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

How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq

Background

Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers.

Results

Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations.

Conclusions

The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12863-021-00974-3.

Evaluating Assisted Gene Flow in Marginal Populations of a High Mountain Species

Many species cannot either migrate or adapt at the rate of temperature increases due to climate warming. Therefore, they need active conservation strategies to avoid extinction. Facilitated adaptation actions, such assisted gene flow, aim at the increase of the evolutionary resilience of species affected by global change. In elevational gradients, marginal populations at the lower elevation edges are experiencing earlier snowmelt and higher temperatures, which force them to adapt to the new conditions by modifying their phenology. In this context, advancing the onset of flowering and seed germination times are crucial to ensure reproductive success and increase seedling survival prior to summer drought. Assisted gene flow may bring adaptive alleles and increase genetic diversity that can help throughout ontogeny. The main aim of this work is to assess the effects that different gene flow treatments could have on the desired trait changes in marginal populations. Accordingly, we established a common garden experiment in which we assayed four different gene flow treatments between Silene ciliata Pourr. (Caryophyllaceae) populations located in similar and different elevation edges, belonging to the same and different mountains. As a control treatment, within-population crosses of low elevation edge populations were performed. The resulting seeds were sown and the germination and flowering onset dates of the resulting plants recorded, as well as the seedling survival. Gene flow between populations falling on the same mountain and same elevation and gene flow from high-elevation populations from a different mountain to low-elevation populations advanced seed germination time with respect to control crosses. No significant effects of gene flow on seedling survival were found. All the gene flow treatments delayed the onset of flowering with respect to control crosses and this effect was more pronounced in among-mountain gene flows. The results of this study highlight two important issues that should be thoroughly studied before attempting to apply assisted gene flow in practical conservation situations. Firstly, among-populations gene flow can trigger different responses in crucial traits throughout the ontogeny of plant species. Secondly, the population provenance of gene flow is determinant and plays a significant role on the effects of gene flow.

Wildlife conservation in a fragmented landscape: the Eurasian red squirrel on the Isle of Wight

Island populations may have a higher extinction risk due to reduced genetic diversity and need to be managed effectively in order to reduce the risk of biodiversity loss. The Eurasian red squirrels (Sciurus vulgaris) in the south of England only survive on three islands (the Isle of Wight, Brownsea and Furzey islands), with the Isle of Wight harbouring the largest population in the region. Fourteen microsatellites were used to determine the genetic structure of red squirrel populations on the Isle of Wight, as well as their relatedness to other populations of the species. Our results demonstrated that squirrels on these islands were less genetically diverse than those in Continental mainland populations, as would be expected. It also confirmed previous results from mitochondrial DNA which indicated that the squirrels on the Isle of Wight were relatively closely related to Brownsea island squirrels in the south of England. Importantly, our findings showed that genetic mixing between squirrels in the east and west of the Isle of Wight was very limited. Given the potential deleterious effects of small population size on genetic health, landscape management to encourage dispersal of squirrels between these populations should be a priority.

Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish

Translocation, the movement of organisms for conservation purposes, can result in unintended introgression if genetic material flows between populations in new ways. The Bluemask Darter Etheostoma akatulo is a federally endangered species of freshwater fish inhabiting the Caney Fork River system and three of its tributaries (Collins River, Rocky River, and Cane Creek) in Tennessee. The current conservation strategy for Bluemask Darters involves translocating the progeny of broodstock from the Collins River (in the west) to the Calfkiller River (in the east) where the species had been extirpated. In this study, we use ddRAD sequence data from across the extant range to assess this translocation strategy in light of population structure, phylogeny, and demography. We also include museum specimen data to assess morphological variation among extant and extirpated populations. Our analyses reveal substantial genetic and phenotypic disparities between a western population in the Collins River and an eastern population encompassing the Rocky River, Cane Creek, and upper Caney Fork, the two of which shared common ancestry more than 100,000 years ago. Furthermore, morphological analyses classify 12 of 13 Calfkiller River specimens with phenotypes consistent with the eastern population. These results suggest that current translocations perturb the evolutionary boundaries between two delimited populations. Instead, we suggest that repopulating the Calfkiller River using juveniles from the Rocky River could balance conflicting signatures of demography, diversity, and divergence. Beyond conservation, the microgeographic structure of Bluemask Darter populations adds another puzzle to the phylogeography of the hyperdiverse freshwater fishes in eastern North America.

Population genetics and geometric morphometrics of the freshwater snail Segmentina nitida reveal cryptic sympatric species of conservation value in Europe

Segmentina nitida Müller 1774 is a rare European freshwater snail of drainage ditches and marshland, which has seen a marked decrease in range (~ 80%) over the last 100 years in the UK. This has been attributed to over-dredging of drainage ditches for land management, conversion of grazing marshes to arable farmland, as well as eutrophication. Segmentina nitida is identified as a priority species in the UK Biodiversity Action Plan (UKBAP) that recommends further research to inform reintroduction and translocation for its conservation. We used nuclear markers (microsatellites and ITS2) and a mitochondrial (COI) marker to investigate population structure in S. nitida individuals sampled from Poland, Germany, Sweden, and the UK to identify differences within and between populations. Data based on 2D landmark-based geometric morphometrics of S. nitida shells was used to determine if phenotypic variation followed genetic differentiation. Two distinct genetic lineages of S. nitida were identified in ITS and COI phylogenies as well as cluster analysis of microsatellite markers, one of these lineages was present in eastern Europe (Poland, Sweden- Lineage 2), and one in western Europe (UK, Germany- Lineage 1), with lineages co-occurring in German populations. No genetic admixture was observed in German populations containing both lineages. These two lineages were also distinct in shape, with lineage 2 individuals having significantly wider shells and taller and wider apertures than those in Lineage 1. ~ 85% of shells assigned to the predicted lineage in a discriminant analysis of Procrustes shape coordinates. We infer that S. nitida includes at least one sympatric cryptic species. We discuss the implications of these findings on the conservation status of S. nitida in the UK and Europe.

Mixing gene pools to prevent inbreeding issues in translocated populations of clonal species

Assisted gene flow by plant translocations is increasingly implemented for restoring populations of critically endangered species. The success in restoring genetically healthy populations may depend on translocation design, in particular the choice of the source populations. Highly clonal populations may show low genetic diversity despite large census sizes, and disrupted and geitonogamous pollination may result in selfing and inbreeding issues in the offspring intended for translocation. We carried out a genetic monitoring of translocated populations of the clonal Dianthus deltoides using 14 microsatellite markers and quantified fitness traits over two generations (transplants, F1 seed progeny and newly established individuals). Inbreeding levels were higher in the offspring used as transplants than in the adult generation of the source populations, as a result of high clonality and pollination disruption leading to self-pollination. The F1 generation in translocated populations showed high genetic diversity maintained across generations, diminished inbreeding levels, low genetic differentiation, pollen flow and genetic mixing between the four sources. New individuals were established from seed germination. Fitness patterns were a combination of inbreeding depression in inbred transplants and F1 progeny, heterosis in admixed F1 progeny, source population adaptive capacities, phenotypic plasticity, maternal effects and site environmental specificities. The strategy in the translocation design to mix several local sources, combined with large founding population sizes and ecological management has proved success in initiating the processes leading to the establishment of genetically healthy populations, even when source populations are highly clonal with low genetic diversity leading to inbreeding issues in the transplants.

An endangered flightless grasshopper with strong genetic structure maintains population genetic variation despite extensive habitat loss

Conservation research is dominated by vertebrate examples but the shorter generation times and high local population sizes of invertebrates may lead to very different management strategies, particularly for species with low movement rates. Here we investigate the genetic structure of an endangered flightless grasshopper, Keyacris scurra, which was used in classical evolutionary studies in the 1960s. It had a wide distribution across New South Wales (NSW) and Victoria in pre-European times but has now become threatened because of land clearing for agriculture and other activities. We revisited remnant sites of K. scurra, with populations now restricted to only one area in Victoria and a few small patches in NSW and the Australian Capital Territory (ACT). Using DArtseq to generate SNP markers as well as mtDNA sequence data, we show that the remaining Victorian populations in an isolated valley are genetically distinct from the NSW populations and that all populations tend to be genetically unique, with large F ST values up to 0.8 being detected for the SNP datasets. We also find that, with one notable exception, the NSW/ACT populations separate genetically into previously described chromosomal races (2n = 15 vs. 2n = 17). Isolation by distance was detected across both the SNP and mtDNA datasets, and there was substantial differentiation within chromosomal races. Genetic diversity as measured by heterozygosity was not correlated with the size of remaining habitat where the populations were found, with high variation present in some remnant cemetery sites. However, inbreeding correlated negatively with estimated habitat size at 25-500 m patch radius. These findings emphasize the importance of small habitat areas in conserving genetic variation in such species with low mobility, and they highlight populations suitable for future translocation efforts.

Conserving the genetic diversity of condemned populations: Optimizing collections and translocation

We consider approaches for conserving genetic diversity from plant populations whose destruction is imminent. We do this using SNP genotype data from two endangered species, Pimelea spicata and Eucalyptus sp. Cattai. For both species, we genotyped plants from a 'condemned' population and designed ex situ collections, characterizing how the size and composition of the collection affected the genetic diversity preserved. Consistent with previous observations, populations where genetic diversity was optimized captured more alleles than populations of equal size chosen at random. This benefit of optimization was larger when the propagation population was small. That is, small numbers of individuals (e.g. 20) needed to be selected carefully to capture a comparable proportion of alleles to optimized populations, but larger random populations (e.g. >48) captured almost as many alleles as optimized populations. We then examined strategies for generating translocation populations based on the horticultural constraints presented by each species. In P. spicata, which is readily grown from cuttings, we designed translocation populations of different sizes, using different numbers of ramets from each member of propagation populations. We then performed simulations to predict the loss of alleles from these populations over 10 generations. Large translocation populations were predicted to maintain a greater proportion of source population alleles than smaller translocation populations, but this effect was saturated beyond 200 individuals. In E. sp. Cattai, we examined strategies to promote the diversity of progeny from a conservation planting scenario with 36 individuals. This included the optimization of the spatial arrangement of the planting and supplementing the diversity of the condemned population with individuals from additional sites. In sum, we studied approaches for designing genetically diverse translocations of condemned populations for two species that require contrasting methods of propagation, illustrating the application of approaches that were useful in different circumstances.

Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

Genomic vulnerability of a dominant seaweed points to future-proofing pathways for Australia's underwater forests

Globally, critical habitats are in decline, threatening ecological, economic and social values and prompting calls for 'future proofing' efforts that enhance resilience to climate change. Such efforts rely on predicting how neutral and adaptive genomic patterns across a species' distribution will change under future climate scenarios, but data is scant for most species of conservation concern. Here, we use seascape genomics to characterise genetic diversity, structure and gene-environmental associations in a dominant forest-forming seaweed, Phyllospora comosa, along its entire latitudinal (12° latitude), and thermal (~14°C) range. Phyllospora showed high connectivity throughout its central range, with evidence of genetic structure and potential selection associated with sea surface temperatures (SSTs) at its rear and leading edges. Rear and leading-edge populations harboured only half the genetic diversity of central populations. By modelling genetic turnover as a function of SST, we assessed the genomic vulnerability across Phyllospora's distributional range under climate change scenarios. Despite low diversity, range-edge populations were predicted to harbour beneficial adaptations to marginal conditions and overall adaptability of the species may be compromised by their loss. Assisted gene flow from range edge populations may be required to enhance adaptation and increase resilience of central and leading-edge populations under warming oceans. Understanding genomic vulnerability can inform proactive restoration and future-proofing strategies for underwater forests and ensure their persistence in changing oceans.

Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management

Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively adaptive loci in order to evaluate the relative effects of genetic drift and local adaptation on population divergence. We sampled individuals across the Utah prairie dog species range and generated 2955 single nucleotide polymorphisms using double digest restriction site-associated DNA sequencing. Genetic diversity was lower in low-elevation sites compared to high-elevation sites. Population divergence was high among sites and followed an isolation-by-distance model. Our results indicate that genetic drift plays a substantial role in the population divergence of the Utah prairie dog, and colonies would likely benefit from translocation of individuals between recovery units, which are characterized by distinct elevations, despite the detection of environmental associations with outlier loci. By understanding the processes that shape genetic structure, better informed decisions can be made with respect to the management of threatened species to ensure that adaptation is not stymied.

Getting the message right on nature-based solutions to climate change

Nature-based solutions (NbS)-solutions to societal challenges that involve working with nature-have recently gained popularity as an integrated approach that can address climate change and biodiversity loss, while supporting sustainable development. Although well-designed NbS can deliver multiple benefits for people and nature, much of the recent limelight has been on tree planting for carbon sequestration. There are serious concerns that this is distracting from the need to rapidly phase out use of fossil fuels and protect existing intact ecosystems. There are also concerns that the expansion of forestry framed as a climate change mitigation solution is coming at the cost of carbon rich and biodiverse native ecosystems and local resource rights. Here, we discuss the promise and pitfalls of the NbS framing and its current political traction, and we present recommendations on how to get the message right. We urge policymakers, practitioners and researchers to consider the synergies and trade-offs associated with NbS and to follow four guiding principles to enable NbS to provide sustainable benefits to society: (1) NbS are not a substitute for the rapid phase out of fossil fuels; (2) NbS involve a wide range of ecosystems on land and in the sea, not just forests; (3) NbS are implemented with the full engagement and consent of Indigenous Peoples and local communities in a way that respects their cultural and ecological rights; and (4) NbS should be explicitly designed to provide measurable benefits for biodiversity. Only by following these guidelines will we design robust and resilient NbS that address the urgent challenges of climate change and biodiversity loss, sustaining nature and people together, now and into the future.

Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian

Revealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.

Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India

The gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G'ST = 0.058, P < 0.05 Jost's D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

Genetic mixing for population management: From genetic rescue to provenancing

Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas’ whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.

Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina

Despite strong support from the media, the reintroduction of animals into natural environments does not always achieve its goal. Alouatta caraya is the primate species facing the greatest hunting pressure due to the illegal pet trade in Argentina. Confiscations of this species are common, as is the voluntary surrender of animals by owners no longer able or willing to care for them. These animals ultimately arrive at rehabilitation centers and, in many cases, are released into natural environments that may differ from the original sites where they were captured. Until recently, the lack of genetic analysis of the individuals involved led to biased relocation decisions. We followed the reintroduction of 12 A. caraya individuals in a protected area (Isla Palacio, Misiones, Argentina). The presence of potential predators such as pumas (Puma concolor) and jaguars (Panthera onca) in this area was confirmed by camera traps, footprints and feces. After the disappearance of four A. caraya at the reintroduction site, we investigated the applicability of genetic assignment tests based on genotypic data to accurately identify predated individuals. Genetic analyses allowed us to determine the predator species (P. onca) and to identify the predated individuals as two of the reintroduced animals. This procedure is promising for identifying the remains of predated individuals, and can contribute to the design of reintroduction policies based on scientific evidence.

Reducing the Extinction Risk of Populations Threatened by Infectious Diseases

Extinction risk is increasing for a range of species due to a variety of threats, including disease. Emerging infectious diseases can cause severe declines in wild animal populations, increasing population fragmentation and reducing gene flow. Small, isolated, host populations may lose adaptive potential and become more susceptible to extinction due to other threats. Management of the genetic consequences of disease-induced population decline is often necessary. Whilst disease threats need to be addressed, they can be difficult to mitigate. Actions implemented to conserve the Tasmanian devil (Sarcophilus harrisii), which has suffered decline to the deadly devil facial tumour disease (DFTD), exemplify how genetic management can be used to reduce extinction risk in populations threatened by disease. Supplementation is an emerging conservation technique that may benefit populations threatened by disease by enabling gene flow and conserving their adaptive potential through genetic restoration. Other candidate species may benefit from genetic management via supplementation but concerns regarding outbreeding depression may prevent widespread incorporation of this technique into wildlife disease management. However, existing knowledge can be used to identify populations that would benefit from supplementation where risk of outbreeding depression is low. For populations threatened by disease and, in situations where disease eradication is not an option, wildlife managers should consider genetic management to buffer the host species against inbreeding and loss of genetic diversity.

Evolutionary principles and genetic considerations for guiding conservation interventions under climate change

Impacts of climate change are apparent in natural systems around the world. Many species are and will continue to struggle to persist in their current location as their preferred environment changes. Traditional conservation efforts aiming to prevent local extinctions have focused on two aspects that theoretically enhance genetic diversity-population connectivity and population size-through 'passive interventions' (such as protected areas and connectivity corridors). However, the exceptionally rapid loss of biodiversity that we are experiencing as result of anthropogenic climate change has shifted conservation approaches to more 'active interventions' (such as rewilding, assisted gene flow, assisted evolution, artificial selection, genetic engineering). We integrate genetic/genomic approaches into an evolutionary biology framework in order to discuss with scientists, conservation managers and decision makers about the opportunities and risks of interventions that need careful consideration in order to avoid unwanted evolutionary outcomes.

Freshwater mussels (Unionidae) brought into captivity exhibit up-regulation of genes involved in stress and energy metabolism

Approximately two thirds of freshwater mussel species in the United States and Canada are imperiled, and populations are declining rapidly. Translocation and captive management are commonly used to mitigate losses of freshwater mussel biodiversity, but these conservation tools may result in decreased growth and increased mortality. This study uses RNA-Seq to determine how translocation into captivity affects gene expression in Amblema plicata. Mussels were collected from the Muskingum River in Ohio, USA and brought into a captive holding facility. RNA was extracted from gill tissue 11 months post translocation from mussels in captivity and the Muskingum River on the same day. RNA was sequenced on an Illumina HiSeq 2500, and differential expression analysis was performed on de novo assembled transcripts. More than 1200 transcripts were up-regulated in captive mussels, and 246 were assigned functional annotations. Many up-regulated transcripts were involved in energy metabolism and the stress response, such as heat shock proteins and antioxidants. More than 500 transcripts were down-regulated in captive mussels, and 41 were assigned functional annotations. We observed an over-representation of down-regulated transcripts associated with immune response. Our work suggests that A. plicata experienced moderate levels of stress and altered energy metabolism and immune response for at least 11 months post translocation into captivity.

Consistent community genetic effects in the context of strong environmental and temporal variation in Eucalyptus

Provenance translocations of tree species are promoted in forestry, conservation, and restoration in response to global climate change. While this option is driven by adaptive considerations, less is known of the effects translocations can have on dependent communities. We investigated the relative importance and consistency of extended genetic effects in Eucalyptus using two species-E. globulus and E. pauciflora. In E. globulus, the dependent arthropod and pathogen canopy communities were quantified based on the abundance of 49 symptoms from 722 progeny from 13 geographic sub-races across 2 common gardens. For E. pauciflora, 6 symptoms were quantified over 2 years from 238 progeny from 16 provenances across 2 common gardens. Genetic effects significantly influenced communities in both species. However, site and year effects outweighed genetic effects with site explaining approximately 3 times the variation in community traits in E. globulus and site and year explaining approximately 6 times the variation in E. pauciflora. While the genetic effect interaction terms were significant in some community traits, broad trends in community traits associated with variation in home-site latitude for E. globulus and home-site altitude for E. pauciflora were evident. These broad-scale trends were consistent with patterns of adaptive differentiation within each species, suggesting there may be extended consequences of local adaptation. While small in comparison to site and year, the consistency of genetic effects highlights the importance of provenance choice in tree species, such as Eucalyptus, as adaptive divergence among provenances may have significant long-term effects on biotic communities.

Genetic Rescue and the Plight of Ponui Hybrids

Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.

The evolutionary consequences of human-wildlife conflict in cities

Human-wildlife interactions, including human-wildlife conflict, are increasingly common as expanding urbanization worldwide creates more opportunities for people to encounter wildlife. Wildlife-vehicle collisions, zoonotic disease transmission, property damage, and physical attacks to people or their pets have negative consequences for both people and wildlife, underscoring the need for comprehensive strategies that mitigate and prevent conflict altogether. Management techniques often aim to deter, relocate, or remove individual organisms, all of which may present a significant selective force in both urban and nonurban systems. Management-induced selection may significantly affect the adaptive or nonadaptive evolutionary processes of urban populations, yet few studies explicate the links among conflict, wildlife management, and urban evolution. Moreover, the intensity of conflict management can vary considerably by taxon, public perception, policy, religious and cultural beliefs, and geographic region, which underscores the complexity of developing flexible tools to reduce conflict. Here, we present a cross-disciplinary perspective that integrates human-wildlife conflict, wildlife management, and urban evolution to address how social-ecological processes drive wildlife adaptation in cities. We emphasize that variance in implemented management actions shapes the strength and rate of phenotypic and evolutionary change. We also consider how specific management strategies either promote genetic or plastic changes, and how leveraging those biological inferences could help optimize management actions while minimizing conflict. Investigating human-wildlife conflict as an evolutionary phenomenon may provide insights into how conflict arises and how management plays a critical role in shaping urban wildlife phenotypes.

Using genetic evaluation to guide conservation of remnant Juniperus communis (Cupressaceae) populations

Many critically endangered plant species exist in small, genetically depauperate or inbred populations, making assisted gene flow interventions necessary for long-term population viability. However, before such interventions are implemented, conservation practitioners must consider the genetic and demographic status of extant populations, which are strongly affected by species' life-history traits. In northwestern Europe, Juniperus communis, a dioecious, wind-pollinated and bird-dispersed gymnosperm, has been declining for the past century and largely exists in small, isolated and senescent populations. To provide useful recommendations for a recovery plan involving translocation of plants, we investigated genetic diversity and structure of populations in Belgium using four microsatellite and five plastid single-nucleotide polymorphism (SNP) markers. We detected no clonality in the populations, suggesting predominantly sexual reproduction. Populations exhibited high genetic diversity (H_e  = 0.367-0.563) and low to moderate genetic differentiation (F_ST  ≤ 0.133), with no clear geographic structure. Highly positive inbreeding coefficients (F_IS  = 0.221-0.507) were explained by null alleles, population substructuring and biparental inbreeding. No isolation by distance was observed among distant populations, but isolation at close geographic proximity was found. Patterns were consistent with high historical gene flow through pollen and seed dispersal at both short and long distances. We also tested four pre-germination treatments among populations to improve germination rates; however, germination rates remained low and only cold-stratification treatments induced germination in some populations. To bolster population regeneration, introductions of cuttings from several source populations are recommended, in combination with in situ management practices that improve seedling survival and with ex situ propagation.

Evaluating wildlife translocations using genomics: A bighorn sheep case study

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

Genetic Consequences of Multiple Translocations of the Banded Hare-Wallaby in Western Australia

Many Australian mammal species now only occur on islands and fenced mainland havens free from invasive predators. The range of one species, the banded hare-wallaby (Lagostrophus fasciatus), had contracted to two offshore islands in Western Australia. To improve survival, four conservation translocations have been attempted with mixed success, and all occurred in the absence of genetic information. Here, we genotyped seven polymorphic microsatellite markers in two source (Bernier Island and Dorre Island), two historic captive, and two translocated L. fasciatus populations to determine the impact of multiple translocations on genetic diversity. Subsequently, we used population viability analysis (PVA) and gene retention modelling to determine scenarios that will maximise demographic resilience and genetic richness of two new populations that are currently being established. One translocated population (Wadderin) has undergone a genetic bottleneck and lost 8.1% of its source population’s allelic diversity, while the other (Faure Island) may be inbred. We show that founder number is a key parameter when establishing new L. fasciatus populations and 100 founders should lead to high survival probabilities. Our modelling predicts that during periodic droughts, the recovery of source populations will be slower post-harvest, while 75% more animals—about 60 individuals—are required to retain adequate allelic diversity in the translocated population. Our approach demonstrates how genetic data coupled with simulations of stochastic environmental events can address central questions in translocation programmes.

Past, current, and potential future distributions of unique genetic diversity in a cold-adapted mountain butterfly

AIM

Climatic changes throughout the Pleistocene have strongly modified species distributions. We examine how these range shifts have affected the genetic diversity of a montane butterfly species and whether the genetic diversity in the extant populations is threatened by future climate change.

LOCATION

Europe.

TAXON

Erebia epiphron Lepidoptera: Nymphalidae.

METHODS

We analyzed mtDNA to map current genetic diversity and differentiation of E. epiphron across Europe to identify population refugia and postglacial range shifts. We used species distribution modeling (SDM) to hindcast distributions over the last 21,000 years to identify source locations of extant populations and to project distributions into the future (2070) to predict potential losses in genetic diversity.

RESULTS

We found substantial genetic diversity unique to specific regions within Europe (total number of haplotypes = 31, number of unique haplotypes = 27, H d = 0.9). Genetic data and SDM hindcasting suggest long-term separation and survival of discrete populations. Particularly, high rates of unique diversity in postglacially colonized sites in England (H d = 0.64) suggest this population was colonized from a now extinct cryptic refugium. Under future climate change, SDMs predict loss of climate suitability for E. epiphron, particularly at lower elevations (<1,000 meters above sea level) equating to 1 to 12 unique haplotypes being at risk under climate scenarios projecting 1°C and 2-3°C increases respectfully in global temperature by 2070.

MAIN CONCLUSIONS

Our results suggest that historical range expansion and retraction processes by a cold-adapted mountain species caused diversification between populations, resulting in unique genetic diversity which may be at risk if distributions of cold-adapted species shrink in future. Assisted colonizations of individuals from at-risk populations into climatically suitable unoccupied habitat might help conserve unique genetic diversity, and translocations into remaining populations might increase their genetic diversity and hence their ability to adapt to future climate change.

Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies

Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically. Several traits, such as high rates of outcrossing, long-distance pollen and seed dispersal, large effective population sizes (N_e ), arborescent stature, low population density, longevity, overlapping generations, and occurrence in late successional communities, may make trees less sensitive to genetic bottlenecks and more resistant to habitat fragmentation or climate change. We recommend that guidelines for genetic conservation strategies be designed differently for tree species versus other types of plant species. Because most tree species fit an LH scenario (low [L] genetic differentiation and high [H] genetic diversity), tree seeds could be sourced from a few populations distributed across the species' range. For the in situ conservation of trees, translocation is a viable option to increase N_e . In contrast, rare herbaceous understory species are frequently HL (high differentiation and low diversity) species. Under the HL scenario, seeds should be taken from many populations with high genetic diversity. In situ conservation efforts for herbaceous plants should focus on protecting habitats because the typically small populations of these species are vulnerable to the loss of genetic diversity. The robust allozyme genetic diversity databases could be used to develop conservation strategies for species lacking genetic information. As a case study of reforestation with several tree species in denuded areas on the Korean Peninsula, we recommend the selection of local genotypes as suitable sources to prevent adverse effects and to insure the successful restoration in the long term.

Genetic divergence and evidence of human-mediated translocation of two-fingered sloths (Choloepus hoffmanni) in Costa Rica

Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanization. Reintroductions from rescue centres are commonplace across the country, yet their genetic diversity and population structure are unknown, and there is currently little consideration of the genetic background prior to intervention or releases. We used microsatellite analysis to undertake the first exploratory investigation into sloth population genetics in Costa Rica. Using data from 98 two-fingered sloths (Choloepus hoffmanni) from four different geographic regions, we determined the presence of four potential genetic groups, three of them with minimal population structuring despite the limited dispersal ability and presence of physical barriers. Sloths from the North appear to represent a highly distinct population that we propose may require management as a discrete unit for conservation. We stress the need for additional analyses to better understand the genetic structure and diversity of North andWest regions and suggest that rescue facilities in Costa Rica should consider the genetic background of rehabilitated sloths when planning future reintroductions. Our results also highlight the threat posed by physical isolation due to widespread urbanization and agriculture expansion for a species with a weak dispersal ability.

Genetic assessment of a conservation breeding program of the houbara bustard (Chlamydotis undulata undulata) in Morocco, based on pedigree and molecular analyses

Protection and restoration of species in the wild may require conservation breeding programs under genetic management to minimize deleterious effects of genetic changes that occur in captivity, while preserving populations' genetic diversity and evolutionary resilience. Here, through interannual pedigree analyses, we first assessed the efficiency of a 21-year genetic management, including minimization of mean kinship, inbreeding avoidance, and regular addition of founders, of a conservation breeding program targeting on Houbara bustard (Chlamydotis undulata undulata) in Morocco. Secondly, we compared pedigree analyses, the classical way of assessing and managing genetic diversity in captivity, to molecular analyses based on seven microsatellites. Pedigree-based results indicated an efficient maintenance of the genetic diversity (99% of the initial genetic diversity retained) while molecular-based results indicated an increase in allelic richness and an increase in unbiased expected heterozygosity across time. The pedigree-based average inbreeding coefficient F remained low (between 0.0004 and 0.003 in 2017) while the proportion of highly inbred individuals (F > .1) decreased over time and reached 0.2% in 2017. Furthermore, pedigree-based F and molecular-based individual multilocus heterozygosity were weakly negatively correlated, (Pearson's r = -.061 when considering all genotyped individuals), suggesting that they cannot be considered as alternatives, but rather as complementary sources of information. These findings suggest that a strict genetic monitoring and management, based on both pedigree and molecular tools can help mitigate genetic changes and allow to preserve genetic diversity and evolutionary resilience in conservation breeding programs.

Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra

Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study, we assess the climate resilience of Themeda triandra, a foundational species and the most widespread plant in Australia, by assessing the relative contributions of spatial, environmental and ploidy factors to contemporary genomic variation. Reduced-representation genome sequencing on 472 samples from 52 locations was used to test how the distribution of genomic variation, including ploidy polymorphism, supports adaptation to hotter and drier climates. We explicitly quantified isolation by distance (IBD) and isolation by environment (IBE) and predicted genomic vulnerability of populations to future climates based on expected deviation from current genomic composition. We found that a majority (54%) of genomic variation could be attributed to IBD, while an additional 22% (27% when including ploidy information) could be explained by two temperature and two precipitation climate variables demonstrating IBE. Ploidy polymorphisms were common within populations (31/52 populations), indicating that ploidy mixing is characteristic of T. triandra populations. Genomic vulnerabilities were found to be heterogeneously distributed throughout the landscape, and our analysis suggested that ploidy polymorphism, along with other factors linked to polyploidy, reduced vulnerability to future climates by 60% (0.25-0.10). Our data suggests that polyploidy may facilitate adaptation to hotter climates and highlight the importance of incorporating ploidy in adaptive management strategies to promote the resilience of this and other foundation species.

Threats from wildlife trade: The importance of genetic data in safeguarding the endangered Four-eyed Turtle (Sacalia quadriocellata)

Wildlife trade has been considered one of the largest threats to biodiversity in Southeast Asia. Many vertebrates, such as pangolins, elephants and turtles have been heavily hunted as a result of high demand from emerging markets in China and other countries in the region. In Vietnam, over-exploitation of turtles over several decades to supply the international trade has extirpated numerous populations and driven several species to the brink of extinction. To reverse this trend, conservation measures, such as re-introduction of confiscated or captive-bred animals to their native habitats, should be implemented to recover severely declined local populations. For species with a complex phylogeographic structure, however, it is crucial to understand geographic patterns of genetically-distinct populations to avoid releasing animals of unknown origin to wrong localities. In this study, we investigate the phylogeographic pattern of the Four-eyed Turtle (Sacalia quadriocellata), a widely traded species, which occurs in southern China, northern and central Laos and much of Vietnam, using samples with known localities and those collected from the local trade. Our range-wide phylogenetic and network study, based on the complete mitochondrial cytochrome b gene, recovered at least three major clades and seven subclades within the species range. Amongst these, two subclades, one from northern Annamites, Vietnam and the other from north-eastern Laos, are newly discovered. The fine scale phylogeographic analysis helped us to assign misidentified sequences from GenBank and those from confiscated animals with unknown origin to well-defined geographic populations. The results highlight the importance of incorporating samples collected from the local trade and the wild in genetic analyses to support both ex-situ and in-situ conservation programmes of highly-threatened species in accordance with the IUCN’s One Plan Approach.

Genetic data and climate niche suitability models highlight the vulnerability of a functionally important plant species from south-eastern Australia

Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south-eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (N e), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support.

Genetic diversity in natural range remnants of the critically endangered hirola antelope

The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.

Evaluating the Impact of Wildlife Shelter Management on the Genetic Diversity of Erinaceus europaeus and E. roumanicus in Their Contact Zone

Simple Summary

Hedgehogs are regularly brought to wildlife shelters. Depending on the area from where animals are accepted, translocation can occur between different regions or populations. In this study, the genetic diversity of wild hedgehog populations was compared with “shelter populations” within central Europe focusing on the western contact zone between both European hedgehog species. Some shelters were hosting both species at the same time, in one this could be shown genetically. Generally, no difference in genetic diversity between shelter individuals and wild populations was found. Two shelters from Innsbruck hosted individuals that probably belong to two subpopulations. This indicates that shelter management-related translocations could facilitate gene flow across a dispersal barrier.

Abstract

Hedgehogs are among the most abundant species to be found within wildlife shelters and after successful rehabilitation they are frequently translocated. The effects and potential impact of these translocations on gene flow within wild populations are largely unknown. In this study, different wild hedgehog populations were compared with artificially created “shelter populations”, with regard to their genetic diversity, in order to establish basic data for future inferences on the genetic impact of hedgehog translocations. Observed populations are located within central Europe, including the species Erinaceus europaeus and E. roumanicus. Shelters were mainly hosting one species; in one case, both species were present syntopically. Apart from one exception, the results did not show a higher genetic diversity within shelter populations, indicating that individuals did not originate from a wider geographical area than individuals grouped into one of the wild populations. Two shelters from Innsbruck hosted individuals that belonged to two potential clusters, as indicated in a distance analysis. When such a structure stems from the effects of landscape elements like large rivers, the shelter management-related translocations might lead to homogenization across the dispersal barrier.

Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning

Translocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.

The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method

Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying F_ST. However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.

Genetic monitoring of translocated plant populations in practice

Plant translocations allow the restoration of genetic diversity in inbred and depauperate populations and help to prevent the extinction of critically endangered species. However, the successes of plant translocations in restoring genetically viable populations and the possible associated key factors are still insufficiently evaluated. To fill this gap, we carried out a thorough genetic monitoring of three populations of Arnica montana that were created or reinforced by the translocation of plants obtained from seeds of two large natural source populations from southern Belgium. We genotyped nine microsatellite markers and measured fitness quantitative traits over two generations (transplants, F1 seed progeny and newly established F1 juveniles). Two years after translocation, the genetic restoration had been effective, with high genetic diversity and low genetic differentiation across generations, extensive contemporary pollen flow, admixture between seed sources in the F1 generation and recruitment of new individuals from seeds. We detected site, seed source and maternal plant effects on plant fitness. The results also suggest that phenotypic plasticity may favour short-term individual survival and long-term adaptive capacity and enhance the evolutionary resilience of the populations to changing environmental conditions. We found no sign of heterosis or outbreeding depression at early life stages in the F1 generation. Our findings emphasize the importance of the translocation design (700 transplants of mixed sources, planted at high density) as well as the preparatory site management for the successful outcome of the translocations, which maximized flowering, random mating, and recruitment from seeds in the first years after translocation.

Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species.