ArticleMolecular biology and evolution2018
Coalescent Analysis of Phylogenomic Data Confidently Resolves the Species Relationships in the Anopheles gambiae Species Complex.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed.
- Multi-omics analysis identifies loci associated with pyrethroid resistance across sister species in the Anopheles gambiae species complex.BMC genomics · 2026Article
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors.Scientific reports · 2026Article
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Chromosomal rearrangements in mosquitoes: from micro- to macroevolution.Current opinion in insect science · 2025Review
- The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- Concatenation fails to describe the anomalous radiation of giant cockroaches (Blattodea: Blaberidae) despite moderate to low discordance.BMC ecology and evolution · 2025Article
- Molecular Prevalence and Identification of ZoonoticVeterinary medicine international · 2025Article
- Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides.Genome biology and evolution · 2024Article
- Major patterns in the introgression history ofeLife · 2023Article
- Efficient Bayesian inference under the multispecies coalescent with migration.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Phylogenomics reveals the history of host use in mosquitoes.Nature communications · 2023Article
- Phylogenomic analysis provides diagnostic tools for the identification ofEvolutionary applications · 2023Article
- Inferring the Direction of Introgression Using Genomic Sequence Data.Molecular biology and evolution · 2023Article
- Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks.Systematic biology · 2023Article
- Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group.BMC biology · 2023Article
- Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Abstract
Deep coalescence and introgression make it challenging to infer phylogenetic relationships among closely related species that arose through radiative speciation events. Despite numerous phylogenetic analyses and the availability of whole genomes, the phylogeny in the Anopheles gambiae species complex has not been confidently resolved. Here we extract over 80, 000 coding and noncoding short segments (called loci) from the genomes of six members of the species complex and use a Bayesian method under the multispecies coalescent model to infer the species tree, which takes into account genealogical heterogeneity across the genome and uncertainty in the gene trees. We obtained a robust estimate of the species tree from the distal region of the X chromosome: (A. merus, ((A. melas, (A. arabiensis, A. quadriannulatus)), (A. gambiae, A. coluzzii))), with A. merus to be the earliest branching species. This species tree agrees with the chromosome inversion phylogeny and provides a parsimonious interpretation of inversion and introgression events. Simulation informed by the real data suggest that the coalescent approach is reliable while the sliding-window analysis used in a previous phylogenomic study generates artifactual species trees. Likelihood ratio test of gene flow revealed strong evidence of autosomal introgression from A. arabiensis into A. gambiae (at the average rate of ∼0.2 migrants per generation), but not in the opposite direction, and introgression of the 3 L chromosomal region from A. merus into A. quadriannulatus. Our results highlight the importance of accommodating incomplete lineage sorting and introgression in phylogenomic analyses of species that arose through recent radiative speciation events.
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