Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record

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provided by Elsevier - Publisher Connector Current Biology 24, 1874–1879, August 18, 2014 ª2014 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2014.06.060 Report Phylogenomic Resolution of the Class Ophiuroidea Unlocks a Global Microfossil Record

Timothy D. O’Hara,1,* Andrew F. Hugall,1 Ben Thuy,2 We used a phylogenomic approach to address these defi- and Adnan Moussalli1 ciencies, obtaining 52 de novo ophiuroid transcriptomes and 1Museum Victoria, GPO Box 666, Melbourne, VIC 3001, three from other echinoderm classes, in addition to three pub- Australia lically available transcriptomes and three genomes (see Table 2Section Pale´ ontologie, Muse´ e National d’Histoire Naturelle du S1 available online). Twenty-nine of the ophiuroid transcrip- Luxembourg, 24 Rue Mu¨ nster, 2160 Luxembourg tomes were obtained from deep-sea (>500 m) samples, to ensure adequate taxonomic representation across the class. We identified and aligned 425 orthologous genes that could Summary be annotated using available sea urchin, hemichordate, or actinopterygian genomes (Table S2). After trimming, we used Our understanding of the origin, evolution, and biogeog- 102,143 amino acid positions to reconstruct a phylogeny of raphy of seafloor fauna is limited because we have insuf- the Echinodermata, with a focus on the ophiuroids (Figure 1). ficient spatial and temporal data to resolve underlying The resulting sequence matrix is 85% complete (Figure S1) processes [1]. The abundance and wide distribution of mod- and is the largest genetic data set ever assembled to analyze ern and disarticulated fossil Ophiuroidea [2], including brittle phylogenetic relationships within echinoderms. We calibrated stars and basket stars, make them an ideal model system for our tree using a series of published and novel fossil discov- global marine biogeography if we have the phylogenetic eries, ranging from the Paleozoic radiation of the echinoderm framework necessary to link extant and fossil morphology classes to the Mesozoic radiation of the crown group Ophiur- in an evolutionary context. Here we construct a phylogeny oidea (Figure 2; Table S3). These include the earliest known from a highly complete 425-gene, 61-taxa transcriptome- fossils that can be assigned to the extant ophiuroid families based data set covering 15 of the 18 ophiuroid families and Gorgonocephalidae, Ophiuridae, Ophiacanthidae, Ophioder- representatives of all extant echinoderm classes. We cali- matidae, Ophiolepididae, Ophiochitonidae, Ophiactidae, and brate our phylogeny with a series of novel fossil discoveries Ophiotrichidae. from the early Mesozoic. We confirm the traditional paleonto- Our large data set has enabled us to reconstruct a phylogeny logical view that ophiuroids are sister to the asteroids and of the echinoderm classes (Figure 1) with full maximum-likeli- date the crown group Ophiuroidea to the mid-Permian hood bootstrap support for 90% of nodes, including all family- (270 6 30 mega-annum). We refute all historical classification to phylum-level nodes, and Bayesian posterior probabilities schemes of the Ophiuroidea based on gross structural char- of 1.000 for all nodes. At the highest level, our tree confirms acters but find strong congruence with schemes based on the traditional paleontological view of echinoderm class evolu- lateral arm plate microstructure [3, 4] and the temporal appear- tion [15], supporting the division of echinoderms into the Pel- ance of various plate morphologies in the fossil record. The matozoa (crinoid) and Eleutherozoa (asteroid + ophiuroid + verification that these microfossils contain phylogenetically echinoid + holothuroid). We recover Asterozoa (asteroid + informative characters unlocks their potential to advance ophiuroid) and Echinozoa (echinoid + holothuroid) clades. our understanding of marine biogeographical processes. The relationship of the Ophiuroidea with other echinoderm classes has been contentious, with previous analyses pairing Results and Discussion them either with the asteroids, with an echinoid-holothuroid clade, or as an independent lineage [8, 10, 16]. The problem The Ophiuroidea contain approximately 2,100 currently is complex, as the fossil record indicates that echinoderm described species, found in most seafloor habitats from the classes arose rapidly in the early Paleozoic but that modern poles to the Equator and from the shoreline to hadal trenches crown groups diversified in the early Mesozoic, and such [2]. They can dominate the megafauna of benthic assemblages ancient rapid radiations are notoriously difficult to disentangle and are sampled by oceanic expeditions frequently enough to [16, 17]. Support for the Asterozoa in our analysis is over- facilitate detailed distributional mapping at large spatial scales whelming and spread across the entire data set (DlnL = 494 [5]. Although complete body fossils are rare, disarticulated support) with a three-to-one majority of individual gene parti- ophiuroid lateral arm plates are abundant as microfossils in tions (Figure S2). We found no evidence of long-branch attrac- paleontological samples and are emerging as a new and rich tion or compositional biases that might confound the overall stratigraphic record to advance our knowledge of deep-sea topology (Figure S2). Notwithstanding the limited taxon sam- paleoecology [6]. Unfortunately, our understanding of the evo- pling for some classes, our echinoderm topology is congruent lution and higher-level systematics of this group is rudimen- with another recent transcriptome study using a different set of tary, being hampered by a constrained body plan, extensive species [10]. homoplasy [2, 3, 7], and deep divergence from other echino- We date the ophiuroid crown-group origin to the mid- derm classes. Previous molecular studies have been limited Permian (270 6 30 mega-annum [Ma]; Figure 3; Table 1). These in their taxon sampling (e.g., [8–10]) or phylogenetic spread dates are broadly congruent across three different analytical [11], and most have been based upon fragments of a small methods and subsets of the data. The chronology and long number of mitochondrial and nuclear ribosomal RNA genes. w200 Ma stem of the Ophiuroidea corroborate fossil evidence of a decline in stem taxa over the Carboniferous and Permian periods [18], including the end-Permian mass extinction event *Correspondence: [email protected] (252 Ma) [19]. Although the fossil record shows a significant Ophiuroid Phylogenomics 1875

Figure 1. Echinoderm Phylogenomic Tree Indicating Ophiuroid Classification Schemes Maximum-likelihood (RAxML) tree of the 102,143 amino acid data set using a 72-partition model. Branch lengths for the outgroup taxa have been shortened for readability. Fast bootstrap support values are only given for nodes without full support. The PhyloBayes topology was identical, with all nodes having a posterior probability of 1.000. The Ophiuroidea are colored blue (for order Ophiurida) and red (Euryalida) [7]. Three higher classification schemes are shown on the right, indicating the better fit of the recent analysis of lateral arm plate morphology of Thuy and Sto¨ hr [4] compared to previous classifications [7, 12]. See Figure S3 for more details. Current Biology Vol 24 No 16 1876

Figure 2. Ophiuroid Fossils Documenting Early Crown-Group Disparity and Dating Calibration Points See Table S3 for more details. Scale bars represent 2 mm in (A)–(D) and 200 mm in (H)–(P). (A) The archetypical ophiuroid ancestor, unnamed fossil Aganaster species from the Early Carboniferous, w350 mega-annum (Ma). (B) Triassic fossil Aspiduriella streichani, 245 Ma, classified as an Ophiurinae but with Euryalida-like vertebrae. (C) The Triassic ophiacanthid fossil Leadagmara gracilispina, 230 Ma. Image from Thuy et al., 2013 [13]. (D) The Cretaceous fossil Ophiactis applegatei (Ophiactidae), 111 Ma. Image from Martin-Medrano et al. 2008 [14]. (E) Detail of arm skeleton of recent Ophiolepis variegata (Ophiolepididae). (F and G) Disassociated lateral arm plates of recent Ophiolepis variegata in external and internal view, showing the most relevant characters. Sa, spine articulation; Or, outer surface ornamentation; Ri, inner ridge; Tp, tentacle opening. (H) Lateral arm plate microfossil of Europacantha paciphila (Ophiacanthidae), 245 Ma. (I) Lateral arm plate microfossil of unnamed Ophiodermatidae, 230 Ma. (J) Lateral arm plate microfossil of Eozonella species (Ophiolepididae), 176 Ma. (K and L) Lateral arm plate and vertebra microfossils of unnamed stem Euryalid, 180 Ma. (M) Lateral arm plate microfossil of unnamed Ophionereididae, 170 Ma. (N) Lateral arm plate microfossil of unnamed Ophiuridae, 114 Ma. (O) Lateral arm plate microfossil of unnamed Ophiotrichidae, 45 Ma. ophiuroid diversification in the early Triassic [19, 20](Figure 2), characters are phylogenetically informative [3]. There has been our phylogeny appears not to show an explosive radiation of only one attempt at a cladistic analysis [7], and previous mo- extant lineages dating from that time, indicating that additional lecular data have been limited and relatively uninformative taxon pruning may have occurred at the end-Triassic extinc- [7–9]. Traditional taxonomic descriptions of fossil species tion event or later. The crown group continued to diversify have been unhelpful, as many lack the detail to place them in over the Mesozoic and Cenozoic, the Ophiotrichidae being a meaningful phylogenetic context with extant taxa [13]. the last family to appear in the fossil record, in the Eocene Thus, modern ophiuroids have been lumped into two orders: (Figure 2O). the Euryalida, which include the basket stars and unbranched We recover three novel clades within the Ophiuroidea serpent stars, having a reduced external skeleton and hour- (marked A, B, and C in Figure 1) and reject previously proposed glass-shaped articulation surfaces on the vertebrae, and the intraclass taxonomies [7, 12, 18](Figure 1). The within-ophiu- Ophiurida, which account for the rest [2]. roid topology was the same with or without outgroups and us- However, we find that the Ophiurida are paraphyletic with ing amino acids or nucleotides. Relationships within the class respect to the Euryalida (Figure 1). Our phylogeny clearly have been problematic. Various classificatory schemes have shows that the euryalids are related to the Ophiuridae and been constructed, but it remains unclear which morphological Ophiomusium (DlnL = 408; Figure S2), although the split Ophiuroid Phylogenomics 1877

Amphiuridae

D Ophiactidae min 111 O Ophiotrichidae

M Ophionereidae min 176 J Ophiolepididae Ophioleucidae

Ophiodermatidae I Ophiomyxidae Ophiocomidae Ophiocypris

crown extant Ophiacanthidae Ophiuroidea H C Clarkcoma

A Ophiophrura Ophiologimus K L Euryalida Asterozoa min 479 B min 180 N Ophiuridae Eleutherozoa min 114 max 521 Ophiophycis Ophiomusium min 482 Asteroidea max 485 max 542 Echinoidea Echinozoa min 501 min 464 Holothuroidea Crinoidea

550 500 450 400 350 300 250 200 150 100 50 Ma

Cambrian Ordovician Silur. Devonian Carboniferous Permian Triassic Jurassic Cretaceous Paleog. Neog.

Figure 3. Echinoderm Chronogram Indicating Extant and Fossil Ophiuroidea PhyloBayes relaxed-clock log-normal model with birth-death prior, using the calibration points (Table S3) marked by black arrows. The Permian-Triassic mass extinction is indicated by the vertical green bar. All analyses estimate the origin of the extant ophiuroids to be 270 6 30 Ma (Table 1; Figure S3). Fossils depicted in Figures 2A–2O are positioned according to their age and inferred phylogenetic positions. Fossil (A) is an ancestral stem ophiuroid, and (C), (H), and (I) are part of the crown-group diversification of clade B, all lying within the 95% confidence limits of the reconstructed node ages. occurred early in the crown-group radiation. The subsequent placement of the arm spines of both the basket stars (euryal- divergence of morphology reflects their ecological specializa- ids) and the family Ophiomyxidae, long united as the Phryno- tion. The euryalids (such as Gorgonocephalus) are typically phiurina [12, 18], are confirmed to be convergent. Surprisingly, active climbers that use their long and frequently branched our two species of Ophiomyxa are placed adjacent to the arms to capture plankton from the water column. The Ophiur- ophiodermatids, which has not been predicted by previous idae and Ophiomusium, on the other hand, have generally studies [3, 4, 7]. Our topology of the Eurylida differs from that adapted to an epibenthic way of life, typically moving horizon- of Okanishi et al. [11] in that Asteronyx is sister to all other eur- tally across muddy seafloors to capture small prey or scav- yalids rather than the Gorgonocephalidae. However, this node enging carrion. We identify the Triassic Aspiduriella streichani in our tree has equivocal support (Figure 1), and more taxon (Figure 2B) as putatively part of the stem group of clade sampling is required. A, classified as an Ophiuridae on the basis of external The prominent tropical shallow-water families Ophiocomi- morphology but with euryalid-like hourglass articulation sur- dae, Ophiodermatidae, Ophionereididae, and Ophiolepididae, faces on the arm vertebrae [21]. Previous reports of euryalid- grouped together in previous taxonomic schemes on the basis like fossils (Eospondylus, Onychaster) from the Paleozoic are of their oral skeletal architecture, are separated into two of our now considered to be stem Ophiuroidea [22]. The basal posi- clades (B and C). Species within the traditional grouping of the tion of clade A is consistent with hypothesis that the most Ophiuridae, Ophiolepididae, and/or Ophioleucidae [12, 24] are recent common ancestors of modern ophiuroids were Ophio- also spread across our phylogeny. Several families are clearly musium-like forms from the late Paleozoic [23](Figure 2A). polyphyletic, particularly the Ophiolepididae, Ophiomyxidae, The incongruence among previous classifications sug- and Ophiocomidae, which has undoubtedly confounded pre- gests substantial parallel diversifications within a constrained vious systematic analyses. In particular, we find that Ophio- morphology. The thick skin covering and ventrolateral cypris tuberculosus falls within the Ophiodermatidae rather Current Biology Vol 24 No 16 1878

Table 1. Estimates of Divergence Times or Stem Length Derived from Lateral arm plates have excellent preservation potential as Three Relaxed-Clock Analyses calcitic microfossils and occur abundantly in marine sediments [28], including those from the deep sea that have been BEAST (Median PhyloBayes (Mean considered devoid of megafaunal remains [6]. They are quan- Extant Crown Group Ma, 95% CI) Ma, 95% CI) PLRS (Ma) tifiable, determinable to genus or even species [27], and also Echinodermata 540 (534–542) 530 (519–540) 542 contain useful phylogenetic information. The combination of Eleutherozoa 509 (504–515) 499 (493–508) 505 a robust phylogeny and extensive fossil deposits will ensure Asterozoa 482 (479–488) 482 (479–490) 479 Echinozoa 471 (465–482) 471 (464–480) 464 that the Ophiuroidea will contribute much to our future under- Ophiuroidea 274 (251–298) 267 (244–301) 255 standing of macroevolutionary processes within the marine Ophiuroid stem length 208 (182–237) 215 (184–244) 224 environment. Ophiuroid clade A 234 (210–258) 242 (224–252) 230 Ophiuroid clade B 213 (188–252) 237 (218–270) 220 Experimental Procedures Ophiuroid clade C 211 (190–235) 221 (205–249) 207 Euryalida 100 (71–133) 139 (113–183) 124 Transcriptomes were prepared from 52 ophiuroid, one crinoid, one holothu- Estimates of divergence times or stem length derived from three relaxed- roid, and one asteroid species (Table S1); sequenced using an Illumina clock analyses. The BEAST analysis of an 80-gene amino acid data set HiSeq PE100 system averaging 20 million paired-end reads per sample; included a single-partition JTT-G uncorrelated log-normal rate variation and de novo assembled using Trinity [29] software into an average of 150 model with birth-death speciation prior and root age limit of 650 mega-an- thousand contigs. Candidate sequences from these assemblies, three pub- num (Ma) (Figure S3). The PhyloBayes analysis of the same 80-gene amino lically available transcriptomes (two echinoids and one asteroid), and two acid data included a CAT-GTR log-normal rate variation model with birth- reference proteomes (hemichordate Saccaglossus and fish Danio) were death divergence time prior and root age limit of 650 Ma. The penalized-like- selected by BLASTx [30] matches against the key sea urchin (Strongylocen- lihood rate smoothing (PLRS) analysis was performed on the full RAxML tree trotus) focal reference proteome (build 3.1), averaging 5,500 unique hits with 210 (Figure 1) using the truncated Newton (TN) algorithm, additive penalty func- an e value cutoff of 10 (Table S4). Because many of our samples were tion (ADD), and optimized smoothing factor of 1.5. small filter feeders, coextraction of contaminating planktonic organisms was an unavoidable and pervasive problem [31, 32]. Moreover, many ophiuroid genes had very low coverage and were fragmented into small contigs, than within the Ophiolepididae, where it has been previously which resulted in better BLASTx match scores for some contaminants than placed [18]. The incongruence between our phylogeny and the underlying real ophiuroid genes. Consequently, certainty of orthology was empirically determined for each gene by phylogenetic assessment (at previous taxonomic schemes based on skeletal characters the nucleotide level) of all candidate contigs and reference protein se- (Figure 1) is indicative of the morphological convergence that quences. A quarter of the examined candidate gene sets were rejected is common throughout the Ophiuroidea. Indeed, Martynov [3] due to paralog complexity, including at least ten with ophiuroid subclade- found that many traditional characters, such as the form of specific duplications. To maintain data matrix completeness, we consid- the genital plates, oral structures, disc armament, and many ered only genes identified from at least two-thirds of taxa. An initial align- arm structures, were not consistent with preexisting morpho- ment of 425 genes (147,953 amino acids) across the 61 taxa was trimmed using the software ALISCORE [33], resulting in 102,143 amino acids in an logical classifications. 85% complete data matrix (Table S2). Our tree contains 15 of the 18 ophiuroid families, which Maximum-likelihood and Bayesian phylogenetic inference were conduct- contain >96% of genera and species, but we have only 38 ed using both the 425-gene and a smaller 80-gene data matrix, with (1) (15%) genera, and we defer a detailed redescription of RAxML [34] fast bootstrap using an exon-based multipartition model opti- higher-level taxa until further taxa have been sequenced. mized by PartitionFinder [35] and (2) PhyloBayes [36] using the CAT-GTR Targeting ethanol-preserved museum specimens with exon- mixture model, with additional Dayhoff6 recoding and heterotachy model analyses. Dating analyses were conducted using BEAST [37], penalized- capture protocols designed from this transcriptome data likelihood rate smoothing (PLRS) [38], and PhyloBayes, applying uniform will allow a future comprehensive redescription of the higher prior fossil-based constraints. Eight of our 15 possible fossil calibrations systematics. (Figures 3 and S3; Table S3) were used in the final analysis to avoid redun- Our three primary ophiuroid clades are not ecologically dancy and unconstrain the crown ophiuroid node. cohesive. Feeding guilds [25] and larval developmental types [26] are spread throughout the phylogeny. However, the Accession Numbers basal lineages of the major clades (including Ophiomusium, Ophiologimus, and Ophioleuce) are now largely confined to The aligned post-ALISCORE data set has been deposited at TreeBase (http://purl.org/phylo/treebase/phylows/study/TB2:S16042) with the bathyal to abyssal depths (200–6,500 m), and fossil ophiu- accession number S16042. roid ossicles are common in deep-sea sediments from the Early Jurassic onward [27], suggesting that at least some of Supplemental Information the radiation of the Ophiuroidea occurred in deep-sea set- tings [6]. Supplemental Information includes three figures, four tables, and Supple- A major finding of this study is that the emerging use of mental Experimental Procedures and can be found with this article online ophiuroid lateral arm morphologies to identify and classify at http://dx.doi.org/10.1016/j.cub.2014.06.060. modern and fossil specimens can now be corroborated Author Contributions against a robust phylogenetic framework. Our phylogeny is consistent with analyses of lateral arm plate synapomorphies T.D.O. and A.M. conceived the study. A.F.H., A.M., and T.D.O. developed [4](Figure 1). The only exception is that our tree suggests the bioinformatics pipeline. A.F.H. processed the transcriptomes. A.F.H. that the similar plate shapes of modern Ophioderma and and T.D.O. produced the aligned data set. A.F.H. performed the phyloge- Ophiolepis [4] are convergent, an interpretation confirmed by nomic analyses. B.T. supplied the fossil interpretation, calibrations, and the morphological disparity of previously unpublished Meso- images. T.D.O. and A.F.H. took the lead in writing the manuscript. zoic fossils (Figures 2I and 2J; Table S3). Moreover, our Acknowledgments crown-group calibration points, based on fossil lateral arm plates, are temporally consistent with our molecular chrono- We thank Sadie Mills (NIWA, New Zealand), Gustav Paulay (University of gram (Figure 3). Florida), Alex Rogers (Oxford University), and David Staples (Museum Ophiuroid Phylogenomics 1879

Victoria) for collection of samples; Sumitha Hunjan (Museum Victoria) for ex- 18. Spencer, W.K., and Wright, C.W. (1966). Asterozoans. In Treatise on tracting RNA; Roger Nilsen (Georgia Genomics Facility) for transcriptome Invertebrate Paleontology, Part U: Echinodermata 3, Volume 1, sequencing; Devi Stuart-Fox (University of Melbourne) for critical assess- Moore, R.C., ed. (Lawrence: Geological Society of America and ment of a manuscript draft; and Mark Miller (CIPRES computing resources) University of Kansas Press), pp. U4–U107. and Luisa Teasdale (Museum Victoria) for assistance with bioinformatics. 19. Chen, Z.Q., and McNamara, K.J. (2006). End-Permian extinction and This work is an output of the project ‘‘National Maps of Biodiversity and subsequent recovery of the Ophiuroidea (Echinodermata). Connectivity’’ of the Marine Biodiversity Hub, funded through the National Palaeogeogr. Palaeoclimatol. Palaeoecol. 236, 321–344. Environmental Research Program and administered through the Australian 20. Twitchett, R.J., and Oji, T. (2005). The Early Triassic recovery of echino- Government Department of the Environment. Specimen line drawings in derms. C. R. Palevol 4, 463–474. Figure 1 were contributed by the Australian Biological Resources Study. 21. Hess, H., and Meyer, C.A. (2008). A new ophiuroid (Geocoma schoenta- lensis sp. nov.) from the Middle Jurassic of northwestern Switzerland Received: March 26, 2014 and remarks on the family Aplocomidae Hess 1965. Swiss J. Geosci. Revised: May 23, 2014 101, 29–40. Accepted: June 23, 2014 22. Hotchkiss, F.C., and Glass, A. (2012). Observations on Onychaster Meek Published: July 24, 2014 & Worthen, 1868 (Ophiuroidea: Onychasteridae) (Famennian – Visean age). Zoosymposia 7, 121–138. 23. Hotchkiss, F.H.C., and Haude, R. (2004). Observations on Aganaster References gregarius and Stephanoura belgica (Ophiuroidea: Ophiolepididae) 1. McClain, C.R., and Hardy, S.M. (2010). The dynamics of biogeographic (Early Caboniferous and Late Devonian age). In Echinoderms: ranges in the deep sea. Proc. Biol. Sci. 277, 3533–3546. Mu¨ nchen: Proceedings of the Eleventh International Echinoderm 2. Sto¨ hr, S., O’Hara, T.D., and Thuy, B. (2012). Global diversity of brittle Conference, T. Heinzeller and J.H. Nebelsick, eds. (Leiden: Balkema), stars (Echinodermata: Ophiuroidea). PLoS ONE 7, e31940. pp. 425–431. 3. Martynov, A.V. (2010). Reassessment of the classification of the 24. Madsen, F.J. (1983). A review of the Ophioleucinae stat. rev. Ophiuroidea (Echinodermata), based on morphological characters. I. (Echinodermata, Ophiuroidea) with the erection of a new genus General character evaluation and delineation of the families Ophiostriatus. Steenstrupia 9, 29–69. Ophiomyxidae and Ophiacanthidae. Zootaxa 2697, 1–154. 25. Warner, G.F. (1982). Food and feeding mechanisms: Ophiuroidea. In 4. Thuy, B., and Sto¨ hr, S. (2011). Lateral arm plate morphology in brittle Echinoderm Nutrition, M. Jangoux and J.M. Lawrence, eds. stars (Echinodermata: Ophiuroidea): new perspectives for ophiuroid (Rotterdam: A.A. Balkema), pp. 161–181. micropalaeontology and classification. Zootaxa 3013, 1–47. 26. McEdward, L.R., and Miner, B.G. (2001). Larval and life-cycle patterns in 5. O’Hara, T.D., Rowden, A.A., and Bax, N.J. (2011). A Southern echinoderms. Can. J. Zool. 79, 1125–1170. Hemisphere bathyal fauna is distributed in latitudinal bands. Curr. 27. Thuy, B. (2013). Temporary expansion to shelf depths rather than an Biol. 21, 226–230. onshore-offshore trend: the shallow-water rise and demise of the mod- 6. Thuy, B., Gale, A.S., Kroh, A., Kucera, M., Numberger-Thuy, L.D., Reich, ern deep-sea brittle-star family Ophiacanthidae (Echinodermata: M., and Sto¨ hr, S. (2012). Ancient origin of the modern deep-sea fauna. Ophiuroidea). Eur. J. Taxonomy 48, 1–242. PLoS ONE 7, e46913. 28. Hess, H. (1962). Mikropala¨ ontologische Untersuchungen an Ophiuren: I. Einleitung. Eclogae Geol. Helv. 55, 595–608. 7. Smith, A.B., Paterson, G.L.J., and Lafay, B. (1995). Ophiuroid phylogeny 29. Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., and higher taxonomy: morphological, molecular and palaeontological perspectives. Zool. J. Linn. Soc. 114, 213–243. Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011). Full-length transcriptome assembly from RNA-Seq data without 8. Janies, D.A., Voight, J.R., and Daly, M. (2011). Echinoderm phylogeny a reference genome. Nat. Biotechnol. 29, 644–652. including Xyloplax, a progenetic asteroid. Syst. Biol. 60, 420–438. 30. Altschul, S.F., Madden, T.L., Scha¨ ffer, A.A., Zhang, J., Zhang, Z., Miller, 9. Perseke, M., Bernhard, D., Fritzsch, G., Bru¨ mmer, F., Stadler, P.F., and W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new Schlegel, M. (2010). Mitochondrial genome evolution in Ophiuroidea, generation of protein database search programs. Nucleic Acids Res. Echinoidea, and Holothuroidea: insights in phylogenetic relationships 25, 3389–3402. of Echinodermata. Mol. Phylogenet. Evol. 56, 201–211. 31. Kocot, K.M., Cannon, J.T., Todt, C., Citarella, M.R., Kohn, A.B., Meyer, 10. Telford, M.J., Lowe, C.J., Cameron, C.B., Ortega-Martinez, O., A., Santos, S.R., Schander, C., Moroz, L.L., Lieb, B., and Halanych, Aronowicz, J., Oliveri, P., and Copley, R.R. (2014). Phylogenomic anal- K.M. (2011). Phylogenomics reveals deep molluscan relationships. ysis of echinoderm class relationships supports Asterozoa. Proc. Biol. Nature 477, 452–456. Sci. 281, 20140479. 32. Hoy, M.A., Yu, F., Meyer, J.M., Tarazona, O.A., Jeyaprakash, A., and Wu, 11. Okanishi, M., and Fujita, T. (2013). Molecular phylogeny based on K. (2013). Transcriptome sequencing and annotation of the predatory increased number of species and genes revealed more robust mite Metaseiulus occidentalis (Acari: Phytoseiidae): a cautionary tale family-level systematics of the order Euryalida (Echinodermata: about possible contamination by prey sequences. Exp. Appl. Acarol. Ophiuroidea). Mol. Phylogenet. Evol. 69, 566–580. 59, 283–296. 12. Matsumoto, H. (1917). A monograph of Japanese Ophiuroidea, 33. Misof, B., and Misof, K. (2009). A Monte Carlo approach successfully arranged according to a new classification. J. Coll. Sci. Imp. Univ. identifies randomness in multiple sequence alignments: a more Tokyo 38, 1–408. objective means of data exclusion. Syst. Biol. 58, 21–34. 13. Thuy, B., Ishida, Y., Doi, E., and Kroh, A. (2013). New ophiacanthid brittle 34. Stamatakis, A., Hoover, P., and Rougemont, J. (2008). A rapid bootstrap stars (Echinodermata: Ophiuroidea) from the Upper Triassic of Japan: algorithm for the RAxML Web servers. Syst. Biol. 57, 758–771. first insights into the origin and evolution of an extant deep-sea group. 35. Lanfear, R., Calcott, B., Ho, S.Y.W., and Guindon, S. (2012). J. Syst. Palaeontol. 11, 515–530. Partitionfinder: combined selection of partitioning schemes and substi- 14. Martin-Medrano, L., Thuy, B., and Garcıá-Barrera, P. (2008). New Albian tution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695–1701. (Early Cretaceous) ophiuroids from the Tlayu´ a Quarry, Puebla, Mexico. 36. Lartillot, N., and Philippe, H. (2004). A Bayesian mixture model for Palaeontology 52, 83–94. across-site heterogeneities in the amino-acid replacement process. 15. Smith, A.B., Peterson, K.J., Wray, G., and Littlewood, D.T.J. (2004). Mol. Biol. Evol. 21, 1095–1109. From bilateral symmetry to pentaradiality: The phylogeny of hemichor- 37. Drummond, A.J., and Rambaut, A. (2007). BEAST: Bayesian evolu- dates and echinoderms. In Assembling the Tree of Life, J. Cracraft and tionary analysis by sampling trees. BMC Evol. Biol. 7, 214. M. Donoghue, eds. (New York: Oxford University Press), pp. 365–383. 38. Sanderson, M.J. (2003). r8s: inferring absolute rates of molecular evolu- 16. Pisani, D., Feuda, R., Peterson, K.J., and Smith, A.B. (2012). Resolving tion and divergence times in the absence of a molecular clock. phylogenetic signal from noise when divergence is rapid: a new look Bioinformatics 19, 301–302. at the old problem of echinoderm class relationships. Mol. Phylogenet. Evol. 62, 27–34. 17. McCormack, J.E., Faircloth, B.C., Crawford, N.G., Gowaty, P.A., Brumfield, R.T., and Glenn, T.C. (2012). Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome Res. 22, 746–754.