Non‐invasive genetic censusing and monitoring of primate populations

American Journal of Primatology, Journal Year: 2018, Volume and Issue: 80(3)

Published: Feb. 19, 2018

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio‐demographic behavioral observations. When direct counts animals are not possible, genetic analysis non‐invasive samples collected from wildlife allows estimates population size with higher accuracy precision than possible using indirect signs. Furthermore, in contrast to traditional survey methods, prolonged periodic sampling across months years enables inference group membership, movement, dynamics, some kin relationships. Data may also be used estimate sex ratios, differences dispersal distances, detect gene flow among locations. Recent advances capture‐recapture models have further improved derived samples. Simulations these methods shown that confidence interval point includes true when assumptions met, therefore this range minima maxima should emphasized monitoring studies. Innovations such as use sniffer dogs anti‐poaching patrols sample collection important ensure adequate sampling, expected development efficient cost‐effective genotyping by sequencing DNAs will automate speed analyses.

Language: Английский

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Fast sequence-based microsatellite genotyping development workflow

PeerJ, Journal Year: 2020, Volume and Issue: 8, P. e9085 - e9085

Published: May 4, 2020

Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown remove many the limitations electrophoresis-based methods and refine inference population genetic diversity structure. We present here a streamlined SSRseq development workflow that includes development, multiplexed marker amplification sequencing, automated bioinformatics data analysis. illustrate its application five groups species across phyla (fungi, plant, insect fish) with different levels genomic resource availability. found relying on previously developed assay is not optimal leads resulting low number reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly assays can be sequenced produce high quality genotypes for 20–40 loci. highlight critical upfront factors consider effective setup in wide range situations. Sequence analysis accounting all linked polymorphisms along sequence quickly generates powerful multi-allelic haplotype-based genotypic dataset, calling new theoretical analytical frameworks extract more information from multi-nucleotide polymorphism systems.

Language: Английский

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Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)

Published: Jan. 30, 2024

Abstract Accurate and efficient microsatellite loci genotyping is an essential process in population genetics that also used various demographic analyses. Protocols for next‐generation sequencing of enable high‐throughput cross‐compatible allele scoring, common issues are not addressed by conventional capillary‐based approaches. To improve this process, we have developed all‐in‐one software, called Seq2Sat ( seq uence to micro sat ellite), C++ support automated genotyping. It directly takes raw reads amplicons conducts read quality control before inferring genotypes based on depth‐of‐read, ratio, sequence composition length. We a module sex identification chromosome–specific locus amplicons. allow greater user access complement autoscoring, SatAnalyzer (micro ellite analyzer ), user‐friendly web‐based platform reads‐to‐report analyses calling genotype autoscoring produces interactive graphs manual editing. allows users troubleshoot multiplex optimization analysing distribution across samples high‐quality library preparation. evaluate its performance, benchmarked our toolkit Seq2Sat/SatAnalyzer against capillary gel method existing MEGASAT, using two datasets. Results showed can achieve >99.70% accuracy ~5 times faster than MEGASAT despite many more informative tables figures being generated. freely available github https://github.com/ecogenomicscanada/Seq2Sat ) dockerhub https://hub.docker.com/r/rocpengliu/satanalyzer ).

Language: Английский

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A mutation associated with resistance to synthetic pyrethroids is widespread in US populations of the tropical lineage of Rhipicephalus sanguineus s.l

Ticks and Tick-borne Diseases, Journal Year: 2024, Volume and Issue: 15(4), P. 102344 - 102344

Published: April 21, 2024

The brown dog tick, Rhipicephalus sanguineus sensu lato (s.l.), is an important vector for Rickettsia rickettsii, causative agent of Rocky Mountain spotted fever. Current public health prevention and control efforts to protect people involve preventing tick infestations on domestic animals in around houses. Primary tools rely acaricides, often synthetic pyrethroids (SPs); resistance this chemical class widespread ticks other arthropods. s.l. a complex that likely contains multiple unique species although the distribution global, there are differences morphology, ecology, perhaps competence among these major lineages. Two lineages within Rh. s.l., commonly referred as temperate tropical, have been documented from locations North America, but thought occupy different ecological niches. To evaluate potential acaricide better define distributions tropical throughout US northern Mexico, we employed highly multiplexed amplicon sequencing approach characterize sequence diversity at: 1) three loci voltage-gated sodium channel (VGSC) gene, which numerous genetic mutations associated with SPs; 2) region gamma-aminobutyric acid-gated chloride gene (GABA-Cl) containing several dieldrin/fipronil species; 3) mitochondrial genes (COI, 12S, 16S). We utilized geographically diverse set Rh collected pets 2013 smaller canines Baja California, Mexico 2021. determined single nucleotide polymorphism (T2134C) domain III segment 6 VGSC, has previously SP was abundant lineage (>50 %) absent lineage, suggesting SPs may be common lineage. found evidence copies GABA-Cl both lineages, some fipronil species, effects patterns currently unknown. widespread, accounting 79 % analyzed present at 13/14 collection sites. co-occurred four states, far north New York. None examined were positive rickettsii or massiliae.

Language: Английский

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Characterizing population structure and documenting rapid loss of genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis) with high throughput microsatellite genotyping

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

The use of molecular markers to assess genetic diversity has become a common component recovery action plans for threatened and endangered species. In this study, we an unusually large number microsatellite (N = 91) characterize the variation Chiricahua Leopard Frogs (Lithobates chiricahuensis) across their range in order understand distribution variation, identify bottlenecks, measure changes over time single, highly-managed population. Populations were best divided into three genetically distinct clusters, with southeastern Arizona New Mexico populations forming clusters. While there is moderate distributed sampled populations, each population on its own shows relatively low allelic diversity. Most displayed strong signals recent bottlenecks or deficiency heterozygous genotypes that typically associated frequent inbreeding. have history no management through translocations harbored greatest unique alleles overall richness, especially subset Mexican populations. Finally, long-term cohort sampling at one specific site (the Southwestern Research Station Portal, Arizona) allowed us demonstrate how rapidly can decrease matter years few founders. This work provide important context conservation agencies, but even suite beyond what typical may not be enough are extremely bottlenecked levels standing

Language: Английский

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Exploring PCR Methodologies in Forensic DNA Profiling

Baghdad Journal of Biochemistry and Applied Biological Sciences, Journal Year: 2025, Volume and Issue: 5(4)

Published: Jan. 20, 2025

Polymerase Chain Reaction (PCR) techniques have revolutionized forensic DNA analysis, enabling the precise amplification of trace samples. This abstract provides a concise overview pivotal role PCR in science. It delves into principles PCR, emphasizing its ability to amplify specific sequences with remarkable sensitivity and specificity. Multiplex variant technique, allows for simultaneous multiple genetic loci, enhancing efficiency investigations. further highlights broad applications criminal investigations, paternity testing, disaster victim identification. Recent advancements, such as MiniSTRs Next-Generation Sequencing (NGS), are elucidated their crucial contributions addressing challenging scenarios. Despite instrumental role, PCR-based analysis is not without challenges, considerations including contamination low-template The concludes aforward-looking perspective on emerging field epigenetics metagenomic offering glimpse promising future analysis. stands an indispensable tool modern science, unraveling identities from most minute traces.

Language: Английский

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Genetic Structure and Differentiation of Hyla savignyi from the Southern Population in Anatolia

Cytology and Genetics, Journal Year: 2025, Volume and Issue: 59(1), P. 127 - 135

Published: Feb. 1, 2025

Language: Английский

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STRyper: A macOS application for microsatellite genotyping and chromatogram management

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(2), P. e0318806 - e0318806

Published: Feb. 20, 2025

Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms microsatellite that is not restricted human genotyping. To fill this gap, I have developed STRyper, macOS whose source code published under General Public License. STRyper only uses libraries, making it very lightweight, responsive, behaving like modern application. Its three-pane window enables easy management viewing imported from FSA HID files, creation size standards marker panels (including bins). features powerful search capabilities (with smart folders) graphical user interface allowing, among others, manual correction DNA ladders individual genotypes drag-and-drop. It also introduces new way mitigate effect variations in electrophoretic conditions on estimated allele sizes.

Language: Английский

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Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus)

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates population size individual dispersal. Amplicon sequencing methods, also known 'genotyping-in-thousands-by sequencing' (GT-seq), now enable the efficient cost-effective genotyping hundreds loci individuals in same run. Here, we develop a GT-seq panel for identification kinship inference Alaska bears. Using genomic data from restriction site-associated DNA hunter-harvested Southcentral (n = 85), identified 170 microhaplotype single nucleotide polymorphism (SNP) that were highly heterozygous local populations. To sexing individuals, included previously published sex-linked locus panel. We empirically validated using samples collected at different spatial scales. These tissues 82) obtained within small geographic area Anchorage, Alaska, which likely to be relatives well geographically widespread locations throughout Alaska. Empirical validation indicated high success genotype reproducibility across replicate subsamples. Computer simulations demonstrated had ample statistical power distinguishing distinct first-order (parent-offspring full-sibling pairs) unrelated individuals. As final proof concept, was used identify close kin sampled urban wild habitats anticipate will useful resource monitoring bear

Language: Английский

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eDNA Approaches for Ecosystem Health Monitoring: Focus on Pathogens, Vectors, and Microbial Assessment

Published: Jan. 1, 2025

Language: Английский

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