Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes

Abstract

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.

Keywords: Pycnogonida; arthropods; diversification; mitogenome; ultraconserved.

Fig. 1.

Exemplars of sea spider diversity. (a) Pallenella harrisi (Callipallenidae). (b) Nymphon grossipes (Nymphonidae). (c) Rhopalorhynchus magdalenae (Colossendeidae). (d) Copulating pair of Pycnogonum litorale (Pycnogonidae) with UV illumination. (e) Stylopallene sp. (Callipallenidae), photograph by Iain Gray. (f) Nymphonella tapetis (Ascorhynchidae sensu lato). (g) Austrodecus glaciale (Austrodecidae). (h) Rhynchothorax australis (Rhynchothoracidae). (i) Anoplodactylus evansi (Phoxichilidiidae). (j) Cilunculus armatus (Ammotheidae), (k) Decolopoda australis (Colossendeidae), photograph by Andrei Utevsky. (l) Colossendeis megalonyx (Colossendeidae). (m) Male of Pallenella sp. (Callipallenidae) with egg clutch.

Fig. 2.

Historical hypotheses of higher-level sea spider relationships based on molecular sequence data. Nodes lacking nodal support (<70% bootstrap support; <0.90 posterior probability) or conflicting across analyses have been collapsed. Brackets correspond to paraphyletic lineages. In Sabroux et al. (2018), both Nymphonidae and Callipallenidae were recovered as polyphyletic. 12S, 12S rRNA; 16S, 16S rRNA; 18S, 18S rRNA; 28S, 28S rRNA; COI, cytochrome c oxidase subunit I; H3, histone H3.

Fig. 3.

Phylogenomic relationships of Pycnogonida based on maximum likelihood analysis of Matrix 3 (ln L = −472,525.59). Colors of branches correspond to families (right). Numbers on nodes indicate bootstrap resampling frequencies for Matrices 1–4 with model fitting using ModelFinder. Quotation marks on Ascorhynchidae reflect the inclusion of the putative ammotheid genus Paranymphon. Bottom left: Sensitivity plot indicating design of matrices and phylogenomic analyses. Inset (gray background): Alternative placements of Nymphonella tapetis.

Fig. 4.

Summary of Hox gene complements of surveyed taxa. Boldface text indicates new embryonic transcriptomes generated for this study. Hox genes for Carcinoscorpius rotundicauda are drawn from Shingate et al. (2020). Hox genes for Endeis spinosa and Nymphon gracile were reported by Manuel et al. (2006) using RACE-PCR. Phylogenetic relationships within Chelicerata are based on Ballesteros and Sharma (2019) and this study. Multiple sequence alignment, gene tree topology, and transcriptomic assemblies are provided in the Dryad Digital Repository.

Fig. 5.

(a) Phylogenomic dating of sea spiders based on the most complete data matrix and a correlated rates molecular clock model. Colors of branches and 95% HPD intervals correspond to families, as in figure 2. Line drawings (inset) correspond to stem-group fossils Palaeoisopus problematicus (top) and Flagellopantopus blocki (bottom). (b) Log lineage through time trajectories for selected Paleozoic aquatic taxa (sources in text). Branching times are truncated at the Cenozoic to mitigate undersampling of recent diversity and/or oversampling of intraspecific terminals.

Fig. 6.

Cephalic appendage evolution in sea spiders, with emphasis on the chelifore. Reconstruction of adult chelifores is mapped on the topology obtained herein, with addition of fossil stem group and crown group representatives. Ancestral state reconstruction is based on equally weighted parsimony. Note the omission of functional adult chelifores in colossendeids with supernumerary segments (a derived state within the genus Colossendeis). Specimens in counterclockwise order from top left: male Austrodecus glaciale, male Endeis spinosa, female Phoxichilidium femoratum, egg-bearing male Ascorhynchus ramipes, male Stylopallene cheilorhynchus, male Nymphon gracile, female Ammothella longipes, female Colossendeis angusta, female Pycnogonum litorale, female Rhynchothorax australis.