Papers

Publications

Published in 2024

Total 2024

J. Stiller. et al. Complexity of avian evolution revealed by family-level genomes. Nature (2024). DOI: https://doi.org/10.1038/s41586-024-07323-1

S. Mirarab. et al. A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences 121, e2319506121 (2024). DOI: https://doi.org/10.1073/pnas.2319506121

G. Chen. et al. Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events. Nature Communications 15.1 (2024): 3151. DOI: https://doi.org/10.1038/s41467-024-47501-3

Published in 2023

Total 2023

K. Wanders. et al. 2023. Polygamy and purifying selection in birds. Evolution 77, 276-288. DOI: https://doi.org/10.1093/evolut/qpac010

R. R. Germain. et al. 2023. Species-specific traits mediate avian demographic responses under past climate change. Nat Ecol Evol. DOI: https://doi.org/10.1038/s41559-023-02055-3

R. R. Germain. et al. 2023. Changes in the functional diversity of modern bird species over the last million years. PNAS 120, 7. DOI: https://doi.org/10.1073/pnas.2201945119

G. Femerling. et al. 2023. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 40, 12. DOI: https://doi.org/10.1093/molbev/msad256

Published in 2022

Total 2022

T. L. Cole. et al. 2022. Genomic insights into the secondary aquatic transition of penguins. Nat Commun 13, 3912. DOI: https://doi.org/10.1038/s41467-022-31508-9

Y. Ji. et al. 2022. Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds. Sci Adv 8, 35. DOI: https://doi.org/10.1126/sciadv.abo0099

X. Li. et al. 2022. Draft genome assemblies of four manakins. Sci Data 9, 564. DOI: https://doi.org/10.1038/s41597-022-01680-0

Published in 2021

Total 2021

S. Andreu-Sánchez. et al. 2021. Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles. GigaScience 10, 1. DOI: https://doi.org/10.1093/gigascience/giaa161

J. Li. et al. 2021. A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. GigaScience 10, 1. DOI: https://doi.org/10.1093/gigascience/giaa142

J. Liu. et al. 2021. A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome research 31, 497. DOI: https://doi.org/10.1101/gr.271569.120

L. Puetz. et al. 2021. Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication. Advanced Genetics 2, 2100018. DOI: https://doi.org/10.1002/ggn2.202100018

Y. Qu. et al. 2021. The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau. PNAS 118. DOI: https://doi.org/10.1073/pnas.2012398118

K. Thorup. et al. 2021. Response of an Afro-Palearctic bird migrant to glaciation cycles. PNAS 118, 52. DOI: https://doi.org/10.1073/pnas.2023836118

M. Wang. et al. 2021. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biology 19, 118. DOI: https://doi.org/10.1186/s12915-021-01052-x

Z. Wang. et al. 2021. Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological Research 42, 51. DOI: https://doi.org/10.24272/j.issn.2095-8137.2020.175

Published in 2020

Total 2020

S. Feng. et al. 2020 Dense sampling of bird diversity increases power of comparative genomics. Nature 587. 252. DOI: https://doi.org/10.1038/s41586-020-2873-9

J. Armstrong. et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587. 246. DOI: https://doi.org/10.1038/s41586-020-2871-y

Published in 2019

Total 2019

E. L. Braun. et al. 2019. Resolving the avian tree of life from top to bottom: the promise and potential boundaries of the phylogenomic era. Avian Genomics in Ecology and Evolution. Springer 151. DOI:10.1007/978-3-030-16477-5_6

T. L. Cole. et al. 2019 Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation. Molecular biology and evolution 36. 784. DOI: 10.1093/molbev/msz017

S. Feng. et al. 2019 The genomic footprints of the fall and recovery of the crested ibis. Current Biology 29, 340. DOI: 10.1016/j.cub.2018.12.008

Y. Hao. et al. 2019 Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. PANS 116, 11851. DOI: 10.1073/pnas.1819657116

Â. M. Ribeiro. et al. 2019 31° South: The physiology of adaptation to arid conditions in a passerine bird. Molecular ecology DOI:10.1111/mec.15176

J. Stiller. et al. 2019 Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies. Diversity 11, 115. DOI: 10.3390/d11070115

M. H. Weissensteiner. et al. 2019 Repetitive DNA: The Dark Matter of Avian Genomics. Avian Genomics in Ecology and Evolution. Springer. 93. DOI:10.1007/978-3-030-16477-5_5

Published in 2018

Total 2018

P. Alström. et al. 2018. Complete species-level phylogeny of the leaf warbler(Aves: Phylloscopidae) radiation. Molecular phylogenetics and evolution 126,141. DOI: 10.1016/j.ympev.2018.03.031

C. Holt. et al. 2018. Improved genome assembly and annotation for the rock pigeon (Columba livia). G3: Genes, Genomes, Genetics 8, 1391. DOI:10.1534/g3.117.300443

H. A. Lewin. et al. 2018. EarthBioGenome Project: Sequencing life for the future of life. PANS. 115, 4325. DOI: 10.1073/pnas.1720115115

M. P. Pedersen. et al. 2018. Phylogeography of a 'great speciator'(Aves:Edolisoma tenuirostre) reveals complex dispersal and diversification dynamicsacross the Indo-Pacific. Journal of biogeography 45, 826. DOI:10.1111/jbi.13182

A.G. Phillips. et al. 2018. Effects of phylogeny and geography on ecomorphological traits in passerine bird clades. Journal of biogeography 45, 2337. DOI:10.1111/jbi.13383

G. Zhang. 2018. The bird's-eye view on chromosome evolution. Genome biology 19, 201. DOI:10.1186/s13059-018-1585-z

Published in 2017

Total 2017

J. Korlach. et al. 2017. De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate andshort reads. GigaScience 6, 85. DOI:10.1093/gigascience/gix085

R. Seki. et al. 2017. Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nature communications 8, 14229. DOI:10.1038/ncomms14229

Published in 2016

Total 2016

D. Almeida. et al. 2016. Whole-genome identification, phylogeny, and evolution of the cytochrome P450 family 2 (CYP2) subfamilies in birds. Genome biology and evolution 8, 1115. DOI:10.1093/gbe/evw041

M. Farre. et al.2016. Novel insights into chromosome evolution in birds, archosaurs, andreptiles. Genome biology and evolution 8, 2442. DOI:10.1093/gbe/evw166

E. D. Jarvis. 2016. Perspectives from the avian phylogenomics project: questions that can be answered with sequencing all genomes of a vertebrate class. AnnualReview of Animal Biosciences 4, 45. DOI:10.1146/annurev-animal-021815-111216

J. P. Machado. et al. 2016 Bone-associated gene evolution and the origin of flightin birds. BMC genomics 17, 371. DOI: 10.1186/s12864-016-2681-7

A.E. Soares. et al. 2016. Complete mitochondrial genomes ofliving and extinct pigeons revise the timing of the columbiform radiation. BMCEvol. Bio. 16, 230. DOI:10.1186/s12862-016-0800-3

Published in 2015

Total 2015

Â. M. Ribeiro et al. 2015. A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. BMC Evol. Bio. 15, 124. DOI:10.1186/s12862-015-0409-y

M. Chakraborty et al. 2015. Core and Shell Song Systems Unique to the Parrot Brain. PLoS ONE 10, 6. DOI:10.1371/journal.pone.0118496

G. Zhang. 2015. Genomics: Bird sequencing project takes off. Nature 522. DOI:10.1038/522034d

K. Nadachowska-Brzyska et al. 2015. Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences. Current Biology 25, 1375. DOI:10.1016/j.cub.2015.03.047

J. Zhang et al. 2015. Improving the ostrich genome assembly using optical mapping data. GigaScience 4, 24. DOI: 10.1186/s13742-015-0062-9

E. D. Jarvis et al. 2015. Phylogenomic analyses data of the avian phylogenomics project. GigaScience 4, 4. DOI:10.1186/s13742-014-0038-1

L. Eöry et al. 2015. Avianbase: a community resource for bird genomics. Genome Biol. 16, 21. DOI:10.1186/s13059-015-0588-2

Avian Phylogenomics Project papers published December 2014

SCIENCE

G. Zhang et al. 2014. Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346, 6215. DOI: 10.1126/science.1251385

E. D. Jarvis et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 6215. DOI: 10.1126/science.1253451

A. R. Pfenning et al. 2014. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science 346, 6215. DOI: 10.1126/science.1256846

O. Whitney et al. 2014. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science 346, 6215. DOI: 10.1126/science.1256780

R. W. Meredith et al. 2014. Evidence for a single loss of mineralized teeth in the common avian ancestor. Science 346, 6215. DOI: 10.1126/science.1254390

Q. Zhou et al. 2014. Complex evolutionary trajectories of sex chromosomes across bird taxa. Science 346, 6215. DOI: 10.1126/science.1246338

R. E. Green et al. 2014. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346, 6215. DOI: 10.1126/science.1254449

S. Mirarab et al. 2014. Statistical binning improves species tree estimation in the presence of gene tree incongruence. Science 346, 6215. DOI: 10.1126/science.1250463

GENOME BIOLOGY

C. C. Weber et al. 2014. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol. 15, 549. DOI: 10.1186/s13059-014-0549-1

C. C. Weber et al. 2014. Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection. Genome Biol. 15, 542. DOI: 10.1186/s13059-014-0542-8

J. Cui et al. 2014. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol. 15, 539. DOI: 10.1186/s13059-014-0539-3

P. V. Lovell et al. 2014. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 15, 565. DOI: 10.1186/s13059-014-0565-1

S. Li et al. 2014. Genomic signatures of near-extinction and rebirth of the Crested Ibis and other endangered bird species. Genome Biol. 15, 557. DOI: 10.1186/s13059-014-0557-1

GIGASCIENCE

C. Li et al. 2014. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the cold Antartic environment. Gigascience 3, 27. DOI: 10.1186/2047-217X-3-27

G. Zhang et al. 2014. Comparative genomic data of the Avian Phylogenomics Project. Gigascience 3, 26. DOI: 10.1186/2047-217X-3-26

S. J. Obrien et al. 2014. The birds of Genome10K. Gigascience 3, 32. DOI: 10.1186/2047-217X-3-32

BMC JOURNALS

M. J. Greenwold et al. 2014. Dynamic evolution of the alpha (alpha) and beta (beta) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. BMC Evol. Bio. 14, 249. DOI: 10.1186/s12862-014-0249-1

Z. Wang et al. 2014. Temporal Genomic Evolution of Bird Sex Chromosomes. BMC Evol. Bio. 14, 250. DOI: 10.1186/s12862-014-0250-8

M. Wirthlin et al. 2014. Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics 15, 1082. DOI: 10.1186/1471-2164-15-1082

M. N. Romanov et al. 2014. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics 15, 1060. DOI: 10.1186/1471-2164-15-1060

PLOS JOURNALS

J. Pereira et al. 2014. Evolutionary genomics and adaptive evolution of the hedgehog gene family (Shh, Ihh, and Dhh) in vertebrates. PLoS ONE 9, 12. DOI: 10.1371/journal.pone.0074132

W. Jaratlerdsiri et al. 2014. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC. PLoS ONE 9, 12. DOI:10.1371/journal.pone.0114631

A. Suh et al. 2014. Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLoS Genet. 10, 12. DOI: 10.1371/journal.pgen.1004559

OTHER JOURNALS

R. Wang et al. 2014. Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners. J. Comp. Neuro. 523, 6. DOI: 10.1002/cne.23719

A. Suh et al. 2014. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biol. Evol. DOI: 10.1093/gbe/evu256

A. Y. Chong et al. 2014. Evolution and gene capture in ancient endogenous retroviruses – insights from the crocodilian genomes. Retrovirology 11, 71. DOI: 10.1186/s12977-014-0071-2

J. C. Opazo et al. 2014. Gene turnover in the avian globin gene families and evolutionary changes in hemoglobin isoform expression. Mol. Bio. Evol. 32. DOI: 10.1093/molbev/msu341


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