Data from: Phenotypic crypticity despite strong phylogenetic divergence: Diversification dynamics in a species complex of Arabian Pristurus geckos
Data files
Apr 10, 2026 version files 240.92 KB
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HeadShape.zip
219.37 KB
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README.md
4.43 KB
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SupplementaryTable1_LinearMeasurements.xlsx
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Abstract
Absence of phenotypic differentiation can challenge the study of diversification by concealing evolutionary divergence through morphological similarity. Such cryptic species diversity is found particularly often in extreme environments, including arid mountain ranges. In the Hajar Mountains of southeastern Arabia, the Pristurus rupestris species complex comprises divergent lineages with notable phenotypic variation. Here, we investigate the evolutionary dynamics of this radiation by integrating geometric morphometric analyses with whole-genome sequencing and phylogenomic reconstructions. We analyzed five species – P. ali, P. assareen, P. feulneri, P. omanensis, and P. rupestris – including all previously identified genetic lineages within those species, and generated a new reference genome for an Old World sphaerodactylid gecko (P. rupestris sensu stricto). Morphometric analyses of comprehensive two- and three-dimensional morphological datasets indicate strong overlap in both body and head shape. Despite considerable phenotypic similarities, our results reveal deep interspecific divergences exceeding 16 million years and contrasting demographic histories. While we detected introgression restricted to specific lineage pairs, phenotypic crypticity persists across the entire complex, suggesting stabilizing selection in harsh environments. Our study highlights the P. rupestris species complex as an ideal model for investigating the role of environmental constraints in limiting morphological divergence and shaping diversification dynamics in arid mountain ecosystems.
Dataset DOI: 10.5061/dryad.jq2bvq8qx
Description of the data and file structure
Here we present an integrative analysis of the diversification dynamics of the extraordinary radiation of Pristurus geckos in the Hajar Mountains, using comprehensive two- and three-dimensional morphological datasets in parallel with whole genome sequencing (WGS) data. In addition to linear measurements, we obtained µ-computed tomography (µCT) scans for 84 individuals covering all five species and 12 genetic lineages of the P. rupestris species complex, and explored the phenotypic variation in this group using a geometric morphometric approach. We assembled a reference genome for P. rupestris and generated WGS data for 28 specimens of the entire radiation, as well as two individuals of the sister species P. flavipunctatus Rüppell, 1835. Using the comprehensive genomic dataset, we performed a range of analyses to investigate the divergence, the role of ongoing and ancient hybridization, and the demographic history of the entire P. rupestris species complex.
For a morphological characterization we obtained nine linear measurements from 84 Pristurus specimens representing all lineages within the P. rupestris complex (Suppl. Table 1). The reference genome assembly of Pristurus rupestris sensu stricto, as well as whole genome sequencing Illumina raw data for 30 specimens comprising the Pristurus rupestris species complex (Pristurus ali, P. assareen, P. feulneri, P. omanensis, and P. rupestris) and P. flavipunctatus are available on NCBI under the BioProject PRJNA1444514. Code for all morphological and phylogenomic analyses is available on https://github.com/thorekop/Pristurus_DiversificationDynamics.
Files and variables
File: HeadShape.zip
Description: Three-dimensional landmark coordinate data representing head shape for each individual. To capture head shape of the 83 Pristurus skull models, we prepared a 3D-landmarking scheme consisting of 15 fixed landmarks, and 24 sliding semilandmarks on equidistant curves (see Suppl. Figure 1 and Suppl. Table 3).
File: SupplementaryTable1_LinearMeasurements.xlsx
Description: This Excel spreadsheet contains an overview of all specimens used for the morphological analyses in the present study. Information regarding specimen assignment to genetic deep lineages, geographic location, region, elevation (in masl), elevation zone (below/above 1,500 masl), sex, specimens used as type material, and 9 linear measurements (specified in the Material and Methods section) are provided.
Variables
Abbreviations for the variables and parameters listed in Supplementary Table 1 (in associated manuscript) are defined here:
- N: number of specimens
- SVL: snout-vent length (snout to the cloaca)
- TrL: trunk length (distance between the internal parts of fore and hind limb insertions)
- HL: head length (snout to anterior-most point of ear opening)
- HH: head height (laterally at anterior-most point of ear opening)
- HW: head width (at anterior-most point of ear opening)
- LHu: humerus length (from elbow to forelimb insertion)
- LUn: ulna length (from wrist to elbow)
- LFe: femur length (from knee to hindlimb insertion)
- LTb: tibia length (from ankle to knee)
Code/software
Code for all morphological and phylogenomic analyses is available on https://github.com/thorekop/Pristurus_DiversificationDynamics.
Access information
Other publicly accessible locations of the data:
- The reference genome assembly of Pristurus rupestris sensu stricto, as well as whole genome sequencing Illumina raw data for 30 specimens comprising the Pristurus rupestris species complex (Pristurus ali, P. assareen, P. feulneri, P. omanensis, and P. rupestris) and P. flavipunctatus are available on NCBI under the BioProject PRJNA1444514. Code for all morphological and phylogenomic analyses is available on https://github.com/thorekop/Pristurus_DiversificationDynamics.