Habitat loss does not always entail negative genetic consequences

Abstract

Although habitat loss has large, consistently negative effects on biodiversity, its genetic consequences are not yet fully understood. In this paper, we assess the genetic consequences of extreme habitat loss driven by mining in two endemic plants from Amazonian Savannas. Our analyses are the first to overcome major methodological limitations like the confounding effect of habitat fragmentation, historical processes underpinning genetic differentiation, time-lags between the onset of disturbances and genetic outcomes, and the need for large numbers of samples, genetic markers and replicated landscapes to ensure sufficient statistical power. We found that both species are remarkably resilient, as genetic diversity and gene flow patterns were unaffected by habitat loss. Our study unambiguously demonstrates that it is not possible to generalize about the genetic consequences of habitat loss, and imply that future conservation efforts need to consider species-specific genetic information.

Combining genotype, phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration

“…The snmf model implements a fast yet accurate likelihood algorithm (Frichot, Mathieu, Trouillon, Bouchard, & François, 2014), while DAPC is a robust genetic clustering method with no assumption about the underlying population genetic model (Jombart & Ahmed, 2011)⁠. Based on previous population genomic studies for other co‐occurring plant species (Carvalho et al., 2019; Lanes et al., 2018; Silva et al., 2020)⁠, we tested from 1 to 10 ancestral populations ( k ). In the case of snmf we performed 10 replicate runs for each value of k , choosing the most likely k based on minimized cross‐entropy.…”

“…We also estimated pairwise F ST using dartR R package (Gruber, Unmack, Berry, & Georges, 2018)⁠, and effective population sizes ( N e ) employing the linkage disequilibrium method implemented in neestimator 2.1 and a lowest allele frequency value of 0.05 (Do et al., 2014)⁠. Finally, we assessed fine‐scale spatial genetic structure in each species within each genetic cluster through local polynomial fitting (LOESS) of Yang's genetic relatedness between pairs of individuals (Yang et al., 2010)⁠ and pairwise geographic distance, as in (Carvalho et al., 2019)⁠.…”

Paths to annihilation: Genetic and demographic consequences of range contraction patterns

“…However, it has been argued that some populations maintain low diversity ancestrally, making this statistic a poor predictor of the population's health. The cheetah (Acinonyx jubatus) and several other species are classic examples of long-term patterns of low genetic diversity without ill effects (O'Brien et al, 1986;Caro & Laurenson, 1994;Caughley, 1994;Merola, 1994;Frankham, 1995;Caro, 2000;Amos & Balmford, 2001).…”

Landscape Genetics of Plants: Challenges and Opportunities

“…Only a minority of landscape genetic studies have been conducted on plants since the inception of the field in the late 1990s ( Storfer et al., 2010 ), and this trend has continued—especially for studies that use optimized circuit theory methods (e.g., Arredondo et al., 2018 ; Alvarado-Serrano et al., 2019 ; Carvalho et al., 2019 ; Grasty et al., 2020 ). This is surprising given that plants offer many advantages for evaluating the effects of specific types of landscape features on effective dispersal.…”