Supplementary information of: Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics

Supplementary information of paper:Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics</div

Supplementary information of: Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider

Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.</p

Supplementary information of: Dynamic Evolution of Size and Color in the Highly Specialized Zodarion Ant-Eating Spiders

   Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defense mechanisms, including myrmecomorphy of different ant species and nocturnality. Using hyRAD, a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed the phylogeny of Zodarion using 52 (~ a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and color, traits that have diversified noticeably and are linked to defense mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and color across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group’s remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.</p

R codes for "Sensitivity of spiders from different ecosystems to lambda-cyhalothrin: effects of phylogeny and climate"

R codes for toxicity data calculations of the manuscript "Sensitivity of spiders from different ecosystems to lambda-cyhalothrin: effects of phylogeny and climate"</p