Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

Systematic Biology, Journal Year: 2017, Volume and Issue: 66(5), P. 857 - 879

Published: March 24, 2017

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as ultimate solution to problem resolving difficult nodes tree life. However, it become clear that analyses these large genomic sets can also result conflicting estimates phylogeny. Here, we early divergences Neoaves, largest clade extant birds, a "model system" understand basis for incongruence among phylogenomic trees. We were motivated by observation trees from two recent avian studies exhibit conflicts. Those used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) sequence data] 48 sometimes including only one taxon each major clade; and 2) fewer ($\sim$ 0.4 Mbp) 198 selected subdivide long branches. types: taxon-poor matrix comprised 68% non-coding sequences whereas coding exons dominated taxon-rich matrix. This difference raises question whether primary reason is number sites, taxa, or type. To test alternative hypotheses assembled novel, comprising 90% 235 bird species. Although increased sampling appeared have positive impact on most important variable was Indeed, analyzing subsets taxa our found actually resulted congruence with previous study (which had majority data) instead largely data). suggest observed differences topology reflect data-type effects due violations models some which may be detect. If estimated using methods reflects problems model fit developing more "biologically-realistic" likely critical efforts reconstruct [Birds; exons; GTR model; fit; Neoaves; DNA; phylogenomics; sampling.].

Language: Английский

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A Phylogenomic Supertree of Birds

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

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A complete and dynamic tree of birds

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

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What makes the Sino‐Himalayan mountains the major diversity hotspots for pheasants?

Journal of Biogeography, Journal Year: 2017, Volume and Issue: 45(3), P. 640 - 651

Published: Dec. 27, 2017

Abstract Aim The Sino‐Himalayas have higher species richness than adjacent regions, making them a global biodiversity hotspot. Various mechanisms, including ecological constraints, energetic diversification rate (DivRate) variation, time‐for‐speciation effect and multiple colonizations, been posited to explain this pattern. We used pheasants (Aves: Phasianidae) as model group test these hypotheses understand the evolutionary processes that generated extraordinary diversity in mountains. Location regions. Taxon Pheasants. Methods Using distribution maps predicted by models ( SDM s) time‐calibrated phylogeny for pheasants, we examined relationships between predictors net primary productivity NPP ), niche (NicheDiv), DivRate, time (EvolTime) colonization frequency using Pearson's correlations structural equation modelling SEM ). reconstructed ancestral ranges at nodes basal/derived patterns reveal mechanisms underlying gradients Sino‐Himalayas. Results found originated Africa early Oligocene (~33 Ma), then colonized Sino‐Himalayan mountains other In Sino‐Himalayas, was strongly related , NicheDiv frequency, but weakly correlated with EvolTime. direct effects of DivRate on were stronger indirectly influenced via its relatively weak. Main conclusions Higher both mechanisms. An increase available niches, rapid diversifications colonizations be key build‐up hotspots Productivity had an important indirect richness, which worked through increased DivRate. Our study offers new insights accumulation provides useful understanding hotspots.

Language: Английский

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A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths

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

Published: Feb. 3, 2021

Language: Английский

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Resolving the Avian Tree of Life from Top to Bottom: The Promise and Potential Boundaries of the Phylogenomic Era

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

Published: Jan. 1, 2019

Language: Английский

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Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

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

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Gray Partridges (Phasianidae: Genera Perdix and Enkuria gen. nov.) from the Early Pleistocene of Crimea and Remarks on the Evolution of the Genus Perdix

Paleontological Journal, Journal Year: 2024, Volume and Issue: 58(3), P. 335 - 352

Published: June 1, 2024

Language: Английский

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Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences

Molecular Phylogenetics and Evolution, Journal Year: 2016, Volume and Issue: 102, P. 320 - 330

Published: June 29, 2016

Language: Английский

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Phylogeny, migration and life history: filling the gaps in the origin and biogeography of the Turdus thrushes

Journal of Ornithology, Journal Year: 2019, Volume and Issue: 160(2), P. 529 - 543

Published: Feb. 15, 2019

Although the biogeographic history of thrushes (Turdidae) has been extensively studied, a concise discussion this topic is still lacking. Therefore, in study we aimed to investigate: (1) evolutionary origin migratory behaviour Turdus context including (2) trans-Atlantic dispersal events, (3) possible colonization routes into Nearctic, and (4) relationships among life traits, ecological factors, strategies within most comprehensive taxon set 72 date. We estimated ancestral ranges studied species, primarily by comparing main models (dispersal-vicariance, dispersal-extinction-cladogenesis, BayArea models), performed phylogenetic generalized least squares analyses identify distribution patterns, diet, body measurements, clutch size, behaviour. found that probable regions for all species were located East Palearctic realm, followed early western Africa, several movements occurred between 11 4 million years ago, which earlier than previously thought. Migration emerged as an genus Turdus, differences size food types significant non-migratory species. Correlated evolution was migration along-latitudinal mobility, type, shift type seasons. conclude may have evolved earlier, simultaneously with radiation thrushes, appearance meridional migration, associated orographic climatic changes. The increased sizes observed documented here could serve important mechanism compensate losses due mortality during migration.

Language: Английский

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