DOI: 10.5061/dryad.4tmpg4fbd
title: Data from: Evolutionary stability inferred for a free ranging lizard with sex-reversal

description: The sex of vertebrates is typically determined genetically, but reptile
 sex can also be determined by incubation temperature. In some reptiles,
 temperature interacts with chromosomal genotype to reverse sex,
 potentially leading to transitions from a chromosomal to a
 temperature-dependent sex determining system. The Central Bearded Dragon,
 Pogona vitticeps, exhibits female heterogamety (ZZ/ZW) but can have its
 sex reversed from ZZ male to ZZ female by high incubation temperatures.
 The species exhibits sex-reversal in the wild and it has been suggested
 that climate change could be increasing the frequency of reversal.
 Transitions to temperature-dependent sex determination require low levels
 of gene flow and high (&gt; 50%) rates of sex-reversal but would have
 increased likelihood if sex-reversed individuals have higher survival and
 greater reproduction compared with concordant ZW females. Here, we combine
 genotype-by-sequencing, identification of phenotypic and chromosomal sex,
 exhaustive field surveys, and radio telemetry to examine levels of genetic
 structure, rates of sex-reversal, movement, space use, and survival of P.
 vitticeps in a location previously identified as a hot spot for
 sex-reversal. We find that the species exhibits low levels of population
 structure (FST ~ 0.001) and a modest (~17%) rate of sex-reversal, and that
 sex-reversed and non-sex-reversed females have similar survival and
 behavioural characteristics to each other. Overall, our data indicate this
 system is evolutionary stable, although we do not rule out the prospect of
 a more gradual transition in sex-determining mechanisms in the future in a
 more fragmented landscape and as global temperatures increase.
description: # Evolutionary stability inferred for a free ranging lizard with
 sex-reversal Data description: Molecular dataset: final.gl.drop A total of
 207 lizards were captured during sampling trips across south west
 queensland and once individuals were genotyped for their chromosomal sex
 this amounted to: ZZf (n = 18), ZWf (n = 98), ZZm (n = 91). Reduced
 representation sequencing (Kilian et al., 2012) was used to genotype
 individuals in order to determine the levels of population genetic
 structure (as an indicator of gene flow) across the study area. Genomic
 DNA from tail tissue and blood samples was extracted using two DNA
 extraction methods appropriate for each sample type: (a) Qiagen's
 Gentra® Puregene® DNA purification kit for tail tips, or (b) Whatman Elute
 quick extraction protocol for blood on WhatmanTM FTATM Elute Cards.
 Specifically, DNA was extracted and sequenced and informative SNP markers
 identified using the commercial provider Diversity Arrays Technology (DArT
 Pty Ltd, Canberra, ACT, Australia,
 [www.diveristyarrays.com](http://www.diveristyarrays.com)). Briefly, SNP
 genotyping was performed using a combination of complexity reduction using
 restriction enzymes, implicit fragment-size selection and
 next-generational sequencing (Kilian et al., 2012). The restriction enzyme
 combination of PstI (recognition sequence 5’-CTGCA|G-3’) and SphI
 (5’-GCATG|C-3’) was used for complexity reduction by double digestion.
 Sequencies were processed using proprietary DArT analytical pipelines
 (Kilian et al., 2012) to yield SNPs that were polymorphic within the set
 of samples. Calling quality was assured by high average read depth per
 locus (medium coverage, average ca 10x). In addition, approximately
 one-third of samples were processed twice from DNA to allelic calls as
 technical replicates. Scoring consistency (repeatability) was used as the
 main selection criteria for high-quality and low error-rate markers.
 Sequences were then filtered using the R package dartR (v.1.1.11; Gruber
 et al., 2018). Loci were removed with a call rate of less than 95%,
 repeatability less than 99%, and if they were monomorphic across all
 individuals. Secondary SNPs, that is, SNPs residing on a single sequence
 tag, were filtered, retaining only one at random. All sex-linked loci were
 filtered. # Genomic data: The script for analysis can be found under the
 folder name "R". Here you will find all models and their checks
 that were used to make figures and used in rmd file. Models from this file
 were saved and then used in Results_figures.Rmd. # Movement Data: Average
 movement rate dataset : Movement.Rates.Winter_divided.csv Reproduction
 movement rate dataset: reproductive.status.csv MCP/KDE dataset:
 MCP.KDE.Morp.Summ.csv Movement rate (m/d) was calculated as the
 straight-line distance between consecutive GPS locations divided by the
 number of days elapsed between relocations. The effect of season, sex
 class, and their interaction on movement rate was compared using the lmer
 function in the lme4 package (Bates et al., 2015) with individual lizard
 as a repeated (random) effect. To determine if reproductive status
 influenced female movement, within-individual variability of movement
 between gravid and non-gravid periods was compared by recording distance
 moved per day for gravid females (2 weeks pre/post lay date) with the
 distances moved while non-gravid (2-6 weeks post lay date). We then tested
 for the effect of reproductive status on distance moved per day (response
 variable) , with reproductive status (gravid or not gravid) as a fixed
 effect, and female ID as a repeated effect. We estimated space use only
 for animals that had a minimum of 15 GPS locations, and estimates were
 log10-transformed for both 100% MCP and 95% KDE to fit normality
 assumptions. The effect of season, sex class, body size (SVL/ cm) and
 their interaction on space use estimates was compared using the lmer
 function in the lme4 package with individual lizard as a repeated (random)
 effect. When results were significant, we followed with pairwise
 comparisons from emmeans package in R (Lenth et al., 2018). Interactions
 (sex class×season) or covariates (SVL/cm) for movement and space use
 estimates that were not significant were removed from further analysis. #
 Survivorship Data: Season_updated.FPT In cases where a tracked lizard was
 found dead, the date of death was determined using the last movement
 recorded by the accelerometer housed on the GPS units. Accelerometers
 recorded average changes in acceleration over a minimum of 120 s
 intervals. Maximum likelihood survival probabilities were estimated using
 known fate models in the program MARK (White & Garrott, 1999) and were
 compared using the Akaike Information Criteria (AICc). Models within &lt;
 2.0 were considered to have support. Time intervals were set seasonally
 (spring, summer, autumn, winter) and sex class was defined as the genotype
 and phenotype combination (ZZf, ZZm, ZWf). We started with a fully
 saturated model in which survival probability was dependent on sex class,
 body size (SVL/cm), mass (g), season (spring, summer, autumn, winter), and
 their interaction, then we fitted a series of reduced-parameters models.