Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 97(4), P. 1511 - 1538

Published: April 12, 2022

Biodiversity underlies ecosystem resilience, function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors global environmental change will require new ways of deriving applying data. A major challenge is that data knowledge are scattered, biased, collected with numerous methods, stored in inconsistent ways. The Group on Earth Observations Observation Network (GEO BON) has developed the Essential Variables (EBVs) as fundamental metrics to help aggregate, harmonize, interpret observation from diverse sources. Mapping analyzing EBVs can evaluate aspects distributed geographically they over time. also intended serve inputs validation forecast status trends biodiversity, support policy decision making. Here, we assess feasibility implementing Genetic Composition (Genetic EBVs), which within-species genetic variation. We review bring together areas field genetics each contributes regional monitoring respect theory, sampling logistics, metadata, archiving, aggregation, modeling, technological advances. propose four EBVs: (i) Diversity; (ii) Differentiation; (iii) Inbreeding; (iv) Effective Population Size (Ne ). rank according their relevance, sensitivity change, generalizability, scalability, availability. outline workflow for generating underlying EBVs, advances needs archiving composition metadata. discuss be operationalized by visualizing space time across species forecasting beyond current observations using various modeling approaches. Our then explores challenges standardization, costs operationalizing well future directions opportunities maximize uptake globally research policy. collection, annotation, availability made past decade, practical standardized framework large-scale reporting. Rapid DNA sequencing technology present opportunities, but regionally globally. With these advances, starting integrated into conservation policy, foundation all species' long-term persistence face change. conclude a summary concrete steps researchers makers advancing operationalization EBVs. technical analytical foundations developed, practitioners should anticipate increasing application efforts emerge scale up

Language: Английский

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Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(3), P. 662 - 680

Published: Jan. 11, 2020

Abstract The genomic era has led to an unprecedented increase in the availability of genome‐wide data for a broad range taxa. Wildlife management strives make use these vast resources enable refined genetic assessments that enhance biodiversity conservation. However, as new platforms emerge, problems remain adapting usually complex approaches genotyping noninvasively collected wildlife samples. Here, we provide practical guidelines standardized development reduced single nucleotide polymorphism (SNP) panels applicable microfluidic degraded DNA samples, such faeces or hairs. We demonstrate how SNP can be optimized efficiently monitor European wildcat ( Felis silvestris S.) populations. show set up modular fashion accommodate informative markers relevant population genetics questions, individual identification, hybridization assessment and detection structure. discuss various aspects regarding implementation framework will allow both molecular ecologists practitioners help bridge gap between genomics applied

Language: Английский

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Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(17), P. 3452 - 3465

Published: July 21, 2018

Abstract Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary for long‐term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of factors. Existing genetic diversity needs to be thoroughly evaluated spatially mapped define units ( CU s ) an context, we address that here. We also propose multidisciplinary approach determine corridors functional connectivity between by including the modelling while controlling isolation distance phylogeographic history. evaluate our on Near Threatened Iberian endemic rodent analysing genotyping‐by‐sequencing (GBS) genomic data from 107 Cabrera voles Microtus cabrerae ), screening entire distribution categories their connectivity: defined six management MU can grouped into four evolutionarily significant ESUs three (putatively) adaptive AUs ). demonstrate different objectively using data, characteristics inform decision‐making. In particular, show vole is very limited eastern Iberia pre‐Pyrenean part Betic geographic nuclei contribute most diversity. argue framework definition essential this strong basis.

Language: Английский

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Contribution to the ecology of the Italian hare (Lepus corsicanus)

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Aug. 4, 2020

Abstract The Italian hare ( Lepus corsicanus ) is endemic to Central-Southern Italy and Sicily, classified as vulnerable due habitat alterations, low density fragmented populations ecological competition with the sympatric European europaeus ). Despite this status , only few local studies have explored its features. We provided some key traits of niche well potential distribution in peninsula. All data derived from genetically validated presences. generated a suitability model using maximum entropy for main competitor, hare. dietary habits were obtained DNA metabarcoding High-Throughput Sequencing on faecal pellets. most relevant environmental variables affecting are shared hare, suggesting competition. variation observed altitudinal statistically significant between two species.The diet all year around includes 344 plant taxa accounted by 62 families. Fagaceae Fabaceae Poaceae Rosaceae Solanaceae (counts > 20,000) represented 90.22% total diet. (60.70%) (67.47%) abundant items occurring Spring/Summer Autumn/Winter diets, respectively. showed richness (N = 266) diversity index values (Shannon: 2.329, Evenness: 0.03858, Equitability: 0.4169) higher than 199, Shannon: 1.818, 0.03096, 0.3435). Our contribution adds important information broaden knowledge (spatial trophic) requirements representing effective support fitting management actions conservation planning.

Language: Английский

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Genetic tools in the management of invasive mammals: recent trends and future perspectives

Mammal Review, Journal Year: 2020, Volume and Issue: 50(2), P. 200 - 210

Published: March 9, 2020

Abstract Invasive non‐native species are now considered to be one of the greatest threats biodiversity worldwide. Therefore, efficient and cost‐effective management invasions requires robust knowledge their demography, ecology impacts, genetic‐based techniques becoming more widely adopted in acquiring such knowledge. We focus on use genetic tools applied mammalian globally, as well inherent advantages disadvantages. cover that used in: 1) detecting monitoring invaders; 2) identifying origins invasive pathways; 3) assessing quantifying negative impacts 4) population potential eradication mammals. highlight changes sequencing technologies, including how Sanger microsatellite genotyping, for tracing pathways respectively, giving way high‐throughput methods. These include emergence environmental DNA (eDNA) metabarcoding early detection mammals, single nucleotide polymorphisms or whole genomes trace sources populations. moving towards trials genome‐editing gene drives control eradicate rodents. Genetic can provide vital information may not accessible with non‐genetic methods, implementation conservation policies (e.g. using systematic eDNA surveillance, identification novel pathogens). However, lack clear communication methods results (including transparency reproducibility) relevant stakeholders prohibitive translating these findings appropriate actions. Geneticists should engage co‐design experiments relation goals

Language: Английский

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Use of a novel camera trapping approach to measure small mammal responses to peatland restoration

European Journal of Wildlife Research, Journal Year: 2021, Volume and Issue: 67(1)

Published: Jan. 12, 2021

Abstract Small mammals, such as small rodents (Rodentia: Muroidea) and shrews (Insectivora: Soricidae), present particular challenges in camera trap surveys. Their size is often insufficient to trigger infra-red sensors, whilst resultant images may be of inadequate quality for species identification. The conventional survey method live-trapping, can both labour-intensive detrimental animal welfare. Here, we describe a using traps monitoring mammals. We show that by attaching the baited tunnel, fixing close-focus lens over lens, reducing flash intensity, pictures or videos obtained sufficient identifying species. demonstrate use comparing occurrences mammals peatland landscape containing (i) plantation forestry (planted on drained former blanket bog), (ii) ex-forestry areas undergoing bog restoration, (iii) unmodified habitat. Rodents were detected only restoration areas, across all odds detecting 7.6 times higher set than bog, 3.7 bog. When absolute abundance estimates are not required, available, this technique provides low-cost labour-efficient has minimal welfare implications.

Language: Английский

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Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 12, 2023

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques use non-invasive sampling with advances in computational approaches can and inform wildlife conservation management. Here, we used fecal DNA to generate low- medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) metagenomic sequences, combining widely available accessible collection cards commonly extraction library building approaches. preservation are easy transport be stored non-refrigerated, avoiding cumbersome costly sample methods. The construction shotgun sequencing approach did not require enrichment targeted amplification. utility potential data generated was demonstrated through scale analyses zoo free-ranging African savanna elephants (

Language: Английский

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Large scale monitoring of terrestrial small mammals using noninvasive sampling and COI barcoding

Mammal Research, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

Language: Английский

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Field testing of different methods for monitoring mammals in Trans-Himalayas: A case study from Lahaul and Spiti

Global Ecology and Conservation, Journal Year: 2019, Volume and Issue: 21, P. e00824 - e00824

Published: Oct. 23, 2019

Combined surveys based on non-invasive genetic methods and camera trapping increase chances of capturing most the elusive species which are otherwise challenging to document, especially in high altitude areas due tough terrains inaccessibility. The Trans–Himalayan mountain ranges India neglected ecosystem context faunal assessment their monitoring. present study provides a comparative performance four i.e., line transects, traps DNA analysis enumerating mammalian diversity Lahaul Spiti (L&S) Indian Trans Himalayan region. We undertook sign surveys, field questionnaire, trapping, collected faeces (n = 471) from trails/transects for analysis. was conducted seven different ranges/blocks L&S. Together all resulted identification 23 mammals with two new records, i.e. Asiatic Black bear (Ursus thibetanus) Leopard cat (Prionailurus bengalensis) Other key detected Brown arctos isabellinus), Snow (Panthera uncia), Tibetian Wolf (Canis lupus). performed best maximum number (19) than other three methods, Questionnaire survey (16), indirect (15) (10). However, no significant differences (Kruskal-Wallis, K 10; P > 0.05) observed among used detection. trap detection varied significantly forest (K 12; < 0.004). aided overcoming issue wrong faecal samples closely related species. Out 471 195 (41%) identification. Through this article, we discussed detecting developing field-tested monitoring protocol specifically Trans-Himalayan recommend use along sampling Trans-Himalayas.

Language: Английский

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Noninvasive Genetic Assessment Is an Effective Wildlife Research Tool When Compared with Other Approaches

Genes, Journal Year: 2021, Volume and Issue: 12(11), P. 1672 - 1672

Published: Oct. 23, 2021

Wildlife research has been indispensable for increasing our insight into ecosystem functioning as well designing effective conservation measures under the currently high rates of biodiversity loss. Genetic and genomic analyses might be able to yield same information on, e.g., population size, health, or diet composition other wildlife methods, even provide additional data that would not possible obtain by alternative means. Moreover, if DNA is collected non-invasively, this technique only minimal no impact on animal welfare. Nevertheless, implementation rate noninvasive genetic assessment in studies rather low. This caused perceived inefficiency material obtained non-invasively comparison with from blood tissues, poorer performance approaches used research. Therefore, aim review was evaluate methods across different types studies. Through a search three scientific databases, 113 relevant were identified, published between years 1997 2020. Overall, most (94%) reported equivalent superior when compared either invasive sampling another method. It also cheaper more time-efficient than techniques. In conclusion, highly approach, whose efficacy are likely improve further future development optimized protocols.

Language: Английский

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