Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

Abstract

Upon publication of this article, it was suggested that some of the entries of the two web-type matrices required revision. We have amended the web data and performed the relevant analyses in order to assess whether such changes overturn any of the web evolution inferences of the study. Seventy-nine out of a total of 1,085 entries were revised with new scores (7.28%) as follows: Twentynine of the entries were conservatively changed to ''?'' to reflect absence of published data on their webs; the remaining 50 entries correct errors or provide new web coding interpretations. State 8 in the matrix for the taxa with transcriptomes has been reworded as ''non-foraging silk-lined burrows.'' After revising the scoring for web building behavior and web architecture, we repeated the relevant comparative analyses using the same methodological approaches described in the original article to reconstruct the evolution of these traits in spiders. Analyses of both the ten-and the three-character-state datasets were carried out with R packages ape [1] and phytools [2], and both revised datasets have been deposited in the Harvard Dataverse repository (https://doi.org/10.7910/ DVN/EJOMZP). Re-analyses of the revised data do not alter our previous conclusions in any significant way. Figures 3 and S2 have been corrected in the article online, and the corrected Figures 3 and S2 are also shown below. The authors apologize to the readers for any inconvenience that this revision may have caused and thank the colleagues that kindly suggested changes.

Phylogenomics and genital morphology of cave raptor spiders (Araneae, Trogloraptoridae) reveal an independent origin of a flow‐through female genital system

“…Both analytical treatments of the dataset resulted in the same topology (Figure a, Figures Supporting Information), which is congruent with the more widely sampled phylogenomic analyses of Fernández et al (). In analyses of concatenated loci, all the clades were recovered with strong support (bootstrap proportions > 95%) for the 50% matrix, and all but one were highly supported for the 75% matrix (Dysdera + Orsolobidae bootstrap proportion = 92%).…”

“…How many times has this functional configuration evolved in spiders? Interpreting the known cases in the light of our results and the densely sampled phylogenetic studies (Fernández et al, ; Wheeler et al, ), we propose that the entelegyne condition evolved no less than six times independently (Figure a): in Pholcidae (Metagonia; Huber, ), Tetrablemmidae (Burger et al, ), Oonopidae (Scaphiella; Burger, ), Ochyroceratidae (Theotima; Machado, ), Trogloraptor (this study), and, of course, Entelegynae. Although the relationships of some of these taxa are not firmly established (especially of Theotima ), it is important to remark that the organization of these functionally flow‐through systems is very different in each taxon.…”

“…Total RNA extraction and postprocessing until transcriptome assembly follow Fernández et al () and Kallal, Fernández, Giribet, and Hormiga (). Orthology assessment was conducted on amino acid sequences using UPhO (Ballesteros & Hormiga, ).…”

“…A total of 28 taxa, including the newly sequenced taxon T. marchingtoni , were analyzed (Table ). We combined the new transcriptomic data from T. marchingtoni with a sample of previous transcriptomic data of species from the study of Fernández et al (), covering the main groups of true spiders (Araneomorphae), its sister group (Mygalomorphae), and a denser coverage of the clade Synspermiata. The tree was rooted between Araneomorphae and Mygalomorphae.…”

“…The results of target‐gene analyses (Wheeler et al, ) are compatible with a close relationship of Trogloraptor with dysderoid spiders, but these analyses place them near the family Caponiidae as well, always with low support perhaps due to the sometimes poor performance of traditional Sanger‐based markers for resolving spider divergences on family level. Phylogenomic data seem to be more successful for tracing some of the more controversial spider divergences (Fernández et al, ; Garrison et al, ). The higher‐level taxonomic diversity of Synspermiata and the dysderoid families is reasonably covered in these studies; thus, we aimed to add transcriptomic data on Trogloraptor to test its suggested phylogenetic position close to Dysderoidea.…”