Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids).

The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (<2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci.

The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.

Hunting the wolf: A molecular phylogeny of the wolf spiders (Araneae, Lycosidae).

Lycosids are a diverse family of spiders distributed worldwide. Previous studies recovered some of the deeper splits of the family, but with little support. We present a broad phylogenetic analysis of the Lycosidae including a wide geographic sampling of representatives and all the subfamilies described to date. Additionally, we extend the amount of molecular data used in previous studies (28S, 12S and NADH) through the inclusion of two additional markers, the nuclear H3 and the mitochondrial COI. We estimated the divergence times through the inclusion of fossils as calibration points and used the phylogenetic hypothesis obtained to explore the evolution of particular traits associated with dispersal capabilities. We recovered most of the currently recognized subfamilies with high nodal support. Based on these results, we synonymize Piratinae and Wadicosinae with Zoicinae and Pardosinae, respectively, and revalidate the subfamily Hippasinae. We corroborated that lycosids are a family with a relatively young origin that diversified with the reduction of tropical forests and the advance of open habitats. We show that a gradual accumulation of behavioral traits associated with ambulatory dispersal made Lycosidae the most vagrant subfamily of spiders, with an impressive ability to disperse long distances which helps to explain the worldwide distribution of some very young clades, such as the members of the subfamily Lycosinae.

Biodiversity and ecosystem functioning in evolving food webs.

We use computer simulations in order to study the interplay between biodiversity and ecosystem functioning (BEF) during both the formation and the ongoing evolution of large food webs. A species in our model is characterized by its own body mass, its preferred prey body mass and the width of its potential prey body mass spectrum. On an ecological time scale, population dynamics determines which species are viable and which ones go extinct. On an evolutionary time scale, new species emerge as modifications of existing ones. The network structure thus emerges and evolves in a self-organized manner. We analyse the relation between functional diversity and five community level measures of ecosystem functioning. These are the metabolic loss of the predator community, the total biomasses of the basal and the predator community, and the consumption rates on the basal community and within the predator community. Clear BEF relations are observed during the initial build-up of the networks, or when parameters are varied, causing bottom-up or top-down effects. However, ecosystem functioning measures fluctuate only very little during long-term evolution under constant environmental conditions, despite changes in functional diversity. This result supports the hypothesis that trophic cascades are weaker in more complex food webs.

Spider phylogenomics: untangling the Spider Tree of Life.

Spiders (Order Araneae) are massively abundant generalist arthropod predators that are found in nearly every ecosystem on the planet and have persisted for over 380 million years. Spiders have long served as evolutionary models for studying complex mating and web spinning behaviors, key innovation and adaptive radiation hypotheses, and have been inspiration for important theories like sexual selection by female choice. Unfortunately, past major attempts to reconstruct spider phylogeny typically employing the "usual suspect" genes have been unable to produce a well-supported phylogenetic framework for the entire order. To further resolve spider evolutionary relationships we have assembled a transcriptome-based data set comprising 70 ingroup spider taxa. Using maximum likelihood and shortcut coalescence-based approaches, we analyze eight data sets, the largest of which contains 3,398 gene regions and 696,652 amino acid sites forming the largest phylogenomic analysis of spider relationships produced to date. Contrary to long held beliefs that the orb web is the crowning achievement of spider evolution, ancestral state reconstructions of web type support a phylogenetically ancient origin of the orb web, and diversification analyses show that the mostly ground-dwelling, web-less RTA clade diversified faster than orb weavers. Consistent with molecular dating estimates we report herein, this may reflect a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125-90 million years ago favoring diversification of spiders that feed on cursorial rather than flying prey. Our results also have major implications for our understanding of spider systematics. Phylogenomic analyses corroborate several well-accepted high level groupings: Opisthothele, Mygalomorphae, Atypoidina, Avicularoidea, Theraphosoidina, Araneomorphae, Entelegynae, Araneoidea, the RTA clade, Dionycha and the Lycosoidea. Alternatively, our results challenge the monophyly of Eresoidea, Orbiculariae, and Deinopoidea. The composition of the major paleocribellate and neocribellate clades, the basal divisions of Araneomorphae, appear to be falsified. Traditional Haplogynae is in need of revision, as our findings appear to support the newly conceived concept of Synspermiata. The sister pairing of filistatids with hypochilids implies that some peculiar features of each family may in fact be synapomorphic for the pair. Leptonetids now are seen as a possible sister group to the Entelegynae, illustrating possible intermediates in the evolution of the more complex entelegyne genitalic condition, spinning organs and respiratory organs.

TESTING ADAPTIVE RADIATION AND KEY INNOVATION HYPOTHESES IN SPIDERS.

We combine statistical and phylogenetic approaches to test the hypothesis that adaptive radiation and key innovation have contributed to the diversity of the order Araneae. The number of unbalanced araneid clades (those whose species numbers differ by 90% or more) exceeds the number predicted by a null Markovian model. The current phylogeny of spider families contains 74 bifurcating nodes, of which 31 are unbalanced. As this is significantly more than the 14.8 expected unbalanced nodes, some of the diversity within the Araneae can be attributed to some deterministic cause (e.g., adaptive radiation). One of the more highly unbalanced (97%) bifurcations divides the orb-weaving spiders into the Deinopoidea and the larger Araneoidea. A simple statistical model shows that the inequality in diversity between the Deinopoidea and the Araneoidea is significant, and that it is associated with the replacement of primitive cribellar capture thread by viscous adhesive thread and a change from a horizontal to a vertical orb-web orientation. These changes improve an orb-web's ability to intercept and retain prey and expand the adaptive zone that orb-weaving spiders can occupy and are, therefore, considered to be "key innovations."