Skip to main content

Kimberley Fish microsatellite genotypes


Miller, Adam; Holland, Owen (2021), Kimberley Fish microsatellite genotypes, Dryad, Dataset,


  1. Dispersal is a critically important process that dictates population persistence, gene flow and evolutionary potential and is an essential element for identifying species conservation risks. This project aims to investigate the contributions of dispersal syndromes and hydrographic barriers on patterns of population connectivity and genetic structure in fishes occupying the particularly rugged and fragmented landscape of the Kimberley Plateau, Western Australia.
  2. We assessed population genetic structure between three neighbouring catchments (the Mitchell, King Edward and Drysdale rivers) in three congeneric groups of freshwater fishes that exhibit varied dispersal syndromes within and among groups: (1) Melanotaenia australis and M. gracilis; (2) Syncomistes trigonicus and S. rastellus; (3) Hephaestus jenkinsi and H. epirrhinos. Within each species we sampled the upper, middle and lower reaches of each catchment and assessed patterns of gene flow between and within catchments using microsatellite markers.
  3. Our results suggest that contemporary connectivity between catchments is greatly limited or absent in all study species, regardless of their dispersal syndromes. However, gene flow within catchments varied in line with predicted dispersal potential with poor dispersers exhibiting limited gene flow and significant genetic structuring.
  4. We conclude that the rugged landscape and historical habitat isolation has contributed to patterns of population fragmentation among fish populations from different river catchments. However, it appears dispersal syndromes influence connectivity and gene flow within catchments, where landscape constraints are not as pervasive.
  5. This study presents a comparative population genetic analysis of freshwater fishes with differing dispersal syndromes and colonisation ability. Our findings provide new insights into factors shaping patterns of biodiversity on the Kimberley Plateau, and the evolutionary uniqueness of fish communities from different river catchments draining the plateau. The results from this study provide a framework for informing the management of the region’s unique freshwater biodiversity.


Total genomic DNA was extracted using a modified Chelex protocol (Walsh et al., 1991). A total of 10 mg of muscle tissue from individual specimens was added to a 0.5 ml microcentrifuge tube containing 150 mL of 5% Chelex solution and 3 mL of Proteinase K (10 mg/mL). Samples were digested at 56˚C for 90 minutes with intermittent vortexing, followed by digestion at 95˚C for 15 minutes with vortexing every 5 minutes. DNA extractions were stored at -20˚C until required for Polymerase Chain Reaction (PCR). Prior to PCR, Chelex extractions were homogenised and centrifuged at 13,000 rpm for 2 min (18,900 RCF). Supernatant was extracted for PCR from the bottom half of the supernatant, above the Chelex resin precipitate. DNA samples were genotyped at 5−16 microsatellite loci, including novel markers developed for Hephaestus and Syncomistes by next generation DNA sequencing following the approach of Miller et al. (2012), and markers previously developed for Melanotaenia by Mondol et al. (2014). In order to distinguish PCR products upon capillary separation, each primer was tagged with a unique fluorescent label during PCR using the method outlined by Blacket et al. (2012). Reaction matrices for PCR amplification consisted of 5 µL Qiagen multiplex mix, 4 µL of primer mix (0.2 µM of each primer) and 2 µL of template DNA. PCR conditions consisted of a 15 min denaturing step at 94˚C, followed by 40 cycles of 94˚C for 30 s, 59˚C for 90 s, and 72˚C for 60 s, with a final extension step of 60˚C for 30 min. Genotyping was performed using an Applied Biosystems 3730 capillary analyser (AGRF, Melbourne Australia), and microsatellite profiles were examined and scored manually using GENEMAPPERTM version 4.0 (Applied Biosystems).

Usage notes

The genotypic data format provided for each species is in GENEPOP format.