Abstract
The anadromous Hilsa shad (Tenualosa ilisha) live in the Bay of Bengal and migrate to the estuaries and freshwater rivers for spawning and nursing of the juveniles. This has led to two pertinent questions: (i) do all Hilsa shad that migrate from marine to freshwater rivers come from the same population? and (ii) is there any relationship between adults and juveniles of a particular habitat? To address these questions, NextRAD sequencing was applied to genotype 31,276 single nucleotide polymorphism (SNP) loci for 180 individuals collected from six strategic locations of riverine, estuarine and marine habitats. FST OutFLANK approach identified 14,815 SNP loci as putatively neutral and 79 SNP loci as putatively adaptive. We observed that divergent local adaptations in differing environmental habitats have divided Hilsa shad into three genetically structured ecotypes: turbid freshwater (Western Riverine), clear freshwater (Eastern Riverine) and brackish-saline (Southern Estuarine-Marine). Our results also revealed that genes involved in neuronal activity may have facilitated the juveniles’ Hilsa shad in returning to their respective natal rivers for spawning. This study emphasized the application of fundamental population genomics information in strategizing conservation and management of anadromous fish such as Hilsa shad that intersect diverse ecotypes during their life-history stages.
Highlights
Anadromous fish migrate from a freshwater breeding habitat to a marine feeding habitat and back to freshwater for spawning and their level of genetic diversity and population divergence is intermediate to that of marine and freshwater species[1,2,3]
Neutral loci did not reveal much genetic structural differences among the Hilsa shad populations, by using 79 adaptive loci, we were still able to observe genetic differences which are so distinctive that they warrant the division of Hilsa shad into three separate ecotypes in Bangladesh waters: (1) marine/brackish represented by two closest relatives at Kuakata and the Meghna Estuary, Bhola, (2) muddy freshwater represented by two closest relatives in the Upper Padma and the Jamuna, and (3) clear freshwater types represented by the Meghna River and its upstream tributaries, Surma-Kushiara
In a conservation management context, it is important to maintain the genetic diversity of Hilsa shad in each location, given that our results have suggested high levels of gene flow within populations but lower variation across most of their range
Summary
NextRAD Sequencing, Annotation and GO Categorization of Neutral and Adaptive Loci. On average, 2 million reads of 150 bp per individual were generated from the 180 nextRAD-genotyped T. ilisha. We have conducted a pairwise comparison of FST values based on 79 putatively adaptive loci between adult and juveniles for five sampling sites except individuals from Meghna estuary in Bhola (Table 5). Juveniles from three sampling sites (Surma-Kushiara, Upper Padma and Jamuna) were observed to show extremely weak genetic differentiation with their respective adults with non-significant zero FST values. PCA based on the adaptive SNPs showed three major clusters (Marine and Estuary, North-Western Riverine and North-Eastern Riverine) without clear separation of the populations according to the collection sites, which is found to be consistent with the NJ clustering, AMOVA analysis and FST values. In contrast with the PCA, NJ clustering and STRUCTURE analyses, our DAPC analysis based on the adaptive SNPs dataset identified four distinct partitioning of populations, the population structure was not explainable by the collection groups (Fig. 8). The DAPC assignment analysis showed that Surma-Kushiara and Chandpur was further divided into two separate clusters
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