Data from: Lizards in pinstripes: morphological and genomic evidence for two new species of scincid lizards within Ctenotus piankai Storr and C. duricola Storr (Reptilia: Scincidae) in the Australian arid zone

The scincid lizard genus Ctenotus is one of the most species-rich genera of squamate reptiles, but few molecular phylogenetic studies have been undertaken on the group. Here we assess molecular and morphological variation within C. piankai and C. duricola, an arid-adapted pair of nominate species characterized by a pattern of thin pale longitudinal lines on a dark background that occur primarily in the western deserts and Pilbara region of Australia. We sequenced mitochondrial DNA and genome-wide restriction-site associated DNA (RAD) from geographically widespread samples of these lizard taxa, with particularly dense sampling from the Pilbara region. Phylogenetic analyses of the mitochondrial cytochrome B gene and approximately 5,000 nuclear loci identified four highly divergent lineages within the two taxa. The four genetically-defined populations were concordant with geography and are distinguishable based on multiple morphological and color pattern characters, despite appearing superficially similar in appearance. Despite limited mtDNA exchange between two lineages in the Pilbara, we found no evidence for ongoing gene flow across the nuclear genome. For the western desert lineages, there was no evidence of introgression for either mtDNA or nDNA in our data. To resolve the taxonomy of the group, we redescribe C. piankai and C. duricola, and recognize the two divergent lineages as new species: C. rhabdotus sp. nov., from the south-eastern Kimberley, Ord, Victoria River and northern Tanami Desert regions of Western Australia and the Northern Territory, and C. pallasotus sp. nov., from the western Pilbara and North West Cape regions of Western Australia.

石龙子科（Scincidae）栉眼蜥属（Ctenotus）是有鳞目爬行动物中物种最丰富的属之一，但针对该类群的分子系统发育研究却极为匮乏。本研究针对一对适应干旱环境的指名物种——C. piankai与C. duricola展开分子与形态变异分析，二者的典型特征为深色底色上分布有纤细浅色纵纹，主要栖息于澳大利亚西部沙漠及皮尔巴拉（Pilbara）地区。我们采集了该蜥蜴类群地理分布范围内的样本，对其线粒体DNA（mitochondrial DNA）及全基因组限制性酶切位点相关DNA（restriction-site associated DNA, RAD）进行测序，其中皮尔巴拉区域的采样密度尤为突出。针对线粒体细胞色素b基因（cytochrome B gene）以及约5000个核基因座（nuclear loci）开展的系统发育分析显示，这两个物种类群内存在4个高度分化的演化支系。这4个基于遗传学界定的种群与地理分布高度吻合，且可通过多种形态及体色花纹特征加以区分，尽管它们的外观看似极为相似。尽管皮尔巴拉地区的两个演化支系间存在有限的线粒体DNA基因交流，但我们并未发现核基因组中存在持续基因流的证据。针对西部沙漠类群的分析结果显示，其线粒体DNA与核DNA均未出现基因渐渗的迹象。为厘清该类群的分类学问题，我们重新描述了C. piankai与C. duricola，并将其中两个分化支系认定为新种：分布于西澳大利亚州及北领地东南部金伯利、奥德河、维多利亚河及塔纳米沙漠北部区域的C. rhabdotus sp. nov.，以及分布于西澳大利亚州西部皮尔巴拉及西北角区域的C. pallasotus sp. nov.。