Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies
(2025) In Molecular Phylogenetics and Evolution 202.- Abstract
Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically... (More)
Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.
(Less)
- author
- Greenwood, Matthew P. LU ; Capblancq, Thibaut ; Wahlberg, Niklas LU and Després, Laurence
- organization
- publishing date
- 2025-01
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Gene conflict, Hybridization, Incomplete lineage sorting, Phylogenetics, Phylogenomics, Species network
- in
- Molecular Phylogenetics and Evolution
- volume
- 202
- article number
- 108222
- publisher
- Elsevier
- external identifiers
-
- scopus:85208196375
- pmid:39477173
- ISSN
- 1055-7903
- DOI
- 10.1016/j.ympev.2024.108222
- language
- English
- LU publication?
- yes
- id
- d03629ad-266b-4d15-a3e2-8b8a3ab2fcd5
- date added to LUP
- 2024-12-03 15:14:44
- date last changed
- 2025-06-04 05:45:58
@article{d03629ad-266b-4d15-a3e2-8b8a3ab2fcd5,
abstract = {{<p>Phylogenetic inference is challenged by genealogical heterogeneity amongst molecular markers. Such discordance is driven predominantly by incomplete lineage sorting (ILS) and interspecific gene flow, and bears attendant consequences for the accurate resolution of species relationships. Understanding the distribution of gene conflict in organismal genomes is, therefore, a key aspect of phylogenetic analysis. In this study, three large phylogenomic datasets (i.e., whole mitogenomes, conserved nuclear protein-coding loci, and genomic windows) are used to probe the extent to which discordance pervades the unresolved phylogeny of Coenonympha (Nymphalidae) butterflies. Gene tree discordance is found to be elevated at multiple historically recalcitrant phylogenetic positions. In particular, species relationships near the crown of Coenonympha and within a rapidly diversifying subclade (the hero group) remain difficult to resolve, suggesting that ILS and gene flow have obscured the evolution of this genus. These findings have implications for the taxonomy of this butterfly group and the study of its diversification history. In addition, this work lends support to a growing body of evidence that gene conflict driven by biological processes stands to confound phylogeny, even when extensive data are used.</p>}},
author = {{Greenwood, Matthew P. and Capblancq, Thibaut and Wahlberg, Niklas and Després, Laurence}},
issn = {{1055-7903}},
keywords = {{Gene conflict; Hybridization; Incomplete lineage sorting; Phylogenetics; Phylogenomics; Species network}},
language = {{eng}},
publisher = {{Elsevier}},
series = {{Molecular Phylogenetics and Evolution}},
title = {{Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies}},
url = {{http://dx.doi.org/10.1016/j.ympev.2024.108222}},
doi = {{10.1016/j.ympev.2024.108222}},
volume = {{202}},
year = {{2025}},
}