Animals
Recent Publications
Complexity of avian evolution revealed by family-level genomes. Stiller, Josefin, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng et al. Nature 629, no. 8013 (2024): 851-860.
A region of suppressed recombination misleads neoavian phylogenomics. Mirarab, Siavash, Iker Rivas-González, Shaohong Feng, Josefin Stiller, Qi Fang, Uyen Mai, Glenn Hickey et al. Proceedings of the National Academy of Sciences 121, no. 15 (2024): e2319506121.
Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Chen, Guangji, Dan Yu, Yu Yang, Xiang Li, Xiaojing Wang, Danyang Sun, Yanlin Lu et al. Nature Communications 15, no. 1 (2024): 3151.
Species-specific traits mediate avian demographic responses under past climate change. Germain, R.R., Feng, S., Chen, G. et al. Nat Ecol Evol 7, 862–872 (2023). https://doi.org/10.1038/s41559-023-02055-3
Changes in the functional diversity of modern bird species over the last million years. Germain, Ryan R., Shaohong Feng, Lucas Buffan, Carlos P. Carmona, Guangii Chen, Gary R. Graves, Joseph A. Tobias et al. Proceedings of the National Academy of Sciences 120, no. 7 (2023): e2201945119.
Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution. Zhang, Xiao, Mark Blaxter, Jonathan MD Wood, Alan Tracey, Shane McCarthy, Peter Thorpe, Jack G. Rayner et al. Nature Communications 15, no. 1 (2024): 5001.
De novo assembly and annotation of Popillia japonica’s genome with initial clues to its potential as an invasive pest. Cucini, Claudio, Sara Boschi, Rebecca Funari, Elena Cardaioli, Nicola Iannotti, Giovanni Marturano, Francesco Paoli et al. BMC genomics 25, no. 1 (2024): 275.
The direction, timing and demography of Popillia japonica (Coleoptera) invasion reconstructed using complete mitochondrial genomes. Nardi, Francesco, Sara Boschi, Rebecca Funari, Claudio Cucini, Elena Cardaioli, Daniel Potter, Shin-Ichiro Asano et al. Scientific Reports 14, no. 1 (2024): 7120.
Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. Stahlke, Amanda R., Jennifer Chang, Sivanandan Chudalayandi, Chan C. Heu, Scott M. Geib, Brian E. Scheffler, Anna K. Childers, and Jeffrey A. Fabrick. G3: Genes, Genomes, Genetics 13, no. 4 (2023): jkad040.
A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect. Coates, Brad S., Kimberly KO Walden, Dimpal Lata, Neetha Nanoth Vellichirammal, Robert F. Mitchell, Martin N. Andersson, Rachel McKay et al. BMC genomics 24, no. 1 (2023): 19.
Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae). Cohen, Zachary P., Lindsey C. Perkin, Sheina B. Sim, Amanda R. Stahlke, Scott M. Geib, Anna K. Childers, Timothy PL Smith, and Charles Suh. G3 13, no. 2 (2023): jkac309.
Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project. Vancaester, Emmelien, and Mark Blaxter. PLoS Biology 21, no. 1 (2023): e3001972.
The genome of Rhyzopertha dominica (Fab.)(Coleoptera: Bostrichidae): adaptation for success. Oppert, Brenda, Anna Muszewska, Kamil Steczkiewicz, Eva Šatović-Vukšić, Miroslav Plohl, Jeffrey A. Fabrick, Konstantin S. Vinokurov et al. Genes 13, no. 3 (2022): 446.
Gene content evolution in the arthropods. Thomas, Gregg WC, Elias Dohmen, Daniel ST Hughes, Shwetha C. Murali, Monica Poelchau, Karl Glastad, Clare A. Anstead et al. Genome biology 21 (2020): 1-14.
Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera. Oeyen, Jan Philip, Patrice Baa-Puyoulet, Joshua B. Benoit, Leo W. Beukeboom, Erich Bornberg-Bauer, Anja Buttstedt, Federica Calevro et al. Genome biology and evolution 12, no. 7 (2020): 1099-1188.
Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies. Zhang, Ru, Jinwu He, Zhiwei Dong, Guichun Liu, Yuan Yin, Xinying Zhang, Qi Li et al. Scientific reports 10, no. 1 (2020): 15882.
Hemimetabolous genomes reveal molecular basis of termite eusociality. Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers et al. Nature ecology & evolution 2, no. 3 (2018): 557-566.
Chromosome-scale genome assembly of the hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest. Koch, Jonathan Berenguer Uhuad, Sheina B. Sim, Brian Scheffler, Jeffrey D. Lozier, and Scott M. Geib. G3: Genes, Genomes, Genetics 14, no. 10 (2024): jkae160.
Repeated shifts in sociality are associated with fine-tuning of highly conserved and lineage-specific enhancers in a socially flexible bee. Jones, Beryl M., Andrew E. Webb, Scott M. Geib, Sheina Sim, Rena M. Schweizer, Michael G. Branstetter, Jay D. Evans, and Sarah D. Kocher. Molecular Biology and Evolution 41, no. 11 (2024): msae229.
Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson)(Hymenoptera: Apidae), an endangered North American pollinator. Koch, Jonathan Berenguer Uhuad, Sheina B. Sim, Brian Scheffler, Scott M. Geib, and Tamara A. Smith. G3: Genes, Genomes, Genetics 13, no. 8 (2023): jkad119.
Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees. Huang, Qiang, Sheina B. Sim, Scott M. Geib, Anna Childers, Junfeng Liu, Xiuxiu Wei, Wensu Han et al. GigaScience 12 (2023): giad056.
Genus-wide characterization of nuclear mitochondrial DNAs in bumblebee (Hymenoptera: Apidae) genomes. Ding, Lele, Huiling Sang, and Cheng Sun. Insects 12, no. 11 (2021): 963.
Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Wright, Charlotte J., Lewis Stevens, Alexander Mackintosh, Mara Lawniczak, and Mark Blaxter. Nature Ecology & Evolution 8, no. 4 (2024): 777-790.
Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements. Zhou, Botong, Ping Hu, Guichun Liu, Zhou Chang, Zhiwei Dong, Zihe Li, Yuan Yin et al. Nature Communications 15, no. 1 (2024): 6303.
A polygenic explanation for Haldane’s rule in butterflies. Xiong, Tianzhu, Shreeharsha Tarikere, Neil Rosser, Xueyan Li, Masaya Yago, and James Mallet. Proceedings of the National Academy of Sciences 120, no. 44 (2023): e2300959120.
Admixture of evolutionary rates across a butterfly hybrid zone. Xiong, Tianzhu, Xueyan Li, Masaya Yago, and James Mallet. Elife 11 (2022): e78135.
The Genetics and Evolution of Leaf Mimicry in Kallima Butterflies. Wang, Shuting, Dequn Teng, Peiwen Yang, Wa Da, Yiming Zhang, Yubo Zhang, Xinshuang Zhang et al. Cell 185, no. 17 (2022): 0092-8674.
Diverse genetic architectures on the Z chromosome underlie the two rules of speciation in Papilio butterfly hybrids. Xiong, Tianzhu, Shreeharsha Tarikere, Neil Rosser, Xueyan Li, Masaya Yago, and James Mallet. bioRxiv (2022): 2022-10.
Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus. Liu, Guichun, Wei Liu, Ruoping Zhao, Jinwu He, Zhiwei Dong, Lei Chen, Wenting Wan, Zhou Chang, Wen Wang, and Xueyan Li. BMC genomics 22 (2021): 1-18.
State of the Amphibia 2020: A review of five years of amphibian research and existing resources. Womack, Molly C., Emma Steigerwald, David C. Blackburn, David C. Cannatella, Alessandro Catenazzi, Jing Che, Michelle S. Koo et al. Ichthyology & Herpetology 110, no. 4 (2022): 638-661.
Comparative analysis of amphibian genomes: An emerging resource for basic and applied research. Kosch, Tiffany A., Andrew J. Crawford, Rachel Lockridge Mueller, Katharina C. Wollenberg Valero, Megan L. Power, Ariel Rodríguez, Lauren A. O'Connell, Neil D. Young, and Lee F. Skerratt. Molecular Ecology Resources (2024): e14025.
A genomic framework to assist conservation breeding and translocation success: A case study of a critically endangered turtle. Nelson, Holly V., Katherine A. Farquharson, Arthur Georges, Elspeth A. McLennan, Jane L. DeGabriel, Melissa Giese, Christopher Ormond et al. Conservation Science and Practice 6, no. 10 (2024): e13204.
Genome-Wide Identification and Expression Analysis of the STAT Family in Reeve’s Turtle (Mauremys reevesii). Song, Yi, Zeshuo Zhou, Shichen Huang, Zhiyuan Li, Xuechi Zhu, Hongming Zhou, Yuxin Jiang, Duminda SB Dissanayake, Arthur Georges, and Lei Xiong. Biochemical Genetics (2024): 1-17.
The genome sequence of the Loggerhead sea turtle, Caretta caretta Linnaeus 1758. Chang, Glenn, Samantha Jones, Sreeja Leelakumari, Jahanshah Ashkani, Luka Culibrk, Kieran O'Neill, Kane Tse et al. F1000Research 12 (2023).
Complete mitochondrial genomes of Eastern Massasauga (Sistrurus catenatus) and North American Racer (Coluber constrictor). Chen, Ying, Amy A. Chabot, Bradley J. Swanson, and Stephen C. Lougheed. bioRxiv (2024): 2024-07.
A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies. Hanrahan, Benjamin J., Kirat Alreja, Andre LM Reis, J. King Chang, Duminda SB Dissanayake, Richard J. Edwards, Terry Bertozzi et al. bioRxiv (2024): 2024-09.
The genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation. Powell, Daniel, Nicola Jackson, Parwinder Kaur, Olga Dudchenko, Erez Lieberman Aiden, Arthur Georges, and Céline Henria Frère. Journal of Heredity (2024): esae054.
Comparison of reptilian genomes reveals deletions associated with the natural loss of γδ T cells in squamates. Morrissey, Kimberly A., Jordan M. Sampson, Megan Rivera, Lijing Bu, Victoria L. Hansen, Neil J. Gemmell, Michael G. Gardner, Terry Bertozzi, and Robert D. Miller. The Journal of Immunology 208, no. 8 (2022): 1960-1967.
Solving an enigma in the tree of life, at the origins of teleost fishes. Parey, Elise, Camille Berthelot, Hugues Roest Crollius, and Yann Guiguen. Comptes Rendus. Biologies 347, no. G1 (2024): 1-8.
ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp. Ventura, Marc, Nati Franch, Rosa Fernández, Javier Palma-Guerrero, Astrid Böhne, Rita Monteiro, Laura Aguilera et al. bioRxiv (2024): 2024-07.
Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution. Weber, Claudia C., Michael Paulini, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Tree of Life Core Informatics team, and Mark L. Blaxter. bioRxiv (2024): 2024-11.
Transcriptomic insights into the antagonistic responses of Antarctic marbled rockcod, Notothenia rossii, to elevated temperature and acidification. Lee, Seungyeon, Seung Chul Shin, and Jin-Hyoung Kim. Ecotoxicology and Environmental Safety 287 (2024): 117249.
Antarctic blackfin icefish genome reveals adaptations to extreme environments. Kim, Bo-Mi, Angel Amores, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Il-Chan Kim, Jun Hyuck Lee et al. Nature ecology & evolution 3, no. 3 (2019): 469-478.
Skin transcriptome profiling reveals the distinctive molecular effects of temperature changes on Antarctic bullhead notothen. Kim, Bo-Mi, Do-Hwan Ahn, Seunghyun Kang, Jihye Jeong, Euna Jo, Bum-Keun Kim, Jin-Hyoung Kim, and Hyun Park. Molecular & Cellular Toxicology 15 (2019): 163-172.
Draft genome of the Antarctic dragonfish, Parachaenichthys charcoti. Ahn, Do-Hwan, Seung Chul Shin, Bo-Mi Kim, Seunghyun Kang, Jin-Hyoung Kim, Inhye Ahn, Joonho Park, and Hyun Park. Gigascience 6, no. 8 (2017): gix060.
The white-spotted bamboo shark genome reveals chromosome rearrangements and fast-evolving immune genes of cartilaginous fish. Zhang, Yaolei, Haoyang Gao, Hanbo Li, Jiao Guo, Bingjie Ouyang, Meiniang Wang, Qiwu Xu et al. Iscience 23, no. 11 (2020).
How many lineages are there of the stingrays genus Hypanus (Myliobatiformes: Dasyatidae) and why does it matter? Petean, Flávia F., Lei Yang, Shannon Corrigan, Sergio MQ Lima, and Gavin JP Naylor. Neotropical Ichthyology 22 (2024): e230046.
Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic. Denton, John SS, Jeff Kneebone, Lei Yang, Arve Lynghammar, David McElroy, Shannon Corrigan, Klara Jakobsdóttir, Carolyn Miri, Mark Simpson, and Gavin JP Naylor. Journal of Fish Biology 104, no. 5 (2024): 1513-1524.
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks. Wu, Jiahong, Fujiang Liu, Jie Jiao, Haoran Luo, Shiyu Fan, Jiao Liu, Hongxiang Wang et al. Cell Genomics 4, no. 8 (2024).
Evolution of vertebrate hormones and their receptors: insights from non-osteichthyan genomes. Kuraku, Shigehiro, Hiroyuki Kaiya, Tomohiro Tanaka, and Susumu Hyodo. Annual Review of Animal Biosciences 11, no. 1 (2023): 163-182.
Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution. Kuraku, Shigehiro. Developmental Biology 477 (2021): 262-272.
A high-quality blue whale genome, segmental duplications, and historical demography. Bukhman, Yury V., Phillip A. Morin, Susanne Meyer, Li-Fang Chu, Jeff K. Jacobsen, Jessica Antosiewicz-Bourget, Daniel Mamott et al. Molecular Biology and Evolution 41, no. 3 (2024): msae036.
Revised taxonomy of eastern North Pacific killer whales (Orcinus orca): Bigg’s and resident ecotypes deserve species status. Morin, Phillip A., Morgan L. McCarthy, Charissa W. Fung, John W. Durban, Kim M. Parsons, William F. Perrin, Barbara L. Taylor, Thomas A. Jefferson, and Frederick I. Archer. Royal Society Open Science 11, no. 3 (2024): 231368.
The genome sequence of the white-beaked dolphin, Lagenorhynchus albirostris (Gray, 1846). Davison, Nicholas J., Phillip Morin, Wellcome Sanger Institute Tree of Life, and Darwin Tree of Life Consortium. Wellcome Open Research 9 (2024): 687.
A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome. McGrath, Nick, Jamie le Roux, Annabel Whibley, Alana Alexander, Ramari Oliphant Stewart, Muriel Johnstone, Karen A. Stockin, and Olin K. Silander. bioRxiv (2024): 2024-05.
A comparison of genomic diversity and demographic history of the North Atlantic and Southwest Atlantic southern right whales. Crossman, Carla A., Michael C. Fontaine, and Timothy R. Frasier. Molecular Ecology 33, no. 20 (2024): e17099.
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus. de Greef, Evelien, Anthony L. Einfeldt, Patrick JO Miller, Steven H. Ferguson, Colin J. Garroway, Kyle J. Lefort, Ian G. Paterson, Paul Bentzen, and Laura J. Feyrer. Molecular Ecology 31, no. 19 (2022): 4919-4931.
The genome sequence of the endemic Mexican common mustached Bat, Pteronotus mexicanus. Miller, 1902 [Mormoopidae; Pteronotus]. Sánchez-de la Vega, Guillermo, Jaime Gasca-Pineda, Anahí Martínez-Cárdenas, Sonja C. Vernes, Emma C. Teeling, Meike Mai, Erika Aguirre-Planter, Luis E. Eguiarte, Caleb D. Phillips, and Jorge Ortega. Gene 929 (2024): 148821.
The genome sequence of the whiskered bat, Myotis mystacinus (Kuhl, 1817). Ryan, Hazel, Sonja C. Vernes, Emma C. Teeling, Meike Mai, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life, and Darwin Tree of Life Consortium. Wellcome Open Research 9 (2024): 684.
The genome sequence of the Brown Long-eared bat, Plecotus auritus (Linnaeus 1758). Millar, Amanda, Sonja C. Vernes, Emma C. Teeling, Meike Mai, Natural History Museum Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life, and Darwin Tree of Life Consortium. Wellcome Open Research 9 (2024): 246.
The genome sequence of the Soprano Pipistrelle, Pipistrellus pygmaeus (Leach, 1825). Ruedi, Manuel, Sonja C. Vernes, Emma C. Teeling, Meike Mai, Wellcome Sanger Institute Tree of Life, and Darwin Tree of Life Consortium. Wellcome Open Research 8 (2023).
Evolutionary constraint and innovation across hundreds of placental mammals. Christmas, Matthew J., Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan et al. Science 380, no. 6643 (2023): eabn3943.
Population dynamics of caribou shaped by glacial cycles before the last glacial maximum. Taylor, Rebecca S., Micheline Manseau, Cornelya FC Klütsch, Jean L. Polfus, Audrey Steedman, Dave Hervieux, Allicia Kelly et al. Molecular Ecology 30, no. 23 (2021): 6121-6143.
Development of SNP-based genomic tools for the Canadian Bison Industry: parentage verification and subspecies composition. Yang, Tianfu, Michelle Miller, David Forgacs, James Derr, and Paul Stothard. Frontiers in genetics 11 (2020): 585999.
The genome of the North American brown bear or grizzly: Ursus arctos ssp. horribilis. Taylor, Gregory A., Heather Kirk, Lauren Coombe, Shaun D. Jackman, Justin Chu, Kane Tse, Dean Cheng et al. Genes 9, no. 12 (2018): 598.
Identification of constrained sequence elements across 239 primate genomes. Kuderna, Lukas FK, Jacob C. Ulirsch, Sabrina Rashid, Mohamed Ameen, Laksshman Sundaram, Glenn Hickey, Anthony J. Cox et al. Nature 625, no. 7996 (2024): 735-742.
Harvesting the fruits of the first stage of the Primate Genome Project. Guo, Yuan-Ting, Yong Shao, Xupeng Bi, Bao-Lin Zhang, Hong Wu, Yang Zhou, Ming-Li Li et al. Zoological Research 44, no. 4 (2023): 725.
Lineage-specific accelerated sequences underlying primate evolution. Bi, Xupeng, Long Zhou, Jin-Jin Zhang, Shaohong Feng, Mei Hu, David N. Cooper, Jiangwei Lin, Jiali Li, Dong-Dong Wu, and Guojie Zhang. Science Advances 9, no. 22 (2023): eadc9507.
Phylogenomic analyses provide insights into primate evolution. Shao, Yong, Long Zhou, Fang Li, Lan Zhao, Bao-Lin Zhang, Feng Shao, Jia-Wei Chen et al. Science 380, no. 6648 (2023): 913-924.
Eighty million years of rapid evolution of the primate Y chromosome. Zhou, Yang, Xiaoyu Zhan, Jiazheng Jin, Long Zhou, Juraj Bergman, Xuemei Li, Marjolaine Marie C. Rousselle et al. Nature Ecology & Evolution 7, no. 7 (2023): 1114-1130.
Comparative genomics reveals the hybrid origin of a macaque group. Zhang, Bao-Lin, Wu Chen, Zefu Wang, Wei Pang, Meng-Ting Luo, Sheng Wang, Yong Shao et al. Science advances 9, no. 22 (2023): eadd3580.
Evolutionary and biomedical insights from a marmoset diploid genome assembly. Yang, Chentao, Yang Zhou, Stephanie Marcus, Giulio Formenti, Lucie A. Bergeron, Zhenzhen Song, Xupeng Bi et al. Nature 594, no. 7862 (2021): 227-233.