Irby Lovette
Director, Fuller Evolutionary Biology Program and Director, Center for Biodiversity Studies and Higher Education
I study the incredible diversity of the world’s birds and work with many different kinds of students through my roles as the Fuller Professor of Ornithology, and the Director of the Fuller Evolutionary Biology Program, the Cornell Museum of Vertebrates, and the Cornell Lab’s Academic Affairs.
I have a hard time deciding what I find most exciting about my profession: making new discoveries about the ways birds have evolved such a wonderful richness of appearances, lifestyles and behaviors; or helping to create opportunities for our inspiring cadres of undergraduates, graduate students, and postdocs, many of whom came to Cornell specifically to study ornithology. Fortunately, in my world these two activities often occur together, since many of our most innovative scientific advances are made by those same student and postdoc researchers! Currently in my area of science I’m particularly impressed by our newfound ability to dissect the genetic basis of bird traits and evolutionary history using cutting-edge comparisons of birds’ entire genomes—I feel like these new big-data tools are giving us a truly novel window on how biodiversity arises, as if we just fired up the equivalent of the “Hubble Telescope” for evolutionary biology.
Recent Publications
2804417
Lovette
1
the-auk
10
date
desc
title
2488
https://www.birds.cornell.edu/home/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%22UZ2ZBR66%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Robinson%20et%20al.%22%2C%22parsedDate%22%3A%222025-10-06%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BRobinson%2C%20B.%20W.%2C%20S.%20Kurtis%2C%20B.%20G.%20Butcher%2C%20S.%20V.%20Edwards%2C%20I.%20J.%20Lovette%2C%20and%20J.%20Walsh%20%282025%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fevolut%5C%2Farticle%5C%2F79%5C%2F9%5C%2F1885%5C%2F8155227%26%23039%3B%26gt%3BThe%20genomic%20basis%20of%20plumage%20polymorphism%20in%20the%20Eastern%20Screech-Owl%20%28%20%26lt%3Bi%26gt%3BMegascops%20asio%26lt%3B%5C%2Fi%26gt%3B%20%29%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BEvolution%26lt%3B%5C%2Fi%26gt%3B%2079%3A1885%5Cu20131899.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22The%20genomic%20basis%20of%20plumage%20polymorphism%20in%20the%20Eastern%20Screech-Owl%20%28%20%3Ci%3EMegascops%20asio%3C%5C%2Fi%3E%20%29%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bryce%20W%22%2C%22lastName%22%3A%22Robinson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sarah%22%2C%22lastName%22%3A%22Kurtis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bronwyn%20G%22%2C%22lastName%22%3A%22Butcher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Scott%20V%22%2C%22lastName%22%3A%22Edwards%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Alison%22%2C%22lastName%22%3A%22Davis%5Cu00a0Rabosky%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Jason%22%2C%22lastName%22%3A%22Wolf%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Understanding%20the%20genetic%20basis%20of%20polymorphic%20traits%20is%20useful%20for%20exploring%20the%20origin%20and%20maintenance%20of%20variable%20phenotypes.%20Previous%20work%20on%20color%20polymorphism%20in%20birds%20has%20evolved%20from%20targeting%20candidate%20genes%20to%20whole-genome%20scans%2C%20consequently%20revealing%20the%20often-complex%20genomic%20architecture%20underlying%20polymorphic%20coloration.%20The%20Eastern%20Screech-Owl%20%28Megascops%20asio%29%20is%20a%20small%20North%20American%20polymorphic%20forest%20owl%20in%20which%20both%20gray%20and%20rufous%20plumage%20morphs%20are%20common%20across%20much%20of%20its%20range.%20We%20used%20whole-genome%20resequencing%20to%20investigate%20the%20genomic%20basis%20of%20this%20polymorphic%20trait%20at%20a%20population%20level%2C%20revealing%20additive%20and%20epistatic%20sources%20of%20this%20color%20and%20pattern%20variation.%20Using%20three%20approaches%2C%20comparisons%20identified%20a%20genome-wide%20suite%20of%20loci%20known%20to%20be%20associated%20with%20coloration%2C%20several%20loci%20associated%20with%20noncoloration%20physiological%20pathways%2C%20and%20using%20a%20regression%20model-based%20approach%20identified%20substantial%20epistatic%20interactions%20between%20loci%20underlying%20variation%20in%20screech-owl%20coloration.%20In%20addition%2C%20we%20uncovered%20evidence%20of%20balancing%20selection%20at%20morph-associated%20loci%2C%20suggesting%20that%20differential%20selection%20on%20morph%20types%20maintains%20their%20relative%20frequency%20in%20this%20species.%20Many%20owls%20show%20similar%20patterns%20of%20color%20polymorphism%2C%20which%20is%20likely%20mediated%20through%20parallel%20and%20equally%20complex%20genomic%20architecture%20under%20similar%20selective%20pressures%20that%20may%20partly%20explain%20how%20this%20trait%20has%20been%20maintained%20over%20evolutionary%20time%20as%20this%20group%20radiated.%22%2C%22date%22%3A%222025-10-06%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1093%5C%2Fevolut%5C%2Fqpaf120%22%2C%22ISSN%22%3A%220014-3820%2C%201558-5646%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fevolut%5C%2Farticle%5C%2F79%5C%2F9%5C%2F1885%5C%2F8155227%22%2C%22collections%22%3A%5B%222LFJB9KN%22%2C%22KH6P374R%22%5D%2C%22dateModified%22%3A%222025-11-04T17%3A44%3A03Z%22%7D%7D%2C%7B%22key%22%3A%22S5V3QFEW%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Rao%20et%20al.%22%2C%22parsedDate%22%3A%222025-09-19%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BRao%2C%20M.%20T.%2C%20B.%20G.%20Butcher%2C%20B.%20W.%20Robinson%2C%20I.%20J.%20Lovette%2C%20and%20J.%20Walsh%20%282025%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fauk%5C%2Fadvance-article%5C%2Fdoi%5C%2F10.1093%5C%2Fornithology%5C%2Fukaf047%5C%2F8258970%26%23039%3B%26gt%3BGenomic%20data%20reveals%20mixed%20support%20for%20the%20current%20subspecies%20designations%20in%20the%20%26lt%3Bi%26gt%3BMegascops%20asio%26lt%3B%5C%2Fi%26gt%3B%20%28Eastern%20Screech-Owl%29%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BOrnithology%26lt%3B%5C%2Fi%26gt%3B%3Aukaf047.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Genomic%20data%20reveals%20mixed%20support%20for%20the%20current%20subspecies%20designations%20in%20the%20%3Ci%3EMegascops%20asio%3C%5C%2Fi%3E%20%28Eastern%20Screech-Owl%29%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mei%20T%22%2C%22lastName%22%3A%22Rao%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bronwyn%20G%22%2C%22lastName%22%3A%22Butcher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bryce%20W%22%2C%22lastName%22%3A%22Robinson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Megascops%20asio%20%28Eastern%20Screech-Owl%29%20is%20a%20non-migratory%20resident%20forest%20owl%20that%20occurs%20across%20a%20broad%20distribution%20throughout%20much%20of%20eastern%20and%20central%20North%20America%20with%205%20subspecies%20generally%20recognized%20across%20the%20range.%20Using%20reduced%20representation%20sequencing%2C%20we%20found%20that%20genetic%20differentiation%20among%20populations%20was%20generally%20low%2C%20with%20only%202%20clear%20genetic%20clusters%20supporting%20that%20M.%20a.%20mccallii%20is%20distinct.%20Beyond%20these%202%20main%20groups%2C%20we%20found%20subtle%20genetic%20clustering%20roughly%20corresponding%20to%20geographic%20region%20and%20the%20currently%20recognized%20subspecies%2C%20suggesting%20mixed%20support%20for%20current%20subspecies%20designations.%20To%20address%20these%20questions%2C%20we%20analyzed%20228%20individuals%20representing%20all%205%20recognized%20subspecies%20at%208%2C220%20single%20nucleotide%20polymorphisms%20%28SNPs%29%20using%20standard%20population%20genetic%20approaches.%20In%20addition%20to%20the%20subtle%20populations%20structuring%20noted%20above%2C%20the%20genetically%20identified%20subpopulations%20also%20varied%20in%20estimated%20effective%20population%20sizes%20and%20metrics%20of%20genetic%20diversity.%20We%20also%20detected%20a%20weak%2C%20but%20significant%2C%20signal%20of%20isolation%20by%20distance%20across%20the%20range%2C%20suggesting%20clinal%20patterns%20of%20genetic%20variation%20across%20this%20broadly%20distributed%20species.%20The%20genetic%20population%20structure%20we%20uncovered%20broadens%20our%20understanding%20of%20subspecies-level%20taxonomic%20classification%20in%20this%20species%20and%20may%20be%20useful%20for%20effective%20conservation%20management%20if%20it%20becomes%20necessary.%22%2C%22date%22%3A%222025-09-19%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1093%5C%2Fornithology%5C%2Fukaf047%22%2C%22ISSN%22%3A%220004-8038%2C%202732-4613%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fauk%5C%2Fadvance-article%5C%2Fdoi%5C%2F10.1093%5C%2Fornithology%5C%2Fukaf047%5C%2F8258970%22%2C%22collections%22%3A%5B%22KH6P374R%22%5D%2C%22dateModified%22%3A%222025-11-03T18%3A16%3A10Z%22%7D%7D%2C%7B%22key%22%3A%22ACIXN3N8%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22C%5Cu00e9spedes%20Arias%20et%20al.%22%2C%22parsedDate%22%3A%222025-08-15%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BC%5Cu00e9spedes%20Arias%2C%20L.%20N.%2C%20A.%20M.%20Cuervo%2C%20C.%20D.%20Cadena%2C%20E.%20Bonaccorso%2C%20C.%20Witt%2C%20I.%20Lovette%2C%20and%20L.%20Campagna%20%282025%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttp%3A%5C%2F%5C%2Fbiorxiv.org%5C%2Flookup%5C%2Fdoi%5C%2F10.1101%5C%2F2025.08.12.667688%26%23039%3B%26gt%3BHistory%20of%20divergence%20and%20gene%20flow%20shaping%20geographic%20variation%20in%20Andean%20warblers%20%28%20%26lt%3Bi%26gt%3BMyioborus%26lt%3B%5C%2Fi%26gt%3B%20%29%26lt%3B%5C%2Fa%26gt%3B.%20%5BOnline.%5D%20Available%20at%20%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22preprint%22%2C%22title%22%3A%22History%20of%20divergence%20and%20gene%20flow%20shaping%20geographic%20variation%20in%20Andean%20warblers%20%28%20%3Ci%3EMyioborus%3C%5C%2Fi%3E%20%29%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laura%20N.%22%2C%22lastName%22%3A%22C%5Cu00e9spedes%20Arias%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9s%20M.%22%2C%22lastName%22%3A%22Cuervo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlos%20Daniel%22%2C%22lastName%22%3A%22Cadena%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elisa%22%2C%22lastName%22%3A%22Bonaccorso%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christopher%22%2C%22lastName%22%3A%22Witt%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Leonardo%22%2C%22lastName%22%3A%22Campagna%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Studying%20how%20genetic%20variation%20is%20structured%20across%20space%2C%20and%20how%20it%20relates%20to%20divergence%20in%20phenotypic%20traits%20relevant%20to%20reproductive%20isolation%2C%20is%20important%20for%20our%20overall%20understanding%20of%20the%20speciation%20process.%20We%20used%20reduced-representation%20genomic%20data%20%28ddRAD-seq%29%20to%20examine%20patterns%20of%20genetic%20variation%20across%20the%20full%20distribution%20of%20an%20Andean%20warbler%20species%20complex%20%28%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Myioborus%20ornatus%5Cu2013melanocephalus%29%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%2C%20which%20includes%20a%20known%20hybrid%20zone%20between%20two%20strikingly%20different%20plumage%20forms.%20Genetic%20structure%20largely%20reflects%20geographic%20variation%20in%20head%20plumage%2C%20some%20of%20which%20corresponds%20to%20major%20topographic%20barriers%20in%20the%20Andes.%20We%20also%20found%20evidence%20of%20isolation%20by%20distance%20shaping%20genetic%20patterns%20across%20the%20group%5Cu2019s%20broad%20latitudinal%20range.%20We%20found%20that%5Cn%20%20%20%20%20%20%20%20%20%20%20%20chrysops%5Cn%20%20%20%20%20%20%20%20%20%20%20%20and%5Cn%20%20%20%20%20%20%20%20%20%20%20%20bairdi%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%2C%20two%20taxa%20with%20marked%20plumage%20differences%20that%20have%20a%20known%20hybrid%20zone%2C%20were%20characterized%20by%20low%20overall%20genetic%20divergence.%20Based%20on%20our%20cline%20analyses%20of%20both%20plumage%20and%20genomic%20hybrid%20indices%2C%20this%20hybrid%20zone%20extends%20for%20approximately%20250%20km%2C%20where%20advanced%20generation%20hybrids%20are%20likely%20most%20common.%20We%20also%20identified%20a%20slight%20difference%20in%20the%20centers%20of%20the%20plumage%20and%20genomic%20clines%2C%20potentially%20suggesting%20the%20asymmetric%20introgression%20of%5Cn%20%20%20%20%20%20%20%20%20%20%20%20chrysops%5Cn%20%20%20%20%20%20%20%20%20%20%20%20-like%20plumage%20traits.%20By%20studying%20genetic%20variation%20in%20a%20phenotypically%20complex%20group%20distributed%20across%20a%20topographically%20complex%20area%2C%20which%20includes%20a%20hybrid%20zone%2C%20we%20were%20able%20to%20show%20how%20both%20geographic%20features%20and%20potentially%20sexually%20selected%20plumage%20traits%20may%20play%20a%20role%20in%20species%20formation%20in%20tropical%20mountains%22%2C%22genre%22%3A%22%22%2C%22repository%22%3A%22Evolutionary%20Biology%22%2C%22archiveID%22%3A%22%22%2C%22date%22%3A%222025-08-15%22%2C%22DOI%22%3A%2210.1101%5C%2F2025.08.12.667688%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22http%3A%5C%2F%5C%2Fbiorxiv.org%5C%2Flookup%5C%2Fdoi%5C%2F10.1101%5C%2F2025.08.12.667688%22%2C%22language%22%3A%22en%22%2C%22collections%22%3A%5B%22KH6P374R%22%5D%2C%22dateModified%22%3A%222025-11-03T18%3A15%3A44Z%22%7D%7D%2C%7B%22key%22%3A%22VSPX6ESR%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Arias%20et%20al.%22%2C%22parsedDate%22%3A%222025-08-15%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BArias%2C%20L.%20C.%2C%20K.%20F.%20P.%20Bennett%2C%20L.%20Campagna%2C%20A.%20W.%20Wood%2C%20E.%20Bonaccorso%2C%20A.%20M.%20Cuervo%2C%20C.%20D.%20Cadena%2C%20I.%20J.%20Lovette%2C%20and%20D.%20P.%20L.%20Toews%20%282025%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttp%3A%5C%2F%5C%2Fbiorxiv.org%5C%2Flookup%5C%2Fdoi%5C%2F10.1101%5C%2F2025.08.12.669906%26%23039%3B%26gt%3BDiversification%20and%20divergence%20in%20Myioborus%20warblers%3A%20insights%20into%20evolutionary%20relationships%20and%20plumage%20genetics%26lt%3B%5C%2Fa%26gt%3B.%20%5BOnline.%5D%20Available%20at%20%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22preprint%22%2C%22title%22%3A%22Diversification%20and%20divergence%20in%20Myioborus%20warblers%3A%20insights%20into%20evolutionary%20relationships%20and%20plumage%20genetics%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laura%20Cespedes%22%2C%22lastName%22%3A%22Arias%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kevin%20F%20P%22%2C%22lastName%22%3A%22Bennett%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Leonardo%22%2C%22lastName%22%3A%22Campagna%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20W%22%2C%22lastName%22%3A%22Wood%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elisa%22%2C%22lastName%22%3A%22Bonaccorso%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andres%20M%22%2C%22lastName%22%3A%22Cuervo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlos%20Daniel%22%2C%22lastName%22%3A%22Cadena%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%20P%20L%22%2C%22lastName%22%3A%22Toews%22%7D%5D%2C%22abstractNote%22%3A%22Genomic%20data%20can%20provide%20valuable%20insights%20into%20the%20evolutionary%20history%20of%20rapidly%20diversifying%20groups%20and%20the%20genetic%20basis%20of%20phenotypic%20differences%20among%20lineages.%20We%20used%20whole-genome%20sequencing%20of%20the%20warbler%20genus%20Myioborus%20to%20investigate%20dynamics%20of%20its%20recent%20diversification%20in%20Neotropical%20mountains.%20We%20found%20that%20mitochondrial%20and%20UCE%20phylogenies%20are%20mostly%2C%20but%20not%20fully%2C%20concordant%2C%20and%20we%20found%20phylogenetic%20support%20for%20a%20pattern%20of%20north-to-south%20and%20low-to-high%20elevation%20colonization%20in%20the%20genus.%20Within%20the%20%20ornatus-melanocephalus%20complex%2C%20which%20showed%20topological%20incongruence%20between%20our%20phylogenies%2C%20we%20found%20that%20genetic%20structure%20generally%20coincides%20with%20geographic%20variation%20in%20plumage%2C%20although%20three%20subspecies%20with%20striking%20plumage%20differences%20exhibit%20low%20mitochondrial%20divergence.%20The%20hybridizing%20taxa%20M.%20o.%20chrysops%20and%20M.%20m.%20bairdi%20show%20very%20shallow%20genomic%20differentiation%2C%20with%20marked%20peaks%20of%20divergence.%20Most%20of%20these%20are%20shared%20with%20other%20parulid%20warbler%20pairs%2C%20pointing%20to%20broad%20genomic%20features%2C%20like%20recombination%20rate%2C%20as%20the%20processes%20shaping%20these%20regions.%20However%2C%20other%20highly%20differentiated%20regions%20were%20unique%20to%20Myioborus%2C%20including%20one%20containing%20the%20gene%20CCDC91%2C%20which%20is%20associated%20with%20melanin-based%20plumage%20differences%20in%20several%20other%20birds.%20Lastly%2C%20we%20found%20higher%20levels%20of%20differentiation%20on%20the%20Z%20chromosome%20relative%20to%20autosomes%2C%20including%20two%20putative%20chromosomal%20inversions.%20Together%2C%20these%20results%20highlight%20the%20interplay%20of%20deep%20ancestral%20divergence%2C%20recent%20hybridization%2C%20and%20shared%20genomic%20architecture%20in%20shaping%20the%20evolution%20of%20phenotypic%20and%20genomic%20diversity%20within%20Myioborus.%22%2C%22genre%22%3A%22%22%2C%22repository%22%3A%22Evolutionary%20Biology%22%2C%22archiveID%22%3A%22%22%2C%22date%22%3A%222025-08-15%22%2C%22DOI%22%3A%2210.1101%5C%2F2025.08.12.669906%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22http%3A%5C%2F%5C%2Fbiorxiv.org%5C%2Flookup%5C%2Fdoi%5C%2F10.1101%5C%2F2025.08.12.669906%22%2C%22language%22%3A%22en%22%2C%22collections%22%3A%5B%22KH6P374R%22%5D%2C%22dateModified%22%3A%222025-11-03T18%3A15%3A44Z%22%7D%7D%2C%7B%22key%22%3A%22ECRQXXPG%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Hooper%20et%20al.%22%2C%22parsedDate%22%3A%222025%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BHooper%2C%20D.%20M.%2C%20K.%20A.%20Lopez%2C%20B.%20G.%20Butcher%2C%20I.%20J.%20Lovette%2C%20and%20S.%20C.%20Griffith%20%282025%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fonlinelibrary.wiley.com%5C%2Fdoi%5C%2F10.1002%5C%2Fece3.72313%26%23039%3B%26gt%3BRecent%20divergence%20and%20microgeographic%20genetic%20structure%20in%20an%20endangered%20Australian%20songbird%3A%20the%20southern%20Black%5Cu2010Throated%20Finch%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BEcology%20and%20Evolution%26lt%3B%5C%2Fi%26gt%3B%2015%3Ae72313.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Recent%20divergence%20and%20microgeographic%20genetic%20structure%20in%20an%20endangered%20Australian%20songbird%3A%20the%20southern%20Black%5Cu2010Throated%20Finch%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%20M.%22%2C%22lastName%22%3A%22Hooper%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kelsie%20A.%22%2C%22lastName%22%3A%22Lopez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bronwyn%20G.%22%2C%22lastName%22%3A%22Butcher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J.%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Simon%20C.%22%2C%22lastName%22%3A%22Griffith%22%7D%5D%2C%22abstractNote%22%3A%22ABSTRACT%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20Anthropogenic%20habitat%20loss%20and%20climate%20change%20threaten%20global%20biodiversity.%20Effective%20conservation%20management%20is%20greatly%20benefited%20by%20a%20detailed%20understanding%20of%20geographic%20structure%2C%20genetic%20diversity%2C%20and%20demography%20of%20threatened%20species.%20The%20black%5Cu2010throated%20finch%2C%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20Poephila%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%20is%20an%20Australian%20songbird%20with%20two%20subspecies%3A%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20atropygialis%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20and%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20.%20The%20southern%20subspecies%2C%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%20has%20experienced%20an%20~80%25%20range%20contraction%20over%20the%20last%20century%20and%20is%20listed%20as%20endangered%2C%20but%20genetic%20surveys%20of%20it%20are%20incomplete.%20Here%2C%20we%20use%20a%20combination%20of%20reduced%20representation%20and%20whole%20genome%20sequencing%20to%20examine%20genetic%20differentiation%2C%20spatial%20genetic%20structure%2C%20and%20demographic%20history%20in%20both%20subspecies%20of%20this%20species.%20We%20find%20that%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20atropygialis%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20and%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20are%20geographically%20isolated%20by%20a%20biogeographic%20barrier%20known%20as%20the%20Einasleigh%20Uplands%20and%20genetically%20distinct%20despite%20a%20history%20of%20divergence%20with%20gene%20flow.%20Since%20they%20last%20shared%20a%20common%20ancestor%20~360%2C000%5Cu2009years%20ago%2C%20the%20two%20subspecies%20have%20experienced%20distinct%20demographic%20trajectories%20over%20the%20last%20~100%2C000%5Cu2009years%2C%20characterized%20by%20population%20expansion%20in%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20atropygialis%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20and%20population%20decline%20in%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20.%20We%20find%20that%20the%20two%20remnant%20population%20centers%20of%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20cincta%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%20from%20the%20Galilee%20Basin%20and%20the%20Townsville%20Coastal%20Plain%2C%20each%20represent%20genetically%20distinct%20lineages%20that%20last%20shared%20appreciable%20levels%20of%20gene%20flow%20~3000%5Cu2009years%20ago.%20Moreover%2C%20we%20report%20striking%20microgeographic%20genetic%20structure%20from%20the%20Townsville%20Coastal%20Plain%20between%20populations%20%26lt%3B%5Cu200920%5Cu2009km%20apart%20associated%20with%20barriers%20to%20dispersal%20caused%20by%20anthropogenic%20habitat%20modification%20over%20the%20last%2050%5Cu2009years%3A%20namely%2C%20the%20construction%20of%20the%20Ross%20River%20Dam.%20Our%20findings%20highlight%20the%20urgent%20need%20for%20a%20conservation%20approach%20that%20prioritizes%20habitat%20restoration%20to%20re%5Cu2010establish%20population%20connectivity%20in%20the%20endangered%20southern%20black%5Cu2010throated%20finch.%22%2C%22date%22%3A%2210%5C%2F2025%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1002%5C%2Fece3.72313%22%2C%22ISSN%22%3A%222045-7758%2C%202045-7758%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fonlinelibrary.wiley.com%5C%2Fdoi%5C%2F10.1002%5C%2Fece3.72313%22%2C%22collections%22%3A%5B%222LFJB9KN%22%2C%22KH6P374R%22%5D%2C%22dateModified%22%3A%222025-11-03T20%3A56%3A28Z%22%7D%7D%2C%7B%22key%22%3A%22G7NEP5I8%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Robinson%20et%20al.%22%2C%22parsedDate%22%3A%222024-07-24%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BRobinson%2C%20B.%20W.%2C%20I.%20J.%20Lovette%2C%20and%20J.%20Walsh%20%282024%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fauk%5C%2Fadvance-article%5C%2Fdoi%5C%2F10.1093%5C%2Fornithology%5C%2Fukae026%5C%2F7720660%26%23039%3B%26gt%3BPlumage%20polymorphism%20in%20raptors%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BOrnithology%26lt%3B%5C%2Fi%26gt%3B%3Aukae026.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Plumage%20polymorphism%20in%20raptors%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bryce%20W%22%2C%22lastName%22%3A%22Robinson%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%5D%2C%22abstractNote%22%3A%22ABSTRACT%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Trait%20polymorphisms%20are%20a%20perennially%20popular%20topic%20of%20study%20in%20ecology%20and%20evolutionary%20biology.%20Plumage%20polymorphisms%20occur%20broadly%20in%20birds%2C%20with%20a%20particularly%20high%20rate%20among%20the%20raptors.%20The%20regularity%20of%20this%20heritable%2C%20melanin-based%20trait%20in%20raptors%20has%20prompted%20research%20into%20its%20potential%20connections%20to%20aspects%20of%20life%20history%20such%20as%20immune%20response%2C%20foraging%20ecology%2C%20and%20mating%20systems.%20Because%20raptors%20are%20a%20non-monophyletic%20grouping%20of%20multiple%20orders%2C%20they%20can%20further%20be%20leveraged%20to%20explore%20the%20eco-evolutionary%20drivers%20of%20recurrent%20plumage%20polymorphism%20phenotypes.%20Here%20we%20characterize%20plumage%20polymorphism%20throughout%20the%20raptors%20and%20review%20the%20existing%20literature%20on%20factors%20involved%20in%20its%20development%20and%20maintenance.%20We%20identify%20patterns%20and%20trends%20in%20this%20past%20body%20of%20research%20and%20discuss%20the%20opportunity%20to%20strengthen%20our%20understanding%20of%20plumage%20polymorphism%20through%20a%20holistic%20research%20approach.%20Specifically%2C%20we%20detail%20the%20likely%20benefits%20of%20applying%20genomic%20tools%20to%20plumage%20polymorphism%20research%20in%20raptors%20while%20encouraging%20both%20a%20focus%20on%20unstudied%20polymorphic%20species%20and%20on%20the%20potential%20interactions%20among%20multiple%20hypotheses%20that%20might%20promote%20plumage%20polymorphism.%22%2C%22date%22%3A%222024-07-24%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1093%5C%2Fornithology%5C%2Fukae026%22%2C%22ISSN%22%3A%220004-8038%2C%202732-4613%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fauk%5C%2Fadvance-article%5C%2Fdoi%5C%2F10.1093%5C%2Fornithology%5C%2Fukae026%5C%2F7720660%22%2C%22collections%22%3A%5B%22SNRZ7X8F%22%5D%2C%22dateModified%22%3A%222024-10-29T02%3A30%3A36Z%22%7D%7D%2C%7B%22key%22%3A%22CJABPNX8%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Carbeck%20et%20al.%22%2C%22parsedDate%22%3A%222023-11-07%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BCarbeck%2C%20K.%2C%20P.%20Arcese%2C%20I.%20Lovette%2C%20C.%20Pruett%2C%20K.%20Winker%2C%20and%20J.%20Walsh%20%282023%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fwww.nature.com%5C%2Farticles%5C%2Fs41467-023-42786-2%26%23039%3B%26gt%3BCandidate%20genes%20under%20selection%20in%20song%20sparrows%20co-vary%20with%20climate%20and%20body%20mass%20in%20support%20of%20Bergmann%26%23039%3Bs%20Rule%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BNature%20Communications%26lt%3B%5C%2Fi%26gt%3B%2014%3A6974.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Candidate%20genes%20under%20selection%20in%20song%20sparrows%20co-vary%20with%20climate%20and%20body%20mass%20in%20support%20of%20Bergmann%27s%20Rule%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Katherine%22%2C%22lastName%22%3A%22Carbeck%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Peter%22%2C%22lastName%22%3A%22Arcese%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christin%22%2C%22lastName%22%3A%22Pruett%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kevin%22%2C%22lastName%22%3A%22Winker%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20Ecogeographic%20rules%20denote%20spatial%20patterns%20in%20phenotype%20and%20environment%20that%20may%20reflect%20local%20adaptation%20as%20well%20as%20a%20species%5Cu2019%20capacity%20to%20adapt%20to%20change.%20To%20identify%20genes%20underlying%20Bergmann%5Cu2019s%20Rule%2C%20which%20posits%20that%20spatial%20correlations%20of%20body%20mass%20and%20temperature%20reflect%20natural%20selection%20and%20local%20adaptation%20in%20endotherms%2C%20we%20compare%2079%20genomes%20from%20nine%20song%20sparrow%20%28%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20Melospiza%20melodia%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%29%20subspecies%20that%20vary%20~300%25%20in%20body%20mass%20%2817%20%5Cu2212%2050%5Cu2009g%29.%20Comparing%20large-%20and%20smaller-bodied%20subspecies%20revealed%209%20candidate%20genes%20in%20three%20genomic%20regions%20associated%20with%20body%20mass.%20Further%20comparisons%20to%20the%20five%20smallest%20subspecies%20endemic%20to%20California%20revealed%20eight%20SNPs%20within%20four%20of%20the%20candidate%20genes%20%28%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20GARNL3%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20RALGPS1%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20ANGPTL2%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%2C%20and%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20COL15A1%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%29%20associated%20with%20body%20mass%20and%20varying%20as%20predicted%20by%20Bergmann%5Cu2019s%20Rule.%20Our%20results%20support%20the%20hypothesis%20that%20co-variation%20in%20environment%2C%20body%20mass%20and%20genotype%20reflect%20the%20influence%20of%20natural%20selection%20on%20local%20adaptation%20and%20a%20capacity%20for%20contemporary%20evolution%20in%20this%20diverse%20species.%22%2C%22date%22%3A%222023-11-07%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1038%5C%2Fs41467-023-42786-2%22%2C%22ISSN%22%3A%222041-1723%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.nature.com%5C%2Farticles%5C%2Fs41467-023-42786-2%22%2C%22collections%22%3A%5B%22PQMMSR8B%22%5D%2C%22dateModified%22%3A%222024-05-14T13%3A36%3A56Z%22%7D%7D%2C%7B%22key%22%3A%22XUMVTBAV%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Garc%5Cu00eda%20et%20al.%22%2C%22parsedDate%22%3A%222023-07-27%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BGarc%5Cu00eda%2C%20N.%20C.%2C%20L.%20Campagna%2C%20A.%20C.%20Rush%2C%20R.%20C.%20K.%20Bowie%2C%20and%20I.%20J.%20Lovette%20%282023%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fevolut%5C%2Farticle%5C%2F77%5C%2F8%5C%2F1818%5C%2F7186177%26%23039%3B%26gt%3BComparative%20genomics%20of%20two%20%26lt%3Bi%26gt%3BEmpidonax%26lt%3B%5C%2Fi%26gt%3B%20flycatchers%20reveal%20candidate%20genes%20for%20bird%20song%20production%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BEvolution%26lt%3B%5C%2Fi%26gt%3B%2077%3A1818%5Cu20131828.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Comparative%20genomics%20of%20two%20%3Ci%3EEmpidonax%3C%5C%2Fi%3E%20flycatchers%20reveal%20candidate%20genes%20for%20bird%20song%20production%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Natalia%20C%22%2C%22lastName%22%3A%22Garc%5Cu00eda%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Leonardo%22%2C%22lastName%22%3A%22Campagna%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andrew%20C%22%2C%22lastName%22%3A%22Rush%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rauri%20C%20K%22%2C%22lastName%22%3A%22Bowie%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Santiago%22%2C%22lastName%22%3A%22Ramirez%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Tracey%22%2C%22lastName%22%3A%22Chapman%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%20%20Whole-genome-level%20comparisons%20of%20sister%20taxa%20that%20vary%20in%20phenotype%20against%20a%20background%20of%20high%20genomic%20similarity%20can%20be%20used%20to%20identify%20the%20genomic%20regions%20that%20might%20underlie%20their%20phenotypic%20differences.%20In%20wild%20birds%2C%20this%20exploratory%20approach%20has%20detected%20markers%20associated%20with%20plumage%20coloration%2C%20beak%20and%20wing%20morphology%2C%20and%20complex%20behavioral%20traits%20like%20migration.%20Here%2C%20we%20use%20genomic%20comparisons%20of%20two%20closely%20related%20suboscine%20flycatchers%20%28Empidonax%20difficilis%20and%20E.%20occidentalis%29%20and%20their%20hybrids%20to%20search%20for%20candidate%20genes%20underlying%20their%20variation%20in%20innate%20vocal%20signals.%20We%20sequenced%20the%20genomes%20of%2020%20flycatchers%20that%20sang%20one%20of%20two%20species-specific%20pure%20song%20types%20and%2014%20putative%20hybrid%20individuals%20with%20intermediate%20song%20types.%20In%20the%20resulting%20genomic%20comparisons%2C%20we%20found%20six%20areas%20of%20high%20differentiation%20that%20may%20be%20associated%20with%20variation%20in%20nonlearned%20songs.%20These%20narrow%20regions%20of%20genomic%20differentiation%20contain%20a%20total%20of%2067%20described%20genes%2C%20of%20which%20three%20have%20been%20previously%20associated%20with%20forms%20of%20language%20impairment%20and%20dyslexia%20in%20humans%20and%2018%20are%20known%20to%20be%20differentially%20expressed%20in%20the%20song%20nuclei%20regions%20of%20the%20avian%20brain%20compared%20with%20adjacent%20parts%20of%20the%20avian%20brain.%20This%20%5Cu201cnatural%20experiment%5Cu201d%20therefore%20may%20help%20identify%20loci%20associated%20with%20song%20differences%20that%20merit%20further%20study%20across%20bird%20lineages%20with%20both%20learned%20and%20innate%20vocalizations.%22%2C%22date%22%3A%222023-07-27%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1093%5C%2Fevolut%5C%2Fqpad096%22%2C%22ISSN%22%3A%220014-3820%2C%201558-5646%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Facademic.oup.com%5C%2Fevolut%5C%2Farticle%5C%2F77%5C%2F8%5C%2F1818%5C%2F7186177%22%2C%22collections%22%3A%5B%22WZ6EF9QJ%22%5D%2C%22dateModified%22%3A%222024-01-23T02%3A57%3A32Z%22%7D%7D%2C%7B%22key%22%3A%22UK32IM33%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Walsh%20et%20al.%22%2C%22parsedDate%22%3A%222023-02-07%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BWalsh%2C%20J.%2C%20S.%20M.%20Billerman%2C%20B.%20G.%20Butcher%2C%20V.%20G.%20Rohwer%2C%20D.%20P.%20L.%20Toews%2C%20V.%20Vila-Coury%2C%20and%20I.%20J.%20Lovette%20%282023%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fwww.nature.com%5C%2Farticles%5C%2Fs42003-023-04532-8%26%23039%3B%26gt%3BA%20complex%20genomic%20architecture%20underlies%20reproductive%20isolation%20in%20a%20North%20American%20oriole%20hybrid%20zone%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BCommunications%20Biology%26lt%3B%5C%2Fi%26gt%3B%206%3A154.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20complex%20genomic%20architecture%20underlies%20reproductive%20isolation%20in%20a%20North%20American%20oriole%20hybrid%20zone%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shawn%20M.%22%2C%22lastName%22%3A%22Billerman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bronwyn%20G.%22%2C%22lastName%22%3A%22Butcher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vanya%20G.%22%2C%22lastName%22%3A%22Rohwer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%20P.%20L.%22%2C%22lastName%22%3A%22Toews%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vicens%22%2C%22lastName%22%3A%22Vila-Coury%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J.%22%2C%22lastName%22%3A%22Lovette%22%7D%5D%2C%22abstractNote%22%3A%22Abstract%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20Natural%20hybrid%20zones%20provide%20powerful%20opportunities%20for%20identifying%20the%20mechanisms%20that%20facilitate%20and%20inhibit%20speciation.%20Documenting%20the%20extent%20of%20genomic%20admixture%20allows%20us%20to%20discern%20the%20architecture%20of%20reproductive%20isolation%20through%20the%20identification%20of%20isolating%20barriers.%20This%20approach%20is%20particularly%20powerful%20for%20characterizing%20the%20accumulation%20of%20isolating%20barriers%20in%20systems%20exhibiting%20varying%20levels%20of%20genomic%20divergence.%20Here%2C%20we%20use%20a%20hybrid%20zone%20between%20two%20species%5Cu2014the%20Baltimore%20%28%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20Icterus%20galbula%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%29%20and%20Bullock%5Cu2019s%20%28%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20I.%20bullockii%5Cn%20%20%20%20%20%20%20%20%20%20%20%20%20%20%29%20orioles%5Cu2014to%20investigate%20this%20architecture%20of%20reproductive%20isolation.%20We%20combine%20whole%20genome%20re-sequencing%20with%20data%20from%20an%20additional%20313%20individuals%20amplityped%20at%20ancestry-informative%20markers%20to%20characterize%20fine-scale%20patterns%20of%20admixture%2C%20and%20to%20quantify%20links%20between%20genes%20and%20the%20plumage%20traits.%20On%20a%20genome-wide%20scale%2C%20we%20document%20several%20putative%20barriers%20to%20reproduction%2C%20including%20elevated%20peaks%20of%20divergence%20above%20a%20generally%20high%20genomic%20baseline%2C%20a%20large%20putative%20inversion%20on%20the%20Z%20chromosome%2C%20and%20complex%20interactions%20between%20melanogenesis-pathway%20candidate%20genes.%20Concordant%20and%20coincident%20clines%20for%20these%20different%20genomic%20regions%20further%20suggest%20the%20coupling%20of%20pre-%20and%20post-mating%20barriers.%20Our%20findings%20of%20complex%20and%20coupled%20interactions%20between%20pre-%20and%20post-mating%20barriers%20suggest%20a%20relatively%20rapid%20accumulation%20of%20barriers%20between%20these%20species%2C%20and%20they%20demonstrate%20the%20complexities%20of%20the%20speciation%20process.%22%2C%22date%22%3A%222023-02-07%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1038%5C%2Fs42003-023-04532-8%22%2C%22ISSN%22%3A%222399-3642%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.nature.com%5C%2Farticles%5C%2Fs42003-023-04532-8%22%2C%22collections%22%3A%5B%229BUGNQUJ%22%5D%2C%22dateModified%22%3A%222024-01-23T02%3A50%3A59Z%22%7D%7D%2C%7B%22key%22%3A%22TL7D8UNN%22%2C%22library%22%3A%7B%22id%22%3A2804417%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Mikles%20et%20al.%22%2C%22parsedDate%22%3A%222023%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BMikles%2C%20C.%20S.%2C%20P.%20Arcese%2C%20I.%20J.%20Lovette%2C%20S.%20M.%20Aguillon%2C%20Y.%20L.%20Chan%2C%20P.%20M.%20Benham%2C%20K.%20Carbeck%2C%20and%20J.%20Walsh%20%282023%29.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-ItemURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Flink.springer.com%5C%2F10.1007%5C%2Fs10592-023-01547-w%26%23039%3B%26gt%3BEvolutionary%20divergence%20and%20adaptive%20capacity%20in%20morphologically%20distinct%20song%20sparrow%20subspecies%26lt%3B%5C%2Fa%26gt%3B.%20%26lt%3Bi%26gt%3BConservation%20Genetics%26lt%3B%5C%2Fi%26gt%3B%2024%3A921%5Cu2013932.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Evolutionary%20divergence%20and%20adaptive%20capacity%20in%20morphologically%20distinct%20song%20sparrow%20subspecies%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chloe%20S.%22%2C%22lastName%22%3A%22Mikles%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Peter%22%2C%22lastName%22%3A%22Arcese%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Irby%20J.%22%2C%22lastName%22%3A%22Lovette%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Stepfanie%20M.%22%2C%22lastName%22%3A%22Aguillon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yvonne%20L.%22%2C%22lastName%22%3A%22Chan%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Phred%20M.%22%2C%22lastName%22%3A%22Benham%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Katherine%22%2C%22lastName%22%3A%22Carbeck%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jennifer%22%2C%22lastName%22%3A%22Walsh%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%2212%5C%2F2023%22%2C%22language%22%3A%22en%22%2C%22DOI%22%3A%2210.1007%5C%2Fs10592-023-01547-w%22%2C%22ISSN%22%3A%221566-0621%2C%201572-9737%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Flink.springer.com%5C%2F10.1007%5C%2Fs10592-023-01547-w%22%2C%22collections%22%3A%5B%22WZ6EF9QJ%22%2C%22PQMMSR8B%22%5D%2C%22dateModified%22%3A%222024-05-14T13%3A38%3A10Z%22%7D%7D%5D%7D
Robinson, B. W., S. Kurtis, B. G. Butcher, S. V. Edwards, I. J. Lovette, and J. Walsh (2025). The genomic basis of plumage polymorphism in the Eastern Screech-Owl ( Megascops asio ). Evolution 79:1885–1899.
Rao, M. T., B. G. Butcher, B. W. Robinson, I. J. Lovette, and J. Walsh (2025). Genomic data reveals mixed support for the current subspecies designations in the Megascops asio (Eastern Screech-Owl). Ornithology:ukaf047.
Céspedes Arias, L. N., A. M. Cuervo, C. D. Cadena, E. Bonaccorso, C. Witt, I. Lovette, and L. Campagna (2025). History of divergence and gene flow shaping geographic variation in Andean warblers ( Myioborus ). [Online.] Available at
Arias, L. C., K. F. P. Bennett, L. Campagna, A. W. Wood, E. Bonaccorso, A. M. Cuervo, C. D. Cadena, I. J. Lovette, and D. P. L. Toews (2025). Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics. [Online.] Available at
Hooper, D. M., K. A. Lopez, B. G. Butcher, I. J. Lovette, and S. C. Griffith (2025). Recent divergence and microgeographic genetic structure in an endangered Australian songbird: the southern Black‐Throated Finch. Ecology and Evolution 15:e72313.
Robinson, B. W., I. J. Lovette, and J. Walsh (2024). Plumage polymorphism in raptors. Ornithology:ukae026.
Carbeck, K., P. Arcese, I. Lovette, C. Pruett, K. Winker, and J. Walsh (2023). Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule. Nature Communications 14:6974.
García, N. C., L. Campagna, A. C. Rush, R. C. K. Bowie, and I. J. Lovette (2023). Comparative genomics of two Empidonax flycatchers reveal candidate genes for bird song production. Evolution 77:1818–1828.
Walsh, J., S. M. Billerman, B. G. Butcher, V. G. Rohwer, D. P. L. Toews, V. Vila-Coury, and I. J. Lovette (2023). A complex genomic architecture underlies reproductive isolation in a North American oriole hybrid zone. Communications Biology 6:154.
Mikles, C. S., P. Arcese, I. J. Lovette, S. M. Aguillon, Y. L. Chan, P. M. Benham, K. Carbeck, and J. Walsh (2023). Evolutionary divergence and adaptive capacity in morphologically distinct song sparrow subspecies. Conservation Genetics 24:921–932.
Center
Biodiversity Studies & Higher Education
Work607-254-2140
Email ijl2@cornell.edu
Website The Lovette Lab