# Publications Download 30 citations download- [BibTeX](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=bibtex) - [EndNote X3 XML](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=endnote8) - [EndNote 7 XML](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=endnote7) - [Endnote tagged](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=tagged) - [Marc](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=marc) - [PubMedId](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=pubmed_id) - [RIS](/bibcite/export?pager_style=no_pager&number_of_items=30&sort_field=bibcite_year--desc&taxonomy_filters=&&&format=ris) ### Working Paper Nicolai M, Debruyn G, Bowie R, Edwards S, Carneiro M, D’Alba L, Shawkey M. [The evolution of brilliant iridescence in birds](https://doi.org/10.21203/rs.3.rs-8020267/v1). 2025. doi:https://doi.org/10.21203/rs.3.rs-8020267/v1 Nicolai M, Debruyn G, Bowie R, Edwards S, Carneiro M, D’Alba L, Shawkey M. [The evolution of brilliant iridescence in birds](https://doi.org/10.21203/rs.3.rs-8020267/v1). 2025. doi:https://doi.org/10.21203/rs.3.rs-8020267/v1 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.researchsquare.com/article/rs-8020267/v1) Colors of iridescent feathers are some of the most striking in nature, but when and how they evolved remains elusive. Using a dataset of 71,536 body patches from 5,755 bird species, we reconstruct the evolution of iridescence. We find that brilliant... - [ descriptionPublisher's Version](https://www.researchsquare.com/article/rs-8020267/v1) ### 2026 Lopez KA, de Carvalho CF, de Lima HS, Naka LN, Amaral FR do, Bravo GA, Edwards S V. [Pangenomes reveal extensive structural variation in a suboscine passerine bird, the Pearly-vented Tody-Tyrant (Hemitriccus margaritaceiventer)](https://doi.org/10.1093/genetics/iyag109). Genetics. 2026. doi:10.1093/genetics/iyag109 Lopez KA, de Carvalho CF, de Lima HS, Naka LN, Amaral FR do, Bravo GA, Edwards S V. [Pangenomes reveal extensive structural variation in a suboscine passerine bird, the Pearly-vented Tody-Tyrant (Hemitriccus margaritaceiventer)](https://doi.org/10.1093/genetics/iyag109). Genetics. 2026. doi:10.1093/genetics/iyag109 - [ descriptionPublisher's Version](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyag109/8666445) - [ descriptionPublisher's Version](https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyag109/8666445) Edwards S V, Li H. [Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics](https://doi.org/10.1098/rspb.2025.2899). Proceedings of the Royal Society B. 2026;293. doi:https://doi.org/10.1098/rspb.2025.2899 Edwards S V, Li H. [Population-scale long-read DNA sequencing: peering under the hood of the new evolutionary genomics](https://doi.org/10.1098/rspb.2025.2899). Proceedings of the Royal Society B. 2026;293. doi:https://doi.org/10.1098/rspb.2025.2899 - [ descriptionPublisher's Version](https://royalsocietypublishing.org/rspb/article/293/2069/20252899/481431/Population-scale-long-read-DNA-sequencing-peering) - [ picture\_as\_pdf\[PDF\]](/sites/g/files/omnuum6356/files/2026-05/rspb.2025.2899.pdf) - [ descriptionPublisher's Version](https://royalsocietypublishing.org/rspb/article/293/2069/20252899/481431/Population-scale-long-read-DNA-sequencing-peering) - [ picture\_as\_pdf\[PDF\]](/sites/g/files/omnuum6356/files/2026-05/rspb.2025.2899.pdf) Sutherland WJ, Burgess ND, Edwards S V, Jones JP, Soltis PS, Tilman D, Allen JM, Andrianandrasana HT, Armour CJ, August T, et al. [Nine changes needed to deliver a radical transformation in biodiversity measurement](https://doi.org/10.1073/pnas.251934512). Proceedings of the National Academy of Sciences. 2026;123(10). Sutherland WJ, Burgess ND, Edwards S V, Jones JP, Soltis PS, Tilman D, Allen JM, Andrianandrasana HT, Armour CJ, August T, et al. [Nine changes needed to deliver a radical transformation in biodiversity measurement](https://doi.org/10.1073/pnas.251934512). Proceedings of the National Academy of Sciences. 2026;123(10). - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/sutherland-et-al-2026-nine-changes-needed-to-deliver-a-radical-transformation-in-biodiversity-measurement.pdf) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/sutherland-et-al-2026-nine-changes-needed-to-deliver-a-radical-transformation-in-biodiversity-measurement.pdf) Fang B, Edwards S V. [Pangenomes: new tools for ecological and evolutionary genomics](https://doi.org/10.1016/j.tree.2025.11.010). Trends in Ecology & Evolution. 2026;41(3):p230–244. doi: https://doi.org/10.1016/j.tree.2025.11.010 Fang B, Edwards S V. [Pangenomes: new tools for ecological and evolutionary genomics](https://doi.org/10.1016/j.tree.2025.11.010). Trends in Ecology & Evolution. 2026;41(3):p230–244. doi: https://doi.org/10.1016/j.tree.2025.11.010 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(25)00344-1) Genomic structural variation is an important component of genetic variation in natural populations. By assembling and analyzing multiple high-quality genomes within a species or clade, pangenomes capture variation that can be missed by reference-based... - [ descriptionPublisher's Version](https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(25)00344-1) Boria RA, Wooldridge B, Kautt AF, Ashing-Giwa K, McFadden S, Kirby C, Edwards S V, Hoekstra HE. [Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes](https://doi.org/10.64898/2026.01.26.699144). bioRxiv. 2026. Boria RA, Wooldridge B, Kautt AF, Ashing-Giwa K, McFadden S, Kirby C, Edwards S V, Hoekstra HE. [Pleistocene climatic oscillations impact the diversification of deer mice (Peromyscus maniculatus) and the independent evolution of ecotypes](https://doi.org/10.64898/2026.01.26.699144). bioRxiv. 2026. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/2026.01.26.699144v1.full_.pdf) A central question in evolutionary biology is whether local adaptation is predictable when a species repeatedly encounters similar environments. The deer mouse, *Peromyscus maniculatus*, has a range of over 13 million km2 in North America and may be found... - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/2026.01.26.699144v1.full_.pdf) Fang B, Edwards S V. [Inferring Species Trees](/publication/inferring-species-trees). Academic Press. 2026:147–157. doi:https://doi.org/10.1016/B978-0-443-15750-9.00174-9 Fang B, Edwards S V. [Inferring Species Trees](/publication/inferring-species-trees). Academic Press. 2026:147–157. doi:https://doi.org/10.1016/B978-0-443-15750-9.00174-9 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/chapter/referencework/abs/pii/B9780443157509001749?via%3Dihub) Species trees are a basic and common type of phylogenetic tree whose tips are species, population and lineages. Inferring species trees is a growing area of research that uses many classical methods of phylogenetic inference, such as Bayesian or maximum... - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/chapter/referencework/abs/pii/B9780443157509001749?via%3Dihub) ### 2025 Orzechowski SC, Doudin D, Shams F, Schmitt J, Drew A, Wilson C, Joseph L, Ezaz T, Edward S V. [Neo-sex chromosomes track the mitochondrial phylogeny and exhibit an extensive added stratum of recombination suppression in honeyeaters (Aves: Meliphagidae)](https://doi.org/10.1093/gbe/evaf215). Genome Biology and Evolution. 2025;17(12). doi:https://doi.org/10.1093/gbe/evaf215 Orzechowski SC, Doudin D, Shams F, Schmitt J, Drew A, Wilson C, Joseph L, Ezaz T, Edward S V. [Neo-sex chromosomes track the mitochondrial phylogeny and exhibit an extensive added stratum of recombination suppression in honeyeaters (Aves: Meliphagidae)](https://doi.org/10.1093/gbe/evaf215). Genome Biology and Evolution. 2025;17(12). doi:https://doi.org/10.1093/gbe/evaf215 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/gbe/article/17/12/evaf215/8323801?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/evaf215.pdf) Mounting discoveries of avian neo-sex chromosomes are providing opportunities to understand the extent of variation in fundamental aspects of avian neo-sex chromosome evolution. We integrated cytogenetic data, long-read assemblies, and whole-genome... - [ descriptionPublisher's Version](https://academic.oup.com/gbe/article/17/12/evaf215/8323801?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/evaf215.pdf) Pegan TM, Sivakumar A, Burns C, Lopez KA, Fang B, Melendez NM, Bartel L, Edwards S V. [The value of structural variants to conservation genomics in the pangenome era](https://doi.org/10.1093/jhered/esaf098). Journal of Heredity. 2025. doi:https://doi.org/10.1093/jhered/esaf098 Pegan TM, Sivakumar A, Burns C, Lopez KA, Fang B, Melendez NM, Bartel L, Edwards S V. [The value of structural variants to conservation genomics in the pangenome era](https://doi.org/10.1093/jhered/esaf098). Journal of Heredity. 2025. doi:https://doi.org/10.1093/jhered/esaf098 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/jhered/advance-article/doi/10.1093/jhered/esaf098/8341471?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/esaf098.pdf) Structural variants (SVs) comprise an axis of genetic diversity with strong consequences for phenotype and fitness, making them a potentially important target for conservation genomics. Here, we review how and why SVs can play a role in conservation... - [ descriptionPublisher's Version](https://academic.oup.com/jhered/advance-article/doi/10.1093/jhered/esaf098/8341471?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/esaf098.pdf) Robinson BW, Kurtis S, Butcher BG, Edwards S V, Lovette IJ, Walsh J. [ The genomic basis of plumage polymorphism in the Eastern Screech-Owl (Megascops asio)](https://doi.org/10.1093/evolut/qpaf120). Evolution. 2025;79(9). doi:https://doi.org/10.1093/evolut/qpaf120 Robinson BW, Kurtis S, Butcher BG, Edwards S V, Lovette IJ, Walsh J. [ The genomic basis of plumage polymorphism in the Eastern Screech-Owl (Megascops asio)](https://doi.org/10.1093/evolut/qpaf120). Evolution. 2025;79(9). doi:https://doi.org/10.1093/evolut/qpaf120 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/evolut/article-abstract/79/9/1885/8155227) Understanding the genetic basis of polymorphic traits is useful for exploring the origin and maintenance of variable phenotypes. Previous work on color polymorphism in birds has evolved from targeting candidate genes to whole-genome scans, consequently... - [ descriptionPublisher's Version](https://academic.oup.com/evolut/article-abstract/79/9/1885/8155227) Khodaei M, Edwards S V, Beerli P. [Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling ](https://doi.org/10.1093/sysbio/syaf015). Systematic Biology. 2025;74(5). doi:https://doi.org/10.1093/sysbio/syaf015 Khodaei M, Edwards S V, Beerli P. [Estimating Genome-Wide Phylogenies Using Probabilistic Topic Modeling ](https://doi.org/10.1093/sysbio/syaf015). Systematic Biology. 2025;74(5). doi:https://doi.org/10.1093/sysbio/syaf015 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/sysbio/article/74/5/850/8125206?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/syaf015.pdf) Methods for rapidly inferring the evolutionary history of species or populations with genome-wide data are progressing, but computational constraints still limit our abilities in this area. We developed an alignment-free method to infer genome-wide... - [ descriptionPublisher's Version](https://academic.oup.com/sysbio/article/74/5/850/8125206?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/syaf015.pdf) Jindal G, Zhu M, Weksler N, Young J, Song B, Solvason J, Le S, Tabin CJ, Sackton T, Edwards SV, et al. [Elucidating the Genetic Basis of Loss of Flight inthe Emu, Dromaius novaehollandiae](https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmor.70059?saml_referrer). 2025. doi:https://doi.org/10.1002/jmor.70059 Jindal G, Zhu M, Weksler N, Young J, Song B, Solvason J, Le S, Tabin CJ, Sackton T, Edwards SV, et al. [Elucidating the Genetic Basis of Loss of Flight inthe Emu, Dromaius novaehollandiae](https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmor.70059?saml_referrer). 2025. doi:https://doi.org/10.1002/jmor.70059 - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmor.70059?saml_referrer) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-07/Journal%20of%20Morphology%20-%202025%20-%20%20-%20Abstracts%20of%20the%20International%20Congress%20of%20Vertebrate%20Morphology%2014%20Virtual%20Meeting%20%2007.pdf) - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/epdf/10.1002/jmor.70059?saml_referrer) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-07/Journal%20of%20Morphology%20-%202025%20-%20%20-%20Abstracts%20of%20the%20International%20Congress%20of%20Vertebrate%20Morphology%2014%20Virtual%20Meeting%20%2007.pdf) Jindal G, Zhu M, Weksler N, Young J, Song B, Solvason J, Le S, Tabin C, Sackton T, Edwards S. [ Elucidating the Genetic Basis of Loss of Flight in the Emu, Dromaius novaehollandiae](https://doi.org/10.1002/jmor.70059). Journal of Morphology. 2025;286. doi:https://doi.org/10.1002/jmor.70059 Jindal G, Zhu M, Weksler N, Young J, Song B, Solvason J, Le S, Tabin C, Sackton T, Edwards S. [ Elucidating the Genetic Basis of Loss of Flight in the Emu, Dromaius novaehollandiae](https://doi.org/10.1002/jmor.70059). Journal of Morphology. 2025;286. doi:https://doi.org/10.1002/jmor.70059 - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/10.1002/jmor.70059) - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/10.1002/jmor.70059) Wu S, Tao Z, Liu L, Marshall CR, Edwards S V, Zhou Z, Rheindt FE. [New fossils imply a deeper origin of modern birds in the Mesozoic ](https://doi.org/10.1093/nsr/nwaf238). National Science Review. 2025;12(7). doi:https://doi.org/10.1093/nsr/nwaf238 Wu S, Tao Z, Liu L, Marshall CR, Edwards S V, Zhou Z, Rheindt FE. [New fossils imply a deeper origin of modern birds in the Mesozoic ](https://doi.org/10.1093/nsr/nwaf238). National Science Review. 2025;12(7). doi:https://doi.org/10.1093/nsr/nwaf238 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/nsr/article/12/7/nwaf238/8158921?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/nwaf238.pdf) Macroevolutionary forces, such as rare catastrophes, have repeatedly disrupted and reset the evolutionary trajectories of Earth's major organismal groups. The Cretaceous–Paleogene (K/Pg) extinction event, approximately 66 Ma, resulted in the demise of ∼75... - [ descriptionPublisher's Version](https://academic.oup.com/nsr/article/12/7/nwaf238/8158921?guestAccessKey=) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/nwaf238.pdf) Beck JN, Baetscher DS, Tobin C, Edwards S V, Sin SYW, Fitzgerald S, Tuttle VJ, Peschon J, Larson WA. [Quantifying impacts of seabird bycatch using genetic assignment: A case study of black-footed albatross in US fisheries](/publication/quantifying-impacts-seabird-bycatch-using-genetic-assignment-case-study-black-footed). Biological Conservation. 2025;303. doi:https://doi.org/10.1016/j.biocon.2025.110965 Beck JN, Baetscher DS, Tobin C, Edwards S V, Sin SYW, Fitzgerald S, Tuttle VJ, Peschon J, Larson WA. [Quantifying impacts of seabird bycatch using genetic assignment: A case study of black-footed albatross in US fisheries](/publication/quantifying-impacts-seabird-bycatch-using-genetic-assignment-case-study-black-footed). Biological Conservation. 2025;303. doi:https://doi.org/10.1016/j.biocon.2025.110965 - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/pii/S0006320725000023) - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/pii/S0006320725000023) Boldgiv B, Lkhagva A, Edwards S, Stenseth NC, Bayarsaikhan J, Altangerel D, Usukhjarga D, Dovchin B, Gombobaatar S, Batsaikhan N, et al. [Global natural history infrastructure requires international solidarity, support, and investment in local capacity](/publication/global-natural-history-infrastructure-requires-international-solidarity-support-and). Proceedings of the National Academy of Sciences. 2025;122(6). doi:https://doi.org/10.1073/pnas.241123212 Boldgiv B, Lkhagva A, Edwards S, Stenseth NC, Bayarsaikhan J, Altangerel D, Usukhjarga D, Dovchin B, Gombobaatar S, Batsaikhan N, et al. [Global natural history infrastructure requires international solidarity, support, and investment in local capacity](/publication/global-natural-history-infrastructure-requires-international-solidarity-support-and). Proceedings of the National Academy of Sciences. 2025;122(6). doi:https://doi.org/10.1073/pnas.241123212 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2411232122) Amid global challenges like climate change, extinctions, and disease epidemics, science and society require nuanced, international solutions that are grounded in robust, interdisciplinary perspectives and datasets that span deep time. Natural history... - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2411232122) Edwards S V, Fang B, Khost D, Kolyfetis GE, Cheek RG, Deraad D, Chen N, Fitzpatrick JW, McCormack JE, Funk C, et al. [Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants](/publication/comparative-population-pangenomes-reveal-unexpected-complexity-and-fitness-effects). 2025. doi:https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1.abstract Edwards S V, Fang B, Khost D, Kolyfetis GE, Cheek RG, Deraad D, Chen N, Fitzpatrick JW, McCormack JE, Funk C, et al. [Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants](/publication/comparative-population-pangenomes-reveal-unexpected-complexity-and-fitness-effects). 2025. doi:https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1.abstract - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1.abstract) Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/10.1101/2025.02.11.637762v1.abstract) Shakya SB, Edwards S V, Sackton TB. [Convergent evolution of noncoding elements associated with short tarsus length in birds](/publication/convergent-evolution-noncoding-elements-associated-short-tarsus-length-birds). 2025. doi:https://doi.org/10.1186/s12915-025-02156-4 Shakya SB, Edwards S V, Sackton TB. [Convergent evolution of noncoding elements associated with short tarsus length in birds](/publication/convergent-evolution-noncoding-elements-associated-short-tarsus-length-birds). 2025. doi:https://doi.org/10.1186/s12915-025-02156-4 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12915-025-02156-4) ### **Background** Convergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various genomic signatures can help identify cases of convergent evolution at the molecular level, including changes in... - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12915-025-02156-4) Edwards SV, Reed M, editors. [New Perspectives in Ornithology: 21st Century Dispatches Across the World of Birds](https://books.google.com/books?hl=en&lr=&id=lyiUEQAAQBAJ&oi=fnd&pg=PP1&dq=info:kpIK_94qtCkJ:scholar.google.com&ots=ByxEJwtRtE&sig=AgLBN_ybZIiYbp1G_j7aiTj3-3E#v=onepage&q&f=false). Oxford University Press; 2025. doi:10.1093/oso/9780197787670.001.0001 Edwards SV, Reed M, editors. [New Perspectives in Ornithology: 21st Century Dispatches Across the World of Birds](https://books.google.com/books?hl=en&lr=&id=lyiUEQAAQBAJ&oi=fnd&pg=PP1&dq=info:kpIK_94qtCkJ:scholar.google.com&ots=ByxEJwtRtE&sig=AgLBN_ybZIiYbp1G_j7aiTj3-3E#v=onepage&q&f=false). Oxford University Press; 2025. doi:10.1093/oso/9780197787670.001.0001 - [ descriptionPublisher's Version](https://books.google.com/books?id=lyiUEQAAQBAJ&lpg=PP1&ots=ByxEJwtRtE&dq=info%3AkpIK_94qtCkJ%3Ascholar.google.com&lr&pg=PR4#v=onepage&q&f=false) - [ descriptionPublisher's Version](https://books.google.com/books?id=lyiUEQAAQBAJ&lpg=PP1&ots=ByxEJwtRtE&dq=info%3AkpIK_94qtCkJ%3Ascholar.google.com&lr&pg=PR4#v=onepage&q&f=false) Fang B, Edwards S V. [Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses](https://doi.org/10.1101/2025.06.27.662071). bioRxiv. 2025. doi:https://doi.org/10.1101/2025.06.27.662071 Fang B, Edwards S V. [Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses](https://doi.org/10.1101/2025.06.27.662071). bioRxiv. 2025. doi:https://doi.org/10.1101/2025.06.27.662071 - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.biorxiv.org/content/10.1101/2025.06.27.662071v1) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/2025.06.27.662071v1.full_.pdf) Germline-restricted chromosomes (GRCs) are unique to germ cells and absent from somatic cells in songbirds. However, their contents, functions, and evolutionary mechanisms remain unclear. We performed comparative genomics on long-read assembled GRCs from... - [ descriptionPublisher's Version](https://www.biorxiv.org/content/10.1101/2025.06.27.662071v1) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/2026-05/2025.06.27.662071v1.full_.pdf) ### 2024 Butler J, McKinney J, Ludington S, Mabogunjie M, Baker P, Singh D, Edwards S, O’Connell L. [Tadpoles rely on mechanosensory stimuli for communication when visual capabilities are poor](https://doi.org/10.1016/j.ydbio.2024.05.006). Developmental Biology. 2024. Butler J, McKinney J, Ludington S, Mabogunjie M, Baker P, Singh D, Edwards S, O’Connell L. [Tadpoles rely on mechanosensory stimuli for communication when visual capabilities are poor](https://doi.org/10.1016/j.ydbio.2024.05.006). Developmental Biology. 2024. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/abs/pii/S0012160624001179) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/tadpoles_rely_on_mechanosensory_stimuli_for_communication_when_visual_capabilities_are_poor_-_sciencedirect.pdf) The ways in which animals sense the world changes throughout development. For example, young of many species have limited visual capabilities, but still make social decisions, likely based on information gathered through other sensory modalities. Poison... - [ descriptionPublisher's Version](https://www.sciencedirect.com/science/article/abs/pii/S0012160624001179) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/tadpoles_rely_on_mechanosensory_stimuli_for_communication_when_visual_capabilities_are_poor_-_sciencedirect.pdf) Thomas G, Gemmell P, Shakya S, Hu Z, Liu J, Sackton T, Edwards S. [Practical guidance and workflows for identifying fast evolving non-coding genomic elements using PhyloAcc](https://doi.org/10.1093/icb/icae056). Integrative and Comparative Biology. 2024:icae056. Thomas G, Gemmell P, Shakya S, Hu Z, Liu J, Sackton T, Edwards S. [Practical guidance and workflows for identifying fast evolving non-coding genomic elements using PhyloAcc](https://doi.org/10.1093/icb/icae056). Integrative and Comparative Biology. 2024:icae056. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/icb/advance-article-abstract/doi/10.1093/icb/icae056/7685531?redirectedFrom=PDF&casa_token=hELo5GYAmf0AAAAA:VF-UEUX9w9TAkr-aKp5kkE_K9k1eWJgaWOmtSX-h17nQ-uzcADNxxiR4jEYAlt8z4eJAq8ZOMxhG) Comparative genomics provides ample ways to study genome evolution and its relationship to phenotypic traits. By developing and testing alternate models of evolution throughout a phylogeny, one can estimate rates of molecular evolution along different... - [ descriptionPublisher's Version](https://academic.oup.com/icb/advance-article-abstract/doi/10.1093/icb/icae056/7685531?redirectedFrom=PDF&casa_token=hELo5GYAmf0AAAAA:VF-UEUX9w9TAkr-aKp5kkE_K9k1eWJgaWOmtSX-h17nQ-uzcADNxxiR4jEYAlt8z4eJAq8ZOMxhG) Edwards S, Cloutier A, Cockburn G, Driver R, Grayson P, Katih K, Baldwin M, Sackton T, Baker A. [A nuclear genome assembly of an extinct flightless bird, the little bush moa](http://doi.org/10.1126/sciadv.adj6823). Science Advances. 2024;10(21):eadj6823. Edwards S, Cloutier A, Cockburn G, Driver R, Grayson P, Katih K, Baldwin M, Sackton T, Baker A. [A nuclear genome assembly of an extinct flightless bird, the little bush moa](http://doi.org/10.1126/sciadv.adj6823). Science Advances. 2024;10(21):eadj6823. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.science.org/doi/full/10.1126/sciadv.adj6823) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/sciadv.adj6823.pdf) We present a draft genome of the little bush moa (*Anomalopteryx didiformis*)—one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand—using ancient DNA recovered from a fossil bone from the South Island. We recover a... - [ descriptionPublisher's Version](https://www.science.org/doi/full/10.1126/sciadv.adj6823) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/sciadv.adj6823.pdf) Stringer E, Gruber B, Sarre S, Wardle G, Edwards S, Dickman C, Greenville A, Duncan R. [Boom-bust population dynamics drive rapid genetic change](https://doi.org/10.1073/pnas.2320590121). Proceedings of the National Academy of Sciences. 2024;121(18):e2320590121. Stringer E, Gruber B, Sarre S, Wardle G, Edwards S, Dickman C, Greenville A, Duncan R. [Boom-bust population dynamics drive rapid genetic change](https://doi.org/10.1073/pnas.2320590121). Proceedings of the National Academy of Sciences. 2024;121(18):e2320590121. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2320590121) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/boom-bust_population_dynamics_drive_rapid_genetic_change_pnas.pdf) Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause... - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2320590121) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/boom-bust_population_dynamics_drive_rapid_genetic_change_pnas.pdf) Thiers B, Roberts T, Rundell R, Spellman G, Fischer G, Nelson G, Bates J, Edwards S, B S, Zaspel J, et al. [Duke’s herbarium merits continued enhancement, not dissolution](https://doi.org/10.1093/biosci/biae031). BioScience. 2024;74(8):507–508. Thiers B, Roberts T, Rundell R, Spellman G, Fischer G, Nelson G, Bates J, Edwards S, B S, Zaspel J, et al. [Duke’s herbarium merits continued enhancement, not dissolution](https://doi.org/10.1093/biosci/biae031). BioScience. 2024;74(8):507–508. - [ descriptionPublisher's Version](https://academic.oup.com/bioscience/article/74/8/507/7657891) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/dukes_herbarium.pdf) - [ descriptionPublisher's Version](https://academic.oup.com/bioscience/article/74/8/507/7657891) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/dukes_herbarium.pdf) Gemmell P, Sackton T, Edwards S, Liu J. [A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011995). PLOS Computational Biology. 2024;20(4). Gemmell P, Sackton T, Edwards S, Liu J. [A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011995). PLOS Computational Biology. 2024;20(4). - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011995) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/journal.pcbi_.1011995.pdf) Genomes contain conserved non-coding sequences that perform important biological functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that associates nucleotide substitution rates with changes in a continuous trait of interest... - [ descriptionPublisher's Version](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011995) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/journal.pcbi_.1011995.pdf) Dinnage R, Sarre S, Duncan R, Dickman C, Edwards S, Greenville A, M W, Gruber B. [slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time](https://doi.org/10.1111/1755-0998.13916). Molecular Ecology Resources. 2024;24(3). Dinnage R, Sarre S, Duncan R, Dickman C, Edwards S, Greenville A, M W, Gruber B. [slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time](https://doi.org/10.1111/1755-0998.13916). Molecular Ecology Resources. 2024;24(3). - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13916) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/molecular_ecology_resources_-_2023_-_dinnage_-_slimr_an_r_package_for_tailor-made_integrations_of_data_in_population.pdf) Software for realistically simulating complex population genomic processes is rev-olutionizing our understanding of evolutionary processes, and providing novel op-portunities for integrating empirical data with simulations. However, the integrationbetween... - [ descriptionPublisher's Version](https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13916) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/molecular_ecology_resources_-_2023_-_dinnage_-_slimr_an_r_package_for_tailor-made_integrations_of_data_in_population.pdf) Sin S, Ke F, Chen G, Huang P-Y, Enbody E, Karubian J, Webster M, Edwards S. [Genetic basis and evolution of structural color polymorphism in an Australian songbird](https://doi.org/10.1093/molbev/msae046). Molecular Biology and Evolution. 2024;41(3):msae046. Sin S, Ke F, Chen G, Huang P-Y, Enbody E, Karubian J, Webster M, Edwards S. [Genetic basis and evolution of structural color polymorphism in an Australian songbird](https://doi.org/10.1093/molbev/msae046). Molecular Biology and Evolution. 2024;41(3):msae046. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://academic.oup.com/mbe/article/41/3/msae046/7615515) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/msae046.pdf) Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (*Malurus leucopterus*), subspecies on two islands have a... - [ descriptionPublisher's Version](https://academic.oup.com/mbe/article/41/3/msae046/7615515) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/msae046.pdf) Jiang Z, Zang W, Ericson PG, Song G, Wu S, Feng S, Drovetski S, Liu G, Zhang D, Saitoh T, et al. [Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)](https://doi.org/10.1186/s12915-024-01848-7). BMC Biology. 2024;22(1):49. Jiang Z, Zang W, Ericson PG, Song G, Wu S, Feng S, Drovetski S, Liu G, Zhang D, Saitoh T, et al. [Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)](https://doi.org/10.1186/s12915-024-01848-7). BMC Biology. 2024;22(1):49. - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12915-024-01848-7) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/s12915-024-01848-7.pdf) - [ descriptionPublisher's Version](https://link.springer.com/article/10.1186/s12915-024-01848-7) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/s12915-024-01848-7.pdf) Wu S, Rheindt F, Zhang J, Wang J, Zhang K, Quan C, Lit Z, Wang M, Wu F, Qu Y, et al. [Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous](https://www.doi.org/10.1073/pnas.2319696121). Proceedings of the National Academy of Sciences. 2024;121(8):e2319696121. Wu S, Rheindt F, Zhang J, Wang J, Zhang K, Quan C, Lit Z, Wang M, Wu F, Qu Y, et al. [Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous](https://www.doi.org/10.1073/pnas.2319696121). Proceedings of the National Academy of Sciences. 2024;121(8):e2319696121. - add\_circle\_outline do\_not\_disturb\_on Abstract - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2319696121) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/wu-et-al-2024-genomes-fossils-and-the-concurrent-rise-of-modern-birds-and-flowering-plants-in-the-late-cretaceous.pdf) The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed the genomes of 124 species across all Neoavian orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding... - [ descriptionPublisher's Version](https://www.pnas.org/doi/abs/10.1073/pnas.2319696121) - [ picture\_as\_pdfPDF](/sites/g/files/omnuum6356/files/wu-et-al-2024-genomes-fossils-and-the-concurrent-rise-of-modern-birds-and-flowering-plants-in-the-late-cretaceous.pdf)