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

Ferreira, Clara Mendes; Sabino-Marques, Helena; Barbosa, Soraia; Costa, Pedro Beschoren da; Encarnação, Cláudia; Alpizar‐Jara, Russell; Pita, Ricardo; Beja, Pedro; Mira, António; Searle, Jeremy B.; Paupério, Joana; Alves, Paulo C.

doi:10.1007/s10344-018-1188-8

Cited by 59 publications

(57 citation statements)

References 89 publications

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“…Genetic noninvasive sampling is increasingly recognized as an efficient and cost-effective tool for monitoring rare and elusive species (Carroll et al, 2018;Ferreira et al, 2018;Waits & Paetkau, 2005).…”

Section: Genotyping Performance In Gnismentioning

confidence: 99%

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

Thaden

Nowak

Tiesmeyer

et al. 2020

Molecular Ecology Resources

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The genomic era has led to an unprecedented increase in the availability of genomewide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how

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Section: Genotyping Performance In Gnismentioning

confidence: 99%

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

Thaden

Nowak

Tiesmeyer

et al. 2020

Molecular Ecology Resources

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“…Various processes can lead to mitonuclear discordance, most commonly sex-biased dispersal, demographic and/or adaptive processes, and these can arise in situ or following isolation (primary vs. secondary contact ;Toews & Brelsford, 2012). Sex-biased dispersal is usually not associated with monogamy, the mating system found in Cabrera voles, and dispersal has not been found to be biased in this species (Barbosa et al, 2017;Brom, Massot, Legendre, & Laloi, 2016;Ferreira et al, 2018;Lawson Handley & Perrin, 2007;Pita et al, 2014). On the other hand, incomplete lineage sorting tends to result in unstructured variation, at odds with the high level of nuclear and mitochondrial structuring observed here (Figure 4).…”

Section: Evolutionarily Significant Unitsmentioning

confidence: 93%

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

et al. 2018

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

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“…Indirect field signs such as hair and faeces can be subjected to genetic non‐invasive sampling (gNIS; Ferreira et al ) to confirm species identification. gNIS has the benefit of collecting genetic information without handling animals, which may cause stress.…”

Section: Detection and Monitoringmentioning

confidence: 99%

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

2020

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

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

Cited by 59 publications

References 89 publications

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

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

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

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

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