Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage-based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species-specific Genotyping-in-Thousands by sequencing (GT-seq) panels. For laboratories involved in large-scale genotyping efforts, diagnosing non-target species and reassigning them to the appropriate monitoring program can be costly and time-consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross-species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species-specific GT-seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species-informative amplicons (16) were newly identified from the four existing GT-seq panels, thus demonstrating a low-cost approach to species identification when using targeted sequencing methods. A species-calling script was developed that is tailored for routine GT-seq genotyping pipelines and automates the identification of non-target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low-frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost-effective approach to species identification for genetic monitoring programs.

A male factor, commonly associated with poor semen quality, is revealed in about 50% of infertile couples. CFTR gene (Cystic Fibrosis Transmembrane Conduction Regulator) variants are one of the common genetic causes of azoospermia-related male infertility. Notably, the spectrum and frequency of pathogenic CFTR variants vary between populations and geographical regions. In this work, we made an attempt to evaluate the allele frequency (AF) of 12 common CFTR variants in infertile Russian men and healthy individuals from different districts of Russia. Because of the limited number of population-based studies on Russian individuals, we characterized the population AFs based on data from the Registry of Russian cystic fibrosis (CF) patients. In addition to the CF patient registry, we estimated the local frequencies of the same set of variants based on the results of genotyping of CF patients in local biocollections (from St. Petersburg and Yugra regions). AFs of common CFTR variants calculated based on registry and biocollection data showed good concordance with directly measured population AFs. The estimated region-specific frequencies of CFTR variants allowed us to uncover statistically significant regional differences in the frequencies of the F508del (c.1521_1523del; p.Phe508del) and CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb; p.Ser18ArgfsX) variants. The data from population-based studies confirmed previous observations that F508del, CFTRdele2,3(21kb), and L138ins (c.413_415dup; p.Leu138dup)variants are the most abundant among infertile patients, and their frequencies are significantly lower in healthy individuals and should be taken into account during genetic monitoring of the reproductive health of Russian individuals.

Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948-1949, 1988-1991, 2013-2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988-1991 and 2013-2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.

Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (Lutra lutra), environmental and legal protection has more recently led to population growth and recolonization of parts of their historic ranges. While heralded as conservation success, only few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s and 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery that (i) gene flow between subpopulations would increase over time, (ii) genetic diversity of previously isolated populations would increase and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main subpopulations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species: that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of the physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasize the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated.

The current extinction crisis requires effective assessment and monitoring tools. Genetic approaches are appealing given the relative ease of field sampling required to estimate genetic diversity characteristics assumed related to population size, evolutionary potential, and extinction risk, and to evaluate hybridization with non-native species simultaneously. However, linkages between population genetic metrics of diversity from survey-style field collections and demographic estimates of population size and extinction risk are still in need of empirical examples, especially for remotely distributed species of conservation concern where the approach might be most beneficial. We capitalized on an exceptional opportunity to evaluate congruence between genetic diversity metrics and demographic-based estimates of abundance and extinction risk from a comprehensive Multiple Population Viability Analysis (MPVA) in a threatened fish, the Lahontan cutthroat trout (LCT). We sequenced non-native trout reference samples and recently collected and archived tissue samples of most remaining populations of LCT (N = 60) and estimated common genetic assessment metrics, predicting minimal hybridization with non-native trout, low diversity, and declining diversity over time. We further hypothesized genetic metrics would correlate positively with MPVA-estimated abundance and negatively with extinction probability. We uncovered several instances of hybridization that pointed to immediate management needs. After removing hybridized individuals, cautious interpretation of low effective population sizes (2-63) suggested reduced evolutionary potential for many LCT populations. Other genetic metrics did not decline over time nor correlate with MPVA-based estimates of harmonic mean abundance or 30-year extinction probability. Our results demonstrate benefits of genetic monitoring for efficiently detecting hybridization and, though genetic results were disconnected from demographic assessment of conservation status, they suggest reduced evolutionary potential and likely a higher conservation risk than currently recognized for this threatened fish. We emphasize that genetic information provides essential complementary insight, in addition to demographic information, for evaluating species status.

The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub-species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the \"hybrid\" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 \"outliers\" (3.6%), for which the proportion of the genome of \"domestic\" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of \"wild\" origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.

Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.

Through using different sources, population reintroductions can create genetically diverse populations at low risk of harmful inbreeding and well equipped for adaptation to future environments. Genetic variation from one source can mask locally nonoptimal alleles from another, thereby enhancing adaptive potential and population persistence. We assessed the outcomes in survival, growth and reproduction of using two differentiated sources (genetically diverse Yarra and moderately diverse Dartmouth) for translocations and stocking to reintroduce the endangered Australian freshwater Macquarie perch Macquaria australasica into the Ovens River. For stocking, same- and different-population parents (\"cross-types\") were used during hatchery production. Genetic samples and data on individual fish were collected over three years of monitoring the Ovens. We genetically assigned Ovens fish to their broodstock parents and tested whether cross-type and genetic dissimilarity between parents are associated with offspring survival, and whether cross-type and parental dissimilarity or individual genetic diversity are associated with somatic growth rates of stocked fish. We genetically identified translocated fish and assessed local recruit ancestry. Of 296 Ovens fish, 31.1% were inferred to be stocked, 1.3% translocated and 67.6% locally born. Cross-type strongly predicted survival of stocked offspring: those with two Yarra parents had the highest survival, followed by offspring with two-population, then Dartmouth, ancestry. Of the Ovens recruits, 59.5% had Yarra, 33.5% two-population and 7.0% Dartmouth ancestry, despite 67% of stocked and 98% of translocated fish originating from Dartmouth. Offspring with two Yarra parents grew faster than offspring of Dartmouth or two-population ancestry. Although Dartmouth fish appear to be less fit in the Ovens compared to Yarra fish, possibly due to deleterious variation or genetic or plastic maladaptation, they contribute to the reintroduced population through local interbreeding with Yarra fish and relatively high survival of stocked offspring of two-population ancestry. Thus, combining compatible stocks is likely to benefit restoration of other wildlife populations.

Molecular approaches to calculate effective population size estimates (Ne) are increasingly used as an alternative to long-term demographic monitoring of wildlife populations. However, the complex ecology of most long-lived species and the consequent uncertainties in model assumptions means that effective population size estimates are often imprecise. Although methods exist to incorporate age structure into Ne estimations for long-lived species with overlapping generations, they are rarely used owing to the lack of relevant information for most wild populations. Here, we performed a case study on an elusive woodland bat, Myotis bechsteinii, to compare the use of the parentage assignment Ne estimator (EPA) with the more commonly used linkage disequilibrium (LD) Ne estimator in detecting long-term population trends, and assessed the impacts of deploying different overall sample sizes. We used genotypic data from a previously published study, and simulated 48 contrasting demographic scenarios over 150 years using the life history characteristics of this species The LD method strongly outperformed the EPA method. As expected, smaller sample sizes resulted in a reduced ability to detect population trends. Nevertheless, even the smallest sample size tested (n = 30) could detect important changes (60%-80% decline) with the LD method. These results demonstrate that genetic approaches can be an effective way to monitor long-lived species, such as bats, provided that they are undertaken over multiple decades.

The study aims to monitor the post-establishment success of the invasive skeleton shrimp Caprella scaura in the Atlantic-Mediterranean transition zone and understand its connectivity with other world areas, providing new information on the status of the introduced population and its global distribution. By using mitochondrial markers (16S and COI) we examined the temporal variation of populations in Cadiz Bay, Spain (hotspot for introductions in Europe) in between 2010 and 2017; as well as their linkage with foreign populations in its native and introduced distribution ranges. Cadiz Bay populations exhibited a connection with several European introduced populations (Iberian Peninsula, Canary Islands, Mediterranean Sea and The Netherlands), eastern USA, Sea of Japan and Australia. We found no evidence to support a Brazilian origin (one potential native area) of the Iberian Peninsula populations. We identified a progressive decrease in haplotype diversity and a low connectivity at the end of the monitoring period in one of the stations. Human-mediated changes in propagule pressure, and unfavorable environmental fluctuations are probably responsible for this. Meanwhile, populations in Cadiz Bay count on numerous foreign donors that could easily refuel the propagule input by exchanging gene flow. This implies that a vector regulation strategy has the potential of compromising the success of established non-native populations, which usually undergo vulnerability periods due to the challenging conditions of marinas. The use of molecular tools in a time series approach is then useful to identify the ideal time window to put in action management measures so that they are cost-effective.