Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype-environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.
Influencia potencial de la divergencia adaptativa a nivel genoma sobre el resultado de la reubicación para conservación en una población aislada de urogallo mayor Resumen Las reubicaciones para conservación son una herramienta importante que se usa con frecuencia para aumentar las poblaciones en declinación o reestablecer las poblaciones erradicadas. Una de las metas de este aumento es incrementar la diversidad genética y reducir el riesgo de depresión endogámica (es decir, rescate genético). Sin embargo, la introducción de individuos de una población con divergencia significativa puede perturbar los rasgos coadaptados y reducir la aptitud local (es decir, depresión exogámica). La información genética es cada vez más accesible para las especies silvestres y puede proporcionar conocimiento único con respecto a la presencia y retención de la variación genética introducida a partir del aumento como un indicador de eficiencia y las similitudes adaptativas como un indicador de la idoneidad de la población de origen y la receptora. Usamos dos conjuntos de datos genéticos para evaluar el aumento de las poblaciones aisladas del urogallo mayor (Centrocercus urophasianus) en la región noroeste de la distribución de la especie (Washington, EUA) y para evaluar de forma retrospectiva la divergencia adaptativa entre la población de origen y la receptora. Desarrollamos dos modelos estadísticos para los datos microsatelitales para así evaluar los resultados del aumento. Usamos un modelo para predecir la diversidad genética después del aumento y comparamos estas predicciones con observaciones del cambio genético. Usamos el segundo modelo para cuantificar el aumento de la reproducción observada atribuida a las reubicaciones (evidencia de la integración poblacional). También caracterizamos la divergencia adaptativa a nivel genoma entre la población de origen y la población receptora. La diversidad genética observada (HO = 0.65) fue mayor de lo que se predijo en la población receptora de no haber ocurrido el aumento (HO = 0.58) pero menor de lo que se predijo en nuestro modelo (HO = 0.75). El aumento de la variación genética compartida entre las dos poblaciones residentes geográficamente aisladas incrementó, lo cual es evidencia de un flujo génico periódico que antes se supuso casi no ocurría. Entre los genes adaptativos candidatos asociados a una FST elevada (143 genes) o a variables ambientales locales (97 y 157 genes para cada método de asociación entre el ambiente y el genotipo, respectivamente) encontramos grupos de genes con funciones relacionadas que pueden influir sobre la habilidad de cada reubicación para usar recursos locales y navegar ambientes desconocidos y su potencial reproductivo, todas posibles razones para la baja retención genética en el aumento.
【摘要】保护性迁移是一项重要的保护工具, 通常用于帮助已衰退或灭绝后重建的种群进行增殖。增殖的目的之一是增加遗传多样性, 降低近交衰退的风险(即遗传拯救)。然而, 从明显分化的种群中引入个体有可能破坏共同适应性状, 降低局部适合度(即远交衰退)。野生动物的遗传数据已越来越容易获取, 这些数据可以提供独特的见解, 如了解通过增殖引入的遗传变异的存在和保留情况以指示有效性, 了解适应性相似性以指示源种群和迁入种群之间是否合适。我们利用两组遗传数据来评估艾草松鸡(Centrocercus urophasianus)分布区西北部(美国华盛顿州)的孤立种群的增殖情况, 并回顾性地评估了源种群和迁入种群之间的适应性分化。我们为微卫星数据开发了两个统计模型来评估增殖结果。我们使用一个模型预测增殖后的遗传多样性, 并将预测结果与观测到的遗传变化进行比较。我们使用第二个模型来量化观测到的迁入带来的繁殖量(证明发生种群融合)。我们还描述了源种群和迁入种群之间的全基因组适应性分化情况。观测到的迁入种群遗传多样性(HO = 0.65)高于未发生增殖的预测值(HO = 0.58), 但低于我们的模型预测值(HO = 0.75)。两个地理上隔离的种群之间共享遗传变异增加, 证明存在以往被认为十分少见的周期性基因流。在与FST升高(143个基因)或当地环境变量(每种基因型‐环境关联方法分别有97个和157个基因)相关的候选适应性基因中, 我们发现了可能会影响迁入个体利用当地资源和适应陌生环境的能力及其繁殖潜力的相关基因, 这些都可能是迁入个体基因保留率低的原因。【翻译:胡怡思;审校:聂永刚】.

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.

The increasing prevalence of hereditary anomalies in Holstein cattle populations presents a pressing issue, leading to concerns such as embryonic mortality and the birth of non-viable offspring. This study addresses the urgency of managing harmful genetic mutations in Holstein cattle by developing alternative diagnostic methods. The research aims to devise effective means to diagnose fertility haplotypes HH1, HH3, HH5, HCD and BY and subfertility syndrome in cattle. To achieve this goal, a range of molecular genetic techniques were employed, including Tetra-Primer ARMS-PCR methods, PCR-RFLP analysis and allele-specific PCR. These methods facilitated the identification of heterozygous carriers of various fertility haplotypes and subfertility syndrome in Holstein cows and servicing bulls. The study reveals the prevalence of these genetic defects within the Republic of Kazakhstan\'s cattle population. HH1, HH3, HH5, HCD and BY fertility haplotypes were found to have occurrence rates ranging from 1.4% to 16.6%, with subfertility syndrome detected in 4.5% of Simmental bulls. The practical significance of this research lies in its contribution to genetic monitoring and management strategies for Holstein cattle populations. By introducing affordable, rapid and accurate diagnostic methods, such as the T-ARMS-PCR, the study provides a valuable tool for controlling and mitigating the spread of harmful genetic mutations, ultimately improving the overall genetic health and productivity of Holstein cattle in the region. This research addresses a critical need in the cattle breeding industry and underscores the importance of genetic monitoring to ensure the long-term viability and sustainability of Holstein cattle populations.

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.

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen\'s d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.
El uso humano del agua, combinado con una megasequía reciente, ha reducido el flujo de los ríos y arroyos en el suroeste de los Estados Unidos y ha provocado la seca periódica de segmentos de ríos que antes eran perennes. Las reducciones en la escorrentía del deshielo y el aumento de la sequía amenazan colectivamente a especies obligatoriamente acuáticas de vida corta, incluyendo la amenazada carpa chamizal (Hybognathus amarus). Esta especie está sujeta a una dinámica poblacional de explosión y colapso, bajo la cual se espera que grandes fluctuaciones en la abundancia reduzcan las estimaciones del tamaño efectivo de la población y erosionen la diversidad genética con el tiempo. Las tasas de pérdida de la diversidad también se ven afectadas por la adición de peces procedentes de criaderos usados para suplementar la población silvestre. Utilizamos datos demográficos y genéticos de individuos silvestres y de criaderos para examinar la relación entre la diversidad genética y el tamaño efectivo de la población con la abundancia durante las últimas dos décadas. La diversidad genética fue baja a principios de los 2000, pero las métricas de diversidad y demografía estabilizaron después de que se inició el programa de criadero y mejoraron las condiciones ambientales. Sin embargo, a partir de 2017, la diversidad alélica disminuyó (d de Cohen = 1,34) y se mantuvo baja a pesar de la suplementación con individuos de criaderos y la breve recuperación de la población silvestre. A lo largo del tiempo, las estimativas de muestras individuales del tamaño efectivo de la población basados en el desequilibrio de ligamiento (LD Ne) estaban asociadas positivamente (r = 0,53) con la abundancia silvestre y la abundancia total, pero a medida que la proporción de desovadores originados en criaderos aumentó, el LD Ne disminuyó (r = -0,55). La megasequía limitó la abundancia de desovadores silvestres e impidió el reabastecimiento de las poblaciones en cautiverio con peces silvestres; por lo tanto, predecimos una población ribereña cada vez más dominada por individuos procedentes de criaderos y una pérdida acelerada de diversidad genética a pesar de la suplementación. Recomendamos un plan de gestión adaptativo y acelerado que integre la gestión del caudal del río y las operaciones de criaderos para frenar el ritmo de pérdida de diversidad genética exacerbada por la megasequía.

Understanding the evolutionary consequences of anthropogenic change is imperative for estimating long-term species resilience. While contemporary genomic data can provide us with important insights into recent demographic histories, investigating past change using present genomic data alone has limitations. In comparison, temporal genomics studies, defined herein as those that incorporate time series genomic data, utilize museum collections and repeated field sampling to directly examine evolutionary change. As temporal genomics is applied to more systems, species and questions, best practices can be helpful guides to make the most efficient use of limited resources. Here, we conduct a systematic literature review to synthesize the effects of temporal genomics methodology on our ability to detect evolutionary changes. We focus on studies investigating recent change within the past 200 years, highlighting evolutionary processes that have occurred during the past two centuries of accelerated anthropogenic pressure. We first identify the most frequently studied taxa, systems, questions and drivers, before highlighting overlooked areas where further temporal genomic studies may be particularly enlightening. Then, we provide guidelines for future study and sample designs while identifying key considerations that may influence statistical and analytical power. Our aim is to provide recommendations to a broad array of researchers interested in using temporal genomics in their work.

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.

Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species\' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.

OBJECTIVE: Few studies have genetically monitored chickens over time, and no research has been conducted on ducks. To ensure the sustainable management of key duck breeds, we used microsatellite markers to monitor Brown Tsaiya ducks over time genetically.
METHODS: The second, fourth, sixth to eighth generations of the Brown Tsaiya duck selected for feeding efficiency and control lines were included in this study to investigate the genetic variations, effective population size, population structure and the differentiation between populations over time with 11 microsatellite markers derived from Brown Tsaiya duck.
RESULTS: The results showed there were a slight decrease in the genetic variations and an increase in within-population inbreeding coefficient (FIS) in both lines, but no consistent increase in FIS was observed in each line. The effective population size in the second and eighth generations was 27.2 for the selected line and 23.9 for the control line. The change in allele richness showed a downward trend over time, and the selected line was slightly lower than the control line in each generation. The number of private alleles (Np) in the selected line were higher than in the control line. Moderate differentiation was observed between the second and eighth generations in the selected line (FST = 0.0510) and the control line (FST = 0.0606). Overall, differentiation tended to increase with each generation, but genetic variation and structure did not change considerably after six generations in the two lines.
CONCLUSIONS: This study provides a reference for poultry conservation and helps to implement cross-generation genetic monitoring and breeding plans in other duck breeds or lines to promote sustainable management.