Conservation Genetics

Wildlife responses to habitat loss and fragmentation are a central concern in the management and conservation of biodiversity. Small and isolated populations are vulnerable, both due to demographic and genetic mechanisms, which are often linked. Thus, understanding how (changes in) genetic diversity, effective population sizes, and levels of inbreeding relate to population size and degree of isolation is key for developing effective conservation strategies. High-density Single Nucleotide Polymorphism (SNP) arrays represent an increasingly cost-efficient tool to achieve the data needed for such analysis. Here, we present the development of a novel 625k SNP array for reindeer Rangifer tarandus and apply this array to assess conservation genetic issues across thirteen Norwegian wild reindeer populations of varying size, isolation, and genetic origin (i.e., semi-domesticated reindeer origin or a mix of wild reindeer and semi-domesticated reindeer origins). Many of these populations are currently completely isolated, with no gene flow from other populations. We genotyped n = 510 individuals sampled by hunters and found that variation in population size across the populations largely predicted their (recent loss of) genetic variation (observed heterozygosity, Ho), as well as effective population size (Ne) and (change in) level of recent inbreeding. For the smallest and most isolated populations, with total population sizes of <50-100 individuals and a high and increasing level of recent inbreeding, estimated loss of genetic variation was as high as 3-10% over the time span of a generation or less, and estimated Ne was as low as six individuals. With the current level of isolation and associated lack of gene flow, and considering their already low genetic diversity, these populations are hardly viable - neither demographically nor genetically - in the long term. These results have direct relevance for the management of Norwegian wild reindeer, recently red-listed as Near Threatened. Yet, these genetic challenges, characterizing many of the small wild reindeer populations in Norway, have been largely ignored by management thus far. Mitigation efforts such as reducing barriers would introduce substantial conservation dilemma due to the aim of avoiding further spread of chronic wasting disease (CWD), as well as potential further domestic introgression into populations with genetically wild reindeer (or mixed) origin. Nevertheless, our cost-efficient and high-density SNP array especially designed for reindeer and caribou offers a powerful genetic tool to include in future monitoring, providing important contributions to management and conservation decisions.

ContextGenetic diversity is essential for the persistence and future adaptation of species. However, human-driven habitat fragmentation results in population isolation, often leading to rapid loss of genetic diversity and adaptive capacity. Genetic management of focal taxa may be overlooked in many threatened species conservation programs. The Endangered southeastern Australian mallee emu-wren Stipiturus mallee is a species that may benefit from genetic management. Its current range encompasses patchily distributed sub-populations, prone to bottlenecks and genetic drift. Thus, the reintroduction to areas from which the species has been locally extirpated requires careful selection of founders to maximise genetic diversity. AimsWe analyse reduced-representation genomic data from seven sampling areas across the global meta-population to design a translocation strategy that maximises heterozygosity and retention of mallee emu-wren allelic diversity. MethodsWe estimated genetic structure, genetic diversity within, and differentiation between subpopulations, thus testing previous inference based on 12 length-variable loci of low population differentiation with 10,840 genome-wide SNP loci. We also estimated effective population sizes to identify populations in need of genetic augmentation, Finally, we used metapop2 simulations to estimate the relative contributions of each population to global genetic diversity of the species and to estimate the source and number of founders that would maximise heterozygosity and allelic richness in a hypothetical newly established population. Key resultsWe found weak genetic structure across all sampling areas, supporting previous conclusions that the global mallee emu-wren population should be considered a single genetic unit for management purposes. Low but significant Weir and Cockerham pairwise FST among locations indicated differentiation between sampling areas, suggesting that contemporary gene flow is restricted. Effective population sizes for the two regions supporting the largest numbers of mallee emu-wrens were below the threshold associated with reduced adaptive potential. ConclusionsThe genetic health and adaptive potential of sampled mallee emu-wren sub-populations are at risk. Implications The global mallee emu-wren meta-population would likely benefit from genetic augmentation, including reciprocal gene flow between extant sub-populations. To maximise genetic diversity in newly established populations, managers should prioritise gene-pool mixing with founders sourced from all sampled areas.

Amphibians are threatened worldwide by various environmental and anthropogenic factors, making non-invasive conservation studies particularly valuable. Newts are one example of a thus challenged amphibian group. In Austria, local population declines of newts have been observed, with the smooth newt (Lissotriton vulgaris) being strongly affected. In this study, skin swabs were used as a non-invasive method to gather DNA, combined with established microsatellite markers. We sampled 139 L. vulgaris individuals at ten sites in North Tyrol, Austria, and, for comparison, 22 L. vulgaris meridionalis individuals in Brixen, Italy. We genotyped all individuals and analysed their population structure. We demonstrate the presence of three distinct L. vulgaris population clusters and find differences in population structure between supposedly introduced allochthonous L. vulgaris individuals and autochthonous populations, as evidenced by differences in Bayesian clustering and elevated values of the fixation index FST. A captive population in a zoological garden, with origins in the Kramsacher Loar in the Tyrolean Unterland (eastern part of Tyrol), performed poorly in terms of conservation genetics, with low genetic diversity (number of alleles) and clear genetic differentiation from populations in the wild (high pairwise FST values with wild individuals, clear separation in cluster analysis). Habitat restoration programs are a crucial aspect of amphibian conservation, as they restore ecosystems that are critical to the animals survival. While breeding programs can play an additional role in the future, they must carefully consider genetic diversity to ensure resilient and viable populations, especially in the face of climate change and chytrid fungus infection. This study emphasizes the significance of considering the geographic origin and genetic diversity of newts in conservation efforts. It also serves as a foundation for future population genetic studies of newts in Austria.

Animal translocations are becoming increasingly popular as a tool for conservationists. Demographic factors can be crucial determinants dictating translocation viability in the short term. Translocated populations pass through artificial bottlenecks and can suffer from founder effects. Reduction in genetic variation relative to their source populations is likely, limiting their adaptive potential. Founder events can increase frequencies of deleterious alleles due to elevated rates of inbreeding and inbreeding depression. Here, we describe the effects of human-driven, serial population translocations on the genetic diversity of critically endangered Anegada iguanas (Cyclura pinguis) in the British Virgin Islands. Though founding populations were extremely small (N=8, N=4), the census sizes of translocated iguana populations increased dramatically over the first twenty years. This implies that these translocations were successful from a demographic perspective despite the small number of animals used, indicating a genetic paradox. To quantify genetic signatures in these bottlenecked populations, blood samples were collected from the source population and two translocated populations and genotyped at 21 microsatellite loci. We found that allele frequencies in translocated populations differed significantly from those of the source, with the translocated populations having less genetic diversity. However, common methods for estimating presence of genetic bottlenecks were non-significant. Estimates of internal relatedness by age class suggest that inbreeding depression may be elevated after translocation, likely reflecting the small initial population sizes associated with these translocation events. Anecdotally, our work shows that translocations may result in subtle genetic erosion that has long-term population viability impacts, even when census size indicates success.

AbstractObtaining genetic information from rare species is challenging for scientists, but it is crucial for understanding animal evolutionary history and informing conservation management initiatives. We present the first example of a collaborative local network that includes zoos and natural history collections to investigate the evolution, systematics, and conservation concerns of olingos (genus Bassaricyon, Procyonidae, Carnivora, Mammalia). We sequenced the entire (1,146 base pairs) cytochrome b gene to phylogenetically identify individuals that have been victims of wildlife trafficking. Unexpectedly, we detected an individual specimen belonging to Bassaricyon medius orinomus (western lowland olingo), which may represent a new geographical record for this taxon in Ecuador. Through our practical experiences, we describe how local collaboration is possible and crucial for promoting wildlife genetic research in the Global South and contributing to protecting the last populations of rare mammals. We also discuss the significance of wild animals under human care as a valuable genetic resource for scientific research, conservation strategies, and informed wildlife management decisions.

Island endemics exhibit low genetic diversity due to founder effects and geographical isolation, increasing their vulnerability to inbreeding depression. The Narcondam Hornbill (Rhyticeros narcondami), restricted to the 6.8 km2 Narcondam island in the Andaman archipelago, has the smallest range size among hornbills, a globally threatened group of birds. We compared the genetic diversity of the Narcondam Hornbill with the Wreathed Hornbill (Rhyticeros undulatus) distributed from the Eastern Himalaya to Bali. We generated DNA sequences for four mitochondrial markers ; Cytochrome B (Cytb), cytochrome c oxidase subunit I (COI), NADH dehydrogenase subunit 2 (ND2) and displacement loop (D-loop) regions) from 14 Narcondam Hornbill faecal samples and for three markers (Cytb, COI and ND2) from 19 Wreathed Hornbill tissue samples from north-east India. Our results suggest markedly lower genetic diversity in the island endemic Narcondam Hornbill compared to the Wreathed Hornbill. Specifically, Cytb and COI showed no genetic variation in the island endemic, compared to three to five haplotypes in the Wreathed Hornbills. In the ND2 region, Narcondam Hornbills showed seven haplotypes among 13 samples compared to the Wreathed Hornbills six haplotypes among eight samples. The observed genetic diversity in the D-loop in the Narcondam Hornbill was lower than other island-endemic hornbill species in the Philippines. The extremely low genetic diversity in the Narcondam Hornbill likely stems from a small founder population and/or past hunting pressures that reduced its numbers to approximately 30% of its current population of 1000 birds, rendering the Narcondam Hornbill susceptible to environmental and human-driven changes.

The Tricolored Blackbird (Agelaius tricolor) is a colonial songbird, found almost exclusively in California, whose total population size has sharply declined over the past century. It is currently under review to be listed as Endangered under both the California and U.S. Endangered Species Acts. Here we assess the genetic diversity of a breeding population in Californias Central Valley, comparing our findings with previously sampled conspecific and congeneric populations. First, we genotyped 50 adults at 9 microsatellite loci in our focal population and estimated allelic and Shannon diversity, observed and expected heterozygosity, and the inbreeding coefficient (FIS). Second, we compared our results to those of the one existing study on Tricolored Blackbird conservation genetics and found that levels of allelic diversity and heterozygosity in our focal population were similar to those of 11 previously studied populations. Unlike the earlier study, which found moderately high mean inbreeding coefficients, we detected no evidence of inbreeding in our focal population. Third, we used 7 of the 9 loci to compare the genetic diversity of our focal population with populations of 2 previously sampled Agelaius congeners. We found that allelic diversity, Shannon diversity, and expected heterozygosity in our Tricolored Blackbird population were most similar to those of an isolated Red-winged Blackbird (A. phoeniceus) population in the Bahamas. We discuss possible reasons for the different results from the conspecific study, outline why the collective findings from both studies support the need for protective measures, and urge conservation action to maintain existing genetic diversity and gene flow before ongoing population losses lead to adverse fitness consequences.

Trends in wildlife crime continue to rise and contribute to the ongoing decline of our planets biodiversity. We applied a genetic approach to ascertain the geographic origin of a suspected Seychelles Magpie-robin confiscated in Singapore during international transit, and to confirm illegal trade of this species. However, mitochondrial analyses revealed this individual to be a subspecies of Oriental Magpie-robin, endemic to the island of Borneo, and bearing similar morphology to the Seychelles species. We thus consider the implications of correct species identification on captive care and repatriation in cases of wildlife confiscation, and emphasise the value of using genetics in wildlife crime investigation.

Caribou, listed as a species at risk across Canada, have experienced a wide range of evolutionary and selective pressures at multiple scales, from large-scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Given these multi-scale evolutionary forces, genetic variation and diversity are expected to be hierarchically structured. Characterising hierarchical population structure is crucial to understanding a species evolutionary history and informing effective conservation and management strategies. In this study, we analysed genomic diversity and variation in woodland caribou (Rangifer tarandus caribou) across western Canada using genotypes from [~]33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo-referenced individuals spanning 45 pre-defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterize hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post-glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post-glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current conservation units for the species in this region. We also observe elevated heterozygosity in the mid-latitudes of the sampled range, indicative of hybridisation following secondary contact during post-glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide-ranging species often experience diverse and complex evolutionary histories and pressures.

Aquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (FST = 0.26 {+/-} 0.02SD) as well as low genetic diversity (HO 0.30) compared to remaining populations (HO 0.64 {+/-} 0.14SD). Although evidence suggests that stocking increased the effective population size of Llyn Padarn in the short term without impacting genetic diversity, the long term effects of such practices are yet to be seen. Results provide baseline data for conservation management, and highlight the need for protection of small isolated populations that are being negatively impacted by the processes of genetic drift due to escalating anthropogenic pressures. Continual monitoring of both Arctic charr and their habitats using a combination of methods will increase the likelihood that these threatened and iconic populations will persist in the future.

The history and population dynamics of feral horse and wild mustang population in the Western United States has led to diverse populations of disparate ancestry. These iconic populations are currently managed by the Bureau of Land Management (BLM) and their genetic history is of great interest for both management and conservation purposes. We examined population genetic parameters using 12 well established microsatellite loci in nearly 8,500 horses representing 235 populations sampled across more than 20 years. Samples were collected by BLM or by members of other management agencies from 10 states. Genetic variability and genetic resemblance to domestic horse breeds using multiple methods were estimated. A wide range of variation levels were observed across the populations. In general, within-population variability was slightly lower than what has been found in domestic horse breeds, but still retains diversity. As expected, levels of population variation correlated to census size. Several populations were sampled longitudinally with intervals between sampling of about 5 years. For these longitudinal samples, there was no trend towards an increase or decline in diversity, indicating consistent management practices. Relationships between populations and domestic breeds ranged from close association to one or two specific breeds to extreme divergence of the feral horses to all breeds examined. Reasons for divergence are mainly related to the founding of the population and subsequent demographic history. Overall, there was a slight tendency for geographically close feral populations to be more similar to each other than to more distant populations. The results of this study show the feral horse populations in the western US have a considerable variation, though management practices can strongly influence variability levels.

1. Understanding critical components of habitat use, such as dietary preferences, is crucial for creating and implementing effective conservation plans. This becomes challenging when species exhibit cryptic behaviours, such as arboreality and nocturnality, as seen in the endangered greater glider (Petauroides spp). Existing methods for determining greater glider diet are inadequate, time consuming and prone to human error. Furthermore, current literature lacks specificity, with most research stating simply that greater gliders are dietary eucalypt specialists, without providing additional insight into which species are eaten. 2. Here, we tested a non-invasive technique using targeted sequencing of species-specific single nucleotide polymorphisms from greater glider faecal samples to identify dietary components across multiple locations in Southeast Queensland. 3. Sequencing identified 17 plant species present in the faecal samples, including Angophora, Acacia and Casuarina spp. that were previously unknown to be feed tree taxa, profoundly increasing our understanding of the habitat requirements of this endangered marsupial. Four of these identified species were out of range of their natural occurrence, suggesting limitations to the accuracy of this technique. 4. This study demonstrates the value of using genomic sequencing for analysing diets of arboreal mammals and makes recommendations for improving the accuracy of this methodology for future studies. Our findings highlight key tree species to be considered important for future greater glider conservation plans and raises the question whether there are local drivers behind the differences in dietary choices across the landscape. Such information will be critical for greater glider conservation, particularly when management planning across multiple habitats.

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.

Whole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) had been widespread across Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater magnitude of loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay. HighlightsO_LIFive regional populations show distinct degrees of population isolation and decline. C_LIO_LIThere has been commensurate loss of genetic diversity, skewed site frequency spectra, reduced migration, and increased inbreeding (FROH). C_LIO_LIAs many state-wide populations decline, the smaller, more remote populations provide a glimpse into the future and a testbed for remediation approaches. C_LI

In this study, samples from 33 Guatemalan Beaded Lizard (Heloderma charlesbogerti) were analyzed for genetic diversity. Twenty-three samples were obtained from wild individuals from two separate population areas, and 10 samples were obtained from captive individuals. Because the seasonally dry tropical forest habitat sampled for this study, is degraded and fragmented, it was hypothesized that beaded lizard populations were small and isolated and would be subject to genetic erosion and an elevated extinction risk. To test this hypothesis, eight microsatellite markers were employed to analyze 22 individual samples from the population of Cabanas, Zacapa, a single individual from the eastern-most population and 10 captive individuals of unknown origin. An average of three alleles per maker was reported for the Cabanas population, evidencing a low genetic diversity. In addition, a recent bottleneck event was detected and an effective population size of 19.6 was estimated. Demographic reconstruction using a Bayesian approach was inconclusive possibly due to a small dataset and shallow coalescence trees obtained with the generated data. No clear structuring pattern was detected for the Cabanas population and most samples from individuals in captivity were found to have similar alleles to the ones from Cabanas. Population designation is challenging without the genotyping of every wild population, but unique alleles were found in captive individuals of unknown origin that could suggest that different genotypes might exist within other, less studied, wild populations. Low genetic diversity, and a small effective population size represent a risk for the Cabanas population facing the threats of isolation, habitat loss and climate change. These findings suggest that genetic management of the Cabanas population might be utilized to avoid high rates of inbreeding and subsequent inbreeding depression.

Cheetahs (Acinonyx jubatus) are majestic carnivores and the fastest land animals; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-interactions and illegal trafficking, there are only approximately 7,100 individuals remaining in the wild. Cheetahs used to roam large parts of Africa, and Western and Southern Asia. Today they are confined to about 9% of their original distribution. To investigate their genetic diversity and conservation status, we generated genome-wide data from historical and modern samples of all four currently recognized subspecies, along with mitochondrial DNA (mtDNA) and major histo-compatibility complex (MHC) data. We found clear genetic differentiation between the sub-species, thus refuting earlier assumptions that cheetahs show only little population differentiation. Our genome-wide nuclear data indicate that cheetahs from East Africa may be more closely related to A. j. soemmeringii than they are to A. j. jubatus. This supports the need for further research on the classification of cheetah subspecies, as East African cheetahs are currently included in the Southern Africa subspecies, A. j. jubatus. We detected stronger inbreeding in individuals of the Critically Endangered A. j. venaticus (Iran) and A. j. hecki (Northwest Africa), and show that overall genome-wide heterozygosity in cheetah is lower than that reported for other threatened and endangered felids, such as tigers and lions. Furthermore, we show that MHC class II diversity in cheetahs is generally higher than previously reported, but still lower than in other felids. Our results provide new and important information for efficient genetic monitoring, subspecies assignments and evidence-based conservation policy decisions.

AimWe used genetic tools to examine the population structure of mountain goats in Alaska, USA and assessed the demographic history of this species in relation to the natural and anthropogenic forces. LocationAlaska, USA TaxonNorth American mountain goat (Oreamnos americanus) MethodsSamples were collected between 2006 - 2020 from harvested animals and live captures. We genotyped 816 mountain goats at 18 microsatellite loci and identified the number of genetically distinct subpopulations across the state and assessed their genetic diversity. We used Bayesian computation software to investigate the demographic history relative to the known biogeographic history of the state. We also simulated island translocation events and compared simulations to empirical data to address the hypothesis that Baranof Island was a cryptic refugia. ResultsWe showed that Alaska has four genetically distinct subpopulations of mountain goats with some additional genetic structure within those subpopulations. The main split of mountain goats between Southcentral and Southeast Alaska occurred [~]14,000 years ago. Simulations of translocation events largely aligned with the current populations observed today except for Baranof Island which showed greater diversity than the translocation simulation. Main ConclusionsThe distribution and genetic structure of mountain goats in Alaska reflects a combination of natural and anthropogenic forces. A rapid northerly expansion through an ice-free corridor in combination with the isolated nature of the landscape led to low diversity and isolation 14,000 years ago in Southcentral Alaska and higher diversity in Southeast Alaska. Two of the three islands where mountain goat translocations have occurred match genetically with their source population, while Baranof Island appears to have a divergent population, consistent with the hypothesis of an endemic or cryptic population prior to the translocation event. This study highlights the value of considering both the natural and anthropogenic forces when assessing the biogeographic history of a species.

AimGenetic diversity contains valuable information about ecological and evolutionary aspects of species. Intraspecific genetic variation is shaped by species natural history traits and by characteristics of geography and climate within their ranges. Amphibians are of ecological and conservation interest because of their global distribution, deep history, trait diversity, and roles within ecological communities. Here, we studied genetic variation within salamanders to investigate predictors of nucleotide diversity and spatial patterns of genetic differentiation. LocationGlobal. Time PeriodPresent. Major Taxa StudiedSalamanders. MethodsWe repurposed mitochondrial DNA sequences and ecological data from open-access databases for 220 salamander species. We calculated nucleotide diversity ({pi}) and tested for isolation by distance (IBD) and isolation by environment (IBE). We analyzed these three variables with random forest and phylogenetic comparative methods using 28 predictors expected to be associated with genetic variation. ResultsWe recovered 8,108 Cytb sequences with their associated geographic coordinates, of which 7,007 sequences were manually curated by us. Range size, lineage age, and sample size were important predictors of genetic variation. We found higher diversity in regions including the Neotropics and central-eastern Europe. The absence of phylogenetic signal in {pi}, IBD, and IBE suggests that genetic variation is shaped by local ecological and geographical factors rather than by shared ancestry. Main ConclusionsOur finding of range size as an important predictor aligns with theoretical expectations that species with larger ranges tend to harbor more genetic diversity. Furthermore, lineage age being an important predictor is in line with the clade-age hypothesis, in which species with longer divergence times have higher genetic diversity because they have had more time to accumulate genetic variation. Our results underscore the importance of integrating spatial data into macrogenetic studies, providing valuable information for future studies and conservation strategies targeting regions with high or low genetic diversity.

In response to growing concerns over human-driven biodiversity loss, rewilding efforts increasingly employ semi-wild herbivores to restore ecosystems. The Exmoor pony is often cited as an ancient breed retaining primitive traits suited for such projects, yet its genetic history remains underexplored. We combined studbook records, mitochondrial DNA (mtDNA) D-loop, and whole mitogenome sequences to evaluate maternal lineage diversity for improved management recommendations and the phylogenetic placement of Exmoor ponies among modern and ancient breeds. We also assessed whether data from multiple breeds already available based on D-loop sequences could be organised into a useful framework for resolving the complex history of modern horse breeds. We identified eight mtDNA haplotypes among 88 Exmoor pony samples, representing all extant maternal lines. While phylogenetic trees based on D-loop sequences lacked resolution, clustering published sequences to a mitogenome-derived haplogroup framework allowed assessment of the distribution and relationships of lineages across diverse horse populations, including ancient DNA samples and Przelwalskis horses. The most basal lineages of Exmoors were traced back to the Pleistocene, supporting their ancient origin and status as a primitive population, with a possible ancestral role in the development of some modern breeds. The founder lineages were found to be polyphyletic, with more derived haplogroups representing subsequent mixture with other domestic horse breeds. Although nuclear genome sequencing is needed to fully assess levels of admixture, we identified new haplotypes, along with rare or basal haplotypes that could be prioritised for conservation in rewilding studies. Our results highlight the potential for broad testing of hypotheses about origins and relationships among horse breeds using short regions of DNA mapped onto a more robust phylogenetic framework resolved through comparison of whole mitogenomes.

AimUnderstanding the processes that underlie the distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, how population structure affects genetic diversity and contributes to a species adaptive potential remain elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. LocationsAtlantic Ocean, Cabo Verde, island of Boavista MethodsHere, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boavista, Cabo Verde). ResultsHypothesis-driven population genetic models suggest the colonization of the Atlantic has occurred in two distinct waves, each corresponding to major mtDNA lineages. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across nesting groups despite significant genetic structure amongst nesting groups. This structure stems from female philopatric behaviour which could further be detected by weak but significant structure amongst beaches separated by only a few kilometres on the island of Boavista. Main conclusionTo explore demographic processes at diverse geographic scales improves understanding the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species adaptive potential and putative response to human-induced selection.