Genetic diversity and restricted genetic connectivity in an endangered marine fish (

Abstract

Determining the genetic diversity and differentiation among populations is a critical element of conservation biology, but for many aquatic, data-deficient species with small population sizes, this is not possible. Closely related species may therefore provide a model. For the first time, using over 4000 single-nucleotide polymorphism loci, we characterise the population genetic diversity and structure of one of the world's rarest marine fish, the spotted handfish (Brachionichthys hirsutus), a species which is also a member of the most threatened marine bony fish family (Brachionichthyidae). Fin clips were taken from 170 live spotted handfish across seven disjunct sites within the only known estuary (in Tasmania, Australia) where multiple populations of the species are found. Spatially discrete populations clustered into three genetic groupings and a significant variance in allele frequencies among populations (overall F ST ¼ 0.043), even at the small scale of the estuary, was observed. Furthermore, low contemporary migration rate estimates suggest low genetic homogeneity between locations. Because of the low genetic connectivity, population clusters of spotted handfish within the estuary should be considered as separate conservation management units. This insight should be considered for management and conservation strategies of other data-deficient and threatened species in the family.

Using eDNA and SCUBA surveys for detection and monitoring of a threatened marine cryptic fish

“…However, the number of transects needed to confirm presence/absence estimated here is highly conservative because these values are based upon locating only a single individual within the search area. In reality, fewer transects would be required to confirm the presence of species that aggregate or tend to live in groups, including the handfishes studied here (Wong et al, 2018; Appleyard et al, 2021).…”

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

“…In addition, the pairwise F ST values obtained were also similar to those obtained by Cao et al (wild populations: F ST < 0.05) with a similar sampling design and 2b-RAD sequencing method [37]. In addition, the pairwise F ST level of S. schlegelii populations (F ST = 0.01356, 0.01360, and 0.01678) was less than many other marine organisms, such as Clupea pallasii (F ST = 0.064-0.106) [38], Acanthopagrus latus (the highest F ST was 0.4288) [39], and Brachionichthys hirsutus (overall F ST = 0.043) [40]. This could confirm that S. schlegelii populations showed relatively low levels of genetic divergence among these two areas (QD, YT, and DL).…”

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

“…This freshwater species is distributed only in Kochi and Miyazaki areas in Japan, where two populations were identified using a set of 780 SNPs obtained from ddRAD-seq (restriction site—associated sequencing) [ 193 ]. In Tasmania, in the small Dervent Estuary, over 4000 SNPs enabled the identification of three main groups of populations of the spotted handfish ( Brachionichthys hirsutus ), which are recommended to be considered as separate conservation management units by the authors [ 194 ]. The threatened populations of subspecies of limpet Patella candei distributed only in the northeast Atlantic Macaronesian islands (e.g., the Canary Islands) have been identified with over 3000 SNP [ 195 ].…”