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Chinook salmon (Oncorhynchus tshawytscha) display remarkable life history diversity, underpinning their ability to adapt to environmental change. Maintaining life history diversity is vital to the resilience and stability of Chinook salmon metapopulations, particularly under changing climates. However, the conditions that promote life history diversity are rapidly disappearing, as anthropogenic forces promote homogenization of habitats and genetic lineages. In this study, we use the highly modified Yuba River in California to understand if distinct genetic lineages and life histories still exist, despite reductions in spawning habitat and hatchery practices that have promoted introgression. There is currently a concerted effort to protect federally listed Central Valley spring-run Chinook salmon populations, given that few wild populations still exist. Despite this, we lack a comprehensive understanding of the genetic and life history diversity of Chinook salmon present in the Yuba River. To understand this diversity, we collected migration timing data and GREB1L genotypes from hook-and-line, acoustic tagging, and carcass surveys of Chinook salmon in the Yuba River between 2009 and 2011. Variation in the GREB1L region of the genome is tightly linked with run timing in Chinook salmon throughout their range, but the relationship between this variation and entry on spawning grounds is little explored in Californias Central Valley. We found that the date Chinook salmon crossed the lowest barrier to Yuba River spawning habitat (Daguerre Point Dam) was tightly correlated with their GREB1L genotype. Importantly, our study confirms that ESA-listed spring-run Chinook salmon are spawning in the Yuba River, promoting a portfolio of life history and genetic diversity, despite the highly compressed habitat. This work highlights the need to identify and protect this life history diversity, especially in heavily impacted systems, to maintain healthy Chinook salmon metapopulations. Without protection, we run the risk of losing the last vestiges of important genetic variation.

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

ABSTRACT Quantifying connectivity between endangered or threatened marine populations is critical information for management and conservation, especially where abundance and productivity differ among such populations. Spatial patterns of such connectivity depend not only on extrinsic factors such as oceanography and bathymetry but also on intrinsic species‐specific factors such as life history, demography and the location of glacial refugia. Nevertheless, population structure is often inferred from related or ecologically similar species. For example, the population structure in most rockfish species (Sebastes spp.) in the Salish Sea and the US West Coast is currently inferred from genetic data of three species that are known to hybridise in Puget Sound. Here, we determined the population structure and connectivity in five Puget Sound Rockfish species (Black [Sebastes melanops], Yellowtail [S. flavidus], Redstripe [S. proriger], Greenstriped [S. elongatus], and Puget Sound Rockfish [S. emphaeus]) from over 12,000 restriction‐site associated DNA sequencing (RADseq) loci. We found species‐specific patterns of genetic differentiation, attributable to both extrinsic and intrinsic factors. Specifically, Black and Puget Sound rockfishes showed no genetic differentiation; Yellowtail and Greenstriped rockfishes were structured according to known geographic barriers; and Redstripe Rockfish revealed evidence for temporal genetic differentiation, suggesting irregular recruitment influences population structure. Only Yellowtail Rockfish followed the federal DPS boundaries generally assumed for rockfish, further emphasizing the importance of species‐specific management for the effective recovery and management of these rockfish populations and of marine species in general. [ABSTRACT FROM AUTHOR]

ABSTRACT Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long‐term population dynamics. Here we took advantage of a rich dataset of seven brook trout (Salvelinus fontinalis) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (N̂$$ \hat{N} $$b) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain N̂badj2$$ {\hat{N}}_{b(adj2)} $$ and subsequently, N̂eadj2$$ {\hat{N}}_{e(adj2)} $$ following Waples et al. (2013). N̂eadj2$$ {\hat{N}}_{e(adj2)} $$ was estimated for the years 2014 to 2019. Census size was estimated by mark recapture using double‐pass electrofishing (N̂cMR$$ {\hat{N}}_{c(MR)} $$) (years 2014–2018) as well as by the Close Kin Mark Recapture approach (N̂cCKMR$$ {\hat{N}}_{c(CKMR)} $$) (years 2015–2017). Within populations, annual variation in N̂eadj2$$ {\hat{N}}_{e(adj2)} $$ (ratio of maximum to minimum N̂eadj2$$ {\hat{N}}_{e(adj2)} $$) ranged from 1.6‐fold to 58‐fold. Over all 7 populations, the median annual variation in N̂eadj2$$ {\hat{N}}_{e(adj2)} $$ was around 5‐fold. These results reflect important interannual changes in the variance in reproductive success and more generally in population dynamics. Within population N̂cMR$$ {\hat{N}}_{c(MR)} $$ varied between years by a (median) factor of 2.7 with a range from 2 to 4.3. Thus, estimated effective size varied nearly twice as much as did estimated census size. Our results therefore suggest that, at least in small populations like those examined in the present study, any single annual estimate of N̂eadj2$$ {\hat{N}}_{e(adj2)} $$ is unlikely to be representative of long‐term dynamics. At least 3–4 annual estimates may be required for an estimate of contemporary effective size to be truly representative. We then compared N̂cMR$$ {\hat{N}}_{c(MR)} $$ to N̂cCKMR$$ {\hat{N}}_{c(CKMR)} $$. For five of the seven populations, the estimates of population abundance based on mark recapture (N̂cMR$$ {\hat{N}}_{c(MR)} $$) were indistinguishable from those based on close kin mark recapture (N̂cCKMR$$ {\hat{N}}_{c(CKMR)} $$). The two populations with discordant N̂cMR$$ {\hat{N}}_{c(MR)} $$ and N̂cCKMR$$ {\hat{N}}_{c(CKMR)} $$ exhibited extremely low N̂eadj2/N̂cMR$$ {\hat{N}}_{e(adj2)}/{\hat{N}}_{c(MR)} $$ ratios and the largest annual variation in N̂eadj2$$ {\hat{\ N}}_{e(adj2)} $$ (58‐fold and 35.4‐fold respectively). These results suggest that sampling effort in these two streams may have been insufficient to properly capture the genetic diversity of the entire population and that individuals sampled were not representative of the population. Our study further validates CKMR as a method for estimating abundance in wild populations and it demonstrates how knowledge of the temporal variation in N̂e$$ {\hat{N}}_e $$ can be used to identify potential sources of discrepancies between N̂cMR$$ {\hat{N}}_{c(MR)} $$ and N̂cCKMR$$ {\hat{N}}_{c(CKMR)} $$. [ABSTRACT FROM AUTHOR]

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co‐occur in spring‐fed tributaries of the Rio Grande in Texas and Mexico. Both N. megalops and N. amabilis are listed as Species of Greatest Conservation Need by the Texas Parks and Wildlife Department. Notropis amabilis is widespread and listed as apparently secure by Texas Parks and Wildlife Department whereas N. megalops has a very limited distribution and has not been ranked by Texas Parks and Wildlife Department because of data deficiency. Morphological differences between these species have been described; however, proper identification in situ remains problematic. Furthermore, given their range of overlap there is potential for hybridization, and limited genetic data have been collected comparing the species. Therefore, reduced representation genomic and mitochondrial sequencing data were used to reassess the distinctness of the species, screen for hybridization, and characterize their relative frequencies throughout their range of overlap. Genomic analyses recovered two distinct genetic groups corresponding to the species (F'CT = 0.89) with no evidence of admixture or introgression. The species were found to co‐occur at three sampling locations, two in the Devils River and one in the Pecos, but not in equal frequencies. Overall, these results provide data and tools for further research on N. megalops needed for accurate conservation policies and management practices. [ABSTRACT FROM AUTHOR]

In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS‐collected whale blow for conservation genetics from a remote location. see also the Perspective by Elena Valsecchi. [ABSTRACT FROM AUTHOR]

The genetic identity and conservation status of lake ecotype of brown trout (Salmo trutta) populations in Slovenia's Alpine lakes Bled and Bohinj have been subjected to changes due to historical stocking practices. We aimed to evaluate the genetic differentiation and origins of these populations to advise for correct conservation strategies. Using microsatellite and mitochondrial DNA analysis on 365 trout specimens, we explored the genetic diversity and structure of these populations, comparing them with potential originators. Results revealed distinct genetic profiles between Bled and Bohinj lake trout, with Bohinj lake trout closely aligned with the native Danubian lineage and Bled lake trout showing a hybrid composition, significantly influenced by hatchery-introduced Atlantic lineage strains. The genetic distinction between these populations underscores the complexity of their conservation, showcasing the impact of human-mediated introductions on natural populations. The urgent need for conservation measures to preserve the Bohinj population's native genetic pool is highlighted, underlining the must to prevent the transfer of individuals from Lake Bled or elsewhere and to reconsider stocking practises in order to prevent further genetic dilution of these iconic European lake dwellers. [ABSTRACT FROM AUTHOR]

ABSTRACT The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de‐extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool. [ABSTRACT FROM AUTHOR]

Ferula huber‐morathii is an endemic and medicinally important plant. This species is distributed in eight Turkish localities, including three newly identified ones. Its extent of occurrence and area of occupancy is determined to be 3963 km2 and 32 km2 respectively. All localities are characterized by East Mediterranean and sub‐Mediterranean precipitation regimes; however, temperatures increase excessively and precipitation decreases during the flowering period of the species. The population sizes are quite small, and the number of reproducing individuals in some populations is below ten. Analyses of ISSR markers showed the percentage of polymorphic loci to be 94% at the species level and 56% at the population level. The level of genetic differentiation (measured by GST) was 0.37 and the estimated level of gene flow among populations (NM) was 0.84. The percentage of variance occurring within and among populations, determined by AMOVA, was 75% and 25%, respectively. STRUCTURE analysis revealed two genetic clusters of individuals with a geographic structure, similar to that found in UPGMA and an ordination analysis. Some populations turned out to have both low numbers of individuals and low genetic diversity. Since many of the populations are subject to anthropogenic disturbance, the species should remain in the EN category. At the same time, it is suggested that a new in‐situ conservation area should be created around nearby dams, situated in the same climate area as the currently known populations. [ABSTRACT FROM AUTHOR]

Out‐planting corals onto coral reefs as a mechanism to increase coral cover on degraded reef systems is an increasing global activity. Current practices typically focus on asexual out‐planting of coral fragments (coral gardening). Newer sexual reproductive approaches are being developed to out‐plant younger corals produced in aquaculture facilities or sea‐based rearing pools to enable assisted evolution or assisted gene flow conservation genetics approaches. Designing out‐planting deployment operations requires decisions to be made on planting density and location in order to maximize future recruitment on both the out‐planted reefs, and on nearby reefs that are connected through oceanographic transport processes. The thinking presented here seeks to unpack how out‐planting density may be influenced, especially by local oceanographic conditions, in order to guide practitioners undertaking restoration projects. [ABSTRACT FROM AUTHOR]

Habitat fragmentation reduces gene flow, causing genetic differentiation and diversity loss in endangered species through genetic drift and inbreeding. However, the impact of habitat fragmentation on ectomycorrhizal (ECM) fungi remains unexplored, despite their critical roles in forest ecosystems. Here, we investigated the population genetic structure and the demographic history of Rhizopogon togasawarius, the ECM fungus specifically colonizing the host tree Pseudotsuga japonica, across its entire distribution range (>200 km). These two species are designated as endangered species on the IUCN Red List since they are found only in small, fragmented forests in Japan. We analysed 236 R. togasawarius individuals from five remaining populations across the Kii Peninsula and the Shikoku Island, separated by a sea channel. Simple sequence repeat analyses using 20 loci revealed strong genetic differentiation among populations (FST = 0.255), even significant in the nearest population pair separated by a distance of only 8 km (FST = 0.075), indicating extremely limited gene flow between populations. DIYABC‐RF analyses implied that population divergence occurred approximately 6000 generations ago between the two regions, and nearly 1500 generations ago between the nearest populations within Shikoku Island, related to past climate events. Because of prolonged genetic isolation, significant inbreeding was confirmed in four of five populations, where effective population sizes became very small (Ne = 9.0–58.0). Although evaluation of extinction risks for microorganisms is challenging, our conservation genetic results indicated that habitat fragmentation increases extinction risk through population genetic mechanisms, and therefore should not be overlooked in biodiversity conservation efforts. [ABSTRACT FROM AUTHOR]

Biodiversity loss has reached critical levels partly due to anthropogenic habitat loss and degradation. These landscape changes are damaging as they can fragment species distributions into small, isolated populations, resulting in limited gene flow, population declines and reduced adaptive potential. Genetic rescue, the translocation of individuals to increase genetic diversity and ultimately fitness, has produced promising results for fragmented populations but remains underutilized due to a lack of long‐term data and monitoring. To promote a better understanding of genetic rescue and its potential risks and benefits over the short‐term, we reviewed and analysed published genetic rescue attempts to identify whether genetic diversity increases following translocation, and if this change is associated with increased fitness. Our review identified 19 studies that provided genetic and fitness data from before and after the translocation; the majority of these were on mammals, and included experimental, natural and conservation‐motivated translocations. Using a Bayesian meta‐analytical approach, we found that on average, genetic diversity and fitness increased in populations post translocations, although there were some exceptions to this trend. Overall, genetic diversity was a positive predictor of population fitness, and in some cases this relationship extended three generations post‐rescue. These data suggest a single translocation can have lasting fitness benefits, and support translocation as another tool to facilitate conservation success. Given the limited number of studies with long‐term data, we echo the need for genetic monitoring of populations post‐translocation to understand whether genetic rescue can also limit the loss of adaptive potential in the long‐term. [ABSTRACT FROM AUTHOR]

Long‐term genetic studies of wild populations are very scarce, but are essential for connecting ecological and population genetics models, and for understanding the dynamics of biodiversity. We present a study of a wild wheat population sampled over a 36‐year period at high spatial resolution. We genotyped 832 individuals from regular sampling along transects during the course of the experiment. Genotypes were clustered into ecological microhabitats over scales of tens of metres, and this clustering was remarkably stable over the 36 generations of the study. Simulations show that it is difficult to determine whether this spatial and temporal stability reflects extremely limited dispersal or fine‐scale local adaptation to ecological parameters. Using a common‐garden experiment, we showed that the genotypes found in distinct microhabitats differ phenotypically. Our results provide a rare insight into the population genetics of a natural population over a long monitoring period. [ABSTRACT FROM AUTHOR]

ABSTRACT Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes, while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state‐of‐the‐art methods. Here, we ask whether a fundamental biogeographic pattern—the latitudinal gradient of species richness in tetrapods—is reflected in the available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last 5 years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes and that reduced representation and whole‐genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics. [ABSTRACT FROM AUTHOR]

Background: Mobulidae is a monophyletic family within the Myliobatiformes that comprises pelagic species represented by manta and devil rays. Among the genus Mobula, the Atlantic Pygmy Devil Ray - Mobula hypostoma - is reported in coastal regions exclusively in tropical and subtropical Atlantic Ocean from 1 to 100 m deep. In Brazil, M. hypostoma is one of the least studied Mobula species. It is regularly misidentified, especially as Mobula thurstoni, and is commonly listed as bycatch, in fishery inventories, or related to opportunistic sightings in the national territory. Methods and results: Here, we describe the complete nucleotide sequence of the mitochondrial genome (mitogenome) from Mobula hypostoma, which is 18,141 bp in length and comprises 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The M. hypostoma mitochondrial genes organisation and mitochondrial genome length are similar to other Mobula species, and the phylogenetic reconstruction indicates M. hypostoma as closely related to Mobula munkiana. Conclusions: The Brazilian mitogenome of M. hypostoma is expected to be a valuable resource for molecular-based species identification, and evolutionary and phylogeography studies. [ABSTRACT FROM AUTHOR]

Many methods are now available to calculate Ne, but their performance varies depending on assumptions. Although simulated data are useful to discover certain types of bias, real empirical data supported by detailed known population histories allow us to discern how well methods perform with actual messy and complex data. Here, we focus on two genomic data sets of grey wolf populations for which population size changes of the past 40–120 years are well documented. We use this background to explore in what detail we can retrieve the known population history from these populations, in the light of pitfalls relating to population history, sampling design and the change in the spatial scale at which Ne is estimated as we go further back in time. The Scandinavian wolf population was founded in the early 1980s from a few individuals and has gradually expanded up to 510 wolves. Although the founder event of the Scandinavian population was detected by GONE, the founding effective population size was strongly overestimated when the most recent samples were used, but less so when older samples were considered. Nevertheless, the present‐day Ne corresponds to theoretical expectations. The western Great Lakes wolf population of Minnesota is the only population in the contiguous United States that persisted throughout the 20th century, surviving intense persecution. We found a good concordance between the estimated Ne and trends in census size data, but the reconstruction of Ne clearly highlights the difficulty of interpreting results in spatially structured populations that underwent demographic fluctuations. [ABSTRACT FROM AUTHOR]

In population genetics idealized Wright‐Fisher (WF) populations are generally considered equivalent to real populations with regard to the major evolutionary processes that influence genotype and allele frequencies. As a result we often model the response of populations by focusing on the effective size Ne. The Diversity Partitioning Theorem (DPT) shows that you cannot model the behavior of a system solely on the basis of a diversity (accounting for unevenness among items) without taking richness into account. I show that the census population size (the number of adults, Nc) is equivalent to a richness, and that the effective size Ne is equivalent to a true diversity. It follows logically from the DPT that we require both Ne and Nc to understand how drift, selection, mutation, and gene flow interact to shape the course of evolution of populations. Here I review evidence that both Nc and Ne affect evolutionary trajectories of populations for neutral and adaptive processes. This also influences how we should consider evolutionary potential and genetic criteria for conservation of populations. The effective size of a population is of huge importance in evolutionary biology, but it should not be the sole focus when population size is concerned. Applied evolutionary studies need to integrate Nc in the equation more consistently when modeling the response to selection, mutation, migration, and drift. [ABSTRACT FROM AUTHOR]

Molecular methods are routinely used to estimate the effective size of populations (Ne). However, underlying model assumptions are frequently violated to an unknown extent. Although simulations can detect sources of bias and help to adjust sampling strategies and analyses methods, additional information from empirical data can also be used to calibrate methods and improve molecular Ne estimation methods. Here, we take advantage of long‐term genetic and ecological monitoring data of the grey wolf (Canis lupus) in Germany, and detailed population genetic studies in Poland, Spain and Portugal to improve Ne estimation strategies in this species, and species with similar life history traits. We first calculated Ne from average lifetime reproductive success and detailed census data from the German population, which served as a baseline to compare to molecular estimates based on linkage disequilibrium and sibship frequency. This yielded a robust Ne/Nc estimation that we used to calibrate molecular estimates of German, Polish and Iberian wolf populations. The linkage disequilibrium method was strongly influenced by spatial genetic structure, much more than the sibship frequency method. When Ne was estimated in local neighbourhoods, both methods yielded comparable results. Estimates of the metapopulation effective size seemed to correspond generally well with the sum of the estimates of local neighbourhoods. Overall, we found that the number of packs is a good proxy of the effective population size. Using this as a rule of thumb, we evaluated for all European wolf populations the Ne 500 indicator and concluded that half of the European wolf populations do not yet fulfil this criterion. [ABSTRACT FROM AUTHOR]

Estimating and understanding the ratio between effective population size (Ne) and census population size (Nc) are pivotal in the conservation of large marine pelagic fish species, including bony fish such as tunas and cartilaginous fish such as sharks, given the challenges associated with obtaining accurate estimates of their abundance. The difficulties inherent in capturing and monitoring these species in vast and dynamic marine environments often make direct estimation of their population size challenging. By focusing on Ne, it is conceivable in certain cases to approximate census size once the Ne/Nc ratio is known, although this ratio can vary and does not always increase linearly, as it is influenced by various ecological and evolutionary factors. Thus, this ratio presents challenges and complexities in the context of pelagic species conservation. To delve deeper into these challenges, firstly, we recall the diverse types of effective population sizes, including contemporary and historical sizes, and their implications in conservation biology. Secondly, we outline current knowledge about the influence of life history traits on the Ne/Nc ratio in the light of examples drawn from large and abundant pelagic fish species. Despite efforts to document an increasing number of marine species using recent technologies and statistical methods, establishing general rules to predict Ne/Nc remains elusive, necessitating further research and investment. Finally, we recall statistical challenges in relating Ne and Nc emphasizing the necessity of aligning temporal and spatial scales. This last part discusses the roles of generation and reproductive cycle effective population sizes to predict genetic erosion and guiding management strategies. Collectively, these sections underscore the multifaceted nature of effective population size estimation, crucial for preserving genetic diversity and ensuring the long‐term viability of populations. By navigating statistical and theoretical complexities, and addressing methodological challenges, scientists should be able to advance our understanding of the Ne/Nc ratio. [ABSTRACT FROM AUTHOR]

Historical periods of rapid climate change and associated direct and indirect impacts such as glaciation and restructuring of drainage systems are important in shaping biodiversity, lineage divergence, and contemporary genetic variation amongst many aquatic taxa. Through an understanding of the impacts of these ancient changes in land‐ and waterscapes on current diversity, practitioners can account for a species' unique evolutionary history when developing conservation strategies.We investigated intraspecific genetic diversity of the critically endangered freshwater mussel, Lampsilis rafinesqueana, endemic to the interior region of the U.S.A. Our study (1) characterises genetic variation within and amongst populations to infer biogeographic history and (2) applies genetic information to potential conservation strategies. We applied restriction‐site associated DNA sequencing and mitochondrial DNA sequencing to investigate genetic diversity within and amongst populations of L. rafinesqueana from across the species' distribution. We then considered this information in the context of historical riverscape processes and applicability to conservation.Variation within rivers was similar, but we found different genetic populations associated with two major ecoregions, the Central Interior Highlands and Osage Plains. The plains population displayed an Ne value approximately 10‐fold lower than the highlands population. Historical demographic modelling suggests the two populations diverged approximately 1.2 million years ago and then both populations underwent a substantial decrease in population size around 19,700 years ago. These two major events are each correlated with known periods of historic rapid climate change.We identified two distinct populations of a federally endangered mussel, L. rafinesqueana. Contemporary genetic diversity of this species was strongly influenced by direct and indirect impacts of rapid historic shifts in climate. The highlands population has undergone a recent expansion, typical of post‐Pleistocene climate change, while also having a much larger Ne value than the plains population. Our results suggest low levels of gene flow amongst the two distinct populations across generations. We recommend that conservation managers for this species take into account relative difference in diversity between populations when developing management strategies. In many species, assisted gene flow amongst genetically unique populations should only be considered in extreme circumstances; however, in L. rafinesqueana, low levels of assisted migration amongst populations may be a valuable tactic to maintain natural levels of genetic variation.Our study shows that biogeographical frameworks can be useful for developing conservation strategies that serve to retain important genomic variation that represents the evolutionary potential of target freshwater species. [ABSTRACT FROM AUTHOR]

Conservation genetics is the use of genetics to understand and mitigate the threats caused by anthropogenic activities, including habitat loss and fragmentation, wildlife trafficking, and emerging diseases. In this review, we discuss the role of primate conservation genetics in the development of effective conservation strategies, emphasizing the importance of maintaining genetic diversity to enhance adaptive potential and prevent extinction. First, we discuss studies of various primate species that exemplify how genetic data have been instrumental in accurately assessing threat levels, identifying trafficked animals and tracing their geographic origin, and studying how habitat loss affects primate populations. Subsequently, we describe the various molecular tools and analytical approaches employed in these studies. Lastly, we provide a bibliographic review of research in conservation genetics over the last 20 years. We conclude with a brief discussion of the limitations and challenges in this field in developing countries and recommendations for future research. [ABSTRACT FROM AUTHOR]

Right whales (genus Eubalaena) were among the first, and most extensively pursued, targets of commercial whaling. However, understanding the impacts of this persecution requires knowledge of the demographic histories of these species prior to exploitation. We used deep whole genome sequencing (~40×) of 12 North Atlantic (E. glacialis) and 10 Southwest Atlantic southern (E. australis) right whales to quantify contemporary levels of genetic diversity and infer their demographic histories over time. Using coalescent‐ and identity‐by‐descent–based modelling to estimate ancestral effective population sizes from genomic data, we demonstrate that North Atlantic right whales have lived with smaller effective population sizes (Ne) than southern right whales in the Southwest Atlantic since their divergence and describe the decline in both populations around the time of whaling. North Atlantic right whales exhibit reduced genetic diversity and longer runs of homozygosity leading to higher inbreeding coefficients compared to the sampled population of southern right whales. This study represents the first comprehensive assessment of genome‐wide diversity of right whales in the western Atlantic and underscores the benefits of high coverage, genome‐wide datasets to help resolve long‐standing questions about how historical changes in effective population size over different time scales shape contemporary diversity estimates. This knowledge is crucial to improve our understanding of the right whales' history and inform our approaches to address contemporary conservation issues. Understanding and quantifying the cumulative impact of long‐term small Ne, low levels of diversity and recent inbreeding on North Atlantic right whale recovery will be important next steps. [ABSTRACT FROM AUTHOR]

A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and barriers to dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced single nucleotide polymorphism (SNP) data are increasingly accessible, presenting an opportunity to study genetic variation across geographic space in myriad species. We present a new inference method that uses geo‐referenced SNPs and a deep neural network to estimate spatially heterogeneous maps of population density and dispersal rate. Our neural network trains on simulated input and output pairings, where the input consists of genotypes and sampling locations generated from a continuous space population genetic simulator, and the output is a map of the true demographic parameters. We benchmark our tool against existing methods and discuss qualitative differences between the different approaches; in particular, our program is unique because it infers the magnitude of both dispersal and density as well as their variation over the landscape, and it does so using SNP data. Similar methods are constrained to estimating relative migration rates, or require identity‐by‐descent blocks as input. We applied our tool to empirical data from North American grey wolves, for which it estimated mostly reasonable demographic parameters, but was affected by incomplete spatial sampling. Genetic based methods like ours complement other, direct methods for estimating past and present demography, and we believe will serve as valuable tools for applications in conservation, ecology and evolutionary biology. An open source software package implementing our method is available from https://github.com/kr‐colab/mapNN. [ABSTRACT FROM AUTHOR]

High‐density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high‐quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander Proteus anguinus, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent Proteus lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (~50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA. [ABSTRACT FROM AUTHOR]

Aim: Human‐induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra‐population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining. Location: We studied two areas: one in semi‐natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species' range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France). Methods: We genotyped 2743 individuals from 128 populations using 11 microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding and genetic relatedness), the extent of genetic differentiation and population affiliations (sPCAs) within the two areas. We also examined fine‐scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS) method. Results: Northern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation. Main Conclusions: These results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures. [ABSTRACT FROM AUTHOR]

The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species. [ABSTRACT FROM AUTHOR]

Understanding genetic structure and diversity among remnant populations of rare species can inform conservation and recovery actions. We used a population genetic framework to spatially delineate gene pools and estimate gene flow and effective population sizes for the endangered California Freshwater Shrimp Syncaris pacifica. Tissues of 101 individuals were collected from 11 sites in 5 watersheds, using non-lethal tissue sampling. Single Nucleotide Polymorphism markers were developed de novo using ddRAD-seq methods, resulting in 433 unlinked loci scored with high confidence and low missing data. We found evidence for strong genetic structure across the species range. Two hierarchical levels of significant differentiation were observed: (i) five clusters (regional gene pools, FST = 0.38–0.75) isolated by low gene flow were associated with watershed limits and (ii) modest local structure among tributaries within a watershed that are not connected through direct downstream flow (local gene pools, FST = 0.06–0.10). Sampling sites connected with direct upstream-to-downstream water flow were not differentiated. Our analyses suggest that regional watersheds are isolated from one another, with very limited (possibly no) gene flow over recent generations. This isolation is paired with small effective population sizes across regional gene pools (Ne = 62.4–147.1). Genetic diversity was variable across sites and watersheds (He = 0.09–0.22). Those with the highest diversity may have been refugia and are now potential sources of genetic diversity for other populations. These findings highlight which portions of the species range may be most vulnerable to future habitat fragmentation and provide management consideration for maintaining local effective population sizes and genetic connectivity. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial genome of Triplophysa erythraea was determined for the first time. Results showed the mitogenome was 16 565 bp, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 2 non-coding regions. The overall base composition of its mitochondrial genome was 28.9% A, 25.2% T, 28.7% C and 17.2% G. Phylogenetic tree revealed that Triplophysa erythraea had the closest relationship with Triplophysa xiangxiensis, which was also found in Xiangxi Tujia and Miao Nationality Autonomous Prefecture, Hunan province. In general, this study provided valuable information for conservation genetics analyses of Triplophysa erythraea and further displayed the evolution of species within the genus Triplophysa. [ABSTRACT FROM AUTHOR]

Giam Malut Hopea ferrea Laness (Dipterocarpaceae) is a woody species that has become endangered due to its habitat destruction and overexploitation. In an effort to support and provide conservation and management of this species, we utilized eight microsatellite loci to investigate the genetic diversity and structure of 234 adult trees across eight populations, encompassing its geographic distribution in Vietnam. The genetic diversity of H. ferrea was found to be low in comparison to other dipterocarps, suggesting a reduction in the number of alleles due to anthropogenic activities. Heterozygosity deficits were identified across all studied populations. Interestingly, the coastal populations exhibited higher genetic diversity compared to the Highlands and southeast populations. Bottleneck effects were detected in the majority of populations, with the exception of the two Highlands populations of Chu Mon Ray and York Don. These effects indicated a reduction in the population sizes. The results of genetic differentiation mirrored the genetic structure and revealed three major clusters corresponding to the three distribution areas of the species. A low level of genetic differentiation among populations (FST=0.146) was detected, consistent with the AMOVA analysis. Geographic distance and anthropogenic activities emerged as the major factors limiting gene exchange among populations. Based on these findings, we propose conservation measures for this endangered species. [ABSTRACT FROM AUTHOR]

Key message: SSR-based characterization revealed a high genetic diversity, negligible genetic differentiation, insignificant inbreeding, and subtle genetic structure in Myrica esculenta populations of Western Himalayas, indicating a high adaptive and evolutionary potential. Myrica esculenta is a high-valued wild edible fruit-bearing tree of sub-Himalayan region experiencing noticeable deterioration in its stand structure. This study aimed to unveil the gene diversity and spatial genetic structure of M. esculenta populations in the Western Himalayas under the state of Uttarakhand (India) using nuclear simple sequence repeat (SSR) markers. By investigating 23 populations at 8 SSR loci, high genetic diversity (expected heterozygosity, He = 0.90; allelic richness, Ar = 13.65) was recorded with little genetic differentiation (fixation index, FST = 0. 025). Bayesian analysis revealed a weak genetic structure with no discrete genetic lineages from which ancestry can be inferred. Furthermore, genetic clustering among populations was conspicuous but not in accordance with their spatial distribution. Geographically separated populations are genetically well connected due to long-distance gene flow via pollen as well as seed. Hence, the meta-population in the Western Himalayas demonstrated a subtle spatial genetic structure with negligible genetic divergence, where genetic admixing is not modulated by geographical constraints. Viewing the substantial anthropogenic pressure over wild populations, conservation strategies must be adopted synergistically based on scientific knowledge. As center of diversity is centered toward the Kumaon region capturing higher allelic richness, we recommend the populations of this region to be prioritized for in situ conservation. Further, it will be important to harvest seeds from genetically diverse populations for raising plantations or ex situ field gene banks. As its fruits are mostly harvested from wild, local communities need to be sensitized and encouraged to establish private plantations or orchards. [ABSTRACT FROM AUTHOR]

Sect. Tuberculata Chang in the genus Camellia (Theaceae Mirb.) is named after the "tubercle-like projections on the surface of the capsule and ovary". Due to complex morphological variations in these taxon and insufficient field investigations, the interspecies relationships are unclear, the species' definitions are vague, and the names are confusing. This is not conducive to the conservation and study of these species. Therefore, herein, we systematically explore the taxonomic status of five sect. Tuberculata species using morphological, pollen morphological, and molecular phylogenetic methods. The results showed that (1) the morphological characteristics of the flower, fruit, and leaves of C. anlungensis and C. leyeensis are similar. Furthermore, the pollen characteristics and pollen wall ornamentation show that there is no significant difference between the two species; (2) there are significant differences between C. acutiperulata and C. anlungensis in terms of leaf shape (elliptic vs. obovate), calyx characteristics (sepal apex pointed vs. sepal oblong), and fruit shape (subglobose folds with shallow verruculose vs. flat folds and verruculose protuberances with pronounced internal cleavage); (3) C. pyxidiacea and C. rubituberculata differ in flower color (white or light color vs. red) and fruit verrucae (obviously deeply cleft vs. shallowly uncracked); (4) a phylogenetic tree based on the chloroplast genome shows that C. anlungensis and C. leyeensis form a single clade (BS = 100%, PP = 1.0) and are on a different branch, with C. acutiperulata on clade II (BS = 100%, PP = 1.0), and C. pyxidiacea and C. rubituberculata clustered on different branches of clade I (BS = 99%, PP = 1.00). Considering the above results together, we propose that C. leyeensis should be treated as a homonym of C. anlungensis, and C. acutiperulata, C. pyxidiacea, and C. rubituberculata should be considered as separate species. Clarifying the taxonomic status of these five species not only advances our understanding of the significance and complexity of the systematic classification of the genus Camellia but also has important implications for diversity conservation and population genetics. [ABSTRACT FROM AUTHOR]

The puma (Puma concolor Linnaeus, 1771) is the top predator with the widest distribution in America. Since the establishment of European settlers on the American continent, puma populations have experienced significant contractions and reductions in their original distribution. In Argentina, the management of the conflict between humans and pumas (direct persecution and habitat modification) focused on reduction or elimination methods, leading to a drastic contraction, even total eradication, of puma populations as seen in Patagonia and the eastern part of the country. Despite the lack of knowledge about puma population demographic trends, there are taxonomic issues that remain controversial and need to be resolved to implement appropriate management and conservation measures. Therefore, the aim of this study was to genetically characterize puma populations in the central-southern region of Argentina using two mitochondrial markers, evaluate their demographic history, compare our results at a macro-regional level, and discuss our findings in a conservation and management context. A total of 203 individuals were used, and a fragment of the control region and another of ND5 were sequenced. The genetic variability obtained was moderate. Substitution rates for each locus and the tMRCA were calculated from calibrated trees. In a concatenated tree, two main phylogenetic clades were identified (posterior probability = 1), although a reciprocal monophyly was not observed, with a divergence time of 228 thousand years and a 95% CI [117-363 thousand years]. When evaluating population structuring, three genetic clusters were found, one characteristic of the Patagonian region and the others in the central part of the country. Calculating the ФST values for pairs resulted in significant structuring between Patagonia and the rest of the populations, suggesting the arid diagonal as a possible barrier to gene flow. When evaluating the demographic history, neutrality tests would support a recent expansion in Patagonia. These findings are crucial in defining two distinct Management Units (MUs) in the southern part of puma distribution and providing valuable information for management and conservation measures for the species. [ABSTRACT FROM AUTHOR]

Crambe sventenii Pett. ex Bramwell & Sunding and Pleudia herbanica (A.Santos & M.Fernández) M.Will, N.Schmalz & Class.-Bockh. are two single-island endemic species from Fuerteventura (Canary Islands), inhabiting the same areas and similar habitats. They are under the "Critically Endangered" category due to historical herbivore pressure, mainly goats, leading to habitat fragmentation and poor population recruitment. The main aim of our study was to provide insights into the conservation genetics and habitat suitability of these two species. For this purpose, we sampled all known populations on the island and developed two new sets of microsatellite markers. Moreover, to assist restoration plans, we performed species distribution models to determine the most suitable areas for reintroduction. While Crambe sventenii is highly fragmented, with low genetic diversity indices in some populations, Pleudia herbanica's genetic structure is quite homogeneous, grouped in three main regions, with signs of inbreeding and an overall low genetic diversity. Both species could present moderate to high levels of autogamy. Our findings can provide guidance to local governments regarding conservation actions to be implemented in the field, like the identification of propagule sources and new suitable areas for restoration. [ABSTRACT FROM AUTHOR]

The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26x and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda. [ABSTRACT FROM AUTHOR]

The conservation of the genetic integrity of Apis mellifera subspecies has emerged as an important objective. In 2019, the Emilia-Romagna region became the first Italian regional authority to issue a law specifically addressing the protection of the native Apis mellifera ligustica subspecies. In this study we analysed a highly informative portion of the mitochondrial DNA (mtDNA), widely used for assessing genetic diversity of honey bee populations. By analysing 1143 honey bees sampled after the introduction of this law, we provided a snapshot of the distribution of mtDNA haplotypes in this region. The two most frequent mtDNA haplotypes were C1 (characteristic of A. m. ligustica) and C2 (characteristic of A. m. carnica), reported in 86.5% and 11.0% of the analysed bees, respectively. About 1.3% and 1.1% of the analysed bees carried mtDNA haplotypes of the A and M lineages (haplotypes A1a, A1e, A4, A26, A65 and two novel ones, A2w and A6a; M3, M3a, M4 and M79). Continued genetic monitoring will be important to assess the impact of this regional law over the coming years. Based on the obtained results, we recommend a more stringent policy to prevent the erosion of the genetic integrity of the native subspecies A. m. ligustica. [ABSTRACT FROM AUTHOR]

Understanding population structure and the extent and distribution of genetic diversity are recognized as central issues in endangered species research, with broad implications for effective conservation management. Advances in whole genome sequencing techniques provide greater resolution of genome-wide genetic diversity and inbreeding. Subspecies of golden eagles (Aquila chrysaetos) in Scotland (A. c. chrysaetos) and Japan (A. c. japonica) are endangered; it is therefore important to understand genetic diversity and inbreeding of these small island populations to increase the chances of conservation success. We investigated this using whole genome sequencing data from golden eagles in Scotland, continental Europe, Japan, and the USA. Following determination of population genetic structure, analysis of heterozygosity and nucleotide diversity revealed reduced levels of genetic diversity together with runs of homozygosity, suggesting evidence of inbreeding attributable to recent shared parental ancestry in the island populations. These results highlight the need to consider genetic reinforcement of small isolated golden eagle populations from neighbouring outbred populations, alongside existing efforts to boost population size through within-island conservation translocations and captive breeding programmes. [ABSTRACT FROM AUTHOR]

We report the rediscovery, a century after its last record, of two specimens of Pristimantis ruidus from approximately 6 km northeast of its type locality, in a montane forest from the western Andes of southern Ecuador. This species, described by John D. Lynch in 1979, based on specimens collected in 1922 by George H. Tate, was previously known only from the type series, all specimens originating from a single locality (Molleturo, Provincia Azuay, Ecuador, 2317 m elev.). The rediscovery occurred in November 2022 in the Reserva de Conservación Quitahuaycu, Molleturo Parish, Azuay Province. The two specimens, both females, are characterised by rough skin with numerous rounded low warts and tubercles on their dorsum, a W-shaped occipital fold, tympanum and tympanic ring not externally visible and by the lack of cranial crests, characters that correspond with the description of the holotype. We evaluate the phylogenetic relationships, based on two mitochondrial genes (12S and 16S rRNA) and one nuclear gene (RAG-1). These analyses reveal Pristimantis ruidus as a member of the subgenus Huicundomantis, being most closely related to P. philipi, a species with a distribution restricted to the paramo of the same mountain region (Macizo del Cajas). Pristimantis ruidus co-exists with Pristimantis jimenezi, three additional species of Pristimantis and one Noblella with uncertain taxonomic status. This rediscovery underscores the urgency of implementing effective conservation and monitoring measures for the few remnants of the original ecosystems from western Ecuador, which face ongoing anthropogenic threats and harbour a diversity that remains insufficiently studied. [ABSTRACT FROM AUTHOR]

It is widely recognized that the examination of haplotypes among sea turtles inhabiting nesting beaches holds significant importance. Yet, an effective conservation effort of a population also requires an investigation of the origin of sea turtles that strand on the shore, especially as many of these result from interactions with fisheries. In consideration of this, we analyzed the haplotypes of 542 stranded individuals from the Eastern Mediterranean and identified a total of 9 different haplotypes. Two of these were new haplotypes, one individual was found in Marmaris, Türkiye, and the other in a stranded species in northern Cyprus. Mixed-stock analysis demonstrated that the majority of the individuals stranded in western Türkiye originated from nesting beaches in the same area (33%), followed by Dalyan, Türkiye (25%), and Cyprus (21%). The partial mixed-stock analysis of individuals stranded in the Dalyan–Dalaman region of Türkiye revealed that most originated from Dalaman (45%) and Dalyan (21%), followed by western Greece (11%). The partial mixed-stock analysis for the Eastern Mediterranean showed that the majority of individuals originated from western Türkiye (69%), followed by Cyprus (11%) and Dalyan (7%). These findings, by quantifying the relative contributions of each region, provide valuable insights for guiding conservation efforts regarding Caretta caretta in the Mediterranean marine environment. [ABSTRACT FROM AUTHOR]

Survival rate is usually the greatest contributor to population growth in long‐lived species, and its accurate estimation along with the evaluation of the factors influencing it is therefore essential for effective conservation. Here, we studied the survival of breeding eastern imperial eagles Aquila heliaca in Hungary between 2011 and 2022 and investigated the effect of poisoning, the leading known anthropogenic cause of mortality. We used the Cormack‐Jolly‐Seber mark‐recapture model to estimate annual apparent survival and encounter probabilities based on the capture histories of 208 males and 411 females. We obtained encounter data from the DNA profiles of shed feathers collected at the nest sites, which we also supplemented with presences inferred from parentage analysis. The most supported model estimated a constant 91.6% annual survival over the study period, but models including the effect of sex and poisoning rate on survival had similar support. Sex difference in survival was less than 1% on average, but the survival of males decreased more with poisoning rate than the survival of females. However, due to smaller encounter probabilities, the estimates for males were less precise compared to females. Males may be more at risk from poisoning than females not only due to their more active foraging behaviour during incubation and chick‐rearing but also due to their smaller body size. Apart from providing direct practical information for the conservation management of imperial eagles, our results also highlight the importance of long‐term studies for estimating population parameters of birds of prey. [ABSTRACT FROM AUTHOR]

Small populations of imperiled species are susceptible to the negative consequences of skewed sex‐ratios. In imperiled species with environmental sex determination such as sea turtles, examining sex ratios across a range of environments and population abundance levels can provide insight into factors that influence population resilience, which can then be the foci of management plans for these species. Breeding sex ratios (the ratio of actively breeding males to females during a reproductive season; BSRs) extrapolated from genetic parentage analyses are a common approach for enumerating sex ratios in sea turtles. Such analyses also allow for the characterization of multiple paternity within sea turtle clutches, which should reflect BSRs and breeding behaviors. We characterized the first BSR for a breeding assemblage of loggerhead sea turtles (Caretta caretta) belonging to the temperate, low‐abundance Northern Gulf of Mexico Recovery Unit using genotypes of 16 microsatellite loci from nesting females and hatchlings. Unlike prior studies at both more‐tropical and more‐temperate, and higher‐abundance, Recovery Units in this region, we found a balanced BSR of 1.3:1 males:female and a low incidence (~17%) of multiple paternity. This suggests that there are relatively few males breeding at this assemblage and within this Recovery Unit. Beaches in this region are expected to produce substantial numbers of male hatchlings based on sand temperature data. The relative dearth of mature males may then be due to hydrologic disturbances that disproportionately affect the fitness and survival of male hatchlings, or due to demographic stochasticity. More work is needed to study the factors that might influence male hatchling production and fitness in this region, particularly as climate change is predicted to lead to feminization in global sea turtle populations. Our work demonstrates the broad utility of characterizing BSRs and other sex ratios across a range of populations in imperiled, environmentally sensitive species. [ABSTRACT FROM AUTHOR]

The overabundance of sika deer has become a significant threat to plant communities across Japan. As a result of the deer overgrazing, rare plants are undergoing a demographic bottleneck, leading to a loss of genetic diversity. Genetic diversity is crucial for the reproductive success of self‐incompatible plants, and it also provides evolutionary potential, which increases their long‐term population viability. Therefore, it is essential to appropriately manage the remaining genotypes to conserve local genetic resources. In this study, we exemplify this, via a conservation genetic analysis of Parasenecio peltifolius populations impacted by deer. Genetic data revealed that the small populations confined to isolated refugial sites consisted of effectively single genets. Recent reproductive failures in these populations may be attributed to the loss of genotypic diversity. Despite the bottlenecks, the remaining genets exhibited high individual heterozygosity, which is a good indicator that they have not been affected by severe inbreeding. Hybrid simulations suggested that interpopulation outbreeding between the unique genotypes can be a viable option to promote sexual reproduction and re‐establish genetic diversity within the local populations. Establishing artificial progenies in botanical gardens can serve as a vital genetic resource for the long‐term viability of threatened P. peltifolius populations. [ABSTRACT FROM AUTHOR]

Estimates of the influence of inbreeding on the fitness of wild animals can guide genetic conservation in rare species. Conservation genetics is important in Mexican wolves (Canis lupus baileyi) because the current population descended from 7 founders and mean inbreeding is relatively high. As an endangered subspecies, Mexican wolves are actively managed using select conflict avoidance measures and by placing captive‐born foster pups into wild litters. We obtained data on inbreeding coefficients of wolf pups and adults based on a pedigree dating to 1957 and data on reproduction for wild wolf packs during 1998–2022. We estimated trends in inbreeding coefficients and the associations between dam, sire, and pup inbreeding coefficients and pup recruitment to age 9 months, and assessed 3 components of recruitment: probability of producing a litter, number of pups produced, and recruitment conditional on successful reproduction. We generated estimates using generalized linear mixed models and bootstrapped estimates of confidence intervals. Mean inbreeding coefficients were high (0.227, SD = 0.047) in the wild population, but we detected no significant evidence of an increase during 2010–2022. Overall, the net associations of dam, sire, and pup inbreeding coefficients with our primary fitness metric, pup recruitment to age 9 months, did not differ from zero. While high inbreeding coefficients are a concern for the long‐term recovery of the subspecies, the stable level of inbreeding, lack of evidence for inbreeding depression, high pup production (5.1 pups/litter, SD = 1.64), and rapid population growth (384% increase from 2010–2022) indicate that inbreeding has not prevented rapid progress towards recovery goals under current management practices. [ABSTRACT FROM AUTHOR]

Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise F ST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct. [ABSTRACT FROM AUTHOR]

Fruit bats (genus Pteropus) are typically island‐endemic species important in seed dispersal and reforestation that are vulnerable to increased extinction risk. An effective method of reducing extinction risk in vulnerable species that cannot be conserved in their native habitat is establishing an ex‐situ captive breeding programme. Due to anthropogenic threats and low population numbers, in the early 1990s, a captive breeding programme was established at Jersey Zoo, British Isles, for Critically Endangered Livingstone's fruit bats (Pteropus livingstonii). Here we use six polymorphic microsatellite loci to assess genetic diversity in the captive breeding population of Livingstone's fruit bats (P. livingstonii), 30 years after the programme's establishment, investigating change over generations and comparing our findings with published data from the wild population. We found no significant difference between the genetic diversity in the captive and wild populations of Livingstone's fruit bats (P. livingstonii), in both expected heterozygosity and allelic richness. The captive population has retained a comparable level of genetic diversity to that documented in the wild, and there has been no significant decline in genetic diversity over the last 30 years. We advise that a full pedigree of the paternal lineage is created to improve the management of the captive breeding programme and further reduce the possibility of inbreeding. However, it appears that the captive breeding programme is currently effective at maintaining genetic diversity at levels comparable to those seen in the wild population, which suggests reintroductions could be viable if genetic diversity remains stable in captivity. Research highlights: The captive breeding programme of Critically Endangered Livingstone's fruit bats shows comparable genetic diversity to current wild populations.This level of genetic diversity has remained stable in the captive population for 30 years, since its first establishment, across four generations of animals.The captive breeding programme of Livingstone's fruit bats is currently managed effectively, minimising inbreeding, and retains reintroduction potential. [ABSTRACT FROM AUTHOR]

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes. [ABSTRACT FROM AUTHOR]

Abstract African pangolins are hunted for their meat and for use in local traditional medicine, as well as for their scales, which are trafficked internationally, especially to growing Asian markets. Pangolin’s population genetic structure can be used to trace the geographic origins of trafficked scales, but substantial sampling gaps across pangolins’ ranges hinder these efforts. In this study, we documented population structure and dynamics in the two species of African pangolin, the white-bellied pangolin (Phataginus tricuspis) and the giant pangolin (Smutsia gigantea) in the underexplored Republic of Congo. Using the mitochondrial control region and two nuclear markers (beta-fibrinogen and titin), we identified high genetic diversity in both species. We document a distinct mitochondrial lineage of the white-bellied pangolin, which was most likely shaped by river barriers together with dynamics of forest refugia related to the climatic shifts during the Pleistocene. We detected population growth in the white-bellied pangolin coinciding with a dry period during the Pleistocene, suggesting some ability for this typically forest-dwelling species to persist under diverse environmental conditions. Using landscape genetics, we found all but one of the pangolins we sampled at bush meat markets originated locally. A single individual appeared to have been imported to Congo from Cameroon. These findings significantly contribute to our understanding of pangolin population biology and local trade dynamics. In addition, our data from a previously unstudied part of pangolins’ ranges will help us to better understand international wildlife trafficking patterns and to target conservation and protection strategies for these highly vulnerable species.

Abstract The conservation of the genetic integrity of Apis mellifera subspecies has emerged as an important objective. In 2019, the Emilia-Romagna region became the first Italian regional authority to issue a law specifically addressing the protection of the native Apis mellifera ligustica subspecies. In this study we analysed a highly informative portion of the mitochondrial DNA (mtDNA), widely used for assessing genetic diversity of honey bee populations. By analysing 1143 honey bees sampled after the introduction of this law, we provided a snapshot of the distribution of mtDNA haplotypes in this region. The two most frequent mtDNA haplotypes were C1 (characteristic of A. m. ligustica) and C2 (characteristic of A. m. carnica), reported in 86.5% and 11.0% of the analysed bees, respectively. About 1.3% and 1.1% of the analysed bees carried mtDNA haplotypes of the A and M lineages (haplotypes A1a, A1e, A4, A26, A65 and two novel ones, A2w and A6a; M3, M3a, M4 and M79). Continued genetic monitoring will be important to assess the impact of this regional law over the coming years. Based on the obtained results, we recommend a more stringent policy to prevent the erosion of the genetic integrity of the native subspecies A. m. ligustica.

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

The aim of this study was to investigate the genomic diversity of the Nero d’Aspromonte (NA) pig population. NA is a subpopulation derived from the Apulo Calabrese (AC) breed that has been reared in total isolation within the Polsi area of Aspromonte, Calabria, Italy. NA is traditionally recognised and used by local farmers for the production of typical products. The growing interest in this subpopulation has led local farmers to create a cooperative to promote NA pig meat and help preserve the cultural heritage associated with this local population. A total of 40 NA pigs were included in our study and genotyped with the Illumina GGP Porcine array. Admixture, TreeMix, and run of homozygosity (ROH) analyses were performed to investigate genetic diversity within the NA subpopulation and its relationship with the AC breed and other Italian pig breeds. The NA population clearly originated from the AC breed. The lower inbreeding and average ROH size in NA compared to AC may indicate that NA differentiated from the original AC genetic pool with the contribution of admixture from other genetic backgrounds in addition to the effects of genetic isolation and genetic drift. The analysis of the genetic diversity of the NA subpopulation showcases the utility of genomic analyses to reconstruct the genetic history of local populations. A specific conservation program for this genetic resource may further support the sustainable development of local pig production systems based on traditional farming practices as a part of agricultural cultural heritage.