DOI: 10.5061/dryad.6p072
title: Data from: Spider phylogenomics: untangling the spider tree of life

description: 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 Tertiary 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, Aviculariodea,
 Theraphosidina, Araneomorphae, Entelygynae, 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, and even
 the new concept of Synspermiata, need revision after the departure of
 Filistatidae and Leptonetidae from the haplogyne clade. 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.
description: Data
 SupermatrixPhylogenetic supermatrix
 data set.superMatrix.txtData partitionsPartitions for accompanying data set.peerj-7476-partitions.txtOutput from EXAMLOutput from EXAML run that includes all genesallGenesinfo1.outallGenesTreeTree file derived from all genes runpHMM spider core orthologsArchive file containing pHMM spider core orthologshmm_dir_STOL2.tar.gz