<scp>MEMGENE</scp>: Spatial pattern detection in genetic distance data

Galpern, Paul; Peres‐Neto, Pedro R.; Polfus, Jean L.; Manseau, Micheline

doi:10.1111/2041-210x.12240

Cited by 97 publications

(127 citation statements)

References 30 publications

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“…In addition, the MEMGENE (Galpern et al, 2014) package in R (http://www.cran.rproject.org/) was used to visualize patterns of spatial genetic variation that may not have been detected with STRUCTURE. Moran's eigenvector maps (MEM) were selected from the geographic locations of individuals and fit against genetic distance data to determine the amount of genetic variation (R 2 adj ) that can be attributed to spatial patterns.…”

Section: Methodsmentioning

confidence: 99%

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Drake

Manseau²,

Klütsch³

et al. 2018

Ran

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Genetic analysis can provide important information on the dynamic and spatial structure of groups of animals or populations. Little is known of the genetic population structure of caribou that inhabit the Lake Superior Coastal Range (LSCR) and the level of gene flow between individuals within the range and beyond. From a landscape perspective, this range is spatially isolated and genetic connectivity within the range is presumed limited due to large water crossings on Lake Superior. This study aims to answer if animal movement can be discerned, using genetic population and relatedness analyses, within and beyond the LSCR. Faecal and hair samples collected between 2005 and 2015 in Pukaskwa National Park were analyzed for genetic markers and compared to 131 unique genotypes previously obtained from both within the LSCR and in the two next closest ranges. Animals from one nearshore island (i.e. Otter) were more closely associated with offshore islands than other mainland caribou, likely a result of past movement and translocation rather than ongoing movement. Conversely, on another nearshore island (i.e. Pic), individuals assigned to a different genetic cluster and were related to animals further north outside the range, demonstrating some connectivity through the discontinuous distribution to the coast. Long-term population declines have been observed in the LSCR despite genetic connectivity within the range and relatively low total habitat disturbance. Restoring connectivity of the LSCR so that it is not isolated from populations to the north is required for the recovery of the mainland portion of the coastal range. These genetic analyses provide some insights on where movements may occur and where landscape restoration efforts may best be directed to enhance connectivity.

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Section: Methodsmentioning

confidence: 99%

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Drake

Manseau²,

Klütsch³

et al. 2018

Ran

Self Cite

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“…In order to bolster our analyses, we used distance‐based Moran's eigenvector maps (MEM; also referred to as PCNM; Borcard and Legendre ) and multivariate regression of genetic distance matrices and the landscape resistance surfaces, implemented in the MEMGENE R package (Galpern et al. ; Appendix S3). This approach differs from Mantel distance regressions as the explanatory variables are not transformed into distances.…”

Section: Methodsmentioning

confidence: 99%

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Roffler

Schwartz

Pilgrim

et al. 2016

Evolutionary Applications

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Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid‐range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long‐term genetic connectivity.

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“…Because Mantel tests can be prone to Type I error (Legendre & Fortin, 2010;Legendre, Fortin, & Borcard, 2015), the matrices described above were also analyzed using distance-based Moran's eigenvector map analysis in the MEMGENE package (Galpern, Peres-Neto, Polfus, & Manseau, 2014) for R. This method finds Moran's eigenvectors in the spatial data (input as geographic, least cost, or resistance distance) using principal coordinates analysis. Then redundancy analysis is used to select a reduced set of vectors based on their contribution as predictors of the response variable (genetic distance (Fisher, 1922) to reveal complex patterns (Griffith & Peres-Neto, 2006;Legendre & Fortin, 2010;Richardson, Brady, Wang, & Spear, 2016).…”

Section: Stmentioning

confidence: 99%

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

Jensen

O'Neil

Iwaniuk

et al. 2019

Ecology and Evolution

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The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.

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MEMGENE: Spatial pattern detection in genetic distance data

Cited by 97 publications

References 30 publications

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Identification of landscape features influencing gene flow: How useful are habitat selection models?

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

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