Evaluation of a trap-and-transport program for a threatened population of steelhead ( Oncorhynchus mykiss ) Abstract Trap-and-transport programs for migratory fish attempt to mitigate for lost habitat blocked by impassable dams. These programs aim to assist with conservation and recovery of declining populations by accessing habitat protected from impacts downstream, such as introgression or competition with hatchery-origin fish. This study examined a trap-and-transport program that supplemented a native population of winter-run steelhead (Oncorhynchus mykiss) above Foster Dam in the South Santiam River, Oregon. The study examined whether outplanted adults transported from 2012 to 2016 reproduced successfully using 268 single nucleotide polymorphisms (SNPs) and an exclusion analysis in CERVUS. Genotypes from two SNPs in the GREB1L gene were used to associate each fish with maturation at return migration: premature migration (summer-run, non-native) or mature migration (winter-run, native). Parentage analyses demonstrated that 51% of outplanted steelhead successfully produced either juvenile or adult offspring. More than 68% of the natural-origin adults outplanted during the study were homozygous for mature migration alleles that are typical of native, winter-run steelhead, however, potential introgression from non-native, summer-run steelhead was detected in 26% of the outplanted adults. These results indicate that transported adult steelhead successfully produced juvenile and adult steelhead, and introgression associated with non-native steelhead may be introduced through the trap-and-transport program.

Population genomics of the peripheral freshwater fish Polynemus melanochir (Perciformes, Polynemidae) in a changing Mekong Delta Abstract The Mekong River is a vital fisheries resource supporting millions of people in mainland Southeast Asia. However, numerous threats have the potential to negatively impact fish populations in this region including overfishing, pollution, climate change and increased urban, agriculture and upstream hydropower development. Although a few studies have examined the population genetic structure of fishes within the upper Mekong River, no known studies have explored that of fishes within the Mekong Delta (MD). Here, we examine the population structure of an important food fish within the MD, Polynemus melanochir, using a panel of 1735 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA (RAD) sequencing across eight locations on the Tien (Mekong) and Hau (Bassac) Rivers in Vietnam. Pairwise FST values, principal component analysis and Structure analysis all indicate high levels of gene flow among the sites sampled across the MD. In contrast to the lack of genetic structure, high levels of relatedness were found, including 26 putatively related pairs, as well as an effective population size (Ne) of less than 500 across the MD. While panmixia indicates that fragmentation of this population is not presently an important threat, a low Neestimate suggests this species may not be resilient to long-term environmental changes in the MD. The reliance on P. melanochir as a food resource may be contingent on management and mitigation of low effective population sizes.

Genetic diversity and differentiation among the species of African mahogany ( Khaya spp.) based on a large SNP array Abstract The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97–100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.

Dispersal, philopatry and population genetic structure of the mainland dibbler, Parantechinus apicalis Abstract Dispersal plays an important role in the population structure and resilience of species. To gain a better understanding of dispersal in the endangered Australian marsupial, the dibbler (Parantechinus apicalis), we screened 199 individuals from seven locations within the Fitzgerald River National Park, Western Australia, for genetic variation at 17 microsatellite loci. There were high levels of genetic variation within all sites (gene diversity ranged from 0.68 to 0.71) as well as significant genetic differentiation between sites less than 19 km apart that were consistent over multiple years (FST = 0.021–0.073). A Bayesian clustering analysis revealed the presence of two genetic clusters separating P. apicalis in the western part from the central and eastern parts of the National Park. There was also evidence of fine-scale population structure with spatial autocorrelation analysis showing positive genetic structure up to distances of 200 m in females. By contrast males did not exhibit significant fine-scale population structure, thus suggesting P. apicalis exhibits female philopatry and male-biased dispersal. We recommend that management should take into account the existence of two subpopulations within the National Park and manage accordingly. Individuals selected for captive breeding and translocation programs, especially females, should be sampled at least 200 m apart to reduce the likelihood of selecting related individuals.

Integrating measures of long-distance dispersal into vertebrate conservation planning: scaling relationships and parentage-based dispersal analysis in the koala Abstract Improved knowledge of dispersal parameters across multiple populations is essential for the effective management of species exposed to ongoing threats from habitat loss, fragmentation and climate change. Currently, management decisions are based on incomplete or insufficient knowledge of key dispersal parameters, especially long-distance dispersal, and its role in maintaining metapopulation connectivity, facilitating range shifts under climate change, or enabling the colonization of new habitats. Using a combination of microsatellite-based population genetic analyses, scaling relationships and parentage-based dispersal analysis we investigated levels and patterns of long-distance dispersal in the koala. Using home range size as a scalar predicted spatial variation in maximum dispersal distance amongst regional populations (range 13.4–43.4 km), while parentage-based dispersal analysis showed that long-distance dispersal (> 11.2 km) accounted for 16.7–18.5% of movements in a focal population. Common movement patterns were discerned, despite varying levels of imprecision and bias, that suggest an important role for long-distance dispersal in maintaining metapopulation connectivity. Our results suggest that implementation of a systematic approach to the estimation of dispersal across multiple populations would benefit koala conservation and management. This will require the use of both empirical and simulation studies to quantify and minimize sources of imprecision and bias that can occur including those related to incomplete sampling, the presence of fine-scale spatial genetic structure and areas of localized inbreeding. As limitations associated with partial sampling are likely to remain an inherent feature of large-scale dispersal studies, a large number of loci should be assayed.

Multiple drivers of interannual oyster settlement and recruitment in the lower Chesapeake Bay Abstract Despite global investment in shellfish restoration activities, relatively little attention has been given to predicting optimal restoration sites and testing these expectations. We used a coupled biological-physical connectivity model as a guide to plant two distinct hatchery-spawned strains of the eastern oyster, Crassostrea virginica, in the Lafayette River, Virginia during the summer of 2013 at two locations corresponding to virtual spawning locations within the connectivity model. We utilized single nucleotide polymorphism markers to test the model predictions by genotyping oysters recruited after planting two hatchery-spawned strains and examining interannual recruitment variability for two successive years. Two spat were identified as hybrids of one of the planted strains and resident oyster genotypes. We also observed a genetic influence from an oyster strain used previously for restoration. Differences in environmental conditions between the two years of monitored recruitment likely affected larval dispersal and survival, contributing to observed interannual differences in the newly recruiting cohorts. Oyster spat from 2013 were genetically more similar to resident adults sampled in the Lafayette River, while the 2014 spat exhibited genotypic frequencies more similar to adults from surrounding rivers. The winds during the spawning seasons differed between years providing conditions for retention in 2013 and mixing of water masses in 2014. We recommend that the monitoring of restoration activities should consider relevant environmental conditions and observe multiple years of recruitment to assess the genetic impacts of restoration plantings and variable reproductive success.

Impact of habitat loss and fragmentation on reproduction, dispersal and species persistence for an endangered Chilean tree Abstract Survival of rare and endangered plant species following habitat loss and fragmentation is dependent upon in situ reproduction and population persistence, and establishment in new sites, so that stochastic, local extirpation does not lead to species extinction. Here we investigate if and how vegetative and sexual reproduction, propagule dispersal, and seedling establishment promote in situ persistence and establishment in new sites for the endangered, endemic Chilean tree Gomortega keule, in a landscape experiencing extensive habitat loss and fragmentation. Genetic analyses show G. keule reproduces vegetatively, producing large clone groups and providing a mechanism for long-term in situ persistence. Abundant seed set was observed, but seedling establishment was rare. At the single site where seedlings were observed, parentage analysis revealed seed dispersal over greater distances, and in a more aggregated pattern, than would be expected from gravity dispersal alone. We hypothesize that G. keulemay represent a ‘seed dispersal anachronism’, wherein the native seed disperser has been lost and possibly replaced by domesticated cattle. The lack of seedling establishment at most sites raises concerns about the ability of existing populations to expand within existing habitat patches or establish at new locations. Globally, habitat loss and fragmentation, coupled with other environmental changes, pose a particular threat to rare species with small populations, because inbreeding and the loss of mutualists can lead to establishment failure and local extirpation. We propose that analysis of a plant’s reproductive strategies as a whole, in its landscape context, is essential for effective species conservation.

Managing the risk of genetic swamping of a rare and restricted tree Abstract Hybridisation is a complex process that has important evolutionary consequences. In the case of rare species, a comprehensive understanding of inter-specific hybridisation can be critical for their conservation and management. Eucalyptus tetrapleura is a rare species of ironbark that is restricted to a 40 km × 100 km area around Grafton on the North Coast of New South Wales (Australia), and is distinctive in that it has four ribs on the sides of its buds and fruits. In recent years, central populations of E. tetrapleurahave been cleared to facilitate upgrades to one of the major highways in eastern Australia. This has led to increased habitat fragmentation, and there are now concerns that the species is at risk of genetic swamping by more common ironbark relatives. In this study, we investigated the population genetics and patterns of gene flow in E. tetrapleura. We used DArTseq to genotype samples collected from across the known distribution of E. tetrapleura, as well as leaf material collected from co-occurring ironbark species. We found that while E. tetrapleura was a distinct evolutionary lineage, there was evidence of gene flow between this species and other ironbarks. Furthermore, many populations that had been identified as E. tetrapleura on the basis of morphology were of hybrid origin, thus the range of the species was much smaller than previously thought. Overall, our findings demonstrate how genomic methods can improve our understanding of admixture across closely related lineages, which can be used to inform the restoration of rare species.

Linking effective population size dynamics to phenotypic traits in the common toad ( Bufo bufo ) Abstract The effective size of a population (Ne) determines the retention of neutral genetic variation in isolated populations, and is therefore a key parameter in conservation genetics. However, while our knowledge on the genetic properties of endangered populations has vastly improved in recent decades, rather little is known about the drivers of variation in Ne/Nc (the ratio between Ne and the population census size Nc) within given species. In the present study, we used eight microsatellite markers to genotype 898 adult common toads (Bufo bufo) obtained over five reproductive seasons from a single population (2004–2006 and 2008–2009), and related annual measures of Ne to cohort-specific population attributes. Consistent with the hypothesis that shifts in fitness-related traits can alter reproductive shares, we observed an increase in annual Ne and Ne/Nc ratios in parallel with a decline in body size in both sexes, and in parallel with an increase in body condition in males. The obtained Ne values also corresponded well with parentage inferences across the 6-year study period, which assigned 46.3% of individuals recorded in 2008 and 2009 to at least one putative parent from the 2004–2006 cohorts. Our study highlights a possible causative link between phenotypic traits such as body size and Ne/Nc, which has the potential to influence the amount of genetic erosion through drift.

Current genetic admixture between relictual populations might enhance the recovery of an elusive carnivore Abstract The present study investigated the natural recovery of the Eurasian otter (Lutra lutra) in France. The otter was widely distributed in France at the dawn of the 20th century, but then its range considerably shrank and became highly fragmented until the early 1970s, just before it was legally protected. However, for more than 25 years, the otter has been reconquering several parts of its original range and is now considered to be in expansion in France. We investigated the genetic differentiation and diversity of several populations from western and central France and northern Spain to gain insight into the recolonisation dynamics of this elusive species. The present study, based on the use of 14 microsatellite markers, revealed that otter populations seem to be split into five distinct groups. The distribution of samples in those five clusters was closely correlated with suspected refugia where the otter probably survived during the 20th century. Admixture was observed between genetic lineages, possibly enhancing their genetic diversity and thus increasing the recolonisation dynamics of these populations. This phenomenon resembles the genetic pattern noted in many invasive exotic species derived from multiple sources and introduction events. Finally, a demographic approach revealed the probable link between historical human pressure and otter population fragmentation patterns.