Sergio Vargas

Barcoding sponges: an overview based on comprehensive sampling.

Background Phylum Porifera includes ∼8,500 valid species distributed world-wide in aquatic ecosystems ranging from ephemeral fresh-water bodies to coastal environments and the deep-sea. The taxonomy and systematics of sponges is complicated, and morphological identification can be both time consuming and erroneous due to phenotypic convergence and secondary losses, etc. DNA barcoding can provide sponge biologists with a simple and rapid method for the identification of samples of unknown taxonomic membership. The Sponge Barcoding Project (www.spongebarcoding.org), the first initiative to barcode a non-bilaterian metazoan phylum, aims to provide a comprehensive DNA barcode database for Phylum Porifera. Methodology/Principal Findings ∼7,400 sponge specimens have been extracted, and amplification of the standard COI barcoding fragment has been attempted for approximately 3,300 museum samples with ∼25% mean amplification success. Based on this comprehensive sampling, we present the first report on the workflow and progress of the sponge barcoding project, and discuss some common pitfalls inherent to the barcoding of sponges. Conclusion A DNA-barcoding workflow capable of processing potentially large sponge collections has been developed and is routinely used for the Sponge Barcoding Project with success. Sponge specific problems such as the frequent co-amplification of non-target organisms have been detected and potential solutions are currently under development. The initial success of this innovative project have already demonstrated considerable refinement of sponge systematics, evaluating morphometric character importance, geographic phenotypic variability, and the utility of the standard barcoding fragment for Porifera (despite its conserved evolution within this basal metazoan phylum).

Phylogeny of Tetillidae (Porifera, Demospongiae, Spirophorida) based on three molecular markers

Tetillidae are spherical to elliptical cosmopolitan demosponges. The family comprises eight genera: namely, Acanthotetilla Burton, 1959, Amphitethya Lendenfeld, 1907, CinachyraSollas, 1886, CinachyrellaWilson, 1925, Craniella Schmidt, 1870, Fangophilina Schmidt, 1880, Paratetilla Dendy, 1905, and Tetilla Schmidt, 1868. These genera are characterized by few conflicting morphological characters, resulting in an ambiguity of phylogenetic relationships. The phylogeny of tetillid genera was investigated using the cox1, 18S rRNA and 28S rRNA (C1-D2 domains) genes in 88 specimens (8 genera, 28 species). Five clades were identified: (i) Cinachyrella, Paratetilla and Amphitethya species, (ii) Cinachyrella levantinensis, (iii) Tetilla, (iv) Craniella, Cinachyra and Fangophilina and (v) Acanthotetilla. Consequently, the phylogenetic analysis supports the monophyly of Tetilla, a genus lacking any known morphological synapomorphy. Acanthotetilla is also recovered. In contrast, within the first clade, species of the genera Paratetilla and Amphitethya were nested within Cinachyrella. Similarly, within the fourth clade, species of the genera Cinachyra and Fangophilina were nested within Craniella. As previously postulated by taxonomists, the loss of ectodermal specialization (i.e., a cortex) has occurred several times independently. Nevertheless, the presence or absence of a cortex and its features carry a phylogenetic signal. Surprisingly, the common view that assumes close relationships among sponges with porocalices (i.e., surface depressions) is refuted.

Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sponges

Vargas, S., Erpenbeck, D., Göcke, C., Hall, K. A., Hooper, J. N. A., Janussen, D. & Wörheide, G. (2012) Molecular phylogeny of Abyssocladia (Cladorhizidae: Poecilosclerida) and Phelloderma (Phellodermidae: Poecilosclerida) suggests a diversification of chelae microscleres in cladorhizid sponges. —Zoologica Scripta, 42, 106–116.

The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data

Halichondrid sponges play a pivotal role in the classification of demosponges as changes in their classification has had direct consequences for the classification of Demospongiae. Historically, the systematics of halichondrids has been unstable. During the 1950s, the order was divided into two subclasses, which were based on empirical and assumed reproductive data. Subsequent morphological and biochemical analyses postulated the re-merging of halichondrid families, but recent molecular data indicate their polyphyly. Here we review the classification history of halichondrid taxa, compare it with the current and predominantly ribosomal molecular data, and support the new phylogenetic hypotheses with mitochondrial data from DNA barcoding.

Molecular paleobiology of early-branching animals: integrating DNA and fossils elucidates the evolutionary history of hexactinellid sponges

Abstract Reconciliation of paleontological and molecular phylogenetic evidence holds great promise for a better understanding of the temporal succession of cladogenesis and character evolution, especially for taxa with a fragmentary fossil record and uncertain classification. In zoology, studies of this kind have largely been restricted to Bilateria. Hexactinellids (glass sponges) readily lend themselves to test such an approach for early-branching (non-bilaterian) animals: they have a long and rich fossil record, but for certain taxa paleontological evidence is still scarce or ambiguous. Furthermore, there is a lack of consensus for taxonomic interpretations, and discrepancies exist between neontological and paleontological classification systems. Using conservative fossil calibration constraints and the largest molecular phylogenetic data set assembled for this group, we infer divergence times of crown-group Hexactinellida in a Bayesian relaxed molecular clock framework. With some notable exceptions, our results are largely congruent with interpretations of the hexactinellid fossil record, but also indicate long periods of undocumented evolution for several groups. This study illustrates the potential of an integrated molecular/paleobiological approach to reconstructing the evolution of challenging groups of organisms.

Diversity in a Cold Hot-Spot: DNA-Barcoding Reveals Patterns of Evolution among Antarctic Demosponges (Class Demospongiae, Phylum Porifera)

Background The approximately 350 demosponge species that have been described from Antarctica represent a faunistic component distinct from that of neighboring regions. Sponges provide structure to the Antarctic benthos and refuge to other invertebrates, and can be dominant in some communities. Despite the importance of sponges in the Antarctic subtidal environment, sponge DNA barcodes are scarce but can provide insight into the evolutionary relationships of this unique biogeographic province. Methodology/Principal Findings We sequenced the standard barcoding COI region for a comprehensive selection of sponges collected during expeditions to the Ross Sea region in 2004 and 2008, and produced DNA-barcodes for 53 demosponge species covering about 60% of the species collected. The Antarctic sponge communities are phylogenetically diverse, matching the diversity of well-sampled sponge communities in the Lusitanic and Mediterranean marine provinces in the Temperate Northern Atlantic for which molecular data are readily available. Additionally, DNA-barcoding revealed levels of in situ molecular evolution comparable to those present among Caribbean sponges. DNA-barcoding using the Segregating Sites Algorithm correctly assigned approximately 54% of the barcoded species to the morphologically determined species. Conclusion/Significance A barcode library for Antarctic sponges was assembled and used to advance the systematic and evolutionary research of Antarctic sponges. We provide insights on the evolutionary forces shaping Antarcticas diverse sponge communities, and a barcode library against which future sequence data from other regions or depth strata of Antarctica can be compared. The opportunity for rapid taxonomic identification of sponge collections for ecological research is now at the horizon.

The phylogeny of Pacifigorgia (Coelenterata, Octocorallia, Gorgoniidae): a case study of the use of continuous characters in the systematics of the Octocorallia

Vargas S., Breedy O. & Guzman H. M. 2010. — The phylogeny of Pacifigorgia (Coelenterata, Octocorallia, Gorgoniidae): a case study of the use of continuous characters in the systematics of the Octocorallia. Zoosystema 32 (1): 5-18. ABSTRACT The Octocorallia constitute a group of organisms that inhabit a wide spectrum of habitats ranging from abyssal to shallow marine environments and from tropical to polar waters. As a subclass, the group is clearly defined and the clade is considered monophyletic based on a series of morphological and molecular synapomorphies. In contrast, the systematic treatment of octocorals below the subclass level is complex given the continuous nature of many of the characters used in their taxonomy. The use of continuous characters for the deduction of phylogenies generally has been considered a philosophical and methodological challenge; within the Octocorallia it has led researchers to rearrange genera, to consider character analysis problematic, or to prefer molecular data sets, which avoid morphological characters, for the study of octocoral phylogenetic relationships. In this study, we assessed the role of continuous morphological variation on the deduction of octocoral phylogenies. Specifically, we analyzed the morphologically diverse genus Pacifigorgia Bayer, 1951 and show that continuous variation, after adequate coding, represents a valuable source of information suitable for phylogenetic inference.

A new family of soft corals (Anthozoa, Octocorallia, Alcyonacea) from the aphotic tropical eastern Pacific waters revealed by integrative taxonomy

The new family Aquaumbridae is described based on distinct morphological characters and supported by a molecular phylogenetic analysis. Aquaumbridae is similar to Nidaliidae, Nepththeidae and Alcyoniidae in having arborescent colonies and lacking axis structure or stolons, but differs from them in having very different sclerite composition and having conspicuous transparent jelly-like lobes. Phylogenetic analysis of two mitochondrial genes, ND2 and mtMutS, strongly supports its placement in a separated clade. Herein we describe Aquaumbra klapferi sp. nov., gen. nov. in the new family. The organisms were obtained from the seamounts, ridges and canyons out of the insular shelf of Isla del Coco, Costa Rica, down to 400 m depth. The new species represents the first discovery of a soft coral in an eastern Pacific oceanic island, and provides hints of the biodiversity of the largely unexplored deep waters of the tropical eastern Pacific.

The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments

Animals have a carefully orchestrated relationship with oxygen. When exposed to low environmental oxygen concentrations, and during periods of increased energy expenditure, animals maintain cellular oxygen homeostasis by enhancing internal oxygen delivery, and by enabling the anaerobic production of ATP. These low-oxygen responses are thought to be controlled universally across animals by the hypoxia-inducible factor (HIF). We find, however, that sponge and ctenophore genomes lack key components of the HIF pathway. Since sponges and ctenophores are likely sister to all remaining animal phyla, the last common ancestor of extant animals likely lacked the HIF pathway as well. Laboratory experiments show that the marine sponge Tethya wilhelma maintains normal transcription under oxygen levels down to 0.25% of modern atmospheric saturation, the lowest levels we investigated, consistent with the predicted absence of HIF or any other HIF-like pathway. Thus, the last common ancestor of all living animals could have metabolized aerobically under very low environmental oxygen concentrations.

How many kinds of sclerite? Towards a morphometric classification of gorgoniid microskeletal components.

Gorgoniid octocorals constitute a diverse group of organisms that inhabit a wide range of marine environments. The group is currently defined by the presence of calcareous sclerites that are less than 0.3 mm in length with regularly arranged warts. Generic and specific classification schemes are based on the presence/absence of different sclerite classes in the sampled specimen as well as the frequency in which each class occurs in the sample. Sclerite classification typically has been difficult because a continuum of sclerite forms is found within and between species. Thus, the use of sclerites for phylogenetic inference and classification is problematic. Herein, we present a methodology to obtain quantitative measurements of large numbers of sclerites and used finite mixture modeling to assess the number of statistically different sclerite classes present in the eastern Pacific octocoral genus Pacifigorgia. We also test the ability of simple neural classifiers (perceptrons) to sort sclerites into the classes traditionally used in octocoral taxonomy. This methodology can be used for other gorgoniids and can be further extended to include shape quantifiers for groups other than those studied here.