Species boundaries to the limit: Integrating species delimitation methods is critical to avoid taxonomic inflation in the case of the Hajar banded ground gecko (Trachydactylus hajarensis)

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genusCerastes

“…Then, for each dataset three independent ipyrad runs were performed using different clustering parameters for both filtered and consensus sequences (step 3 and 6 in ipyrad, respectively): 0.85, 0.89 and 0.92, selecting the clustering that maximized the number of samples without significantly reducing the number of loci retained (0.85 with the outgroup and 0.89 for both datasets without the outgroup). Then, following recommendations from O’Leary et al, (2018), we used Radiator (Gosselin et al, 2017), Plink2 (Chang et al, 2015) and VCFr (Knaus & Grünwald, 2017) implemented in a custom script (https://github.com/BernatBurriel/Post_processing_filtering) from Burriel-Carranza et al, (2023a) to filter iteratively and alternatively low-quality samples and loci. For all datasets, values of missing data allowance ranged from 98% to 60% of missing genotype call rate and missing data per individual, decreasing 2% between iterations.…”

“…We used BEAST2 v.2.6.4 (Bouckaert et al, 2019) to reconstruct a Bayesian Inference (BI) time-calibrated tree. We calibrated the phylogeny dating the deepest node in the phylogeny (between Echis and Cerastes ), as suggested by Stange et al, (2018) and also implemented in previous studies focused on reptiles (Burriel-Carranza et al, 2023a, 2023b; Thanou et al 2023), with a normal distribution from a mean age of 28 million years ago (Mya) (Šmíd & Tolley, 2019) and encompassing a 95% HPD interval (25.65-31.55 Mya). We selected a GTR model with four gamma categories (base frequencies and proportion of invariant sites were estimated), and a relaxed clock LogNormal was used with a coalescent constant population tree prior.…”

“…Arid areas are often inhabited by specialized arid-adapted species, showing high levels of inter-and intra-specific diversity and endemicity (e.g., Burriel-Carranza et al, 2023b;Garcia-Porta et al, 2017;Metallinou et al, 2012Metallinou et al, , 2015Velo-Antón et al 2018). Much attention has been focused on arid areas from Australia and North America, while North Africa and Arabia have been traditionally neglected despite an increasing number of biodiversity studies carried out in the last decade (e.g., Brito et al, 2014;Carranza et al, 2018;Metallinou et al, 2012Metallinou et al, , 2015Gonçalves et al, 2018a;Martínez-Freiría et al, 2017;Šmíd et al, 2021a;Tejero-Cicuéndez et al, 2022b;Burriel-Carranza et al, 2019, 2023a, 2023b. These studies have reported high levels of cryptic diversity in these relatively underexplored regions and have emphasized vicariant processes as the primary factor driving speciation/diversification.…”

“…Traditionally, mitochondrial markers have been widely used in phylogenetic and/or phylogeographic approaches to infer the evolutionary history of species (Brown, 2002). However, mitonuclear discordances have been widely reported in many taxa (e.g., Dinis et al, 2019; Burriel-Carranza et al, 2023a; Hinojosa et al, 2019; Mochales-Riaño et al, 2023; Zaidi & Makova, 2019), mainly due to incomplete lineage sorting, sex-biased asymmetries, introgression, or different selection pressures on mitochondrial and nuclear genomes (Toews & Brelsford, 2012). Extensive discussion about this topic has led to the general agreement that the use of genomic data can efficiently resolve the evolutionary relationships of target species (e.g., Mao et al, 2019), as well as to infer other mechanisms, like introgression, which may influence the evolutionary trajectory of species (Cahill et al, 2015; Green et al, 2010).…”