Loss of genetic variation and effective population size of Kirikuchi charr: implications for the management of small, isolated salmonid populations

The genetic status and rescue measure for a geographically isolated population of Amur tigers

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.

Exploring Less Invasive Visual Surveys to Assess the Spatial Distribution of Endangered Mediterranean Trout Population in a Small Intermittent Stream

Monitoring the conservation status of endangered freshwater fish using less invasive methods poses challenges for ecologists and conservationists. Visual surveys have been proposed as an alternative to electrofishing, which is a standard methodology that can cause injuries, physiological stress and post-release mortality in organisms. To test the efficacy of visual methods, a study was conducted in an intermittent stream of Sardinia (Italy). Two visual methods were employed: a visual survey from streambanks (VSS) and an underwater visual survey (UVS) using cameras. The aims of this study were (1) to compare the effectiveness of these methods in detecting patch occupancy patterns and (2) to investigate the effect of environmental variables on the detection probability of Mediterranean native trout. Environmental variables characterizing pool habitats were recorded, and generalized linear models (GLMs) were employed to assess the correlation between these variables and trout presence/absence. GLM analysis revealed that UVS had higher detection probability with larger pool volume, whereas submerged macrophytes negatively affected detection probability. Detection from streambanks (VVS) was negatively affected by a high turbulence rate. In conclusion, our study suggests the utility of visual methods to describe patterns of patch occupancy of Mediterranean trout. However, methods can be differently affected by environmental variables. Therefore, monitoring programs using these methods should consider these factors to ensure a reliable description of within-stream trout distribution in intermittent streams.

Pug-Headedness Anomaly in a Wild and Isolated Population of Native Mediterranean Trout Salmo trutta L., 1758 Complex (Osteichthyes: Salmonidae)

Skeletal anomalies are commonplace among farmed fish. The pug-headedness anomaly is an osteological condition that results in the deformation of the maxilla, pre-maxilla, and infraorbital bones. Here, we report the first record of pug-headedness in an isolated population of the critically endangered native Mediterranean trout Salmo trutta L., 1758 complex from Sardinia, Italy. Fin clips were collected for the molecular analyses (D-loop, LDH-C1* locus. and 11 microsatellites). A jaw index (JI) was used to classify jaw deformities. Ratios between the values of morphometric measurements of the head and body length were calculated and plotted against values of body length to identify the ratios that best discriminated between malformed and normal trout. Haplotypes belonging to the AD lineage and the genotype LDH-C1*100/100 were observed in all samples, suggesting high genetic integrity of the population. The analysis of 11 microsatellites revealed that observed heterozygosity was similar to the expected one, suggesting the absence of inbreeding or outbreeding depression. The frequency of occurrence of pug-headedness was 12.5% (two out of 16). One specimen had a strongly blunted forehead and an abnormally short upper jaw, while another had a slightly anomaly asymmetrical jaw. Although sample size was limited, variation in environmental factors during larval development seemed to be the most likely factors to trigger the deformities.

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

Background

The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites.

Results

A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation.

Conclusions

The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation.

Loss of genetic diversity at an MHC locus in the endangered Tokyo bitterling Tanakia tanago (Teleostei: Cyprinidae)

Genetic diversity at a major histocompatibility complex (MHC) class II B gene was examined for two wild and three captive populations of the endangered Tokyo bitterling Tanakia tanago. A specific primer set was first developed to amplify the MHC II B exon 2 locus. Using single strand conformation polymorphism (SSCP) and sequencing analysis, 16 DAB3 alleles were detected with 56 nucleotide substitutions in the 276-bp region. In the putative antigen-binding sites of exon 2, the rate of nonsynonymous substitutions was significantly higher than that of synonymous substitutions (dN/dS = 2.79), indicating positive selection on the retention of polymorphism. The population from the Handa Natural Habitat Conservation Area and that from the Tone River system exhibited low variation (one and three alleles, respectively), whereas the captive population that originated from a mix of three distinct populations had the highest amounts of variation (14 alleles). The levels of heterozygosity at the MHC varied considerably among populations and showed significant correlations with those at putative neutral microsatellite markers, suggesting that genetic drift following a bottleneck has affected MHC variability in some populations. Comparisons between endangered and non-endangered fish species in previous reports and the present results indicate that the number of MHC alleles per population is on average 70% lower in endangered species than non-endangered species. Considering the functional consequence of this locus, attention should be paid to captive and wild endangered fish populations in terms of further loss of MHC alleles.

Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla)

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.