Complete mitochondrial genomes of three reef forming Acropora corals (Acroporidae, Scleractinia) from Chagos Archipelago, Indian Ocean

We present the first mitochondrial genomes from Chagos Archipelago, Indian Ocean, of three putative species of reef forming Acropora (Acropora aff. tenuis, Acropora aff. cytherea and Acropora aff. orbicularis). The circular genome consists respectively of 18,334 bp, 18,353 bp and 18,584 bp. All mitochondrial genomes recovered comprise 13 protein-coding genes, two transfer RNA genes and two ribosomal RNA genes, with an overall GC content ranging from 37.9% to 38.0%. These new genomic data contribute to our increased understanding of genus Acropora and its species boundaries, ultimately aiding species monitoring and conservation efforts

Complete mitochondrial genome of the geniculate calcified red alga, Corallina officinalis (Corallinales, Rhodophyta)

peerreview_statement: The publishing and review policy for this title is described in its Aims & Scope. aims_and_scope_url: http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=tmdn20© 2016 The Author(s). Published by Taylor & Francis. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published pd

Evolution of mitochondrial and nuclear genomes in Pennatulacea

We examine the phylogeny of sea pens using sequences of whole mitochondrial genomes and the nuclear ribosomal cluster generated through low coverage Illumina sequencing. Taxon sampling includes 30 species in 19 genera representing 13 families. Ancestral state reconstruction shows that most sea pen mitochondrial genomes have the ancestral gene order, and that Pennatulacea with diverse gene orders are found in a single clade. The monophyly of Pennatulidae and Protoptilidae are rejected by both the mitochondrial and nuclear dataset, while the mitochondrial dataset further rejects monophyly of Virgulariidae, and the nuclear dataset rejects monophyly of Kophobelemnidae. We show discordance between nuclear ribosomal gene cluster phylogenies and whole mitochondrial genome phylogenies and highlight key Pennatulacea taxa that could be included in cnidarian genome-wide studies to better resolve the sea pen tree of life. We further illustrate how well frequently sequenced markers capture the overall diversity of the mitochondrial genome and the nuclear ribosomal genes in sea pens

Phylogenetics and Mitogenome Organisation in Black Corals (Anthozoa: Hexacorallia: Antipatharia): An Order-Wide Survey Inferred From Complete Mitochondrial Genomes

Black corals (Anthozoa: Antipatharia) are an ecologically and culturally important group of deep-sea cnidarians. However, as the majority of species inhabit depths >50 m, they are relatively understudied. The inaccessibility of well-preserved tissue for species of interest has limited the scope of molecular analysis, and as a result only a small number of antipatharian mitochondrial genomes have been published. Using next generation sequencing, 18 complete and five partial antipatharian mitochondrial genomes were assembled, increasing the number of complete mitochondrial genomes to 22. This includes species from six antipatharian families, four of which were previously unrepresented, enabling the first family-level, full mitochondrial gene analysis over the whole order. The circular mitogenomes ranged in size from 17,681 to 21,669 bp with the large range in size due to the addition of an intron in COX1 in some species and size variation of intergenic regions. All mitogenomes contained the genes standard to all hexacoral mitogenomes (13 protein coding genes, two rRNAs and two tRNAs). The only difference in gene content is the presence of the COX1 intron in five families. The most variable mitochondrial gene is ND4 which may have implications for future barcoding studies. Phylogenetic analysis confirms that Leiopathidae is sister to all other families. Families Antipathidae, Cladopathidae and Schizopathidae are polyphyletic, supporting previous studies that call for a taxonomic revision

Environmental drivers and the distribution of cold-water corals in the global ocean

Species distribution models (SDMs) are useful tools for describing and predicting the distribution of marine species in data-limited environments. Outputs from SDMs have been used to identify areas for spatial management, analyzing trawl closures, quantitatively measuring the risk of bottom trawling, and evaluating protected areas for improving conservation and management. Cold-water corals are globally distributed habitat-forming organisms that are vulnerable to anthropogenic impacts and climate change, but data deficiency remains an ongoing issue for the effective spatial management of these important ecosystem engineers. In this study, we constructed 11 environmental seabed variables at 500 m resolution based on the latest multi-depth global datasets and high-resolution bathymetry. An ensemble species distribution modeling method was used to predict the global habitat suitability for 10 widespread cold-water coral species, namely, 6 Scleractinian framework-forming species and 4 large gorgonian species. Temperature, depth, salinity, terrain ruggedness index, carbonate saturation state, and chlorophyll were the most important factors in determining the global distributions of these species. The Scleractinian Madrepora oculata showed the widest niche breadth, while most other species demonstrated somewhat limited niche breadth. The shallowest study species, Oculina varicosa, had the most distinctive niche of the group. The model outputs from this study represent the highest-resolution global predictions for these species to date and are valuable in aiding the management, conservation, and continued research into cold-water coral species

Genetic structure of the tall sea pen Funiculina quadrangularis in NW Scottish sea lochs

The tall sea pen Funiculina quadrangularis has a patchy distribution around the UK, being found in sheltered waters below 20 m depth on the northwest coast of Scotland and Ireland. The limited distribution and sensitivity to bottom fishing activities make F. quadrangularis vulnerable to reduction in population numbers that may lead to genetic isolation and reduced diversity. Because of this vulnerability and low resilience to physical disturbance, the tall sea pen is recognised as a Species of Principle Importance under the Natural Environment and Rural Communities Act, 2006, UK. (http://www.legislation.gov.uk/ukpga/2006/16/contents) and is also on the Biodiversity Action Plan list of Priority Species for the UK. In the Mediterranean it is recognised as a sensitive and essential fish habitat because it forms habitat for several commercially important crustaceans. The aim of this study was to understand the current state of the genetic structure and gene flow of F. quadrangularis in areas of NW Scotland. We developed 10 microsatellite markers and used them to genotype 176 samples from four populations. Overall, our results suggest that there is high genetic diversity and high gene flow between colonies of F. quadrangularis in and among locations in Loch Linnhe and Loch Duich. As a result of the high rates of gene flow, genetic differentiation between sites was low. This may provide resilience to human impacts if distant populations have a high connectivity. However, care must be taken, as small but significant isolation by distance was found between the most geographically distant sites and only a small part of the species range was examined in this study. The genetic tools developed here will provide a foundation for wider studies of this vulnerable species

Seafloor habitats across geological boundaries in Disko Bay, central West Greenland

In this paper we describe seafloor terrain of nearly the entire Disko Bay region and provide scientific baseline information about surface geology and sedimentary environments that can support the seafloor management plan in Greenland. Our study utilized multiple datasets of multibeam bathymetry and backscatter, seismic profiles and ground-truthing consisting of video footage from drop camera and benthic video sled, as well as sediment samples from grab and corers. Our results revealed that the key geological units in Disko Bay characterize the scale of geomorphic features, which in turn affects the distribution and complexity of habitat zones. The NE sub-region is underlain by Cretaceous sandstone and characterized by large-scale landforms, mainly vast flat areas draped by glacial lineations, bedrock ridges and pockmark fields. This setting promotes less topographically complex habitats, i.e. coarse plain, muddy/sandy plain with dropstones, and muddy plain. The SW sub-region is characterized by Precambrian Gneiss and Paleoproterozoic metasedimentary rocks with complex system of small-scale geomorphic features, such as cross-cutting channels. This results in topographically complex habitats in the area, such as rocky bank, coarse rugged terrain, and rocky slopes. Two distinctive habitat areas, associated with potential gas seeps, i) southern pockmark field and ii) western zoanthid-sponge wall, were discovered at the geological boundary separating the two sub-regions. Our study highlights the importance of seafloor habitat mapping and analyses by providing fundamental geophysical knowledge necessary to comply with long-term sustainable use of marine resources in Greenland

A comparison of multispectral aerial and satellite imagery for mapping intertidal seaweed communities

Habitat‐forming seaweeds are vital components of marine ecosystems, supporting immense diversity and providing ecosystem services. Reports of major changes in the distribution and abundance of large brown seaweeds in the north‐east Atlantic are an increasing cause for concern, but a lack of consistent monitoring over time is a key impediment in obtaining reliable evidence of change. There is an urgent need to recognize change rapidly and efficiently in marine communities, which are increasingly affected by pressures of human population growth, climate change, and ocean acidification. Here, the potential for remote monitoring of seaweed habitats is investigated using freely available, high‐resolution aerial and satellite imagery. Three sources of imagery were used: (i) Channel Coastal Observatory (CCO) aerial imagery; (ii) aerial images from the Bing webmap server; and (iii) RapidEye multispectral satellite data. The study area, the Thanet Coast, is an area of chalk outcrop in south‐east England of high conservation status, and includes three Marine Conservation Zones. Eight habitat classes, including brown, red, and green algal zones, were recognized based on ground‐truthing surveys. A multi‐class classification model was developed to predict habitat classes based on the chromatic signature derived from the aerial images. The model based on the high‐resolution CCO imagery gave the best outcome (with a kappa value of 0.89). Comparing predictions for images in 2001 and 2013 revealed habitat changes, but it is unclear as to what extent these are natural variability or real trends. This study demonstrates the potential value for long‐term monitoring with remote‐sensing data. Repeated, standardized coastal aerial imaging surveys, such as those performed by CCO, permit the rapid assessment and re‐assessment of habitat extent and change. This is of value to the conservation management of protected areas, particularly those defined by the presence or extent of specific habitats

Community composition of epibenthic megafauna on the West Greenland Shelf

Epibenthic organisms are a critical component of the marine environment, functioning as ecosystem engineers, habitat and food for other organisms. Our knowledge of the diversity, complexity and sensitivities of these habitats is limited, particularly at higher latitudes and greater depths. The West Coast of Greenland is the site of a commercially important shrimp trawl fishery, but there are few published records describing the benthic community structure of the region. Here we report results from benthic camera surveys conducted at 119 sites, over 3 years, spanning 1400 km of the West Greenland continental shelf (61–725 m depth). A total of 29 classes of epibenthic taxa were identified from the images. There are significant differences of composition and diversity in sites with hard and soft substrate. Hard-substrate communities are relatively diverse with higher abundances and are characterised by sessile, attached groups such as Hydrozoa, Anthozoa, Bryozoa and Porifera. Soft-sediment sites are less diverse and dominated by Polychaeta and have specialist Malacostraca such as the commercially exploited shrimp, Pandalus borealis. Distribution patterns and variation in epibenthic megafauna are related to substrate and the environmental parameters depth, temperature and current speed. This study represents the first quantitative characterisation of epibenthic megafaunal assemblages on the West Greenland continental shelf. These data constitute an important baseline, albeit in a region heavily impacted by trawl fisheries, and demonstrate the utility of benthic photography for examining and monitoring seabed diversity and change