ArticleMolecular ecology2016
Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis.
Article in Molecular ecology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed.
- Comparative Analysis ofGenes · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression.PLoS computational biology · 2024Article
- Evaluation of the Relative Performance of the Subflattenings Method for Phylogenetic Inference.Bulletin of mathematical biology · 2023Article
- Inference of Gene Flow between Species under Misspecified Models.Molecular biology and evolution · 2022Article
- Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2.BMC ecology and evolution · 2021Article
- Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow.Systematic biology · 2021Article
- Morphological ghosts of introgression in Darwin's finch populations.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Phylogenomic assessment of the role of hybridization and introgression in trait evolution.PLoS genetics · 2021Article
- The Legacy of Recurrent Introgression during the Radiation of Hares.Systematic biology · 2021Article
- Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.Systematic biology · 2021Article
- Biased Gene Retention in the Face of Introgression Obscures Species Relationships.Genome biology and evolution · 2020Article
- Alternative views of biological species: reproductively isolated units or genotypic clusters?National science review · 2020Article
- Integrated likelihood for phylogenomics under a no-common-mechanism model.BMC genomics · 2020Article
- Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure.Genome biology and evolution · 2020Article
- Integrated species-phenon trees: visualizing infraspecific diversity within lineages.Scientific reports · 2019Article
- Hybridization increases population variation during adaptive radiation.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life.BMC evolutionary biology · 2019Article
- Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae).Proceedings. Biological sciences · 2019Article
- Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae).Systematic biology · 2019Article
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4 authors.
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Abstract
The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyse the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of 'network thinking' and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.
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