DOI: 10.5061/dryad.zw3r228cc
title: Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

description: 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.
description: 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).
description: Excel and R.