Ecological genomics and adaptation to environmental change

Rapid environmental and climatic change represents a clear and urgent challenge for conservation and evolutionary biologists – this is particularly so in aquatic ecosystems, which are experiencing some of the fastest rates of change. Understanding the genetic basis of adaptation in the wild is central to predict how organisms will respond to global crises such as climate change, habitat loss, resistance to antibiotics, or invasive species. It is also key for biodiversity management since it informs on the distribution of functional diversity and on the evolutionary potential of populations.

We are implementing a research program in ecological genomics to understand population adaptations and responses to environmental change in ecologically important aquatic organisms including fishes, abalones, whales and dolphins. Our projects involve collaborations with research teams with international leadership standing in aquatic genomics and use study systems with well-known natural history so the most meaningful biological results can be obtained.

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Research Projects

– “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.

Select Publications

– McCairns RJS, Smith S, Sasaki M, Bernatchez L, Beheregaray LB (2016) The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. Evolutionary Applications doi:10.1111/eva.12363.

– Brauer CJ, Hammer MP, Beheregaray LB (2016) Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Molecular Ecology doi: 10.1111/mec.13830

– Lean J, Hammer MP, Unmack PJ, Adams M, Beheregaray LB (2016) Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system. Heredity In press

 – Attard CRM, Möller LM, Sasaki M, Hammer MP, Bice C, Brauer C, Carvalho D, Harris J, Beheregaray LB (2016) A novel holistic framework for genetic-based captive breeding and reintroduction programs. Conservation Biology 30, 1060-1069.

– Cooke GM, Landguth EL, Beheregaray LB (2014) Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone. Evolution doi: 10.1111/evo.12410.

– Perini V, Carvalho DC, Beheregaray LB, Prosdocimi F (2015) The complete mitochondrial genome of the southern purple-spotted gudgeon Mogurnda adspersa (Perciformes: Eleotridae) through pyrosequencing. Mitochondrial DNA doi: 10.3109/19401736.2014.895995.

– Smith S, Bernatchez L, Beheregaray LB (2013) RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species. BMC Genomics 2013, 14:375. (Highly Accessed)

– Hammer MP, Bice CM, Hall A, Frears A, Watt A, Whiterod NS, Beheregaray LB, Harris JO, Zampatti BP (2013) Freshwater fish conservation in the face of critical water shortages in the southern Murray–Darling Basin, Australia. Marine and Freshwater Research 64, 807–821.

– Amaral AR, Beheregaray LB, Bilgmann K, Freitas L, Robertson KM, Sequeira M, Stockin KA, Coelho MM, Möller LM (2012) Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Molecular Ecology 21, 4854-4871.

– Cooke GM, Chao NL, Beheregaray LB (2012) Natural selection in the water: freshwater invasion and adaptation by water colour in the Amazonian pufferfish. Journal of Evolutionary Biology 25, 1305-1320.

 – Cooke GM, Chao NL, Beheregaray LB (2012) Divergent natural selection with gene flow along major environmental gradients in Amazonia: Insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus. Molecular Ecology  –  Paper recommended by F1000, read review here

– Teske PR, Papadopoulos I, Mmonwa K, Matumba T, McQuaid C, Barker NP, Beheregaray LB (2011) Climate-driven genetic divergence of limpets with different life histories across a southeast African marine biogeographic disjunction: different processes, same outcome. Molecular Ecology 20, 5025-5041.

– Prosdocimi F, Carvalho DC, Almeida RN, Beheregaray LB (2011) The complete mitochondrial genome for two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae) Molecular Biology Reports doi: 10.1007/s11033-011- 1034-5.

– Banks SC, Ling SD, Johnson CR, Piggott MP, Williamson JE & Beheregaray LB (2010) Genetic structure of a recent climate-change driven range expansion. Molecular Ecology 19, 2011–2024.

– Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. Journal of Biology 6, 1-5.

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