RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fishDascyllus trimaculatus

Abstract

Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak genetic differentiation between the Northwestern (Red Sea and Arabian Sea) and Western Indian Ocean biogeographic provinces. Loci potentially under selection (outlier loci) revealed a similar pattern but with a much stronger signal of genetic structure between regions. The Oman population appears to be genetically distinct from all other populations included in the analysis. While we could not clearly identify the mechanisms driving these patterns (isolation, adaptation or both), the datasets indicate that population-level divergences are largely concordant with biogeographic boundaries based on species composition. Our data can be used along with genetic connectivity of other species to identify the common genetic breaks that need to be considered for the conservation of biodiversity and evolutionary processes in the poorly studied Western Indian Ocean region.

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

“…The outlier loci suggest adaptive responses to potential environmental factors, such as salinity, which vary on regional scales, while neutral loci are influenced by genetic drift [52]. Given that the divergences revealed by the outlier dataset are discordant with the neutral loci, these loci should be driven by the effects of selection and not by the isolation alone [53].…”

“…The shallow sea (SS), deep sea (DS) and Meghna estuary (ME) populations are genetically homogenized, based on clustering patterns in multivariate (PCA, DAPCs) and individual analyses (STRUCTURE, NJ phylogenetics). It is also possible that physical barriers between the different environments are semipermeable, allowing for constraint dispersal, while the environmental contrasts between these habitats reinforce those barriers through selection [53]. The expansions of founder populations may also occur after isolation, which further induces adaptation, if colonizing individuals carry beneficial mutated genes [58].…”

“…We observed that the Hilsa shad from the deep sea (DS) and upper Jamuna river (UJR) collection sites in the outlier loci dataset, as detected by F ST OutFLANK (F ST = 0.315, p ≤ 0.001), was an order magnitude greater than those in the putatively neutral loci dataset (F ST = 0.003, p ≤ 0.001). While it is difficult to distinguish between differentiations caused by selection or drift processes [53], it is noteworthy that these processes are mutually inclusive and likely act in concert on populations found around the region, given its complex anadromous life cycle. The presence of two major clusters of Hilsa shad in Bangladesh was substantiated by these analyses of the outlier datasets, which could not be revealed in previous studies utilizing mainly neutral markers.…”

“…In this study, different cluster analyses revealed that Hilsa shad individuals collected from nine geographical locations are divided into two genetic clusters, in which one cluster is dominated by the marine (deep sea, DS; shallow sea, SS) and estuarine (Meghna estuary, ME) water individuals and another cluster is dominated by the different freshwater riverine (MR, Meghna river; SKR, Surma-Kushiara river; LPR, lower Padma river; UPR, upper Padma river; LJR, lower Jamuna river; UJR, upper Jamuna river) individuals. The distinction between these two major clusters indicates that the gene flow among them is restricted due to a limited dispersal and selection processes, which operate at various scales throughout the heterogeneous environment [53] and likely influences their divergence. More elaborately, such discrimination of Hilsa shad individuals from different geographical locations divided into two genetic clusters can be interpreted by two different ways.…”

“…More elaborately, such discrimination of Hilsa shad individuals from different geographical locations divided into two genetic clusters can be interpreted by two different ways. Firstly, the genetic discrimination may correspond to the alternative multi-locus genotypes that are maintained by strong divergent selection pressures in a spatially heterogeneous environment in which many factors could impose selection pressures, and those selection pressures could act at one or more life history stages [53]. Secondly, the observed two genetic clusters may correspond to the intense spawning site fidelity for two geographically isolated spawning grounds, one in the freshwater habitats and another one in the brackish water estuary as reported by the previous studies [5][6][7].…”