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Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

Cloutier, Alison, Sackton, Timothy B, Grayson, Phil, Clamp, Michele, Baker, Allan J, Edwards, Scott V·2019·Systematic Biology
DOI 10.1093/sysbio/syz019PMC PMC6857515

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Abstract

Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

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  • Relaxing the assumption of a single topology for all loci improved on the performance of PhyloAcc, particularly in situations such as the loss of flight in paleognaths that also experience high levels of ILS.

    “R el axing the as s umptio n o f a single topology for a l l loci improve d on t he per for mance of PhyloAcc, p art icu l arly in situ ations such as the loss of flight in p a le og nat hs t hat also exper ien ce high leve ls of ILS ( C lout ier et al . 2019 ; Sac kt on et al. 2019).”

    From Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc (2024) · cites this paper as Cloutier et al. 2019

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Metadata

Authors
Cloutier, A., Sackton, T. B., Grayson, P., Clamp, M., Baker, A. J., & Edwards, S. V.
Affiliations
  • Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
  • Informatics Group, Harvard University, 28 Oxford Street, Cambridge, MA 02138, USA
  • Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario M5S 3B2, Canada
Venue
Systematic Biology
Publisher
Oxford University Press (OUP)
Published
2019-04-23
Volume
68
Issue
6
Pages
937-955
ISSN
  • 1063-5157
  • 1076-836X
DOI
10.1093/sysbio/syz019
PMC
PMC6857515
Cited by
124
References
5
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor, 1 d)

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