Genetic variation and structure in Scandinavian red deer (<i>Cervus elaphus</i>): influence of ancestry, past hunting, and restoration management

Höglund, Jacob; Cortázar-Chinarro, María; Jarnemo, Anders; Thulin, Carl‐Gustaf

doi:10.1111/bij.12049

Cited by 16 publications

(10 citation statements)

References 51 publications

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“…Höglund et al . ), population genetic measures like those of AR and H e were higher than SS‐10RS/SS‐35 specific panels, while F IS was lower. A similar trend was observed in relation to our panel of ten most polymorphic species‐specific loci (SS‐10MP), suggesting that cross‐specific amplification of microsatellites produces an ascertainment bias in the overall levels of genetic variability, when compared with randomly selected specific markers.…”

Section: Discussionmentioning

confidence: 84%

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications

Queirós

Godinho

Lopes

et al. 2014

Molecular Ecology Resources

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Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.

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Section: Discussionmentioning

confidence: 84%

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications

Queirós

Godinho

Lopes

et al. 2014

Molecular Ecology Resources

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“…The studied fenced and managed population (PE) showed significant higher allelic richness and observed heterozygosity than the DN and FG/CP populations and nonsignificant differences with respect to CB (see Supporting information, Fig. The admixture of founder individuals from different geographical regions has been related to increased genetic diversity in isolated and captive red deer populations (Haanes et al, 2010;Höglund et al, 2013) and can explain this high genetic variability. Several explanations are possible for this observation.…”

Section: Structure and Genetic Diversitymentioning

confidence: 95%

“…Several explanations are possible for this observation. The admixture of founder individuals from different geographical regions has been related to increased genetic diversity in isolated and captive red deer populations (Haanes et al, 2010;Höglund et al, 2013) and can explain this high genetic variability. Moreover, the tendency of balanced sex ratios and age structures in fenced estates These factors (initial heterozygosity and Ne), together with the generation interval, have been noted as the principal drivers maintaining genetic diversity (Frankham, 1995).…”

Section: Structure and Genetic Diversitymentioning

confidence: 99%

The impact of management practices and past demographic history on the genetic diversity of red deer (Cervus elaphus): an assessment of population and individual fitness

Queirós

Vicente

Boadella

et al. 2013

Biol J Linn Soc Lond

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The influences of management practices and past demographic history on genetic diversity are of critical relevance to sustainable practices and the conservation of wildlife populations. The red deer (Cervus elaphus) is an interesting model species to address these questions because it has a wide geographical distribution and it has been intensively managed for humans in the last decades. In the present study, we have analyzed the impact of recent management practices on the genetic diversity of Iberian red deer populations and assessed the genetic variation effects on population and individual fitness-related traits. Four populations subjected to distinct management systems were selected: Cabañeros (CB) and Doñana (DN), not hunted populations; Fraga/Caspe (FG/CP), open hunting area with very low or absent management; and PE, fenced private hunting estate founded 31 years ago through the introduction of deer of different origins. Ten microsatellites were amplified in a total of 172 individuals. Additionally, several fitness-related traits such as the presence of tuberculosis compatible lesions (TBCL), spleen weight (SW), and body length (BL) were estimated. We found a marked genetic variation and differentiation among populations, suggesting a strong population structure. In the fenced population, the introduction of genetically distinct animals has led to high genetic variability (no evidence of inbreeding) despite intensive management. Lower levels of genetic diversity were observed in two historically isolated natural populations (DN and FG/CP). The past demographic history of Iberian populations appears to be more relevant than the current management policy in shaping the genetic variability of natural populations. Population genetic diversity may correlate with life-history traits and disease susceptibility, which could compromise the conservation and management of these wildlife populations. Although no significant effects of individual genetic diversity (general and local effect hypotheses) were observed on TBCL, SW and BL, some single-locus effects had almost significant trends for the TBCL and SW traits.

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“…DNA from all these samples was extracted and analyzed originally for other studies [17,18]. We were given full permission to use the extracts.…”

Section: Samplesmentioning

confidence: 99%

An eDNA-Based SNP Assay for Ungulate Species and Sex Identification

Nichols

Spong

2017

Diversity

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Many processes in wild populations are difficult to study. Genetic data, often non-invasively collected, may provide a solution to these difficulties and are increasingly used to study behavioral, demographic, ecological, and evolutionary processes. Moreover, the improved sensitivity of genetic methods now allows analyses of trace amounts of DNA left by animals in their environment (e.g., saliva, urine, epithelial cells). Environmental DNA (eDNA) thus offers new opportunities to study a range of historic and contemporary questions. Here, we present a species and sex diagnostic kit for studying browsing in a multispecies temperate ungulate assemblage. Using mitochondrial sequences deposited in Genbank, we developed four single nucleotide polymorphisms (SNPs) for identifying four temperate ungulate species. We also sequenced portions of the Amelogenin gene on the X-and Y-chromosomes and developed six SNPs (three on the X-chromosome and three on the Y-chromosome) for sex determination. We tested the SNP assays on high and low quality/quantity DNA samples.

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Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry, past hunting, and restoration management

Cited by 16 publications

References 51 publications

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications

Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross‐specific and species‐specific amplifications

The impact of management practices and past demographic history on the genetic diversity of red deer (Cervus elaphus): an assessment of population and individual fitness

An eDNA-Based SNP Assay for Ungulate Species and Sex Identification

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