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  • 1
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    Comparative population genomics in animals uncovers the determinants of genetic diversity (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-21
    Description: Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Romiguier, J -- Gayral, P -- Ballenghien, M -- Bernard, A -- Cahais, V -- Chenuil, A -- Chiari, Y -- Dernat, R -- Duret, L -- Faivre, N -- Loire, E -- Lourenco, J M -- Nabholz, B -- Roux, C -- Tsagkogeorga, G -- Weber, A A-T -- Weinert, L A -- Belkhir, K -- Bierne, N -- Glemin, S -- Galtier, N -- England -- Nature. 2014 Nov 13;515(7526):261-3. doi: 10.1038/nature13685. Epub 2014 Aug 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] Department of Ecology and Evolution, Biophore, University of Lausanne, 1015 Lausanne, Switzerland. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] UMR 7261, Institut de Recherches sur la Biologie de l'Insecte, Centre national de la recherche scientifique, Universite Francois-Rabelais, 37200 Tours, France. ; UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France. ; Aix-Marseille Universite, Institut Mediterraneen de Biodiversite et d'Ecologie marine et continentale (IMBE) - CNRS - IRD - UAPV, 13007 Marseille, France. ; Department of Biology, University of South Alabama, Mobile, Alabama 36688-0002, USA. ; UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, Universite Lyon 1, CNRS, 69622 Lyon, France. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] The School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. ; 1] UMR 5554, Institute of Evolutionary Sciences, University Montpellier 2, Centre national de la recherche scientifique, Place E. Bataillon, 34095 Montpellier, France [2] Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25141177" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ecology ; *Evolution, Molecular ; Genetic Variation/*genetics ; *Genetics, Population ; Genome/*genetics ; *Genomics ; *Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Seabed classification for trawlability determined with a multibeam echo sounder on Snakehead Bank in the Gulf of Alaska (2021)
    In:  weber@ccom.unh.edu | http://aquaticcommons.org/id/eprint/14495 | 403 | 2014-02-13 04:21:26 | 14495 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-06-26
    Description: Rockfishes (Sebastes spp.) tend to aggregate near rocky, cobble, or generally rugged areas that are difficult to survey with bottom trawls, and evidence indicates that assemblages of rockfish species may differ between areas accessible to trawling and those areas that are not. Consequently, it is important to determine grounds that are trawlable or untrawlable so that the areas where trawl survey results should be applied are accurately identified. To this end, we used multibeam echosounder data to generate metrics that describe the seafloor: backscatter strength at normal and oblique incidence angles, the variation of the angle-dependent backscatter strength within 10° of normal incidence, the scintillation of the acoustic intensity scattered from the seafloor, and the seafloor rugosity. We used these metrics to develop a binary classification scheme to estimate where the seafloor is expected to be trawlable. The multibeam echosounder data were verified through analyses of video and still images collected with a stereo drop camera and a remotely operated vehicle in a study at Snakehead Bank, ~100 km south of Kodiak Island in the Gulf of Alaska. Comparisons of different combinations of metrics derived from the multibeam data indicated that the oblique-incidence backscatter strength was the most accurate estimator of trawlability at Snakehead Bank and that the addition of other metrics provided only marginal improvements. If successful on a wider scale in the Gulf ofAlaska, this acoustic remote-sensing technique, or a similar one, could help improve the accuracy of rockfish stock assessments.
    Keywords: Biology ; Ecology ; Fisheries
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 68-77
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  • 3
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    Effect of environmental conditions on the distribution of Pacific mackerel (Scomber japonicus) larvae in the California Current system (2021)
    In:  http://aquaticcommons.org/id/eprint/8692 | 403 | 2012-06-07 14:48:59 | 8692 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-06-25
    Description: We modeled the probability of capturing Pacif ic mackerel(Scomber japonicus) larvae as a function of environmental variables for the Southern California Bight (SCB) most years from 1951 through 2008 and Mexican waters offshore ofBaja California from 1951 through 1984. The model exhibited acceptable fit, as indicated by the area under a receiver-operating-characteristic curve of 0.80 but was inconsistentwith the zero catches that occurred frequently in the 2000s. Two types of spawners overlapped spatially within the survey area: those that exhibited peak spawning duringApril in the SCB at about 15.5°C and a smaller group that exhibited peak spawning in August near Punta Eugenia, Mexico, at 20°C or greater. The SCB generally had greater zooplankton than Mexican waters but less appropriate (lower) geostrophic f lows. Mexican waters generallyexhibited greater predicted habitat quality than the SCB in cold years. Predicted quality of the habitat in the SCB was greater from the 1980s to 2008 than in the earlier years of the survey primarily because temperatures and geostrophic flows were more appropriate for larvae. However, stocksize the previous year had a larger effect on predictions than any environmental variable, indicating that larval Pacific mackerel did not fully occupy the suitable habitat during most years.
    Keywords: Biology ; Ecology ; Fisheries
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 85-97
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  • 4
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    Evaluation of rockfish abundance in untrawlable habitat: combining acoustic and complementary sampling tools (2021)
    In:  http://aquaticcommons.org/id/eprint/8966 | 403 | 2012-08-03 19:12:20 | 8966 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-06-29
    Description: Rockfishes (Sebastes spp.) are an important component ofNorth Pacific marine ecosystems and commercial fisheries. Because the rocky, high-relief substrate that rockfishes often inhabit is inaccessible to standard survey trawls, population abundance assessments for many rockfish species are difficult. As part of a large study to classify substrate and compare complementary sampling tools, we investigated the feasibility of using an acoustic survey in conjunction with a lowered stereo-video camera, a remotely operated vehicle, and a modified bottom trawl to estimate rockfish biomass in untrawlable habitat. The SnakeheadBank south of Kodiak Island, Alaska, was surveyed repeatedly over 4 days and nights. Dusky rockfish (S. variabilis), northern rockfish (S. polyspinis), and harlequin rockfish (S. variegatus) were the most abundantspecies observed on the bank. Backscatter attributed to rockfish were collected primarily near the seafloor at a mean height off the bottom of 1.5 m. Total rockfish backscatter and the height of backscatter off the bottomdid not differ among survey passes or between night and day. Biomass estimates for the 41 square nautical-milearea surveyed on this small, predominantly untrawlable bank were 2350 metric tons (t) of dusky rockfish, 331 t of northern rockfish, and 137 t of harlequin rockfish. These biomass estimates are 5–60 times the densityestimated for these rockfish species by a regularly conducted bottom trawl survey covering the bank and the surrounding shelf. This finding shows that bottom trawl surveys can underestimate the abundance of rockfishesin untrawlable areas and, therefore, may underestimate overall population abundance for these species.
    Keywords: Biology ; Ecology ; Fisheries
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 332-343
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  • 5
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    Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System (2021)
    Frontiers Media
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., Armenteros, M., Soule, M. K., Longnecker, K., Kujawinski, E. B., & Apprill, A. Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System. Frontiers in Marine Science, 7, (2020): 582161, https://doi.org/10.3389/fmars.2020.582161.
    Description: Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina (JR), Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used liquid chromatography mass spectrometry (LC-MS) to quantify specific known metabolites of interest (targeted metabolomics approach) and to survey trends in metabolite feature composition (untargeted metabolomics approach) from surface and reef depth (6 – 14 m) seawater overlying nine forereef sites in JR. We found that untargeted metabolite feature composition was surprisingly similar between reef depth and surface seawater, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within JR. Additionally, we quantified 32 of 53 detected metabolites using the targeted approach, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and xanthosine, displayed interesting trends by depth. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. Xanthosine concentrations were significantly higher in surface reef seawater. 5′-methylthioadenosine (MTA) concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.
    Description: This work was supported by the Dalio Foundation (now “OceanX”) and the National Science Foundation (OCE-1736288) (award to Amy Apprill). The mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility with instrumentation funded by the National Science Foundation (grant OCE-1058448 to EK and MK) and the Simons Foundation (Award ID #509042, EK). Lastly, a portion of the publication fees was supported by the Massachusetts Institute of Technology (MIT) Open Access Article Publication Subvention fund from MIT Libraries.
    Keywords: Metabolomics ; Coral reefs ; Microorganisms ; Ecology ; DOM cycling
    Repository Name: Woods Hole Open Access Server
    Type: Article
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