Ecological genomics and adaptation to environmental change

– “Evolution, adaptation and resilience of Australian freshwater fishes” 
ARC Future Fellowship (FT130101068 2014-2017),  CI: L Beheregaray (Flinders). 

This project integrates comparative ecological genomics (in the wild and in the lab), phenotypic data and
spatially-explicit modelling approaches to assess adaptation and vulnerability of aquatic biodiversity to
environmental change. The focus is on a family of Australian freshwater fishes that evolved in response to
hydrological disturbance and shows contemporary patterns of biodiversity shaped by hydroclimatic variation
and anthropogenic pressures. I expect to disclose a positive correlation between family-wide adaptive
capacity and variance in ecological disturbance. This work will address fundamental and novel questions
about factors shaping adaptation and resilience along naturally and anthropogenically disturbed ecosystems.

GENERAL AIM: To understand and predict adaptive responses and vulnerability to environmental change in a family
of Australian freshwater fishes that evolved in response to strong hydrologic disturbance.

– “Seascape genomics of abalones: a spatial analysis of neutral and adaptive variation in species challenged by climate change”
Seafood CRC 2012/714,  CI: L Beheregaray (Flinders); PI: N Robinson (Nofima, Norway); J Sandovall-Castillo (Flinders); Collaborators:  A Hart, L Strain (Western Australian Fisheries), J Strugnell (La Trobe).

The integration of ecological genomics and oceanographic datasets provides the means to elucidate the spatial distribution of both neutral and adaptive variation in marine populations. This information is particularly relevant for clarifying the relative role of ecological and evolutionary processes in shaping population persistence and for informing conservation actions, including translocations.  We used RAD-seq to discover and characterise SNPs and conduct a genome wide scan of neutral and putatively adaptive variation in Roe’s abalone (Haliotis roei).  Populations of this species experienced catastrophic mortalities (including regional extinctions) associated to an extreme marine heatwave event along the western Australian coast during the summer of 2010/11. We genotyped 400 abalones sampled from ten localities along the southwest and southern coasts of Australia using 31,008 SNPs. Analyses based on the entire SNP dataset indicate that the species is characterized by substantial gene flow and little if any population differentiation along the vast sampled area. In marked contrast to these results, three genetically distinct population groups can be clearly defined based on SNPs that potentially carry the signature of natural selection (i.e. ‘outlier’ loci used as candidates to characterize population adaptations). These loci were annotated using the transcriptome of a closely related abalone (H. laeviegata) to determine adaptive functions. Interestingly, these candidate loci are related to genes associated with heat stress or general immune tolerance. We also disclosed evidence of putatively adaptive variation spatially associated with thermal gradients along the sampled area. Our study provides key information for ongoing restocking efforts in this species and contributes to our understanding of local adaptation and population resilience to climate change in a commercially important broadcast spawner.

– “Comparative Evolutionary Genomics of Australian Rainbowfishes“
ARC Discovery (D110101207 & DP150102903), CI: L Beheregaray (Flinders); PI: L Bernatchez (Universite Laval, Canada); Collaborators: P Unmack (U Canberra);  S Smith (Flinders & U Vienna); S McCairns (U Helsinki).

 This project uses an evolutionarily young and ecologically important fish clade to understand adaptive resilience and to test predictions derived from the ‘climatic variability hypothesis’ for the major climatic regions of mainland Australia. Correlative surveys along landscapes and mechanistic experimental studies will be integrated to implement a comparative evolutionary genomics framework capable of assessing the genetic basis of adaptation and the evolutionary resilience of populations and lineages. This will clarify climatic and geographic correlates of adaptation across a vast area of Australia and will disentangle plastic from evolutionary responses to environmental change in an emerging model system for adaptation research.

– “Genomics for Persistence of Australian Freshwater Fish”
ARC Linkage (LP110200017, 2011-2014), CIs: P Sunnucks (Monash), M Lintermans (U canberra), C Sgro (Monash), L Beheregaray (Flinders); PIs: F Allendorf & G Luikart (U Montana), F Lyon (Arthur Rylah Institute). Partners: ACTEW Corporation, Fisheries Victoria, Melbourne Water, University of Montana, Victorian Department of Sustainability and Environment.

This project assembled an outstanding multidisciplinary team to apply genomics to a suite of Australian native freshwater fish to address the range of typical management needs. Working with key freshwater management agencies, we will develop genomic measures of ecological-genetic functions and evolutionary potential for managing Australian freshwater fish.