Understanding the exchange of individuals between wildlife populations, particularly those with naturally fragmented habitats, is important for the effective management of these species. This is of particular consequence when the species is of conservation concern, and isolated populations may be lost due to pressures from predation or competition, or catastrophic events such as wildfire. Here we demonstrate the use kinship and population structure analysis to show potential recent movement between colonies in metapopulations of yellow-footed rock-wallaby ( Petrogale xanthopus Gray 1854) at two sites in the Grey Range of Queensland, and at four sites in the Gawler Ranges of South Australia. These colonies are also compared to a single colony from the Flinders Ranges, a connected landscape of rock-wallaby habitat. Using reduced representation next-generation sequencing, we acquired and filtered a set of ~ 17,000 single-nucleotide polymorphisms to examine population genetic variation, structure and relationships within populations, and also identify putative migrants. Initial STRUCTURE analysis re-confirmed each population should be considered separately. Tests of population genetic variation identify several colonies appearing to be experiencing genetic erosion, also with low calculated effective population sizes (N e = 4.5–36.6). Pairwise comparisons of individual relatedness (relatedness coeffiecients; r ) implied several contemporary movement events between colonies within both the Gawler and Grey Ranges ( r > 0.125), which was then affirmed with tests for putative first generation migrants. These results are of particular note in South Australia, where threat abatement (management of key predators and competitors) may facilitate dispersion. Additionally, in Queensland, colonies are separated by anthropogenic barriers: predator exclusion fencing designed to exclude dingoes ( Canis familiaris ) from grazing land, which may hinder dispersal. This work highlights the usefulness of population genetics to inform management outcomes in wildlife, in this case, highlighting the need for threatened species management at the landscape level.
The spatiotemporal genetic variation at early plant life stages may substantially affect the natural recolonization of human-altered areas, which is crucial to understand plant and habitat conservation. In animal-dispersed plants, dispersers’ behavior may critically drive the distribution of genetic variation. Here, we examine how genetic rarity is spatially and temporally structured in seedlings of a keystone pioneer palm (Chamaerops humilis) and how the variation of genetic rarity could ultimately affect plant recruitment. We intensively monitored the seed rain mediated by two medium-sized carnivores during two consecutive seasons in a Mediterranean human-altered area. We genotyped 143 out of 309 detected seedlings using 12 microsatellite markers. We found that seedlings emerging from carnivore-dispersed seeds showed moderate to high levels of genetic diversity and no evidence of inbreeding. We found inflated kinship among seedlings that emerged from seeds within a single carnivore fecal sample, but a dilution of such FSGS at larger spatial scales (e.g. latrine). Seedlings showed a significant genetic sub-structure and the sibling relationships varied depending on the spatial scale. Rare genotypes arrived slightly later throughout the dispersal season and tended to be spatially isolated. However, genetic rarity was not a significant predictor by itself which indicates that, at least, its influence on seedling survival was smaller than other spatiotemporal factors. Our results suggest strong C. humilis resilience to genetic bottlenecks due to human disturbances. We highlight the study of plant-animal interactions from a genetic perspective since it provides crucial information for plant conservation and the recovery of genetic plant resilience.
The clouded apollo ( Parnassius mnemosyne ) used to have a wide distribution in Fennoscandia. Recent population declines have, however, led to regional extinctions and in Sweden it is currently one of the most endangered butterflies, confined to three geographically separated metapopulations: Blekinge, Roslagen and Västernorrland. Especially the Blekinge population has declined dramatically and few imagines have been observed during recent census efforts (< 10 in some localities). The clouded apollo is subject to a species action plan which includes both habitat restorations and captive breeding to produce individuals for release and reintroductions. Here, we apply whole-genome resequencing of clouded apollo individuals collected in the three natural populations and the captive population in Sweden and apply population genomic approaches to get a better understanding of the genetic structure and levels of genetic diversity in the species. We find that the clouded apollo populations in the different geographic regions have similar, but comparatively low levels of genetic diversity and we find evidence for significant genetic differentiation between the northernmost population and the populations in southern Sweden. Additional analysis, including previously available mitochondrial data, unveil that a bi-directional re-colonization of Fennoscandia after the latest glacial maximum most likely is the explanation for the considerable differentiation between some Swedish populations. Finally, we find evidence for population sub-structure in one of the Swedish populations. The results provide insights into the genetic consequences of population size declines and fragmentation in general and provide important information for direct conservation actions for the clouded apollo in Sweden in particular.
The Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion.
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
Genetic diversity is critical to a population’s ability to overcome gradual environment change. Large-bodied wildlife existing in regions with relatively high human population density are vulnerable to isolation-induced genetic drift, population bottlenecks, and loss of genetic diversity. Moose ( Alces americanus americanus ) in eastern North America have a complex history of drastic population changes. Current and potential threats to moose populations in this region could be exacerbated by loss of genetic diversity and connectivity among subpopulations. Existing genetic diversity, gene flow, and population clustering and fragmentation of eastern North American moose are not well quantified, while physical and anthropogenic barriers to population connectivity already exist. Here, single nucleotide polymorphism (SNP) genotyping of 507 moose spanning five northeastern U.S. states and one southeastern Canadian province indicated low diversity, with a high proportion of the genomes sharing identity-by-state, with no consistent evidence of non-random mating. Gene flow estimates indicated bidirectionality between all pairs of sampled areas, with magnitudes reflecting clustering and differentiation patterns. A Discriminant Analysis of Principal Components analysis indicated that these genotypic data were best described with four clusters and indicated connectivity across the Saint Lawrence River and Seaway, a potential physical barrier to gene flow. Tests for genetic differentiation indicated restricted gene flow between populations across the Saint Lawrence River and Seaway, and between many sampled areas facing expanding human activity. These results document current genetic variation and connectivity of moose populations in eastern North America, highlight potential challenges to current population connectivity, and identify areas for future research and conservation.
A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringlet Erebia manto, which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priority. Using several thousand nuclear genomic markers, we evaluated to which degree the bubastis lineage from the Alps and the vogesiaca lineage from the Vosges, are genetically isolated from the widespread manto lineage. Our results suggest that both lineages are genetically as strongly differentiated from manto as other taxonomically well separated sibling species in this genus from each other, supporting a delineation of bubastis and vogesiaca as independent species. Given the restricted and isolated range of vogesiaca as well as the disjunct distribution of bubastis, our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes.
Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal ( Pusa hispida saimensis ) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal ( Pusa hispida botnica ) reference population ( p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.
Captive propagation is widely used for the conservation of imperiled populations. There have been concerns about the genetic effects of such propagation, but few studies have measured this directly at a genomic level. Here, we use moderate-coverage (10X) genome sequences from 80 individuals to evaluate the genomic distribution of variation of several paired groups of Chinook salmon (Oncorhynchus tshawytscha). These include (1) captive- and natural-origin fish separated by at least one generation, (2) fish within the same generation having high fitness in captivity compared to those with high fitness in the wild, and (3) fish listed as different Evolutionarily Significant Units (ESUs) under the US Endangered Species Act. The distribution of variation between high-fitness captive and high-fitness natural fish was nearly identical to that expected from random sampling, indicating that differential selection in the two environments did not create large allele frequency differences within a single generation. In contrast, the samples from distinct ESUs were clearly more divergent than expected by chance, including a peak of divergence near the GREB1L gene on chromosome 28, a gene previously associated with variation in time of return to fresh water. Comparison of hatchery- and natural-origin fish within a population fell between these extremes, but the maximum value of FST was similar to the maximum between ESUs, including a peak of divergence on chromosome 8 near the slc7a2 and pdgfrl genes. These results suggest that efforts at limiting genetic divergence between captive and natural fish in these populations have successfully kept the average divergence low across the genome, but at a small portion of their genomes, hatchery and natural salmon were as distinct as individuals from different ESUs.
Magnolia odoratissima is a highly threatened species, with small distribution and scattered populations due to habitat fragmentation and human activity. In this study, the genetic diversity and population structure of the five remaining natural populations and two cultivated populations of M. odoratissima were analyzed using single nucleotide polymorphisms (SNPs) derived from specific-locus amplified fragment sequencing. A total of 180,650 SNPs were identified in seventy M. odoratissima individuals. The Nei’s and Shannon-Wiener diversity index across all M. odoratissima population were 0.35 and 0.51, respectively, while the observed heterozygosity (Ho) and expected heterozygosity (He) were 0.27 and 0.34, respectively. Our results suggest that M. odoratissima has relatively high genetic diversity at the genomic level. The FST and AMOVA indicated that high genetic differentiation exists among populations, and a phylogenetic neighbor-joining tree, Bayesian model–based clustering and discriminant function analysis of principal component all divided the M. odoratissima individuals into three distinct clusters. The Treemix analysis showed that there was low gene flow among the natural populations. Demographic history inferences indicated show that three clusters of M. odoratissima experienced at least three bottlenecks and resulted in a decrease of effective population size. Our results suggest that three distinct evolutionary significant units should be set up to conserve this critically endangered species.
Estimates of susceptibility to inbreeding depression for total fitness are needed for predicting the cost of inbreeding and for use in population viability analyses, but no such valid estimates are available for any wild invertebrate population. I estimated the number of lethals equivalents for total fitness in recently wild-caught populations of Drosophila melanogaster using published data on the total fitness of homozygosity versus heterozygosity for each of the major chromosomes (the X, second, and third) under competitive conditions. As there are no data for the fitness effects of homozygosity for the small fourth chromosome which represents 1.0% of the euchromatic genome, this was accounted for by attributing the homozygosity for the three large chromosome to an inbreeding coefficient of 0.99 when computing lethal equivalents for total fitness. Total genomic homozygosity is predicted to be essentially lethal in D. melanogaster. The corresponding haploid lethal equivalents estimate for total fitness was 5.04. The lethal equivalent value lies within the range for vertebrates but tends to be higher than for most outbreeding plants which are often purged as they exhibit up to 20% selfing (by definition). As D. melanogaster has its genome sequenced and annotated and has lethal equivalent estimates for total fitness for individual chromosomes as well as its total genome, it provides an excellent opportunity for evaluating genomic estimates of mutation load.
The main aim of ex situ programmes in conservation is to provide a suitable source of individuals for future reintroductions or reinforcement of existing populations. A fundamental prerequisite is creating and maintaining healthy and sustainable captive populations that show high levels of phenotypic and genetic similarity to their wild counterparts. The Eurasian lynx (Lynx lynx) is a model of a locally extinct species that has been subject to long-term captive breeding and of past and ongoing reintroduction efforts. To test for genetic suitability of ex situ population, a comparative genetic evaluation including in situ populations was undertaken. The assignment analysis of 97 captive lynx from 45 European zoos, wildlife parks and private breeds was performed using 124 lynx from different wild Eurasian populations belonging to three evolutionary lineages: the Carpathian, the Northern, and the Siberian lynx. The results showed a high proportion of Siberian lynx (51%) in the European captive lynx population. Remaining captive animals were assigned to either the Carpathian (28%), or the Northern lynx lineage (13%). Admixture between lineages was rather low (8%). Notably, no or very low difference in genetic diversity was detected between the wild and captive lynx populations. Our results support the potential of the captive population to provide genetically suitable individuals for genetic rescue programmes. The transfer of genes between isolated populations, including those in captivity, should become an important management tool to preserve genetic variability and prevent inbreeding depression in native and reintroduced populations of this iconic predator.
Sky island species face climate-driven and anthropogenic habitat loss and population fragmentation, and are therefore vulnerable to genetic erosion. We conducted a genetic study of the cryptic and threatened alpine she-oak skink (Cyclodomorphus praealtus) throughout its range, across two regions of the mainland Australian Alps; an extensive high elevation plateau in the north (‘Kosciuszko Plateau’) and several smaller plateaus in the south (‘southern plateaus’). We investigated whether extensive potential habitat across Kosciuszko Plateau supported larger, connected populations with better genetic health than more fragmented southern plateaus. Our analyses of genome-wide markers confirmed effective isolation of the two regions. We identified three populations from the southern plateaus, largely aligning with discrete landforms, and four populations on Kosciuszko Plateau. Only one individual, from the southern-most population, showed evidence of admixture between the two regions. Across its range, C. praealtus populations had low genetic diversity and small effective population sizes. In contrast to our expectations, Kosciuszko Plateau populations were smaller, with greater genetic differentiation and a higher degree of inbreeding than the southern populations. We detected admixture between populations on Kosciuszko Plateau, while the southern plateaus had limited admixture. We found no evidence of local adaptation, suggesting plateaus represent interglacial refugia. Our results suggest that C. praealtus has little capacity to withstand further disturbance or rapid environmental changes. Maintaining or restoring habitat quality in occupied and suitable connecting habitats across the species’ range is paramount. ‘Genetic rescue’ should be investigated as an option to mitigate the effects of isolation and improve population resilience.
There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures.
The online version contains supplementary material available at 10.1007/s10592-022-01483-1.
The maintenance of genetic variation is crucial at the margins of a species’ distribution range where plants grow in a suboptimal environment and often put less effort into sexual recruitment. The main focus of this study was on exploring the variation in genetic patterns and plant fitness of the long-lived clonal legume Trifolium alpestre in marginal populations in comparison to the distribution centre with the purpose to plan adequate conservation actions for this species. We used highly variable microsatellite loci to explore genetic patterns in 16 populations of varied size in Trifolium alpestre at the different parts of its range (marginal/central populations in Estonia, Poland and Czechia) of this species. We also studied overall genetic structure and population divergence, and historical and contemporary gene flow within each region. To estimate the potential for sexual reproduction at the marginal and central area, we measured the amount and weight of seeds produced in Estonian and Czech populations. Our study revealed high HE and AR in all studied populations that were unconnected with population size, and the occurrence of unique alleles both in central as well as in marginal northernmost (Estonian) populations. Overall genetic structure reflected the geographical location of populations. Very weak population structure together with high historical migration at the distribution margin imply a past, more continuous occurrence of T. alpestre in the northernmost region. Recent bottlenecks, lowered seed production and lighter seeds in marginal populations point to the local suboptimal conditions and indicate the need to pay more attention to management to prevent loss of genotypes and maintain diverse populations in this region.
Globally, wildlife populations are becoming increasingly small and isolated. Both processes contribute to an elevated risk of extinction, notably due to genetic factors related to inbreeding depression and a loss of adaptive potential. Wildlife translocation is a valuable conservation tool to reintroduce species to previously occupied areas, or augment existing populations with genetically divergent animals, thereby improving the viability of endangered populations. However, understanding the genetic implications of mixing gene pools is key to avoid the risk of outbreeding depression, and to maximise translocation effectiveness. In this study we used mitochondrial and microsatellite DNA collected from 110 black rhinoceroses (Diceros bicornis minor) in Kruger National Park, South Africa, to determine levels of genetic diversity, inbreeding and relatedness. We compared this diversity with the two source populations (KwaZulu-Natal, South Africa and Zambezi River, Zimbabwe) using data from previously published studies, and assessed changes in the relative contribution of source lineages since their reintroduction in the 1970s. Our results show that Kruger’s black rhinoceroses are genetically more diverse than those from KwaZulu-Natal, with levels closer to those from the Zambezi Valley. Furthermore, our findings indicate a relative increase in the Zimbabwean lineage since reintroduction, suggesting a possible selective advantage. From a conservation perspective, our results demonstrate the benefits of mixing multiple source populations to restore gene flow, improve genetic diversity and thereby help protect small, isolated populations from extinction.
Historic and contemporary data can shed light on a species’ conservation status and work together to address two main goals in conservation biology: (1) identifying species under extinction risk and (2) the forces shaping this process. Museomics is the study of historical DNA acquired from museum specimens that allows researchers to answer myriad questions across many taxa. Museomics is an effective way to understand how populations have been affected by human and climate factors from a historic perspective. Here, our goal is to investigate changes in wild populations of two small carpenter bee species (Ceratina calcarata and C. dupla) across a 50-year time span. We sampled museum specimens and recent collections to determine their genetic diversity, population structure, effective population size, signatures of selection, and local adaptation. Both species displayed reduced genetic diversity and effective population size through time. We identified signatures of adaptation in both species across human-altered land use and climate change scenarios. We found signatures of selection in genes related to biochemical defense, insecticide, and thermal tolerance, which are consistent with the observed increase in agricultural land use development and rising temperatures over the past 50 years. Our findings suggest that these species are facing population inbreeding, possibly attributable to human land-use change and agrochemicals in their environment. Overall, this study highlights the use of museomics to understand species declines, threats to populations, and targets for remediation.
EX situ conservation management is an effective method that conserves endangered species that are on the decline owing to anthropogenic alteration of natural habitats. This entails the management of a captive population while maintaining its genetic variability and preventing its adaptation to the captive environment. However, implementation of such efforts is largely limited to experimental animals and zoo-managed animals with pedigree information. In this study, ex situ management of endangered Itasenpara bitterling (Acheilognathus longipinnis) was conducted, while practicing recommended conservation procedures, for the purpose of conserving this species. In this 11 year long study, we conducted multi-locus microsatellite DNA analyses to evaluate the genetic dynamics of an ex situ captive population of A. longipinnis, as well as the wild A. longipinnis population of the Kiso River. Genetic diversity generally varied between yearly cohorts in each of the captive sub-populations, and some showed a stable increasing trend with generations. When all sub-populations were considered as one population, genetic diversity was maintained at a high value, while effective population size generally reached target values, thereby preventing inbreeding. These results were achieved by maintaining multiple captive sub-populations and exchanging individuals between them. Simultaneously, the introduction of additional individuals from the wild population produced genetic variability in the captive population. These fluctuating patterns of genetic diversity in the captive A. longipinnis population were desirable compared to previously predicted values. Consequently, these findings show that the current ex situ conservation program is suitable for maintaining the genetic composition of the captive population of A. longipinnis.
The negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.
Conservation genetics is a relatively new discipline, and yet has rapidly evolved in the last decade with massive advances in sequencing technologies. Here, we review the newest edition of an influential textbook in the field, “Conservation and the Genomics of Populations”, which seeks to bridge the transition from population genetics to genomics and its application to conservation management. This textbook—complete with 24 chapters (one completely new), 25 guest boxes, and two new authors over the previous edition—navigates the rich and sometimes complex history of conservation and population genetics, while also providing a comprehensive catalog of how genomics broadens our understanding of diversity in a changing world. Despite some sections requiring an advanced understanding of population genetic theory, we foresee this text being used as a reference for conservation geneticists and for teaching upper level undergraduate or graduate students. While we anticipate the field of conservation genetics will continue to rapidly advance with new technologies, this textbook provides a strong foundation of population genetics, while also celebrating the new horizon of genomics for conservation management.
Genetic diversity of organisms is an indicator of their long-term survival and can potentially be shaped by the extent of geneflow between populations. Geographical features and anthropogenic interferences can both obstruct and also facilitate animal movement, directly or indirectly. Such patterns have not been extensively studied across grasslands in the Indian subcontinent which is a mosaic of both natural and man-made topography. This study looks at genetic variation in an endemic ungulate, the Antilope cervicapra or blackbuck, throughout its distribution range. Using mitochondrial and nuclear (microsatellite) information, we find that different markers shed light on different aspects of their evolutionary history. Absence of robust geographical clustering in mitochondrial DNA indicate recent isolation in these populations, while lack of shared haplotypes between sampling locations suggests female philopatry. Nuclear data shows the presence of three genetic clusters in this species, pertaining to the Northern, Southern and Eastern regions of India. Our study also shows that an ancestral stock separated into two groups that gave rise to the North and South clusters and the East population was derived from the South at a later time period. Both microsatellite and mitochondrial data indicate that the population from the Eastern part of India is genetically distinct and the species as a whole shows signatures of having undergone recent genetic expansion. In spite of immense losses in grassland habitats across India, blackbucks seem to have well-adapted to human altered landscapes and their numbers are beginning to show an upward trend.
Knowledge of the magnitude and geographic patterns of genetic diversity is instrumental for recovery of endangered tree species whose persistence is limited by genetic variation. One such species is American chestnut (Castanea dentata), which has experienced a dramatic reduction in population size in North America in association with the spread of the parasitic fungus, Cryphonectria parasitica, causing chestnut blight. To examine the impact of the bottleneck and role of genetic diversity on population dynamics and recovery, we conducted a population genetic assessment of native American chestnut populations in the understudied northern range in Canada and along a transect towards the center of the U.S. range. Leaf tissue from 13 natural populations in Canada (N = 7) and northern U.S. (N = 6) were genetically characterized using 16 microsatellite loci and compared to a sample of reference Castanea species. Genetic diversity and population structure were assessed within and among populations to determine population connectivity and the presence of admixture with other Castanea spp. Populations throughout the range displayed high genetic diversity and significant inbreeding, with no significant difference in diversity between those at the center and edge of the range. We found evidence of infrequent interspecific hybridization in some Canadian populations but no relationship between admixture and tree health, assessed in a previous demographic survey. Unexpectedly, Canadian populations clustered separately from U.S. populations. American chestnut appears to have retained substantial genetic diversity following the population bottleneck, which is at odds with the limited incidence of blight resistance/tolerance in extant populations.
Narrowly endemic species are particularly vulnerable to catastrophic events. Compared to widespread species, they may also be less capable of adapting to shifts in environmental pressures as a result of specialisation on a narrow range of local condition and limited ability to disperse. However, life-history traits, such as preferential outcrossing and high fecundity can maintain genetic diversity and evolutionary potential, and boost species resilience. The endangered Grevillea bedggoodiana (Enfield Grevillea) is an understorey shrub restricted to an area of ca. 150 km 2 in southeastern Australia with a legacy of large-scale anthropogenic disturbance. Prior to this study little was known about its biology and population structure. Here, its breeding system was assessed through a controlled pollination experiment at one of its central populations, and eight populations were sampled for genetic analysis with microsatellite markers. The species was found to be preferentially out-crossing, with no evidence of pollination limitation. In most populations, allelic richness, observed heterozygosity and gene diversity were high (Ar: 3.8-6.3; H o : 0.45-0.65, H e : 0.60 − 0.75). However, the inbreeding coefficients were significant in at least four populations, ranging from F i-0.061 to 0.259 despite high outcrossing rates. Estimated reproductive rates varied among sampled populations but were independent of gene diversity and inbreeding. Despite its small geographic range, the species' populations showed moderate differentiation (AMOVA: F ST = 0.123), which was largely attributable to isolation by distance. We interpret these results as suggesting that G. bedggoodiana is reproductively healthy and has maintained high levels of genetic diversity despite recent disturbance.
Assessments of genetic diversity for imperiled species can provide a baseline for determining the relative impacts of contemporary anthropogenic threats (e.g., habitat fragmentation) on population connectivity and identify historical factors contributing to population structure. We conducted a population genetics and phylogeographic assessment of the imperiled Pristine Crayfish (Cambarus pristinus) sampled throughout its range encompassing two morphologically distinct forms. Pristine Crayfish exhibit a disjunct distribution throughout lower order tributaries suggesting they are headwater-adapted species. The two morphologically distinct forms of the Pristine Crayfish are found in the upper Caney Fork (nominal Caney Fork form) and the Big Brush Creek and Cane Creek systems (Sequatchie form). We used 19 microsatellite loci and the cytochrome oxidase subunit I (COI) gene to assess population connectivity and genetic diversity of the Pristine Crayfish. Haplotypes recovered from the COI gene revealed that historic connectivity was maintained within each form of the Pristine Crayfish. However, the divergence between forms was higher (2.3%) than within forms (< 2.0%), suggesting each form is on an independent evolutionary trajectory, supporting recognition of the Sequatchie form as a distinct taxon. Microsatellite analyses for the Caney Fork form recovered a high degree of population isolation and support for six genetically isolated population. In addition, genetic diversity metrics per population and for the Caney Fork form were low suggesting that the Caney Fork form is at an increased risk of extinction under anthropogenic disturbances. We suggest that each form receive continued listing protection and conservation resources and that the Sequatchie form be treated as a unique taxon.
Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus , and the endemic Irish hare, L. timidus hibernicus . Roadkill hares ( n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin ( Tf ) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus . Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus , 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus ). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus ). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
Identifying units for appropriate management and conservation of rare species is an important and challenging process, and population genetics can inform this decision making. Using Phlox hirsuta, a rare species restricted to serpentine soils in Northern California and with a geographic range of less than 15 km, we examined genetic variation within and among populations, using tunable Genotyping-by-Sequencing (tGBS) to generate single nucleotide polymorphisms (SNPs) as well as 11 microsatellite loci, to identify population structure, patterns of migration and selection, and units for conservation. Multiple methods recognized three geographically structured population clusters. The species has undergone a recent genetic bottleneck, and the increase in population size may be influenced by the changing climate. Patterns of gene flow are greater from south to north than in the opposite direction. Some of the genes under selection are putatively involved in adaptation to edaphic conditions, and genes under selection differ among the populations. Four population units were identified as suitable for conservation purposes based on various partitions of the SNPs.
Within-species, biodiversity can be organized in units, ranging from subspecies to evolutionarily significant units (ESUs), populations and social groups. To define ESUs, researchers often focus on the concordant distribution of traits that exhibit likely adaptive significance, including genetic and ecological variation. Caribou is a Species at Risk in Canada, and are conserved at the level of both subspecies and designatable units (DUs), which are conceptually similar to ESUs. However, the use of genomics has been suggested to provide better delineation of units that are based upon variation of genes—not just neutral genetic markers. Here, we analyzed single nucleotide polymorphisms (SNPs) for 190 caribou belonging to two recognized subspecies and four DUs found throughout western Canada. We confirmed two major genetic clusters, which we refer to as the Northern Caribou and Southern Caribou, characterized by divergence at numerous SNPs and genes with known functions in other mammals. Notably, the distribution of these two clusters did not fully overlap with currently recognized subspecies. A discrepancy with current classification was detected for Mountain DUs, which were thought to belong to the Woodland subspecies, but with significant northern-type ecological traits described in the literature, indicating more work is needed to refine our understanding of this transitional zone. We also detected genetic signals of male-biased dispersal, which may be natural or affected by habitat fragmentation effects on females. This work illustrates the value of genomics in rethinking subspecies and conservation unit designations and better conserve biodiversity within terrestrial species at risk.
Restoring levels of genetic diversity in small and declining populations is increasingly being considered in biodiversity conservation. Evidence-based genetic management requires assessment of risks and benefits of crossing populations. Because risks are challenging to assess experimentally, e.g. through multi-generational crosses, decision-support approaches utilize proxy risk factors such as time since separation of lineages. However, the paucity of empirical datasets on fitness consequences of longer separation times tends to favour crossing lineages with conservatively short separations, restricting wildlife managers’ options. Here, we assessed the genetic outcomes of interbreeding in the wild between lineages of a threatened Australian freshwater fish (Macquarie perch) separated by an estimated 119,000–385,000 years of evolution in distinct environments. Fish belonging to the Murray-Darling Basin (MDB) lineage escaped from Cataract Dam—into which they were translocated in ~ 1915—into the Cataract River, where they interbred with the local Hawkesbury-Nepean Basin (HNB) lineage. Analyses of reduced-representation genomic data revealed no evidence of genetic incompatibilities during interbreeding of the two lineages in the Cataract River: assignment to genotypic clusters indicated a spectrum of hybrid types including second generation hybrids and backcrosses to both parental lineages. Thus, no adverse effects were detected from genetic mixing of populations separated by > 100,000 years. We are not advocating purposely crossing the two lineages for management purposes under present cost–benefit considerations, because there are currently sufficient intra-lineage source populations to beneficially mix. Instead, this study presents a useful calibration point: two morphologically different lineages evolved in different habitats for 119,000–385,000 years can successfully interbreed.
Surveying and quantifying the bushmeat crisis in Africa requires up-front, reliable species-level identification. We conducted a comprehensive survey of 31 trading places where bushmeat are sold in Côte d’Ivoire (West Africa) and two seizures from Europe, using a multi-gene DNA-typing approach and a dedicated species-assignment pipeline (DNAbushmeat). We identified 47 wild and five domestic species-level taxa from 348 collected carcasses, including mammals (15 Cetartiodactyla, 10 Rodentia, seven Carnivora, seven Primates, two Pholidota, two Lagomorpha, one Hyracoidea, one Chiroptera), reptiles (two Squamata), birds (one Bucerotiformes, one Galliformes, one Otidiformes) and fish (one Perciformes). Our DNA-based approach allowed the detection of two separate lineages of red-flanked duikers (Cephalophus rufilatus), a yet unreferenced cane rat (but possibly Thryonomys gregorianus) and two cryptic species of Gambian rat (Cricetomys). We also observed important levels of intraspecific diversity in several mammals and squamates, suggesting additional cryptic diversity within bushmeat species from Côte d’Ivoire. More than half of the bushmeat carcasses were inaccurately identified, with European customs peaking at 100% inaccuracy. Our study also explored the use of diversity indices among bushmeat markets to identify ‘hotspot’ market places where biodiversity would be the most impacted. Overall, 12 protected species (including pangolins, crocodiles, primates and antelopes) were impacted by the bushmeat trade in Côte d’Ivoire, indicating weak law enforcement related to game protection. We suggest that the recognition of the bushmeat sector by the state and its DNA-based surveillance is necessary to reach a sustainable management of the bushmeat trade in Côte d’Ivoire.
Despite the global crisis facing migratory benthic fishes, conservation genetic knowledge of these species remains scarce. In this study, we conducted a population genetic analysis using seven microsatellite loci to obtain basic information for determining conservation units and priorities of Cottus hangiongensis in Shiretoko, a mountainous peninsula where sculpin habitats are thought to be in decline throughout the region. The genetic structure was clearly divided between west and east coastal populations, and there was little recent migration between them. The western populations, which are closer to the center of the species’ range, had significantly higher genetic diversity than the eastern populations. However, a bottleneck analysis and the inference of demographic history using approximate Bayesian computation showed that only the west group had experienced a significant recent bottleneck, probably due to recent habitat losses. These results suggest that the western and eastern populations should be different conservation units and that the western populations should be prioritized for conservation despite their high genetic diversity. This study contributes to the conservation genetics of diadromous sculpin and reiterates the importance of analyzing not only the current levels but also temporal changes in assessing genetic diversity.
Rafflesia species (Rafflesiaceae) are among the flagship plants of South-East Asian countries in which they occur. Three species of Rafflesia, i.e. Rafflesia patma, R. rochussenii, and R. zollingeriana, are known from Java, Indonesia. All three species are threatened with extinction due to human activities that cause habitat loss and fragmentation. Conservation efforts such as determining conservation units for prioritization of those species have been difficult due to the lack of data on their population genetics. Availability of genetic information is important to develop appropriate conservation measures. Our study evaluates genetic diversity and structure of the three Rafflesia species using a total of 166 samples across the island. We used single nucleotide polymorphism (SNP) markers obtained via MIG-seq. The three species of Rafflesia in Java bear much lower genetic diversity compared to what was previously shown for R. speciosa and R. lagascae on Borneo, the Philippines and the Malayan Peninsula. Low genetic diversity within the Javanese Rafflesia species, particularly in R. patma and R. zollingeriana, is attributed to bottleneck events and population expansion in the past. We also provide evidence of clonality and existence of different genotypes within Tetrastigma host plants in two species of Rafflesia. Scattered and fragmented populations as reconstructed in the genetic structure analyses are important to be considered in designing appropriate conservation strategies. Furthermore, we demonstrate how the establishment of Rafflesia ex-situ collections can conserve genetic diversity that may no longer be present in nature and could be used in future reintroduction programs.
Understanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy ( Acanthocladium dockeri ) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and 'Critically Endangered' Kemp's ridley (L. kempii). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp's (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management.
The online version contains supplementary material available at 10.1007/s10592-022-01465-3.
In the present context of the ramping up of the global biodiversity crisis, improving our understanding on the genetic and biogeographic patterns of ill-known taxa is central to conservation planning. This is especially relevant for geographically isolated populations that suffer from little or no gene flow and an increased extinction risk. The few studies available on the molecular phylogeny and phylogeographic diversity of Frigatebirds have only focused on populations of three species, Fregata magnificens, F. andrewsi from Christmas Islands and F. minor in the Galapagos. To improve our knowledge on these tropical seabirds, our study aimed at assessing worldwide phylogeographic patterns and relationships among all five extant species of the genus Fregata. To accomplish it, we sampled museum specimens corresponding to 18 frigatebird populations spatially distributed by Brazil, Mexico, Ascension Islands, Cabo Verde and the Indo-Pacific region, and fresh samples from Cabo Verde, and amplified them for a mtDNA cytochrome b fragment. We complemented our dataset with previously available data representing a total of 36 populations in this study. Similar to the well-known endemic populations of the Galapagos and Christmas Island, the isolated ultraperipheral populations in the Atlantic were shown to be genetically divergent from their main populations for the three widespread species, F. magnificens, F. ariel and F. minor. We provide the first genetic data for F. ariel, whilst building upon the existing knowledge of the genetic patterns of F. magnificens, F. aquila and F. minor. Furthermore, our molecular data comes in support of most but not all the morphologically recognized frigatebird subspecies. This study provides important genetic insights into the evolutionary history of the genus Fregata and acts as a baseline for future molecular work and conservation efforts.
European (Anguilla anguilla) and American eel (A. rostrata) are panmictic catadromous fish species, which have experienced recent drastic population declines amounting to just a few percent recruitment relative to levels prior to 1980. However, little is known about the extent of recent population declines relative to historical fluctuations. We analyzed demographic histories of the species using a method for reconstructing skyline plots based on site frequency spectra, in this case derived from restriction site-associated DNA (RAD) markers. The results showed very high effective population sizes ranging in the millions for most of the time span covered. Both species experienced ancient declines coinciding with the time of speciation (ca. 170,000 generations ago) and at a later stage where secondary contact occurred (ca. 90,000 generations ago). Whereas the demographic histories of the species were similar most of the time, they followed widely different trajectories from ca. 70,000 to 40,000 generations ago. However, for the past ca. 30,000 generations both species have shown demographic stability, even across glacial and interglacial periods. We discussed the possible environmental factors, including ocean current changes and geomagnetism reversal that could have affected demographic history and further suggest that southward displacement of spawning regions and continental distribution could explain the apparent stability even during glaciations. The recent declines appear unprecedented against a backdrop of long-term demographic stability, underpinning concerns that low density of spawners in the huge spawning region could lead to detrimental Allee Effects.
Invasive species prevention involves avoiding two aspects: introduction and secondary spread. The latter is essential in places that can become hubs for spreading invasive species. Lake Biwa, the largest lake in Japan, is an important area for biodiversity and fisheries. However, several invasive fish and crustaceans were established in the lake last century. One of the conservation problems in the Lake Biwa region is the unresolved suspicion that the native freshwater shrimp Neocaridina denticulata have been replaced with alien Neocaridina species. To verify whether exotic species have replaced the native Neocaridina population in this region, we estimated the population structure of Neocaridina spp., collected from 19 sites in and around Lake Biwa, based on genome-wide SNPs and mitochondrial DNA. The three detected genetic clusters were characterized by quantitative analysis of multiple morphological traits. Two clusters were identified as non-native N. davidi and the other as native N. denticulata. However, species discrimination based solely on morphological analysis was difficult, highlighting the importance of genetic analysis. We rediscovered the native populations in the region for the first time in a century; however, in 11 sites, the invasive species were dominant. These findings suggest that the native populations are in a critical situation. Furthermore, fishery resource stocking throughout Japan from Lake Biwa can cause the secondary spread of the invasive shrimps from the lake, acting as a hub, to other parts of the country.
India led the global tiger conservation initiatives and has doubled its wild tiger population to 2967 (2603–3346) since 2006. As the extant habitats are shrinking continuously, the persistence of these growing populations can only be ensured through focused landscape-scale conservation planning across all the existing tiger landscapes of Indian. We used intensive field-sampling, genetic analyses and GIS modelling to investigate tiger population structure, source-recipient dynamics and functionality of the existing corridors across the Indian part of Terai-Arc landscape (TAL). Using a 13 microsatellite marker panel we identified 219 individual tigers across Indian TAL. Further genetic analyses revealed three weakly, but significantly differentiated tiger subpopulations, termed as ‘Tiger Genetic Blocks (TGBs)’. Genetic migrant detection and gene flow analyses distinguished seven source and 10 recipient areas within this landscape. Circuitscape analyses ascertained total 19 (10 high, three medium and six low conductance) corridors across this landscape, of which 10 require immediate conservation attention. Overall, the tiger populations residing in the western, central and eastern TAL still maintain functional connectivity through these corridors. We suggest urgent management plan involving habitat recovery and protection of ~ 2700 sq. km. identified area to establish landscape connectivity. Further, mitigation measures associated with ongoing linear infrastructure developments and transboundary coordination with Nepal will ensure habitat and genetic connectivity and long-term sustainability of tigers in this globally important landscape.
Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout (Oncorhynchus clarkii) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity
between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.
Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
Biological invasions can pose a severe threat to coastal ecosystems, but are difficult to track due to inaccurate species identifications and cryptic diversity. Here, we clarified the cryptic diversity and introduction history of the marine amphipod Ampithoe valida by sequencing a mtDNA locus from 683 individuals and genotyping 10,295 single-nucleotide polymorphisms (SNPs) for 349 individuals from Japan, North America and Argentina. The species complex consists of three cryptic lineages: two native Pacific and one native Atlantic mitochondrial lineage. It is likely that the complex originated in the North Pacific and dispersed to the north Atlantic via a trans-arctic exchange approximately 3 MYA. Non-native A. valida in Argentina have both Atlantic mitochondrial and nuclear genotypes, strongly indicating an introduction from eastern North America. In two eastern Pacific estuaries, San Francisco Bay and Humboldt Bay, California, genetic data indicate human-mediated hybridization of Atlantic and Pacific sources, and possible adaptive introgression of mitochondrial loci, nuclear loci, or both. The San Francisco Bay hybrid population periodically undergoes population outbreaks and profoundly damages eelgrass Zostera marina thalli via direct consumption, and these ecological impacts have not been documented elsewhere. We speculate that novel combinations of Atlantic and Pacific lineages could play a role in A. valida’s unique ecology in San Francisco Bay. Our results reinforce the notion that we can over-estimate the number of non-native invasions when there is cryptic native structure. Moreover, inference of demographic and evolutionary history from mitochondrial loci may be misleading without simultaneous survey of the nuclear genome.
The adoption of measures to protect the viability of threatened populations should be supported by empirical data identifying appropriate conservation units and management strategies. The global population of the majorera limpet, P. candei candei d’Orbigny, 1840, is restricted to the Macaronesian islands in the NE Atlantic, including near-to-extinct and healthy populations in Fuerteventura and Selvagens, respectively. The taxonomic position, genetic diversity and intra- and interspecifc relationships of these populations are unclear, which is hindering the implementation of a recovery plan for the overexploited majorera limpet on Fuerteventura. In this study, ddRAD-based genome scanning was used to overcome the limitations of mitochondrial DNA-based analysis. As a result, P. candei candei was genetically diferentiated from the closely related P. candei crenata for the first time. Moreover, genetic diferentiation was detected between P. candei candei samples from Selvagens and Fuerteventura, indicating that translocations from the healthy Selvagens source population are inadvisable. In conclusion, the majorera limpet requires population-specifc management focused on the preservation of exceptional genetic diversity with which to face future environmental challenges.
The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei ) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions. To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.
Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse ( Reithrodontomys raviventris ), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.
Few studies have evaluated the genetic status of medicinal plants exposed to commercial harvesting. Here, we examine the genetic variability of Pilocarpus microphyllus, an endemic and threatened medicinal plant species from the eastern Amazon, across its largest remaining wild population. Popularly known as jaborandi, species of Pilocarpus genus are the unique known natural source of pilocarpine, an alkaloid used to treat glaucoma and xerostomia. However, Populations of P. microphyllus has experienced a severe decline in the last decades. Using RAD sequencing, we identified a total of 5,266 neutral and independent SNPs in 277 individuals collected from the Carajás National Forest (CNF). We quantified genetic diversity and gene flow patterns and estimated the minimum number of individuals necessary to establish a germplasm bank. Our results revealed high genetic diversity and four spatially distinct clusters of P. microphyllus with substantial admixture among them. Geographic distance and temperature dissimilarity were the factors that best explained the relatedness patterns among individuals. Additionally, our findings indicate that at least 40 matrices sampled randomly from each population would be required to conserve genetic diversity in the long term. In short, P. microphyllus showed high levels of genetic diversity and an effective population size (NE) sufficient to reduce the likelihood of extinction due to inbreeding depression. Our results indicate that diversity has been maintained despite the continuous harvesting of raw leaf material in the area over recent decades. Finally, the results provide information essential for the design of a germplasm bank to protect the endangered medicinal plant species.
Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander (Gyrinophilus subterraneus), estimated the population trend from historic and current survey data, and assessed the current potential for water quality threats to the cave habitat. Our genomic data (mtDNA sequence and ddRADseq-derived SNPs) reveal two, distinct evolutionary lineages within General Davis Cave corresponding to G. subterraneus and its widely distributed sister species, Gyrinophilus porphyriticus, that are also differentiable based on morphological traits. Genomic models of evolutionary history strongly support asymmetric and continuous gene flow between the two lineages, and hybrid classification analyses identify only parental and first generation cross (F1) progeny. Collectively, these results point to a rare case of sympatric speciation occurring within the cave, leading to strong support for continuing to recognize G. subterraneus as a distinct and unique species. Due to its specialized habitat requirements, the complete distribution of G. subterraneus is unresolved, but using survey data in its type locality (and currently the only known occupied site), we find that the population within General Davis Cave has possibly declined over the last 45 years. Finally, our measures of cave and surface stream water quality did not reveal evidence of water quality impairment and provide important baselines for future monitoring. In addition, our unexpected finding of a hybrid zone and partial reproductive isolation between G. subterraneus and G. porphyriticus warrants further attention to better understand the evolutionary and conservation implications of occasional hybridization between the species.
Eighty nine (42%) of Canada’s 215 freshwater fish species have been assessed as at risk by the Committee on the Status of Endangered Wildlife in Canada. This study examines genomic population structure of the at-risk Grass Pickerel (Esox americanus vermiculatus), a small (≤ 33 cm) predatory fish that in Canada has a range spanning approximately 114,000 km² of southern Ontario. Within this range it occupies approximately ten sites that are mostly shallow, weedy, and slow-flowing. Its populations and habitat are declining. This study defines population clusters and quantifies genomic diversity within and between populations based on > 5500 loci and > 950 SNPs from genomes of 66 individuals representing the subspecies’ entire Canadian range. Ordination and STRUCTURE analyses revealed four major geographic/genomic clusters centered in the Georgian Bay-Severn River, southeastern shore of Lake Huron, Niagara Peninsula, and upper St. Lawrence River. Major clusters were distinguished by relatively high Hudson Fst values (0.205–0.480), with Georgian Bay-Severn River being consistently most distinct. The Niagara Peninsula major cluster contained an additional three discernable sub-clusters differentiated by Fst values as great or greater than major clusters, despite spanning only ca. 200 km². Genomically distinct Niagara sub-clusters occurred in Abino Drain, Big Forks Creek, and Tea Creek. Samples from sites between both major and minor clusters exhibited admixture from adjacent clusters. Despite current management of Grass Pickerel under a single designatable unit throughout its Canadian range, we map considerable geographic population structure that should help guide the designation of additional conservation units.
Comparative population genetic studies of closely related taxa provide a powerful framework for evaluating if and to what degree a species of conservation concern has been negatively impacted by factors such as habitat fragmentation, decreased population connectivity, inbreeding and genetic drift. In this study, we take advantage of a paired sampling strategy to compare the population genetics of the geographically restricted, federally threatened Cheat Mountain salamander (Plethodon nettingi) to those of its partially sympatric, but much more widely distributed congener, the red-backed salamander (P. cinereus), where the two species overlap in the Appalachian mountains of West Virginia. Mitochondrial DNA haplotype and nucleotide diversity were lower in P. nettingi, as were a variety of metrics of nuclear genetic diversity estimated from microsatellite data. Population differentiation and structuring were greater in P. nettingi, suggesting reduced gene flow following fragmentation. Significant inbreeding and evidence of recent population bottlenecks were also seen in P. nettingi and estimated population sizes were smaller. Estimates of contemporary gene flow, as measured through kinship, also showed more restricted gene flow in P. nettingi. Overall, our comparative study provides strong evidence that the small and highly fragmented nature of its geographic distribution has resulted in a suite of negative genetic consequences for the federally threatened Cheat Mountain salamander. Management efforts aimed at enhancing the genetic health and long-term viability of this species should focus on increasing population connectivity through establishment of forest habitat corridors where possible and exploring the potential merits of translocations.
Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.
Cerrado is one of the largest biomes in Brazil and has undergone constant changes in its landscape over the years. Modifications driven by the expansion of agriculture and uncontrolled deforestation endanger the permanence of several species in the territory. Ecological imbalances demand the application of methodologies that seek the conservation of species, however, conflicts between theoretical expectations and empirical observations have suggested the need for studies that carefully assess the impacts of fragmentation on different species. In this study, we investigated the impact of changes in the seed and pollen dispersal of an isolated population of Caryocar brasiliense Camb. through in silico analyzes, in order to evaluate their impact on genetic variability of populations. We simulated different scenarios with changes in seed dispersal and pollination patterns in an isolated population. Populations with well preserved pollinators had lower rates of inbreeding and maintained greater genetic diversity over time, even in the absence of the seed disperser. In contrast, in scenarios with reduction of pollen dispersal distance or pollination efficiency, populations had an increase in inbreeding and in extinction probability, and reduction in genetic diversity over time. Small areas of conservation of C. brasiliense can harbor viable populations only if pollination service is maintained, so conservation strategies must consider both tree and pollinator protection.