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

Abstract

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.

The active spread of adaptive variation for reef resilience

“…Estimates of natural levels and directions of gene flow can inform the design of optimal deployment of PALs through AGF or deployment of offspring from crosses between northern and more southern corals (Harrisson et al, 2016;Pavlova et al, 2017). Estimates of gene flow will also help inform how fast PALs may spread naturally following intervention, thereby providing guidance for the number and location of reefs where migrants harboring PALs can be best deployed.…”

“…AGF and selective breeding may introduce genotypes that are not adapted to local environmental conditions other than temperature at the receiving location ("local is best", Rehfeldt et al, 2017) and introduce trade-offs between different traits. One concern is that the single or repeated pulse of PALs will erode or alter local adaptation among coral populations, as other loci adapted to the source reef conditions will also enter the receiving population (Drury, Manzello, et al, 2017;Drury, Schopmeyer, et al, 2017;Kenkel et al, 2013;Pavlova et al, 2017;Polato et al, 2010;Webber & Scott, 2012). Meta-analyses across highly divergent taxa including plants, animals, fungi, and protists revealed that local populations gain ~50% fitness advantage in their native environment compared to migrants (Hereford, 2009).…”

Not just a migration problem: Metapopulations, habitat shifts, and gene flow are also important for fishway science and management

“…Several population‐level metrics are reported, including probability of extinction over the modelled time period. With translocation of suitable genotypes, Pavlova et al () found that the probability of extinction in the smallest populations could be maintained at or near zero for 100 years, a substantial improvement on a “do‐nothing” scenario.…”

Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool‐breeding amphibians

“…Above these scales, sample sizes are greater, but drift–migration equilibrium may take longer to occur, and stochastic processes weaken correlations. Understanding the scale dependence of IBD may be important to understanding why different studies on a specific species obtain different IBD inferences and help to inform whether an IBD study has sufficient power to identify effects of landscape features on population connectivity. Urbanization's influence on isolation and genetic diversity : We hypothesized that greater urbanization will affect metapopulation dynamics by increasing among‐population isolation and reducing within‐population genetic diversity for both species, relative to patterns in less‐urbanized areas (Frankham, ; Kenney, Allendorf, Mcdougal, & Smith, ; Pavlova et al, ). We further hypothesize that the substantive differences in life history and vagility of our focal species will contribute to different effects of the same landscape features (Moyle, ; Phillipsen et al, ).…”