Retention Of Genetic Diversity Research Articles

Development of genetic markers for reproductive management of toucans.

Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.

Management of diversity and inbreeding when importing new stock into an inbred population.

This article relates to breeding programs that seek to manage genetic diversity. The method maximizes a multicomponent objective function, applicable across breeding scenarios. However, this paper focuses on breeding decisions following immigration of 10 unrelated individuals into a highly inbred simulated population (F ≈ 0.34). We use Optimal Contribution Selection to maximize retention of genetic diversity. However, some treatments add Coancestry Assortative Mating (CAM). This helps to avoid early dilution of immigrant genetic material, maximizing its ability to contribute to genetic diversity in the longer term. After 20 generations, this resulted in considerably increased genetic diversity, with mean coancestries 59% of what random pairing gave. To manage progeny inbreeding, common practice is to reject matings above an upper limit. As a suboptimal rules-based approach, this resulted in 26% decreased genetic diversity and 8% increased inbreeding in the long term, compared with random pairing. In contrast, including mean progeny inbreeding as a continuous variable in the overall objective function decreased final inbreeding by 37% compared with random pairing. Adding some emphasis on selection for a single trait resulted in a similar pattern of effects on coancestry and inbreeding, with 12% higher trait response under CAM. Results indicate the properties of alternative methods, but we encourage users to do their own investigations of particular scenarios, such as including inbreeding depression. Practical implementation of these methods is discussed: they have been widely adopted in domestic animal breeding and are highly flexible to accommodate a wide range of technical and logistical objectives and constraints.

Genetic Relationship Between Founders of a Threatened Freshwater Turtle in a Mexican Wildlife Management Unit. A Conservation Strategy

Management Units for Wildlife Conservation (UMAs according to its Spanish acronym), are used for the ex-situ reproduction of freshwater turtles. These areas, often administered by local communities, are dedicated to conservation and sustainable management. The critically endangered freshwater turtle Dermatemys mawii has been successfully reproduced in several UMAs; however, no genetic management plan has been developed to maintain offspring genetic variability. Therefore, this study aims to determine the kinship relationship and homozygosity through the loci index of founder individuals in three UMAs devoted to the reproduction of D. mawii for the establishment of breeding groups. We collected skin samples of D. mawii in 2017 from 117 founder individuals from three UMAs located in the state of Tabasco, southeast Mexico. Ten specific D. mawii microsatellite markers were used for genotyping the founder individuals. We estimated the pedigree relationship between founders and proposed the formation of three breeding groups to optimize the use of related and non-related individuals to meet UMA-specific objectives and evaluated the genetic diversity retention of the breeding groups. The breeding groups were integrated as follows: 1) conservation breeding group consisting of 16 unrelated females and 7 unrelated males that presented a lower level of homozygosity (< 0.4); 2) research breeding group consisting of 45 females and 16 males that were unrelated or presented a half-sibling relationship and with a medium level of homozygosity (<0.6); and 3) a sustainable breeding group comprising 29 females and 4 males that were not necessarily unrelated and with a high level of homozygosity (> 0.6). Genetic diversity retention (Ho, He) was highest for the conservation breeder group and research breeder group. UMAs can create 3 breeding groups with different objectives: 1) species conservation, 2) research, and 3) sustainable use of species. All breeding groups can retain genetic diversity. Our proposal can enrich conservation actions and sustainable use for D. mawii at both national and international levels, specifically within the Mesoamerican corridor.

Genetic viability and habitat suitability of the critically endangered southern muriqui (Brachyteles arachnoides) in the Atlantic Forest's fragmented landscapes under land use and climate change scenarios

The joint effects of climate change and landscape fragmentation to the genetic viability of isolated populations has barely been addressed for the Atlantic Forest fauna. Therefore, this work explored the potential habitat suitability for the southern muriqui (Brachyteles arachnoides), by modeling climate change, landscape fragmentation, and genetic diversity loss of the species. Maxent was used to model its potential distribution in 2050, with two climate change scenarios. A land use and land cover change model was applied to describe current and future forest fragmentation patterns, and a Population and Habitat Viability Analysis (PHVA) was used to describe the retention of genetic diversity of the southern muriqui. Although PHVA modeling provided a low risk of extinction of the southern muriqui, climate change and fragmentation could result in the loss of >65% of the suitable forest patches, and reduce the habitat suitability to only 11% of the potential distribution area, which could lead to future genetic diversity loss and decreased capacity of self-sustained populations. In both climate change scenarios, the suitable areas for the southern muriqui in Paraná and Rio de Janeiro states will decrease more drastically. Areas where the primate occurs in the interior of São Paulo and Rio de Janeiro states will disappear or be climatically disconnected from the core potential habitat. Alike preventing further deforestation, Atlantic Forest restoration actions are needed to connect the viable populations for compensating the projected land use and climate change impacts to the long term persistence of the southern muriqui.

Modelling Genetic Benefits and Financial Costs of Integrating Biobanking into the Captive Management of Koalas.

Simple SummaryManaged wildlife breeding faces high costs and genetic diversity challenges associated with caring for small populations. Biobanking (freezing of sex cells and tissues for use in assisted breeding) and associated reproductive technologies could help alleviate these issues in koala captive management by enhancing retention of genetic diversity in captive-bred animals and lowering program costs through reductions in the size of the required live captive colonies. Australia’s zoos and wildlife hospitals provide rare opportunities to refine and cost-effectively integrate these tools into conservation outcomes for koalas due to extensive already-existing infrastructure, technical expertise, and captive animals.Zoo and wildlife hospital networks are set to become a vital component of Australia’s contemporary efforts to conserve the iconic and imperiled koala (Phascolarctos cinereus). Managed breeding programs held across zoo-based networks typically face high economic costs and can be at risk of adverse genetic effects typical of unavoidably small captive colonies. Emerging evidence suggests that biobanking and associated assisted reproductive technologies could address these economic and genetic challenges. We present a modelled scenario, supported by detailed costings, where these technologies are optimized and could be integrated into conservation breeding programs of koalas across the established zoo and wildlife hospital network. Genetic and economic modelling comparing closed captive koala populations suggest that supplementing them with cryopreserved founder sperm using artificial insemination or intracytoplasmic sperm injection could substantially reduce inbreeding, lower the required colony sizes of conservation breeding programs, and greatly reduce program costs. Ambitious genetic retention targets (maintaining 90%, 95% and 99% of source population heterozygosity for 100 years) could be possible within realistic cost frameworks, with output koalas suited for wild release. Integrating biobanking into the zoo and wildlife hospital network presents a cost-effective and financially feasible model for the uptake of these tools due to the technical and research expertise, captive koala colonies, and ex situ facilities that already exist across these networks.

Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number.

The release of captive‐bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters Crassostrea virginica. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large‐scale hatchery‐based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long‐term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine‐scale genetic structure and local adaptation in broadcast‐spawning marine species and provide novel information for the management of an important fisheries resource.

One size does not fit all: Genetic considerations from the Missouri elk restoration

AbstractPopulation restoration is an inherently costly conservation practice typically reliant on animal translocations. There are many approaches to translocation and consideration is paid to understanding how various translocation models influence restoration success. Translocation strategies are often designed to meet site‐specific objectives, minimize cost, and maximize success. We investigated genetic diversity retention associated with the low‐founder, multi‐release, single admixed stock translocation model of the Missouri elk (Cervus canadensis) restoration in 2011–2013. We further estimated effective population size and projected future losses in genetic diversity if the restored Missouri elk herd is maintained at the population size objective with no immigration from neighboring states. We observed relatively high levels of genetic diversity retention as evidenced by minimal losses in allelic richness and expected heterozygosity. Our projections indicated 90% genetic diversity retention within the Missouri population for roughly 130 years. Where number of progeny or source stocks are limited by resource or disease considerations, use of a relatively low‐founder, single admixed source may enable retention of genetic variation, while minimizing costs.

Multiparental populations in line development: Genetic gain, diversity, and practical limitations

AbstractNew homozygous lines are usually developed from biparental crosses. To my knowledge, biparental and multiparental crosses have not been directly compared as breeding populations. My objective in this simulation study was to determine whether a set of several biparental populations or a single multiparental population is superior in terms of genetic gain and diversity of the best ensuing lines. Multiparental populations were simulated from p = 4, 6, and 8 parents and were compared with the corresponding p(p – 1)/2 biparental populations (i.e., diallel). Each of 250 quantitative trait loci had p alleles. Parental selection was mimicked via a Better Half model, wherein only the better crosses (e.g., four out of six with p = 4) were made. Genetic gains were equal between the Better Half model and the full diallel despite the larger population size with the latter. Current timelines for cultivar development in different species impose a limit on the number of generations available for creating multiparental populations, and the results indicated only a minimal (if any) increase in genetic gain when lines were developed from multiparental populations instead of biparental populations. The main benefit from multiparental populations was a better retention of genetic diversity among the selected lines. It remains to be seen whether this higher diversity among new lines from multiparental populations would lead to larger or more‐sustained gains in future lines.

A novel framework for evaluating in situ breeding management strategies in endangered populations.

Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.

Blanding's Turtle Demography and Population Viability

AbstractIn anticipation of U.S. federal status classification (warranted, warranted but precluded, not warranted), scheduled for 2023, we provide population viability analysis of the Blanding's turtle Emydoidea blandingii, a long-lived, late-maturing, semi-aquatic species of conservation concern throughout its range. We present demographic data from long-term study of a population in northeastern Illinois and use these data as the basis for viability and sensitivity analyses focused on parameter uncertainty and geographic parameter variation. We use population viability analysis to identify population sizes necessary to provide population resiliency to stochastic disturbance events and catastrophes, and demonstrate how alternative definitions of ‘foreseeable future' might affect status decisions. Demographic parameters within our focal population resulted in optimistic population projections (probability of extinction = 0% over 100 y) but results were less optimistic when catastrophes or uncertainty in parameter estimates were incorporated (probability of extinction = 3% and 16%, respectively). Uncertainty in estimates of age-specific mortality had the biggest impact on population viability analysis outcomes but uncertainty in other parameters (age of first reproduction, environmental variation in age-specific mortality, percent of females reproducing, clutch size) also contributed. Blanding's turtle demography varies geographically and incorporating this variation resulted in both mortality- and fecundity-related parameters affecting population viability analysis outcomes. Possibly, compensatory variation among demographic parameters allows for persistence across a wide range of parameter values. We found that extinction risk decreased and retention of genetic diversity increased rapidly with increasing initial population size. In the absence of catastrophes, demographic conservation goals could be met with a smaller initial population size than could genetic conservation goals; ≥20–50 adults were necessary for extinction risk <5%, whereas ≥50–110 adults were necessary to retain >95% of existing genetic diversity over 100 y. These thresholds shifted upward when catastrophes were included; ≥50–200 adults were necessary for extinction risk <5% and ≥110 to >200 adults were necessary to retain >95% of existing genetic diversity over 100 y. Impediments to Blanding's turtle conservation include an incomplete understanding of geographic covariation among demographic parameters, the large amount of effort necessary to estimate and monitor abundance, and uncertainty regarding the impacts of increasingly frequent extreme weather events.

Integrating biobanking minimises inbreeding and produces significant cost benefits for a threatened frog captive breeding programme

AbstractCaptive breeding is an integral part of global conservation efforts despite high costs and adverse genetic effects associated with unavoidably small population sizes. Supplementing captive‐bred populations with biobanked founder sperm to restore genetic diversity offers a solution to colony size, costs and inbreeding, yet is rarely done, partly due to a lack of concrete examples or awareness amongst the conservation community of the huge potential benefits. We present a model system of the cost and genetic benefits achieved by incorporating biobanking into captive breeding of Oregon spotted frogs (Rana pretiosa). Backcrossing with frozen sperm every generation resulted in very large reductions in required programme expenditure compared to traditional captive breeding. This model supports the view that integration of biobanking into captive breeding would make longstanding and previously unachievable genetic diversity retention targets feasible (90% source population heterozygosity for a minimum of 100 years) at much reduced costs. This study suggests that the credibility of captive breeding as a conservation strategy would be enhanced by integrating genome storage and assisted breeding to produce far larger numbers of animals of higher genetic quality. This innovation would justify increased public and agency support for captive breeding.

Wild at heart: Programs to diminish negative ecological and evolutionary effects of conservation hatcheries

Hatchery programs are critical for conservation and management of many imperiled fishes. Most traditional aquaculture programs negatively affect ecological performance, genetic, and phenotypic diversity of hatchery-origin fish compared with wild counterparts. Here, we synthesize outcomes of three conservation programs aimed at enhancing ‘wildness’. Each program focuses on a different species: lake sturgeon, razorback sucker, and Rio Grande silvery minnow. These species differ in key life history traits including size and age at sexual maturity, reproductive and migratory behavior, and habitat requirements. Threats to persistence of the focal taxa, however, exemplify common pressures experienced by freshwater fishes worldwide. Conservation hatchery programs for lake sturgeon, razorback sucker, and Rio Grande silvery minnow capitalize on natural spawning in the wild followed by collections of wild-fertilized eggs/larvae for hatchery rearing. Individuals are repatriated to the wild after rearing to body sizes less susceptible to mortality. Protocols include collections of eggs or larvae across the entire spawning period and at appropriate geographic scales to maximize retention of genetic diversity and, to increase the likelihood of preserving variation for heritable life history traits. Using direct and indirect evidence we show that hatchery programs that allow individuals to fulfill parts of the life-cycle in their native habitats can be conducted without compromising genetic diversity. Adoption of similar strategies in other imperiled fishes would improve understanding of species life history, and provide an incentive to protect native habitats so they may eventually support self-sustaining populations.

Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Abstract The objective of this study was to use pedigree analysis to evaluate the population structure and retention of genetic diversity in a flock of Muzaffarnagari sheep in India. Pedigrees of 5955 animals born between 1974 and 2003 was used to estimate the generation interval, pedigree completeness, and rate and level of inbreeding. Effective population size and parameters characterizing probabilities of gene origin were computed for lambs born between 2001 and 2003. The average numbers of equivalent complete generations were 3.41 and 5.00 for the whole and reference populations, respectively. The mean generation interval was 3.42 years. Average inbreeding coefficients for animals in the whole and reference populations were 1.79 and 1.23 %, respectively, and the rate of inbreeding was 0.68 % per generation. The average additive relationships for all animals and those in the reference population were 3.93 and 6.43 %, respectively. The realized effective population size, estimated from either the increase in coancestry between pairs of individuals or by regression of the average inbreeding coefficient on number of equivalent complete generations was approximately 76. Probabilities of gene origin were estimated by calculating effective numbers of founders (fe), ancestors (fa), founder genomes (fg), and non-founder genomes (fng) (33, 30, 15.4, and 28.9, respectively). The 10 most influential ancestors accounted for 50 % of the genetic variability, with a maximum individual contribution 6.53 %. The fe/fa ratio in the reference population was 1.10, indicating that occasional bottlenecks had occurred. Approximately 3.2 % of the initial heterozygosity had disappeared from the population. The results revealed that although there was some evidences of bottlenecks and genetic drift, considerable genetic variability remained in the population.

Establishing population boundaries and conservation proposals for Coleocephalocereus purpureus, a critically endangered cactus species microendemic from Caatinga biome

Coleocephalocereus purpureus (Buining & Brederoo) F. Ritter is a rare columnar cactus species endemic to four small habitat patches of a south-eastern caatinga inselberg elements located in Eastern Brazil. C. purpureus was listed as Critically Endangered by IUCN by habitat loss due to quarrying activities. Here, we used ten microsatellite markers to estimate genetic diversity and structure of C. purpureus populational groups to perform a remaining genetic diversity diagnosis and to define population boundaries. Our estimates of genetic diversity indicated that C. purpureus displayed moderated levels of genetic diversity, even though the species populational groups are small and fragmented. All genetic structuring approaches revealed that there is a clear differentiation in two populations isolated by the Jequitinhonha River, named here as South and North populations. The South population corresponds to a unique group placed in a disturbed non-protected area and the North population comprises three groups, including the admixtured and managed group placed in a Conservation Unit. As priority actions for the retention of genetic diversity of C. purpureus populations, we propose (i) that the isolated population should be considered as a prior for conservation efforts and managed as an independent unit; (ii) maintaining the integrity of the habitat within the four small patches that constitute the range of the species; (iii) continuous monitoring of genetic diversity of the populational groups; (iii) improve the quality of local pollinator habitats in order to avoid the inbreeding; and (iv) ex-situ conservation actions should be considered, especially the transfer of C. purpureus representatives to botanical gardens as well formation of a seed bank.

Assessing the benefits and risks of translocations in depauperate species: A theoretical framework with an empirical validation

Abstract Conservation translocations are becoming more common to assist in the management of threatened native species. While many translocation programs focus on maximizing survival in newly established populations, consideration is also required for the persistence of source populations. Here, we present and test a theoretical framework that assesses the translocation trade‐off between increasing a species probability of survival and decreasing a species’ overall genetic diversity. We anticipate that (a) the genetic diversity of translocated populations will be reduced compared to the source due to a failure to capture and retain genetic diversity and (b) the genetic diversity of the source population will decline due to the removal of founder individuals. We test this framework with an empirical study of redfin blue eye Scaturiginichthys vermeilipinnis, a critically endangered fish species which has undergone several replicate translocations, established with founders sourced from a single remnant population. Several generations after reintroduction, we show that the predicted survival of the species has improved as a result of these translocations. While the species’ genetic diversity has been retained across all populations combined (translocated and source), we show that genetic diversity in each individual population (including the source) is reduced compared to the source population prior to translocation. Synthesis and applications. Conservation translocations can provide great benefits to species survival, enabling extinction risk to be spread across multiple populations. Translocated populations, however, often harbour reduced genetic diversity compared to source populations and initiating translocated populations can decrease the genetic diversity of source populations, placing them at an increased risk of extinction. The framework presented here enables the trade‐off between extinction risk and retention of genetic diversity to be established. This will enable the optimal conservation strategy to be employed to increase the long‐term persistence and evolutionary potential of a species.

Seeking compromise across competing goals in conservation translocations: The case of the ‘extinct’ Floreana Island Galapagos giant tortoise

Abstract Conservation translocation projects must carefully balance multiple, potentially competing objectives (e.g. population viability, retention of genetic diversity, delivery of key ecological services) against conflicting stakeholder values and severe time and cost constraints. Advanced decision support tools would facilitate identifying practical solutions. We examined how to achieve compromise across competing objectives in conservation translocations via an examination of giant tortoises in the Galapagos Islands with ancestry from the extinct Floreana Island species (Chelonoidis niger). Efforts have begun to populate Floreana Island with tortoises genetically similar to its historical inhabitants while balancing three potentially competing objectives – restoring ecosystem services (sustaining a high tortoise population size), maximizing genome representation of the extinct C. niger species and maintaining a genetically diverse population – under realistic cost constraints. We developed a novel approach to this conservation decision problem by coupling an individual‐based simulation model with generalized additive models and global optimization. We identified several incompatibilities among programme objectives, with quasi‐optimal single‐objective solutions (sets of management actions) differing substantially in programme duration, translocation age, incubation temperature (determinant of sex ratio) and the number of individuals directly translocated from the source population. Quasi‐optimal single‐objective solutions were able to produce outcomes (i.e. population size and measures of genetic diversity and C. niger genome representation) to within 75% of their highest simulated outcomes (e.g. highest population size achieved across all simulations) within a cost constraint of c. $2m USD, but these solutions resulted in severe declines (up to 74% reduction) in outcomes for non‐focal objectives. However, when all programme objectives were equally weighted to produce a multi‐objective solution, all objectives were met to within 90% of the highest achievable mean values across all cost constraints. Synthesis and applications. Multi‐objective conservation translocations are likely to encounter complex trade‐offs and conflicts among programme objectives. Here, we developed a novel combination of modelling approaches to identify optimal management strategies. We found that solutions that simultaneously addressed multiple, competing objectives performed better than single‐objective solutions. Our model‐based decision support tool demonstrates that timely, cost‐effective solutions can be identified in cases where management objectives appear to be incompatible.

The Tapanuli orangutan: Status, threats, and steps for improved conservation

The Tapanuli orangutan: Status, threats, and steps for improved conservation

Impacts of stocking and its intensity on effective population size in Brook Charr (Salvelinus fontinalis) populations

Effective population size (Ne) is a measure of the genetic size of a population and a crucial parameter for wildlife population management since it is strongly related to retention of genetic diversity in time and/or to inbreeding levels. Many exploited fish populations are stocked with the purpose of increasing population sizes to sustain important fishing pressures. However, stocking hatchery-reared fish could at the same time increase population census size and decrease Ne. Our study aimed at characterizing how stocking affected Ne in supplemented populations of Brook Charr (Salvelinus fontinalis) in Quebec and at assessing how this relationship varied with the intensity of stocking (e.g. number of stocking events, number of fish stocked/ha, proportion of domestic genetic background). We estimated Ne with the linkage disequilibrium method in 54 populations (3361 sampled individuals analyzed at 20 microsatellites) with various levels of stocking intensity. We found that stocked lakes have significantly lower Ne than unstocked lakes. However, we found little evidence of an additional effect of stocking intensity on Ne of stocked lakes. Our results suggest that stocking may have a negative impact on Ne but that more intense stocking does not necessarily translate into lower Ne. However, even though low Ne in stocked populations could be attributed to an effect of stocking, it is also likely that stocked lakes consist of poor environments that translate into low Ne.

Extinction vortex dynamics of top predators isolated by urbanization.

Extinction risk is elevated in small, isolated populations due to demographic and genetic interactions. Therefore, it is critical to model these processes realistically in population viability analyses (PVA) to inform local management and contribute to a greater understanding of mechanisms within the extinction vortex. We conducted PVA's for two small mountain lion populations isolated by urbanization in southern California to predict population growth, extinction probability, and loss of genetic diversity with empirical data. Specifically, we (1) provide the first PVA for isolated mountain lions in the Santa Ana Mountains (SAM) that considers both demographic and genetic risk factors and (2) test the hypothesis that variation in abundance and mortality between the SAM and Santa Monica Mountains (SMM) result in differences in population growth, loss of heterozygosity, and extinction probability. Our models predicted 16-21% probability of local extinction in the SAM due purely to demographic processes over 50yr with current low levels or no immigration. Our models also predicted that genetic diversity will further erode in the SAM such that concern regarding inbreeding depression is warranted unless gene flow is increased, and that if inbreeding depression occurs, rapid local extinction will be highly likely. Dynamics of the two populations were broadly similar, but they also exhibited differences driven by larger population size and higher mortality in the SAM. Density-independent scenarios predicted a rapidly increasing population in the SMM, whereas growth potential did not differ from a stable trend in the SAM. Demographic extinction probability and loss of heterozygosity were greater in the SMM for density-dependent scenarios without immigration. However, higher levels of immigration had stronger, positive influences on both demographic viability and retention of genetic diversity in the SMM driven by lower abundance and higher adult survival. Our results elucidate demographic and genetic threats to small populations within the extinction vortex, and how these vary relative to demographic structure. Importantly, simulating seemingly attainable increases in connectivity was sufficient to greatly reduce extinction probability. Our work highlights that conservation of large carnivores is achievable within urbanized landscapes, but requires land protection, connectivity, and strategies to promote coexistence with humans.

Cross-specific markers reveal retention of genetic diversity in captive-bred pygmy hog, a critically endangered suid

As part of the species recovery plan for the critically endangered pygmy hog (Porcula salvania), a conservation-breeding program was initiated, to bolster its wild population. For successful conservation-breeding, it is essential to maintain 90% of the founder genetic diversity over time. Therefore, in the present study, we assessed the genetic diversity of a captive population of pygmy hog across generations using a set of ten, cross-specific microsatellite markers. Our results indicated a genetically heterozygous captive population (HE = 0.603), with stable expected heterozygosities across generations. However, the most recent generation showed a significant decrease in individual heterozygosities, implying possible genetic inbreeding. The current findings warrant a need for genetic evaluation to inform future conservation-breeding decisions. In addition, we also designed and tested primers for PCR-based species and sex-identification in the pygmy hog. The markers standardised in the present study would also help in evaluating the survival and ecology of the reintroduced populations.