Genetic introgression of cultured rainbow trout in the Mexican native trout complex

Genetic Diversity and Population Structure of Portunustrituberculatus in Released and Wild Populations Based on Microsatellite DNA Markers from the Yangtze Estuary

Portunus trituberculatus is an important economic species of crab that is artificially bred and released in the Yangtze River Estuary and its adjacent sea areas. Based on six microsatellite markers, we investigate the genetic diversity and structure of 101 P. trituberculatus specimens collected from two hatcheries in Nantong and Zhoushan that participated in stock enhancement in the year 2019. We compared these with 124 wild specimens caught from 13 localities in the estuary. Analysis of several genetic diversity parameters (NA, RS, I, HO, HE, FIS, and FST) for the 15 populations demonstrates that both released and wild populations possess relatively rich genetic diversity. Furthermore, the released groups demonstrate no less genetic variation between themselves than do the wild crabs. Most FIS values are greater than zero, which shows inbreeding is common among specimens with geographically open sites. However, insufficient sampling may have led to a wide distribution of null alleles, a Hardy–Weinberg test disequilibrium in microsatellite markers PN22 and P04, and a lack of crab genetic diversity in site 14. All populations (except locality 14) have not suffered the bottleneck effect. Four subgroups can be seen to roughly spread longitudinally along the sample area by performing pairwise comparisons of genetic distance and FST values among the populations. No obvious topological heterogeneity is discovered among the four subgroups in a phylogenetic tree. The existence of genetic exchange and differentiation among the subgroups is also verified using structure analysis. Therefore, based on this evidence, we propose that the hatchery stock enhancements performed in Nantong and Zhoushan result in no reduction in genetic diversity for wild populations in the Yangtze Estuary in 2019.

Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris)

The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole-genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long-term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome-wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, π), while the number of segregating sites (Watterson's theta, θw) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co-occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.

Phylogeography and Population Genetics of Vicugna vicugna: Evolution in the Arid Andean High Plateau

The vicuña (Vicugna vicugna) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000-520,000 animals) is the result of population recovery programs established in response to 500 years of overexploitation. Despite the vicuña's ecosystemic, economic and social importance, studies about their genetic variation and history are limited and geographically restricted. Here, we present a comprehensive assessment of the genetic diversity of vicuña based on samples collected throughout its distribution range corresponding to eleven localities in Peru and five in Chile representing V. v. mensalis, plus four localities each in Argentina and Chile representing V. v. vicugna. Analysis of mitochondrial DNA and microsatellite markers show contrasting results regarding differentiation between the two vicuña types with mitochondrial haplotypes supporting subspecies differentiation, albeit with only a few mutational steps separating the two subspecies. In contrast, microsatellite markers show that vicuña genetic variation is best explained as an isolation by distance pattern where populations on opposite ends of the distribution present different allelic compositions, but the intermediate populations present a variety of alleles shared by both extreme forms. Demographic characterization of the species evidenced a simultaneous and strong reduction in the effective population size in all localities supporting the existence of a unique, large ancestral population (effective size ∼50,000 individuals) as recently as the mid-Holocene. Furthermore, the genetic variation observed across all localities is better explained by a model of gene flow interconnecting them rather than only by genetic drift. Consequently, we propose space "continuous" Management Units for vicuña as populations exhibit differentiation by distance and spatial autocorrelation linked to sex biased dispersal instead of population fragmentation or geographical barriers across the distribution.

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multidecade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world's most widely introduced invasive fish, across the Northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11°C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially nonhybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories.

Genetic effects of released swimming crab (Portunus trituberculatus) on wild populations inferred from mitochondrial control region sequences

Along the coast of Shandong Province in China, an extensive hatchery-release programme has been conducted for more than 10 years. However, no information has been reported concerning the long-term effects on the wild population resulting from the release of large numbers of juveniles in Portunus trituberculatus. In this study, sequence variation of swimming crab P. trituberculatus based on the mitochondrial control region was investigated for 946 swimming crabs at the releasing sites from 2012 to 2014. The result showed that the wild P. trituberculatus was characterized by high genetic diversity indices, and not significantly different from the previous study. Low F_ST values were estimated among the groups of different years and different sites, which suggested no genetic differentiation found in the wild population after the stock enhancement programme. Hence, the long-term extensive hatchery release programme has not affected the genetic structure of wild P. trituberculatus populations along the coast of Shandong Province.

Genetic Structure of Pacific Trout at the Extreme Southern End of Their Native Range

Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately also facing threats to their continued existence. Previous work has described one endemic species, the Mexican golden trout (O. chrysogaster), and one endemic subspecies, Nelson’s trout (O. mykiss nelsoni), in Mexico, but previous work indicated that there is vastly more biodiversity in this group than formally described. Here we conducted a comprehensive genetic analysis of this important group of fishes using novel genetic markers and techniques to elucidate the biodiversity of trout inhabiting northwestern Mexico, examine genetic population structure of Mexican trout and their relationships to other species of Pacific trout, and measure introgression from non-native hatchery rainbow trout. We confirmed substantial genetic diversity and extremely strong genetic differentiation present in the Mexican trout complex, not only between basins but also between some locations within basins, with at least four species-level taxa present. We also revealed significant divergence between Mexican trout and other trout species and found that introgression from non-native rainbow trout is present but limited, and that the genetic integrity of native trout is still maintained in most locations. This information will help to guide effective conservation strategies for this important group of fishes.