Dataset
Data from: Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)
18 Jun 2024
Abstract
As an old group that has diversified in South America over millions of
years, the tinamous (Palaeognathae: Tinamidae) are of high interest for
understanding the evolution of birds and the assembly of the Neotropical
biota. However, there are currently no complete species-level phylogenies
of this group. Most prior work has been based on either morphological data
or a small number of molecular markers, each of which has limited
capability for reconstructing the tinamou phylogeny. Therefore, the
interrelationships of most tinamou species are uncertain. We analyzed 80
whole genomes from a mix of historical study skins and frozen tissues,
including all 46 recognized species of tinamous, to (1) reconstruct their
interrelationships, (2) estimate the timeframe of tinamou evolution, and
(3) examine the effects of incomplete lineage sorting (ILS) and ancestral
introgression on genome evolution. We compared results for coding (BUSCO)
and ultraconserved element (UCE) loci, as well as sex-linked and autosomal
markers, and used fossil-calibrated tip-dating to estimate divergence
times. Tinamous diverged from their sister-group, the extinct Moas, 50-60
mya, and their crown divergence occurred roughly 30-40 mya, followed by
constant diversification rates until the present. Phylogenetic
reconstructions were largely robust across methods and datasets. Only one
clade in the genus Crypturellus displayed substantial species-tree
discordance across the different data sets. To investigate the impacts of
introgression on this discordance, we quantified introgression for 100kb
non-overlapping windows across the genome and identified pervasive
genome-wide introgression. The distribution of this introgression across
the genome was dependent on the assumed phylogeny applied to the f-branch
model. When assuming one of these topologies in the f-branch model,
patterns of introgression matched theoretical predictions about genome
architecture. Overall, we present the most complete phylogeny for tinamous
to date, identify an unrecognized species, and provide a case study for
species-level phylogenomic analysis using whole genomes
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Details
- Title
- Data from: Whole-genomes illuminate the drivers of gene tree discordance and the tempo of tinamou diversification (Aves: Tinamidae)
- Creators
- Lukas Musher - Drexel UniversityTherese Catanach - Drexel UniversityThomas Valqui - Centro de Ornitología y BiodiversidadAlexandre Aleixo - Vale Technological InstituteKevin Johnson - University of Illinois Urbana-ChampaignJason Weckstein - Drexel University
- Publisher
- Dryad
- Grant note
- 1855812 / National Science Foundation (https://ror.org/021nxhr62) 2203228 / National Science Foundation (https://ror.org/021nxhr62)
- Resource Type
- Dataset
- Language
- English
- Academic Unit
- Biodiversity, Earth, and Environmental Science (BEES); Ornithology
- Other Identifier
- 991022133561804721