Assessing the benefits and risks of translocations in changing environments: a genetic perspective

Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation

Biodiversity conservation requires conserving evolutionary potential-the capacity for wild populations to adapt. Understanding genetic diversity and evolutionary dynamics is critical for informing conservation decisions that enhance adaptability and persistence under environmental change. We review how emerging landscape genomic methods provide plant conservation programs with insights into evolutionary dynamics, including local adaptation and its environmental drivers. Landscape genomic approaches that explore relationships between genomic variation and environments complement rather than replace established population genomic and common garden approaches for assessing adaptive phenotypic variation, population structure, gene flow, and demography. Collectively, these approaches inform conservation actions, including genetic rescue, maladaptation prediction, and assisted gene flow. The greatest on-the-ground impacts from such studies will be realized when conservation practitioners are actively engaged in research and monitoring. Understanding the evolutionary dynamics shaping the genetic diversity of wild plant populations will inform plant conservation decisions that enhance the adaptability and persistence of species in an uncertain future.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains

BACKGROUND

Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely.

RESULTS

Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins.

CONCLUSION

Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

Thirty years of conservation breeding: Assessing the genetic diversity of captive Livingstone's fruit bats

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

Guiding seed movement: environmental heterogeneity drives genetic differentiation in Plathymenia reticulata, providing insights for restoration

Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).

Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations

As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.

Swinging back from the brink? Polygamous mating strategies revealed for an iconic threatened freshwater fish

Catastrophic fish death events are increasing in frequency and severity globally. A series of major recent fish deaths in the semi-arid lower Darling-Baaka river system (LDBR) of Australia are emblematic of these issues with tens of millions of native fish perishing. In 2018-2019 there was a major death event for Australia's largest freshwater fish, Murray cod (Maccullochella peelii). To aid the recovery and guide restoration activities of local Murray cod populations, it is essential to gather information on the mating strategies and effective population size following the fish death event. After the fish deaths, we collected larvae during the 2020 and 2021 breeding seasons and used single nucleotide polymorphisms (SNPs) to provide insight mating strategies and to estimate effective population size. Larvae were detected in both years along the entire length of the LDBR. Sixteen percent of the inferred breeding individuals were found to contribute to multiple pairings, confirming a complex and polygamous mating system. A high frequency of polygamy was evident both within and between years with 100 % polygamy identified among parents that produced offspring in both 2020 and 2021 and 95 % polygamy identified among parents involved in multiple spawning events within years. Post-larval Murray cod samples collected between 2016 and 2021 were co-analysed to further inform kinship patterns. Again, monogamy was rare with no confirmed cases of the same male-female pair contributing to multiple breeding events within or between seasons. Effective population size based on Murray cod collected after the fish death event was estimated at 721.6 (CI 471-1486), though this has likely declined following a subsequent catastrophic fish death event in the LDBR in March 2023. Our data provide insight into the variability of Murray cod mating strategies, and we anticipate that this knowledge will assist in planning conservation actions to ultimately help recover a species in crisis.

The high cost of movement in an arid working landscape for an endangered amphibian

Connectivity is essential for the maintenance of genetic diversity and stability of wildlife populations. Drought and changing precipitation regimes have caused natural aquatic amphibian breeding habitats to disappear or become isolated and have led to the replacement of natural surface water with artificial livestock water tanks. Terrestrial movement is the only means of responding to aquatic threats in arid landscapes and to allow population connectivity. Aridity may present an impenetrable barrier in hydrologically fragmented environments. We used a facultatively paedomorphic and federally endangered salamander to assess the challenges of movement across arid working lands. Sonoran tiger salamanders (Ambystoma mavortium stebbinsi) are endemic to the San Rafael Valley of southeastern Arizona, United States of America, where they depend on livestock water tanks as breeding habitat. The ecology of this species' metamorphs outside of stock tanks is virtually unknown. To assess survival on the landscape during terrestrial movement we used radio-transmitters to track 78 adult metamorphosed salamanders over 2 years. Sonoran tiger salamanders moved up to 1 km from the tank edge, and average distances moved of over 400 m were higher than most Ambystoma species. However, during the study period, none reached neighboring stock tanks. We found high mortality due to predation and desiccation. Individuals that dispersed to terrestrial habitat in summer survived longer than individuals that dispersed in spring. High mortality suggests terrestrial movement is exceptionally risky and may contribute to isolated subpopulations and elevated levels of inbreeding. Conservation actions that improve and maintain artificial aquatic habitats as well as increase connectivity may improve long-term management for pond-breeding amphibians in arid regions.

Identifying predictors of translocation success in rare plant species

The fundamental goal of a rare plant translocation is to create self-sustaining populations with the evolutionary resilience to persist in the long term. Yet, most plant translocation syntheses focus on a few factors influencing short-term benchmarks of success (e.g., survival and reproduction). Short-term benchmarks can be misleading when trying to infer future growth and viability because the factors that promote establishment may differ from those required for long-term persistence. We assembled a large (n = 275) and broadly representative data set of well-documented and monitored (7.9 years on average) at-risk plant translocations to identify the most important site attributes, management techniques, and species' traits for six life-cycle benchmarks and population metrics of translocation success. We used the random forest algorithm to quantify the relative importance of 29 predictor variables for each metric of success. Drivers of translocation outcomes varied across time frames and success metrics. Management techniques had the greatest relative influence on the attainment of life-cycle benchmarks and short-term population trends, whereas site attributes and species' traits were more important for population persistence and long-term trends. Specifically, large founder sizes increased the potential for reproduction and recruitment into the next generation, whereas declining habitat quality and the outplanting of species with low seed production led to increased extinction risks and a reduction in potential reproductive output in the long-term, respectively. We also detected novel interactions between some of the most important drivers, such as an increased probability of next-generation recruitment in species with greater seed production rates, but only when coupled with large founder sizes. Because most significant barriers to plant translocation success can be overcome by improving techniques or resolving site-level issues through early intervention and management, we suggest that by combining long-term monitoring with adaptive management, translocation programs can enhance the prospects of achieving long-term success.

Population status and genetic assessment of mugger (Crocodylus palustris) in a tropical regulated river system in North India

For rewilding the depleted crocodylian populations in India, a targeted 'one-species one area' based conservation approach was adopted in the early-1970s. Suitable habitats were identified and designated as protected areas, specifically targeted to recover a particular crocodylian species. A ~ 610 km stretch of Chambal River in the Ganga River Basin was declared as National Chambal Sanctuary to restore the 'Critically Endangered' gharial (Gavialis gangeticus), where active management of mugger (Crocodylus palustris) was discouraged. In the present study, we examined the population trends, occupancy, and genetic status of mugger by conducting population monitoring and genetic assessment to understand the status of potentially competitive mugger in the Sanctuary. Our finding suggests that the mugger population has notably increased and colonised the Sanctuary. We observed a moderate level of genetic diversity in the mugger, which was relatively higher compared to the gharial in the Sanctuary. The rapid colonization of ecological generalist mugger raises concerns about potential competition with ecological specialist gharial threatening its long-term sustainability. Considering the coexistence dynamics between the species, it is essential to extend adaptive management strategies for mugger to ensure successful recovery of gharial population in the Sanctuary.

Assessment of the Genetic Diversity and Structure of the Korean Endemic Freshwater Fish Microphysogobio longidorsalis (Gobioninae) Using Microsatellite Markers: A First Glance from Population Genetics

Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic conservation data for M. longidorsalis. We analyzed 19 microsatellite loci in six populations of M. longidorsalis in South Korea to characterize their population structure and genetic diversity. The genetic diversity of the microsatellites was 0.741-0.779, which is lower than that of other freshwater fishes. The pairwise genetic differentiation of microsatellite (FST) values ranged from 0.007 to 0.041, suggesting low genetic differentiation between the populations. The Jojongicheon stream population (CP) had an effective population size of <100. Therefore, conservation efforts are required to prevent inbreeding depression in M. longidorsalis. Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis.

Species conservation in the era of genomic science

The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.

Importance of Genetic-Fitness Correlations for the Conservation of Amphibians

Endangered animals suffer from isolation of their habitats. Isolation leads to a reduction in population size as well as a decrease in genetic diversity and a concomitant increase in the risk of extinction. Amphibians are the most endangered vertebrate class. Besides habitat loss, fragmentation and isolation, amphibians are threatened by emerging diseases e.g., chytrid fungus or Ranavirus. By employing experiments, researchers investigate whether changes in genetic diversity within or among isolated populations affect amphibian fitness. While genetic diversity estimates are based on molecular markers, typically microsatellites, fitness is mostly measured as tadpole performance in rearing experiments often under varying environmental conditions. Tadpole performances (e.g., body mass, growth rate and survival) have been found to be negatively affected by low genetic diversity, as several studies have found a positive association between genetic diversity and these fitness traits. Moreover, infection with pathogens also seems to be more likely in individuals or populations with lower genetic diversity. Overall, these genetic-fitness correlations seem to be more pronounced or detectable in smaller, declining populations but not in larger populations. Genomic studies, which sample a larger fraction of the genome, are still scarce in the conservation genetic literature on amphibians. These are likely to increase in upcoming years and may reveal adaptive variants that protect against dangerous pathogens or environmental changes. Altogether, genetic-fitness correlation studies should be a priority in order to develop effective management plans for the genetic rescue of isolated, imperilled amphibian populations.

Fine-scale spatial genetic structure and dispersal among Italian smooth newt populations in a rural landscape

Amphibians are particularly sensitive to habitat loss and fragmentation caused by the intensification and modernization of farming occurring in the second half of the twentieth century in the Mediterranean basin. However, artificial water bodies, associated with traditional husbandry, proved to be important surrogate for amphibian feeding and reproduction. Here, multilocus genotypes were used to investigate the spatial population structure of Lissotriton vulgaris meridionalis and the role of drinking troughs in supporting viable breeding populations within a rural landscape interested by traditional husbandry and agriculture. Our genetic analysis highlighted the conservation value and the potential stepping-stone function of artificial aquatic sites in the dispersal of the species and for the gene flow maintenance. Indeed, populations of drinking troughs show allelic richness and heterozygosity levels comparable to those from natural ponds and there is no great evidence of genetic bottlenecks. A complex system of artificial aquatic sites and few natural wetlands was identified sustaining a well-structured network of demes highly interconnected with themselves and natural aquatic sites. The conservation of the identified genetic clusters may be useful to prevent further population declines and future loss of genetic diversity within the study area characterized by scarce natural wetlands that frequently dried because of agricultural practices and strong seasonality. Site-specific protection measures are needed to contrast the progressive disappearance of drinking troughs observed in the last years in Italy because of the abandonment of traditional farming practices in favour of modern agriculture and intensive farming.

Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer

The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.

A RETROSPECTIVE ANALYSIS OF MORBIDITY AND MORTALITY IN THE CAPTIVE LEADBEATER'S POSSUM (GYMNOBELIDEUS LEADBEATERI) POPULATION FROM 1970 TO 2021

The Leadbeater's possum (Gymnobelideus leadbeateri) is a critically endangered nocturnal marsupial with a restricted range in the Central Highlands of Victoria, Australia. There are two genetically distinct populations divided by location: highland and lowland. Lowland possums exist in one remnant swamp forest and entered captivity in 2012 when ∼60 individuals remained. Today, with less than 20 lowland individuals remaining, any information that informs the yet-unsuccessful breeding program is critical. This study encompasses a retrospective analysis of the causes of mortality and significant histological lesions in captive highland and lowland individuals across seven institutions internationally from 1970 to 2021. During this time, 245 possums lived in captivity. Postmortem records exist for 99 animals, including 349 histopathology diagnoses from 80 reports and 264 gross necropsy diagnoses from 78 reports. Diagnoses were assigned into two categories based on the importance to the individual (causing death or morbidity to a single animal [n = 194]), or importance to the wider population (causing death or morbidity to more than one animal or was related to reproduction [n = 155]). Individual animals had multiple diagnoses, which were tallied as individual data points. Renal disease was diagnosed 57 times; the most common finding was chronic nephropathy (43/57). Cardiovascular disease was diagnosed 33 times; atherosclerosis associated with obesity was common (n = 10/33). Both categories suggest causal association with captive husbandry but elicit no comment on the lack of success of the breeding program. Reproductive disease was diagnosed 36 times in 24 animals (14 females and 10 males). In females, 11 cases of uterine inflammation and associated clinical signs were associated with ascending infection or neoplasia. Of the seven lowland male possums with mortality data, five were infertile (azoospermia or testicular atrophy). More investigation into the reproductive health of this population is indicated to understand the lack of success in the current breeding program.

Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur

Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer

Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

Losing the forest for the tree? On the wisdom of subpopulation management

Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.

Return to 1616: Multispecies Fauna Reconstruction Requires Thinking Outside the Box

Conservation translocations have become increasingly popular for 'rewilding' areas that have lost their native fauna. These multispecies translocations are complex and need to consider the requirements of each individual species as well as the influence of likely interactions among them. The Dirk Hartog Island National Park Ecological Restoration Project, Return to 1616, aspires to restore ecological function to Western Australia's largest island. Since 2012, pest animals have been eradicated, and conservation translocations of seven fauna species have been undertaken, with a further six planned. Here, we present a synthesis of the innovative approaches undertaken in restoring the former faunal assemblage of Dirk Hartog Island and the key learnings gathered as the project has progressed.

Genomics of founders for conservation breeding: the Jasper caribou case

Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10592-023-01540-3.

Are Urban Populations of a Gliding Mammal Vulnerable to Decline?

Small populations are at high risk of extinction, and they are likely to need management intervention. Successful management, however, relies on sufficient long-term demographic data in order to determine whether apparent declines are natural fluctuations or the product of threatening processes. In this study, we monitored a small urban population of squirrel gliders (Petaurus norfolcensis) in Queensland, Australia, over a 16 year period. A reference population in a larger forest patch was also studied in order to investigate whether its demographic trends were similar. Using mark-recapture data to generate estimates of apparent survival and population size, we found evidence of a decline within the small population but not in the reference population over the monitoring period. We suggest that the influence of multiple factors may have led to the decline, but, ultimately, that the genetic condition of the small population may be responsible. Understanding demographic trends is an important context for management interventions of small populations, although causes of decline need to be identified for successful management. The squirrel glider provides a useful case study for small urban populations and particularly for arboreal mammals.

Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States

Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.

Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Effective conservation planning of Iberian amphibians based on a regionalization of climate-driven range shifts

Amphibians are severely affected by climate change, particularly in regions where droughts prevail and water availability is scarce. The extirpation of amphibians triggers cascading effects that disrupt the trophic structure of food webs and ecosystems. Dedicated assessments of the spatial adaptive potential of amphibian species under climate change are, therefore, essential to provide guidelines for their effective conservation. I used predictions about the location of suitable climates for 27 amphibian species in the Iberian Peninsula from a baseline period to 2080 to typify shifting species' ranges. The time at which these range types are expected to be functionally important for the adaptation of a species was used to identify full or partial refugia; areas most likely to be the home of populations moving into new climatically suitable grounds; areas most likely to receive populations after climate adaptive dispersal; and climatically unsuitable areas near suitable areas. I implemented an area prioritization protocol for each species to obtain a cohesive set of areas that would provide maximum adaptability and where management interventions should be prioritized. A connectivity assessment pinpointed where facilitative strategies would be most effective. Each of the 27 species had distinct spatial requirements but, common to all species, a bottleneck effect was predicted by 2050 because source areas for subsequent dispersal were small in extent. Three species emerged as difficult to maintain up to 2080. The Iberian northwest was predicted to capture adaptive range for most species. My study offers analytical guidelines for managers and decision makers to undertake systematic assessments on where and when to intervene to maximize the persistence of amphibian species and the functionality of the ecosystems that depend on them.

Implications of past and present genetic connectivity for management of the saltwater crocodile ( Crocodylus porosus )

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey ≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.

Conservation through Collaboration: Regional Conservation Programs of the North Carolina Zoo

In response to rapid biodiversity losses in recent decades, zoos have become more engaged in conservation issues. Solutions to conservation challenges are complex and require collaborative efforts across organizations. Zoos can be effective partners that can contribute diverse expertise and resources to protect wildlife and their habitats. While zoos often partner with international organizations to facilitate field-based conservation projects on the exotic animals they exhibit, some of the most meaningful conservation and education initiatives are conducted locally in partnership with local organizations. A core part of the mission of the North Carolina Zoo (Asheboro, NC, USA) is the conservation of wildlife and their natural habitats, both regionally and internationally. The goal of this article is to review the North Carolina Zoo’s regional conservation programs and the importance of partnerships with other local organizations in accomplishing shared goals. North Carolina Zoo plays an important role in regional conservation by protecting and managing natural lands, protecting declining amphibians through headstarting and habitat management, rehabilitating native wildlife, and working on local outreach and sustainability projects to reduce impacts on natural resources and inspire others to get involved in conservation. These programs were developed through partnerships with local and state government agencies, academic institutions, non-profit organizations, other zoos and aquariums, schools, libraries, and businesses. These collaborations have been instrumental in developing and implementing successful projects by pooling limited resources and sharing crucial expertise. They demonstrate how zoos are evolving to become leaders and partners in conservation, research, and education to protect local species and natural resources.

Facilitated Adaptation as A Conservation Tool in the Present Climate Change Context: A Methodological Guide

Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating to locations where their ecological niche is preserved or by adapting to the new environment. While the first response has been used to develop, discuss and implement the strategy of assisted migration, facilitated adaptation is only beginning to be considered as a potential approach. Here, we present a review of the conceptual framework for facilitated adaptation, integrating advances and methodologies from different disciplines. Briefly, facilitated adaptation involves a population reinforcement that introduces beneficial alleles to enable the evolutionary adaptation of a focal population to pressing environmental conditions. To this purpose, we propose two methodological approaches. The first one (called pre-existing adaptation approach) is based on using pre-adapted genotypes existing in the focal population, in other populations, or even in closely related species. The second approach (called de novo adaptation approach) aims to generate new pre-adapted genotypes from the diversity present in the species through artificial selection. For each approach, we present a stage-by-stage procedure, with some techniques that can be used for its implementation. The associated risks and difficulties of each approach are also discussed.

Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts

In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E. amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E. risdonii seed, yet in some hybrid patches small individuals resembling E. risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E. risdonii and E. amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F₁ /F₂ hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F₁ /F₂ -like genotypes to those dominated by E. risdonii-backcross genotypes, and (iii) the E. risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E. risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E. amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E. risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.

Multiplexed ISSR Genotyping by Sequencing (MIG-Seq)

Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.

Resident wild koalas show resilience to large-scale translocation of bushfire-rescued koalas

Wildlife translocation is increasingly utilized as a conservation management action, to mitigate the immediate negative effects of habitat loss and fragmentation (e.g. from land clearing or bushfires). Previous research has shown that stress responses can help or hinder survival in translocated wildlife and determine the efficacy of translocation as a conservation action. Yet these translocated animals are only one side of the equation, with translocation also potentially impacting the animals in the recipient population. We measured physiological markers of stress (faecal cortisol metabolite concentrations and neutrophil-lymphocyte ratios) and assessed health condition in a wild koala population one year after a major translocation of bushfire-rescued koalas on Kangaroo Island. We expected to find a high population density at the site (>0.75 koalas per hectare) and that resident koalas would show signs of chronic stress and ill health as a result of territorial conflict over food trees and reproductive opportunities. In contrast, we found that only one-fifth of the population remaining at the site were translocated koalas. The overall population density was also much lower (0.21 koalas per hectare) than anticipated. With no evidence of mass mortality at the site, we suggest that the majority of translocated koalas dispersed away from the site. Our stress marker measurements did not differ between the wild koalas and a sample of captive (non-display) koalas at the nearby Kangaroo Island Wildlife Park and were generally low compared to other studies. Veterinary examinations found that most koalas were in good body condition with very few diagnostic indicators of systemic ill health. Overall, our results suggest that, if there is adequate landscape-scale habitat connectivity and opportunity for dispersal, translocated koalas are likely to disperse from the site of release, with limited impacts on recipient koala populations at translocation release sites.

Examining the spatiotemporal variation of genetic diversity and genetic rarity in the natural plant recolonization of human-altered areas

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.

Capturing Genetic Diversity in Seed Collections: An Empirical Study of Two Congeners with Contrasting Mating Systems

Plant mating systems shape patterns of genetic diversity and impact the long-term success of populations. As such, they are relevant to the design of seed collections aiming to maximise genetic diversity (e.g., germplasm conservation, ecological restoration). However, for most species, little is known empirically about how variation in mating systems and genetic diversity is distributed. We investigated the relationship between genetic diversity and mating systems in two functionally similar, co-occurring species of Hakea (Proteaceae), and evaluated the extent to which genetic diversity was captured in seeds. We genotyped hundreds of seedlings and mother plants via DArTseq, and developed novel implementations of two approaches to inferring the mating system from SNP data. A striking contrast in patterns of genetic diversity between H. sericea and H. teretifolia was revealed, consistent with a contrast in their mating systems. While both species had mixed mating systems, H. sericea was found to be habitually selfing, while H. teretifolia more evenly employed both selfing and outcrossing. In both species, seed collection schemes maximised genetic diversity by increasing the number of maternal lines and sites sampled, but twice as many sites were needed for the selfing species to capture equivalent levels of genetic variation at a regional scale.

Understanding Local Adaptation to Prepare Populations for Climate Change

Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.

Genomic trajectories of a near-extinction event in the Chatham Island black robin

Background

Understanding the micro-­evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.

Results

We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.

Conclusion

Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.

Risks, benefits, and knowledge gaps of non-native tree species in Europe

Changing ecosystem conditions and diverse socio-economical events have contributed to an ingrained presence of non-native tree species (NNTs) in the natural and cultural European landscapes. Recent research endeavors have focused on different aspects of NNTs such as legislation, benefits, and risks for forestry, emphasizing that large knowledge gaps remain. As an attempt to fulfill part of these gaps, within the PEN-CAFoRR COST Action (CA19128) network, we established an open-access questionnaire that allows both academic experts and practitioners to provide information regarding NNTs from 20 European countries. Then, we integrated the data originating from the questionnaire, related to the country-based assessment of both peer-reviewed and grey literature, with information from available datasets (EUFORGEN and EU-Forest), which gave the main structure to the study and led to a mixed approach review. Finally, our study provided important insights into the current state of knowledge regarding NNTs. In particular, we highlighted NNTs that have shown to be less commonly addressed in research, raising caution about those characterized by an invasive behavior and used for specific purposes (e.g., wood production, soil recultivation, afforestation, and reforestation). NNTs were especially explored in the context of resilient and adaptive forest management. Moreover, we emphasized the assisted and natural northward migration of NNTs as another underscored pressing issue, which needs to be addressed by joint efforts, especially in the context of the hybridization potential. This study represents an additional effort toward the knowledge enhancement of the NNTs situation in Europe, aiming for a continuously active common source deriving from interprofessional collaboration.

The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba

The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites H_E = 0.44, and SNP H_E = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite F_IS = 0.12, SNP F_IS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all N_e < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.

Strong bidirectional gene flow between fish lineages separated for over 100,000 years

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.

Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species

BACKGROUND AND AIMS

Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted.

METHODS

We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status.

KEY RESULTS

All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids.

CONCLUSIONS

Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.

Using PVA and captive breeding to balance trade-offs in the rescue of the island dibbler onto a new island ark

In the face of the current global extinction crisis, it is critical we give conservation management strategies the best chance of success. Australia is not exempt from global trends with currently the world’s greatest mammal extinction rate (~ 1 per 8 years). Many more are threatened including the dibbler (Parantechinus apicalis) whose remnant range has been restricted to Western Australia at just one mainland site and two small offshore islands—Whitlock Island (5 ha) and Boullanger Island (35 ha). Here, we used 14 microsatellite markers to quantify genetic variation in the remaining island populations from 2013 to 2018 and incorporated these data into population viability analysis (PVA) models, used to assess factors important to dibbler survival and to provide guidance for translocations. Remnant population genetic diversity was low (< 0.3), and populations were highly divergent from each other (pairwise F_STs 0.29–0.52). Comparison of empirical data to an earlier study is consistent with recent declines in genetic diversity and models projected increasing extinction risk and declining genetic variation in the next century. Optimal translocation scenarios recommend 80 founders for new dibbler populations—provided by captive breeding—and determined the proportion of founders from parental populations to maximise genetic diversity and minimise harvesting impact. The goal of our approach is long-term survival of genetically diverse, self-sustaining populations and our methods are transferable. We consider mixing island with mainland dibblers to reinforce genetic variation.

Genetic diversity and genetic structure of Puya raimondii (Bromeliaceae) for its conservation in the Peruvian Andes

Puya raimondii is an endemic species from the high Andes of Peru and Bolivia. In Peru it is distributed from 8.068501°S, 16.170280°W to 16.180580°S, 70.658873°W, between 3600 and 4800 m, living in extreme climatic conditions typical of the Puna, where it plays an important ecological role. Despite the wide distribution of P. raimondii populations in Peru, they appear to be fairly uniform morphologically. The following questions arise: Will the current molecular tools be able to show differences between the numerous populations? Are the conservation areas established for P. raimondii sufficient since they harbor the existing variability? To answer these questions, this work aimed to evaluate the genetic diversity and genetic structure in a northern population, Pachapaqui (Ancash department), a central population, Yanacancha (Junin), and a southern population, Lampa - Choconchaca sector (Puno), using microsatellite markers (SSR) specific for the species. The genetic diversity parameters used included number of alleles (A), exclusive alleles (RA), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphic content index (PIC). The results showed that the total number of A varied from 2 - 13, the He values were 0 ‒ 0.723 and Ho 0 ‒ 0.929, with an average He of 0.217, indicating a moderate to high genetic diversity, being the population of Lampa-Choconchaca sector, the one that presented the greatest allelic diversity and the greatest genetic diversity. The Hardy-Weinberg test showed that the populations are in HW disequilibrium, the statistical analysis indicates 65% of the genetic variation at the population level and values of FST (0.426) and RST (0.650) that indicate high genetic differentiation among populations, with two genetic groups (K=2) that correspond to the populations of northern-central and southern Peru. The results provide useful information to establish conservation strategies for P. raimondii, which lead to the creation of an additional conservation area to protect the populations in southern Peru.

Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour-a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F₁ and F₄  generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F₁ to F₄ . Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.