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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Species composition and chemical characterization of Sargassum influx at six different locations along the Mexican Caribbean coast

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 795, P. 148852 - 148852

Published: July 3, 2021

Language: Английский

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A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

Evolutionary Applications, Journal Year: 2020, Volume and Issue: 13(6), P. 1195 - 1213

Published: March 3, 2020

Abstract Rivers are fascinating ecosystems in which the eco‐evolutionary dynamics of organisms constrained by particular features, and biologists have developed a wealth knowledge about freshwater biodiversity patterns. Over last 10 years, our group used holistic approach to contribute this focusing on causes consequences intraspecific diversity rivers. We conducted empirical works temperate permanent rivers from southern France, we broadened scope findings using experiments, meta‐analyses, simulations. demonstrated that (genetic) follows spatial pattern (downstream increase diversity) is repeatable across taxa (from plants vertebrates) river systems. This can result interactive processes teased apart appropriate simulation approaches. further experimentally showed matters for functioning ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. means losing yield major ecological effects. Our work impact multiple human stressors revealed that—in studied systems—stocking domestic (fish) strains strongly consistently alters natural patterns diversity. highlighted need specific analytical tools tease spurious actual relationships wild. Finally, original conservation strategies at basin scale based systematic planning framework appeared pertinent preserving identified several important research avenues should facilitate understanding local adaptation rivers, identification sustaining biodiversity–ecosystem function relationships, setting reliable plans.

Language: Английский

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Resolving fine‐scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

Evolutionary Applications, Journal Year: 2020, Volume and Issue: 13(5), P. 1055 - 1068

Published: Jan. 24, 2020

The resiliency of populations and species to environmental change is dependent on the maintenance genetic diversity, as such, quantifying diversity central combating ongoing widespread reductions in biodiversity. With advent next-generation sequencing, several methods now exist for resolving fine-scale population structure, but comparative performance these assignment has rarely been tested. Here, we evaluate sequenced microsatellites a single nucleotide polymorphism (SNP) array resolve structure critically important salmonid north eastern Canada, Arctic Charr (

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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High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae)

Plant Ecology and Evolution, Journal Year: 2025, Volume and Issue: 158(1), P. 43 - 52

Published: Jan. 22, 2025

Background and aims – Anadenanthera colubrina is a Neotropical native forest tree species with significant ecological importance in Seasonally Dry Tropical Forests. Developing genetic markers for this relevant conservation, breeding, evolutionary studies. Previously available A. consisted of few microsatellites. Next-generation sequencing (NGS) strategies allow simple cost-effective development new SSR loci from low-coverage whole genome shotgun sequencing. The main aim was to develop microsatellite sequence-based high-throughput genotyping (SSRseq) the characterize their information content against traditional capillary electrophoresis-based data by estimating amount molecularly accessible size homoplasy each locus. Additionally, reliability these population analysis assessed two age classes (reproductively mature trees seedlings) typical location Argentina. Key results Sixty primer pairs targeting microsatellites were designed, which 25 validated allelic error rates < 3% genotype missingness 20%. A significantly higher number alleles per locus heterozygosity detected SSRseq considering sequence polymorphisms compared analysing same based on (length) only. Size homoplasy, calculated as proportion mismatches between datasets relative differing length, averaged 97.85% over all loci. High levels diversity adults seedlings Paranaense forests, exceeding those reported previous studies using SSRs. generated increase resolution capillary-based genotyping, allowing more accurate inference eco-evolutionary processes non-model species.

Language: Английский

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Genetic Conservation and Population Management of Non‐Human Primates: Parentage Determination Using Seven Microsatellite‐Based Multiplexes

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

Published: April 1, 2025

ABSTRACT Conservation of non‐human primates receives much attention, with nearly 350 the more than 520 recorded primate species classified as threatened. To conduct effective population management, monitoring genetic diversity within is key importance, it can offer insights into levels inbreeding groups or populations. examine kinship macaque breeding housed at Biomedical Primate Research Centre, located in Rijswijk, The Netherlands, we have developed seven microsatellite‐based multiplexes for parentage analysis. These comprise a unique set 23 short tandem repeats (STR) distributed across 15 chromosomes. Extensive validation has been conducted 2217 Indian rhesus ( Macaca mulatta ) and 759 long‐tailed macaques M. fascicularis ), demonstrating that these STR markers are highly polymorphic segregate. Most exhibit information content (PIC) value above 0.5, illustrating they informative valuable providing us reliable determination. Beyond macaques, manifested also suitable addressing issues apes other Old World monkey species. Furthermore, this assay works on DNA isolated from both invasive non‐invasive derived material (e.g., hair follicles potentially feces). Thus, present here validated analysis support future colony management objectives various captive populations and, given applicability techniques, could be free‐ranging

Language: Английский

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Insights into the population genetics of an extreme habitat specialist, the wood ant commensal Formicoxenus nitidulus

Ecological Entomology, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

Abstract Habitat specialists, particularly those that are poor dispersers, highly susceptible to population isolation as a result of habitat fragmentation. Population can lead inbreeding, resulting in reduced genetic diversity and an increased risk local extinction. The shining guest ant, Formicoxenus nitidulus , lives only within the nests its wood ant hosts. It is thus extreme specialist, dependent on patchy nesting sites already fragmented woodland habitat. We aimed generate first data genetics this species, characterise degree isolation. developed eight novel nuclear microsatellite markers generated mitochondrial DNA sequence COI region samples from seven UK F. populations collected three hosts: Formica aquilonia lugubris rufa . These be used future studies species across wider geographic range may have utility other closely related species. found clear differentiation between Scottish English F populations. six largest study were genetically diverse showed signs effective within‐site dispersal. Our show often host multiple colonies. has been maintained specialist at also demonstrate single nest high conservation importance for colonies it supports.

Language: Английский

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Relating Equanimity to Mindfulness

Mindfulness, Journal Year: 2021, Volume and Issue: 12(11), P. 2635 - 2644

Published: Sept. 24, 2021

Abstract A recent surge of interest in equanimity as an important and transformative dimension the cultivation mindfulness can benefit from discerning different types recognized Buddhist traditions, such between a divine abode or immeasurable absence compulsive reactivity by way likes dislikes. In order to provide early background more fine-grained understanding construct equanimity, present article surveys key passages on their relationship mindfulness.

Language: Английский

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Landscape effects on taxonomic and functional diversity of dung beetle assemblages in a highly fragmented tropical forest

Forest Ecology and Management, Journal Year: 2021, Volume and Issue: 496, P. 119390 - 119390

Published: June 1, 2021

Language: Английский

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