The identification of genetically distinct populations is central to the management and conservation of wild populations. Whole-genome-sequencing allows for high-resolution assessment of genetic structure, demographic connectivity and the impacts of selection acting on different parts of the genome. Here, we utilise population genomics to investigate the genetic structure of the Australasian snapper or Tāmure (Chrysophrys auratus), an ecologically, economically, and culturally important (taonga) marine fish. We analysed over four million high-quality SNPs obtained by whole-genome sequencing from 382 individuals collected across its New Zealand range. We identified two genetic clusters (an eastern and western cluster) with genetic disjunctions around on either side of the North Island of New Zealand. These genetic clusters do not match the current fisheries management areas. Pairwise-FST and ADMIXTURE analyses showed the presence of directional gene flow occurring at both genetic disjunctions from the East to the West cluster. We hypothesize that major ocean currents are limiting the dispersal of snapper at these genetic disjunctions. The heterogeneous coastal environment is also likely driving evolutionary change. A genome scan identified four significantly divergent genomic regions between genetic clusters. A diverse pattern of genetic variation in these regions implies that different evolutionary processes drive local adaptation in these clusters. Identification of candidate genes in these regions also provides a tentative connection to which traits may be under selection. Our results provide novel insights into New Zealand’s coastal environment influences evolutionary processes, and valuable information for effective management of the snapper fisheries.
The outcome of hybridization is of major interest in evolutionary and conservation biology. Here, we investigate (i) the genomic signal of the hybridization dynamics, (ii) the strength of reproductive barriers preventing copulation in heterospecific and hybrid crosses, and (iii) the population dynamics (stability of species proportions) of the two damselfly species Ischnura elegans and I. graellsii in two differently aged Spanish hybrid regions. RAD sequencing in these hybrid regions and in allopatric populations was used to generate 5,702 SNPs to quantify population diversity and population differentiation, and a subset of 381 species-specific SNPs to analyze individual ancestry and the proportion of individuals in different hybrid classes. Our individual ancestry results showed the presence of F1 and F2 hybrids, in line with on-going hybridization and bidirectional backcrossing in both hybrid regions, with almost complete absence of genetically pure I. elegans and I. graellsii. Different admixture-class distributions were in part explained by 1) different mean strength of reproductive barriers in the hybrid regions, with stronger barrier in the older hybrid region, 2) local dynamics (continuous recolonization events), 3) proximity to introduction site, and 4) time elapsed since colonization. Consistent with theoretical expectations, introgression maintained (in the younger hybrid region) or increased genetic diversity (in the older hybrid region), and reduced genetic differentiation between local populations in both hybrid regions. Whether this will facilitate the ongoing range expansion of I. elegans in Spain is an interesting avenue for future research.
1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper