Supplemental Data — Climatic swings triggered incipient postglacial speciation of flightless Calosoma beetles in Western Balkan sky islands

Supplemental data — Climatic swings triggered incipient postglacial speciation of flightless Calosoma beetles in Western Balkan sky islands Cody Raul Cardenas (1), Jérémy Gauthier (1,2), Hélène Mottaz (1), Julia Bilat (1), Slavčo Hristovski (3), & Emmanuel F.A. Toussaint (1) 1 — Natural History Museum of Geneva, Geneva, Switzerland2 — Naturéum - State Museum of Natural Sciences, Lausanne, Switzerland3 — Institute of Biology, Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, Skopje, North Macedonia Manuscript Abstract:Climatic changes drastically shape the ecology and evolution of lineages across landscapes. In mountainous regions, climatic oscillations drive fine-scale biome shifts and modulate habitat availability along elevation gradients; thereby governing population connectivity. Highland cold-adapted lineages with low dispersal capacity are an ideal system to study the impact of past climates on geographic range shifts and genomic signatures. Here we focus on the flightless highland species Calosoma (Callisthenes) pentheri endemic from the Western Balkan mountains, presenting a disjunct geographic distribution. We predict that glacial and interglacial periods were drove allopatry through cycles of allopatric isolation and secondary contact, leaving a genomic signature among populations. Using HyRAD museomics combined with a newly sequenced reference genome we generated 10,794 single nucleotide polymorphisms and 2,278 loci and reconstruct the evolutionary history of this lineage. Admixture and phylogenomic analyses demonstrate clear delineation between the lineages reflecting their distribution along the Western Balkans. Genomic features and divergence estimations suggest these two lineages are distinct species that diverged in the late Miocene with little interspecific, but occasional intraspecific, admixture since the Pliocene. The diversification of these species in the Balkans was likely driven by isolation in sky island glacial refugia during the Miocene to Pliocene. Subsequent secondary contact during Pleistocene glacial periods might have occurred but did not result in introgression. Climatic oscillations during Quaternary ice ages similarly triggered admixture between populations of each moassif. These species harbors intermediate stages along the speciation continuum, representing a model system for in-depth studies of climate-driven evolution in sky islands. Dataset breif summary: Contains compressed directories which include suppelmental data used in analyses. alignment_files.zip Each file is a standard alignment file either a newick or nexus file for the folllowing datasets: ml_filt, ml_nohist, divergence_loci, divergence_model, basic_snp, no_Hist, no_Ts, and no_Ts, and no_Ts_no_Hist. The locus based anlayses (ml_filt, ml_nohist, divergence_loci, and divergence_model) also include nexus files for the partitions. The basic_snp, no_Hist, no_Ts, and no_Ts, and no_Ts_no_Hist data sets contain the vcf files from which the SNP phylip files resulted. BEAST_files.zip These contain the replicate logs, ops, and treeannotated files for each replicate analysis of the beast file. The *.xml file for each analysis contains the run parameters and alignment and partitioning. popgen_analysis.zip This file contains the two population genetic analysis *.vcf files and subsequent R analysis in Rmd format for each dataset: coal-const and yule. strucutre_data.zip The structure files generated from the respective popgen_analays/*.Rmd used in the structure analysis (penrel & subspp). trees.zip Each analays tree generated for the ml_filt, ml_nohist, divergence_loci, divergence_model, basic_snp, no_Hist, no_Ts, and no_Ts, and no_Ts_no_Hist datasets. When appropraite, locus trees and runtrees are included in the analysis.