Temporal variation in the genetic composition of an endangered marsupial reflects reintroduction history

The loss of genetic variation and genetic divergence from source populations are common problems for reintroductions that use captive animals or a small number of founders to establish a new population. This study evaluated the genetic changes occurring in a captive and a reintroduced population of the dibbler (Parantechinus apicalis) that were established from multiple source populations over a twelve-year period, using 21 microsatellite loci. While the levels of genetic variation within the captive and reintroduced populations were relatively stable, and did not differ significantly from the source populations, their effective population size reduced 10–16-fold over the duration of this study. Evidence of some loss of genetic variation in the reintroduced population coincided with genetic bottlenecks that occurred after the population had become established. Detectable changes in the genetic composition of both captive and reintroduced populations were associated with the origins of the individuals introduced to the population. We show that interbreeding between individuals from different source populations lowered the genetic relatedness among the offspring, but this was short-lived. Our study highlights the importance of sourcing founders from multiple locations in conservation breeding programs to avoid inbreeding and maximize allelic diversity. The manipulation of genetic composition in a captive or reintroduced population is possible with careful management of the origins and timings of founder releases

Mixing genetically and morphologically distinct populations in translocations: Asymmetrical introgression in a newly established population of the boodie (Bettongia lesueur)

The use of multiple source populations provides a way to maximise genetic variation and reduce the impacts of inbreeding depression in newly established translocated populations. However, there is a risk that individuals from different source populations will not interbreed, leading to population structure and smaller effective population sizes than expected. Here, we investigate the genetic consequences of mixing two isolated, morphologically distinct island populations of boodies (Bettongia lesueur) in a translocation to mainland Australia over three generations. Using 18 microsatellite loci and the mitochondrial D-loop region, we monitored the released animals and their offspring between 2010 and 2013. Despite high levels of divergence between the two source populations (FST = 0.42 and ϕST = 0.72), there was clear evidence of interbreeding between animals from different populations. However, interbreeding was non-random, with a significant bias towards crosses between the genetically smaller-sized Barrow Island males and the larger-sized Dorre Island females. This pattern of introgression was opposite to the expectation that male–male competition or female mate choice would favour larger males. This study shows how mixing diverged populations can bolster genetic variation in newly established mammal populations, but the ultimate outcome can be difficult to predict, highlighting the need for continued genetic monitoring to assess the long-term impacts of admixture

Disentangling the Genetic Relationships of Three Closely Related Bandicoot Species across Southern and Western Australia

The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus, and I. fusciventer, has been ongoing and hampered by limited sampling in studies to date. Identification of taxonomic units remains a high priority, as all are threatened to varying extents by ongoing habitat loss and feral predation. To aid diagnosis of conservation units, we increased representative sampling of I. auratus and I. fusciventer from Western Australia (WA) and investigated genetic relationships of these with I. obesulus from South Australia (SA) and Victoria (Vic) using microsatellite markers and mitochondrial DNA. mtDNA analysis identified three major clades concordant with I. obesulus (Vic), I. auratus, and I. fusciventer; however, I. obesulus from SA was polyphyletic to WA taxa, complicating taxonomic inference. Microsatellite data aided identification of evolutionarily significant units consistent with existing taxonomy, with the exception of SA I. obesulus. Further, analyses indicated SA and Vic I. obesulus have low diversity, and these populations may require more conservation efforts than others to reduce further loss of genetic diversity

Data from: Population density and size influence pollen dispersal pattern and mating system of the predominantly outcrossed Banksia nivea (Proteaceae) in a threatened ecological community

Gene flow is a critical component of plant mating systems and influences population fitness, yet pollen dispersal can be highly variable and influenced by natural and anthropogenic fragmentation. Gene flow through pollen dispersal was investigated in two populations of contrasting size and habitat context in Banksia nivea ssp. uliginosa, a rare species in the Busselton ironstone threatened ecological community with a naturally fragmented distribution. Paternity analysis was conducted with seven microsatellite loci to determine mating system parameters and patterns of pollen dispersal. Outcrossing was high in both populations with a similar level of selfing for both populations despite differences in population size, density and vegetation matrix. Most mating occurred within 10 m of a mother plant in the small, clumped population, while more dispersed mating, up to 50 m from a mother plant, was recorded in the large, less dense population. Our results show that population density and size are important influences on mating system parameters and level of pollen dispersal

Banksia nivea genotype

Genotypes of mature plants and seeds of Banksia nivea spp. uliginos

Population Genomics of Bettongia lesueur: Admixing Increases Genetic Diversity with no Evidence of Outbreeding Depression

Small and isolated populations are subject to the loss of genetic variation as a consequence of inbreeding and genetic drift, which in turn, can affect the fitness and long-term viability of populations. Translocations can be used as an effective conservation tool to combat this loss of genetic diversity through establishing new populations of threatened species, and to increase total population size. Releasing animals from multiple genetically diverged sources is one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using high-resolution genomic markers through double-digest restriction site-associated sequencing (ddRAD-seq) and life history data collected over nine years of monitoring, this study investigates the genetic and fitness consequences of admixing two genetically-distinct subspecies of Bettongia lesueur in a conservation translocation. Using single nucleotide polymorphisms (SNPs) identified from 215 individuals from multiple generations, we found an almost 2-fold increase in genetic diversity in the admixed translocation population compared to the founder populations, and this was maintained over time. Furthermore, hybrid class did not significantly impact on survivorship or the recruitment rate and therefore we found no indication of outbreeding depression. This study demonstrates the beneficial application of mixing multiple source populations in the conservation of threatened species for minimizing inbreeding and enhancing adaptive potential and overall fitness

Species-specific SNP arrays for non-invasive genetic monitoring of a vulnerable bat

Abstract Genetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44–50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach

Genotype

Microsatellite loci of Parantechinus apicali

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

Abstract 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 FSTs 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

Mixing Genetically and Morphologically Distinct Populations in Translocations: Asymmetrical Introgression in A Newly Established Population of the Boodie (Bettongia lesueur)

The use of multiple source populations provides a way to maximise genetic variation and reduce the impacts of inbreeding depression in newly established translocated populations. However, there is a risk that individuals from different source populations will not interbreed, leading to population structure and smaller effective population sizes than expected. Here, we investigate the genetic consequences of mixing two isolated, morphologically distinct island populations of boodies (Bettongia lesueur) in a translocation to mainland Australia over three generations. Using 18 microsatellite loci and the mitochondrial D-loop region, we monitored the released animals and their offspring between 2010 and 2013. Despite high levels of divergence between the two source populations (FST = 0.42 and ϕST = 0.72), there was clear evidence of interbreeding between animals from different populations. However, interbreeding was non-random, with a significant bias towards crosses between the genetically smaller-sized Barrow Island males and the larger-sized Dorre Island females. This pattern of introgression was opposite to the expectation that male&ndash;male competition or female mate choice would favour larger males. This study shows how mixing diverged populations can bolster genetic variation in newly established mammal populations, but the ultimate outcome can be difficult to predict, highlighting the need for continued genetic monitoring to assess the long-term impacts of admixture