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

Abstract

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxonspecific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

Dynamic evolution of size and colour in the highly specializedZodarionant-eating spiders

“…As a result, we deemed branches with low support or clear conflict among analyses as unreliable and did not use them for ancestral state reconstruction analyses. Secondly, we observed a relatively high level of agreement between the topologies obtained in our study and those from a previous phylogenomic analysis of Zodarion [13]. It is worth mentioning that although that analysis included only half the number of Zodarion species used in the present study, it was based on a larger dataset comprising up to 870 ddRAD (double-digest restriction-siteassociated DNA) loci and only fresh samples.…”

Ecological specialization and reproductive isolation among closely related sympatric ant‐eating spiders

“…Although it looks clear that all the remarkable differences that we recorded between the black and yellow morphotypes of Z. nitidum are connected and evolved as part of the diverging lifestyles of both forms, because these traits are connected, it is difficult to determine the polarity of the change. Having in mind that in a recent phylogenomic analysis of Zodarion (Ortiz et al, 2022), Zodarion luctuosum , which is a black species and has diurnal activity (Pekár, unpublished), was strongly recovered as sister to Z. nitidum , if we assume that its black colouration is indicative of myrmecomorphy, then it is likely that the lifestyle character states of black Z. nitidum are ancestral. In this context, prey shift towards non‐ Messor ants that are easier to catch during the evening hours and/or avoidance of the diurnal activity hours due to predator pressure could have driven the divergence of the yellow morphotype from the ancestral lifestyle.…”

“…Recent studies of trophic ecology have shown that Zodarion species display prey specialization on different ant species, from exploiting mostly one species to successfully preying on phylogenetically diverse ants (Ortiz et al, 2022;Pekár et al, 2005Pekár et al, , 2012Pekár, Petráková, et al, 2018). Records of Zodarion prey include a rich number of ant species in the subfamilies Myrmicinae, Formicinae and Dolichoderinae, having in common to be ground middle-to largesized ants, co-occurring in the same microhabitat with the spiders, and being large enough to provide them camouflage from potential predators and abundant food from every hunting event (Pekár et al, 2014).…”

“…Because in the context of Zodarion 's biology, the colour pattern is likely to have a noticeable impact on the spider's lifestyle, we predicted that the colour diversification in Z. nitidum is a sign of a deeper biological divergence. We hypothesized that the dark form is diurnal, imitating and catching black Messor ants (Myrmicinae), a common prey for other species of the genus, and abundant in the habitats where Z. nitidum occurs (Ortiz et al, 2022; Pekár et al, 2012; Pekár, Petráková, et al, 2018). We also hypothesized that, in contrast, the lighter morphotype might avoid predators by displaying nocturnal activity, and therefore could be able to exploit other ant species.…”

Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude

“…We then used an integrative taxonomic approach combining DNA barcoding of over 1500 specimens with high‐resolution morphometric data for the most common mitochondrial MOTUs, as well as analysing selected specimens of nearly all MOTUs with genome‐wide double digest restriction site‐associated DNA sequencing (ddRAD‐seq) data. RAD‐seq has been applied in population genomics, phylogeography and phylogenomics (Combosch and Vollmer, 2015; Ortiz et al., 2021; Reitzel et al., 2013; Weiss et al., 2022), as well as species delimitation (Ivanov et al., 2018; Weigand et al., 2017; Weiss et al., 2018), where its main advantage is providing information from multiple loci across the entire genome compared to commonly used single‐locus nuclear markers (Andrews et al., 2016; Baird et al., 2008). Furthermore, as correct mate recognition is one of the crucial aspects characterising a distinct species, we also investigated the MOTU composition of precopulatory mating pairs.…”