Validating the use of non-invasively sourced DNA for population genetic studies using pedigree data

Wedrowicz, Faye; Mosse, Jennifer; Wright, Wendy; Hogan, Fiona

doi:10.5194/we-17-9-2017

Cited by 4 publications

(3 citation statements)

References 38 publications

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“…Targeting shorter regions of DNA can thus increase amplification success (Waits and Paetkau 2005). The quality of DNA derived from sambar deer scats may be assessed by amplification with the SE47/SE48 pair in a similar fashion to that conducted by Hogan et al (2008) for owl feathers and Wedrowicz et al (2017) for koala scats.…”

Section: Discussionmentioning

confidence: 99%

A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)

Davies¹,

Wright²,

Wedrowicz³

et al. 2020

Aust. Mammalogy

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Invasive sambar deer (Rusa unicolor) are having significant detrimental impacts on natural environments in south-eastern Australia. Little, however, is known about their ecology, limiting evidence-based management strategies directed at reducing deer impacts. Genetic data, generated from DNA isolated from deer scats, can be used to fill ecological knowledge gaps. This study outlines a non-invasive genetic sampling strategy by which good-quality DNA from a single deer scat can be used to determine (1) species of origin, (2) sex and (3) a unique DNA profile. DNA from deer tissue and sambar deer scat samples were used to develop and optimise molecular methods to collect reliable genetic information. A DNA toolbox is presented that describes how to find, collect and store scat samples, isolate DNA and use molecular markers to generate informative genetic data. Generating genetic data using this approach will support studies aimed at acquiring ecological knowledge about sambar deer. Such knowledge will be critical for developing evidence-based recommendations to improve on-ground management decisions for sambar deer.

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Section: Discussionmentioning

confidence: 99%

A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)

Davies¹,

Wright²,

Wedrowicz³

et al. 2020

Aust. Mammalogy

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“…Each paper was attributed to 15 groupings ( Table S1 ), of which 41 papers were some form of population genetic/genomic study. A full assessment of the 41 population genetic papers resulted in a further five groupings: population genetics (N = 24; Table 1 ); development of methods for using scat DNA (N = 4; [ 73 , 74 , 75 , 76 ]); DNA profiling (N = 3; [ 77 , 78 , 79 ]); differentiation of populations using mitochondrial DNA (N = 8; [ 52 , 80 , 81 , 82 , 83 , 84 , 85 , 86 ], and phylogenetics (N = 2; [ 87 , 88 ]. Of the 24 population genetics studies, two were reviews ( Table 1 ).…”

Section: Systematic Reviewmentioning

confidence: 99%

Koala Genome Survey: An Open Data Resource to Improve Conservation Planning

Hogg

Silver

McLennan

et al. 2023

Genes

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Genome sequencing is a powerful tool that can inform the management of threatened species. Koalas (Phascolarctos cinereus) are a globally recognized species that captured the hearts and minds of the world during the 2019/2020 Australian megafires. In 2022, koalas were listed as ‘Endangered’ in Queensland, New South Wales, and the Australian Capital Territory. Populations have declined because of various threats such as land clearing, habitat fragmentation, and disease, all of which are exacerbated by climate change. Here, we present the Koala Genome Survey, an open data resource that was developed after the Australian megafires. A systematic review conducted in 2020 demonstrated that our understanding of genomic diversity within koala populations was scant, with only a handful of SNP studies conducted. Interrogating data showed that only 6 of 49 New South Wales areas of regional koala significance had meaningful genome-wide data, with only 7 locations in Queensland with SNP data and 4 locations in Victoria. In 2021, we launched the Koala Genome Survey to generate resequenced genomes across the Australian east coast. We have publicly released 430 koala genomes (average coverage: 32.25X, range: 11.3–66.8X) on the Amazon Web Services Open Data platform to accelerate research that can inform current and future conservation planning.

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“…Genetic monitoring in particular can be a powerful research tool, as it is capable of providing the same information as other methods, for instance, population size estimates [10,11], species detection [12,13], individual identification [14,15], or diet composition [16][17][18]. Moreover, DNA analyses can deliver multitude of data that might be difficult or impossible to obtain with other methods, e.g., on relatedness among individual animals [19,20], population structure [21][22][23], origin of invasive species [24][25][26][27], hybridization [28][29][30][31], past and present population sizes [7,32,33], or gene flow [26,27,31,[34][35][36][37][38][39].…”

Section: Introductionmentioning

confidence: 99%

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

Zemanova

2021

Genes

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

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Validating the use of non-invasively sourced DNA for population genetic studies using pedigree data

Cited by 4 publications

References 38 publications

A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)

A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)

Koala Genome Survey: An Open Data Resource to Improve Conservation Planning

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

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