Genetic and genomic monitoring with minimally invasive sampling methods

Evolutionary Applications, Journal Year: 2018, Volume and Issue: 11(7), P. 1094 - 1119

Published: Feb. 2, 2018

Abstract The decreasing cost and increasing scope power of emerging genomic technologies are reshaping the field molecular ecology. However, many modern approaches (e.g., RAD ‐seq) require large amounts high‐quality template DNA . This poses a problem for an active branch conservation biology: genetic monitoring using minimally invasive sampling ( MIS ) methods. Without handling or even observing animal, methods collection hair, skin, faeces) can provide information on individuals populations. Such samples typically yield low‐quality and/or quantities , restricting type that be used. Despite this limitation, is effective tool estimating population demographic parameters diversity in natural Genetic likely to become more important future as populations undergoing anthropogenically driven declines, which unlikely abate without intensive adaptive management efforts often include approaches. Here, we profile expanding suite platforms compatible with producing genotypes from considering factors such development costs error rates. We evaluate how powerful new will enhance our ability investigate questions answered monitoring, abundance, structure relatedness. As period unusually rapid transition, also highlight importance legacy data sets recommend address challenges moving between traditional next‐generation platforms. Finally, consider could move beyond future. For example, assessing microbiomes epigenetic markers greater understanding relationship their environment.

Language: Английский

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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Sept. 1, 2017

Abstract Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance SNP noninvasive from grey wolves, European wildcats brown bears, compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% 97% wolf, cat bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified same individuals provided almost identical estimates pairwise differentiation. found that for which all loci were scored had no disagreements across three replicates (except one locus wolf sample). Thus, argue call rate (amplification success) can be used proxy genotype quality, allowing reduction replication effort when high. Furthermore, cycle threshold values real-time PCR to guide choice protocols amplification. Finally, provide general guidelines successful degraded technology.

Language: Английский

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Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysis

Mammal Review, Journal Year: 2018, Volume and Issue: 49(2), P. 97 - 112

Published: Dec. 22, 2018

Abstract Accurate analyses of the diets predators are key to understand trophic interactions and defining conservation strategies. Diets commonly assessed through analysis non‐invasively collected scats, use faecal DNA ( fDNA ) can reduce species misidentifications that could lead biased ecological inference. We review scientific literature since publication first paper on amplifying , in order assess trends genetic non‐invasive sampling gNIS for predator identification scat‐based diet studies North American European terrestrial mammalian carnivores (Carnivora). quantify error rates morphology‐based identification. then provide an overview how applying would improve research other areas carnivore ecology. found identity was verified by using only 8% 400 based scats. The median percentage false positives (i.e. samples wrongly identified as belonging target species) 18%, consistent regardless species’ body size. did not find increasing trend over time, despite existing technical capability identify almost all species. New directions include employing high‐throughput sequencing HTS metabarcoding species, individual predator, entire assemblage consumed items, microbiome pathogens. conclude protocols metagenomic approaches hold great promise elevating a fundamental cornerstone future ecology biology mammals.

Language: Английский

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More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(6), P. 1505 - 1516

Published: June 10, 2020

Abstract Noninvasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates and error rates. The information lost when may lead to decreased precision in animal population densities, which could misguide conservation management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative traditionally used microsatellites as SNPs allow amplification shorter DNA fragments, are less prone errors produce results that easily shared among laboratories. Here, we outline detailed protocol for cost‐effective accurate noninvasive SNP using multiplexed amplicon sequencing optimized degraded DNA. We validated this method individual identification 216 scats, 18 hairs 15 tissues from coyotes ( Canis latrans ) 26 SNPs. Our rate scat samples was 93%, 100% hair tissue, representing substantial increase compared previous microsatellite‐based studies while remaining at cost under $5 per PCR replicate (excluding labour). accuracy genotypes further corroborated scats matching known, GPS‐collared were always located within territory known individual. also show different levels multiplexing produced similar results, product cleanup strategies can effects on success. By making more affordable, efficient, use monitor conserve free‐ranging populations.

Language: Английский

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Detecting and analysing intraspecific genetic variation with eDNA: From population genetics to species abundance

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(15), P. 4118 - 4132

Published: May 30, 2023

Abstract Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies explored the potential these detect within‐species variation, allowing population assessments abundance estimates from samples. However, we currently lack a framework outlining key considerations specific generating, analysing applying data two purposes. Here, discuss how various markers differ with regard information detectability samples analysis of differs common tissue‐based analyses. We then outline it may be possible obtain absolute by detecting intraspecific variation mixtures under multiple scenarios. also major causes contributing allele detection frequency errors data, their consequences population‐level analyses bioinformatic remove erroneous sequences. This review summarizes advances required harness full eDNA‐based inform questions ecology, evolutionary biology conservation management.

Language: Английский

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SSR‐seq: Genotyping of microsatellites using next‐generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

Ecology and Evolution, Journal Year: 2018, Volume and Issue: 8(22), P. 10817 - 10833

Published: Oct. 25, 2018

Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next-generation sequencing (NGS) makes it easy to obtain also information for the loci of interest. This avoids misinterpretations that otherwise could arise due size homoplasy. Here, an NGS strategy described allows genotype hundreds individuals at many custom-designed SSR simultaneously, combining multiplex PCR, barcoding, Illumina sequencing. We created three different datasets which alleles were coded according (a) length repetitive region, (b) total length, (c) identity, order evaluate eventual benefits from having data hand, not only data. For each dataset, genetic diversity statistics, as well FST RST values, calculated. The number per locus, observed expected heterozygosity, highest identity because single-nucleotide polymorphisms insertions/deletions flanking regions motif. Size homoplasy found be very common, amounting 44.7%-63.5% (mean over all loci) study species. Thus, obtained by offers a better resolution than traditional way more accurate evolutionary interpretations.

Language: Английский

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Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics

Ecology and Evolution, Journal Year: 2019, Volume and Issue: 9(5), P. 2814 - 2832

Published: Feb. 14, 2019

By applying second-generation sequencing technologies to microsatellite genotyping, sequence information is produced which can result in high-resolution population genetics analysis populations and increased replicability between runs laboratories. In the present study, we establish an approach study genetic structure patterns of two European hedgehog species Erinaceaus europaeus E. roumanicus. These are usually associated with human settlements good models anthropogenic impacts on diversity wild populations. The short repeats genotyping by (SSR-GBS) method presented uses amplicon sequences determine genotypes for allelic variants be defined according both length single nucleotide polymorphisms (SNPs). To evaluate whether complete improved definition, compared this datasets based solely information. We identified a total 42 markers were successfully amplified species. Overall, resulted higher number alleles, as well greater differentiation Additionally, slightly clearer division some potential hybrids. There was degree within species, although only roumanicus related geographical distance. statistically significant results obtained SSR-GBS demonstrate that it superior electrophoresis-based methods SSR genotyping. Moreover, reproducibility throughput lower effort possibility include degraded DNA into analysis, allow continued relevance during genomic era.

Language: Английский

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Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals

European Journal of Wildlife Research, Journal Year: 2018, Volume and Issue: 64(4)

Published: July 17, 2018

Genetic non-invasive sampling (gNIS) may provide valuable information for population monitoring, as it allows inferences of density and key behavioural traits such dispersal, kinship reproduction. Despite its enormous potential, gNIS has rarely been applied to small mammals, which live-trapping is still the most commonly used method. Here we evaluated applicability cost-effectiveness compared with live-trapping, monitor a metapopulation an Iberian endemic elusive rodent: Cabrera vole (Microtus cabrerae). We genetic diversity, dispersal movements inferred using both methods. For that, optimised microsatellite markers individual identification M. cabrerae, tissue (n = 31) faecal samples 323) collected from in south-western Iberia. An initial set 20 loci was samples, 11 were selected amplify samples. Overall, revealed higher number identified individuals (65) than (31), estimated diversity similar data tissues gNIS. Kinship analysis showed relationships events when including gNIS, indicated absence sex-biased dispersal. The total cost (fieldwork analysis) each genotype obtained through three times greater Our strongly supports high potential monitoring populations and/or threatened mammals. also illustrate how this tool can be logistically feasible conservation.

Language: Английский

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Application of microsatellite genotyping by sequencing (SSR-GBS) to measure genetic diversity of the East African Oreochromis niloticus

Conservation Genetics, Journal Year: 2018, Volume and Issue: 20(2), P. 357 - 372

Published: Dec. 17, 2018

Microsatellites play an important role when investigating population and ecological genetics, although high effort in development genotyping constitute a technical constraint remains major bottleneck. Here we use microsatellite approach utilizing sequences of amplicons for allele calling (SSR-GBS) based on Illumina that requires less time. The consist highly polymorphic loci, sequencing multiplexed PCR amplified microsatellites Miseq PE 300 platform bioinformatic treatment the sequenced data using custom scripts. procedure allows automation calling, which can be more reliably replicated thereby removes biases might prevent concatenation datasets from different analyses. Additionally, methodology enhances information content beyond traditional amplicon length (AL) approaches. Using 26 newly developed markers SSR-GBS investigate genetic assessment anthropogenically altered populations East African Nile tilapia to show potential this approach. More precisely, compare genotypic generated considering AL whole (WAI). We found genotypes WAI are not only able recover higher number alleles but also detailed structure pattern. discuss capability importance perspectives implementation future conservation studies. specifically, demonstrate how current techniques contribute useful studies concerning resources sustainable exploitation tilapia.

Language: Английский

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The Evolution of Variance Control

Trends in Ecology & Evolution, Journal Year: 2019, Volume and Issue: 35(1), P. 22 - 33

Published: Sept. 11, 2019

Language: Английский

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