Genomic stock structure of the marine teleost tarakihi (Nemadactylus macropterus) provides evidence of fine-scale adaptation and a temperature-associated cline amid panmixia

Abstract

Tarakihi (Nemadactylus macropterus) is an important fishery species with widespread distribution around New Zealand and off the southern coasts of Australia. However, little is known about whether the populations are locally adapted or genetically structured. To address this, we conducted whole-genome resequencing of 175 tarakihi from around New Zealand and Tasmania (Australia) to obtain a dataset of 7.5 million genome-wide and high-quality single nucleotide polymorphisms (SNPs). Variant filtering, FST-outlier analysis, and redundancy analysis (RDA) were used to evaluate population structure, adaptive structure, and locus-environment associations. A weak but significant level of neutral genetic differentiation was found between tarakihi from New Zealand and Tasmania (FST = 0.0054–0.0073, P ≤ 0.05), supporting the existence of at least two separate reproductive stocks. No clustering was detected among the New Zealand populations (FST < 0.001, P = 0.77). Outlier-based, presumably adaptive variation suggests fine-scale adaptive structure between locations around central New Zealand off the east (Wairarapa, Cape Campbell, and Hawke's Bay) and the west coast (Tasman Bay/Golden Bay and Upper West Coast of South Island). Allele frequencies from 55 loci were associated with at least one of six environmental variables, of which 47 correlated strongly with yearly mean water temperature. Although genes associated with these loci are linked to various functions, the most common functions were integral components of membrane and cilium assembly. Projection of the RDA indicates the existence of a latitudinal temperature cline. Our work provides the first genomic insights supporting panmixia of tarakihi in New Zealand and evidence of a genomic cline that appears to be driven by the temperature gradients, together providing crucial information to inform the stock assessment of this species, and to widen the insights of the ecological drivers of adaptive variation in a marine species.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

“…for other marine teleost species in New Zealand previously (e.g. [54][55][56]). Interestingly, the F ST values between the two clusters were unexpectedly high, denoting pronounced genetic divergence between the two clusters.…”

Comparative genomics of tarakihi (Nemadactylus macropterus) and five New Zealand fish species: assembly contiguity affects the identification of genic features but not transposable elements

“…DNA was isolated from five specimens each belonging to a different fish species (king tarakihi, blue moki, butterfish, barracouta, and kahawai) for the respective de novo genome assemblies (Figure 1). The fish were sampled opportunistically, based on availability, as part of a sampling campaign for the genome assembly and population genomics of tarakihi (Papa, Morrison, et al, 2021; Papa, Wellenreuther, et al, 2021). The king tarakihi specimen was collected by a commercial fishing trawler around Three King Islands at a depth between 140 and 250 m. The standard length was 477 mm, weight was 1,900 g, and it was identified as a female by observation of the gonads.…”

“…The king tarakihi specimen was not blasted because there were no sequences available for this species on NCBI. The specimen was already identified with high confidence using morphology and based on the phylogenetic position of the sequence data (see Papa, Morrison, et al (2021)).…”

Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context

“…Barriers to gene flow for many marine species have been detected using neutral markers (Wei et al, 2013;Schiavina et al, 2014;Silva et al, 2016;Silva & Gardner, 2016;Diopere et al, 2018;Singh et al, 2018). On the other hand, a higher number of significant associations are found between adaptive genetic variability and environmental variability that determines in situ natural selection on populations (Diopere et al, 2018;Muir et al, 2020;Boulanger et al, 2022;Papa et al, 2022). The relationship between environment and target species may be assessed via quick seascape genomics protocols and considered when managing the target species and/or marine resources within the marine community over time.…”

“…SNPs can be neutral or under selection, depending on their location in the genome, and both categories of markers have been used in population genetics studies successfully (Vu et al, 2021;Chao et al, 2021). For population genetics studies neutral molecular markers are selected (Truong et al, 2022), although the two categories of SNPs are usually complimentary tools that can provide comprehensive information about genetic patterns or evidence of local adaptation for certain species/populations (Carreras et al, 2017;Miller et al, 2019;Asaduzzaman et al, 2020;Saha et al, 2021;Mejía-Ruíz et al, 2020;Papa et al, 2022).…”