Sampling for conservation genetics: how many loci and individuals are needed to determine the genetic diversity of plant populations using AFLP?

Leipold, Martin; Tausch, Simone; Hirtreiter, Markus; Poschlod, Peter; Reisch, Christoph

doi:10.1007/s12686-018-1069-1

Cited by 21 publications

(15 citation statements)

References 30 publications

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“…Despite the relatively low success in using outlined ddRAD sequencing methods, the declining costs and time associated with obtaining such data allows researchers to process many samples at once for thousands of markers and obtain large enough datasets to answer important population questions. Specifically, our sample dataset was large enough to capture ≥95% of the local nesting black duck population's genetic diversity (Nazareno et al 2017, Leipold et al 2020). Moreover, simulations across studies established that late generation hybrids into the F7 backcross stage are accurately assessed when using >1,000 loci (Boecklen and Howard 1997, Lavretsky et al 2019 c , Caniglia et al 2020, Leipold et al 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Specifically, our sample dataset was large enough to capture ≥95% of the local nesting black duck population's genetic diversity (Nazareno et al 2017, Leipold et al 2020). Moreover, simulations across studies established that late generation hybrids into the F7 backcross stage are accurately assessed when using >1,000 loci (Boecklen and Howard 1997, Lavretsky et al 2019 c , Caniglia et al 2020, Leipold et al 2020). Although we demonstrate the limitations posed by strong familial structure on ADMIXTURE and PCA analyses, coupling these with co‐ancestry assignments and sibship analyses allows researchers to make robust inferences into population structure and diversity, and provides confidence in assigning purity levels across sampled individuals (Wang 2018, O'Connell et al 2019).…”

Section: Discussionmentioning

confidence: 99%

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Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina

et al. 2021

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North Carolina, USA, represents the southern extent of the American black duck's (Anas rubripes) breeding range. Mallards (A. platyrhynchos) are present on the breeding grounds of the American black duck and hybridization is observed between these species; therefore, we assessed the genetic integrity, hybridization rates, and population structure of this local breeding population. We extracted genomic and mitochondrial DNA from chorioallantoic membranes and contour feathers from monitored black duck nests. We then prepared the extracted DNA for analysis using high-throughput DNA sequencing methods (ddRAD-seq). First, we assessed nuclear and mitochondrial population structure, genetic diversity, and differentiation across samples from North Carolina, and compared them against 199 genetically vetted mallards, black ducks, and mallard × black duck hybrids that served as genetic references. Next, we tested for parentage and sibling relationship and overall relatedness of black ducks in North Carolina. We recovered strong population structure and high co-ancestry across genetic markers due to interrelatedness among sampled nests in North Carolina and concluded that black ducks have been locally breeding in this area for a prolonged period of time. Despite a high level of interrelatedness among our samples, nucleotide diversity was similar to the reference continental black duck population, suggesting little effect of genetic drift, including inbreeding. Additionally, we conclude that molecular diversity of black ducks in North Carolina is maintained at reference population levels through the influx of genetic material from unrelated, migrating male black ducks. Finally, we report a hybridization level of 47.5%, covering 3 filial generations. Of identified hybrids, 54.7% and 53% were the direct result of interbreeding between black ducks and captive-reared or wild mallards, respectively. We conclude that because of high rates of interspecific hybridization and successive backcrossing events, introgression from wild and feral mallards is occurring into this population of breeding black ducks and requires careful consideration in future management efforts.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina

et al. 2021

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“…For molecular analyses we took leaf samples from 16 individuals per population and species to cover more than 90% of the total genetic diversity (Leipold et al 2020).…”

Section: Methodsmentioning

confidence: 99%

Surrounding landscape structures, rather than habitat age, drive genetic variation of typical calcareous grassland plant species

et al. 2020

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Context Land use change reduced calcareous grasslands throughout Europe during the last decades. Subsequent fragmentation and habitat deterioration led, moreover, to a massive biodiversity decline. To counteract this alarming development, a clear understanding of genetic variation patterns, as fundamental level of biodiversity, becomes inevitable. Objectives The aim of our study was to identify the drivers of genetic variation in common calcareous grassland plant species. More specifically, we tested whether genetic diversity or differentiation of Asperula cynanchica, Campanula rotundifolia, and Linum catharticum depend on habitat age, landscape structure, habitat quality, and/or population size. Methods We investigated 912 individuals, 304 per study species, from 19 calcareous grasslands across the Swabian Alb in Baden-Württemberg (Germany) using AFLP analyses. Results We observed no significant influence of habitat age on genetic diversity and differentiation. Habitat quality also had no impact on genetic diversity and population size only showed weak effects. However, genetic diversity strongly depended on landscape structure represented by distance to the nearest settlement, total area of surrounding calcareous grasslands, and their connectivity. Conclusions Migratory sheep herding is considered as main land use in calcareous grasslands on the Swabian Alb and thus, landscape structures in the study region may describe movement patterns of grazing livestock. In this study, genetic variation in calcareous grassland populations was strongly affected by surrounding landscape structures and subsequent grazing patterns. Therefore, we assume that moderate grazing intensities over the long term may increase levels of genetic diversity, whereas periods of overgrazing or abandonment could lower genetic diversity.

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“…At each study site, plant leaf material of up to 16 healthy individuals of each species was collected for genetic analysis in order to cover more than 90% of the total genetic diversity present (Leipold et al, 2020). In total, we sampled 953 individuals ( Supplementary Table 3).…”

Section: Study Species and Samplingmentioning

confidence: 99%

Genetic Variation of Typical Plant Species in Hay Meadows: The Effect of Land Use History, Landscape Structure, and Habitat Quality

et al. 2020

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Global changes in land use are threatening the diversity of many ecosystems on both the intra- and interspecific levels. Among these ecosystems are the species-rich hay meadows, which have drastically declined in quality and quantity, due to land use intensification or abandonment in recent decades. The remaining genetic resources of their plant species must therefore be protected. To determine the driving forces impacting genetic variation in common hay meadow species (Dactylis glomerata, Heracleum sphondylium, and Trifolium pratense), we used data on the land use history, historic and present landscape structure and habitat quality. Our results showed average genetic diversity within the study sites, with low differentiation levels and a high gene flow among grasslands. Land use history, landscape structure and habitat quality were found to be related to the distribution of genetic diversity in the studied species, highlighting the complex forces acting in these ecosystems and showing the specific impact of litter accumulation on genetic diversity. Both historic and current environmental variables influence genetic diversity, demonstrating the importance of the land use history of a habitat. The most important group of variables impacting genetic variation in all three species was the landscape structure (e.g., distance to the nearest-located urban area or grassland). Also important was the influence of litter cover on genetic diversity in D. glomerata, which provides an interesting starting point for further research.

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Sampling for conservation genetics: how many loci and individuals are needed to determine the genetic diversity of plant populations using AFLP?

Cited by 21 publications

References 30 publications

Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina

Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina

Surrounding landscape structures, rather than habitat age, drive genetic variation of typical calcareous grassland plant species

Genetic Variation of Typical Plant Species in Hay Meadows: The Effect of Land Use History, Landscape Structure, and Habitat Quality

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