Genetic approaches are likely to play a major role in conservation in the future, given the extent of habitat fragmentation and the rate of human-driven environmental change. We are working in the emerging fields of restoration genetics (i.e. based on a few dozen molecular markers) and restoration genomics (i.e. based on thousands of markers) to address genetic problems typically found in small populations while attempting at restoring threatened biodiversity in the wild.
Our restoration efforts include work with both ‘genetic-based captive breeding’ and ‘genetic rescue’ programs. The aim of ‘genetic-based captive breeding’ is to preserve as much as possible the genetic diversity found in wild populations. By working out family relationships (or pedigrees) we can design crosses in the laboratory between unrelated individuals to prevent inbreeding in captive populations before their reintroduction in the wild. Another way of conserving genetic diversity that is slowly becoming more popular is ‘genetic rescue’ in the wild – also known as translocations. Here, individuals are moved between recently isolated populations to restore connectivity or to supplement local levels of both neutral and adaptive (i.e. ecologically relevant) genetic diversity.
In a separate but complementary research program we are implementing range-wide studies of landscape genomics in select organisms, such as ecologically surrogate species of freshwater fishes. Landscape genomic studies aim to assess associations between genome-wide levels of variation of populations and environmental heterogeneity. We are studying how land use, natural and artificial barriers, habitat type, hydrological regime and climate change shape genome-wide diversity (both neutral and adaptive), connectivity and evolutionary potential.
Our work has targeted both threatened and non-threatened fish species from coastal and inland catchments of Australia and Brazil. In Australia, we implemented and run large conservation and landscape genomic programs in collaboration with government agencies responsible for biodiversity inventories, protection and management of aquatic resources (examples below).
Australia is an arid nation that has water as a critical resource and some of the world’s most impacted freshwater ecosystems. We have built collaborations with government departments, aquatic ecologists, industry partners and conservation stakeholders to address issues about management of freshwater resources and policies regarding reintroduction and recovery of threatened species. Some of our research projects have united native fish conservation stakeholders to address key questions in conservation and management of freshwater biodiversity.
We have pioneered the use of riverscape genetics in Australia to establish links between anthropogenic and environmental factors and fish biodiversity (see publications list). Our conservation management research includes work with catadromous species in the wild and used for restocking programs. We are also working on conservation breeding and restoration genetics of endangered fishes from the Murray-Darling Basin using information from both neutral and adaptive genetic diversity.
Some examples include:
– ARC Linkage (LP100200409) “Restoration Genetics of Five Endangered Fish Species from the Murray-Darling Basin”
CIs: L Beheregaray & J Harris (Flinders); PI: M Adams (SA Museum). Partners: Department for Environment and Natural Resources SA (DEWNR SA), SA Murray Darling Basin Natural Resource Management Board (MDB NRM), South Australian Museum, Native Fish Australia (NFA); Fisheries Division of Primary Industries and Resources South Australia (PIRSA Fisheries). Other team members and collaborators: M Hammer (NFA), A Hall, A Watt (DEWNR SA), A Frears (MDB NRM), J McPhail (PIRSA Fisheries), F Prosdocimi (UERJ, Brazil); L Moller, D Carvalho, S Smith, J Sandoval-Castillo, M Sasaki, C Brauer, T Cole and H Ling (Flinders).
– ARC Linkage (LP0667952) “Phylogeography, Conservation Genetics and Stocking Management of Perches and Basses”
CI: L Beheregaray (Flinders); PI: D Gilligan (NSW DPI). Partners: NSW Department of Primary Industries (DPI) Fisheries. Other team members and collaborators: : L Faulks, K Shaddick, T Schwartz (Macquarie), D Jerry (James Cook University), C Burridge (UTAS), W Fulton (DPI Fisheries VIC).
– ARC Linkage (LP110200017) “Genomics for Persistence of Australian Freshwater Fish”
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.
– 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.
– 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
– Sandoval-Castillo J, Attard CRM, Marri A , J. Brauer C, Möller LM, Beheregaray LB (2016) SWINGER: a user-friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information. Molecular Ecology Resources In press
– Brauer CJ, Hammer MP, Beheregaray LB (2016) Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin. Molecular Ecology 25, 5093-5113.
– Attard CRM, Brauer CJ, Van Zoelen J, Sasaki M, Hammer MP, Morrison L, Harris JO, Möller LM, Beheregaray LB (2016) Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (Nannoperca australis). Conservation Genetics doi: 10.1007/s10592-016-0873-y
– Cole TL, Hammer MP, Unmack PJ, Teske PR, Brauer CJ, Adams M, Beheregaray LB (2016) Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray-Darling Basin, Australia. Conservation Genetics doi: 10.1007/s10592-016-0868-8
– Sasaki M, Hammer MP, Unmack PJ, Adams M, Beheregaray LB (2016) Population genetics of a widely distributed small freshwater fish with varying conservation concerns: the southern purple-spotted gudgeon, Mogurnda adspersa. Conservation Genetics doi: 10.1007/s10592-016-0829-2.
– Faulks LK, Gilligan DM, Beheregaray LB (2015) “Ragged mountain ranges, droughts and flooding rains”: The evolutionary history and conservation of Australian freshwater fishes. In: Austral Ark. Eds. Stow A, Mclean N & Holwell G. Cambridge University Press, Cambridge, UK.
– Beheregaray LB, Cooke GM, Chao NL, Landguth EL (2015) Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia. Frontiers in Genetics 5, 477
– Bracamonte SE, Smith S, Hammer M, Pavey SA, Sunnucks P, Beheregaray LB (2015) Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations. Fish and Shellfish Immunology In press
– Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beheregaray LB (2013) Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems. PLoS ONE 8(12): e82953.
– 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 In press
– Faulks LK, Gilligan DM, Beheregaray LB (2011) The role of anthropogenic vs. natural in-stream structures in determining connectivity and genetic diversity in an endangered freshwater fish, Macquarie perch (Macquaria australasica). Evolutionary Applications 19, 4723–4737.
– Shaddick K, Burridge CP, Jerry DR, Gilligan DM, Truong K, Beheregaray LB (2011) Historical divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum). Canadian Journal of Fisheries and Aquatic Sciences 68, 304–318.
– Faulks LK, Gilligan DM, Beheregaray LB (2010) Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia’s arid zone, the golden perch (Macquaria ambigua). Molecular Ecology 19, 4723-4737.
-Shaddick K, Burridge CP, Jerry DR, Schwartz TS, Truong K, Gilligan DM, Beheregaray LB (2011) A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum. Journal of Fish Biology 79, 1214–1235.
– 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.
– Carvalho DC, Rodriguez-Zarate CJ, Hammer MP, Beheregaray LB (2011) Development of 21 microsatellite markers for the threatened Yarra pygmy perch (Nannoperca obscura) through 454 shot-gun pyrosequencing. Conservation Genetics Resources 3, 601-604.
– Carvalho DC, Beheregaray LB (2011) Rapid development of microsatellites for the endangered Neotropical catfish Conorhynchus conirostris using a modest amount of 454 shot-gun pyrosequencing. Conservation Genetics Resources 3, 373-375.
– Faulks LK, Gilligan DM, Beheregaray LB (2010) Evolution and maintenance of divergent lineages in an endangered freshwater fish, Macquaria australasica. Conservation Genetics 11, 921–934.
– Faulks LK, Gilligan DM, Beheregaray LB (2010) Clarifying an ambiguous evolutionary history: range-wide phylogeography of an Australian freshwater fish, Golden Perch (Macquaria ambigua). Journal of Biogeography 37, 1329–1340.
– Rourke M, Gilligan D, Attard C, Teske P, Beheregaray LB (2009) Isolation and characterisation of microsatellite loci in the Australian freshwater catfish. Conservation Genetics Resources 2, 245-248.
– Carvalho DC, de Oliveira DAA, dos Santos JE, Teske P, Beheregaray LB, Schneider H & Sampaio I (2009) Genetic chracterization of native and introduced populations of the neotropical cichlid genus Cichla in Brazil. Genetics and Molecular Biology 32, 3, 601-607.
– Faulks L, Gilligan D, Beheregaray LB (2008) Phylogeography of a threatened freshwater fish (Mogurnda adspersa) in eastern Australia: conservation implications. Marine and Freshwater Research 59, 89-96.