Basics of Population Genetics: Quantifying Neutral and Adaptive Genetic Variation for Landscape Genetic Studies

Waits, Lisette P.; Storfer, Andrew

doi:10.1002/9781118525258.ch03

Cited by 17 publications

(19 citation statements)

References 141 publications

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“…Pairwise measures of genetic differentiation are usually computed from allele frequencies at the population‐level and from genotypes at the individual level. In both cases, numerous metrics may be considered (Waits & Storfer, ). Additionally, individual‐based genetic distances may also be calculated from transformed genetic data, such as individual ancestry values computed from clustering algorithms (e.g., Balkenhol et al., ; Murphy et al., ).…”

Section: How To Infer the Environmental And Individual Effects On Nonmentioning

confidence: 99%

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

et al. 2018

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Dispersal is a central process in ecology and evolution. At the individual level, the three stages of the dispersal process (i.e., emigration, transience and immigration) are affected by complex interactions between phenotypes and environmental factors. Condition- and context-dependent dispersal have far-reaching consequences, both for the demography and the genetic structuring of natural populations and for adaptive processes. From an applied point of view, dispersal also deeply affects the spatial dynamics of populations and their ability to respond to land-use changes, habitat degradation and climate change. For these reasons, dispersal has received considerable attention from ecologists and evolutionary biologists. Demographic and genetic methods allow quantifying non-effective (i.e., followed or not by a successful reproduction) and effective (i.e., with a successful reproduction) dispersal and to investigate how individual and environmental factors affect the different stages of the dispersal process. Over the past decade, demographic and genetic methods designed to quantify dispersal have rapidly evolved but interactions between researchers from the two fields are limited. We here review recent developments in both demographic and genetic methods to study dispersal in wild animal populations. We present their strengths and limits, as well as their applicability depending on study objectives and population characteristics. We propose a unified framework allowing researchers to combine methods and select the more suitable tools to address a broad range of important topics about the ecology and evolution of dispersal and its consequences on animal population dynamics and genetics.

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Section: How To Infer the Environmental And Individual Effects On Nonmentioning

confidence: 99%

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

et al. 2018

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“…SNPs have low mutation rates (10 × 10 −8 to 10 × 10 −9 ; Nachman & Crowell, 2000), much lower than microsatellites (0.001 to 0.005; Pinto et al, 2013), whereas AFLP mutation rates can exceed those of microsatellites (Kuchma, Vornam, & Finkeldey, 2011). As a consequence, AFLPs respond more strongly to recent demographic events than SNPs, whose polymorphisms may actually reflect the effects of recent to intermediate evolutionary events (Waits & Storfer, 2016). The possibility of different responses by AFLPs and SNPs is supported by the recent comparison of genetic diversities in Arabidopsis between SNP and microsatellites (Fischer et al, 2017).…”

Section: The Usefulness and The Limits Of Snp Markers For Partitionmentioning

confidence: 99%

Partitioning genetic and species diversity refines our understanding of species–genetic diversity relationships

Pfeiffer

Ford

Housset

et al. 2018

Ecology and Evolution

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Disentangling the origin of species–genetic diversity correlations (SGDCs) is a challenging task that provides insight into the way that neutral and adaptive processes influence diversity at multiple levels. Genetic and species diversity are comprised by components that respond differently to the same ecological processes. Thus, it can be useful to partition species and genetic diversity into their different components to infer the mechanisms behind SGDCs. In this study, we applied such an approach using a high‐elevation Andean wetland system, where previous evidence identified neutral processes as major determinants of the strong and positive covariation between plant species richness and AFLP genetic diversity of the common sedge Carex gayana. To tease apart putative neutral and non‐neutral genetic variation of C. gayana, we identified loci putatively under selection from a dataset of 1,709 SNPs produced using restriction site‐associated DNA sequencing (RAD‐seq). Significant and positive relationships between local estimates of genetic and species diversities (α‐SGDCs) were only found with the putatively neutral loci datasets and with species richness, confirming that neutral processes were primarily driving the correlations and that the involved processes differentially influenced local species diversity components (i.e., richness and evenness). In contrast, SGDCs based on genetic and community dissimilarities (β‐SGDCs) were only significant with the putative non‐neutral datasets. This suggests that selective processes influencing C. gayana genetic diversity were involved in the detected correlations. Together, our results demonstrate that analyzing distinct components of genetic and species diversity simultaneously is useful to determine the mechanisms behind species–genetic diversity relationships.

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“…We calculated genetic distances (ranging from 0, no genetic difference, to 1, maximum genetic difference) between all pairs of Capercaillie individuals as 1 − (the proportion of shared alleles) (Hazlitt et al 2004) using GENALEX 6.41 (Peakall and Smouse 2006). We considered the proportion of shared alleles as the measurement of genetic distance because of its widespread and successful application in individual-based landscape genetic analysis (Waits and Storfer 2016).…”

Section: Study Species and Genetic Data Setmentioning

confidence: 99%

Three‐dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity

Milanesi

Holderegger

Bollmann

et al. 2017

Ecology

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Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality.

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Basics of Population Genetics: Quantifying Neutral and Adaptive Genetic Variation for Landscape Genetic Studies

Cited by 17 publications

References 141 publications

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

Partitioning genetic and species diversity refines our understanding of species–genetic diversity relationships

Three‐dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity

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