Cited by 240Evolution and Paleontology StudiesPlant Diversity and EvolutionGenetic diversity and population structure

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

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Moyle, Robert G., Oliveros, Carl H., Andersen, Michael J., Hosner, Peter A., Benz, Brett W., Manthey, Joseph D., Travers, Scott L., Brown, Rafe M. +1 more·2016·Nature Communications

Abstract

Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Here, we combine the first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, and geologically informed biogeographic reconstructions to provide a well-supported evolutionary hypothesis for the group. We show that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates. This burst of diversification occurred coincident with extensive island formation in Wallacea, which provided the first dispersal corridor out of Australia, and resulted in independent waves of songbird expansion through Asia to the rest of the globe. Our results reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.

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  • Separate Asian origin of Ostromia and Archaeopteryx lineages implies dispersal happened in several independent waves.

    “The separate Asian origin of the lineages of Ostromia and Archaeopteryx implied by the biogeographic analysis indicates that this dispersal might have happened in several independent waves, as has recently been suggested for the evolution of oscine passerines in the Cenozoic [70].”

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Research works printed but not linked: 47

  1. Barker F. K., Cibois A., Schikler P., Feinstein J. & Cracraft J. Phylogeny and diversification of the largest avian radiation. Proc. Natl Acad. Sci. USA 101, 11040– 11045 (2004). 15263073 PMC503738
  2. Ericson P. G. P.. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proc. R. Soc. B Biol. Sci. 269, 235– 241 (2002). PMC1690883 11839192
  3. Barker F. K. in Living Dinosaurs: The Evolutionary History of Modern Birds eds Dyke G., Kaiser G. 235– 256John Wiley & Sons (2011).
  4. Jønsson K. A., Fabre P.-H., Ricklefs R. E. & Fjeldså J. Major global radiation of corvoid birds originated in the proto-Papuan archipelago. Proc. Natl Acad. Sci. USA 108, 2328– 2333 (2011). 21262814 PMC3038755
  5. Aggerbeck M., Fjeldså J., Christidis L., Fabre P. H. & Jønsson K. A. Resolving deep lineage divergences in core corvoid passerine birds supports a proto-Papuan island origin. Mol. Phylogenet. Evol. 70, 272– 285 (2014). 24125832
  6. Jetz W., Thomas G. H., Joy J. B., Hartmann K. & Mooers A. O. The global diversity of birds in space and time. Nature 491, 444– 448 (2012). 23123857
  7. Ericson P. G. P., Klopfstein S., Irestedt M., Nguyen J. M. T. & Nylander J. A A. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evol. Biol. 14, 8 (2014). 24422673 PMC3917694
  8. Selvatti A. P., Gonzaga L. P. & Russo C. A. D. M. A Paleogene origin for crown passerines and the diversification of the Oscines in the New World. Mol. Phylogenet. Evol. 88, 1– 15 (2015). 25837731
  9. Gibb G. C.. New Zealand passerines help clarify the diversification of major songbird lineages during the Oligocene. Genome Biol. Evol. 7, evv196 (2015). PMC5635589 26475316
  10. Burleigh J. G., Kimball R. T. & Braun E. L. Building the avian tree of life using a large-scale, sparse supermatrix. Mol. Phylogenet. Evol. 84, 53– 63 (2015). 25550149
  11. Fregin S., Haase M., Olsson U. & Alström P. New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers. BMC Evol. Biol. 12, 157 (2012). 22920688 PMC3462691
  12. Alstrom P.. Discovery of a relict lineage and monotypic family of passerine birds. Biol. Lett. 10, 20131067 (2014). 24598108 PMC3982435
  13. Cracraft J. in The Howard & Moore Complete Checklist of the Birds of the World 4th Edition Vol. 2, (eds Dickinson E., Christidis L. xvii– xvi ((Aves Press, Eastbourne, UK, 2014).
  14. Jarvis E. D.. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320– 1331 (2014). 25504713 PMC4405904
  15. Cracraft J. Avian evolution, Gondwana biogeography and the Cretaceous-Tertiary mass extinction event. Proc. Biol. Sci. 268, 459– 469 (2001). 11296857 PMC1088628
  16. Faircloth B. C.. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61, 717– 726 (2012). 22232343
  17. Schodde R. & Christidis L. Relicts from Tertiary Australasia: undescribed families and subfamilies of songbirds (Passeriformes) and their zoogeographic signal. Zootaxa 3786, 501– 522 (2014). 24869551
  18. Fuchs J., Fjeldså J., Bowie R. C. K., Voelker G. & Pasquet E. The African warbler genus Hyliota as a lost lineage in the Oscine songbird tree: Molecular support for an African origin of the Passerida. Mol. Phylogenet. Evol. 39, 186– 197 (2006). 16182572
  19. Müller R. D., Gaina C. & Clark S. in Billion-Year Earth History of Australia and Neighbours in Gondwanaland eds Veevers J. J., Morgan P. 18– 28Gemoc Press (2000).
  20. Toussaint E. F. A.. The towering orogeny of New Guinea as a trigger for arthropod megadiversity. Nat. Commun. 5, 4001 (2014). 24874774
  21. Chaves J. A., Weir J. T. & Smith T. B. Diversification in Adelomyia hummingbirds follows Andean uplift. Mol. Ecol. 20, 4564– 4576 (2011). 21981387
  22. Ribas C. C., Moyle R. G., Miyaki C. Y. & Cracraft J. The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots. Proc. R. Soc. Lond. 274, 2399– 2408 (2007). PMC2274971 17686731
  23. Glenn T. C.. Adapterama I: universal stubs and primers for thousands of dual-indexed Illumina libraries (iTru & iNext), Preprint at http://biorxiv.org/content/early/2016/06/15/049114 (2016). PMC6791352 31616586
  24. Faircloth B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786– 788 (2015). 26530724
  25. Grabherr M. G.. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644– 652 (2011). 21572440 PMC3571712
  26. Chifman J. & Kubatko L. Quartet inference from SNP data under the coalescent model. Bioinformatics 30, 3317– 3324 (2014). 25104814 PMC4296144
  27. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540– 552 (2000). 10742046
  28. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312– 1313 (2014). 24451623 PMC3998144
  29. Aberer A. J., Kobert K. & Stamatakis A. ExaBayes: massively parallel bayesian tree inference for the whole-genome era. Mol. Biol. Evol. 31, 2553– 2556 (2014). 25135941 PMC4166930
  30. Chifman J. & Kubatko L. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. J. Theor. Biol. 374, 35– 47 (2015). 25791286
  31. Snir S. & Rao S. Quartet MaxCut: a fast algorithm for amalgamating quartet trees. Mol. Phylogenet. Evol. 62, 1– 8 (2012). 21762785
  32. Seo T. K. Calculating bootstrap probabilities of phylogeny using multilocus sequence data. Mol. Biol. Evol. 25, 960– 971 (2008). 18281270
  33. Liu L. & Yu L. Phybase: an R package for species tree analysis. Bioinformatics 26, 962– 963 (2010). 20156990
  34. Liu L., Yu L. & Edwards S. V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 10, 302 (2010). 20937096 PMC2976751
  35. Mirarab S.. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30, i541– i548 (2014). 25161245 PMC4147915
  36. Liu L., Xi Z., Wu S., Davis C. & Edwards S. V. Estimating phylogenetic trees from genome-scale data. Ann. N. Y. Acad. Sci. 1360, 36– 53 (2015). 25873435
  37. Parham J. F.. Best practices for justifying fossil calibrations. Syst. Biol. 61, 346– 359 (2012). 22105867 PMC3280042
  38. Mitchell K. J., Cooper A. & Phillips M. J. Comment on ‘Whole-genome analyses resolve early branches in the tree of life of modern birds'. Science 349, 1460 (2015). 26404819
  39. Cracraft J.. Response to Comment on ‘Whole-genome analyses resolve early branches in the tree of life of modern birds '. Science 349, 1460 (2015). 26404820
  40. Inoue J., Donoghue P. C. J. & Yang Z. The impact of the representation of fossil calibrations on bayesian estimation of species divergence times. Syst. Biol. 59, 74– 89 (2010). 20525621
  41. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586– 1591 (2007). 17483113
  42. Ree R. H., Moore B. R., Webb C. O. & Donoghue M. J. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59, 2299– 2311 (2005). 16396171
  43. Ree R. H. & Smith S. A. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 57, 4– 14 (2008). 18253896
  44. Clark J. R.. A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages. Syst. Biol. 57, 693– 707 (2008). 18853357
  45. Matzke N. J. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Syst. Biol. 63, 951– 970 (2014). 25123369
  46. Yu Y., Harris A. J. & He X. S-DIVA (Statistical Dispersal-Vicariance Analysis): a tool for inferring biogeographic histories. Mol. Phylogenet. Evol. 56, 848– 850 (2010). 20399277
  47. Landis M. J., Matzke N. J., Moore B. R. & Huelsenbeck J. P. Bayesian analysis of biogeography when the number of areas is large. Syst. Biol. 62, 789– 804 (2013). 23736102 PMC4064008

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Authors
Moyle, R. G., Oliveros, C. H., Andersen, M. J., Hosner, P. A., Benz, B. W., Manthey, J. D., Travers, S. L., Brown, R. M., & Faircloth, B. C.
Affiliations
  • University of Kansas (US)
  • University of New Mexico (US)
  • University of Florida (US)
  • American Museum of Natural History (US)
  • Louisiana State University (US)
Corresponding author
Moyle, Robert G.
Venue
Nature Communications
Published
2016-08-30
Volume
7
Issue
1
Pages
12709-12709
ISSN
2041-1723 (ISSN-L)
OpenAlex
W2510851398
Cited by
240
References
5
Citations by year
2026: 10 · 2025: 12 · 2024: 15 · 2023: 22 · 2022: 15 · 2021: 21 · 2020: 29 · 2019: 45 · 2018: 30 · 2017: 37 · 2016: 4
FWCI
32.15
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Civil War Book Review (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • KU ScholarWorks (University of Kansas) (submittedVersion, cc-by)
Funders
  • National Science Foundation (1146345, 1241181, P20GM103638, 1337899)
  • Yale University
  • University of Washington
  • Louisiana State University
  • National Institutes of Health
  • Burke Museum, University of Washington
  • National Institute of General Medical Sciences (P20GM103638)
  • Division of Environmental Biology (1241181, 1146345)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
songbirds, oscine passerines, avian diversification, Wallacea, tectonic collision, uplift, island formation, biogeography, dispersal corridors, Oligocene, Miocene, fossil calibration, genome-scale phylogeny, global radiation
MeSH terms
Animals, Asia, Australia, Fossils, Phylogeny, Population Dynamics, Genome, Sequence Analysis, DNA, Songbirds, Genomics, Biodiversity, Genetic Speciation

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