Practical genetic management

Many of these publications are open access or otherwise readily available on the internet for example via ResearchGate.

However, if you would like papers to which you do not have access

please email Paul.Sunnucks@monash.edu /  Alexandra.Pavlova@monash.edu

Practical genetic management - Papers:

Helmeted honeyeater

Pavlova A, Petrovic S, Harrisson KA, Cartwright K, Dobson E, Hurley LL, Lane M, Magrath MJL, Miller KA, Quin B, Winterhoff M, Yen JDL, and Sunnucks P (2023) Benefits of genetic rescue of a critically endangered subspecies from another subspecies outweigh risks: Results of captive breeding trials. Biological Conservation 284:110203 https://doi.org/10.1016/j.biocon.2023.110203. Code available at https://doi.org/10.5281/zenodo.7735233, data at https://doi.org/10.26180/22139813  

Robledo-Ruiz DA, Gan HM, Kaur P, Dudchenko O, Weisz D, Khan R, Lieberman Aiden E, Osipova E, Hiller M, Morales HE, Magrath MJL, Clarke RH, Sunnucks P, Pavlova A. 2022. Chromosome-length genome assembly and linkage map of a Critically Endangered Australian bird: the helmeted honeyeater.  GigaScience 11.

Explainer video  |  Blog  |  Press release

Robledo-Ruiz DA, Pavlova A, Clarke RH, Magrath MJL, Quin B, Harrisson KA, Gan HM, Low GW, Sunnucks P. (2022) A novel framework for evaluating in-situ breeding management strategies in endangered populations. Molecular Ecology Resources, 22, 239-253.    https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13476   

Video abstract

Harrisson KA, Magrath MJL, Yen JDL, Pavlova A, Murray N, Quin B, Menkhorst P, Miller KA, Cartwright K, Sunnucks P. (2019) Lifetime fitness costs of inbreeding and being inbred in a critically endangered bird.  Current Biology 29, 1-7.

Harrisson KA, Pavlova A, Gonçalves da Silva A, Rose B, Bull JK, Lancaster ML, Murray ND, Quin B, Menkhorst P, Magrath M, Sunnucks P (2016) Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies.  Molecular Ecology, 25, 1242–1258 https://doi.org/10.26180/25777902 

Pavlova A, Selwood P, Harrisson KA, Murray N, Quin B, Menkhorst P, Smales I and Sunnucks P  (2014) Integrating phylogeography and morphometrics to assess conservation merits and inform conservation strategies for an endangered subspecies of a common species. Biological Conservation, 174, 136–146. https://doi.org/10.26180/25778121

Leadbeater’s possum

Zilko JP, Harley D, Hansen B, Pavlova A, Sunnucks P. (2020). Accounting for cryptic population structure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial.  Molecular Ecology 29, 2978–2993.  Full text via ResearchGate   Data available at https://doi.org/10.26180/5ef6ec4550f3b  

Zilko JP, Harley D, Pavlova A, Sunnucks P.  Applying population viability analysis to inform genetic rescue that preserves locally unique genetic variation in a critically endangered mammal.  Diversity,13, 382. https://doi.org/10.3390/d13080382. Data available at https://doi.org/10.26180/15019797 

Plants

Brown's Banksia

Rodger YS, Dillon R, Monroe K, Pavlova A, Coates DJ, Byrne M, Sunnucks P. (2024). Benefits of outcrossing and their implications for genetic management of an endangered species with mixed mating system. Restoration Ecology, 32, e14057. https://doi.org/10.1111/rec.14057. Data available at https://doi.org/10.26180/24532861   

Button wrinklewort

Rodger YS, Pavlova A, Sinclair S, Pickup M, Sunnucks P. (2021) Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy.  Heredity, 126, 846-858.    

Blog  https://doi.org/10.1038/s41437-021-00413-0. Data available at https://doi.org/10.26180/5ea1603edd3a1. 

Fish

Macquarie perch

Pavlova A, Pearce L, Sturgiss F, Lake E, Sunnucks P, Lintermans M. (2024) Immediate genetic augmentation and enhanced habitat connectivity are required to secure the future of an iconic endangered freshwater fish population. Evolutionary Applications 17, e70019. https://doi.org/10.1111/eva.70019. Genetic data available in Dryad at https://doi.org/10.5061/dryad.j3tx95xqc, all data in Bridges at https://doi.org/10.26180/25467973.

Pavlova A, Schneller N, Lintermans M, Beitzel M, Robledo-Ruiz D, Sunnucks P. (2024) Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression. Evolutionary Applications, 17, e13679. https://doi.org/10.1111/eva.13679. Data available at https://doi.org/10.26180/19376570. 

Yen JDL, Todd CR, Sharley J, Harris A, Geary WL, Kelly E, Pavlova A, Hunt TL, Ingram B, Lyon J, Tonkin Z. (2022) Establishing new populations in water-secure locations may benefit species persistence more than interventions in water-stressed locations. Biological Conservation, 276, 109812. https://doi.org/10.1016/j.biocon.2022.109812  

Pavlova A, Harrisson KA, Turakulov R, Lee YP, Ingram BA, Gilligan D, Sunnucks P, Gan HM.  (2022). Labile sex chromosomes in the Australian freshwater fish family Percichthyidae. Molecular Ecology Resources, 22, 1639-1655. https://doi.org/10.1111/1755-0998.13569. Authorea preprint https://doi.org/10.22541/au.162696809.95212733/v1. Full text via ResearchGate Data available at https://doi.org/10.26180/5ea1736cc3553 and https://doi.org/10.26180/13551713 

Lutz ML, Sunnucks P, Chapple DG, Gilligan D, Lintermans M, and Pavlova A (2022) Strong bidirectional gene flow between fish lineages separated for over 100,000 years. Conservation Genetics 23:1105-1113 https://rdcu.be/cXwco. Data available at https://doi.org/10.26180/16553151. 

Lutz M, Tonkin Z, Yen JDL, Johnson G, Ingram BA, Sharley J, Lyon J, Chapple DG, Sunnucks P, Pavlova A (2021). Using multiple sources during reintroduction of a locally extinct population benefits survival and reproduction of an endangered freshwater fish. Evolutionary Applications, 14:950–964. https://doi.org/10.1111/eva.13173. Data available at https://doi.org/10.26180/5ea1736cc3553 

Pavlova A, Beheregaray LB, Coleman R, Gilligan D, Harrisson KA, Ingram BA, Kearns J, Lamb AM, Lintermans M, Lyon JP, Nguyen TTT, Sasaki M, Tonkin Z, Yen JDL and Sunnucks P (2017) Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: a call for assisted gene flow. Evolutionary Applications 10, 531–550

Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan D, Lintermans M, Sunnucks P (2017) Purifying selection and drift shaped Pleistocene evolution of mitochondrial genome in an endangered Australian freshwater fish. Heredity 118, 466-476

Murray cod

Harrisson KA, Amish S, Pavlova A, Narum S, Telonis-Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan D, Ingram B, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. (2017) Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity.  Molecular Ecology, 26: 6253–6269.

Harrisson KA, Yen JDL, Pavlova A, Rourke ML, Gilligan D, Ingram BA, Lyon J, Tonkin Z, Sunnucks P (2016) Identifying environmental correlates of intra-specific genetic variation. Heredity 117, 155-164.

Harrisson KA, Pavlova A, Gan HM, Lee YP, Austin CM and Sunnucks P (2016) Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species. Heredity 116, 506 – 515.

Other

Nguyen TT and Sunnucks P. (2012) Strong population genetic structure and its management implications in the mud carp Cirrhinus molitorella, an indigenous freshwater species subject to an aquaculture and culture-based fishery. Journal of Fish Biology, 80:651.

Coleman RA, Gauffre B, Pavlova A, Beheregaray LB, Kearns J, Lyon J, Sasaki M, Leblois R, Sgro C and Sunnucks P (2018) Artificial barriers prevent genetic recovery of small isolated populations of a low mobility freshwater fish Heredity 120, 515-532 View the paper here http://rdcu.be/ExoC. 

Eltham copper butterfly

Roitman M, Gardner MG, New TR, Nguyen TTT, Roycroft EJ, Sunnucks P, Yen AL, Harrisson KA. (2017) Assessing the scope for genetic rescue of an endangered butterfly: the case of the Eltham copper. Insect Conservation and Diversity 10, 399–414

Arabian Oryx

Marshall TC, Sunnucks P, Greth A, Spalton A & Pemberton JM (1999) Genetic analysis of Arabian oryx (Oryx leucoryx) using microsatellite markers. Animal Conservation 2: 269-278.

Marsupials

Beckman J, Banks SC, Sunnucks P, Lill A, Taylor AC (2007). Phylogeography and environmental correlates of a cap on reproduction: teat number in a small marsupial, Antechinus agilis. Molecular Ecology, 16, 1069-1083.

Taylor AC, Sunnucks P & Cooper DW (1999) Retention of reproductive barriers and reproductive synchronisation in introduced sympatric Macropus spp. in New Zealand. Animal Conservation 2: 195-202.

Sunnucks P & Taylor AC (1997) Gender of pouch young related to maternal weight in Macropus eugenii and M. parma (Marsupialia: Macropodidae). Australian Journal of Zoology 45: 573-578.

Wombats

Banks SC, Hoyle SD, Horsup A, Sunnucks P, Wilton A & Taylor AC (2003) Demographic monitoring of an entire species by genetic analysis of non-invasively collected material. Animal Conservation, 6, 101-108.

Sloane M, Sunnucks P, Beheregaray LB, Alpers DL & Taylor AC (2000) Highly reliable genetic identification of individual northern hairy-nosed wombats from remotely collected hairs: a feasible censusing method. Molecular Ecology 9, 1233-1240.

Taylor AC, Horsup A, Johnson CN, Sunnucks P & Sherwin W (1997) Unusual relatedness structure detected by microsatellite analysis, and parentage analysis in an endangered marsupial, the Northern Hairy-nosed wombat, Lasiorhinus krefftii. Molecular Ecology 6: 9-20.

Alpers DL, Walker FM, Taylor AC, Sunnucks P, Bellman S, Hansen BD, and Sherwin WB (2016). Evidence of subdivisions on evolutionary timescales in a large, declining marsupial distributed across a phylogeographic barrier. PLoS ONE 11: e0162789