Chapter 11: Vulnerability of benthic invertebrates of the Great Barrier Reef to climate change

This chapter deals with benthic invertebrates inhabiting the extensive inter-reef soft bottom habitats and those occurring on the reef, excluding corals. For the remainder of the chapter, the term ‘benthic invertebrate’ refers to all invertebrates excluding corals. An assessment of the impacts of climate change on non-coral benthic invertebrates poses particular challenges: i) benthic invertebrates include an extraordinary diversity of marine organisms, including many microscopic, infaunal, boring or ephemeral species that can be difficult to sample and are poorly known taxonomically; ii) benthic invertebrates employ a diversity of reproductive strategies, broadly including planktotrophy (development through feeding larvae), lecithotrophy (development through non-feeding larvae) and direct development (release of post-metamorphic juveniles), as well as asexual reproduction, making broad generalisations of dispersal capabilities difficult; iii) factors determining species distributions are poorly known for most species; iv) benthic invertebrates exhibit a tremendous variety of lifestyles and forms, including colonial, sedentary and errant species; v) many species include either a pelagic larval or adult stage, so effects of climate change may vary during their lives (see McKinnon et al. chapter 6 for comments on planktonic forms); and, vi) research on the biogeography of benthic invertebrates on the Great Barrier Reef (GBR) is strongly biased towards commercial or destructive species.This is Chapter 11 of Climate change and the Great Barrier Reef: a vulnerability assessment. The entire book can be found at http://hdl.handle.net/11017/13

CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida)

DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance.Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates.We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Background: Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. Results: We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. Conclusions: Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications

Bearing the wrong identity: A case study of an Indo-Pacific common shallow water sponge of the genus Neopetrosia (Haplosclerida; Petrosiidae).

Sponges of the order Haplosclerida are often abundant and characteristic components of Indo-Pacific reefs, but are often misidentified, because of the lack of clear distinctive morphological characters. Neopetrosia exigua is an example of a haplosclerid sponge that is very common in Indonesian shallow coral reef environments but bears several different names. In the present study we investigated type material of several Indo-Pacific Neopetrosia species with a similar morphology and examined freshly collected specimen materials including specimens that are deposited at several institutions. In addition, we used molecular phylogenetic methods for assisting the morphological examinations. We conclude that the true identity of Neopetrosia exigua should be Neopetrosia chaliniformis. Likewise, N. exigua and N. pacifica should be considered as junior synonyms of N. chaliniformis. In conclusion, we advocate that molecular barcoding could significantly aid on sponge species' delimitation that possess limited morphological characters.Conservation Biolog

Expanded sampling of New Zealand glass sponges (Porifera: Hexactinellida) provides new insights into biodiversity, chemodiversity, and phylogeny of the class

Glass sponges (Hexactinellida) constitute important parts of ecosystems on the deep-sea floor worldwide. However, they are still an understudied group in terms of their diversity and systematics. Here, we report on new specimens collected during RV Sonne expedition SO254 to the New Zealand region, which has recently emerged as a biodiversity hotspot for hexactinellids. Examination of the material revealed several species new to science or so far unknown from this area. While formal taxonomic descriptions of a fraction of these were published earlier, we here briefly report on the morphology of the remaining new species and use the collection to greatly expand the molecular phylogeny of the group as established with ribosomal DNA and cytochrome oxidase subunit I markers. In addition, we provide a chemical fingerprinting analysis on a subset of the specimens to investigate if the metabolome of glass sponges contains phylogenetic signal that could be used to supplement morphological and DNA-based approaches

Comparative genomics and the nature of placozoan species.

Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites

Molecular Phylogenetic Evaluation of Classification and Scenarios of Character Evolution in Calcareous Sponges (Porifera, Class Calcarea)

Calcareous sponges (Phylum Porifera, Class Calcarea) are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU) rDNA and the almost complete large subunit (LSU) rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae) and Leucettidae and between Leucascandra (Jenkinidae) and Sycon carteri (Sycettidae). According to our results, the taxonomy of Calcarea is in desperate need of a thorough revision, which cannot be achieved by considering morphology alone or relying on a taxon sampling based on the current classification below the subclass level

Rare and common genetic determinants of metabolic individuality and their effects on human health

Garrod’s concept of ‘chemical individuality’ has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant–metabolite associations (P < 1.25 × 10−11) within 330 genomic regions, with rare variants (minor allele frequency ≤ 1%) explaining 9.4% of associations. Jointly modeling metabolites in each region, we identified 423 regional, co-regulated, variant–metabolite clusters called genetically influenced metabotypes. We assigned causal genes for 62.4% of these genetically influenced metabotypes, providing new insights into fundamental metabolite physiology and clinical relevance, including metabolite-guided discovery of potential adverse drug effects (DPYD and SRD5A2). We show strong enrichment of inborn errors of metabolism-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of the inborn errors of metabolism. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential etiological relationships

Global Diversity of Sponges (Porifera)

With the completion of a single unified classification, the Systema Porifera (SP) and subsequent development of an online species database, the World Porifera Database (WPD), we are now equipped to provide a first comprehensive picture of the global biodiversity of the Porifera. An introductory overview of the four classes of the Porifera is followed by a description of the structure of our main source of data for this paper, the WPD. From this we extracted numbers of all ‘known’ sponges to date: the number of valid Recent sponges is established at 8,553, with the vast majority, 83%, belonging to the class Demospongiae. We also mapped for the first time the species richness of a comprehensive set of marine ecoregions of the world, data also extracted from the WPD. Perhaps not surprisingly, these distributions appear to show a strong bias towards collection and taxonomy efforts. Only when species richness is accumulated into large marine realms does a pattern emerge that is also recognized in many other marine animal groups: high numbers in tropical regions, lesser numbers in the colder parts of the world oceans. Preliminary similarity analysis of a matrix of species and marine ecoregions extracted from the WPD failed to yield a consistent hierarchical pattern of ecoregions into marine provinces. Global sponge diversity information is mostly generated in regional projects and resources: results obtained demonstrate that regional approaches to analytical biogeography are at present more likely to achieve insights into the biogeographic history of sponges than a global perspective, which appears currently too ambitious. We also review information on invasive sponges that might well have some influence on distribution patterns of the future