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

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

This data is published in 'Thavornkanlapachai, R.; Mills, H.R.; Ottewell, K.; Dunlop, J.; Sims, C.; Morris, K.; Donaldson, F.; Kennington, W.J. 2019. Mixing genetically and morphologically distinct populations in translocations: Asymmetrical introgression in a newly established population of the boodie (Bettongia lesueur). Genes'. The file contains microsatellite data, mtDNA sequences and morphological measurements

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

This data is published in 'Thavornkanlapachai, R.; Mills, H.R.; Ottewell, K.; Dunlop, J.; Sims, C.; Morris, K.; Donaldson, F.; Kennington, W.J. 2019. Mixing genetically and morphologically distinct populations in translocations: Asymmetrical introgression in a newly established population of the boodie (Bettongia lesueur). Genes'. The file contains microsatellite data, mtDNA sequences and morphological measurements

Dibbler raw microsatellite genotype

20 Microsatellite loci of dibbler (Parantechinus apicalis) published in the paper 'Thavornkanlapachai, R.; Mills, H.R.; Ottewell, K.; Friend, J.A.; Kennington, W.J. Temporal variation in the genetic composition of an endangered marsupial reflects reintroduction history, Diversity, Under Review.' The aim of the paper to assess reintroduction outcomes at the Peniup Nature Reserve sourcing from multiple source populations in the Fitzgerald River National Park in Western Australia. The released animals were captive bred at Perth Zoo and were released over multiple years between 2001-2010. The founders of the captive populations were collected from the western (Twertup) and eastern (Hamersley Moir and Moir Track) side of Fitzgerald River National Park. The source and reintroduced populations were also undergone regular monitoring over multiple years. This data contains columns of year of collection, population names, lab ID which contains sex information and genotype scores. Missing genotype is labelled as zero

Degree of fragmentation and population size do not adversely affect reproductive success of a rare shrub species, Banksia nivea (Proteaceae), in a naturally fragmented community

Fragmentation of plant communities is generally considered to be detrimental to the survival of the constituent species, especially those that are rare. We investigated the effects of fragmentation on reproductive biology in nine populations of the rare taxon Banksia nivea subsp. uliginosa, differing in size and habitat context. Small mammals were the main pollinator, with lower contributions from honeybees and birds (honeyeaters). There was no significant relationship between population size, fruit set and seed germinability. Fruit set was marginally highest (25.5 ± 3.4) in medium size populations and was variable over years. Lower fruit set (1.0 ± 0.6) in the smallest population may be due to inbreeding depression or lack of pollinators in a degraded habitat, but low fruit set was also observed in the largest population despite high levels of gene flow, possibly due to low pollinator visitation rate in a low-density population. Seeds from all populations had high germination success (>93.4%). Predation occurred in up to 56% of fruit and increased with increasing population size, but was not significantly different between populations of different size. Our study provided evidence that the reproductive output in species in a naturally fragmented landscape system may be resilient to reduced population size and other influences of anthropogenic fragmentation

Genotype

Microsatellite loci of Parantechinus apicali

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

Development and optimisation of molecular assays for microsatellite genotyping and molecular sexing of non-invasive samples of the ghost bat, Macroderma gigas

The ghost bat (Macroderma gigas) is endemic to Australia but is under threat, with scarce information available on the genetic health of remaining populations. Here, we develop molecular assays for microsatellite genotyping and molecular sexing of non-invasive samples as a genetic monitoring tool to identify individuals, measure genetic diversity and investigate spatial and temporal patterns of habitat use by ghost bats. We identified novel microsatellites through high-throughput sequencing on the Illumina MiSeq platform. Of 48 loci tested, six markers were added to five previously developed microsatellite loci. We developed three Y-linked (DDX3Y, Zfy and SRY) and one X-linked markers (Zfx) to enable molecular identification of sex. To assess performance, all 11 microsatellite and four sex-linked markers were amplified in three multiplex reactions in 160 M. gigas faecal samples from the Pilbara region, Western Australia. The combined markers offered a high level of individual discrimination (PIDsibs = 0.00002) and we detected 19 bats in total (11 males, 4 females and 4 sex undetermined). The number of alleles per locus ranged from 5 to 14 and the average observed and expected heterozygosity across loci were Ho = 0.735 (0.58–0.91) and uHe = 0.785 (0.59–0.89) respectively. Our molecular assays allowed identification of individuals from faecal samples at multiple time points and spatial locations and enabled us to elucidate patterns of habitat usage at the study site. This study highlights the value of our molecular assays as a potential capture-mark-recapture technique for population monitoring for this species

Contemporary pollen-mediated gene immigration reflects the historical isolation of a rare, animal-pollinated shrub in a fragmented landscape

Fragmentation is generally considered to have negative impacts on widespread outbreeders but impacts on gene flow and diversity in patchy, naturally rare, self-compatible plant species remain unclear. We investigated diversity, gene flow and contemporary pollen-mediated gene immigration in the rare, narrowly distributed endemic shrub Calothamnus quadrifidus ssp. teretifolius. This taxon occurs in an internationally recognized biodiversity hotspot subjected to recent human-induced fragmentation and the condition of the remnants ranges from intact to highly degraded. Using microsatellites, we found that inbreeding, historically low gene flow and significant population differentiation have characterized the genetic system of C. quadrifidus ssp. teretifolius. Inbreeding arises from self-pollination, a small amount of biparental inbreeding and significant correlation of outcross paternity but fecundity was high suggesting populations might have purged their lethals. Paternity analyses show that pollinators can move pollen over degraded and intact habitat but populations in both intact and degraded remnants had few pollen parents per seed parent and low pollen immigration. Genetic diversity did not differ significantly between intact and degraded remnants but there were signs of genetic bottlenecks and reduced diversity in some degraded remnants. Overall, our study suggests human-induced fragmentation has not significantly changed the mating system, or pollen immigration to, remnant populations and therefore genetic connectivity need not be the highest conservation priority. Rather, for rare species adapted to higher levels of inbreeding, conservation efforts may be best directed to managing intact habitats and ecosystem processes