An elevational shift facilitated the Mesoamerican diversification of Azure‐hooded Jays (Cyanolyca cucullata) during the Great American Biotic Interchange DOI Creative Commons
John E. McCormack,

Molly M. Hill,

Devon A. DeRaad

et al.

Ecology and Evolution, Journal Year: 2023, Volume and Issue: 13(8)

Published: Aug. 1, 2023

The Great American Biotic Interchange (GABI) was a key biogeographic event in the history of Americas. rising Panamanian land bridge ended isolation South America and ushered period dispersal, mass extinction, new community assemblages, which sparked competition, adaptation, speciation. Diversification across many bird groups, elevational zonation others, ties back to events triggered by GABI. But exact timing these is still being revealed, with recent studies suggesting much earlier time window for faunal exchange, perhaps as early 20 million years ago (Mya). Using time-calibrated phylogenetic tree, we show that jay genus Cyanolyca emblematic dispersal trends, an early, pre-land from Mesoamerica 6.3-7.3 Mya, followed back-colonization C. cucullata 2.3-4.8 likely after complete. As species came into contact Mesoamerica, they avoided competition due prior shift lower elevation ancestor cucullata. This allowed integrate itself Mesoamerican highland avifauna, our phylogeny suggests already populated higher-elevation, congeneric dwarf-jays (C. argentigula, pumilo, mirabilis, nanus). outcome fortuitous could continue colonizing areas farther north during Pleistocene. Resultingly, four lineages became isolated allopatric, regions Panama Mexico, diverging genetics, morphology, plumage, vocalizations. At least two are best described mitrata cucullata). Continued study will further document influence GABI help clarify how vicariance shaped modern-day assemblages

Language: Английский

A Phylogenomic Supertree of Birds DOI Creative Commons
Rebecca T. Kimball, Carl H. Oliveros, Ning Wang

et al.

Diversity, Journal Year: 2019, Volume and Issue: 11(7), P. 109 - 109

Published: July 10, 2019

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal tree life, but it remains challenging move from a clear understanding evolutionary history, in part due computational challenges phylogenetic estimation using genome-scale data. Supertree methods solve challenge because they facilitate divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees computationally efficient manner. Here, we combined information capture and whole-genome phylogenies supertree methods. However, available phylogenomic trees had limited overlap so used taxon-rich (but not phylogenomic) megaphylogenies weave them together. This allowed us construct supertree, with support values, included 707 bird species (~7% avian diversity). We estimated branch lengths mitochondrial these estimate divergence times. Our time-calibrated supports radiation all three major clades (Palaeognathae, Galloanseres, Neoaves) near Cretaceous-Paleogene (K-Pg) boundary. The will permit continued addition taxa this as new are published, could be applied other well.

Language: Английский

Citations

134
A complete and dynamic tree of birds DOI Creative Commons
Emily Jane McTavish, Jeff Gerbracht, Mark T. Holder

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 22, 2024

Abstract We present a complete, time-scaled, evolutionary tree of the world’s bird species. This unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using Open Tree synthesis algorithm. The remaining are placed in based on curated taxonomic information. tips this complete aligned to Clements Taxonomy used by eBird other resources, cross-mapped systems including Life (Open Tree), National Center Biotechnology Information (NCBI), Global Biodiversity Facility (GBIF). total number named varies 10,824 11,017 across taxonomy versions we applied (v2021, v2022 v2023). share trees each version. procedure, software data-stores generate public reproducible. presented here is Aves v1.2 can be easily updated with new information as published. demonstrate types large scale analyses data resource enables linking geographic phylogeny calculate regional diversity birds world. will release translation tables annually. procedure describe developing any group interest. Significance statement Birds charismatic - well loved, highly studied. Many phylogenies elucidating avian relationships every year. have united hundreds create all birds. While variety resources aggregate huge collections trait, behavior location birds, previously barriers these history limited opportunities do exciting analyses. bridged that gap, developed system allows us update our understanding evolution generated. workflow needed group.

Language: Английский

Citations

9
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets DOI Creative Commons

Xiaodong Jiang,

Scott V. Edwards, Liang Liu

et al.

Systematic Biology, Journal Year: 2020, Volume and Issue: 69(4), P. 795 - 812

Published: Jan. 31, 2020

A statistical framework of model comparison and validation is essential to resolving the debates over concatenation coalescent models in phylogenomic data analysis. set tests are here applied developed evaluate compare adequacy substitution, concatenation, multispecies (MSC) across 47 sets collected tree life. Tests for substitution assumption topologically congruent gene trees suggest that a poor fit models, rejected by 44% loci, 38% widespread. Logistic regression shows proportions GC content informative sites both negatively correlated with loci. Moreover, substantial violation consistently observed six major groups (birds, mammals, fish, insects, reptiles, others, including other invertebrates). In contrast, among those loci adequately described given model, proportion rejecting MSC 11%, significantly lower than models. Although conducted on reduced due computational constraints, Bayesian strongly favor all sets; rarely holds more 10 Thus, large sets, comparisons expected model. We also found have little effect species estimation. Our study reveals value analysis, as well need further improvements multilocus tools phylogenetic inference. [Bayes factor; validation; prior; trees; independent Metazoa; posterior predictive simulation.].

Language: Английский

Citations

59
A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths DOI
Rebecca T. Kimball, Peter A. Hosner, Edward L. Braun

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 158, P. 107091 - 107091

Published: Feb. 3, 2021

Language: Английский

Citations

45
Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era DOI
Edward L. Braun, Joël Cracraft, Peter Houde

et al.

Springer eBooks, Journal Year: 2019, Volume and Issue: unknown, P. 151 - 210

Published: Jan. 1, 2019

Language: Английский

Citations

50
How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes) DOI Open Access
Peter A. Hosner, Joseph A. Tobias, Edward L. Braun

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2017, Volume and Issue: 284(1854), P. 20170210 - 20170210

Published: May 3, 2017

Dispersal ability is a key factor in determining insular distributions and island community composition, yet non-vagile terrestrial organisms widely occur on oceanic islands. The landfowl (pheasants, partridges, grouse, turkeys, quails relatives) are generally poor dispersers, but the Old World quail (

Language: Английский

Citations

49
Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements DOI Creative Commons
De Chen, Peter A. Hosner,

Donna L. Dittmann

et al.

BMC Ecology and Evolution, Journal Year: 2021, Volume and Issue: 21(1)

Published: Nov. 22, 2021

Abstract Background Divergence time estimation is fundamental to understanding many aspects of the evolution organisms, such as character evolution, diversification, and biogeography. With development sequence technology, improved analytical methods, knowledge fossils for calibration, it possible obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, best ways leverage large amounts data divergence has not been well explored. A potential solution focus on a subset which can significantly reduce computational burdens avoid problems with heterogeneity that may bias Results In this study, we obtained thousands ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives all genera, determine times throughout history. We tested effects different “gene shopping” schemes using carefully, previously validated, set fossils. Our results found commonly used clock-like be suitable UCE (or other types) where some loci have little information. suggest use partitioning (e.g., PartitionFinder) selection tree-like partitions good strategies select UCEs. tree largely consistent clock studies mitochondrial nuclear loci. our increased taxon sampling, well-resolved topology, carefully vetted fossil calibrations, high quality tree. Conclusions provide backbone combined more records further facilitate Galliformes resource comparative biogeographic group.

Language: Английский

Citations

37
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales DOI
Carl R. Hutter, Kerry A. Cobb, Daniel M. Portik

et al.

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(3), P. 1100 - 1119

Published: Sept. 27, 2021

Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because conflicting signal among genomic regions. Selection different types molecular markers from regions is required overcome these challenges. For evolutionary studies frogs, we introduce publicly available FrogCap suite resources, which a large collection ~15,000 that unifies previous genetic efforts. designed be modular, such subsets and SNPs can selected based on desired phylogenetic scale. uses variety marker include exons introns, ultraconserved elements, previously sequenced Sanger markers, span up 10,000 bp alignment lengths; addition, demonstrate potential for SNP-based analyses. We tested using 121 samples distributed across five scales, comparing probes consensus- or exemplar genome-based approach. Using consensus design more resilient issues with sensitivity, specificity, missing data than picking an genome sequence. also impact bait kit sizes (20,020 vs. 40,040) depth coverage found triple 20,020 kit. observed sequence capture success (i.e., data, markers/bases, length, informative sites) scales. The incorporation effective deep shallow population genetics studies. Having demonstrated FrogCap's utility modularity, conclude new resources are efficacious projects variable timescales.

Language: Английский

Citations

34
Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic DOI
Michael Forthman, Christine W. Miller, Rebecca T. Kimball

et al.

Zoologica Scripta, Journal Year: 2019, Volume and Issue: 48(4), P. 520 - 534

Published: May 12, 2019

Abstract Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, inference many lineages dominated by has not yet benefited NGS, which can complement Sanger studies. One such lineage, whose relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given lack consensus on higher‐level importance robust phylogeny evolutionary hypothesis testing, we use large set comprised hundreds ultraconserved element (UCE) loci infer (excluding Stenocephalidae Hyocephalidae), with emphasis families Coreidae Alydidae. We generated three sets including alignments that contained sampled least 50%, 60%, or 70% total taxa, inferred using maximum likelihood summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive analyses coreoids were also re‐evaluated within our molecular framework. recovered 439–970 per (16%–36% targeted) combined this previously UCE 12 taxa. All sets, regardless analytical approach, yielded topologically similar strongly supported trees, exception outgroup position Hydarinae. monophyletic Coreoidea, Rhopalidae highly as sister group Alydidae + Coreidae. Neither nor monophyletic; coreid subfamilies Hydarinae Pseudophloeinae more closely related than other subfamilies. Coreinae paraphyletic respect Meropachyinae. Most traits homoplastic several clades defined few, if any, synapomorphies. Our results demonstrate utility phylogenomic approaches generating hypotheses taxa long‐standing problems highlight novel insights may come approaches.

Language: Английский

Citations

41
When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes) DOI Creative Commons
Rebecca T. Kimball, Marisa Guido, Peter A. Hosner

et al.

Gene, Journal Year: 2021, Volume and Issue: 801, P. 145841 - 145841

Published: July 16, 2021

Language: Английский

Citations

31