Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7,500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 ultraconserved element loci and 1,071 exon loci. Library preparation and target enrichment were performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ± 187 loci). Parsimony informative sites ranged from 26 to 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The per cent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7% to 30%. Maximum-likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Redesigning the baits with improved affinities to capture loci within each subclass will provide a valuable toolset to address systematic questions, further our understanding of the timing of diversifications and help resolve long-standing controversial relationships in the class Anthozoa.

Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648–894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for interpretation of the Precambrian environment and the early evolution of metazoans.

46Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of 47 marine metazoans that occur from shallow to deep waters worldwide. However, our 48 understanding of the evolutionary relationships among the ~7500 species within this class is 49 hindered by the lack of phylogenetically informative markers that can be reliably sequenced 50 across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 51Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was 52 performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing 53and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci 54 recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 55 138 loci) than hexacorals (475 ±187 loci). Phylogenetically informative sites ranged from 26-56 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, 57 Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, 58and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum 59 likelihood analyses recovered highly resolved trees with topologies matching those supported by 60 other studies, including the monophyly of the order Scleractinia. Our results demonstrate the 61 utility of this target-enrichment approach to resolve phylogenetic relationships from relatively 62 old to recent divergences. Re-designing the baits with improved affinities to capture loci within 63 each sub-class will provide a valuable toolset to address systematic questions and further our 64

BackgroundAntarctica is surrounded by the Antarctic Circumpolar Current (ACC), the largest and strongest current in the world. Despite its potential importance for shaping biogeographical patterns, the distribution and connectivity of deep-sea populations across the ACC remain poorly understood. In this study we conducted the first assessment of phylogeographical patterns in deep-sea octocorals in the South Pacific and Southern Ocean, specifically a group of closely related bottlebrush octocorals (Primnoidae: Tokoprymno and Thourella), as a test case to study the effect of the ACC on the population structure of brooding species. We assessed the degree to which the ACC constitutes a barrier to gene flow between northern and southern populations and whether the onset of diversification of these corals coincides with the origin of the ACC (Oligocene-Miocene boundary).ResultsBased on DNA sequences of two nuclear genes from 80 individuals and a combination of phylogeographic model-testing approaches we found a phylogenetic break corresponding to the spatial occurrence of the ACC. We also found significant genetic structure among our four regional populations. However, we uncovered shared haplotypes among certain population pairs, suggesting long-distance, asymmetrical migration. Our divergence time analyses indicated that the separation of amphi-ACC populations took place during the Middle Miocene around 12.6 million years ago, i.e., after the formation of the ACC.ConclusionWe suggest that the ACC constitutes a semi-permeable barrier to these deep-sea octocorals capable of separating and structuring populations, while allowing short periods of gene flow. The fluctuations in latitudinal positioning of the ACC during the Miocene likely contributed to the diversification of these octocorals. Additionally, we provide evidence that the populations from each of our four sampling regions could actually constitute different species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0574-z) contains supplementary material, which is available to authorized users.

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Morphological traits that appear multiple times when mapped onto molecular phylogenies have been associated with character lability. In an ecological context, functional characters, if labile, could confer advantages for adaptation to specific habitats. Bamboo corals are long-lived, deep-sea octocorals characterized by an obvious modularity, which affords diverse branching morphologies in the Keratoisidinae subfamily. We reconstructed molecular phylogenies using 16S (mitochondrial) and ITS2 (nuclear) ribosomal DNA, and obtained 39 ITS2 and 22 16S sequences from 22 different specimens. The molecular topologies showed Keratoisidinae genera as polyphyletic. Twelve morphological characters were chosen to make the ancestral character reconstruction, none of which exhibited character states forming monophyletic groups when mapped onto molecular phylogenies. The different character states appeared as having been gained and lost multiple times. Modular organisms such as bamboo corals could have higher character evolvability than unitary organisms. Complexity arising from simple body plans is a typical characteristic in most modular organisms, such as plants and colonial marine invertebrates. However, bamboo corals may also exhibit phenotypic plasticity associated with continuous characters, given that they can respond to extrinsic controls. Our results also have direct repercussions on Isididae taxonomy, since morphological characters have been used for their classification. Consequently, we suggest that the current taxonomy of the group is re-evaluated and that the different mechanisms regulating modularity and character evolution in bamboo corals are explored.

During three expeditions to the island (2009 and 2010), the diversity, abundance and status of octocorals were explored. Seven species of octocorals were recorded: Leptogorgia alba, Pacifigorgia cf. lacerata, Pacifigorgia sp.1 y Pacifigorgia sp.2, Muricea cf. fruticosa, Muricea sp., and the invasive species Carijoa riisei. Octocorals form dense aggregations in rocky walls and cliffs, with higher abundances between 10 and 20 m, reaching up to 20 colonies m-2. The most abundant species was Pacifigorgia cf. lacerata with a dominance of more than 60 % and a frequency of occurrence of 100 % for all visited sites. According to depth, three well-defined zones were determined for most sites. A deep zone between 25 and 40 m with an exclusive dominance of L. alba, a shallow assemblage between 7 and 20 m dominated by Pacifigorgia spp., and a transition zone between 18 and 25 m with a mixture of L. alba and P. cf. lacerata. Surprisingly, during November 2009, diseases of possible fungal origin visibly affected populations of Leptogorgia and Pacifigorgia. Subsequently, during February 2010 the same populations of octocorals were monitored and up to 66 % of the colonies were already dead in some locations. Leptogorgia had a significant reduction at El Arrecife site, while Pacifigorgia cf. lacerata had high mortality at La Nevera and El Freezer sites, and a recovery in El Arrecife. There was a notable improvement in disease prevalence by July 2010 with less than 10 % of diseased colonies. The invasive species C. riisei was observed in La Catedral and El Monstruo bank. Thus, this information increases considerably the knowledge of octocorals on Malpelo Island and is the first warning of possible threats against local octocoral populations, such as fungal diseases and the invasive octocoral C. riisei.

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