Geology topics

Paul A. Hohenlohe

Publications and source records attributed to Paul A. Hohenlohe.

11 recordsLinked to original sources

USGS2026

Genetic structure in a previously extirpated population of gray wolves following reintroduction and natural recolonization

Genetic structuring in wildlife populations is driven by barriers that restrict gene flow as well as the history of population demography. Mechanisms driving genetic structuring can be nuanced in group-living species, such as gray wolves ( Canis lupus ). Behavioral factors, such as social affiliation and resistance, natal habitat imprinting, and trade-offs between dispersal from natal packs and territorial biding, affect habitat selection of wolves despite landscape barriers providing little resistance to their extensive dispersal capabilities. Wolves were previously extirpated from Idaho, USA, and current populations are the result of both reintroductions in 1995 and 1996 and natural dispersal from Canada. In this context we examined genetic structure of wolves in Idaho using 101 individuals genotyped at 18 nuclear DNA microsatellite loci and a subset of 38 individuals genotyped at 1019 single nucleotide polymorphism markers. We hypothesized panmictic (i.e., random mating) genetic structure in Idaho due to the long-distance dispersal abilities of gray wolves. Contrary to our hypothesis, we found three genetic clusters of gray wolves in Idaho, primarily supported by SNP markers. Microsatellite data suggested similar patterns, but permutation tests indicated these differences were not statistically significant. The extent of differentiation and evidence of gene flow, however, suggests that the three genetic clusters are not wholly isolated from one another. The distinctions between clusters spatially align with areas of reintroduction into central Idaho and Yellowstone National Park, as well ongoing natural recolonization from adjacent populations in Canada and Montana. Wolves at the periphery of analysis areas showed more admixture than those in the core, consistent with territoriality and mating behaviors contributing to genetic structuring. We demonstrate how management history, including reintroduction efforts, and animal behavior may interact and contribute to patterns of genetic structure in wild populations.

Idaho, Montana, Wyoming↗

USGS2025

Genetic variation and metapopulation structure inform recovery goals in a threatened species

Background: Monitoring genetic parameters is important for setting effective conservation and management strategies, particularly for small, fragmented, and isolated populations. Small, isolated populations face increased rates of genetic drift and inbreeding, which increase extinction risk especially when gene flow is limited. Methods: Here, we applied a Genotyping-in-Thousands by sequencing (GT-seq) panel to inform recovery action for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ). We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals. Results: We delineated three types of conservation units: (1) three evolutionarily significant units that represent long-term population structure and variation, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective population sizes per management unit were small overall (mean 38.16, range 2.3–220.9), indicating that recovery goals of 10 subpopulations with N e > 500 have not been reached. Conclusions: Our results support the maintenance of connectivity within evolutionarily significant units through the restoration of dispersal corridors. Next steps could include further sampling of some subpopulations with low sample sizes, unsampled subpopulations, and subpopulations that are geographically isolated. Genotyping future samples with the same GT-seq panel would help to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change.

Idaho↗

USGS2024

Development and validation of a GT-seq panel for genetic monitoring in a threatened species using minimally invasive sampling

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals.

Ecology and Evolution↗

USGS2023

A pragmatic approach for integrating molecular tools into biodiversity conservation

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

Conservation Science and Practice↗

USGS2021

The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels ( Urocitellus brunneus —NIDGS, and U . endemicus —SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype–environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographical barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.

Idaho↗

USGS2021

Authors’ reply to letter to the editor: Continued improvement to genetic diversity indicator for CBD

We appreciate the encouraging response to our call for indicators for genetic diversity within the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity, CBD (Laikre et al. 2020 ; Hoban et al. 2020 ). In agreement with us, Frankham ( 2021 ) highlights the urgent necessity for the CBD to include an indicator that tracks the maintenance of genetic diversity within populations of all species—wild and domestic. Draft CBD Headline indicators (which all CBD Parties will need to report) do not include genetic diversity within populations of wild species (CBD/SBSTTA/24/3Add.1).

Conservation Genetics↗

USGS2021

Effective population size remains a suitable, pragmatic indicator of genetic diversity for all species, including forest trees

Fady & Bozzano highlight some challenges to a proposed Convention on Biological Diversity (CBD) indicator of genetic diversity based on effective population size, Ne ( Fady and Bozzano, 2020 ; Hoban et al., 2020 ). We appreciate the thoughtful debate and concur that genetic diversity indicators must be reliable and scalable. We fully agree that “genetic diversity should be better considered in the CBD post-2020 framework to prevent the irreplaceable loss of biodiversity… existing indicators are far from satisfactory.” As Fady & Bozzano state, Ne is essential for monitoring vital aspects of genetic diversity: loss of genetic diversity due to drift (genetic erosion), inbreeding rate (genetic health), and potential for adaptation and long term survival (resilience) ( Fady and Bozzano, 2020 ).

Biological Conservation↗

USGS2020

Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics . Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.

Biological Conservation↗

USGS2016

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Proceedings of the Royal Society B: Biological Sci↗

USGS2013

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.

Molecular Ecology↗

USGS2012

RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays

Hybridization with introduced rainbow trout threatens most native westslope cutthroat trout populations. Understanding the genetic effects of hybridization and introgression requires a large set of high-throughput, diagnostic genetic markers to inform conservation and management. Recently, we identified several thousand candidate single-nucleotide polymorphism (SNP) markers based on RAD sequencing of 11 westslope cutthroat trout and 13 rainbow trout individuals. Here, we used flanking sequence for 56 of these candidate SNP markers to design high-throughput genotyping assays. We validated the assays on a total of 92 individuals from 22 populations and seven hatchery strains. Forty-six assays (82%) amplified consistently and allowed easy identification of westslope cutthroat and rainbow trout alleles as well as heterozygote controls. The 46 SNPs will provide high power for early detection of population admixture and improved identification of hybrid and nonhybridized individuals. This technique shows promise as a very low-cost, reliable and relatively rapid method for developing and testing SNP markers for nonmodel organisms with limited genomic resources.

Molecular Ecology Resources↗