Cryptic species can be phylogenetically old despite strong sex-biased dispersal

The impact of strongly differentiated populations on species delimitation due to limited or sex-biased dispersal remains challenging and under-explored in the framework of integrative taxonomy. The Mediterranean chafer beetle genus Pachypus is remarkable for its extreme female philopatry, with entirely wingless and subterranean females. This makes Pachypus an interesting case study. Based on a dataset of over 900 protein-coding genes (metazoan universal single-copy orthologs; mzl-USCOs), we investigated phylogeny, species delimitation, gene flow, and population differentiation to provide an integrative assessment of species boundaries. Integrative consideration of all results led to the recognition of 14 mostly morphologically cryptic species, including several new taxa. Most inferred speciation events occurred in the time between the end of the Messinian salinity crisis (about 5.3 million years ago) and the early Pleistocene. Phylogenetically old species and lack of recent speciation w..., Metazoan single-copy orthologs (mzl-USCOs) were sequenced in 171 Pachypus individuals by targeted enrichment and mapped against the reference sequences with bwa. Phylogenetic analyses were conducted with IQ-TREE and ASTRAL. Time-calibrated phylogenetic trees were constructed with MCMCTree. Species delimitation was performed with BPP, tr2, SODA, GMYC and PTP. Population clustering was performed with ADMIXTURE, and intra-population differentiation and gene flow were analysed with ADMIXTOOLS and Dsuite., , # Cryptic species can be phylogenetically old despite strong sex-biased dispersal

Supplementary files for study \"Cryptic species or metapopulations? Post-Messinian speciation of ancient Tyrrhenian philopatric Pachypus chafer beetles despite repeated hybridization\", L. Dietz et al., submitted

For questions, contact Dirk Ahrens ([[e-mail]](mailto:[e-mail])) or Lars Dietz ([[e-mail]](mailto:[e-mail]))

Each ZIP file contains a folder with several files containing alignments, phylogenetic trees, or other data. For more information on these files, please consult the accompanying description files.

All alignments, including SNP datasets, are in FASTA format and can be opened with standard alignment viewers. Except in the alignments from the Scarabaeoidea dataset, ambiguity codes (R, Y, W, S, M, K) stand for positions inferred to be heterozygous.

Phylogenetic trees are in NEWICK format and can be opened in a standard phylogenetic tr...,