A Revisited Phylogeography of Nautilus Pompilius

The cephalopod genus Nautilus is considered a “living fossil” with a contested number of extant and extinct species, and a benthic lifestyle that limits movement of animals between isolated seamounts and landmasses in the Indo-Pacific. Nautiluses are fished for their shells, most heavily in the Philippines, and these fisheries have little monitoring or regulation. Here, we evaluate the hypothesis that multiple species of Nautilus (e.g., N. belauensis, N. repertus and N. stenomphalus) are in fact one species with a diverse phenotypic and geologic range. Using mitochondrial markers, we show that nautiluses from the Philippines, eastern Australia (Great Barrier Reef), Vanuatu, American Samoa, and Fiji fall into distinct geographical clades. For phylogenetic analysis of species complexes across the range of nautilus, we included sequences of Nautilus pompilius and other Nautilus species from GenBank from localities sampled in this study and others. We found that specimens from Western Australia cluster with samples from the Philippines, suggesting that interbreeding may be occurring between those locations, or that there is limited genetic drift due to large effective population sizes. Intriguingly, our data also show that nautilus identified in other studies as N. belauensis, N. stenomphalus, or N. repertus are likely N. pompilius displaying a diversity of morphological characters, suggesting that there is significant phenotypic plasticity within N. pompilius

Widespread Presence of Human BOULE Homologs among Animals and Conservation of Their Ancient Reproductive Function

Sex-specific traits that lead to the production of dimorphic gametes, sperm in males and eggs in females, are fundamental for sexual reproduction and accordingly widespread among animals. Yet the sex-biased genes that underlie these sex-specific traits are under strong selective pressure, and as a result of adaptive evolution they often become divergent. Indeed out of hundreds of male or female fertility genes identified in diverse organisms, only a very small number of them are implicated specifically in reproduction in more than one lineage. Few genes have exhibited a sex-biased, reproductive-specific requirement beyond a given phylum, raising the question of whether any sex-specific gametogenesis factors could be conserved and whether gametogenesis might have evolved multiple times. Here we describe a metazoan origin of a conserved human reproductive protein, BOULE, and its prevalence from primitive basal metazoans to chordates. We found that BOULE homologs are present in the genomes of representative species of each of the major lineages of metazoans and exhibit reproductive-specific expression in all species examined, with a preponderance of male-biased expression. Examination of Boule evolution within insect and mammalian lineages revealed little evidence for accelerated evolution, unlike most reproductive genes. Instead, purifying selection was the major force behind Boule evolution. Furthermore, loss of function of mammalian Boule resulted in male-specific infertility and a global arrest of sperm development remarkably similar to the phenotype in an insect boule mutation. This work demonstrates the conservation of a reproductive protein throughout eumetazoa, its predominant testis-biased expression in diverse bilaterian species, and conservation of a male gametogenic requirement in mice. This shows an ancient gametogenesis requirement for Boule among Bilateria and supports a model of a common origin of spermatogenesis

Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

Abstract Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine-terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions

Global Diversity of Ascidiacea

The class Ascidiacea presents fundamental opportunities for research in the fields of development, evolution, ecology, natural products and more. This review provides a comprehensive overview of the current knowledge regarding the global biodiversity of the class Ascidiacea, focusing in their taxonomy, main regions of biodiversity, and distribution patterns. Based on analysis of the literature and the species registered in the online World Register of Marine Species, we assembled a list of 2815 described species. The highest number of species and families is found in the order Aplousobranchia. Didemnidae and Styelidae families have the highest number of species with more than 500 within each group. Sixty percent of described species are colonial. Species richness is highest in tropical regions, where colonial species predominate. In higher latitudes solitary species gradually contribute more to the total species richness. We emphasize the strong association between species richness and sampling efforts, and discuss the risks of invasive species. Our inventory is certainly incomplete as the ascidian fauna in many areas around the world is relatively poorly known, and many new species continue to be discovered and described each year

The Magnitude of Global Marine Species Diversity

Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are ∼226,000 eukaryotic marine species described. More species were described in the past decade (∼20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are ∼170,000 synonyms, that 58,000–72,000 species are collected but not yet described, and that 482,000–741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7–1.0 million marine species. Past rates of description of new species indicate there may be 0.5 ± 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century

Apoptosis as Potential Cause for Notochord Cell Loss in Molgula occulta

The evolution of the chordate body plan is still unresolved. Notochord evolution can be studied with two tunicates—the tailed M. oculata and the tailless M. occulta. The tailed M. oculata has 40 notochord cells that are converged and extended. The tailless M. occulta does not form a tail in their larval stage as it only has 20 notochord cells that have not converged or extended. A hypothesis for the loss of notochord cells in M. occulta is that the notochord cells are being destroyed by apoptosis (programmed cell death). In this study, preparations for studying programmed cell death (PCD) using two genes Programmed cell death 2 (PDCD2) and Programmed cell death interacting protein 6 (PCDIP6) were made for in situ hybridizations. A cell death assay and in situ hybridizations will be done in the future on a variety of developmental stages of both the tailed and tailless species to assess differential regulation of the PCD genes. These studies elucidate if differential regulation of PCD is potentially the cellular mechanism for the loss of a tail in M. occulta

Molecular Searching for Gill Slits in Echinoderms: Hox1 expression in Strongylocentrotus purpuratus

The formation of gill slits is a homologous trait in most deuterostomes (including hemichordates, tunicates, lancelets, and vertebrates), however is not present in the Phylum Echinodermata. Thus, there may be a difference in gene order or gene expression. The anterior Hox1 gene is responsible for gill slit formation (among other things), and is present in all deuterostomes, but perhaps in a different context. In this study, I performed phylogenetic analysis to determine how similar Hox1 was in echinoderms and hemichordates. My results show that they are divergent genes and therefore a laboratory experiment is possible. The next step would be to observe and compare Hox1 expression in both an echinoderm and a hemichordate

Wnt Pathway in Sand Dollar Dendraster excentricus Clones

Although regeneration has been described in many deuterstomes, little is known about the molecular pathways involved in regeneration and cloning in the echinoderms (Rychel and Swalla, 2008). Larval cloning occurs in the sand dollar Dendraster excentricus in the presence of predatory threat and food stress (Vaughn, 2007). The molecular pathways involved in the process of limb patterning in development and in cloning may be analogous (Mueoka and Bryant, 1982). The goal of this research project is to determine the role of Wnt expression in newly cloned larval Dendraster excentricus

Origin of the Gonad: A phylogenetic analysis of SoxB1 Tracing back human sex-determining gene Sry to an orthologue involved in echinoid metamorphosis

Until twenty-five years ago, the sex determining factor in humans had yet to be identified. The Sox family of transcription factors were identified after the human sex-determining gene SRY was sequenced and compared to other genomes (Bowles et al., 2000). SOX genes have been discovered across the Metazoans but with varying function. Looking at related invertebrate organisms can offer insights into the primary gene function and the evolution of the gene. Echinoderm life cycles begin with a larval, bilaterally symmetric shape which then transforms into a radially symmetric juvenile—a radical metamorphosis! The role of Sox transcription factors in the process of metamorphosis has been described in Strongylocentrotus purpuratus and in this project I will do research on metamorphosis with other echinoids to see if they are similar