Identifying environmental correlates of intraspecific genetic variation

Abstract

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow

“…We used an individual‐based Bayesian modelling approach to identify environmental variables that were correlated with spatial distribution of genetic variation (Harrisson, Yen, et al., ). The model was based on the 16 populations from the MDB and the HNB (translocated Yarra and Cataract Dam and admixed Cataract River samples were excluded).…”

Underlying trends confound estimates of fish population responses to river discharge

“…Many factors confound population responses to discharge (Palmer & Ruhi, 2019; Thompson et al., 2018; Wenger et al., 2011). These include extrinsic factors, such as the introduction of non‐native species, sedimentation, and loss of habitat (Thompson et al., 2018), as well as factors intrinsic to populations, such as age structure and individual or population genetic diversity (Harrisson et al., 2016; Pavlova et al., 2017). Extrinsic and intrinsic factors can drive population trends independently of discharge but also interact with discharge.…”

Combining Bayesian genetic clustering and ecological niche modeling: Insights into wolf intraspecific genetic structure

“…Genetic variation is key for the long‐term persistence and survival of species and populations. Its distribution across species ranges can reveal intraspecific information that is not necessarily represented in simple species occurrence patterns (Harrisson et al, ; Kovach et al, ). For instance, understanding the distribution of intraspecific genetic variation and how it relates to environmental factors can assist conservation management to assess species responses to environmental conditions and global change (Thomassen et al, ).…”

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Genetic variation is key for the long-term persistence and survival of species and populations. Its distribution across species ranges can reveal intraspecific information that is not necessarily represented in simple species occurrence patterns (Harrisson et al, 2016;Kovach et al, 2015). For instance, understanding the distribution of intraspecific genetic variation and how it relates to environmental factors can assist conservation management to assess species responses to environmental conditions and global change (Thomassen et al, 2010).Recently, Gotelli and Stanton-Geddes (2015) proposed the use of ecological niche models (ENMs), also known as habitat suitability models or species distribution models, for intraspecific genetic groups identified by Bayesian clustering, in order to account for the genetic diversity occurring within species.

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“…The approach of Gotelli and Stanton-Geddes (2015) has so far only been applied in handful of studies (Harrisson et al, 2016;Ikeda et al, 2017;Marcer et al, 2016;Shinneman, Means, Potter, & Hipkins, 2016) , and the relationship between genetic distances among genetically defined clusters (e.g., genetic differentiation F ST ; Dupanloup, Schneider, & Excoffier, 2002;Jombart, Devillard, Dufour, & Pontier, 2008) and distances or similarities among their ecological niches (e.g., niche overlap) has not been tested so far. Moreover, none of these studies specifically investigated the environmental factors differing among genetic clusters.…”