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

Abstract

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 (MecicobothriumandHexurella)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.

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

“…Targeting mitochondrial genomes via Illumina sequencing, Cotoras et al () successfully recovered partial mitochondrial genomes from spider samples collected from the 1940s, with a 242‐bp fragment recovered from the oldest specimen collected in 1925 (92 years old). Most recently several UCE sequence capture studies have included museum specimens in phylogenomic analyses (Hedin et al, ; Hedin, Derkarabetian, Blair, et al, ; Hedin, Derkarabetian, Ramírez, et al, ), including one study specifically focusing on the utility of museum specimens (Wood et al, ). In these studies, successful sequencing of UCEs from the museum specimens was limited to those that were up to ~30 years old.…”

“…Bossert and Danforth () demonstrated that some UCE loci are shared across all arthropod UCE probe sets designed to date and correspond to genes with known function. Similarly, the vast majority (>98%) of arachnid UCEs were shown to be exonic in origin and annotated to genes with known functions (Hedin et al, ), making sequence capture of UCEs in arachnids essentially exon capture with the potential sequencing of adjacent intronic regions. The additional context the annotations and exon/intron boundaries provide for arachnid (or other arthropod) UCE origins is beneficial for downstream analyses, for example as an additional way to ensure sequence orthology for questionable sequences from museum specimens.…”

“…The ability to incorporate museum specimens into modern molecular systematics offers plenty of research possibilities, as evidenced by the plethora of studies published in recent years. One obvious benefit in systematics is the inclusion of rare, difficult to collect, endangered or extinct taxa in phylogenomic analyses (Hedin et al, ; Hedin, Derkarabetian, Blair, et al, ; Hedin, Derkarabetian, Ramírez, et al, ; Oliveros et al, ; Tsai et al, ; Wood et al, ), or even datasets consisting entirely of museum specimens (Tsai et al, ). One important consideration will be the proportion of specimens in the final dataset that are historical museum specimens.…”

“…To assess nonorthology, gene trees were reconstructed for all individual locus alignments with RAxML version 8 (Stamatakis, ) using the gtrgamma model and the rapid bootstrap algorithm with 200 bootstrap replicates. Potential nonorthologs were evidenced by highly divergent congeneric or confamilial sequences and/or by inspecting preliminary gene trees (Hedin et al, ); sequences that resulted in paraphyletic Opiliones suborders or families (i.e., universally supported lineages) and/or extremely long branch lengths were considered nonorthologs or contaminants and removed from subsequent analyses. We were very conservative when considering the oldest museum specimens.…”

“…Ethanol‐preserved collections include some vertebrate taxa, the great majority of non‐insect arthropods and most soft‐bodied invertebrates, including cnidarians, annelids and most non‐dried molluscs, among many other groups, representing a large proportion of specimens held in museum collections worldwide. Recent studies utilizing sequence capture of UCEs in arachnids have successfully included some historical ethanol‐preserved museum specimens in phylogenomic analyses (Hedin, Derkarabetian, Alfaro, Ramírez, & Bond, ; Hedin, Derkarabetian, Blair, et al, ; Hedin, Derkarabetian, Ramírez, et al, ; Wood et al, ) using standard extraction and sequence capture protocols, but success was limited to specimens collected within the last ~30 years, despite some attempts targeting older specimens.…”