Gonzalez, Vanessa L, additional, Kweskin, Matthew P, additional, Taylor, Adam M, additional, Wilson, Seth B, additional, Stewart, Russell J, additional, Zhou, Xin, additional, Holzenthal, Ralph, additional, Pauls, Steffen U, additional, and Frandsen, Paul B, additional

Published
2021
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27. Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-making Caddisflies (Insecta: Trichoptera)

Author

Olsen, Lindsey K., primary, Heckenhauer, Jacqueline, additional, Sproul, John S., additional, Dikow, Rebecca B., additional, Gonzalez, Vanessa L., additional, Kweskin, Matthew P., additional, Taylor, Adam M., additional, Wilson, Seth B., additional, Stewart, Russell J., additional, Zhou, Xin, additional, Holzenthal, Ralph, additional, Pauls, Steffen U., additional, and Frandsen, Paul B., additional

Published
2020
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30. Additional file 8 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 8: Table S9. Transposable elements (TE) found in Hyposter didymator segments, IVSPERs and neighboring regions. The LOLA package [86] was used to assess if some particular TE were enriched close to viral circles or IVSPER. Genomics positions were enlarged to 10 kbp at each segments ends and sampled against 1000 other similar regions from the genome, then used it a random reference. LOLA identifies overlaps and calculates enrichment for each TE. For each pairwise comparison, a series of columns describe the results of the statistical test (pvalueLog: -log10(pvalue) from the fisher’s exact result; oddsRatio: result from the fisher’s exact test; q-value transformation to provide false discovery rate (FDR) scores automatically). Some TE are enriched around viral locations, but after FDR correction, nothing was significant.

Published
2020
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31. Additional file 10 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 10:. DRJs analysis. Figure S3. Examples of the different types of DRJ position. a. Proviral segment with two copies of a single direct repeat (DRJ1L and DRJ1R), one at each end of the segment. b. Proviral segment with two distinct repeated sequences (DRJ1, in yellow and DRJ2, in green), each present in two copies (DRJ1L and DRJ1R, DRJ2L and DRJ2R). c. Proviral segment with two repeated sequences, each present in two or more copies. DRJ1s in yellow, DRJ2s in green, HdIV genes represented by arrows. Table S11. DNA motifs found in the direct repeated sequences flanking the IV segments inserted in wasp genomes. Analysis was performed using the DNAMINDA2 webserver ( http://bmbl.sdstate.edu/DMINDA2/annotate.php ); the input dataset was composed of 99 DRJ sequences (right junctions of HdIV and CsIV segments). A total of 89 motifs were obtained; only those whose occurrence exceed 70% of the DRJs are reported. Table S12. Result of genome search using motifs predicted with DMINDA 2.0 webserver. Occurrence rate of motifs predicted with DMINDA 2.0 webserver in DRJs and whole genome sequences. Each of the two motifs was search among the 6 bp kmers present in the whole genome (201,969,604) and in the DRJs (33,930). The significance was evaluated using a Chi2 (taking into account the ratio of these motifs / all the other motifs in the DRJS and in the genome).

Published
2020
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32. Additional file 9 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 9: Table S10. List of direct repeat junctions (DRJ) found at the ends or within proviral segments genes identified in Hyposoter didymator and Campoletis sonorensis genome scaffolds. Are indicated the scaffold name, the name of the proviral segment, its length and position in the scaffold, the name of the DRJ, its size and position in the scaffold and the DRJ sequence. Nucleotide identities are indicated for each pair of DRJ.

Published
2020
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33. Additional file 6 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 6: Figure S1. H. didymator proviral loci corresponding to two segments previously described as “distinct” but sharing part of their sequence [36]. Segments Hd2a (GenBank: KJ586332.1) and Hd2b (GenBank: KJ586327.1) co-localize in the same genome locus here named Hd2; segments Hd11a (KJ586322.1) and Hd11b (KJ586302.1) co-localize in the same genome locus here named Hd11; Hd17a (KJ586314.1) and Hd17b (KJ586316.1) co-localize in the same genome locus here named Hd17; Hd20a (KJ586312.1) and Hd20b (KJ586297.1) co-localize in the same genome locus here named Hd20; Hd26a (KJ586301.1) and Hd26b (KJ586306.1) co-localize in the same genome locus here named Hd26; and finally, Hd31 (KJ586299.1) and Hd34 (KJ586295.1) co-localize in the same genome locus here named Hd31-34. Each proviral locus was characterized by the presence of two different direct repeated sequences (DRJ1 and DRJ2) at the extremities of each of the overlapping segments. Scale bar: 1000 nt.

Published
2020
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34. Additional file 5 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 5: Table S7. List of ichnoviral genes identified in Hyposoter didymator and Campoletis sonorensis genome scaffolds containing at least on ichnovirus sequence. Are indicated the scaffold name, the name of the proviral segment or of the Ichnovirus structural protein encoding region (IVSPER) found in the scaffold, its length and position in the scaffold, the name of the gene, its position in the scaffold, if it contains or not introns, the size of the predicted protein, then the NCBI blast P search results (NCBI accession number and ID of the best match, the blast P e-value and the percentage of identities). Last column indicates comments, or notes reporting discrepancies in the genomic sequence compared with the original CDS sequence in NCBI database.

Published
2020
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35. Additional file 4 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 4: Table S6. List of scaffolds in Hyposoter didymator and Campoletis sonorensis genomes containing at least on ichnovirus sequence. Are indicated the scaffold name and length, the name of the proviral segment or of the Ichnovirus structural protein encoding region (IVSPER) found in the scaffold, its length and position in the scaffold, the name of the direct repeats flanking the segment or within the segment, and the name of the genes predicted in each viral locus. DRJ, direct repeat junction; R, right; L, left; int, internal.

Published
2020
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36. Additional file 2 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 2:. Orthogroups analyses. Table S2. Orthofinder clustering metrics. G50: cluster size at which 50% of genes are in an orthogroup (OG) of that size or greater. O50: fewest number of orthogroups required to reach G50; G50 (assigned genes) = 16; G50 (all genes) = 14; O50 (assigned genes) = 3063; O50 (all genes) = 4112. Species carrying a PDV are indicated with an asterisk. Species carrying polydnaviruses are indicated by asterisks. Table S3. Number of orthogroups shared by each species-pair (i.e. the number of orthogroups which contain at least one gene from each of the species-pairs). Species carrying a PDV are indicated with an asterisk. Table S4. Number of species-specific orthogroups. Number of orthogroups specific to one or groups of species.

Published
2020
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37. Additional file 3 of Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

Author

Legeai, Fabrice, Santos, Bernardo F., Robin, Stéphanie, Bretaudeau, Anthony, Dikow, Rebecca B., Lemaitre, Claire, Jouan, Véronique, Ravallec, Marc, Jean-Michel Drezen, Tagu, Denis, Baudat, Frédéric, Gabor Gyapay, Zhou, Xin, Shanlin Liu, Webb, Bruce A., Brady, Seán G., and Volkoff, Anne-Nathalie

Abstract

Additional file 3:. Table S5. Synteny blocks between pairwise comparisons of multiple parasitoid genomes. Synteny blocks were computed using SynChro [89], a tool based on a simple algorithm that computes Reciprocal Best-Hits (RBH) to reconstruct the backbones of the synteny blocks. Species carrying polydnaviruses are indicated by asterisks. [Ichn.]: Ichneumonid; [Braco.]: Braconid.

Published
2020
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39. Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps

Author

Legeai, Fabrice, primary, Santos, Bernardo F., additional, Robin, Stéphanie, additional, Bretaudeau, Anthony, additional, Dikow, Rebecca B., additional, Lemaitre, Claire, additional, Jouan, Véronique, additional, Ravallec, Marc, additional, Drezen, Jean-Michel, additional, Tagu, Denis, additional, Gyapay, Gabor, additional, Zhou, Xin, additional, Liu, Shanlin, additional, Webb, Bruce A., additional, Brady, Seán G., additional, and Volkoff, Anne-Nathalie, additional

Published
2019
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40. An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Author

Jones, Katy E., primary, Fér, Tomáš, additional, Schmickl, Roswitha E., additional, Dikow, Rebecca B., additional, Funk, Vicki A., additional, Herrando‐Moraira, Sonia, additional, Johnston, Paul R., additional, Kilian, Norbert, additional, Siniscalchi, Carolina M., additional, Susanna, Alfonso, additional, Slovák, Marek, additional, Thapa, Ramhari, additional, Watson, Linda E., additional, and Mandel, Jennifer R., additional

Published
2019
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41. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa)

Author

Ohdera, Aki, primary, Ames, Cheryl L, additional, Dikow, Rebecca B, additional, Kayal, Ehsan, additional, Chiodin, Marta, additional, Busby, Ben, additional, La, Sean, additional, Pirro, Stacy, additional, Collins, Allen G, additional, Medina, Mónica, additional, and Ryan, Joseph F, additional

Published
2019
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43. The Compositae Tree of Life in the age of phylogenomics

Author

Mandel, Jennifer R., Barker, Michael S., Bayer, Randall J., Dikow, Rebecca B., Gao, Tian-Gang, Jones, K.E., Keeley, Sterling, Kilian, Norbert, Ma, Hong, Siniscalchi, Carolina M., Susanna de la Serna, Alfonso, Thapa, Ramhari, Watson, Linda, Funk, Vicki A., Smithsonian Institution, W. Harry Feinstone Center for Genomic Research, National Museum of Natural History Smithsonian Institution, and Smithsonian Institute for Biodiversity Genomics

Subjects
Phylogenetics, Sequence capture, Gene-tree, Next-generation sequencing, Nuclear, Genomes, Chloroplast, Hyb-Seq, Transcriptomes
Abstract

6 p., figuras -- Contiene material suplementario, Comprising more than 25 000 species, the Sunflower Family (Compositae or Asteraceae) is the largest family of flowering plants. Many of its lineages have experienced recent and rapid radiations, and the family has a deep and widespread history of large-scale gene duplications and polyploidy. Many of the most important evolutionary questions about the family's diversity remain unanswered due to poor resolution and lack of support for major nodes of the phylogeny. Our group has employed a phylogenomics approach using Hyb-Seq that includes sequencing ∼1000 low-copy number nuclear markers, plus partial plastomes for large numbers of species. Here we discuss our progress to date and present two phylogenies comprising nine subfamilies and 25 tribes using concatenated and coalescence-based analyses. We discuss future plans for incorporating high-quality reference genomes and transcriptomes to advance systematic and evolutionary studies in the Compositae. While we have made great strides toward developing tools for employing phylogenomics and resolving relationships within Compositae, much work remains. Recently formed global partnerships will work to solve the unanswered evolutionary questions for this megafamily., The authors thank the Undersecretary for Science, Smithsonian Institution, for the Next Generation Sequencing SmallGrant to VAF. This research was also supported in part by the W. Harry Feinstone Center for Genomic Research,University of Memphis. Portions of the computational workwere conducted in and with the support of the L.A.B. facilities of the National Museum of Natural History and the newlyorganized Smithsonian Institute for Biodiversity Genomics.CMS is supported by a FAPESP scholarship (2016/12446-1).

Published
2017

44. Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor).

Author

Tsuchiya, Mirian T N, Dikow, Rebecca B, Koepfli, Klaus-Peter, Frandsen, Paul B, Rockwood, Larry L, and Maldonado, Jesús E

Subjects
*RACCOON, *NUCLEOTIDE sequencing, *GENES, *CLIMATE change, *GENOMES
Abstract

Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection. [ABSTRACT FROM AUTHOR]

Published
2021
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45. The Compositae Tree of Life in the age of phylogenomics

Author

Mandel, Jennifer R., primary, Barker, Michael S., additional, Bayer, Randall J., additional, Dikow, Rebecca B., additional, Gao, Tian‐Gang, additional, Jones, Katy E., additional, Keeley, Sterling, additional, Kilian, Norbert, additional, Ma, Hong, additional, Siniscalchi, Carolina M., additional, Susanna, Alfonso, additional, Thapa, Ramhari, additional, Watson, Linda, additional, and Funk, Vicki A., additional

Published
2017
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46. The Compositae Tree of Life in the age of phylogenomics

Author

Smithsonian Institution, W. Harry Feinstone Center for Genomic Research, National Museum of Natural History Smithsonian Institution, Smithsonian Institute for Biodiversity Genomics, Mandel, Jennifer R., Barker, Michael S., Bayer, Randall J., Dikow, Rebecca B., Gao, Tian-Gang, Jones, K.E., Keeley, Sterling, Kilian, Norbert, Ma, Hong, Siniscalchi, Carolina M., Susanna de la Serna, Alfonso, Thapa, Ramhari, Watson, Linda, Funk, Vicki A., Smithsonian Institution, W. Harry Feinstone Center for Genomic Research, National Museum of Natural History Smithsonian Institution, Smithsonian Institute for Biodiversity Genomics, Mandel, Jennifer R., Barker, Michael S., Bayer, Randall J., Dikow, Rebecca B., Gao, Tian-Gang, Jones, K.E., Keeley, Sterling, Kilian, Norbert, Ma, Hong, Siniscalchi, Carolina M., Susanna de la Serna, Alfonso, Thapa, Ramhari, Watson, Linda, and Funk, Vicki A.

Abstract

Comprising more than 25 000 species, the Sunflower Family (Compositae or Asteraceae) is the largest family of flowering plants. Many of its lineages have experienced recent and rapid radiations, and the family has a deep and widespread history of large-scale gene duplications and polyploidy. Many of the most important evolutionary questions about the family's diversity remain unanswered due to poor resolution and lack of support for major nodes of the phylogeny. Our group has employed a phylogenomics approach using Hyb-Seq that includes sequencing ∼1000 low-copy number nuclear markers, plus partial plastomes for large numbers of species. Here we discuss our progress to date and present two phylogenies comprising nine subfamilies and 25 tribes using concatenated and coalescence-based analyses. We discuss future plans for incorporating high-quality reference genomes and transcriptomes to advance systematic and evolutionary studies in the Compositae. While we have made great strides toward developing tools for employing phylogenomics and resolving relationships within Compositae, much work remains. Recently formed global partnerships will work to solve the unanswered evolutionary questions for this megafamily.

Published
2017

48. Reciprocal genomic evolution in the ant-fungus agricultural symbiosis

Author

Nygaard, Sanne, Hu, Haofu, Li, Cai, Schiøtt, Morten, Chen, Zhensheng, Yang, Zhikai, Xie, Qiaolin, Ma, Chunyu, Deng, Yuan, Dikow, Rebecca B., Rabeling, Christian, Nash, David Richard, Wcislo, William T., Brady, Seán G., Schultz, Ted R., Zhang, Guojie, Boomsma, Jacobus Jan, Nygaard, Sanne, Hu, Haofu, Li, Cai, Schiøtt, Morten, Chen, Zhensheng, Yang, Zhikai, Xie, Qiaolin, Ma, Chunyu, Deng, Yuan, Dikow, Rebecca B., Rabeling, Christian, Nash, David Richard, Wcislo, William T., Brady, Seán G., Schultz, Ted R., Zhang, Guojie, and Boomsma, Jacobus Jan

Abstract

The attine ant-fungus agricultural symbiosis evolved over tens of millions of years, producing complex societies with industrial-scale farming analogous to that of humans. Here we document reciprocal shifts in the genomes and transcriptomes of seven fungus-farming ant species and their fungal cultivars. We show that ant subsistence farming probably originated in the early Tertiary (55-60 MYA), followed by further transitions to the farming of fully domesticated cultivars and leaf-cutting, both arising earlier than previously estimated. Evolutionary modifications in the ants include unprecedented rates of genome-wide structural rearrangement, early loss of arginine biosynthesis and positive selection on chitinase pathways. Modifications of fungal cultivars include loss of a key ligninase domain, changes in chitin synthesis and a reduction in carbohydrate-degrading enzymes as the ants gradually transitioned to functional herbivory. In contrast to human farming, increasing dependence on a single cultivar lineage appears to have been essential to the origin of industrial-scale ant agriculture.

Published
2016

49. Reciprocal genomic evolution in the ant–fungus agricultural symbiosis

Author

Nygaard, Sanne, primary, Hu, Haofu, additional, Li, Cai, additional, Schiøtt, Morten, additional, Chen, Zhensheng, additional, Yang, Zhikai, additional, Xie, Qiaolin, additional, Ma, Chunyu, additional, Deng, Yuan, additional, Dikow, Rebecca B., additional, Rabeling, Christian, additional, Nash, David R., additional, Wcislo, William T., additional, Brady, Seán G., additional, Schultz, Ted R., additional, Zhang, Guojie, additional, and Boomsma, Jacobus J., additional

Published
2016
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50. Genome sequence and population declines in the critically endangered greater bamboo lemur (<italic>Prolemur simus</italic>) and implications for conservation.

Author

Hawkins, Melissa T. R., Culligan, Ryan R., Frasier, Cynthia L., Dikow, Rebecca B., Hagenson, Ryan, Lei, Runhua, and Louis, Edward E.

Subjects
NUCLEOTIDE sequencing, GREATER bamboo lemur, SINGLE nucleotide polymorphisms, ANIMAL population density, CLIMATE change
Abstract

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19 k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~ 900,000 to one million individuals) between approximately 60,000–90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60–90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~ 1700 km2. The decline in effective population size of 89–99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations. [ABSTRACT FROM AUTHOR]

Published
2018
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