Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)

Abstract

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

Habitat Loss Does Not Always Entail Negative Genetic Consequences

“…Yang’s genetic relatedness between pairs of individuals (Yang et al, 2010) was used as a proxy for recent gene flow, given that it represents the number of common ancestors in the recent past (Wang, 2017). Although relatedness is not a direct measure of gene flow, it has been widely used to describe genetic connectivity among individuals (Storfer et al, 2010; Balkenhol et al, 2016; Monteiro et al, 2019) and a recent simulation study showed that it is among the most accurate individual-based genetic distance metric for landscape genetic studies (Shirk et al, 2017). Resistance to gene flow due to mining was modeled using land cover maps for different years (2016, 2014, 2011, and 1979) containing only the major land cover classes of our study region: Montane savanna (Canga), forest (evergreen forest), and mine.…”

“…In spite of ample evidence showing that habitat loss has large, consistently negative effects on biodiversity (Fahrig, 2003), very few studies have assessed the consequences of habitat amount on genetic variation (DiLeo and Wagner, 2016; Monteiro et al, 2019). Habitat loss can potentially impact the demographics of natural populations, reducing population size, gene flow, and genetic diversity, and thereby increasing inbreeding and extinction risk (Allendorf et al, 2013).…”

Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

“…These analyses project genetic variation into unsampled locations for which data on the driver are available, using the driver as a surrogate of genetic variation (Wasserman et al ., 2012; Hanson et al ., 2017). This has practical utility for highlighting migration corridors to limit genetic erosion (DiLeo & Wagner, 2016; Monteiro et al ., 2019), identifying priority conservation areas aimed at protecting within‐species genetic composition [e.g. conservation planning (Paz‐Vinas et al ., 2018; Hanson et al ., 2020)], or modeling population vulnerability and changes in adaptive capacity due to environmental change (Fitzpatrick & Keller, 2015; Martins et al ., 2018; Razgour et al ., 2018; Vranken et al ., 2021).…”

Habitat loss does not always entail negative genetic consequences

“…Yang's genetic relatedness between pairs of individuals (Yang et al, 2010) was used as a proxy for recent gene flow, given that it represents the number of common ancestors in the recent past (Wang, 2017). Although relatedness is not a direct measure of gene flow, it has been widely used to describe genetic connectivity among individuals (Balkenhol et al, 2016;Monteiro et al, 2019;Storfer et al, 2010) and a recent simulation study showed that it is among the most accurate individual-based genetic distance metric for landscape genetic studies (Shirk et al, 2017). Resistance to gene flow due to mining was modeled using land cover maps for different years (2016, 2014, 2011 and 1979) containing only the major land cover classes of our study region: Montane Savanna (Canga), Forest (evergreen forest) and Mine.…”