Identifying environmental correlates of intraspecific genetic variation

Harrisson, Katherine A.; Yen, Jian D. L.; Pavlova, Alexandra; Rourke, Meaghan L.; Gilligan, Dean M.; Ingram, Brett A.; Lyon, Jarod; Tonkin, Zeb; Sunnucks, Paul

doi:10.1038/hdy.2016.37

Cited by 9 publications

(7 citation statements)

References 57 publications

(71 reference statements)

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“…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).…”

Section: Methodsmentioning

confidence: 99%

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

Pavlova

Beheregaray

Coleman

et al. 2017

Evolutionary Applications

134

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Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population “uniqueness” often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small‐scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.

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Section: Methodsmentioning

confidence: 99%

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

Pavlova

Beheregaray

Coleman

et al. 2017

Evolutionary Applications

134

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“…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.…”

Section: Introductionmentioning

confidence: 99%

Underlying trends confound estimates of fish population responses to river discharge

et al. 2021

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Conservation management of freshwater ecosystems often focuses on mitigating or reversing the negative effects of altered patterns of river discharge. Assessments of management interventions frequently focus on direct, short‐term responses to discharge without consideration of underlying population trends that span multiple years. We sought to determine the effects on fish populations of annual variation in river discharge and water temperature after accounting for underlying population trends. We used data on five native and one non‐native fish species, collected over 7–20 years in seven rivers in the Murray‐Darling Basin, south‐eastern Australia. Population trends explained 3.4%–24.6% of the total variation in abundance and biomass of our six study species, while discharge and water temperature explained a further 1.2%–11.4% of this variation. However, population trends confounded the effects of discharge and water temperature, which suggests that the effects of annual discharge conditions may be contingent on past conditions and factors intrinsic to populations (e.g. age structure). Failing to account for population trends led to a combination of plausible and implausible associations with discharge and water temperature. Plausible associations included positive associations with the magnitude of spring discharge and negative associations with the number of days where discharge was below the long‐term 10th percentile. Determining whether estimated associations are real or artefactual requires a greater focus on the processes that underpin multiyear population trends. Our results highlight the potential for underlying trends in populations to confound the short‐term effects of discharge. Potential confounding of short‐ and long‐term changes in populations underscores the need to assess responses to river discharge in the context of overarching environmental conditions, including factors other than discharge.

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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, ; 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, ).…”

Section: Introductionmentioning

confidence: 99%

“…

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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mentioning

confidence: 99%

“…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.…”

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confidence: 99%

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

Milanesi

Caniglia

Fabbri

et al. 2018

Ecology and Evolution

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The distribution of intraspecific genetic variation and how it relates to environmental factors is of increasing interest to researchers in macroecology and biogeography. Recent studies investigated the relationships between the environment and patterns of intraspecific genetic variation across species ranges but only few rigorously tested the relation between genetic groups and their ecological niches. We quantified the relationship of genetic differentiation (F ST) and the overlap of ecological niches (as measured by n‐dimensional hypervolumes) among genetic groups resulting from spatial Bayesian genetic clustering in the wolf (Canis lupus) in the Italian peninsula. Within the Italian wolf population, four genetic clusters were detected, and these clusters showed different ecological niches. Moreover, different wolf clusters were significantly related to differences in land cover and human disturbance features. Such differences in the ecological niches of genetic clusters should be interpreted in light of neutral processes that hinder movement, dispersal, and gene flow among the genetic clusters, in order to not prematurely assume any selective or adaptive processes. In the present study, we found that both the plasticity of wolves—a habitat generalist—to cope with different environmental conditions and the occurrence of barriers that limit gene flow lead to the formation of genetic intraspecific genetic clusters and their distinct ecological niches.

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Identifying environmental correlates of intraspecific genetic variation

Cited by 9 publications

References 57 publications

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

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

Underlying trends confound estimates of fish population responses to river discharge

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

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