The use and misuse of regression models in landscape genetic analyses

Peterman, William E.; Pope, Nathaniel S.

doi:10.1111/mec.15716

Cited by 44 publications

(30 citation statements)

References 91 publications

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“…The proportion of shared alleles was better explained by the model including the pairwise Euclidean distances among individuals than by the model including the pairwise LCPs across the resistance surface. Pairwise genetic data are known to be noisy, and therefore, inferences are often challenging (Peterman & Pope, 2020). Among individuals, the landscape's resistance arguably did not exert a meaningful effect.…”

Section: Discussionmentioning

confidence: 99%

Assessment of drivers of spatial genetic variation of a ground‐dwelling bird species and its implications for conservation

Kunz

Klinga

Sittenthaler

et al. 2021

Ecology and Evolution

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In modern wildlife ecology, spatial population genetic methods are becoming increasingly applied. Especially for animal species in fragmented landscapes, preservation of gene flow becomes a high priority target in order to restore genetic diversity and prevent local extinction. Within Central Europe, the Alps represent the core distribution area of the black grouse, Lyrurus tetrix. At its easternmost Alpine range, events of subpopulation extinction have already been documented in the past decades. Molecular data combined with spatial analyses can help to assess landscape effects on genetic variation and therefore can be informative for conservation management. Here, we addressed whether the genetic pattern of the easternmost Alpine black grouse metapopulation system is driven by isolation by distance or isolation by resistance. Correlative ecological niche modeling was used to assess geographic distances and landscape resistances. We then applied regression‐based approaches combined with population genetic analyses based on microsatellite data to disentangle effects of isolation by distance and isolation by resistance among individuals and subpopulations. Although population genetic analyses revealed overall low levels of genetic differentiation, the ecological niche modeling showed subpopulations to be clearly delimited by habitat structures. Spatial genetic variation could be attributed to effects of isolation by distance among individuals and isolation by resistance among subpopulations, yet unknown effects might factor in. The easternmost subpopulation was the most differentiated, and at the same time, immigration was not detected; hence, its long‐term survival might be threatened. Our study provides valuable insights into the spatial genetic variation of this small‐scale metapopulation system of Alpine black grouse.

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Section: Discussionmentioning

confidence: 99%

Assessment of drivers of spatial genetic variation of a ground‐dwelling bird species and its implications for conservation

Kunz

Klinga

Sittenthaler

et al. 2021

Ecology and Evolution

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“…MLPE uses individual-based genetic distances as the response and environmental resistances as fixed effects, with an additional random effect matrix of pairwise individual comparisons to control for their nonindependence (Balkenhol et al, 2016;Trumbo et al, 2019). Although MLPE has received criticism regarding its power to accurately capture how landscape features impact gene flow (Peterman & Pope, 2021), our goal here was to test the validity of a priori hypotheses regarding scrub-jay dispersal across habitat types (Langin et al, 2015), rather than finding the best supported resistance model. Additionally, MLPE is an effective method to infer associations between landscape features and gene flow (Kozakiewicz et al, 2019;Shirk et al, 2017;Trumbo et al, 2019).…”

Section: Is Gene Flow Restricted Between Habitat Types?mentioning

confidence: 99%

Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species

et al. 2022

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“…Arrows depict causal relationships. The dotted circle represents an unsampled variable the importance of thoughtful hypothesis testing (Hickerson, 2014;Peterman & Pope, 2021). However, it becomes even more critical in the context of complex geoclimatic settings and when working to establish causal relationships between earth processes and evolution.…”

Section: The Problem Of Epiphenomenamentioning

confidence: 99%

Towards a unified framework to study causality in Earth–life systems

Dolby

2021

Molecular Ecology

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There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.

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The use and misuse of regression models in landscape genetic analyses

Cited by 44 publications

References 91 publications

Assessment of drivers of spatial genetic variation of a ground‐dwelling bird species and its implications for conservation

Assessment of drivers of spatial genetic variation of a ground‐dwelling bird species and its implications for conservation

Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species

Towards a unified framework to study causality in Earth–life systems

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