Conservation Genetics

Population management using gene drive: molecular design, models of spread dynamics and assessment of ecological risks Abstract CRISPR gene drive has recently been proposed as a promising technology for population management, including in conservation genetics. The technique would consist in releasing genetically engineered individuals that are designed to rapidly propagate a desired mutation or transgene into wild populations. Potential applications in conservation biology include the control of invasive pest populations that threaten biodiversity (eradication and suppression drives), or the introduction of beneficial mutations in endangered populations (rescue drives). The propagation of a gene drive is affected by different factors that depend on the drive construct (e.g. its fitness effect and timing of expression) or on the target species (e.g. its mating system and population structure). We review potential applications of the different types of gene drives for conservation. We examine the challenges posed by the evolution of resistance to gene drives and review the various molecular and environmental risks associated with gene drives (e.g. propagation to non target populations or species and unintended detrimental ecosystem impacts). We provide some guidelines for future gene drive research and discuss ethical, biosafety and regulation issues.

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.

Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus : implications for forest management and species conservation Abstract Comparative landscape genetic studies provide insights into whether relationships between landscape features and patterns of spatial genetic structure differ among populations, species, habitat types, and regions. For species with fragmented distributions, especially when management practices contribute to fragmentation, tests of the factors structuring population connectivity are particularly important for understanding continued risks. We determined levels of genetic diversity and tested the relationships of landscape-scale vegetative, geographic, and climate variables with genetic distance in two congeneric, endemic salamander species with status of concern. Using microsatellite data for 326 Rhyacotriton kezeri and 557 Rhyacotriton variegatus individuals collected from 17 to 29 localities, respectively, we implemented a model of landscape resistance based on circuit theory. The northernmost portions of each species' range is more fragmented than areas to the south, leading to the prediction that these areas would have relatively lower genetic diversity in response. Due to reliance of both species upon cold-water habitats, we predicted that landscape variables maintaining cool, moist microhabitats would be correlated with gene flow. Genetic structure was high overall and trended toward increasing with the proportion of the forested landscape. Based on maximum likelihood population effects models across genetic clusters and species, land cover and roads were the best predictors of genetic distance, even though the degree of fragmentation differed across each species' geographic range. Our results suggest that forest cover is essential for dispersal in these salamanders, indicating negative effects of fragmentation resulting from timber harvest and other forest disturbances.

Impacts of stocking and its intensity on effective population size in Brook Charr ( Salvelinus fontinalis ) populations Abstract Effective population size (Ne) is a measure of the genetic size of a population and a crucial parameter for wildlife population management since it is strongly related to retention of genetic diversity in time and/or to inbreeding levels. Many exploited fish populations are stocked with the purpose of increasing population sizes to sustain important fishing pressures. However, stocking hatchery-reared fish could at the same time increase population census size and decrease Ne. Our study aimed at characterizing how stocking affected Ne in supplemented populations of Brook Charr (Salvelinus fontinalis) in Québec and at assessing how this relationship varied with the intensity of stocking (e.g. number of stocking events, number of fish stocked/ha, proportion of domestic genetic background). We estimated Ne with the linkage disequilibrium method in 54 populations (3361 sampled individuals analyzed at 20 microsatellites) with various levels of stocking intensity. We found that stocked lakes have significantly lower Ne than unstocked lakes. However, we found little evidence of an additional effect of stocking intensity on Ne of stocked lakes. Our results suggest that stocking may have a negative impact on Ne but that more intense stocking does not necessarily translate into lower Ne. However, even though low Ne in stocked populations could be attributed to an effect of stocking, it is also likely that stocked lakes consist of poor environments that translate into low Ne.

Predicting population extinctions in Darwin's finches Abstract Genetic data are increasingly used for fast, efficient, and cost-effective monitoring of natural populations and assessment of extinction risk in species management. A single modern molecular snapshot is typically used to infer population size and vulnerability, yet for species with unknown and potentially complex genetic metapopulation structure, this technique may not effectively predict vulnerability. Darwin's finches, which are well-represented in museum collections, offer a unique opportunity to test the effectiveness of predicting extinction vulnerability in species with complex structure, such as naturally fragmented populations. In this study, we compared ancient DNA from ~ 100 year old extinct and extant Darwin's finch populations in the Galápagos Islands to determine whether single time point genetic assessments in the past accurately predicted extinction risk, or if other factors such as metapopulation dynamics could mask population declines. Of eight extinct populations, only one had significantly reduced genetic variation compared to an extant population of similar characteristics. Contrary to our prediction that populations would have decreased genetic diversity prior to extinction when compared to persisting populations, at least one measure of genetic diversity was significantly higher in six of the eight extinct populations when compared to extant populations. Simulations lend support to the hypothesis that unaccounted for metapopulation structure may explain the observed pattern in many species. Therefore, models of genetic diversity reflecting population extinction potential may be inadequate for highly-mobile species with metapopulation dynamics such as the Galápagos finches.

Genetic structure of an abundant small mammal is influenced by low intensity urbanization Abstract Urban development can fragment and degrade habitat, and such habitat alterations can have profound effects on wildlife, including influencing population genetics. We used nine microsatellite loci to determine the effects of urbanization on genetic diversity and genetic structure in a native small mammal, Merriam's kangaroo rat, in areas in and around Las Cruces, NM, an expanding low density urban center. We found that Merriam's kangaroo rats in urban areas had increased genetic differentiation among populations as compared to wildland animals, and detected some evidence of lower genetic diversity in urban areas, indicating that the population genetics of a common and abundant wildlife species can be impacted by low density urbanization. Our results suggest that although abundant and common wildlife such as Merriam's kangaroo rats may persist in urban environments, these animals may still be influenced by more subtle effects of urbanization, such as genetic isolation.

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.

Messing about on the river: the role of geographic barriers in shaping the genetic structure of Bornean small mammals in a fragmented landscape Abstract Landscape features may restricting dispersal and gene flow, and increase demographic isolation among sub-populations. In addition, landscape features may represent potential dispersal barriers depending on species vagility. To predict the persistence of populations and to formulate adequate conservation measures it is essential to understand the ability of species to transverse landscape barriers. Using population genetic techniques we assessed the importance of physical barriers along the Kinabatangan River for a suite of non-volant small mammals. Cytochrome b sequence variation was examined for each of the 19 species sampled across both riverbanks. Haplotype networks and molecular variance analyses indicated contrasting patterns of genetic isolation between riversides for different taxa. Genetic isolation between riversides ranged from moderate to complete in tree shrews and squirrels, whereas no isolating effect could be detected in murids and gymnures. Although genetic divergence between forest fragments on the same side of the river could only be studied in a subset of six species, the results suggest an additional dispersal barrier for two of these studied species. While barrier effects of a paved road and tributaries could not be verified, large oil palm plantations seem to have disrupted gene flow in these species. Furthermore, the findings suggest higher genetic connectivity on the more continuously forested compared to the more fragmented riverside, and underline the importance of forest corridors as essential conservation measures to maintain genetic diversity in a fragmented landscape such as that along the Kinabatangan River.

History matters: contemporary versus historic population structure of bobcats in the New England region, USA Abstract Habitat fragmentation and genetic bottlenecks can have substantial impacts on the health and management of wildlife species by lowering diversity and subdividing populations. Population genetic comparisons across time periods can help elucidate temporal changes in populations and the processes responsible for the changes. Bobcats (Lynx rufus) are wide-ranging carnivores and are currently increasing in abundance across an expanding range. Bobcat populations in New England have fluctuated in the past century in response to changes in their prey base, harvest pressure, and landscape development. We genotyped contemporary (2010–2017) and historic (1952–1964) bobcats from New England and Quebec, Canada at a suite of microsatellite loci and tested for differences in diversity, effective population size, and gene flow. Over 20 generations separated the sampling periods, and the intervening years were marked by drastic changes in land use and species management regimes. We found a general decrease in genetic diversity and differing population genetic structure through time. Effective population size decreased at the end of the historic period, coincident with a spike in harvest, but rebounded to greater numbers in the contemporary period. Our results suggest that bobcat populations in the region are robust, but development and range dynamics may play a significant role in population structure. Our study also highlights the benefits of a historical perspective in interpreting contemporary population genetic data.

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.

Alexandros Sfakianakis
Anapafseos 5 . Agios Nikolaos
Crete.Greece.72100
2841026182

6948891480

alsfakia@gmail.com