Plio‐Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open‐Habitat Bird Lineages DOI Creative Commons
Pascale Lubbe, Nicolas J. Rawlence, Nicolás Dussex

et al.

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 9, 2025

ABSTRACT In a changing environment, vacant niches can be filled either by adaptation of local taxa or range‐expanding invading species. The relative tempo these patterns is key interest in the modern age climate change. Aotearoa New Zealand has been hotspot biogeographic research for decades due to its long‐term isolation and dramatic geological history. An island with high levels faunal endemicity, it system well suited studying effects situ evolution versus dispersal determining assemblages, while turbulent history provide valuable insights into evolutionary impacts environmental changes. Such investigations are urgent importance given predicted change human rapidly affecting environments globally. Here, we analyse divergence dates nearly all endemic bird species from their overseas relatives assess role changes driving speciation colonisation, special regard cooling during Pliocene Pleistocene. We uncover wave colonisation events Australian open‐habitat adapted since that peaked at beginning Furthermore, highlight an even distribution forest‐adapted through time, consistent millions years extensive forest cover. Finally, note parallels modern‐day establishment new populations Australia suggest this largely influenced anthropogenic land‐use patterns. This contributes growing body work recognising long‐lasting Pleistocene on Zealand's avifauna, reinforces biological invasions as response conditions.

Language: Английский

An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life DOI Creative Commons
Heiner Kuhl,

Carolina Frankl‐Vilches,

Antje Bakker

et al.

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 38(1), P. 108 - 127

Published: July 22, 2020

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny birds are still resolved controversially in different analyses or considered unresolvable. To address this problem, we produced an avian tree life, which includes molecular sequences one several species ∼90% currently recognized family-level taxa (429 species, 379 genera) including all 106 nonpasserines and 115 passerines (Passeriformes). The unconstrained noncoding 3-prime untranslated region (3'-UTR) those coding yielded trees. In contrast sequences, 3'-UTR resulted well-resolved stable topology. contained, unexpectedly, transcription factor binding motifs that were specific for taxa. tree, grebes flamingos sister clade other Neoaves, subdivided into five clades. All nonpasserine placed with robust statistical support long-time enigmatic hoatzin (Opisthocomiformes), was found being taxon Caprimulgiformes. comparatively late radiation clades songbirds (oscine Passeriformes) contrasts attenuated diversification nonpasseriform since Miocene. This correlates evolution vocal production learning, important speciation factor, is ancestral evolved convergent only hummingbirds parrots. As 3'-UTR-based phylotranscriptomics suggest procedure will also resolve all-species life.

Language: Английский

Citations

157
Origin and Evolution of Birds DOI
Gary Ritchison

Fascinating life sciences, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 154

Published: Jan. 1, 2023

Language: Английский

Citations

44
Revised Evolutionary and Taxonomic Synthesis for Parrots (Order: Psittaciformes) Guided by Phylogenomic Analysis DOI
Brian Tilston Smith, Gregory Thom, Leo Joseph

et al.

Bulletin of the American Museum of Natural History, Journal Year: 2024, Volume and Issue: 2024(468)

Published: June 28, 2024

Parrots (Order: Psittaciformes) are a diverse clade that is easily distinguishable from other birds. Despite the clear characters define Psittaciformes (hooked bills, zygodactylous feet, and plumage often predominantly green or red), relative morphological uniformity among parrots has made taxonomic classification fraught endeavor for over century. Parrot systematics were propelled forward when DNA sequencing data shed insights into higher- species-level relationships. However, despite these significant advances, major gaps in taxon sampling uncertainty relationships remained due to inferring phylogenetic with short fragments of DNA. Recent work using genome-wide molecular markers nearly complete parrot brought clarity many remaining outstanding questions on Here, we build this by including four additional species present revision better aligned its evolutionary tree. We infer maximum likelihood time-calibrated phylogenies parrots, accounts 106 genera, compare how our findings relate previous work, highlight future areas research. The family-group nomenclature propose reflects deep divergences diagnosable synapomorphies commensurate across comparable ranks psittaciform clades. erect three new names at rank tribe (Brotogerini Smith, Thom, Joseph, 2024; Neophemini Schodde, Mason, Bolbopsittacini 2024). elevate one subfamily cacatuid genus Probosciger restrict usage recently introduced Touitini type Touit. At shallower scales, recognition more rather than fewer genera addresses issues paraphyly high discordance genomic those levels. support reinstatements older generic advocated recent decades, further reinstate five valid, available not widely used literature if all (Licmetis, Gymnopsittacus, Clarkona, Suavipsitta, Cardeos). advocate retention Vini Lesson, 1833, Coriphilus Wagler, 1832, based preliminary examination showing substantially frequent former. redraw limits some cases (e.g., Bolborhynchus parrotlets allies) includes recognizing proposed Psittacula sensu lato ringneck parakeets. Our revised longstanding have arisen through acquisition genetic data. It provides context temporal origins clades phenotypic diversification throughout their history. hope it will be benchmark guiding study as well downstream analyses fields.

Language: Английский

Citations

20
Late Cretaceous neornithine from Europe illuminates the origins of crown birds DOI
Daniel J. Field, Juan Benito, Albert Chen

et al.

Nature, Journal Year: 2020, Volume and Issue: 579(7799), P. 397 - 401

Published: March 18, 2020

Language: Английский

Citations

132
Pennaraptoran Theropod Dinosaurs Past Progress and New Frontiers DOI
Michael Pittman, Xing Xu

Bulletin of the American Museum of Natural History, Journal Year: 2020, Volume and Issue: 440(1), P. 1 - 1

Published: Aug. 21, 2020

Language: Английский

Citations

71
Data Types and the Phylogeny of Neoaves DOI Creative Commons
Edward L. Braun, Rebecca T. Kimball

Birds, Journal Year: 2021, Volume and Issue: 2(1), P. 1 - 22

Published: Jan. 5, 2021

The phylogeny of Neoaves, the largest clade extant birds, has remained unclear despite intense study. difficulty associated with resolving early branches in Neoaves is likely driven by rapid radiation this group. However, conflicts among studies may be exacerbated data type analyzed. For example, analyses coding exons typically yield trees that place Strisores (nightjars and allies) sister to remaining while non-coding where Mirandornites (flamingos grebes) Neoaves. Our understanding effects hampered fact previous have used different taxa, loci, types data. Herein, we provide strong corroboration hypothesis for comparing based on derived from same taxa gene regions. A simple analytical method known minimize biases due base composition (coding nucleotides as purines pyrimidines) resulted exon increased congruence topology using concatenated analyses. These results improve our resolution neoavian point a challenge—data effects—that an important factor phylogenetic birds (and many other taxonomic groups). Using results, summary identifies well-corroborated relationships highlights specific nodes future efforts should focus.

Language: Английский

Citations

62
Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes) DOI
David Černý, Rossy Natale

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 177, P. 107620 - 107620

Published: Aug. 28, 2022

Language: Английский

Citations

57
Phylogenomic Analysis of the Parrots of the World Distinguishes Artifactual from Biological Sources of Gene Tree Discordance DOI
Brian Tilston Smith, Jon Merwin, Kaiya L. Provost

et al.

Systematic Biology, Journal Year: 2022, Volume and Issue: 72(1), P. 228 - 241

Published: Aug. 2, 2022

Abstract Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources topological discordance. We examined how the information content tips subclades impacts parrots (Order: Psittaciformes), a diverse highly threatened clade nearly 400 species. Using ultraconserved elements from 96% clade’s species-level diversity, we estimated concatenated species for 382 ingroup taxa. found that topologies was most common at nodes dating between late Miocene Pliocene, taxonomic level genus. Accordingly, used two metrics characterize assess degree which conflict being driven by lower-quality samples. Most instances nonmonophyletic genera could be objectively identified using these metrics. For still discordant after tip-based filtering, machine learning approach determine whether or noise more important predictor supporting alternative topologies. when favored one topologies, variable poorly performing models topology. In sum, show gene discordance, likely phenomenon many sets, can distinguished quantifying each tip modeling factors support [Historical DNA; learning; museomics; Psittaciformes; tree.]

Language: Английский

Citations

41
Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds DOI
Ekaterina Osipova,

Rico Barsacchi,

Tom Brown

et al.

Science, Journal Year: 2023, Volume and Issue: 379(6628), P. 185 - 190

Published: Jan. 12, 2023

Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of long-tailed hermit and screened for genes that have been specifically inactivated in ancestral hummingbird lineage. We discovered FBP2 (fructose-bisphosphatase 2), which encodes gluconeogenic muscle enzyme, was lost during time period when flight evolved. show knockdown an avian cell line up-regulates glycolysis enhances mitochondrial respiration, coincident with increased mitochondria number. Furthermore, involved respiration organization up-regulated expression muscle. Together, these results suggest loss likely key step evolution required true flight.

Language: Английский

Citations

23
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