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

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae) DOI Open Access

Guanwei Lan,

Jiaojiao Yu, Juan Liu

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(1), P. 90 - 90

Published: Jan. 11, 2024

Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, conducted first comprehensive comparative analysis of Muscicapidae birds and reconstructed phylogenetic relationships between related groups. The T. was 16,723 size, it possessed typical avian structure organization. Most PCGs were initiated strictly start codon ATG, while COX1 ND2 started GTG. RSCU statistics showed that CUA, CGA, GCC relatively high frequency mitogenome. cyanurus shared very similar mitogenomic features. All 13 mitogenomes had experienced purifying selection. Specifically, ATP8 highest rate evolution (0.13296), whereas lowest (0.01373). monophylies Muscicapidae, Turdidae, Paradoxornithidae strongly supported. clade ((Muscicapidae + Turdidae) Sturnidae) Passeriformes supported by both Bayesian Inference Maximum likelihood analyses. latest taxonomic status many complex histories also For example, Monticola gularis, indicus, allocated to Turdidae literature; our topologies clearly their membership Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, fulvifrons formerly classified into Paradoxornithidae; Culicicapa ceylonensis originally as member results are consistent position Stenostiridae. Our study enriches genetic data provides new insights molecular phylogeny birds.

Language: Английский

Citations

8
Aspects of diversity, paleobiology, and morphology of wing-propelled diving birds DOI Creative Commons
Junya Watanabe

Geobios, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

1
Phylogenetic supertree reveals detailed evolution of SARS-CoV-2 DOI Creative Commons
Tingting Li, Dongxia Liu,

Yadi Yang

et al.

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Dec. 22, 2020

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship still ambiguous. Several reports attempted to figure out this critical issue genome-based phylogenetic analysis, yet limited progress was obtained, principally owing disability these methods reasonably integrate information from all genes SARS-CoV-2. Supertree method based on multiple trees can produce overall reasonable tree. However, supertree has been barely used for analysis viruses. Here we applied matrix representation with parsimony (MRP) pseudo-sequence study evolution Compared other methods, showed more resolution power coronaviruses. In particular, MRP firmly disputes bat RaTG13 be last common ancestor SARS-CoV-2, which implied tree viral genome sequences. Furthermore, discovery mutation in achieved analysis. Taken together, provided inference relative normal full-length genomic

Language: Английский

Citations

52
Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution DOI Creative Commons
Juan C. García–R, Emily Moriarty Lemmon, Alan R. Lemmon

et al.

Diversity, Journal Year: 2020, Volume and Issue: 12(2), P. 70 - 70

Published: Feb. 7, 2020

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does general timescale evolution. Here, we disentangle deep phylogenetic structure rails using anchored phylogenomics. We analysed set 393 loci from 63 species, representing approximately 40% extant familial diversity. Our phylogenomic analyses reconstruct phylogeny robustly infer previously contentious relationships. Concatenated maximum likelihood coalescent species-tree approaches recover identical topologies strong node support. results are concordant previous studies small DNA datasets, but they also supply an additional resolution. dating analysis provides contrasting divergence times fossils Bayesian non-Bayesian approaches. study refines history rails, offering foundation for future birds.

Language: Английский

Citations

50
Early origin of sweet perception in the songbird radiation DOI
Yasuka Toda, Meng‐Ching Ko, Qiaoyi Liang

et al.

Science, Journal Year: 2021, Volume and Issue: 373(6551), P. 226 - 231

Published: July 9, 2021

From savory to sweet Seeing a bird eat nectar from flower is common sight in our world. The ability detect sugars, however, not ancestral the lineage, where most species were carnivorous. Toda et al. looked at receptors within largest group of birds, passerines or songbirds, and found that emergence detection involved single shift receptor for umami (see Perspective by Barker). This ancient change facilitated sugar just feeding but also across songbird group, way was different from, though convergent with, hummingbirds. Science , abf6505, this issue p. 226 ; see abj6746, 154

Language: Английский

Citations

48
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
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life DOI Creative Commons
Luna L. Sánchez‐Reyes, Emily Jane McTavish, Brian C. O’Meara

et al.

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(2), P. 470 - 485

Published: March 1, 2024

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us study natural processes in many areas biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction chronogram is difficult resource-consuming task. Here we present DateLife, phylogenetic software implemented as an R package Shiny web application available at www.datelife.org, provides services efficient easy discovery, summary, reuse, reanalysis node age mined from curated database expert, peer-reviewed, openly chronograms. The main DateLife workflow starts one or more scientific taxon names provided by user. Names are processed standardized unified taxonomy, run name match across its local Open Tree Life's repository, extract all chronograms contain least two queried names, along their metadata. Finally, ages matching mapped using the congruification algorithm corresponding nodes tree topology, either extracted synthetic phylogeny Congruified secondary calibrations date chosen without initial lengths, different dating methods such BLADJ, treePL, PATHd8, MrBayes. We performed cross-validation test compare resulting analysis (i.e, calibrations) those original obtained primary calibrations), found DateLife's estimates consistent chronograms, largest variation occurring around topologically deeper nodes. Because results any only good input, highlight importance considering context input help increase awareness existing disparities among alternative hypotheses dates same diversification support exploration effect downstream analyses, providing framework informed interpretation results.

Language: Английский

Citations

7
The early origin of a birdlike inner ear and the evolution of dinosaurian movement and vocalization DOI
Michael Hanson, Eva A. Hoffman,

Mark A. Norell

et al.

Science, Journal Year: 2021, Volume and Issue: 372(6542), P. 601 - 609

Published: May 6, 2021

Reptiles, including birds, exhibit a range of behaviorally relevant adaptations that are reflected in changes to the structure inner ear. These include capacity for flight and sensitivity high-frequency sound. We used three-dimensional morphometric analyses large sample extant extinct reptiles investigate ear correlates locomotor ability hearing acuity. Statistical revealed three vestibular morphotypes, best explained by categories-quadrupeds, bipeds simple fliers (including bipedal nonavialan dinosaurs), high-maneuverability fliers. Troodontids fall with Archaeopteryx among low-maneuverability Analyses cochlear shape single instance elongation, on stem Archosauria. suggest this transformation coincided origin both high-pitched juvenile location, alarm, hatching-synchronization calls adult responses them.

Language: Английский

Citations

35
Phylogenetic definitions for 25 higher-level clade names of birds DOI Creative Commons
George Sangster, Edward L. Braun, Ulf S. Johansson

et al.

Avian Research, Journal Year: 2022, Volume and Issue: 13, P. 100027 - 100027

Published: Jan. 1, 2022

Knowledge of the higher-level phylogenetic relationships birds has grown substantially during past two decades due to application genomic data. However, nomenclature taxa not become more stable, lack regulation taxon names above level superfamily by ICZN, and usage rank-based nomenclature, which is tied clades in a phylogeny. Lack instability impede effective communication among systematists. We review support for avian using set 10 phylogenomic data sets, identify that are supported congruency at least four these. provide formal definitions these based on rules recently published PhyloCode. The 25 here defined minimum-crown-clade (n ​= ​23), minimum-clade ​1) maximum-crown-clade definitions. Five new introduced here: Dinocrypturi, Pteroclimesites, Musophagotides, Phaethoquornithes Pelecanes. also diagnostic apomorphies relevant clades, known synonyms homonyms. By establishing link between well-supported hypotheses, our will solid basis stabilization nomenclature.

Language: Английский

Citations

25
A supermatrix phylogeny of the world’s bees (Hymenoptera: Anthophila) DOI Creative Commons
Patricia Henríquez‐Piskulich,

Andrew F. Hugall,

Devi Stuart‐Fox

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 190, P. 107963 - 107963

Published: Nov. 14, 2023

The increasing availability of large molecular phylogenies has provided new opportunities to study the evolution species traits, their origins and diversification, biogeography; yet there are limited attempts synthesise existing phylogenetic information for major insect groups. Bees (Hymenoptera: Anthophila) a group pollinators that have worldwide distribution, wide variation in ecology, morphology, life-history including sociality. For these reasons, as well economic importance pollinators, numerous studies family genus-level relationships been published, providing an opportunity assemble bee 'tree-of-life'. We used publicly available genetic sequence data, phylogenomic reconciled taxonomic database, produce concatenated supermatrix phylogeny Anthophila comprising 4,586 species, representing 23% 82% genera. At family, subfamily, tribe levels, support expected was robust, but between within some genera remain uncertain. Within families, sampling ranged from 67 100% coverage lower (17-41%). Our mostly reproduces found recent with few exceptions. provide summary differences current state data its gaps. discuss advantages limitations this (available online at beetreeoflife.org), which may enable insights into long standing questions about evolutionary drivers bees, potentially insects more generally.

Language: Английский

Citations

14