Resolving evolutionary relationships in closely related nonmodel organisms: a case study using chromosomally distinct members of a black fly species complex. (19th January 2017)

• Record Type: Journal Article
• Authors: CONFLITTI, IDA M.; SHIELDS, GERALD F.; MURPHY, ROBERT W.; CURRIE, DOUGLAS C.
• Is Part Of: Systematic entomology. Volume 42:Number 3(2017)
• Page Start: 489
• Page End: 508
• Publication Date: 2017-01-19
• Subjects: Insects -- Classification -- Periodicals; Entomology -- Periodicals; 595.7012
• DOI: 10.1111/syen.12226
• Languages: English
• ISSNs: 0307-6970

Abstract

Abstract: Coalescent‐based analyses have been recommended for species delimitation and tree reconstruction. Yet, despite recent advances in molecular methods, acquiring sufficient genetic data often precludes coalescent‐based analyses in nonmodel organisms. We show that these methods are accessible to questions in nonmodel systems. Specifically, we use coalescent‐based analyses to investigate evolutionary independence and relationships among chromosomally distinct members (sibling species) of a black fly (Diptera: Simuliidae) species complex. Our dataset consists of nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) markers – the former developed using the black fly transcriptome and available genomes from model relatives. We show that individual gene trees exhibit considerable discordance among one another and reveal little about potential species limits. Consistent species tree topologies are obtained from analyses of nuDNA, both with and without the inclusion of mtDNA data. Nodes on the tree receive robust support with the addition of mtDNA. Coalescent‐based species validation approaches recognize all sibling species. However, unlike species tree analyses, the addition of mtDNA data does not improve or alter the results. Thus, analyses of nuDNA alone can validate sibling species. Contrary to these results, population genetic patterns of neutral diversity, within‐locus recombination, and linkage disequilibrium suggest that sibling species represent a single species with high levels of nucleotide polymorphism, large effective population sizes, and extensive gene flow. Demographic patterns inferred from neutrality tests integrate seemingly disparate results by showing signatures of gene flow among structured populations that are expanding in size. Thus, admixture associated with geographic range expansions may be assimilating sibling species into a single genetic lineage.