Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

Population Genetics of New Zealand Pagrus auratus and Genetic Variation of an Aquaculture Broodstock

<p>Fisheries and aquaculture are major contributors of nutrition and animal protein worldwide. Understanding the genetic variation and differentiation within and between wild populations is important for both sustainable fisheries management and selection of aquaculture broodstock. This study determined the genetic variation and differentiation of New Zealand Pagrus auratus based on mitochondrial DNA control region sequencing and microsatellite DNA genotyping. Low but significant differentiation was measured between several sample sites, but otherwise the population was genetically panmictic. The M-ratio test and Fu’s Fs statistics indicate that there may have been historical bottlenecks at all sample sites and a more recent bottleneck in the Tasman Bay. Two South Island sites were identified that had not been through recent bottlenecks and were not significantly differentiated from the Tasman Bay, which may provide a source of gene flow to aid its genetic recovery. Comparison of the broodstock and wild genetic variation indicate that the broodstock represented most of the genetic variation found in high frequency in wild populations, but further wild-caught individuals may be needed, based on the criteria used in several previous studies. Simulations indicate that adding approximately 20 and 48 wild-caught individuals from multiple populations to the current broodstock was needed to represent all genetic variation above a target frequency of 0.05 in the Tasman Bay and all sample sites, respectively.</p>

High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.

Pedigree analysis for conservation of genetic diversity and purging

SummaryWe present an approach to describe and evaluate changes in genetic diversity and to calculate bounds for improvement. This pedigree-based analysis was applied to the Kromfohrländer dog (FCI Gr9 Sec10). Pedigrees trace back to the foundation of the breed and were available for 5527 individuals. Based on this dataset the population structure and historical bottlenecks were studied. Distributions of allele frequencies were estimated by Monte Carlo simulation. To monitor changes in mating systems throughout the breeding history, the homozygosity of alleles was compared with their expectations in Hardy–Weinberg equilibrium. Different breeding lines were identified by hierarchical cluster analysis and were characterized by ancestor contributions. Our calculations showed that the founder event in 1945 was followed by two bottlenecks. One was caused by strong selection in a very small population, and the other was triggered by rigorous disease management. The necessary amount of purging that arised due to the bottlenecks was also discussed.

Allozyme and microsatellite diversity in natural and domestic populations of turbot (Scophthalmus maximus) in comparison with other Pleuronectiformes

Twelve microsatellite and 28 allozyme loci were employed to analyse genetic diversity in natural and domestic populations of turbot (Scophthalmus maximus) from northwest Spain in comparison with other flatfish species with similar habitat, life history, and geographic distribution—the brill (Scophthalmus rhombus) and the flounder (Platichthys flesus). These species had shown much higher allozyme diversity than turbot in previous studies, and were used as a reference to check for putative historical bottlenecks in turbot. Significantly lower genetic variability in turbot than in brill and flounder was confirmed with allozymes, but not with the highly variable microsatellite loci. This intermarker discrepancy could be explained by different mutation rates in relation with historical bottlenecks along turbot evolution. A significantly lower genetic diversity was observed in a domestic strain of turbot than in natural populations of this species. This sample evidenced a strong family structure from microsatellite data, which suggests caution against the use of commercial batches for broodstock foundation in turbot farming. A strong concordance was found across the two categories of markers used when analysing the pattern of genetic subdivision at a local scale within the three species analysed, low and nonsignificant genetic differentiation being observed between Atlantic and Cantabric areas.