Conservation Genetics

Small populations are increasingly common on the landscape, and many face rising probabilities of extinction. Demographic factors alone can drive a small population into an extinction vortex, but genetic factors such as inbreeding and genetic drift lead to reductions in genetic diversity and expression of deleterious alleles, further impacting fitness. Populations on islands are also impacted by founder effects, minimal gene flow, and habitat constraints, yet naturally small, island populations have persisted through many generations despite all these factors. This suggests that island biota may operate at smaller viable population sizes than their mainland counterparts while avoiding extinction vortices. Using 26 microsatellites, we describe the genetic diversity and population structure of 13 subpopulations of a large island vertebrate, the endangered Turks and Caicos rock iguana (Cyclura carinata), found on a range of small cays (0.151-374ha). Most subpopulations had decreased genetic variation but limited evidence of inbreeding despite small island size. Even with water barriers limiting gene flow, some subpopulations in geographical proximity are functioning as a metapopulation while others are not. These subpopulations are not in danger of extirpation, even though census size could be as low as 10 individuals. We believe this study shows that C. carinata has a low population size threshold for long-term persistence that can inform the species' future management, such as with conservation translocations. Furthermore, this project anecdotally adds more evidence to how island populations persist through selection despite genetic drift.

Here we describe substantial range shifts of historically differentiated wolf populations and formation of novel sympatric zones during the recent decade in Central Europe. This region provides a natural laboratory for testing alternative scenarios of population interactions from continued isolation or restricted gene flow to progressive population fusion, while prompting a reassessment of their geographic ranges. Based on sampling across the Czech Republic and Slovakia obtained from large-scale monitoring programmes over five wolf years (2020/21_2024/25), complemented by comparative material from neighbouring regions, we analysed mitochondrial haplotypes, autosomal microsatellite genotypes and sex-linked loci. The Central European population with Baltic ancestry predominated across large parts of Central Europe including the Bohemian Massif with enclaves in the Western Carpathians. The Carpathian population was predominant in Slovakia, with a smaller satellite occurrence in the northern part of the Bohemian Massif. Alpine population was centred in the Alps but extended into southern parts of Bohemian Massif and Central German Uplands. Following the sporadic occurrence of admixed individuals, broad mosaic and dynamic sympatric zones have formed in the Czech Republic and Slovakia in the last decade. These scenarios could be facilitated by the presence of intermediate habitats and isolation of the Bohemian Massif structural basin, framed by a massive ring fault system. Recent-immigration estimates are asymmetric, with the largest mean contributions from the Alpine to the Central European population and from the Central European to the Carpathian population, with the second case potentially linked to source-sink dynamics driven by the hunting pressure within the Carpathian population (whereas the others are protected year-round). Whether increasing admixture will enhance viability of populations (that currently have small effective sizes) through genetic rescue or carry risks of outbreeding depression remains uncertain, highlighting the need for continued transboundary monitoring within conservation biology framework.

EU has reclassified the sika deer (Cervus nippon) as an undesirable invasive species based on reports that hybridization with the indigenous red deer (C. elaphus) may produce fertile offspring. Since sika-derived DNA previosuly introduced into the red deer population (introgression) cannot be removed, the crucial question is whether new (F1) hybridisation occur. To address this, we analysed the chromosomes in 56 sika and 22 red deer. All red deer had a chromosome number 2n=68. In contrast, the chromosome number in sika ranged from 64 to 67, due to the variable presence of two sika-specific Robertsonian translocations (ROB1,ROB2). In the free-ranging sika population in Jutland, >90% of the sika deer were homozygote for at least one of these ROBs, excluding that they could be F1-hybrids. Moreover, ROB2 was in Hardy-Weinberg equilibrium, further supporting the absence of gene flow between the two species. In contrast, ROB1 was in Hardy-Weinberg disequilibrium, suggesting negative fitness of heterozygotes, including potential F1-hybrids. In Jaegersborg Deer Park, the eight examined sika deer had the same genotype (absence of ROB1, homozygosity of ROB2), supporting that it is a founder population which may have been isolated for [~]100 years. Again, none of these can be F1-hybrids due to the homozygosity of ROB2. We conclude that F1-hybridisation between sika and red deer either does not occur or occur very rarely in Denmark. The study establish the Danish sika-populations as unique models for adressing important biological questions: What underlies the absence of hybridisation? Why are ROBs frequent in sika deer but not in the closely related red deer? How fast do new species/subspecies develop in isolated founder populations? Which factors determine, that some ROBs have little heterozygous effects, whereas others are selected against, with implications for the role of ROBs as genetic barriers promoting speciation, and for fertility problems in some human ROB carriers.

Urbanization has been previously shown to affect evolution of plants and animals by restricting gene flow, increasing genetic drift, and causing divergent selection between rural and urban populations, however, the effect of urbanization on terrestrial gastropod evolution has only been minimally researched. Most research on terrestrial gastropods primarily focusing on invasive pest species, and little attention is given to native species like Ariolimax columbianus (Pacific banana slug). There is no current published research on the phylogeography of A. columbianus. In this study, surface epithelial cells from 66 Ariolimax columbianus individuals were collected from 11 locations around Corvallis, Oregon, and one site in northern California. These samples were amplified and sequenced at two loci: cytochrome oxidase 1 (CO1) and the internal transcribed spacer 2 (ITS-2). This data was used to generate maximum-likelihood phylogenetic trees to better understand the population genetics of these local native gastropods. The CO1 phylogenetic analysis showed two major haplotypes around the city of Corvallis - northwestern and southern, while the ITS-2 phylogenetic analysis showed three general haplotypes around the city - northern, western, and southern. The results in this study show the presence of genetic breaks between many of these populations, possibly due to a combination of factors including anthropogenic fragmentation, natural barriers, and the low active dispersal ability of A. columbianus. However, the extent that each of those factors has on disrupting gene flow and explaining patterns of genetic variation in this species requires further research. The present study acts as a foundation for the development of future research on banana slug phylogenetics and population genetic structure.

Rosa gallica L., the French rose, is a perennial, tetraploid, heterozygous species that naturally propagates by seed and sucker. It occurs in the wild, primarily in Europe, and also exists as cultivated varieties. R. gallica cultivars were extensively bred and cultivated in France at the beginning of the 19th century. Although several hypotheses have been proposed regarding the species expansion based on historical records, none have been assessed using molecular data. Indeed, its genetic diversity has so far been investigated only at local or regional scales, hindering the identification of the evolutionary factors shaping its present-day distribution. Using 29 sequenced microsatellites, we genotyped a comprehensive sample of 1618 individuals, including wild R. gallica from 219 sites across the species range, rose cultivars, and specimens from other Rosa species. We then detected clonal lineages and characterized the range-wide genetic diversity and structure, aiming to disentangle the roles of natural and human factors in shaping the distribution of R. gallica, with particular focus on France. French diversity appears particularly structured compared to the rest of the range, suggesting multiple origins within France. Populations in South Alps, Central Eastern Europe, and Eastern France appear to have recolonized naturally from a single southern glacial refugium. In contrast, populations in the western part of France likely resulted from more recent natural or human-mediated dispersal. Finally, clonal lineages containing both wild and cultivated individuals were predominantly found in France, highlighting the role of human-mediated dispersal in 28 of the 98 French sites studied. These findings show that the present-day natural range of R. gallica was shaped primarily by post-glacial recolonization, but also reveal a contribution of human activities to its recent dispersal, particularly in France, where cultivated varieties were intensively bred and exchanged.

A central goal when assessing patterns of population structure for conservation is to identify populations with unique genetic compositions. The use of genomic sequencing to identify distinct populations has become an increasingly popular method of delineating conservation units. Reduced costs associated with sequencing make it possible to generate larger, more informative datasets to assess genetic diversity within and among populations. In species that exhibit nest-site philopatry, genetic population structure can emerge on much finer scales, particularly in maternally inherited mitochondrial genomes. We demonstrate the feasibility and insight gained by using whole mitochondrial genome sequencing for evaluating population genetic structure and comparing to previous single marker studies in a vulnerable turtle. We used whole mitochondrial genome sequences from diamond-backed terrapin (Malaclemys terrapin) to evaluate whether nest-site philopatry generates fine-scale genetic structure among M. terrapin nesting beaches in western Mobile Bay (Alabama, USA). We then compared haplotype diversity between the Alabama population and M. terrapin populations from the Atlantic and Gulf coasts and evaluated the utility of using whole mitochondrial genomes rather than a subset of loci to characterize unique haplotypic diversity. We found no genetic structure associated with nest-site philopatry within Alabama, but none of the haplotypes in this region were shared with other Gulf Coast sites. This genetic structure is consistent with strong female natal philopatry within western Mobile Bay relative to the Gulf of Mexico and suggests that the Mobile Bay population is genetically unique relative to other M. terrapin populations and merits a unique conservation and management plan.

Detecting dugongs at low densities remains a major challenge for conservation monitoring, particularly in remote or turbid coastal habitats where conventional surveys are difficult. Environmental DNA (eDNA) offers a complementary approach, but robust species-specific tools are needed before it can be confidently applied to dugong surveillance. We developed and analytically validated a quantitative PCR TaqMan assay for detecting dugong (Dugong dugon) eDNA and evaluated its performance across controlled aquarium conditions in Australia and Abu Dhabi, and wild populations in northern Australia and the Arabian/Persian Gulf. The assay detected dugong eDNA in aquarium and field samples, with Sanger sequencing confirming amplification of dugong mitochondrial DNA from positive field detections. Our assay provides a robust and geographically transferable tool for targeted dugong eDNA detection, performing reliably across contrasting coastal environments and widely separated populations. This approach can strengthen local-scale surveillance of low-density or difficult-to-detect dugong populations.

Understanding how contemporary population declines affect the genomic diversity and structure of threatened species is important for effective conservation. The Eurasian curlew (Numenius arquata) is experiencing severe population declines across Europe, with Ireland among the most extreme, showing declines exceeding 90% over 40 years. Genomic data are increasingly incorporated into policy and used to assess conservation status by estimating genetic diversity, differentiation, inbreeding, effective population size, and adaptive divergence. Such data for curlew is scarce, and the population structure among northern and north-western European breeding populations remains unclear. To address this, we generated whole-genome resequencing data for 56 curlews across Ireland, Britain and Sweden. Irish and British populations showed minimal interpopulation differentiation, but both were substantially differentiated from Sweden. This was apparent from principal component analysis, and admixture and FST analyses. Measures of genetic diversity (nucleotide diversity, heterozygosity, Watterson's{theta} ) were similar across populations. A slightly elevated Tajima's D in Ireland, along with elevated FROH in Ireland and Britain relative to Sweden, may be the early genomic signs of recent population declines. We identified locally selected candidate genes. These had putative roles in metabolic processes, the immune response, and were potentially associated with distinct migratory behaviours and environmental conditions. We find a potential lag in genomic effects of decline being detectable following population contraction. We also show highly migratory species can exhibit differentiation in ecologically relevant traits, potentially driven by high site fidelity. These findings warrant consideration in translocation planning and broader conservation strategies.

Due to the sparse and uneven availability of genomic resources, it remains challenging to appraise genomic attributes for species of conservation concern. While long-read sequencing enables assessment of genetic diversity at unprecedented scale, accessing high-quality tissues remains a challenge for non-model species. Here, we explore an alternative sampling strategy for tissues where "gold-standard" cryopreservation is infeasible. Focusing on the Australian scincid lizard Cryptoblepharus pulcher, we compare DNA obtained from various ethanol-preserved tissue types and DNA extraction kits, and ask whether high-molecular weight DNA can still be retrieved. PacBio HiFi sequencing of the most promising sample yielded a highly contiguous reference-level assembly, validating this approach in vertebrates, specifically lizards. After scaffolding the assembly to chromosome-level, we then used a comparative approach to shed light on the evolution and demise of C. egeriae, a closely related, now Extinct-in-the-Wild species. Surprisingly, despite being a wide-spread continental analogue with a similar ecology, C. pulcher has lower genetic diversity and long-term historical population size than C. egeriae, an island endemic. However, C. pulcher also shows fewer runs-of-homozygosity, supporting prior reports that C. egeriae experienced recent inbreeding. Together, these findings demonstrate that a practical and cost-effective preservation strategy can still yield high-quality genomic resources in vertebrates, as well as valuable insights that are relevant in an age of biodiversity decline.

Genomic data can assist conservation planning, but implementation of genetic-based recommendations is rare. Closing this "conservation genetics gap" is crucial for restoration and translocation decisions, particularly for highly fragmented ecosystems like pine barrens. We first analyze the conservation genetics gap in pine barren management organizations using a survey. We then analyze whole-genome data to characterize population structure and diversity in the pine barren keystone plant Lupinus perennis. We find little genetic difference among L. perennis populations in the Northeast United States. While populations show signs of isolation by distance (rho = 0.785, p = 0.001), we find no correlation between population size and heterozygosity (Estimate = 0.003, p = 0.357) or inbreeding (Estimate = 0.028, p = 0.416). We also find no effect of seed source population on forecasted effective population size in restoration simulations. These findings and our recommendation that managers consider non-local seed provenancing for L. perennis restorations in the Northeast have been integrated into SWAP policy in two states. We generally recommend practitioners record seed provenance, save genetic material for future testing, and incorporate fitness metrics into restoration monitoring. To effectively close the conservation genetics gap, researchers providing conservation recommendations must consult with practitioners before designing experiments.

Kashmir voles (Hyperacrius) are poorly studied fossorial arvicolines of the southern Himalayan slopes, with two species recognized. We sequenced Cytb from voles collected in northern Pakistan and combined these data with existing GenBank sequences, yielding 194 tips spanning nearly all arvicoline genera. We analyzed five data sets with maximum likelihood and compared external measurements among species using principal component and linear discriminant analyses. We recovered five well-supported clades of Hyperacrius separated by ~12-14% p-distance, which we treat as distinct species. We recognize clade 1 as H. wynnei, and populations referred to H. w. traubi are genetically indistinguishable from H. w. wynnei. We recognize H. zygomaticus, new rank (clade 2), and tentatively allocate clade 5 to H. brachelix. Clades 3 and 4 likely represent undescribed species. Morphometric analyses of external measurements clearly distinguish H. wynnei but not clades 3 and 4 (overall classification accuracy 70.3%). Phylogenetic analyses including nuclear genes placed Hyperacrius as sister to a clade containing Microtini, Arvicola, Lagurini, Dinaromys, and Ellobiusini, whereas mitochondrial analyses weakly allied it with Ellobiusini. Its traditional placement in Clethrionomyini is thus unsupported, although its exact position remains unresolved. Alticola is nonmonophyletic, with A. macrotis sequences nested within Clethrionomys, likely reflecting mitochondrial capture.

Batoids (rays, skates, and relatives) are among the most threatened cartilaginous fishes globally, yet the molecular diversity of Peruvian taxa remains poorly evaluated. Furthermore, regional barcode sequences for high-conservation-priority taxa, such as sawfish, manta, and devil rays, are often restricted to private records, hindering essential phylogeographic and population structure assessments. To bridge this gap, we developed BATOseq-PE, the first public genetic reference library for Peruvian marine batoids, covering 14 species sequenced in vitro from local specimens, complemented by a novel in silico assembled mitogenome for Notoraja martinezi. This open-access repository contributes 73 novel COI barcodes, providing robust taxonomic resolution across 15 molecular operational taxonomic units (MOTUs) and Barcode Index Numbers (BINs). Notably, we provide the first Peruvian public records for high-priority species such as Mobula munkiana, Mobula thurstoni, Myliobatis peruviana, Rostroraja velezi, and the first global public barcodes for N. martinezi and Zapteryx xyster. By coupling BATOseq-PE with global datasets, we conducted the first multi-taxa screening for delimitation and phylogeographic assessments on Peruvian batoids, revealing a cryptic lineage within R. velezi and genetic connectivity patterns suggesting female philopatry in Mobula mobular. Finally, by integrating nucleotide diversity into a Genetic Diversity Risk Indicator (GDRI) alongside ecological and fishery data, we identified an alarming trend where heavy fishing pressure overlaps with extinction risk and depleted genetic diversity, allowing us to suggest data-driven, tailored management strategies. BATOseq-PE represents a valuable resource to accelerate taxonomic and population assessments, ultimately fostering ray conservation through the integration of genetic frameworks into fishery management.

Understanding patterns of evolution and divergence in populations is important for defining conservation units and informing taxonomy. However, when populations have low genetic diversity, or are closely related, genetic differentiation can be difficult to detect, particularly when relying on small numbers of genetic markers. Whole-genome sequencing allows for genome-wide identification of both neutral and outlier variation, improving the resolution of subtle population structure and providing insight into evolutionary processes. Here, we investigated genomic differentiation in a recently diverged and highly threatened albatross complex, the Antipodean (D. antipodensis antipodensis) and Gibson's albatross (D. a. gibsoni), using genome-wide neutral and outlier datasets. Whole-genome resequencing of 86 individuals sampled across Antipodes Island (D. a. antipodensis) and the Auckland Islands (D. a. gibsoni) identified 381,176 neutrally evolving and 57 independently segregating outlier (putatively adaptive) SNPs. Analyses of both datasets revealed significant genetic differentiation between the Antipodean and Gibson's albatross, no evidence of contemporary gene flow and evidence of selective sweeps suggesting local adaptation. Within-population structure was also identified for the Gibson's albatross, with genetic differentiation among sample sites from different islands (Adams Island and Disappointment Island). Patterns of heterogenous differentiation across the genome suggest the taxa are on different evolutionary trajectories. Together with existing morphological and behavioural evidence, these genomic results support reassessment of their conservation and taxonomic status. More broadly, this study demonstrates the value of combining neutral and putatively adaptive genomic variation to resolve subtle population structure in recently diverged taxa.

Understanding genetic connectivity among marine populations is central to conservation biology, informing how exploited species are managed, and how marine protected area (MPA) networks are designed. The queen conch (Aliger gigas) is a large, heavily exploited Caribbean gastropod listed under CITES Appendix II and provides an ideal system for examining connectivity in species with high dispersal potential. Its extended pelagic larval phase promotes gene flow across broad spatial scales, limiting detectable population structure. Here we used low-coverage whole-genome sequencing (lcWGS) of queen conch sampled from three regions within United States waters, Florida (FL), Puerto Rico (PR), and the US Virgin Islands (VI), to characterize connectivity and to evaluate the implications for management. Using genotype-likelihood approaches, we inferred patterns across principal component analysis, admixture analysis, pairwise FST, contemporary migration, and historical coalescent-based demographic modeling. Genome-wide analyses revealed little structure with individuals from all three regions intermixed in ordination space and similar ancestry profiles, consistent with high gene flow. In contrast, analyses restricted to the upper tail of the FST distribution recovered geographically concordant structure, resolving FL, PR, and VI as distinguishable groups, with PR individuals showing intermediate, admixed ancestry between FL and VI. Estimates of contemporary migration indicated a partially open system in which 72-98% of each population's ancestry was locally derived, with substantial bidirectional gene flow between PR and VI, moderate immigration from VI into FL and VI to PR, and negligible direct exchange from FL to either PR or VI. Historical demographic analyses suggest long-term genetic effective population sizes (Ne) on the order of 2.2-7.6 x 105; individuals and a hierarchical population divergence during the early Pleistocene (~ 2 Mya) with ongoing symmetric migration among the three populations, with the strongest historical connectivity between PR and VI with 10 diploid migrants per generation (2Nm = 20.0). Together, these results indicate that queen conch populations across US waters are neither fully panmictic nor completely isolated. Instead, they form a connected population system in which substantial gene flow occurs alongside geographically differentiated genomic variation. These findings argue against treating the US range as either a single management unit or as a set of completely independent stocks. They also highlight the potential importance of the US Virgin Islands within the regional connectivity network and suggest that highly differentiated loci could be useful for developing forensic SNP panels to identify the geographic origin of queen conch products and support enforcement against illegal, unreported, and unregulated fishing.

Among Madagascar primates, the sportive lemurs (family Lepilemuridae) have seen their species diversity increase from eight in 2005 to 26 in 2009 mostly by applying the phylogenetic species concept to DNA barcode data. Despite the genus being speciose, only one case of sympatry is known from northern Madagascar, where two sportive lemur species described based on low mtDNA divergence, Lepilemur ankaranensis and Lepilemur milanoii, were found to co-occur at the center of their joint distribution range. Here, to clarify the taxonomy of these two species and examine their sympatry, we apply an integrative taxonomic framework to genomic and morphological data from 84 individuals of L. ankaranensis and L. milanoii, encompassing their entire distribution range and the forest of Analafiana, beyond their southernmost limit. Using clustering, multivariate, and isolation by distance analyses, we find no evidence of a sympatric zone and show that despite clear genetic differentiation between regions, the genomic and morphological diversity of the L. ankaranensis, L. milanoii-Analafiana group is clinal and explained by geographic distance. These results clarify that L. milanoii is a junior synonym of L. ankaranensis and that the Analafiana forest population belongs to L. ankaranensis, extending its distribution. It further implies that the 'sympatric' zone, the Andrafiamena forest, hosts conspecific individuals with slightly differentiated mtDNA backgrounds, rather than slightly differentiated sympatric species. Lastly, we re-evaluate the IUCN conservation metrics of L. ankaranensis, which continue to qualify as Endangered (EN) under the B1ab(i-v) criteria.

Arctic ecosystems are undergoing rapid climate warming, providing an opportunity to examine molecular evolution under environmental stress. Here, we used whole-genome resequencing to assess population structure, genetic diversity, and recent demographic history in the snowy owl (Bubo scandiacus), a highly mobile Arctic apex predator classified as Vulnerable by the IUCN. We analysed genome-wide data from individuals sampled across the species' circumpolar range using a chromosome-level reference genome. Population genomic analyses revealed an absence of detectable population structure, indicating extensive gene flow and near-panmixia across continents. Genome-wide nucleotide diversity was low ({pi}= 2.47 x 10^(-4)), while runs of homozygosity were dominated by short tracts, indicating limited standing genetic variation despite little evidence for recent close inbreeding. Our demographic inference revealed a sustained decline in effective population size over the past ~1,600 years, a pronounced reduction coinciding with the Medieval Warm Period followed by a partial recovery during the subsequent cooler interval. This direct, measurable effect of past climate warming on effective population size raises concerns for the long-term survival of the snowy owl. Our results demonstrate that high connectivity and low levels of recent inbreeding have not necessarily buffered this species against climate-driven demographic erosion of genetic diversity. This study highlights the value of using whole-genome population genomics to inform genomic monitoring and conservation decision-making in rapidly changing environments.

Urban and rural woodlands have become important habitats for wildlife, providing opportunities for ecological and ethological adaptation to changing environmental conditions. Due to limited tree resources in anthropogenic woodlands, different species are often forced to interact more closely, and one possible outcome of such interactions is hybridisation. Recent studies have shown that hybrids between the uncommon Syrian Woodpecker (Dendrocopos major) and the often common Great Spotted Woodpecker (Dendrocopos syriacus) are relatively widespread, yet rare, in sympatric populations (Bakai et al. 2026). To understand the factors determining their occurrence in rural and urban landscapes, we conducted an intensive survey across Europe. We examined the effects of environmental factors, particularly woodland characteristics, as well as the co-occurrence of hybrids with the parental species and European Starlings (Sturnus vulgaris) (hereafter Starling). Spatial analyses revealed that the parental species generally have allotopic distributions, with Syrian Woodpeckers (hereafter SW) being more common in scattered woodlands in both rural and urban landscapes, while Great Spotted Woodpeckers (hereafter GW) are more commonly associated with denser woodlands and forests. Although in some areas the two species can co-occur, which provides opportunities for interspecific hybridisation, hybrid offspring showed no clear preference for any particular woodland type. However, they tended to occur in proximity to one of the parental species, usually the species that was locally rarer. Starlings were not identified as a factor influencing hybrid distribution. These results suggest that hybrids have a relatively broad ecological tolerance, potentially facilitated by heterosis. These findings contribute to our understanding of the factors influencing interspecific hybridisation and may have implications for the management of urban and rural woodlands to preserve habitats for the SW, an uncommon and strictly protected species in the west of the European Union.

Megadiverse countries concentrate most of the World's biodiversity. These countries encompass different levels of research infrastructure, and nearly all of them have been historically committed to the Convention of Biological Diversity, often setting precedents and leading new approaches. Here, we ask whether the assessment of genetic diversity indicators provide novel insights for biodiversity management and conservation in one of those countries, Mexico. We evaluated the first national application of the Kunming-Montreal Global Biodiversity Framework (GBF), genetic diversity indicators in Mexico. The data covered 97 taxa across diverse ecosystem types and taxonomic groups, including crop wild relatives, to assess the capacity of genetic diversity indicators to provide novel insights, as well as their relevance for strengthening national conservation strategies. We calculated two indicators: the proportion of populations with an effective population size greater than 500 (Ne 500) and the proportion of populations maintained (PM). Data were sufficient to estimate the Ne 500 indicator for 47 taxa and the PM for 28 taxa, with mean indicator values of 0.217 and 0.936, respectively. Species' geographic range was positively associated with Ne 500, whereas national endemicity had no significant effect. Comparisons with the IUCN Red List and Mexico's national extinction-risk legislation revealed that genetic vulnerability occurs even among taxa not currently recognized as threatened. Our findings highlight a gap in legal recognition of genetic diversity protection that could be strengthened by incorporating population-level assessments focused on maintaining adaptive potential in the long-term. Additionally, the indicators allowed to highlight conservation concerns within crop wild relatives, though fully realizing their potential requires integrating the entire wild-to-domesticated complex. The Mexican experience highlights that the main challenge for scaling the monitoring of genetic diversity is not only generating new data, but integrating existing information into systems that strengthen collaboration and communication among researchers, local communities, and government institutions.

Aim: Given that much of Earth's biodiversity is contained within species, inferring intraspecific genetic diversity and identifying its ecological correlates is essential for understanding evolutionary processes and informing conservation. Here, we investigate broad-scale variation in species-level mitochondrial genetic diversity and evaluate the relative importance of alternative ecological hypotheses proposed to explain it. Location: Brazilian Atlantic Forest, Iberian Peninsula, northwestern Africa, Arabian Peninsula, Madagascar and Australian Monsoonal Tropics. Taxon: Amphibians and reptiles Methods: We assembled a comprehensive dataset by integrating and manually curating mitochondrial sequences, occurrence records, environmental data and species traits from multiple open-access sources. We used multiple mitochondrial genes to estimate mean nucleotide diversity for each study species and quantified regional variation in genetic diversity. We then used random forests models to evaluate the relative importance of selected variables representing hypotheses related to water-energy availability, topography, historical climatic stability, land-cover characteristics, species geographic characteristics, life-history traits, evolutionary history and conservation status. Results: The final dataset comprised 247 amphibians and 295 reptiles, for which 43 and 52 explanatory variables were evaluated, respectively. Overall, the strongest support was found for hypotheses related to life-history traits, topographic heterogeneity and water-energy availability. In amphibians, higher genetic diversity was associated with smaller body size and greater environmental heterogeneity, particularly broader elevational and precipitation gradients. In reptiles, genetic diversity was primarily associated with life-history traits, with species of smaller body size and lower reproductive output exhibiting higher diversity. Long-term climatic stability showed comparatively little explanatory power for both taxa. Main conclusions: Our comprehensive study demonstrates that integrating extensive manual data curation with comparative macrogenetic analyses provides a robust framework for identifying broad-scale ecological correlates of mitochondrial genetic diversity. These findings improve our understanding of the factors associated with contemporary patterns of genetic diversity and provide a foundation for future conservation assessments in data-limited systems.

The Atlantic surfclam, Spisula solidissima solidissima supports multimillion dollar harvests in the western North Atlantic, including Georges Bank and Mid-Atlantic Bight populations along the continental shelf. Surfclam populations in this part of the Exclusive Economic Zone (3-200 nm from shore) are managed as a single unit, but demographic connectivity has never been tested directly. This study analyzed >8,500 SNPs in 548 Atlantic surfclams sampled across the USA harvested range to infer population structure, genomic diversity, and gene flow patterns. Genomic analyses included eight sampled and 10 reference Spisula solidissima similis samples, a morphologically cryptic nominal subspecies previously known only from nearshore habitats. Novel morphologically cryptic population structure was identified in S.s. solidissima. One operational taxonomic unit (OTU-A) was found only in the inshore region of southern New England, south of Cape Cod. The other population unit, OTU-B, was found offshore and in Cape Cod Bay. The federal fishing grounds only had OTU-B clams. Populations within each OTU were connected by gene flow, justifying current fishery management practices. Nearshore state waters had mixed OTU stocks. Hybridization was analyzed between the two OTUs and between the two subspecies based on nuclear SNPs and asymmetrical mitochondrial DNA introgression. Finally, we demonstrated the utility of a novel SNP panel for diagnosing all three taxa and their hybrids.