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At least 73 records · Page 4Linked to original sources
USGS2014

A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

Molecular Ecology Resources↗
USGS2016

Detecting the movement and spawning activity of bigheaded carps with environmental DNA

Bigheaded carps are invasive fishes threatening to invade the Great Lakes basin and establish spawning populations, and have been monitored using environmental DNA (eDNA). Not only does eDNA hold potential for detecting the presence of species, but may also allow for quantitative comparisons like relative abundance of species across time or space. We examined the relationships among bigheaded carp movement, hydrography, spawning and eDNA on the Wabash River, IN, USA. We found positive relationships between eDNA and movement and eDNA and hydrography. We did not find a relationship between eDNA and spawning activity in the form of drifting eggs. Our first finding demonstrates how eDNA may be used to monitor species abundance, whereas our second finding illustrates the need for additional research into eDNA methodologies. Current applications of eDNA are widespread, but the relatively new technology requires further refinement.

Molecular Ecology Resources↗
USGS2016

SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate

Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5′ and 3′ untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep ( Ovis canadensis ) exon capture data and directly from the domestic sheep genome ( Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep ( Ovis dalli dalli ) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches ( lositan and bayescan ), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.

Molecular Ecology Resources↗
USGS2016

Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA

A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species’ presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp ( Ctenopharyngodon idella ) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty – indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis, and forensic and clinical diagnostics.

Molecular Ecology Resources↗
USGS2017

eDNAoccupancy: An R package for multi-scale occupancy modeling of environmental DNA data

In this article we describe eDNAoccupancy, an R package for fitting Bayesian, multi-scale occupancy models. These models are appropriate for occupancy surveys that include three, nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit, and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). eDNAoccupancy allows users to specify and fit multi-scale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analyzing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.

Molecular Ecology Resources↗
USGS2019

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high-throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced-representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long-term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.

Molecular Ecology Resources↗
USGS2020

A GT-seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non-model organisms

Targeted amplicon sequencing methods, such as genotyping-in-thousands by sequencing (GT-seq), facilitate rapid, accurate, and cost-effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT-seq panels is nontrivial, but studies describing trade-offs associated with different steps of GT-seq panel development are rare. Here, we construct a dual-purpose GT-seq panel for walleye ( Sander vitreus ), discuss trade-offs associated with different development and genotyping approaches, and provide suggestions for researchers constructing their own GT-seq panels. Our GT-seq panel was developed using an ascertainment set consisting of restriction site-associated DNA data from 954 individuals sampled from 23 populations in Minnesota and Wisconsin, USA. We conducted simulations to test the utility of all loci for parentage analysis and genetic stock identification and designed 600 primer pairs to maximize joint accuracy for these analyses. We then performed three rounds of primer optimization to remove loci that overamplified and our final panel consisted of 436 loci. We also explored different approaches for DNA extraction, multiplexed polymerase chain reaction (PCR) amplification, and cleanup steps during the GT-seq process and discovered the following: (i) inexpensive Chelex extractions performed well for genotyping; (ii) the exonuclease I and shrimp alkaline phosphatase (ExoSAP) procedure included in some current protocols did not improve results substantially and was probably unnecessary; and (iii) it was possible to PCR amplify panels separately and combine them prior to adapter ligation. Well-optimized GT-seq panels are valuable resources for conservation genetics and our findings and suggestions should aid in their construction in myriad taxa.

Minnesota, Wisconsin↗
USGS2020

Detecting population declines via monitoring the effective number of breeders (Nb)

Estimating the effective population size and effective number of breeders per year ( N b ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of N b in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. N b estimates were biased by ~5%–10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence N b estimation. Precision was higher for 100 SNPs ( H ≈ 0.30) than for 15 microsatellites ( H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when N b was small ( N b < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe ) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that N b = 50 when the true N b = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject N b = 500 when the true N b = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in N b when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate N b for age structured populations ( https://github.com/popgengui/agestrucnb/ ), which should help biologists develop sensitive monitoring programmes for early detection of changes in N b and population declines.

Molecular Ecology Resources↗
USGS2022

Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons

Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon ( Scaphirhynchus albus ) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon ( S. platorynchus ) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site-associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced-representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.

Molecular Ecology Resources↗
USGS2023

A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)

The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new pipeline for capture and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline captured targeted loci accurately, and given its unbiased nature, can be used with any target capture probe set. Moreover, due to its low computational demand, this new pipeline may be ideal for users with limited resources and when high-coverage sequencing outputs are required. We demonstrate the utility of our approach by incorporating WGS data into the first comprehensive phylogenomic reconstruction of the freshwater mussel family Margaritiferidae. We also provide a catalogue of well-curated functional annotations of these previously uncharacterized freshwater mussel-specific target regions, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set.

Molecular Ecology Resources↗
USGS2023

Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding

Diet analysis is a vital tool for understanding trophic interactions and is frequently used to inform conservation and management. Molecular approaches can identify diet items that are impossible to distinguish using more traditional visual-based methods. Yet, our understanding of how different variables, such as predator species or prey ration size, influence molecular diet analysis is still incomplete. Here, we conducted a large feeding trial to assess the impact that ration size, predator species, and temperature had on digestion rates estimated with visual identification, qPCR, and metabarcoding. Our trial was conducted by feeding two rations of Chinook salmon ( Oncorhynchus tshawytscha ) to two piscivorous fish species (largemouth bass [ Micropterus salmoides ] and channel catfish [ Ictalurus punctatus ]) held at two different temperatures (15.5 and 18.5°C) and sacrificed at regular intervals up to 120 h from the time of ingestion to quantify the prey contents remaining in the digestive tract. We found that ration size, temperature, and predator species all influenced digestion rate, with some indication that ration size had the largest influence. DNA-based analyses were able to identify salmon smolt prey in predator gut samples for much longer than visual analysis (~12 h for visual analysis vs. ~72 h for molecular analyses). Our study provides evidence that modelling the persistence of prey DNA in predator guts for molecular diet analyses may be feasible using a small set of controlling variables for many fish systems.

Molecular Ecology Resources↗
USGS2023

A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis)

Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single-nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome-wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold-adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large-scale analyses. We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern.

Molecular Ecology Resources↗
USGS2023

A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats

The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the use of CRISPR/Cas tools in the surveillance of the causative agents of wildlife diseases has not been prominent. This study presents the development of a minimally invasive, field-applicable and user-friendly CRISPR/Cas-based biosensor for the detection of Pseudogymnoascus destructans ( Pd ), the causative fungal agent of white-nose syndrome (WNS), an infectious disease that has killed more than five million bats in North America since its discovery in 2006. The biosensor assay combines a recombinase polymerase amplification (RPA) step followed by CRISPR/Cas12a nuclease cleavage to detect Pd DNA from bat dermal swab and guano samples. The biosensor had similar detection results when compared to quantitative PCR in distinguishing Pd- positive versus negative field samples. Although bat dermal swabs could be analysed with the biosensor without nucleic acid extraction, DNA extraction was needed when screening guano samples to overcome inhibitors. This assay can be applied to help with more rapid delineation of Pd- positive sites in the field to inform management decisions. With further optimization, this technology has broad translation potential to wildlife disease-associated pathogen detection and monitoring applications.

Molecular Ecology Resources↗
USGS2025

Cgsim: An R package for simulation of population genetics for conservation and management applications

Wildlife conservation and management increasingly considers genetic information to plan, understand and evaluate implemented population interventions. These actions commonly include conservation translocation and population reductions through removals. Change in genetic variation in response to management actions can be unintuitive due to the influence of multiple interacting drivers (e.g. genetic drift, life history traits, environmental stochasticity). Simulation is an excellent tool to understand the predicted consequences of different proposed or implemented actions. However, the genetic simulators that are robust to a wide variety of life history traits also have a steep learning curve to appropriately parameterize common management actions. To fill this gap, we have developed cgsim, an R package for simulating the genetic consequences of common management interventions for populations of wildlife species. We developed a set of functions to specifically understand the effects of four main aspects of managing small, declining or isolated populations: loss of genetic diversity to drift, augmenting existing populations (e.g. translocation), population reduction through targeted removals and population catastrophes driven by stochastic extrinsic forces. Our single population simulation model is individual-based, and flexible to a range of life history traits. Here we validate cgsim through comparison of simulations to theoretical expectations of genetic diversity loss and illustrate its applied utility by focusing on a recently published empirical example for the Greater Sage-Grouse. Cgsim is available as an R package at: https://doi.org/10.5066/P1BXBEXJ .

Molecular Ecology Resources↗
USGS2025

Sensitive environmental DNA methods for low-risk surveillance of at-risk bumble bees

Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis ). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.

Central Appalachian Mountains↗
USGS2026

GT-Seq panel development for species identification and parentage analysis of closely related hybridising Scaphirhynchus sturgeons

Hatchery supplementation is vital for conserving dwindling fish populations. Effective augmentation requires distinguishing hatchery-origin from wild individuals and accurately identifying species, particularly in systems where closely related species coexist. Genetic monitoring is key to quantifying genetic differences, but conventional markers do not distinguish hybrids, especially backcrosses. Misidentifying hybrids in hatchery programs compromises wild gene pools because hatchery broodstock contributes to numerous offspring being released into the wild. Here, we present a workflow for developing and evaluating the Genotyping-in-Thousands by sequencing (GT-seq) single nucleotide polymorphism (SNP) panel for North American river sturgeons ( Scaphirhynchus spp.). This panel is designed to detect complex hybrid classes and to determine parent-offspring relationships. Our species identification panel (S-loci) contains 155 SNPs selected for high genetic differentiation (F ST ) between Pallid Sturgeon ( S. albus ) and Shovelnose Sturgeon ( S. platorynchus ), and the parentage assignment panel (P-loci) includes 112 SNPs with high heterozygosity within Pallid Sturgeon. Simulation analyses demonstrated that our GT-seq S-loci panel reliably classifies pure species, F1, F2 and backcross hybrids, even with up to 70% missing data. The P-loci panel achieves high-confidence parentage assignment with ≥ 80% typed loci, with performance influenced by the proportion of sampled parents. Overall, the novel Scaphirhynchus GT-seq panel developed in this study represents a robust and efficient tool for detecting hybridisation, assigning parentage and providing critical information for management decisions in ongoing Pallid Sturgeon conservation.

lower Mississippi River, Missouri River↗
USGS2021

Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species

Co‐distributed species may exhibit similar phylogeographic patterns due to shared environmental factors or discordant patterns attributed to the influence of species‐specific traits. Although either concordant or discordant patterns could occur due to chance, stark differences in key traits (e.g., dispersal ability) may readily explain differences between species. Multiple species’ attributes may affect genetic patterns, and it is difficult to isolate the contribution of each. Here we compare the relative importance of two attributes, range size and niche breadth, in shaping the spatial structure of genetic variation in four sedge species (genus Carex ) from the Rocky Mountains. Within two pairs of co‐distributed species, one species exhibits narrow niche breadth, while the other species has broad niche breadth. Furthermore, one pair of co‐distributed species has a large geographical distribution, while the other has a small distribution. The four species represent a natural experiment to tease apart how these attributes (i.e., range size and niche breadth) affect phylogeographic patterns. Investigations of genetic variation and structure revealed that range size, but not niche breadth, is related to spatial genetic covariation across species of montane sedges. Our study highlights how isolating key attributes across multiple species can inform their impact on processes driving intraspecific differentiation.

Molecular Ecology↗
USGS2008

Cytonuclear genetic architecture in mosquitofish populations and the possible roles of introgressive hybridization

Spatial genetic structure in populations of mosquitofish ( Gambusia ) sampled throughout the south-eastern United States was characterized using mitochondrial (mt) DNA and allozyme markers. Both sets of data revealed a pronounced genetic discontinuity (along a broad path extending from south-eastern Mississippi to north-eastern Georgia) that corresponds to a recently recognized distinction between the nominal forms G. affinis to the west and G. holbrooki to the east. However, several populations from the general contact region exhibited unusual allelic associations in high frequency, suggestive of evolutionary processes within a zone of introgressive hybridization. These involve: (i) cytonuclear profiles representing combinations of nuclear and mitochondrial genotypes that tended to be more nearly species-specific and concordant elsewhere; and (ii) significant nuclear gametic disequilibria, perhaps attributable to positive assortative mating and/or differential fitnesses of homospecific vs. recombinant genotypes. However, outside this suspected hybrid region, ‘heterospecific’ genetic markers also appeared in low frequency, thus complicating interpretations. These discordant alleles on a broader geographic scale may reflect: (a) the retention of polymorphisms from an ancestral gene pool; (b) occasional evolutionary convergence (especially with respect to electrophoretic mobility of allozyme alleles); (c) the ‘footprints’ of a moving hybrid zone; or (d) differential introgressive penetrance across the current hybrid region.

Molecular Ecology↗