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RESEARCH ARTICLE (Open Access)
Contents Vol 76(14)

Species delineation, phylogeography and conservation of temperate perches (Actinopterygii: Percichthyidae) from an endemism and climate change hotspot

Michael P. Hammer A , David L. Morgan B , Stephen J. Beatty B , Mark G. Allen B , Peter J. Unmack https://orcid.org/0000-0003-1175-1152 C D , Sean J. Buckley E F G , Luciano B. Beheregaray https://orcid.org/0000-0003-0944-3003 E , Jon Murphy H and Mark Adams https://orcid.org/0000-0002-6010-7382 I J *
+ Author Affiliations
- Author Affiliations

A Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, NT 0801, Australia.

B Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia.

C Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.

D School of Biological Sciences, Monash University, Clayton, Vic. 3800, Australia.

E Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA 5001, Australia.

F School of Biological Sciences, University of Western Australia, Perth, WA 6000, Australia.

G Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia.

H Deceased, formerly at Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia.

I Evolutionary Biology Unit, South Australian Museum, North Terrace Adelaide, SA 5000, Australia.

J School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia.

* Correspondence to: mark.adams@adelaide.edu.au

Handling Editor: Michael Joy

Marine and Freshwater Research 76, MF24257 https://doi.org/10.1071/MF24257
Submitted: 13 November 2024  Accepted: 23 August 2025  Published: 22 September 2025

© 2025 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

Context

The south-western corner of Australia is a biodiversity hotspot that includes a freshwater fauna with a high proportion of endemic species. The temperate perches comprise nearly half of the obligate freshwater fishes of the region, representing important components of local ecosystems and are of significant conservation concern.

Aims

Provide a spatially comprehensive molecular genetic assessment of species boundaries and major substructure for all local members of the family to better understand the interplay of ecology and environment across a common landscape.

Methods

Nuclear markers (allozymes) and matrilineal (cytb) datasets were generated to infer genetic groupings and any instances of hybridisation or introgression in relation to the current taxonomy, regional geography and ecological understanding.

Key results

There were contrasting patterns of diversification across genera, with Nannoperca housing four likely species-level splits, Nannatherina having three distinct geographically and ecologically separated subpopulations, and Bostockia comprising several refugial subpopulations that appear partially introgressed. Repeated genetic patterns were identified across particular biogeographic features, most notably the Margaret River and Shannon River.

Conclusions

This study highlighted the value of comparative range-wide molecular studies to inform taxonomy, ecology and conservation planning.

Implications

These analyses pave the way for taxonomic revision, management of key habitat refuges, and other conservation actions.

Keywords: allozymes, aquatic biodiversity, biogeography, conservation genetics, cryptic species, freshwater fishes, mtDNA, species delineation.

References

Adams M, Hammer M (2024) Species delineation, phylogeography, and conservation of WA perches. Zenodo 2024, ver. 1 [Dataset, published 24 October 2024].
| Crossref | Google Scholar |

Adams M, Raadik TA, Burridge CP, Georges A (2014) Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room? Systematic Biology 63(4), 518-533.
| Crossref | Google Scholar | PubMed |

Adams M, Hammer MP, Unmack PJ, Raadik TA, Jense C, Burridge CP (2023) Multi-gene insights into the taxonomy and conservation of Tasmania’s galaxiid fishes. Marine and Freshwater Research 74(13), 1113-1128.
| Crossref | Google Scholar |

Allan JD, Flecker AS (1993) Biodiversity conservation in running waters: identifying the major factors that threaten destruction of riverine species and ecosystems. BioScience 43(1), 32-43.
| Crossref | Google Scholar |

Allen GR, Midgley SH, Allen M (2002) ‘Field guide to the freshwater fishes of Australia.’ (Western Australian Museum: Perth, WA, Australia)

Allen MG, Beatty SJ, Morgan DL (2017) Aquatic fauna refuges in Margaret River and Cape to Cape region of Australia’s Mediterranean-climatic Southwestern Province. FiSHMED Fishes in Mediterranean Environments 2, 1-27.
| Google Scholar |

Allen MG, Morgan DL, Close PG, Beatty SJ (2020) Too little but not too late? Biology of a recently discovered and imperilled freshwater fish in a drying temperate region and comparison with sympatric fishes. Aquatic Conservation: Marine and Freshwater Ecosystems 30(7), 1412-1423.
| Crossref | Google Scholar |

Appleyard SA, Maher S, Pogonoski JJ, Bent SJ, Chua X-Y, McGrath A (2021) Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches. Journal of Fish Biology 98(5), 1421-1432.
| Crossref | Google Scholar | PubMed |

Arratia G, Quezada-Romegialli C (2019) The South American and Australian percichthyids and perciliids. What is new about them? Neotropical Ichthyology 17(1), e180102.
| Crossref | Google Scholar |

Arthington AH, Dulvy NK, Gladstone W, Winfield IJ (2016) Fish conservation in freshwater and marine realms: status, threats and management. Aquatic Conservation: Marine and Freshwater Ecosystems 26(5), 838-857.
| Crossref | Google Scholar |

Atkinson R, Power R, Lemon D, O’Hagan R, Dovey D, Kinny D (2008) The Australian hydrological geospatial fabric–development methodology and conceptual architecture. Water for a Healthy Country. CSIRO, Canberra, ACT, Australia.

Austin CM, Ryan SG (2002) Allozyme evidence for a new species of freshwater crayfish of the genus Cherax Erichson (Decapoda: Parastacidae) from the south-west of Western Australia. Invertebrate Systematics 16(3), 357-367.
| Crossref | Google Scholar |

Beatty S, Morgan DL (2019) Little pygmy perch Nannoperca pygmaea. In ‘The IUCN Red List of Threatened Species 2019’. e.T122906197A123382291. (International Union for Conservation of Nature and Natural Resources) Available at https://www.iucnredlist.org/species/122906197/123382291

Beatty SJ, Morgan DL, Rashnavadi M, Lymbery AJ (2011) Salinity tolerances of endemic freshwater fishes of south-western Australia: implications for conservation in a biodiversity hotspot. Marine and Freshwater Research 62(1), 91-100.
| Crossref | Google Scholar |

Beatty SJ, Morgan DL, Lymbery AJ (2014) Implications of climate change for potamodromous fishes. Global Change Biology 20(6), 1794-1807.
| Crossref | Google Scholar | PubMed |

Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. Journal of Biology 6, 9.
| Crossref | Google Scholar | PubMed |

Beheregaray LB, Pfeiffer LV, Attard CRM, Sandoval-Castillo J, Domingos FMCB, Faulks LK, Gilligan DM, Unmack PJ (2017) Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua). Molecular Phylogenetics and Evolution 111, 65-75.
| Crossref | Google Scholar | PubMed |

Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Orti G (2017) Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17, 162.
| Crossref | Google Scholar |

Blom MPK, Horner P, Moritz C (2016) Convergence across a continent: adaptive diversification in a recent radiation of Australian lizards. Proceedings of the Royal Society of London – B. Biological Sciences 283(1832), 20160181.
| Crossref | Google Scholar |

Brooks E, Slender AL, Cu S, Breed MF, Stangoulis JCR (2022) A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri). Conservation Genetics 23(6), 1027-1037.
| Crossref | Google Scholar |

Buckley SJ, Domingos FMCB, Attard CRM, Brauer CJ, Sandoval-Castillo J, Lodge R, Unmack PJ, Beheregaray LB (2018) Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation. Royal Society Open Science 5(6), 172125.
| Crossref | Google Scholar | PubMed |

Buckley SJ, Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beatty SJ, Morgan DL, Beheregaray LB (2024) Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot. Heredity 133, 149-159.
| Crossref | Google Scholar |

Castelnau FL (1873) Contribution to the ichthyology of Australia. Number III. Supplement to the fishes of Victoria. Proceedings of the Zoological and Acclimatisation Society of Victoria 2, 37-58.
| Google Scholar |

Davies PM, Stewart BA (2013) Aquatic biodiversity in the Mediterranean climate rivers of southwestern Australia. Hydrobiologia 719, 215-235.
| Crossref | Google Scholar |

Dudgeon D, Arthington AH, Gessner MO, Kawabata Z-I, Knowler DJ, Lévêque C, Naiman RJ, Prieur-Richard A-H, Soto D, Stiassny MLJ, Sullivan CA (2006) Freshwater biodiversity: importance, threats, status and conservation challenges. Biological Reviews 81(2), 163-182.
| Crossref | Google Scholar | PubMed |

Duffy R, Ledger J, Dias J, Snow M (2014) The critically endangered hairy marron, Cherax tenuimanus Smith, 1912: a review of current knowledge and actions required to prevent extinction of a species. Journal of the Royal Society of Western Australia 97, 297-306.
| Google Scholar |

Ebner BC, Morgan DL, Kerezsy A, Hardie S, Beatty SJ, Seymour JE, Donaldson JA, Linke S, Peverell S, Roberts D, Espinoza T, Marshall N, Kroon FJ, Burrows DW, McAllister RRJ (2016) Enhancing conservation of Australian freshwater ecosystems: identification of freshwater flagship fishes and relevant target audiences. Fish and Fisheries 17(4), 1134-1151.
| Crossref | Google Scholar |

Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14(8), 2611-2620.
| Crossref | Google Scholar | PubMed |

Feckler A, Zubrod JP, Thielsch A, Schwenk K, Schulz R, Bundschuh M (2014) Cryptic species diversity: an overlooked factor in environmental management? Journal of Applied Ecology 51(4), 958-967.
| Crossref | Google Scholar |

Fricke R, Eschmeyer WN, Van der Laan R (2024) Escmeyer’s catalog of fishes. Electronic version. (California Academy of Sciences) Available at http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp [Verified 12 October 2024]

General Bathymetric Chart of the Ocean (2024) Bathymetric data services. (GBCO) Available at https://download.gebco.net/ [Verified 12 October 2024]

Guildea C, Hitchen Y, Duffy R, Dias PJ, Ledger JM, Snow M, Kennington WJ (2015) Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda: Parastacidae) in the wild. PLoS ONE 10(3), e0121075.
| Crossref | Google Scholar | PubMed |

Hammer M (2001) Molecular systematics and conservation biology of the southern pygmy perch Nannoperca australis (Günther, 1861) (Teleostei: Percichthyidae) in south-eastern Australia. BSc(Hons) thesis, Adelaide University, Adelaide, SA, Australia.

Hammer MP, Adams M, Unmack PJ, Walker KF (2007) A rethink on Retropinna: conservation implications of new taxa and significant genetic sub-structure in Australian smelts (Pisces: Retropinnidae). Marine and Freshwater Research 58(4), 327-341.
| Crossref | Google Scholar |

Hammer MP, Unmack PJ, Adams M, Johnson JB, Walker KF (2010) Phylogeographic structure in the threatened Yarra pygmy perch Nannoperca obscura (Teleostei: Percichthyidae) has major implications for declining populations. Conservation Genetics 11, 213-223.
| Crossref | Google Scholar |

Hammer MP, Adams M, Hughes JH (2013) Evolutionary processes and biodiversity. In ‘Ecology of Australian Freshwater Fishes’. (Eds P Humphries, K Walker) pp. 49–79. (CSIRO Publishing: Melbourne, Vic., Australia)

Hammer MP, Unmack PJ, Adams M, Raadik TA, Johnson JB (2014) A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia. Biological Journal of the Linnean Society 111(3), 521-540.
| Crossref | Google Scholar |

Hammer MP, Allen GR, Martin KC, Adams M, Ebner BC, Raadik TA, Unmack PJ (2018) Revision of the Australian Wet Tropics endemic rainbowfish genus Cairnsichthys (Atheriniformes: Melanotaeniidae), with description of a new species. Zootaxa 4413(2), 271-294.
| Crossref | Google Scholar | PubMed |

Hammer MP, Adams M, Thacker CE, Johnson JB, Unmack PJ (2019a) Comparison of genetic structure in co-occurring freshwater eleotrids (Actinopterygii: Philypnodon) reveals cryptic species, likely translocation and regional conservation hotspots. Molecular Phylogenetics and Evolution 139, 106556.
| Crossref | Google Scholar |

Hammer MP, Allen GR, Martin KC, Adams M, Unmack PJ (2019b) Two new species of dwarf rainbowfishes (Atheriniformes: Melanotaeniidae) from northern Australia and southern New Guinea. Zootaxa 4701(3), 201-234.
| Crossref | Google Scholar |

Hasselman DJ, Argo EE, McBride MC, Bentzen P, Schultz TF, Perez-Umphrey AA, Palkovacs EP (2014) Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species. Molecular Ecology Resources 23(5), 1137-1152.
| Crossref | Google Scholar |

Hending D (2025) Cryptic species conservation: a review. Biological Reviews 100(1), 258-274.
| Crossref | Google Scholar | PubMed |

Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35(2), 518-522.
| Crossref | Google Scholar | PubMed |

Horner P, Adams M (2007) ‘A molecular-systematic assessment of species boundaries in Australian Cryptoblepharus (Reptilia: Squamata: Scincidae): a case study for the combined use of allozymes and morphology to explore cryptic biodiversity. Supplement 3. The Beagle.’ (Museums and Art Galleries of the Northern Territory)

Hourston M, Ledger J, Vercoe P, Lawrence C (2014) Native and non-native fishes in wetlands of the Swan Coastal Plain, Western Australia. Journal of the Royal Society of Western Australia 97(2), 331-341.
| Google Scholar |

Hughes JM, Schmidt DJ, Finn DS (2009) Genes in streams: a molecular approach to understanding movement of freshwater fauna and their riverine habitat. BioScience 59(7), 573-583.
| Crossref | Google Scholar |

Humphries P (2023) ‘Life and times of the murray cod.’ (CSIRO Publishing: Melbourne, Vic., Australia)

International Union for Conservation of Nature (2024) The IUCN Red List of Threatened Species. Version 2024-1. (IUCN) Available at http://www.iucnredlist.org

Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14), 1801-1806.
| Crossref | Google Scholar | PubMed |

Jerry DR, Eliphinstone MS, Baverstock PR (2001) Phylogenetic relationships of Australian members of the family Percichthyidae inferred from mitochondrial 12S rRNA sequence data. Molecular Phylogenetics and Evolution 18(3), 335-347.
| Crossref | Google Scholar | PubMed |

Jusaitis M, Adams M (2005) Conservation implications of clonality and limited sexual reproduction in the endangered shrub Acanthocladium dockeri (Asteraceae). Australian Journal of Botany 53(6), 535-544.
| Crossref | Google Scholar |

Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14(6), 587-589.
| Crossref | Google Scholar | PubMed |

Klunzinger MW, Lopes-Lima M, Gomes-dos-Santos A, Froufe E, Lymbery AJ, Kirkendale L (2021) Phylogeographic study of the West Australian freshwater mussel, Westralunio carteri, uncovers evolutionarily significant units that raise new conservation concerns. Hydrobiologia 848(12), 2951-2964.
| Crossref | Google Scholar |

Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources 15(5), 1179-1191.
| Crossref | Google Scholar | PubMed |

Kuiter RH, Allen GR (1986) A synopsis of the Australian pygmy perches (Percichthyidae) with the description of a new species. Revue Francaise Aquariologie 12(4), 109-116.
| Google Scholar |

Lintermans M (2007) ‘Fishes of the Murray–Darling Basin: an introductory guide.’ (Murray–Darling Basin Commission: Canberra, ACT, Australia)

Lintermans M, Geyle HM, Beatty S, Brown C, Ebner BC, Freeman R, Hammer MP, Humphreys WF, Kennard MJ, Kern P, Martin K, Morgan DL, Raadik TA, Unmack PJ, Wager R, Woinarski JCZ, Garnett ST (2020) Big trouble for little fish: identifying Australian freshwater fishes in imminent risk of extinction. Pacific Conservation Biology 26(4), 365-377.
| Crossref | Google Scholar |

Liu C, Comte L, Olden JD (2017) Heads you win, tails you lose: life-history traits predict invasion and extinction risk of the world’s freshwater fishes. Aquatic Conservation: Marine and Freshwater Ecosystems 27(4), 773-779.
| Crossref | Google Scholar |

McCulloch AR (1929) A check-list of the fishes recorded from Australia. Australian Museum Memoirs 5(1–2), 1-329.
| Google Scholar |

McDowall RM (Ed.) (1996) ‘Freshwater fishes of south-eastern Australia’, 2nd edn. (Reed Books: Sydney, NSW, Australia)

McFarlane SE, Pemberton JM (2019) Detecting the true extent of introgression during anthropogenic hybridization. Trends in Ecology & Evolution 34(4), 315-326.
| Crossref | Google Scholar |

Morgan DL (2019) Western pygmy perch Nannoperca vittata. In ‘The IUCN Red List of Threatened Species 2019’. e.T123358592A123382821. (International Union for Conservation of Nature and Natural Resources) Available at https://www.iucnredlist.org/species/123358592/123382821

Morgan DL (2020) Nightfish Bostockia porosa. In ‘The IUCN Red List of Threatened Species 2020’. e.T123358443A123382766. (International Union for Conservation of Nature and Natural Resources) Available at https://www.iucnredlist.org/species/123358443/123382766

Morgan DL, Beatty SJ (2008) The Donnelly River catchment: an important refuge for all of south-western Australia’s endemic freshwater fishes and the pouched lamprey (Geotria australis). Western Australian Naturalist 26(2), 112-127.
| Google Scholar |

Morgan DL, Beatty S (2019) Balston’s pygmy perch Nannatherina balstoni. In ‘The IUCN Red List of Threatened Species 2019’. e.T14320A123378416. (International Union for Conservation of Nature and Natural Resources) Available at https://www.iucnredlist.org/species/14320/123378416

Morgan DL, Gill HS (2000) Fish associations within the different inland habitats of lower south-western Australia. Records of the Western Australian Museum 20(1), 31-37.
| Google Scholar |

Morgan DL, Gill HS, Potter IC (1995) Life cycle, growth and diet of Balston’s pygmy perch in its natural habitat of acidic pools in south-western Australia. Journal of Fish Biology 47(5), 808-825.
| Crossref | Google Scholar |

Morgan DL, Gill HS, Potter IC (1998) Distribution, identification and biology of freshwater fishes in south-western Australia. Records of the Western Australian Museum 56, 1-97.
| Google Scholar |

Morgan DL, Hambleton SJ, Gill HS, Beatty SJ (2002) Distribution, biology and likely impacts of the introduced redfin perch (Perca fluviatilis) (Percidae) in Western Australia. Marine and Freshwater Research 53(8), 1211-1221.
| Crossref | Google Scholar |

Morgan DL, Thorburn DC, Gill HS (2003) Salinization of southwestern Western Australian rivers and the implications for the inland fish fauna – the Blackwood River, a case study. Pacific Conservation Biology 9(3), 161-171.
| Crossref | Google Scholar |

Morgan DL, Gill HS, Maddern MG, Beatty SJ (2004) Distribution and impacts of introduced freshwater fishes in Western Australia. New Zealand Journal of Marine and Freshwater Research 38(3), 511-523.
| Crossref | Google Scholar |

Morgan D, Beatty S, Lymbery A, Adams M, Murphy J (2010) Aquatic fauna values of the Mitchell and Quickup Rivers. Report to the Water Corporation of Western Australia. Centre for Fish & Fisheries Research, Murdoch University, Perth, WA, Australia.

Morgan DL, Beatty SJ, Klunzinger MW, Allen MG, Burnham QF (2011) ‘A field guide to freshwater fishes, crayfishes & mussels of south-western Australia.’ (Sercul and Centre for Fish and Fisheries Research, Murdoch University: Perth, WA, Australia)

Morgan DL, Beatty SJ, Adams M (2013) Nannoperca pygmaea, a new species of pygmy perch (Teleostei: Percichthyidae) from Western Australia. Zootaxa 3637(4), 401-411.
| Crossref | Google Scholar |

Morgan DL, Beatty SJ, Allen MG, Keleher JJ, Moore GI (2014a) Long live the King River perchlet (Nannatherina balstoni). Journal of the Royal Society of Western Australia 97, 307-312.
| Google Scholar |

Morgan DL, Unmack PJ, Beatty SJ, Ebner BC, Allen MG, Keleher JJ, Donaldson JA, Murphy J (2014b) An overview of the ‘freshwater fishes’ of Western Australia. Journal of the Royal Society of Western Australia 97(2), 263-278.
| Google Scholar |

Morrongiello JR, Beatty SJ, Bennett JC, Crook DA, Ikedife DNEN, Kennard MJ, Kerezsy A, Lintermans M, McNeil DG, Pusey BJ, Rayner T (2011) Climate change and its implications for Australia’s freshwater fish. Marine and Freshwater Research 62(9), 1082-1098.
| Crossref | Google Scholar |

Mossop KD, Lemmon AR, Lemmon EM, Eytan R, Adams M, Unmack PJ, Date KS, Morales HE, Hammer MP, Wong BBM, Chapple DG (2023) Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes. Molecular Phylogenetics and Evolution 182, 107757.
| Crossref | Google Scholar | PubMed |

Murphy JC (2010) Defining the genetic structure of freshwater fishes in the south west of Western Australia: implications for conservation. BSc(Hons) thesis, Murdoch University, Perth, WA, Australia.

Musyl MK, Keenan CP (1992) Population genetics and zoogeography of Australian freshwater golden perch, Macquaria ambigua (Richardson 1845) (Teleostei: Percichthyidae), and electrophoretic identification of a new species from the Lake Eyre Basin. Australian Journal of Marine and Freshwater Research 43(6), 1585-1601.
| Crossref | Google Scholar |

Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GA, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403(6772), 853-858.
| Crossref | Google Scholar | PubMed |

Near TJ, Eytan RI, Dornburg A, Kuhn KL, Moore JA, Davis MP, Wainwright PC, Friedman M, Smith WL (2012) Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Sciences 109(34), 13698-13703.
| Crossref | Google Scholar |

Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32(1), 268-274.
| Crossref | Google Scholar | PubMed |

Nock CJ, Elphinstone MS, Rowland SJ, Baverstock PR (2010) Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae). Marine and Freshwater Research 61(9), 980-991.
| Crossref | Google Scholar |

Ogston G, Beatty SJ, Morgan DL, Pusey BJ, Lymbery AJ (2016) Living on burrowed time: aestivating fishes in south-western Australia face extinction due to climate change. Biological Conservation 195, 235-244.
| Crossref | Google Scholar |

Page TJ, Choy SC, Hughes JM (2005) The taxonomic feedback loop: symbiosis of morphology and molecules. Biology Letters 1(2), 139-142.
| Crossref | Google Scholar | PubMed |

Pen LJ, Potter IC (1990) Biology of nightfish, Bostockia porosa Castelnau, in a south-western Australian River. Australian Journal of Marine and Freshwater Research 41(5), 627-645.
| Crossref | Google Scholar |

Pen LJ, Potter IC (1991) Biology of the western pygmy perch, Edelia vittata, and comparisons with two other teleost species endemic to south-western Australia. Environmental Biology of Fishes 31, 365-380.
| Crossref | Google Scholar |

Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2), 945-959.
| Crossref | Google Scholar | PubMed |

Pusey BJ, Kennard MJ (2001) Guyu wujalwujalensis, a new genus and species (Pisces: Percichthyidae) from north-eastern Queensland. Ichthyological Exploration of Freshwaters 12(1), 17-28.
| Google Scholar |

Reid AJ, Carlson AK, Creed IF, Eliason EJ, Gell PA, Johnson PTJ, Kidd KA, MacCormack TJ, Olden JD, Ormerod SJ, Smol JP, Taylor WW, Tockner K, Vermaire JC, Dudgeon D, Cooke SJ (2019) Emerging threats and persistent conservation challenges for freshwater biodiversity. Biological Reviews 94(3), 849-873.
| Crossref | Google Scholar | PubMed |

Reyjol Y, Hugueny B, Pont D, Bianco PG, Beier U, Caiola N, Casals F, Cowx I, Economou A, Ferreira T, Haidvogl G, Noble R, De Sostoa A, Vigneron T, Virbickas T (2007) Patterns in species richness and endemism of European freshwater fish. Global Ecology and Biogeography 16(1), 65-75.
| Crossref | Google Scholar |

Richardson BJ, Baverstock PR, Adams M (1986) ‘Allozyme electrophoresis: a handbook for animal systematics and population studies.’ (Academic Press: Sydney, NSW, Australia)

Ruzzante DE, Walde SJ, Cussac VE, Dalebout ML, Seibert J, Ortubay S, Habit E (2006) Phylogeography of the Percichthyidae (Pisces) in Patagonia: roles of orogeny, glaciation, and volcanism. Molecular Ecology 15(10), 2949-2968.
| Crossref | Google Scholar | PubMed |

Saddlier S, Koehn JD, Hammer MP (2013) Let’s not forget the small fishes – conservation of two threatened species of pygmy perch in south-eastern Australia. Marine and Freshwater Research 64(9), 874-886.
| Crossref | Google Scholar |

Sayer CA, Fernando E, Jimenez RR, Macfarlane NBW, Rapacciuolo G, Böhm M, Brooks TM, Contreras-MacBeath T, Cox NA, Harrison I, Hoffmann M, Jenkins R, Smith KG, Vié J-C, Abbott JC, Allen DJ, Allen GR, Barrios V, Boudot J-P, Carrizo SF, Charvet P, Clausnitzer V, Congiu L, Crandall KA, Cumberlidge N, Cuttelod A, Dalton J, Daniels AG, De Grave S, De Knijf G, Dijkstra K-DB, Dow RA, Freyhof J, García N, Gessner J, Getahun A, Gibson C, Gollock MJ, Grant MI, Groom AER, Hammer MP, Hammerson GA, Hilton-Taylor C, Hodgkinson L, Holland RA, Jabado RW, Juffe Bignoli D, Kalkman VJ, Karimov BK, Kipping J, Kottelat M, Lalèyè PA, Larson HK, Lintermans M, Lozano F, Ludwig A, Lyons TJ, Máiz-Tomé L, Molur S, Ng HH, Numa C, Palmer-Newton AF, Pike C, Pippard HE, Polaz CNM, Pollock CM, Raghavan R, Rand PS, Ravelomanana T, Reis RE, Rigby CL, Scott JA, Skelton PH, Sloat MR, Snoeks J, Stiassny MLJ, Tan HH, Taniguchi Y, Thorstad EB, Tognelli MF, Torres AG, Torres Y, Tweddle D, Watanabe K, Westrip JRS, Wright EGE, Zhang E, Darwall WRT (2025) One-quarter of freshwater fauna threatened with extinction. Nature 638(8049), 138-145.
| Crossref | Google Scholar | PubMed |

Thacker CE, Geiger DL, Unmack PJ (2022) Species delineation and systematics of a hemiclonal hybrid complex in Australian freshwaters (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris). Royal Society Open Science 9, e220201.
| Crossref | Google Scholar |

Tibbets CA, Dowling TE (1996) Effects of intrinsic and extrinsic factors on population fragmentation in three species of North American minnows (Teleostei: Cyprinidae). Evolution 50(3), 1280-1292.
| Crossref | Google Scholar | PubMed |

Tims AR, Saupe EE (2023) Forecasting climate-driven habitat changes for Australian freshwater fishes. Diversity and Distributions 29(5), 641-653.
| Crossref | Google Scholar |

Tims AR, Unmack PJ, Hammer MP, Brown C, Adams M, McGee MD (2024) Museum genomics reveals the hybrid origin of an extinct crater lake endemic. Systematic Biology 73(3), 506-520.
| Crossref | Google Scholar |

Trifinopoulos J, Nguyen L-T, Von Haeseler A, Minh BQ (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44(W1), W232-W235.
| Crossref | Google Scholar | PubMed |

Unmack PJ (2001) Biogeography of Australian freshwater fishes. Journal of Biogeography 28(9), 1053-1089.
| Crossref | Google Scholar |

Unmack PJ, Hammer MP, Adams M, Dowling TE (2011) A phylogenetic analysis of pygmy perches (Teleostei: Percichthyidae) with an assessment of the major historical influences on aquatic biogeography in southern Australia. Systematic Biology 60(6), 797-812.
| Crossref | Google Scholar | PubMed |

Unmack PJ, Hammer MP, Adams M, Dowling TE, Johnson JB (2013) The role of continental shelf width in determining freshwater phylogeographic patterns in south-eastern Australian pygmy perches (Teleostei: Percichthyidae). Molecular Ecology 22(6), 1683-1699.
| Crossref | Google Scholar | PubMed |

Unmack PJ, Sandoval-Castillo J, Hammer MP, Adams M, Raadik TA, Beheregaray LB (2017) Genome-wide SNPs resolve a key conflict between sequence and allozyme data to confirm another threatened candidate species of river blackfishes (Teleostei: Percichthyidae: Gadopsis). Molecular Phylogenetics and Evolution 109, 415-420.
| Crossref | Google Scholar | PubMed |

Unmack PJ, Adams M, Bylemans J, Hardy CM, Hammer MP, Georges A (2019) Perspectives on the clonal persistence of presumed ‘ghost’ genomes in unisexual or allopolyploid taxa arising via hybridization. Scientific Reports 9(1), 4730.
| Crossref | Google Scholar | PubMed |

Unmack PJ, Adams M, Hammer MP, Johnson JB, Gruber B, Gilles A, Young M, Georges A (2022) Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery. Biological Journal of the Linnean Society 135(1), 117-137.
| Crossref | Google Scholar |

Unmack PJ, Cook BD, Johnson JB, Hammer MP, Adams M (2023) Phylogeography of a widespread Australian freshwater fish, western carp gudgeon (Eleotridae: Hypseleotris klunzingeri): cryptic species, hybrid zones, and strong intra-specific divergences. Ecology and Evolution 13(11), e10682.
| Crossref | Google Scholar | PubMed |

Valenzuela-Aguayo F, McCracken GR, Diaz G, Manosalva A, Habit E, Ruzzante DE (2022) Connectivity, diversity, and hybridization between two endemic fish species (Percilia spp.) in a complex temperate landscape. Conservation Genetics 23(1), 23-33.
| Crossref | Google Scholar |