Pedigree-based assessment of recent population connectivity in a threatened rattlesnake

How Can Genomics Help or Hinder Wildlife Conservation?

Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.

Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.

Inferring population connectivity in eastern massasauga rattlesnakes (Sistrurus catenatus) using landscape genetics

Assessing the environmental factors that influence the ability of a threatened species to move through a landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited, making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the eastern massasauga rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity was impacted by both contemporary land-cover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and least-cost paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmented landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.

Temporal sampling and network analysis reveal rapid population turnover and dynamic migration pattern in overwintering regions of a cosmopolitan pest

Genetic makeup of insect pest is informative for source-sink dynamics, spreading of insecticide resistant genes, and effective management. However, collecting samples from field populations without considering temporal resolution and calculating parameters related to historical gene flow may not capture contemporary genetic pattern and metapopulation dynamics of highly dispersive pests. Plutella xylostella (L.), the most widely distributed Lepidopteran pest that developed resistance to almost all current insecticides, migrates heterogeneously across space and time. To investigate its real-time genetic pattern and dynamics, we executed four samplings over two consecutive years across Southern China and Southeast Asia, and constructed population network based on contemporary gene flow. Across 48 populations, genetic structure analysis identified two differentiated insect swarms, of which the one with higher genetic variation was replaced by the other over time. We further inferred gene flow by estimation of kinship relationship and constructed migration network in each sampling time. Interestingly, we found mean migration distance at around 1,000 km. Such distance might have contributed to the formation of step-stone migration and migration circuit over large geographical scale. Probing network clustering across sampling times, we found a dynamic P. xylostella metapopulation with more active migration in spring than in winter, and identified a consistent pattern that some regions are sources (e.g., Yunnan in China, Myanmar and Vietnam) while several others are sinks (e.g., Guangdong and Fujian in China) over 2 years. Rapid turnover of insect swarms and highly dynamic metapopulation highlight the importance of temporal sampling and network analysis in investigation of source-sink relationships and thus effective pest management of P. xylostella, and other highly dispersive insect pests.

The relevance of pedigrees in the conservation genomics era

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

Genomic signatures of inbreeding and mutation load in a threatened rattlesnake

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load) and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely related yet outbred Western massasauga rattlesnakes (Sistrurus tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of runs of homozygosity of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared to S. catenatus, presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped species-level drift effects within S. catenatus populations were in general more frequent and more often found in homozygous genotypes than in S. tergeminus, suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.

Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake

Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species' range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.