Abstract

BackgroundThe Drosophila simulans species complex continues to serve as an important model system for the study of new species formation. The complex is comprised of the cosmopolitan species, D. simulans, and two island endemics, D. mauritiana and D. sechellia. A substantial amount of effort has gone into reconstructing the natural history of the complex, in part to infer the context in which functional divergence among the species has arisen. In this regard, a key parameter to be estimated is the initial isolation time (t) of each island species. Loci in regions of low recombination have lower divergence within the complex than do other loci, yet divergence from D. melanogaster is similar for both classes. This might reflect gene flow of the low-recombination loci subsequent to initial isolation, but it might also reflect differential effects of changing population size on the two recombination classes of loci when the low-recombination loci are subject to genetic hitchhiking or pseudohitchhikingMethodology/Principal Findings New DNA sequence variation data for 17 loci corroborate the prior observation from 13 loci that DNA sequence divergence is reduced in genes of low recombination. Two models are presented to estimate t and other relevant parameters (substitution rate correction factors in lineages leading to the island species and, in the case of the 4-parameter model, the ratio of ancestral to extant effective population size) from the multilocus DNA sequence data.Conclusions/SignificanceIn general, it appears that both island species were isolated at about the same time, here estimated at ∼250,000 years ago. It also appears that the difference in divergence patterns of genes in regions of low and higher recombination can be reconciled by allowing a modestly larger effective population size for the ancestral population than for extant D. simulans.

Highlights

  • The study of speciation genetics can be imperfectly divided into two categories: the study of genes that directly contribute to speciation and population genetic analyses that aim to reconstruct the natural historical context in which speciation occurs

  • Calibrating a molecular clock by the divergence of the complex from D. melanogaster, and assuming that this split occurred,3 mya [1], prior studies of the D. simulans complex indicated that D. sechellia and D. mauritiana were initially isolated from the mainland species approximately 500 and 250 kya, respectively [2]

  • Polymorphism at all LR loci is low for both D. simulans and D. mauritiana (Tables 2 and 3); this suggests that these regions of low recombination are shared by the species

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Summary

Introduction

The study of speciation genetics can be imperfectly divided into two categories: the study of genes that directly contribute to speciation and population genetic analyses that aim to reconstruct the natural historical context in which speciation occurs. A substantial amount of effort has gone into reconstructing the natural history of the complex, in part to infer the context in which functional divergence among the species has arisen. In this regard, a key parameter to be estimated is the initial isolation time (t) of each island species. Loci in regions of low recombination have lower divergence within the complex than do other loci, yet divergence from D. melanogaster is similar for both classes This might reflect gene flow of the lowrecombination loci subsequent to initial isolation, but it might reflect differential effects of changing population size on the two recombination classes of loci when the low-recombination loci are subject to genetic hitchhiking or pseudohitchhiking

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