Incorporating evolutionary adaptation in species distribution modelling reduces projected vulnerability to climate change

Authors: Alex Bush, Karel Mokany, Renee Catullo, Ary Hoffmann, Vanessa Kellermann, Carla Sgrò, Shane McEvey, and Simon Ferrier

Published in: Ecology Letters, volume 19, issue 12 (December 2016)

Abstract

Based on the sensitivity of species to ongoing climate change, and numerous challenges they face tracking suitable conditions, there is growing interest in species’ capacity to adapt to climatic stress.

Here, we develop and apply a new generic modelling approach (AdaptR) that incorporates adaptive capacity through physiological limits, phenotypic plasticity, evolutionary adaptation and dispersal into a species distribution modelling framework.

Using AdaptR to predict change in the distribution of 17 species of Australian fruit flies (Drosophilidae), we show that accounting for adaptive capacity reduces projected range losses by up to 33% by 2105. We identify where local adaptation is likely to occur and apply sensitivity analyses to identify the critical factors of interest when parameters are uncertain.

Our study suggests some species could be less vulnerable than previously thought, and indicates that spatiotemporal adaptive models could help improve management interventions that support increased species’ resilience to climate change.

Citation

Bush A, Mokany K, Catullo R, Hoffmann A, Kellermann V, Sgrò C, McEvey S, Ferrier S (2016) Incorporating evolutionary adaptation in species distribution modelling reduces projected vulnerability to climate change. Ecology Letters, PDF DOI

Thermal plasticity in Drosophila melanogaster populations from eastern Australia: quantitative traits to transcripts

Authors: Allannah S Clemson, Carla M Sgrò, and Marina Telonis-Scott

Published in: Journal of Evolutionary Biology, volume 29, issue 12 (December 2016)

Abstract

The flexibility afforded to genotypes in different environments by phenotypic plasticity is of interest to biologists studying thermal adaptation because of the thermal lability of many traits. Differences in thermal performance and reaction norms can provide insight into the evolution of thermal adaptation to explore broader questions such as species distributions and persistence under climate change.

One approach is to study the effects of temperature on fitness, morphological and more recently gene expression traits in populations from different climatic origins. The diverse climatic conditions experienced by Drosophila melanogaster along the eastern Australian temperate-tropical gradient are ideal given the high degree of continuous trait differentiation, but reaction norm variation has not been well studied in this system.

Here, we reared a tropical and temperate population from the ends of the gradient over six developmental temperatures and examined reaction norm variation for five quantitative traits including thermal performance for fecundity, and reaction norms for thermotolerance, body size, viability and 23 transcript-level traits.

Despite genetic variation for some quantitative traits, we found no differentiation between the populations for fecundity thermal optima and breadth, and the reaction norms for the other traits were largely parallel, supporting previous work suggesting that thermal evolution occurs by changes in trait means rather than by reaction norm shifts.

We examined reaction norm variation in our expanded thermal regime for a gene set shown to previously exhibit G×E for expression plasticity in east Australian flies, as well as key heat-shock genes.

Although there were differences in curvature between the populations suggesting a higher degree of thermal plasticity in expression patterns than for the quantitative traits, we found little evidence to support a role for genetic variation in maintaining expression plasticity.

Citation

Clemson AS, Sgrò CM, Telonis-Scott M (2016) Thermal plasticity in Drosophila melanogaster populations from eastern Australia: quantitative traits to transcripts. Journal of Evolutionary Biology, PDF DOI

Cross-study comparison reveals common genomic, network, and functional signatures of desiccation resistance in Drosophila melanogaster

Authors: Marina Telonis-Scott, Carla M Sgrò, Ary A Hoffmann and Philippa C Griffin

Published in: Molecular Biology and Evolution (early view)

Abstract

Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categories, genetic pathways, and interaction networks.

Here we report on the genomic overlap for natural desiccation resistance from a Pool-genome-wide association study experiment and a selection experiment in flies collected from the same region in southeastern Australia in different years.

We identified over 600 single nucleotide polymorphisms associated with desiccation resistance in flies derived from almost 1,000 wild-caught genotypes, a similar number of loci to that observed in our previous genomic study of selected lines, demonstrating the genetic complexity of this ecologically important trait.

By harnessing the power of cross-study comparison, we narrowed the candidates from almost 400 genes in each study to a core set of 45 genes, enriched for stimulus, stress, and defense responses.

In addition to gene-level overlap, there was higher order congruence at the network and functional levels, suggesting genetic redundancy in key stress sensing, stress response, immunity, signaling, and gene expression pathways. We also identified variants linked to different molecular aspects of desiccation physiology previously verified from functional experiments.

Our approach provides insight into the genomic basis of a complex and ecologically important trait and predicts candidate genetic pathways to explore in multiple genetic backgrounds and related species within a functional framework.

Citation

Telonis-Scott M, Sgrò CM, Hoffmann AA, Griffin PC (2016) Cross-study comparison reveals common genomic, network and functional signatures of desiccation resistance in Drosophila melanogasterMolecular Biology and Evolution PDF DOI

Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits

Authors: Marina Telonis-Scott, Allannah S Clemson, Travis K Johnson and Carla M Sgrò

Published in: Molecular Ecology, volume 23, issue 24 (December 2014)

Abstract

The cellular stress response has long been the primary model for studying the molecular basis of thermal adaptation, yet the link between gene expression, RNA metabolism and physiological responses to thermal stress remains largely unexplored.

We address this by comparing the transcriptional and physiological responses of three geographically distinct populations of Drosophila melanogaster from eastern Australia in response to, and recovery from, a severe heat stress with and without a prestress hardening treatment.

We focus on starvin (stv), recently identified as an important thermally responsive gene. Intriguingly, stv encodes seven transcripts from alternative transcription sites and alternative splicing, yet appears to be rapidly heat inducible.

First, we show genetic differences in upper thermal limits of the populations tested. We then demonstrate that the stv locus does not ubiquitously respond to thermal stress but is expressed as three distinct thermal and temporal RNA phenotypes (isoforms). The shorter transcript isoforms are rapidly upregulated under stress in all populations and show similar molecular signatures to heat-shock proteins. Multiple stress exposures seem to generate a reserve of pre-mRNAs, effectively ‘priming’ the cells for subsequent stress.

Remarkably, we demonstrate a bypass in the splicing blockade in these isoforms, suggesting an essential role for these transcripts under heat stress. Temporal profiles for the weakly heat responsive stv isoform subset show opposing patterns in the two most divergent populations. Innate and induced transcriptome responses to hyperthermia are complex, and warrant moving beyond gene-level analyses.

Citation

Telonis-Scott, M, Clemson AS, Johnson TK, Sgrò, CM (2014) Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits,
Molecular Ecology, 23: 6135–6151. PDF DOI