Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data

Abstract

Next-generation sequencing technologies are rapidly transforming molecular systematic studies of non-model animal taxa. The arachnid order Opiliones (commonly known as “harvestmen”) includes more than 6,400 described species placed into four well-supported lineages (suborders). Fossil plus molecular clock evidence indicates that these lineages were diverging in the late Silurian to mid-Carboniferous, with some fossil harvestmen representing the earliest known land animals. Perhaps because of this ancient divergence, phylogenetic resolution of subordinal interrelationships within Opiliones has been difficult. We present the first phylogenomics analysis for harvestmen, derived from comparative RNA-Seq data for eight species representing all suborders. Over 30 gigabases of original Illumina short-read data were used in de novo assemblies, resulting in 50–80,000 transcripts per taxon. Transcripts were compared to published scorpion and tick genomics data, and a stringent filtering process was used to identify over 350 putatively single-copy, orthologous protein-coding genes shared among taxa. Phylogenetic analyses using various partitioning strategies, data coding schemes, and analytical methods overwhelmingly support the “classical” hypothesis of Opiliones relationships, including the higher-level clades Palpatores and Phalangida. Relaxed molecular clock analyses using multiple alternative fossil calibration strategies corroborate ancient divergences within Opiliones that are possibly deeper than the recorded fossil record indicates. The assembled data matrices, comprising genes that are conserved, highly expressed, and varying in length and phylogenetic informativeness, represent an important resource for future molecular systematic studies of Opiliones and other arachnid groups.

Carboniferous araneomorph spiders reinterpreted as long-bodied harvestmen

“…This would make these specimens the oldest known laniatorids, and extend the range of the suborder back more than 250 million years from the previous oldest examples in Eocene (c.45À49 Ma) Baltic amber described by Koch & Berendt (1854) and revised by Ubick & Dunlop (2005). Time-calibrated estimates of phylogeny (Giribet et al 2010;Sharma & Giribet 2011Hedin et al 2012) strongly imply that laniatorids should have been present in some form during the Carboniferous; the latest estimates for the origins of Laniatores range between c.355.5 Ma fig. 3B) and 410.3 Ma , which corresponds to somewhere in the early DevonianÀearly Carboniferous.…”

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

“…direct sperm transfer; median ocelli; paired tarsal claws), and spiders (e.g. unsegmented opisthosoma; venom glands; labidognathous chelicerae), and these evolutionary trends have been robustly validated by phylogenomic data [14,54,[59][60][61][62][63][64]. In the case of scorpions, barring the clear separation of buthids from non-buthid lineages, there has been little agreement as to how scorpion families are related.…”

Cross-bracing uncalibrated nodes in molecular dating improves congruence of fossil and molecular age estimates

“…However, we add the caveat that biochemical and functional analysis of the Metasiro americanus hemocyanin is required to assess whether it constitutes a true hemocyanin subunit or a runaway gene with a novel function. We further note that the discovery of a hemocyanin in this apulmonate arachnid may have been made uniquely possible by sequencing a large number of developmental stages for this species, as evidenced by numerous sequences in its transcriptome with gene ontogeny pertaining to developmental processes [63], in contrast to larger libraries based on one or two developmental stages [64].…”

“…To resolve this discordance in the literature with new empirical data, we searched for hemocyanin sequences in the transcriptomic libraries of 14 Opiliones species spanning all suborders [56,63,64]. We identified a single copy of hemocyanin in the transcriptome of Metasiro americanus, a member of the suborder Cyphophthalmi (the lineage sister to the remaining suborders [64,65]).…”

“…We identified a single copy of hemocyanin in the transcriptome of Metasiro americanus, a member of the suborder Cyphophthalmi (the lineage sister to the remaining suborders [64,65]). Phylogenetic placement of this hemocyanin sequence, tentatively named "Hc2FD", indicates that it diverged prior to the split between the paralogs Hc5A/D and Hc2/F.…”