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1. Specimen collection is essential for modern science.

Author

Nachman, Michael, Beckman, Elizabeth, Bowie, Rauri, Cicero, Carla, Conroy, Chris, Hayes, Tyrone, Koo, Michelle, Lacey, Eileen, Martin, Christopher, McGuire, Jimmy, Patton, James, Spencer, Carol, Wake, Marvalee, Wang, Ian, Achmadi, Anang, Álvarez-Castañeda, Sergio, Andersen, Michael, Arroyave, Jairo, Austin, Christopher, Barker, F, Barrow, Lisa, Barrowclough, George, Bates, John, Bauer, Aaron, Bell, Kayce, Bell, Rayna, Bronson, Allison, Brown, Rafe, Burbrink, Frank, Burns, Kevin, Cadena, Carlos, Cannatella, David, Castoe, Todd, Chakrabarty, Prosanta, Colella, Jocelyn, Cook, Joseph, Cracraft, Joel, Davis, Drew, Davis Rabosky, Alison, DElía, Guillermo, Dumbacher, John, Dunnum, Jonathan, Edwards, Scott, Esselstyn, Jacob, Faivovich, Julián, Fjeldså, Jon, Flores-Villela, Oscar, Ford, Kassandra, Fuchs, Jérôme, Fujita, Matthew, Good, Jeffrey, Greenbaum, Eli, Greene, Harry, Hackett, Shannon, Hamidy, Amir, Hanken, James, Haryoko, Tri, Hawkins, Melissa, Heaney, Lawrence, Hillis, David, Hollingsworth, Bradford, Hornsby, Angela, Hosner, Peter, Irham, Mohammad, Jansa, Sharon, Jiménez, Rosa, Joseph, Leo, Kirchman, Jeremy, LaDuc, Travis, Leaché, Adam, Lessa, Enrique, López-Fernández, Hernán, Mason, Nicholas, McCormack, John, McMahan, Caleb, Moyle, Robert, Ojeda, Ricardo, Olson, Link, Kin Onn, Chan, Parenti, Lynne, Parra-Olea, Gabriela, Patterson, Bruce, Pauly, Gregory, Pavan, Silvia, Peterson, A, Poe, Steven, Rabosky, Daniel, Raxworthy, Christopher, Reddy, Sushma, Rico-Guevara, Alejandro, Riyanto, Awal, Rocha, Luiz, Ron, Santiago, Rovito, Sean, Rowe, Kevin, Rowley, Jodi, Ruane, Sara, Salazar-Valenzuela, David, Shultz, Allison, and Sidlauskas, Brian

Subjects
Animals, Museums, Specimen Handling, Natural History
Abstract

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Published
2023

2. Complexity of avian evolution revealed by family-level genomes

Author

Stiller, Josefin, Feng, Shaohong, Chowdhury, Al-Aabid, Rivas-González, Iker, Duchêne, David A., Fang, Qi, Deng, Yuan, Kozlov, Alexey, Stamatakis, Alexandros, Claramunt, Santiago, Nguyen, Jacqueline M. T., Ho, Simon Y. W., Faircloth, Brant C., Haag, Julia, Houde, Peter, Cracraft, Joel, Balaban, Metin, Mai, Uyen, Chen, Guangji, Gao, Rongsheng, Zhou, Chengran, Xie, Yulong, Huang, Zijian, Cao, Zhen, Yan, Zhi, Ogilvie, Huw A., Nakhleh, Luay, Lindow, Bent, Morel, Benoit, Fjeldså, Jon, Hosner, Peter A., da Fonseca, Rute R., Petersen, Bent, Tobias, Joseph A., Székely, Tamás, Kennedy, Jonathan David, Reeve, Andrew Hart, Liker, Andras, Stervander, Martin, Antunes, Agostinho, Tietze, Dieter Thomas, Bertelsen, Mads F., Lei, Fumin, Rahbek, Carsten, Graves, Gary R., Schierup, Mikkel H., Warnow, Tandy, Braun, Edward L., Gilbert, M. Thomas P., Jarvis, Erich D., Mirarab, Siavash, and Zhang, Guojie

Published
2024
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3. Editorial: Biodiversity across Afromontane environments

Author

Hořák, David, Clark, Vincent Ralph, Njabo, Kevin Y, and Fjeldså, Jon

Subjects
Ecological Applications, Biological Sciences, Ecology, Evolutionary Biology, Environmental Sciences, forest, grassland, savanna, plants, animals, endemism, Afromontane, Afro-alpine, Evolutionary biology, Ecological applications
Published
2023

4. 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 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

Subjects
Biological Sciences, Genetics, General Science & Technology
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

5. Diversification of flowering plants in space and time

Author

Dimitrov, Dimitar, Xu, Xiaoting, Su, Xiangyan, Shrestha, Nawal, Liu, Yunpeng, Kennedy, Jonathan D., Lyu, Lisha, Nogués-Bravo, David, Rosindell, James, Yang, Yong, Fjeldså, Jon, Liu, Jianquan, Schmid, Bernhard, Fang, Jingyun, Rahbek, Carsten, and Wang, Zhiheng

Published
2023
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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-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

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Life on Land, Animals, Birds, Chickens, Conservation of Natural Resources, Datasets as Topic, Finches, Genome, Genomics, Humans, Phylogeny, Selection, Genetic, Synteny, General Science & Technology
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

7. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

Author

Thomas, Jessica E, Carvalho, Gary R, Haile, James, Rawlence, Nicolas J, Martin, Michael D, Ho, Simon YW, Sigfússon, Arnór Þ, Jósefsson, Vigfús A, Frederiksen, Morten, Linnebjerg, Jannie F, Castruita, Jose A Samaniego, Niemann, Jonas, Sinding, Mikkel-Holger S, Sandoval-Velasco, Marcela, Soares, André ER, Lacy, Robert, Barilaro, Christina, Best, Juila, Brandis, Dirk, Cavallo, Chiara, Elorza, Mikelo, Garrett, Kimball L, Groot, Maaike, Johansson, Friederike, Lifjeld, Jan T, Nilson, Göran, Serjeanston, Dale, Sweet, Paul, Fuller, Errol, Hufthammer, Anne Karin, Meldgaard, Morten, Fjeldså, Jon, Shapiro, Beth, Hofreiter, Michael, Stewart, John R, Gilbert, M Thomas P, and Knapp, Michael

Subjects
Biological Sciences, Ecology, Genetics, Life on Land, Animals, Charadriiformes, DNA, Ancient, DNA, Mitochondrial, Extinction, Biological, Genetic Variation, Genome, Mitochondrial, Humans, Phylogeny, Population Dynamics, 19th century extinction, ancient DNA, evolutionary biology, genetics, genomics, hunting, paleogenetics, seabird exploitation, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

Published
2019

9. Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation

Author

Soares, André ER, Novak, Ben J, Haile, James, Heupink, Tim H, Fjeldså, Jon, Gilbert, M Thomas P, Poinar, Hendrik, Church, George M, and Shapiro, Beth

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Generic health relevance, Animals, Base Sequence, Bayes Theorem, Biological Evolution, Columbidae, Extinction, Biological, Genetic Variation, Genome, Mitochondrial, High-Throughput Nucleotide Sequencing, Phylogeny, Sequence Analysis, DNA, Ancient DNA, time calibrated phylogeny, Pezophaps solitaria, Raphus cucullatus, Passenger pigeon, Ecology, Evolutionary biology
Abstract

BackgroundPigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group's evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context.ResultsWe used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves.ConclusionsOur analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously.

Published
2016

14. Calibrating the genomic clock of modern birds using fossils

Author

Claramunt, Santiago, Braun, Edward L., Cracraft, Joel, Fjeldså, Jon, Ho, Simon Y. W., Houde, Peter, Nguyen, Jacqueline M. T., Stiller, Josefin, Claramunt, Santiago, Braun, Edward L., Cracraft, Joel, Fjeldså, Jon, Ho, Simon Y. W., Houde, Peter, Nguyen, Jacqueline M. T., and Stiller, Josefin

Published
2024

16. Comparative genomics reveals insights into avian genome evolution and adaptation

Author

Zhang, Guojie, Li, Cai, Li, Qiye, Li, Bo, Larkin, Denis M, Lee, Chul, Storz, Jay F, Antunes, Agostinho, Greenwold, Matthew J, Meredith, Robert W, Ödeen, Anders, Cui, Jie, Zhou, Qi, Xu, Luohao, Pan, Hailin, Wang, Zongji, Jin, Lijun, Zhang, Pei, Hu, Haofu, Yang, Wei, Hu, Jiang, Xiao, Jin, Yang, Zhikai, Liu, Yang, Xie, Qiaolin, Yu, Hao, Lian, Jinmin, Wen, Ping, Zhang, Fang, Li, Hui, Zeng, Yongli, Xiong, Zijun, Liu, Shiping, Zhou, Long, Huang, Zhiyong, An, Na, Wang, Jie, Zheng, Qiumei, Xiong, Yingqi, Wang, Guangbiao, Wang, Bo, Wang, Jingjing, Fan, Yu, da Fonseca, Rute R, Alfaro-Núñez, Alonzo, Schubert, Mikkel, Orlando, Ludovic, Mourier, Tobias, Howard, Jason T, Ganapathy, Ganeshkumar, Pfenning, Andreas, Whitney, Osceola, Rivas, Miriam V, Hara, Erina, Smith, Julia, Farré, Marta, Narayan, Jitendra, Slavov, Gancho, Romanov, Michael N, Borges, Rui, Machado, João Paulo, Khan, Imran, Springer, Mark S, Gatesy, John, Hoffmann, Federico G, Opazo, Juan C, Håstad, Olle, Sawyer, Roger H, Kim, Heebal, Kim, Kyu-Won, Kim, Hyeon Jeong, Cho, Seoae, Li, Ning, Huang, Yinhua, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Bertelsen, Mads F, Derryberry, Elizabeth, Warren, Wesley, Wilson, Richard K, Li, Shengbin, Ray, David A, Green, Richard E, O’Brien, Stephen J, Griffin, Darren, Johnson, Warren E, Haussler, David, Ryder, Oliver A, Willerslev, Eske, Graves, Gary R, Alström, Per, Fjeldså, Jon, Mindell, David P, Edwards, Scott V, Braun, Edward L, Rahbek, Carsten, Burt, David W, Houde, Peter, and Zhang, Yong

Subjects
Human Genome, Biotechnology, Genetics, Adaptation, Physiological, Animals, Biodiversity, Biological Evolution, Birds, Conserved Sequence, Diet, Evolution, Molecular, Female, Flight, Animal, Genes, Genetic Variation, Genome, Genomics, Male, Molecular Sequence Annotation, Phylogeny, Reproduction, Selection, Genetic, Sequence Analysis, DNA, Synteny, Vision, Ocular, Vocalization, Animal, Avian Genome Consortium, General Science & Technology
Abstract

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Published
2014

30. Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

Author

Fuchs, Jérôme, Fjeldså, Jon, and Bowie, Rauri CK

Abstract

Abstract Background The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (Phyllastephus debilis) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies albigula (green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies rabai (grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (Phyllastrephus debilis) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages. Results We found significant biometric differences between the lowland (rabai) and montane (albigula) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago. Our coalescent analyses suggest that limited gene flow, mostly from the subspecies rabai to albigula, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of rabai further inland. Conclusion The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend albigula be elevated to species rank.

Published
2011

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