Habitat association predicts population connectivity and persistence in flightless beetles: a population genomics approach within a dynamic archipelago

Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable vs. dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact-soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic-habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable vs. dynamic habitat specialists.

Methods
For a detailed description of data collection and processing, please refer to the relevant manuscript:

Meramveliotakis, E., Ortego, J., Anastasiou, I., Vogler, A. P., Papadopoulou, A. (ACCEPTED; Sep-2024) Habitat association predicts population connectivity and persistence in flightless beetles: a population genomics approach within a dynamic archipelago. Molecular Ecology

Briefly, 318 samples were collected from 47 sampling sites (24 demes of the compact-soil "geophilous" Eutagenia clade and 23 demes of the sand-obligate "psammophilous" Eutagenia clade) across 14 Cyclades islands (Aegean, Greece). Each specimen was individually preserved in 100% ethanol and stored at -20°C. DNA extraction was performed following a commercial bead-based protocol (Biosprint® 96 DNA Blood kit, Qiagen®) as implemented in the automated KingFisher Flex system (Thermo Fisher scientific). Library preparation followed the double-digest Restriction site Associated DNA sequencing (ddRADseq) protocol of Peterson et al. (2012) (PLOS One, 7: e37135) with small modifications (Papadopoulou and Knowles, 2017; Evolution, 71: 2901-2917). DNA was double-digested with restriction enzymes EcoRI and Msel, unique barcodes (10bp) and adaptors were ligated to the digested fragments and individually barcoded products were pooled into libraries of 72-80 samples each. Each library was size-selected between 350 to 450 bp using a Pippin Prep™ instrument (Sage Science Inc.). Following size-selection, the fragments were PCR-amplified (8-10 amplification cycles) using high-fidelity DNA polymerase (iProof™ , Bio-Rad) and they were sequenced on the Illumina HiSeq2500 platform (single-end, 150bp reads) at the Centre for Applied Genomics (SickKids, Toronto, Ontario, Canada). Demultiplexing of the raw Illumina reads, de novo assembly to putative loci and genotype calling, was performed using the STACKS2 v2.64 pipeline (Rochette et al., 2019; Molecular Ecology, 28: 4737-4754).