Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia

Abstract

Tropical forests have undergone repeated fragmentation and expansion during Pleistocene glacial and interglacial periods, respectively. The effects of this repeated forest fragmentation in driving vicariance in tropical taxa have been well studied. However, relatively little is known about how often this process results in allopatric speciation, since it may be inhibited by recurrent gene flow during repeated secondary contact, or to what extent Pleistocene-dated speciation results from ecological specialization in the face of gene flow. Here, divergence times and gene flow between three closely-related mosquito species of the Anopheles dirus species complex endemic to the forests of Southeast Asia, are inferred using coalescent based Bayesian analysis. An Isolation with Migration model is applied to sequences of two mitochondrial and three nuclear genes, and 11 microsatellites. The divergence of An. scanloni has occurred despite unidirectional nuclear gene flow from this species into An. dirus. The inferred asymmetric gene flow may result from the unique evolutionary adaptation of An. scanloni to limestone karst habitat, and therefore the fitness advantage of this species over An. dirus in regions of sympatry. Mitochondrial introgression has led to the complete replacement of An. dirus haplotypes with those of An. baimaii through a recent (approximately 62 kya) selective sweep. Speciation of An. baimaii and An. dirus is inferred to have involved allopatric divergence throughout much of the Pleistocene. Secondary contact and bidirectional gene flow has occurred only within the last 100 000 years, by which time the process of allopatric speciation seems to have been largely completed.

Genetic population structure of the malaria vector Anopheles baimaii in north-east India using mitochondrial DNA

“…The start time of population expansion under the sudden expansion model was estimated using the same mutation rate as in earlier studies to enable a direct comparison with previous estimates for a single NE Indian population of An. baimaii [5,20]. However, since there is no calibrated rate for Anopheles , the estimated expansion time should be considered as very approximate.…”

“…baimaii in NE India has undergone expansion, a mismatch distribution was calculated in Arlequin 3.1 and compared with the expectations of the sudden expansion model. The time of expansion was estimated under the sudden expansion model assuming the mutation rate of 1.15 × 10 -8 /site/year as used by Morgan et al [5] and a generation time of 0.1 years reported for Anophelines (Maharaj, 2003) [46]. …”

“…Anopheles baimaii also occurs widely in Southeast Asia, extending from NE India into the hills of Bangladesh, through Myanmar and into north-western and southern Thailand [4]. Studies using microsatellites, mitochondrial and nuclear sequence data [5] indicated that An. baimaii had a more confined, westerly distribution until it spread eastwards making secondary contact ~62 kyr with a closely related species, An.…”

“…baimaii in NE India [2,3,16-18], its genetic diversity and population structure have been little studied within this region. Studies of genetic population structure on a broader geographical scale throughout Southeast Asia using mtDNA [19,20], microsatellites [21] and sequences of nuclear genes [5] have revealed low, but significant, structuring in An. baimaii and a lack of population structure in An.…”

Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish,Belodontichthys truncatusKottelat & Ng, 1999 (Siluriformes: Siluridae), from Mekong Basin

“…Previous studies found a significant influence from the Pleistocene glaciation on genetic diversity, genetic structure, and demographic history in many Southeast Asian floras and faunas [e.g., [21][22][23]]. During the Pleistocene glaciations, climatic and environmental conditions in Southeast Asia were cooler and drier [24].…”