Tenualosa ilisha is a popular anadromous and significant trans-boundary fish. For sustainable management and conservation of this fish, drawing an appropriate picture reflecting population status of this species is very essential based on their all-strategic habitats in Bangladesh. In this study, 139 samples from 18 sites were collected and cross-species gene enrichment method was applied. Like most of the Clupeiforms, nucleotide diversity of this shad was very low (0.001245–0.006612). Population differences between most of the locations were low and not significant (P > 0.05). However, P values of a few locations were significant (P < 0.05) but their pairwise FST values were very poor (0.0042–0.0993), which is inadequate to recognize any local populations. Our study revealed that the presence of a single population in the Bangladesh waters with some admixtured individuals, which may contain partial genes from other populations. Most of the individuals were admixed without showing any precise grouping in the ML IQtree and Network, which might due to their highly migratory nature. Fishes from haors and small coastal rivers were not unique and no genetic differences between migratory cohorts. The hilsa shad fishery should be managed considering it as a single panmictic population in Bangladesh with low genetic diversity.

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Siniperca undulata and S. obscura (Centrarchiformes: Sinipercidae) are small Chinese perches, living in creeks and streams in southern China. While they have sympatric distribution and occupy similar macrohabitat, their body sizes and ecological niches have many differences. Determining the genome sequences of S. undulata and S. obscura would provide us an essential data set for better understanding their genetic makeup and differences that may play important roles in their adaptation to different niches. We determined the genome sequences of both S. undulata and S. obscura using 10× genomics technology and the next-generation sequencing. The assembled genomes of S. undulata and S. obscura were 744 and 733 Mb, respectively. Gene family analysis revealed that there were no overlap between S. undulata and S. obscura in terms of rapid expanding and rapid contracting genes families, which were related to growth, immunity, and mobility. Positive selection analyses also cooperated that the function of selected genes involve growth, athletic ability, and immunity, which may explain the preference of different niches by S. undulata and S. obscura. Pairwise sequentially Markovian coalescent analyses for the two species suggested that populations of both S. undulata and S. obscura showed a rising trend between 90 and 70 Ka probably due to the mild environment during the last interglacial period. A stage of population shrinking occurred from 70 to 20 Ka, which was in with the Tali glacial period in eastern China (57–16 Ka).

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