DOI: 10.5061/dryad.t76hdr7zm
title: The demise of a wonder: evolutionary history and conservation assessments of the Wonder Gecko Teratoscincus keyserlingii (Gekkota, Sphaerodactylidae) in Arabia

description: Effective biodiversity conservation planning starts with the genetic
 characterization within and among focal populations, in order to
 understand the likely impact of threats for ensuring the long-term
 viability of the species. The Wonder Gecko, Teratoscincus keyserlingii, is
 one of nine members of the genus. The species is distributed in Iran,
 Afghanistan and Pakistan, with a small isolated population in the United
 Arab Emirates (UAE), where it is classified nationally as Critically
 Endangered. Within its Arabian range, anthropogenic activity is
 directly linked to the species’ decline, highly localized and severely
 fragmented populations. Here we describe the evolutionary history of
 Teratoscincus, by reconstructing its phylogenetic relationships and
 estimating its divergence times and ancestral biogeography. For
 conservation implications of T. keyserlingii we evaluate the genetic
 structure of the Arabian population using genomic data. The presentstudy
 supports the monophyly of most species and reveals considerable
 intraspecific variability in T. microlepis and T. keyserlingii, which
 necessitate broad systematic revisions. The UAE population of T.
 keyserlingii likely arrived from southern Iran during the Pleistocene and
 no internal structure was recovered within, implying a single population
 status. Regional conservation of T. keyserlingii requires improved land
 management and natural habitat restoration in the species’ present
 distribution, and the expansion of current protected areas, or the
 establishment of new areas with suitable habitats for the species, mostly
 in northern Abu Dhabi Emirate.
description: We collected
 ddRAD data for 26 samples of <i>Teratoscincus keyserlingii</i>
 from the UAE, following the protocol, adaptors, and indices of Peterson et
 al. (2012). We double-digested 500 ng of genomic DNA for each sample with
 20 units each of two restriction enzymes (SbfI and MspI, New England
 Biolabs) for 6 h at 37 °C. Fragments were purified with Agencourt AMPure
 beads before ligation of barcoded Illumina adapters. Samples with unique
 adapters were pooled, and each pool of eight samples was size-selected for
 a distribution of fragments with a peak of 480 bp, using E-Gel SizeSelect
 2% agarose gels (Thermo Fisher Scientific). Illumina multiplexing indices
 were ligated to individual samples using a Phusion polymerase kit
 (high-fidelity Taq polymerase, New England Biolabs). Final pools were
 sequenced on an Illumina NexSeq 500, under a 50 bp single-end read
 protocol at the UPF Genomics Core Facility, Barcelona, Spain.
 We processed raw
 Illumina reads using the program iPyRAD v.0.7.8. We demultiplexed samples
 using their unique barcode and adapter sequences. Sites with Phred quality
 scores under 99% (Phred score=33) were changed into ‘N’ characters, and
 reads with ≥3 N’s were discarded. Within the iPyRAD pipeline, the filtered
 reads for each sample were clustered using VSEARCH v.2.4.3 and aligned
 with MUSCLE v.3.8.31. We assembled the ddRADseq data using a clustering
 threshold of 92%. As an additional filtering step, consensus sequences
 that had low coverage (&lt;6 reads), excessive undetermined or
 heterozygous sites (&gt;3) or too many haplotypes (&gt;2) were
 discarded. The consensus sequences were clustered across samples using the
 within-sample clustering threshold (92%). Again, alignment was done with
 MUSCLE, applying a paralog filter that removes loci with excessive shared
 heterozygosity among samples (paralog filter=200). The maximum number of
 SNPs per locus was set to 6. We generated final datasets that included no
 missing data, i.e. with all loci present for all samples.