Seed set in the studied Trollius europaeus populations

Data on the number of produced seeds from Trollius europaeus populations. Number of ovules (column ovules_sum) and developing seeds (column seed_sum) were counted in five carpels per fruit

Morphological data

Morphological dat

Final DNA sequence assembled

Final DNA sequence assemble

Ecological data

Ecological dat

AFLP matrix

AFLP matri

Data_Sheet_4_Life-history traits drive spatial genetic structuring in Dinaric cave spiders.PDF

The subterranean ecosystem exerts strong selection pressures on the organisms that thrive in it. In response, obligate cave-dwellers have developed a series of morphological, physiological, and behavioral adaptations, such as eye reduction, appendage elongation, low metabolic rates or intermittent activity patterns, collectively referred to as troglomorphism. Traditionally, studies on cave organisms have been hampered by the difficulty of sampling (i.e., small population sizes, temporal heterogeneity in specimen occurrence, challenges imposed by the difficult-to-access nature of caves). Here, we circumvent this limitation by implementing a museomics approach. Specifically, we aim at comparing the genetic population structures of five cave spider species demonstrating contrasting life histories and levels of troglomorphism across different caves in the northern Dinarides (Balkans, Europe). We applied a genome-wide hybridization-capture approach (i.e., HyRAD) to capture DNA from 117 historical samples. By comparing the population genetic structures among five species and by studying isolation by distance, we identified deeper population structuring and more pronounced patterns of isolation by distance in the highly troglomorphic Parastalita stygia and Stalita pretneri ground dwellers, while the three web-building Troglohyphantes species, two of which can occasionally be found in surface habitats, showed less structured populations compatible with higher dispersal ability. The spatial distribution of genetic groups revealed common phylogeographic breaks among lineages across the studied species, which hint at the importance of environmental features in driving dispersal potential and shaping underground diversity.</p

A. Combined Bayesian half-compatible consensus tree of <i>Horismenus</i> based on mitochondrial and nuclear DNA regions.

<p>The species of parasitoid wasps defined by the Bayesian Poisson tree process coupled with the evolutionary placement algorithm and node supports are represented. Bayesian posterior probabilities and bootstrap support values are displayed below branches. Please see text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0136063#pone.0136063.t001" target="_blank">Table 1</a> for abbreviations. <b>B</b>. Barplot of the nucleotide diversities of each species. This analysis does not include information provided by the gaps and species that are not represented have a nucleotide diversity of zero.</p

Tritrophic relationships.

<p><i>Phaseolus species</i>: Depicted at the top of the figure are three wild bean species sorted into categories based on the other beans found in their immediate environment. <i>Phaseolus lunatus</i> with a red background is found on the far left with its sympatric partner, <i>P</i>. <i>vulgaris</i> in green. To their right, <i>P</i>. <i>vulgaris</i> (again in green) is depicted alone as it is found at median altitudes to be in allopatry. This is followed by <i>P</i>. <i>vulgaris</i> (in green) and <i>P</i>. <i>coccineus</i> (in blue) found in sympatry and finally <i>P</i>. <i>coccineus</i> (in blue) alone to represent where it is found in allopatry. <i>Altitude range</i>: Directly beneath these is an altitude measure on the y-axis. The bars indicate the range of altitudes within which each of the above categories was collected. <i>Bruchine species</i>: Beneath this are the most common bruchine beetle speces that attack each one of the <i>Phaseolus</i> categories. <i>Horismenus profile</i>: Photos on the left identify the three species of described <i>Horismenus</i> wasp found emerging from bean seeds. Blue bars indicate emergence from the first field season (2006–7) and pink bars indicate emergence from the second field season (2007–8). Numbers below in gray are the number of emerging wasps from that category for that season. The pink and blue bars are the proportions of each wasp species to emerge from that category in each season and will all add to 1.</p

Phylogenetic markers and models of evolution.

<p>* one individual of <i>H</i>. <i>cyaenoviridis</i> has one long indel</p><p>Phylogenetic markers used in the current study and models of evolution applied in Bayesian analyses of the full (128 specimens) and reduced dataset (38 specimens).</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