Conservation and the Genomics of Populations

Oxford University Press eBooks, Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

Abstract Loss of biodiversity is among the greatest problems facing world today. Conservation and Genomics Populations gives a comprehensive overview essential background, concepts, tools needed to understand how genetic information can be used conserve species threatened with extinction, manage ecological or commercial importance. New molecular techniques, statistical methods, computer programs, principles, methods are becoming increasingly useful in conservation biological diversity. Using balance data theory, coupled basic applied research examples, this book examines phenotypic variation natural populations, principles mechanisms evolutionary change, interpretation from these conservation. The includes examples plants, animals, microbes wild captive populations. This third edition has been thoroughly revised include advances genomics contains new chapters on population genomics, monitoring, genetics practice, as well sections climate emerging diseases, metagenomics, more. More than one-third references were published after previous edition. Each 24 Appendix end Guest Box written by an expert who provides example presented chapter their own work. for advanced undergraduate graduate students genetics, resource management, biology, professional biologists policy-makers working wildlife habitat management agencies. Much will also interest nonprofessionals curious about role

Language: Английский

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Recovery of a marine keystone predator transforms terrestrial predator–prey dynamics

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(5)

Published: Jan. 23, 2023

Sea otters (Enhydra lutris) and wolves (Canis lupus) are two apex predators with strong cascading effects on ecosystem structure function. After decades of recovery from near extirpation, their ranges now overlap, allowing sea to interact for the first time in scientific record. We intensively studied during 2015 2021 an island system colonized by 2000s 2013. wolf colonization, we quantified shifts foraging behavior DNA metabarcoding 689 scats stable isotope analyses, both revealing a dietary switch Sitka black-tailed deer (Odocoileus hemionus), terrestrial situ primary prey, otters. Here show unexpected result reintroduction restoration otters, which became abundant marine subsidy following population recovery. The availability allowed persist continue reproduce, subsequently nearly eliminating deer. Genotypes 390 telemetry data 13 confirmed fidelity constituting one highest known densities upending standardly accepted density predictions based ungulate abundance. Whereas subsidies other systems generally derived lower trophic levels, here nearshore predator key prey species linked food webs recently deglaciated rapidly changing ecosystem. These results underscore that may serve as unanticipated nutrient pathway recipient ecosystems even resulting cross-boundary cascades.

Language: Английский

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Wildlife parasitology: sample collection and processing, diagnostic constraints, and methodological challenges in terrestrial carnivores

Parasites & Vectors, Journal Year: 2024, Volume and Issue: 17(1)

Published: March 13, 2024

Abstract Wild terrestrial carnivores play a crucial role as reservoir, maintenance, and spillover hosts for wide parasite variety. They may harbor, shed, transmit zoonotic parasites of veterinary importance domestic hosts. Although wild are globally distributed comprise many different species, some living in close proximity to human settlements, only few studies have investigated using non-specific techniques. Access samples be challenging species protected, others secretive, possibly explaining the data paucity. Considering carnivores’ health ecological role, combined with lack specific diagnostic methodologies, this review aims offer an overview methods investigation carnivores, providing precise techniques collection analysis fecal, blood, tissue samples, environmental impact on said limitations researchers currently face analyzing carnivores. In addition, paper offers information how factors affect detection postmortem insects can used estimate time death highlight insect larvae. The contains literature available procedures emphasizes need method standardization Graphical

Language: Английский

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The Rapid Rise of Next-Generation Natural History

Frontiers in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 9

Published: July 21, 2021

Many ecologists have lamented the demise of natural history and attributed this decline to a misguided view that is outdated unscientific. Although there perception focus in ecology conservation shifted away from descriptive research training toward hypothetico-deductive research, we argue has entered new phase call “next-generation history.” This renaissance characterized by technological statistical advances aid collecting detailed observations systematically over broad spatial temporal extents. The increased exponentially last decade include electronic sensors such as camera-traps acoustic recorders, aircraft- satellite-based remote sensing, animal-borne biologgers, genetics genomics methods, community science programs. Advances statistics computation aided analyzing growing quantity reveal patterns nature. These robust next-generation datasets transformed anecdotal into collected collectively constitute foundation for can be leveraged applied management. are encouraging scientists conduct embrace descriptions nature remain critically important component scientific endeavor. Finally, these engaging non-scientists alike with documentations wonders Thus, celebrate people experience directly.

Language: Английский

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Variable strategies to solve risk–reward tradeoffs in carnivore communities

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(35)

Published: Aug. 24, 2021

Significance An incomplete understanding of the total influence competitively dominant predators exert on subordinate species hinders our ability to anticipate effects that changing carnivore populations will have ecological communities. Here, we show cougars are architects a complex behavioral game risk and reward, because or cooccurring carnivores both provisioned preyed by predators. Each considered here employed different strategy approach risk–reward tradeoff, suggesting there multiple viable solutions game. By not considering multitude other carnivores, missing important linkages in terrestrial food webs.

Language: Английский

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A systematic review of DNA‐based methods in authentication of game and less common meat species

Comprehensive Reviews in Food Science and Food Safety, Journal Year: 2023, Volume and Issue: 22(3), P. 2112 - 2160

Published: March 29, 2023

Abstract Despite the numerous studies on food safety and authenticity, especially for meat products, not enough have been conducted focusing exclusively game species other unusual animals. As a result of European horse scandal, is currently target many authenticity studies. With this review, we aim to present various DNA‐based methods that used by researchers identify, detect, quantify game, uncommon animals, wildlife species. Polymerase chain reaction (PCR) considered standard method DNA analysis in testing. However, paper, several may or involve PCR technique. For purpose, systematically reviewed 131 articles selected according criteria such as animal species, analysis, year publication, so forth. The our study shows most studied PCR‐ non‐PCR‐based conservation. study, can find detailed information about frequent adulterants regular products techniques identify them.

Language: Английский

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Metabarcoding of fecal DNA shows dietary diversification in wolves substitutes for ungulates in an island archipelago

Ecosphere, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 1, 2021

Abstract Although ungulates are the main prey of wolves ( Canis lupus ) throughout their range, substantial dietary diversity may allow to persist even when declining or rare. Alexander Archipelago ligoni inhabit distinct mainland and island biogeographic units, each with a unique assemblage available prey. We quantified variability in wolf diets across archipelago using DNA metabarcoding 860 scats collected during 2010–2018 12 study sites. hypothesized that would increase niche breadth as proportion ungulate species decreased, but this could be mediated by availability coastal resources. Application achieved fine taxonomic resolution remains identified 55 diet items representing from 42 genera 29 families, many previously undetected diets. Overall, made up largest were also most variable between sites (occurrence per item index [O/I] = 0.130–0.851). On islands, Sitka black‐tailed deer Odocoileus hemionus consumed species, whereas moose Alces alces mountain goats Oreamnos americanus contributed more Wolves responded biogeographical variation primary altering foraging patterns. increased number widened declined rather than switch one few individual items. Across all combined, beaver Castor canadensis ; O/I 0.125), marine mammals (O/I 0.113), black bears Ursus 0.067) important alternate In areas where had become scarce, sea otters Enhydra lutris particularly important, case becoming suggesting ongoing expansion otter populations postreintroduction restores an food source for these cryptic predators. Here, we show extensive elucidate regional consumer–resource interactions archipelagic landscape.

Language: Английский

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Whole-genome resequencing identifies exonic single-nucleotide variations in terpenoid biosynthesis genes of the medicinal and aromatic plant common sage (Salvia officinalis L.)

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: 71(8), P. 4171 - 4181

Published: Feb. 18, 2024

Abstract Common sage ( Salvia officinalis L.), the type species of genus , is a historically acknowledged medicinal and aromatic plant that utilized in several different industries for manufacturing diverse end products, including food, pharmaceuticals, cosmetics, personal hygiene products insect repellants. The medical uses essential oil terpenoids have made these secondary metabolites focus medical/pharmaceutical chemistry research. In present work, common genome was resequenced assembled, protein-encoding gene content annotated. terpenoid biosynthesis repertoire, which includes 75 terpene synthase 67 backbone pathway genes, predicted located on assembly scaffolds, revealing tandem duplication blocks chromosomes. Variant analysis identified 188 variable single-nucleotide loci coding sequences genes. A total 24,570 polymorphisms were exome, representing database potential targeted genotyping Given activity highly prone to modulation by point mutations genotype plays an important role complex traits composition, constitute candidate functional markers can be associated with compositional future

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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Development of a Noninvasive Genotyping‐In‐Thousands (GTseq) Panel for Long‐Term Conservation of Western Great Lakes Gray Wolves (Canis lupus)

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

Published: April 1, 2025

ABSTRACT The application of noninvasive genetic methods toward the field conservation has increased our understanding many wildlife populations that are difficult to sample, allowing for better management. In molecular ecology, use sampling became widely feasible with advent microsatellites, a highly polymorphic, short‐length marker could be genotyped from low‐quality DNA sources. Despite decades use, microsatellite panels continue suffer high genotyping error rates, allelic dropout, and limited reproducibility across laboratories. To address these issues, single nucleotide polymorphisms (SNPs) offer advantages such as lower avoidance dropout due consistent allele length, automated calling through bioinformatic pipelines, reducing human subjectivity error. Given SNPs provide relative microsatellites marker, SNP specifically, method genotyping‐in‐thousands by sequencing (GTseq) gained popularity. Here, we developed GTseq panel western Great Lakes canids comprised 196 loci, capable species identification, accurately inferring sex (97.2%), identifying unique individuals (probability identity = 6.71e −41 ), assigning relationships (false positive rate 9.34e −14 genotypes low (0.39%). an attempt improve success samples, found while increasing number PCR cycles yielded higher percentage it also on‐target reads in negative controls. We suggest approaching this manipulation caution emphasize importance including reporting Further, quantitative was powerful estimate host‐specific concentrations, enabling conservative sample selection library preparation respect affordability.

Language: Английский

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