Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

Abstract

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

Evidence for population genetic structure in two exploited Mekong River fishes across a natural riverine barrier

“…The ability to detect neutral genetic differentiation between Pakse and the other locations sampled here is likely due to the improved sampling of the genome provided by RADseq as compared to previous studies using low‐throughput methods (Hurwood et al ., 2007; Iranawati, 2014), rather than to recently emerging population structure. High‐throughput methods similar to those utilized in this study are increasing in use in the Mekong (Ackiss et al ., 2019; Dang et al ., 2019) and are needed to measure baseline genetic diversity, population size and structuring for fishes in this rapidly changing riverscape.…”

“…Ferierra et al ., 2017; Gouskov et al ., 2016; Khedkar et al ., 2014; Ruzich et al ., 2019); nonetheless, examples from heavily dammed rivers, such as the Columbia and Fraser Rivers of northwest North America, have shown that migratory fish populations are particularly vulnerable to negative effects such as severe inbreeding and complete extirpation upstream of dams (Ferguson et al ., 2011). In the 3S Basin, a population of the catfish Hemibagrus spilopterus sampled upstream of dams on the Srepok River was found to have diminished effective population size and elevated relatedness and inbreeding (Ackiss et al ., 2019).…”

“…Extirpation of local populations has been observed in the Columbia River system following the blocking of upstream spawning grounds by dams (Ferguson et al ., 2011) and freshwater fish are approximately four times more likely than marine to be classified as vulnerable to extinction (Olden et al ., 2007). Incipient extirpation due to damming has been detected in at least one species of economically important catfish in the Mekong Basin (Ackiss et al ., 2019).…”

Mixed-stock analysis in the age of genomics: Rapture genotyping enables evaluation of stock-specific exploitation in a freshwater fish population with weak genetic structure

“…Genomics is emerging as an influential tool for managing and conserving freshwater fishes globally (Tibihika et al 2020; Biesack et al 2020). In Africa and Asia, genomics has become an important tool to quantify diversity and identify critically endangered populations (Malinsky et al 2018; Ackiss et al 2019). In Europe, genomics has become central to domestication of native species for aquaculture (Toomey et al 2020).…”

Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

“…This heterozygosity deficiency is also recorded in P . pelagicus populations in Malaysia [50], and in other marine and freshwater organisms due to widespread habitat loss, degradation and fragmentation [32,96,97]. Significant relatedness and sib-ships have been observed in marine populations due to biophysical larval behavior [98,99], self-recruitment [31,100], and overexploitation/restocking [101].…”