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The tomato genome sequence provides insights into fleshy fruit evolution
Get PDFTomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.This is an open access article, available to all readers online, published under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/). The attached file is the published version of the article.NHM Repositor
The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758
Get PDFCopyright: © 2020 Mead D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.Copyright: © 2020 Mead D et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The attached file is the published pdf.NHM Repositor
Understanding the microscale spatial distribution and mineralogical residency of Re in pyrite: Examples from carbonate-hosted Zn-Pb ores and implications for pyrite Re-Os geochronology
Get PDFAccurate and precise geochronology using the Re-Os isotopic system in pyrite is an invaluable tool for developing and confirming genetic models of ore systems. However, as a bulk method, the results produced by pyrite Re-Os geochronology are commonly complex, and many imprecise isochrons exist in the literature. Using LA-ICPMS methods it is now possible to map and quantify Re distribution at the ppb level, allowing an unprecedented look into the Re-Os systematics of pyrite-bearing ore.
Two samples from the Lisheen Zn-Pb ore deposit in Ireland showing disparate Re-Os isotopic behavior were investigated. In-situ sulfur isotope measurements using SIMS, an analytical technique not previously attempted on the Irish deposits, was used to supplement the Re-Os dataset. A massive pyrite sample from the Main Zone produced a precise, low-scatter isochron (346.6 ± 3.0 Ma, MSWD = 1.6). The Re distribution in this sample is relatively homogeneous, with the Re budget dominated by pyrite containing 1–5 ppb Re, but the δ34S varies significantly from −45.2‰ to 8.2‰. A second, more paragenetically complex, sample from the Derryville Zone produced a younger age with high scatter (322 ± 11 Ma, MSWD = 206) and this also displays a large variation in δ34S (−53‰ to +4‰). The cores of grains of main-stage iron sulfide are depleted in trace elements and show low Re abundances (<10 ppb) but have been altered in an irregular fashion leading to Re-enriched domains that exceed 100 ppb. Additionally, micron-scale molybdenite crystals, found in close association with altered sulfides, contain Re at levels that locally exceed 10 ppm. The highly scattered (MSWD = 206) and younger age (322 Ma), produced by the Derryville Zone sample are interpreted to result from mixing of different generations of sulfide, potentially involving fluids associated with Variscan deformation (<310 Ma). Therefore, the Re-Os data produced from the Derryville Zone sample does not reflect the timing of iron sulfide mineralization, even though a relatively precise age was obtained.
A second Re-Os dataset from Zn-Pb mineralization at Hawker Creek, Nunavut, Canada was produced from massive pyrite that displays low Re concentrations (<1 ppb). However, on grain boundaries and in fractures, silicate-rich material contains Re at levels that can locally exceed 500 ppb. Analyses of fracture-free pyrite produced by bulk separation using magnetic separation yielded the oldest model age (1083 Ma), whereas mineral separates containing the highest fracture density produced the youngest age (413 Ma).
In general, therefore, the complexities of pyrite Re-Os geochronology can result from impurities in mineral separates. Attempts to eliminate impurities through different mineral separation techniques (e.g. crushing, heavy liquid separation, magnetic separation, acid leaching) are frequently only partially successful and therefore full characterization of any resulting mineral separates is extremely important. We conclude that LA-ICPMS mapping of Re and Mo distributions is essential for the identification of such impurities. Although other trace element LA-ICPMS maps, in-situ sulfur isotope measurements, and petrographic evidence were of limited use in assessing the Re budget of a sample, they are invaluable in linking the documented Re distribution obtained through LA-ICPMS to Re-Os geochronological results.© 2019 Elsevier B.V. All rights reserved. The attached document is the author(’s’) final accepted/submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it.NHM Repositor
From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean
Get PDFMarine bacteria regulate fluxes of matter and energy essential for pelagic and
benthic organisms and may also be involved in the formation and maintenance of
commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields
is predicted to have substantial effects on biodiversity and physicochemical conditions
in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea
sediments and associated polymetallic nodules has received relatively little attention.
We examined bacterial communities using high-throughput sequencing of bacterial 16S
rRNA gene fragments from samples collected in the water column, sediment, and
polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern
Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S
rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae
(Alphaproteobacteria) had higher relative abundances in the nodule and sediment
habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had
higher relative abundance in nodule samples, but were less abundant in sediment
and water column samples. Bacterial communities in sediments and associated with
nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water
column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial
OTUs clustering among Prochlorococcus and Synechococcus were detected in both
sediments and nodules, with greater representation among nodule samples. Such results
suggest that vertical export of typically abundant photic-zone microbes may be an
important process in delivery of water column microorganisms to abyssal habitats,
potentially influencing the structure and function of communities in polymetallic nodule
fields.Copyright © 2017 Lindh, Maillot, Shulse, Gooday, Amon, Smith and Church. This
is an open-access article distributed under the terms of the Creative Commons
Attribution License (CC BY). The use, distribution or reproduction in other forums
is permitted, provided the original author(s) or licensor are credited and that the
original publication in this journal is cited, in accordance with accepted academic
practice. No use, distribution or reproduction is permitted which does not comply
with these terms.NHM Repositor
Observations of organic falls from the abyssal Clarion-Clipperton Zone in the tropical eastern Pacific Ocean
No full textOrganic falls can form nutrient-rich, ephemeral hotspots of productivity and biodiversity at the deep-sea floor, especially in food-poor abyssal plains. We report here the first wood falls and second carcass fall recorded from the Clarion-Clipperton Zone in the tropical eastern Pacific Ocean, an area that could be mined for polymetallic nodules in the future. A small cetacean fall in the mobile-scavenger stage likely recently arrived on the seafloor was observed, whereas most of the wood falls were highly degraded. There were multiple species in attendance at the wood falls including organic-fall specialists such as Xylophagaidae molluscs. Many of the taxa attending the carcass fall were known mobile scavengers that regularly attend bait parcels in the Pacific Ocean. These results further confirm that wood falls can occur at large distances (>1450 km) from major land masses, providing an adequate supply of wood to the abyssal seafloor for colonization by wood-boring molluscs and associated fauna. Organic falls may be regionally abundant and are likely to influence species and habitat diversity in the abyssal areas of the Clarion-Clipperton Zone.The attached is the author's accepted version of the paper. If you wish the cite from this paper your are advised to consult the published pdf: https://doi.org/10.1007/s12526-016-0572-4NHM Repositor
Successful Blue Economy Examples With an Emphasis on International Perspectives
Get PDFCareful definition and illustrative case studies are fundamental work in developing a Blue Economy. As blue research expands with the world increasingly understanding its importance, policy makers and research institutions worldwide concerned with ocean and coastal regions are demanding further and improved analysis of the Blue Economy. Particularly, in terms of the management connotation, data access, monitoring, and product development, countries are making decisions according to their own needs. As a consequence of this lack of consensus, further dialogue including this cases analysis of the blue economy is even more necessary. This paper consists of four chapters: (I) Understanding the concept of Blue Economy, (II) Defining Blue economy theoretical cases, (III) Introducing Blue economy application cases and (IV) Providing an outlook for the future. Chapters (II) and (III) summarizes all the case studies into nine aspects, each aiming to represent different aspects of the blue economy. This paper is a result of knowledge and experience collected from across the global ocean observing community, and is only made possible with encouragement, support and help of all members. Despite the blue economy being a relatively new concept, we have demonstrated our promising exploration in a number of areas. We put forward proposals for the development of the blue economy, including shouldering global responsibilities to protect marine ecological environment, strengthening international communication and sharing development achievements, and promoting the establishment of global blue partnerships. However, there is clearly much room for further development in terms of the scope and depth of our collective understanding and analysis.This is an open-access
article distributed under the terms of the Creative Commons Attribution License
(CC BY). The use, distribution or reproduction in other forums is permitted, provided
the original author(s) and the copyright owner(s) are credited and that the original
publication in this journal is cited, in accordance with accepted academic practice. No
use, distribution or reproduction is permitted which does not comply with these terms.NHM Repositor
Deep-Sea Debris in the Central and Western Pacific Ocean
Get PDFMarine debris is a growing problem in the world’s deep ocean. The naturally slow biological and chemical processes operating at depth, coupled with the types of materials that are used commercially, suggest that debris is likely to persist in the deep ocean for long periods of time, ranging from hundreds to thousands of years. However, the realized scale of marine debris accumulation in the deep ocean is unknown due to the logistical, technological, and financial constraints related to deep-ocean exploration. Coordinated deep-water exploration from 2015 to 2017 enabled new insights into the status of deep-sea marine debris throughout the central and western Pacific Basin via ROV expeditions conducted onboard NOAA Ship Okeanos Explorer and RV Falkor. These expeditions included sites in United States protected areas and monuments, other Exclusive Economic Zones, international protected areas, and areas beyond national jurisdiction. Metal, glass, plastic, rubber, cloth, fishing gear, and other marine debris were encountered during 17.5% of the 188 dives from 150 to 6,000 m depth. Correlations were observed between deep-sea debris densities and depth, geological features, and distance from human-settled land. The highest densities occurred off American Samoa and the main Hawaiian Islands. Debris, mostly consisting of fishing gear and plastic, were also observed in most of the large-scale marine protected areas, adding to the growing body of evidence that even deep, remote areas of the ocean are not immune from human impacts. Interactions with and impacts on biological communities were noted, though further study is required to understand the full extent of these impacts. We also discuss potential sources and long-term implications of this debris.This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.NHM Repositor
A morphological revision of Keraterpeton, the earliest horned nectridean from the Pennsylvanian of England and Ireland.
No full textThe aquatic diplocaulid nectridean Keraterpeton galvani is the commonest taxon
represented in the Jarrow Coal assemblage from Kilkenny, Ireland. The Jarrow locality has
yielded the earliest known Carboniferous coal-swamp fauna in the fossil record and is, therefore,
of importance in understanding the history and diversity of the diplocaulid clade. The morphology
of Keraterpeton is described in detail with emphasis on newly observed anatomical features. A
reconstruction of the palate includes the presence of interpterygoid vacuities and new morphological
details of the pterygoid, parasphenoid and basicranial region. The hyoid apparatus comprising an
ossified basibranchial element has not been reported previously in nectrideans. The structure of the
scapulocoracoid and primitive nature of the humerus is described and the presence of a five-digit
manus confirmed. Previously unrecognised accessory dermal ossifications are present in the pectoral
girdle. Keraterpeton longtoni from the Bolsovian in Staffordshire, England, is also described
and newly figured. The primitive condition in diplocaulids is defined on the basis of the earliest
occurrence at Jarrow and discussed in relation to functional morphology and mode of life. The
evolution of the diplocaulid clade is assessed in relation to the revised diagnoses that define the
primitive condition in Keraterpeton.© The Royal Society of Edinburgh 2019
The attached document is the author(’s’) final accepted/submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it.NHM Repositor
The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis
Get PDFBackground
Acoels are simply organized unsegmented worms, lacking hindgut and anus. Several publications over recent years challenge the long-held view that acoels are early offshoots of the flatworms. Instead a basal position as sister group to all other bilaterian animals was suggested, mainly based on molecular evidence. This led to the view that features of acoels might reflect those of the last common ancestor of Bilateria, and resulted in several evo-devo studies trying to interpret bilaterian evolution using acoels as a proxy model for the "Urbilateria".
Results
We describe the first complete mitochondrial genome sequence of a member of the Acoela, Symsagittifera roscoffensis. Gene content and circular organization of the mitochondrial genome does not significantly differ from other bilaterian animals. However, gene order shows no similarity to any other mitochondrial genome within the Metazoa. Phylogenetic analyses of concatenated alignments of amino acid sequences from protein coding genes support a position of Acoela and Nemertodermatida as the sister group to all other Bilateria. Our data provided no support for a sister group relationship between Xenoturbellida and Acoela or Acoelomorpha. The phylogenetic position of Xenoturbella bocki as sister group to or part of the deuterostomes was also unstable.
Conclusions
Our phylogenetic analysis supports the view that acoels and nemertodermatids are the earliest divergent extant lineage of Bilateria. As such they remain a valid source for seeking primitive characters present in the last common ancestor of Bilateria. Gene order of mitochondrial genomes seems to be very variable among Acoela and Nemertodermatida and the groundplan for the metazoan mitochondrial genome remains elusive. More data are needed to interpret mitochondrial genome evolution at the base of Bilateria.© 2010 Mwinyi et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.NHM Repositor
On the front line of modern data-management and Open Access publishing: Two years of PhytoKeys – the fastest growing journal in plant systematics
Get PDFPhytoKeys was launched on the 1st of November 2010 as a novel, peer-reviewed, openaccess outlet for plant biodiversity research (Penev et al. 2010a). The journal quickly
gained the support of the international botanical community and since its launch continues to grow in reputation and volume.This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published pdf.NHM Repositor