DOI: 10.5061/dryad.3r2280gh8
title: Kimberley Fish microsatellite genotypes

description: 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. 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. 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. 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. 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.
description: Total genomic DNA was
 extracted using a modified Chelex protocol (Walsh <i>et
 al.</i>, 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
 <i>Hephaestus </i>and <i>Syncomistes </i>by next
 generation DNA sequencing following the approach of Miller et al. (2012),
 and markers previously developed for <i>Melanotaenia </i>by
 Mondol <i>et al.</i> (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
 <i>et al.</i> (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 GENEMAPPER<sup>TM</sup>
 version 4.0 (Applied Biosystems).
description: The genotypic data format provided for each species is in GENEPOP
 format.