Search results for " data"
showing 10 items of 7516 documents
The Chlamydomonas genome reveals the evolution of key animal and plant functions
2007
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the a…
Genome Economization in the Endosymbiont of the Wood Roach Cryptocercus punctulatus Due to Drastic Loss of Amino Acid Synthesis Capabilities
2011
Cockroaches (Blattaria: Dictyoptera) harbor the endosymbiont Blattabacterium sp. in their abdominal fat body. This endosymbiont is involved in nitrogen recycling and amino acid provision to its host. In this study, the genome of Blattabacterium sp. of Cryptocercus punctulatus (BCpu) was sequenced and compared with those of the symbionts of Blattella germanica and Periplaneta americana, BBge and BPam, respectively. The BCpu genome consists of a chromosome of 605.7 kb and a plasmid of 3.8 kb and is therefore approximately 31 kb smaller than the other two aforementioned genomes. The size reduction is due to the loss of 55 genes, 23 of which belong to biosynthetic pathways for amino acids. The …
The efficacy of whole human genome capture on ancient dental calculus and dentin
2019
Objectives Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. Results Total DNA from calculus exceeded that of dentin in all cases, and altho…
Identifying small pelagic Mediterranean fish schools from acoustic and environmental data using optimized artificial neural networks
2019
Abstract The Common Fisheries Policy of the European Union aims to exploit fish stocks at a level of Maximum Sustainable Yield by 2020 at the latest. At the Mediterranean level, the General Fisheries Commission for the Mediterranean (GFCM) has highlighted the importance of reversing the observed declining trend of fish stocks. In this complex context, it is important to obtain reliable biomass estimates to support scientifically sound advice for sustainable management of marine resources. This paper presents a machine learning methodology for the classification of pelagic species schools from acoustic and environmental data. In particular, the methodology was tuned for the recognition of an…
Moving Toward a Strategy for Addressing Climate Displacement of Marine Resources: A Proof-of-Concept
2020
Realistic predictions of climate change effects on natural resources are central to adaptation policies that try to reduce these impacts. However, most current forecasting approaches do not incorporate species-specific, process-based biological information, which limits their ability to inform actionable strategies. Mechanistic approaches, incorporating quantitative information on functional traits, can potentially predict species- and population-specific responses that result from the cumulative impacts of small-scale processes acting at the organismal level, and can be used to infer population-level dynamics and inform natural resources management. Here we present a proof-of-concept study…
Spatial variations in Ba/Cashell fingerprints of Glycymeris pilosa along the eastern Adriatic Sea
2020
Abstract The long living Glycymeris pilosa bivalve is an interesting target species for the sclerochronological research in the Mediterranean Sea. In this study, Ba/Cashell and Mg/Cashell variations were studied along the coast of the eastern Adriatic Sea. Specimens were collected alive by SCUBA and skin diving during several occasions in 2014, 2015 and 2016 from five sites including Pag, Pasman Channel, Cetina, Živogosce and Drace. Element-to-Cashell ratios were measured by LA-ICP-MS in line scan mode in three specimens of each site, ranging in age from 7 to 21. In addition, chemical analysis was conducted on three ontogenetically older specimens (68-97 years-old) from Drace. Mg/Cashell an…
Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space
2018
Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographicall…
Helminth communities of loggerhead turtles (Caretta caretta) from Central and Western Mediterranean Sea: the importance of host's ontogeny.
2009
We investigated the factors providing structure to the helminth communities of 182 loggerhead sea turtles, Caretta caretta, collected in 6 localities from Central and Western Mediterranean. Fifteen helminth taxa (10 digeneans, 4 nematodes and 1 acanthocephalan) were identified, of which 12 were specialist to marine turtles; very low numbers of immature individuals of 3 species typical from fish or cetaceans were also found. These observations confirm the hypothesis that phylogenetic factors restrict community composition to helminth species specific to marine turtles. There were significant community dissimilarities between turtles from different localities, the overall pattern being compat…
Circummed pine forest database: An electronic archive for mediterranean and submediterranean pine forest vegetation data
2019
Large thematic databases of vegetation plots are increasingly needed for vegetation studies and biodiversity research. In this paper, we present the CircumMed Pine Forest Database (GIVD ID: EU-00-026), which in November 2018, comprised records from 6317 pine-dominated vegetation plots (relevés) and associated vegetation types from 20 countries of the Mediterranean Basin, Near East and Crimea. These vegetation plots were collected through a detailed literature search for plots not previously included in the European Vegetation Archive (EVA), in order to fill geographic gaps in data coverage. The database comprises Mediterranean (including Oromediterranean) pine-forest vegetation plots from b…
Analysis of trematode parasite communities in fish eye lenses by pyrosequencing of naturally pooled DNA.
2011
Infections by multiple parasite species are common in nature and have important consequences for between species interactions and coevolutionary dynamics with the host populations. For example ecological and evolutionary factors underlying the structure of parasite communities determine the range of hosts a parasite can infect and set the basis for both evolution of host defences and parasite virulence as well as management of diseases. Studies investigating these factors have been facilitated in the recent past by genetic methods which surmount difficulties of traditional morphological taxonomy in identifying individual parasite species. Here we take a step further and present a novel meth…