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

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 T.; Parent, Carole A.; Pacheco, George; Sinding, Mikkel Holger S.; Puetz, Lara; Cavill, Emily Louisa; Ribeiro, Ângela Maria; Eckhart, Leopold; Fjeldså, Jon; Hosner, Peter A.; Brumfield, Robb T.; Christidis, Les; Bertelsen, Mads F.; Sicheritz-Pontén, Thomas; Tietze, Dieter Thomas; Robertson, Bruce C.; Song, Gang; Borgia, Gerald; Claramunt, Santiago; Lovette, Irby J.; Cowen, Saul; Njoroge, Peter; Dumbacher, John P.; Ryder, Oliver A.; Fuchs, Jérôme; Bunce, Michael; Burt, David W.; Cracraft, Joel; Meng, Guanliang; Hackett, Shannon J.; Ryan, Peter G.; Jønsson, Knud A.; Jamieson, Ian G.; Fonseca, Rute R. da; Braun, Edward L.; Houde, Peter; Mirarab, Siavash; Suh, Alexander; Hansson, Bengt; Ponnikas, Suvi; Sigeman, Hanna; Stervander, Martin; Frandsen, Paul B.; Zwan, Henriëtte van der; Sluis, Rencia van der; 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; Obiol, Joan Ferrer; Rozas, Julio; Riutort, Marta; Tigano, Anna; Friesen, Vicki L.; Dalén, Love; Urrutia, Araxi O.; Székely, Tamás; Liu, Yang; Campana, Michael G.; Corvelo, André; Fleischer, Robert C.; Rutherford, Kim; Gemmell, Neil J.; Dussex, Nicolás; Mouritsen, Henrik; Thiele, Nadine; Delmore, Kira E.; Liedvogel, Miriam; Franke, André; Hoeppner, Marc P.; Krone, Oliver; Fudickar, Adam M.; Milá, Borja; Ketterson, Ellen D.; Fidler, Andrew E.; Friis, Guillermo; Parody-Merino, Ángela M.; Battley, Phil F.; Cox, Murray P.; Lima, Nicholas Costa Barroso; Prosdocimi, Francisco; Parchman, Thomas L.; 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, Thomas B.; Camenisch, Glauco; Keller, Lukas F.; DaCosta, Jeffrey M.; Hauber, Márk 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 Luis Padovan; Vasconcelos, Ana Tereza Ribeiro de; Mello, Claudio V.; Weir, Jason T.; Haussler, David; Li, Qiye; Yang, Huanming; Wang, Jian; Lei, Fumin; Rahbek, Carsten; Gilbert, Martin; Graves, Gary R.; Jarvis, Erich D.; Paten, Benedict; Zhang, Guojie

doi:10.1038/s41586-021-03473-8

Cited by 7 publications

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Beyond genes‐for‐behaviour: The potential for genomics to resolve long‐standing questions in avian brood parasitism

Rönkä,

Eroukhmanoff,

Kulmuni

et al. 2024

Ecology and Evolution

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Behavioural ecology by definition of its founding ‘Tinbergian framework’ is an integrative field, however, it lags behind in incorporating genomic methods. ‘Finding the gene/s for a behaviour’ is still rarely feasible or cost‐effective in the wild but as we show here, genomic data can be used to address broader questions. Here we use avian brood parasitism, a model system in behavioural ecology as a case study to highlight how behavioural ecologists could use the full potential of state‐of‐the‐art genomic tools. Brood parasite–host interactions are one of the most easily observable and amenable natural laboratories of antagonistic coevolution, and as such have intrigued evolutionary biologists for decades. Using worked examples, we demonstrate how genomic data can be used to study the causes and mechanisms of (co)evolutionary adaptation and answer three key questions for the field: (i) Where and when should brood parasitism evolve?, (ii) When and how should hosts defend?, and (iii) Will coevolution persist with ecological change? In doing so, we discuss how behavioural and molecular ecologists can collaborate to integrate Tinbergen's questions and achieve the coherent science that he promoted to solve the mysteries of nature.

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Beyond genes‐for‐behaviour: The potential for genomics to resolve long‐standing questions in avian brood parasitism

Rönkä,

Eroukhmanoff,

Kulmuni

et al. 2024

Ecology and Evolution

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Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development

Padilla-Morales,

Acuña-Alonzo,

Kilili

et al. 2024

Nat Commun

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In mammals, sexual size dimorphism often reflects the intensity of sexual selection, yet its connection to genomic evolution remains unexplored. Gene family size evolution can reflect shifts in the relative importance of different molecular functions. Here, we investigate the associate between brain development gene repertoire to sexual size dimorphism using 124 mammalian species. We reveal significant changes in gene family size associations with sexual size dimorphism. High levels of dimorphism correlate with an expansion of gene families enriched in olfactory sensory perception and a contraction of gene families associated with brain development functions, many of which exhibited particularly high expression in the human adult brain. These findings suggest a relationship between intense sexual selection and alterations in gene family size. These insights illustrate the complex interplay between sexual dimorphism, gene family size evolution, and their roles in mammalian brain development and function, offering a valuable understanding of mammalian genome evolution.

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Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

McCullough,

Eliason,

Hackett

et al. 2024

Preprint

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The flora and fauna of island systems, especially those in the Indo-Pacific, are renowned for their high diversification rates and outsized contribution to the development of evolutionary theories. The total diversity of geographic radiations of many Indo-Pacific fauna is often incompletely sampled in phylogenetic studies due to the difficulty in obtaining single island endemic forms across the Pacific and the relatively poor performance of degraded DNA when using museum specimens for inference of evolutionary relationships. New methods for production and analysis of genome-wide datasets sourced from degraded DNA are facilitating insights into the complex evolutionary histories of these influential island faunas. Here, we leverage whole genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic "Great Speciators." We find that whole genome datasets do not outright resolve the evolutionary relationships of this clade: four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree building methods did not find a single well-supported and concordant species-level topology. We then uncover evidence of widespread incomplete lineage sorting and both ancient and contemporary gene flow and demonstrate how these factors contribute to conflicting evolutionary histories. Our complete taxonomic sampling allowed us to further identify a novel case of mitochondrial capture between two allopatric species, suggesting a potential historical (but since lost) hybrid zone as islands were successively colonized. Taken together, these results highlight how increased genomic and taxon sampling can reveal complex evolutionary patterns in rapid island radiations.

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

Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Cited by 7 publications

References 0 publications

Beyond genes‐for‐behaviour: The potential for genomics to resolve long‐standing questions in avian brood parasitism

Beyond genes‐for‐behaviour: The potential for genomics to resolve long‐standing questions in avian brood parasitism

Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development

Phylogenomics of a genus of ‘Great Speciators’ reveals rampant incomplete lineage sorting, gene flow, and mitochondrial capture in island systems

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