Conservation Genetics

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. keule may 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.

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 Ne estimate 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.

A morphologically cryptic salamander reveals additional hidden diversity: evidence for ancient genetic divergence in Webster's salamander, Plethodon websteri Abstract We investigated the genetic diversity and phylogenetic structure of Webster's salamander (Plethodon websteri), an understudied species of conservation concern and one of the first morphologically cryptic salamander species described solely on the basis of molecular techniques. Using a combination of mitochondrial and microsatellite data, we discovered significant genetic differentiation across the known distribution (ɸST > 0.868 and FST = 0.261−0.652, p < 0.001), and identified at least two highly divergent clades. These clades, referenced herein as the Semlitsch and Type Locality clades, are of late Miocene origin (approximately 5.3 million years old) and are composed of several geographically and genetically distinct populations. Together, our observations suggest that previously unrecognized species-level diversity may exist in P. websteri, with populations potentially representing distinct but undescribed taxa. We hypothesize that divergence within P. websteri likely resulted from a culmination of radical changes in climate, hydrology, and geology over deep time. Moreover, our results add to mounting evidence suggesting that P. websteri does not belong within the P. welleri group, but instead forms its own discrete species complex separate and genetically distant from P. welleri. This study provides a starting point for future work and reiterates that relationships among, and species-level diversity within, eastern species of Plethodon require additional investigation and potential reevaluation.

Population genetic assessment of two critically endangered freshwater mussel species, Tennessee bean Venustaconcha trabalis and Cumberland bean Venustaconcha troostensis Abstract The Cumberland bean Venustaconcha troostensis (Conrad in Academy of Natural Sciences of Philadelphia. http://biodiversitylibrary.org/page/16346317/, 1834) and Tennessee bean V. trabalis (Lea in Proc Acad Nat Sci Phila 13:38–41, 1861) are both endangered freshwater mussel species endemic to the Cumberland and Tennessee river basins, respectively. These species are closely related and morphologically similar in appearance, and now exist only in small, fragmented populations relative to their historical abundances and distributions throughout the southeastern United States. A critical management need is to understand genetic differences among populations, so that informed decisions can be made to promote demographic and genetic viability of remaining populations. Against this background, we conducted a population genetic analysis by assessing variation at eight microsatellite DNA loci across 127 individuals. Our results showed five population clusters across five rivers, V. trabalis in the Clinch, Obed-Emory, Holston, and Hiwassee rivers; and V. troostensis in the Cumberland river. There was moderate to high differentiation among populations based on FST (range 0.09 − 0.18) and high differentiation among populations based on Jost's D (range 0.33 − 0.67). The highest differentiation was observed between populations in the Cumberland and Tennessee River basins (mean FST = 0.155, mean D = 0.559). Analysis of allele frequencies suggest that all populations likely have lost genetic diversity and are bottlenecked to various degrees. Linkage disequilibrium-based estimates of recent-current effective population sizes (Ne) ranged from 42 in the Cumberland River population to 130 individuals in the Hiwassee River population, suggesting that populations have become small and fragmented by natural historical processes and by man-made impediments to gene flow. Using approximate Bayesian computation to estimate Ne over longer-term coalescent time, median posterior distributions of Ne ranged from 7130 for the Clinch River population to 901 for the Holston River population. The inferences gained in this study may warrant action by conservation managers to artificially cross extant stocks within basins for purposes of genetic and demographic augmentation. However, based on our initial results, we do not recommend interspecific mixing of individuals between the Cumberland and Tennessee River basins.

Conservation implications of widespread polyploidy and apomixis: a case study in the genus Pomaderris (Rhamnaceae) Abstract Polyploidy resulting from whole genome duplication is common in plants and is increasingly being recognised as a critical factor in conservation actions, particularly when within-species variation in ploidy exists. Pomaderris(Rhamnaceae), a genus of 70 species endemic to Australia and New Zealand, has many species listed as threatened and that are subject to conservation management but of unknown ploidy. To provide a better understanding of polyploidy in the genus we sampled 36 of 70 species of Pomaderris and used flow cytometry to establish genome sizes and infer ploidy. Additionally, to examine within-species variation, we screened 104 individuals of eight rare species subject to conservation management. We did not find evidence for infraspecific variation in ploidy, suggesting that from a cytological perspective, conspecific individuals from the screened populations do not need to be kept geographically separated in conservation management. There is, however, considerable variation among species, with genome sizes suggesting the occurrence of diploidy, triploidy, tetraploidy and hexaploidy. Finding several species to be triploid but capable of seed production, we then explored reproductive biology using the flow cytometric seed screen. Results suggested that triploid species produce seeds asexually, as previously reported for two New Zealand congeners. While asexual reproduction through apomixis is generally a means of odd-ploid taxa overcoming sterility, we found that more than half of examined diploids and tetraploids also produced seeds asexually. Asexual reproduction means genetic diversity is potentially low, and these results should therefore be considered in future conservation actions and seed sampling designs.

The role of landscape and history on the genetic structure of peripheral populations of the Near Eastern fire salamander, Salamandra infraimmaculata , in Northern Israel Abstract Genetic studies on core versus peripheral populations have yielded many patterns. This diversity in genetic patterns may reflect diversity in the meaning of "peripheral populations" as defined by geography, gene flow patterns, historical effects, and ecological conditions. Populations at the lower latitude periphery of a species' range are of particular concern because they may be at increased risk for extinction due to global climate change. In this work we aim to understand the impact of landscape and ecological factors on different geographical types of peripheral populations with respect to levels of genetic diversity and patterns of local population differentiation. We examined three geographical types of peripheral populations of the endangered salamander, Salamandra infraimmaculata, in Northern Israel, in the southernmost periphery of the genus Salamandra, by analyzing the variability in 15 microsatellite loci from 32 sites. Our results showed that: (1) genetic diversity decreases towards the geographical periphery of the species' range; (2) genetic diversity in geographically disjunct peripheral areas is low compared to the core or peripheral populations that are contiguous to the core and most likely affected by a founder effect; (3) ecologically marginal conditions enhance population subdivision. The patterns we found lead to the conclusion that genetic diversity is influenced by a combination of geographical, historical, and ecological factors. These complex patterns should be addressed when prioritizing areas for conservation.

A quantitative genetic analysis of life-history traits and lifetime reproductive success in reintroduced Chinook salmon Abstract Reintroductions are widely implemented as a means of reestablishing wild populations and genetic parentage methods can be used in concert with these efforts to monitor and evaluate efficacy. In addition to understanding demographic outcomes, reconstructed pedigrees, when combined with phenotypic data, can provide insight into the adaptive potential of reintroduced individuals. Here, we examined the heritability and evolvability of life-history traits and lifetime reproductive success in two threatened Chinook salmon populations undergoing reintroduction to historical habitats above dams in Oregon, USA, using previously-developed multigenerational genetic pedigrees. All of the examined life-history traits: length-at-maturity, age-at-maturity, and arrival timing to the spawning grounds, and lifetime reproductive success exhibited significant narrow-sense heritabilities and evolvabilities. There was also a detectable influence of parental effects (i.e., paternal or maternal effects) on life-history trait variation, suggesting that in addition to genetic effects, nongenetic inheritance mechanisms are influencing life-history diversity in the populations. Additionally, our analyses revealed evidence of natural selection on the date of reintroduction, although the form and intensity of selection differed between the two populations; the forms of selection also point to the potential for phenotype-environment mismatch under some conditions. Overall, our results suggest that these threatened Chinook salmon populations exhibit significant adaptive potential, a factor that should be important to the longer-term success of recovery efforts.

Genetic mixture analyses in support of restoration of a high value recreational fishery for rainbow trout ( Oncorhynchus mykiss ) from a large lake in interior British Columbia Abstract Genetic mixture analysis is an important tool to apportion catch amongst potential component populations contributing to a fishery. We used variation at 10 microsatellite DNA loci to assess the level of genetic divergence between two ecotypes of rainbow trout (Oncorhynchus mykiss) that naturally co-occur in Kootenay Lake, southeastern British Columbia, and to exploit such divergence in a mixture analysis. One form, "Gerrard" rainbow trout, historically matured at sizes greater than 60 cm and 5 kg, spawns at a lake outlet after upstream migration in a large river tributary to Kootenay Lake, and is highly prized in the recreational fishery. The other form, "non-Gerrard" rainbow trout, is also native to the lake and matures at smaller sizes and spawns in numerous small streams tributary to Kootenay Lake. Recent declines in growth rate of Gerrard rainbow trout, however, has made them difficult to identify by size in fishery samples. Gerrard (N = 130, 6 sites) and non-Gerrard trout N = 312, 15 sites) were highly divergent from one another (FST = 0.14, P < 0.001) and constituted distinct genetic groups in model-based clustering analyses. Genetic mixture analyses of fishery samples indicated a high degree of accuracy in estimating mixture proportions; 100% Gerrard simulated fisheries were estimated to contain 99.9% Gerrards (95% confidence intervals of 99.8–100%) while 100% non-Gerrard rainbow trout simulated fisheries were estimated to contain 100.0% non-Gerrard trout (100–100%). Across eight fishery creel samples obtained between 2015 and 2017 (N = 527 fish), mixture analysis estimated the fishery to contain an average of 73.4% (95% confidence interval = 68.4–74.6%) Gerrard and 26.6% (23.4–31.6%) non-Gerrard trout. Realistic fishery simulations demonstrated strong agreement with empirical results; the average simulated values for Gerrards was 73.4% (65.9–80.0%) and for non-Gerrards was 26.8% (20.0–34.1%). Assignment tests resulted in an average 98.5% (± 0.066%) assignment confidence; 385 fish from the fishery samples were assigned to the Gerrard group (0.73) and 142 (0.27) to the non-Gerrard rainbow trout genetic group. Fitting length-at-age data for genetically assigned fishery samples to a von Bertalanffy growth model found greatest support for a model employing ecotype-specific L∞ (= 59.6 and 52.9 cm for Gerrards and non-Gerrards, respectively, both P < 0.001), and t0 (= − 1.36 and − 2.58, respectively, both P < 0.05), but a common K (= 0.189, P < 0.001). Our mixture analyses are being used to monitor catches and better understand the feeding and migration biology of these sympatric ecotypes of rainbow trout.

Beyond Bonferroni revisited: concerns over inflated false positive research findings in the fields of conservation genetics, biology, and medicine Abstract In 2006, Narum published a paper in Conservation Genetics emphasizing that Bonferroni correction for multiple testing can be highly conservative with poor statistical power (high Type II error). He pointed out that other approaches for multiple testing correction can control the false discovery rate (FDR) with a better balance of Type I and Type II errors and suggested that the approach of Benjamini and Yekutieli (BY) 2001 provides the most biologically relevant correction for evaluating the significance of population differentiation in conservation genetics. However, there are crucial differences between the original Benjamini and Yekutieli procedure and that described by Narum. After carefully reviewing both papers, we found an error due to the incorrect implementation of the BY procedure in Narum (Conserv Genet 7:783–787, 2006) such that the approach does not adequately control FDR. Since the incorrect BY approach has been increasingly used, not only in conservation genetics, but also in medicine and biology, it is important that the error is made known to the scientific community. In addition, we provide an overview of FDR approaches for multiple testing correction and encourage authors first and foremost to provide effect sizes for their results; and second, to be transparent in their descriptions of multiple testing correction. Finally, the impact of this error on conservation genetics and other fields will be study-dependent, as it is related to the number of true to false positives for each study.

Broad-scale patterns of genetic diversity and structure in a foundational salt marsh species black needlerush ( Juncus roemerianus ) Abstract Clonal and genetic diversity in foundational plant species are critical for species resiliency and ecosystem processes, both of which contribute to restoration success; however, genetic data is often lacking for common plant species used in many restoration practices. Only a few plant species dominate salt marshes, ecologically and economically valuable ecosystems targeted for restoration due to global decline. Despite being a foundational species in southeastern United States salt marshes black needlerush (Juncus roemerianus Scheele) is understudied, especially in comparison to the co-occurring smooth cordgrass (Spartina alterniflora Loisel). We used a panel of 18 microsatellite markers on 849 samples of J. roemerianus collected at 17 sites across a majority of the species range from Mississippi to South Carolina to measure clonal and genetic diversity and characterize population structure. Results are consistent with previous genetic studies on J. roemerianus and other clonal plant species in that clonal and genetic diversity were higher than expected based on life history literature, with an average genotypic diversity (GD) of 0.67 and average observed heterozygosity (HO) of 0.56. Differences in diversity between the ecologically and environmentally divergent Gulf (GD = 0.64, HO = 0.52) and Atlantic (GD = 0.80, HO = 0.45) coasts suggest that life history strategy may vary by environment. Hierarchical structure was apparent across the study area, with STRUCTURE analyses identifying three genetic clusters that further subdivided into five clusters and a broad transition zone. The scale of this genetic differentiation should be considered in sourcing plants for salt marsh restoration efforts.