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Dryad

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Citation

Alves, Fernanda et al. (2023), Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird, Dryad, Dataset, https://doi.org/10.5061/dryad.zw3r228cc

Abstract

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as ‘satellites’ of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Methods

We sampled nestlings and adult birds between 2012 and 2019. Nestling samples were collected during nest monitoring for other studies (e.g Edworthy et al. 2019; Alves et al. 2020) and adult birds were captured using mist-nets. To ensure the same individual was not resampled, we banded all birds using bands supplied by the Australian Bird and Bat Banding Scheme.  We collected blood using brachial venepuncture in accordance with guidelines approved by Australian National University Animal Ethics Permits 2012/34 and A2017/38 and Tasmanian Government Scientific Permits TFA13956, TFA14295, and TFA18255. Blood was stored either in 70% ethanol or on FTA paper (WhatmanTM). 

DNA extraction and single nucleotide polymorphism (SNP) genotyping were performed by Diversity Arrays Technology Pty. Ltd. (DArT; Canberra, Australia; https://www.diversityarrays.com/), using DartSeq™ protocols, which are independent from reference genome sequence availability (Jaccoud et al. 2001; Kilian et al. 2012). DartSeq is a genome complexity reduction technology that digests genomic DNA using pairs of restriction enzymes (cutters).

Usage notes

Excel and R.

Funding

NRM South through funding from the Australian Government

Holsworth Wildlife Research Endowment

Mohamed bin Zayed Species Conservation Fund, Award: 172516602

BirdLife Australia, Award: Professor Allen Keast Research Award

Kingborough Council

Research School of Biology, Australian National University

Ecological Society of Australia