Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Carbonate "clumped" isotope signatures in aragonitic scleractinian and calcitic gorgonian deep-sea corals

Deep-sea corals are a potentially valuable archive of the temperature and ocean chemistry of intermediate and deep waters. Living in near-constant temperature, salinity, and pH and having amongst the slowest calcification rates observed in carbonate-precipitating biological organisms, deep-sea corals can provide valuable constraints on processes driving mineral equilibrium and disequilibrium isotope signatures. Here we report new data to further develop "clumped" isotopes as a paleothermometer in deep-sea corals as well as to investigate mineral-specific, taxon-specific, and growth-rate-related effects. Carbonate clumped isotope thermometry is based on measurements of the abundance of the doubly substituted isotopologue (COO2)-C-13-O-18-O-16 in carbonate minerals, analyzed in CO2 gas liberated on phosphoric acid digestion of carbonates and reported as Delta(47) values. We analyzed Delta(47) in live-collected aragonitic scleractinian (Enallopsammia sp.) and high-Mg calcitic gorgonian (Isididae and Coralliidae) deep-sea corals and compared results to published data for other aragonitic scleractinian taxa. Measured Delta(47) values were compared to in situ temperatures, and the relationship between Delta(47) and temperature was determined for each group to investigate taxon-specific effects. We find that aragonitic scleractinian deep-sea corals exhibit higher values than high-Mg calcitic gorgonian corals and the two groups of coral produce statistically different relationships between Delta(47)-temperature calibrations. These data are significant in the interpretation of all carbonate clumped isotope calibration data as they show that distinct Delta(47)-temperature calibrations can be observed in different materials recovered from the same environment and analyzed using the same instrumentation, phosphoric acid composition, digestion temperature and technique, CO2 gas purification apparatus, and data handling. There are three possible explanations for the origin of these different calibrations. The offset between the corals of different mineralogy is in the same direction as published theoretical predictions for the offset between calcite and aragonite although the magnitude of the offset is different. One possibility is that the deep-sea coral results reflect high-Mg and aragonite crystals attaining nominal mineral equilibrium clumped isotope signatures due to conditions of extremely slow growth. In that case, a possible explanation for the attainment of disequilibrium bulk isotope signatures and equilibrium clumped isotope signatures by deep-sea corals is that extraordinarily slow growth rates can promote the occurrence of isotopic reordering in the interfacial region of growing crystals. We also cannot rule out a component of a biological "vital effect" influencing clumped isotope signatures in one or both orders of coral. Based on published experimental data and theoretical calculations, these biological vital effects could arise from kinetic isotope effects due to the source of carbon used for calcification, temperature-and pH-dependent rates of CO2 hydration and/or hydroxylation, calcifying fluid pH, the activity of carbonic anhydrase, the residence time of dissolved inorganic carbon in the calcifying fluid, and calcification rate. A third possible explanation is the occurrence of variable acid digestion fractionation factors. Although a recent study has suggested that dolomite, calcite, and aragonite may have similar clumped isotope acid digestion fractionation factors, the influence of acid digestion kinetics on Delta(47) is a subject that warrants further investigation

Gas flux and carbonate occurrence at a shallow seep of thermogenic natural gas

The Coal Oil Point seep field located offshore Santa Barbara, CA, consists of dozens of named seeps, including a peripheral ∼200 m2 area known as Brian Seep, located in 10 m water depth. A single comprehensive survey of gas flux at Brian Seep yielded a methane release rate of ∼450 moles of CH4 per day, originating from 68 persistent gas vents and 23 intermittent vents, with gas flux among persistent vents displaying a log normal frequency distribution. A subsequent series of 33 repeat surveys conducted over a period of 6 months tracked eight persistent vents, and revealed substantial temporal variability in gas venting, with flux from each individual vent varying by more than a factor of 4. During wintertime surveys sediment was largely absent from the site, and carbonate concretions were exposed at the seafloor. The presence of the carbonates was unexpected, as the thermogenic seep gas contains 6.7% CO2, which should act to dissolve carbonates. The average δ13C of the carbonates was −29.2 ± 2.8‰ VPDB, compared to a range of −1.0 to +7.8‰ for CO2 in the seep gas, indicating that CO2 from the seep gas is quantitatively not as important as 13C-depleted bicarbonate derived from methane oxidation. Methane, with a δ13C of approximately −43‰, is oxidized and the resulting inorganic carbon precipitates as high-magnesium calcite and other carbonate minerals. This finding is supported by 13C-depleted biomarkers typically associated with anaerobic methanotrophic archaea and their bacterial syntrophic partners in the carbonates (lipid biomarker δ13C ranged from −84 to −25‰). The inconsistency in δ13C between the carbonates and the seeping CO2 was resolved by discovering pockets of gas trapped near the base of the sediment column with δ13C-CO2 values ranging from −26.9 to −11.6‰. A mechanism of carbonate formation is proposed in which carbonates form near the sediment–bedrock interface during times of sufficient sediment coverage, in which anaerobic oxidation of methane is favored. Precipitation occurs at a sufficient distance from active venting for the molecular and isotopic composition of seep gas to be masked by the generation of carbonate alkalinity from anaerobic methane oxidation. Figure Processes modulating carbonate formation at Brian Seep (California) during times of high and low sediment burde

Uranium-series dating and growth characteristics of the deep-sea scleractinian coral: Enallopsammia rostrata from the Equatorial Pacific

The deep-sea coral, Enallopsammia rostrata, a member of the Dendrophylliidae family, is a major structure-forming species that creates massive dendroid colonies, up to 1 m wide and 0.5 m tall. Living colonies of E. rostrata have been collected using the PISCES submersibles from three locations from 480 to 788 m water depth in the Line Islands (similar to 160 degrees W) in the Equatorial Pacific. We have applied to these colonies a high sensitivity, low blank technique to determine U-series ages in small quantities (70 +/- 15 mg) of modern and near modern calcareous skeletons using MC-ICP-MS (Multi-collector Inductively Coupled Plasma Mass Spectrometer). The application of this method to living slow-growing colonies from a range of sites as well as the observations of axial growth patterns in thin sections of their skeletons offer the first expanded and well constrained data on longevity, growth pattern and mean growth rates in E. rostrata. Absolute dated specimens indicate life spans of colonies ranging from 209 +/- 8 yrs to 605 +/- 7 yrs with radial growth rates from 0.012 to 0.072 mm yr(-1) and vertical extension rates from 0.6 to 1.9 mm yr(-1). The linear growth rates reported here are lower than those reported for other deep-sea scleractinian corals (Lophelia pertusa and Madrepora oculata). The U-series dating indicates that the growth ring patterns of E. rostrata are not consistent with annual periodicity emphasizing the importance of absolute radiometric dating methods to constrain growth rates. Slow accretion and extreme longevity make this species and its habitat especially vulnerable to disturbances and impacts from human activities. This dating method combined with observation of growth patterns opens up new perspectives in the field of deep-sea corals since it can provide quantitative estimates of growth rates and longevity of deep-sea corals in general

Uranium-series dating and growth characteristics of the deep-sea scleractinian coral: Enallopsammia rostrata from the Equatorial Pacific

The deep-sea coral, Enallopsammia rostrata, a member of the Dendrophylliidae family, is a major structure-forming species that creates massive dendroid colonies, up to 1 m wide and 0.5 m tall. Living colonies of E. rostrata have been collected using the PISCES submersibles from three locations from 480 to 788 m water depth in the Line Islands (∼160°W) in the Equatorial Pacific. We have applied to these colonies a high sensitivity, low blank technique to determine U-series ages in small quantities (70 ± 15 mg) of modern and near modern calcareous skeletons using MC-ICP-MS (Multi-collector Inductively Coupled Plasma Mass Spectrometer). The application of this method to living slow-growing colonies from a range of sites as well as the observations of axial growth patterns in thin sections of their skeletons offer the first expanded and well constrained data on longevity, growth pattern and mean growth rates in E. rostrata. Absolute dated specimens indicate life spans of colonies ranging from 209 ± 8 yrs to 605 ± 7 yrs with radial growth rates from 0.012 to 0.072 mm yr-1 and vertical extension rates from 0.6 to 1.9 mm yr-1. The linear growth rates reported here are lower than those reported for other deep-sea scleractinian corals (Lophelia pertusa and Madrepora oculata). The U-series dating indicates that the growth ring patterns of E. rostrata are not consistent with annual periodicity emphasizing the importance of absolute radiometric dating methods to constrain growth rates. Slow accretion and extreme longevity make this species and its habitat especially vulnerable to disturbances and impacts from human activities. This dating method combined with observation of growth patterns opens up new perspectives in the field of deep-sea corals since it can provide quantitative estimates of growth rates and longevity of deep-sea corals in general

A National Status Report on United States Coral Reefs Based on 2012-2018 Data From National Oceanic and Atmospheric Administration's National Coral Reef Monitoring Program

National Oceanic and Atmospheric Administration's Coral Reef Conservation Program supports the National Coral Reef Monitoring Program (NCRMP) in the United States Pacific, Atlantic, Caribbean, and Gulf of Mexico. NCRMP conducts standardized observations of biological, climatic, and socioeconomic indicators across American Samoa, Guam, the Main Hawaiian Islands, the Northwestern Hawaiian Islands, the Northern Mariana Islands, the Pacific Remote Islands, Florida, the Flower Garden Banks, Puerto Rico, and the United States Virgin Islands. NCRMP provides periodic, national-level assessments of the status of United States coral reef ecosystems and communities connected to them. In 2014, NCRMP partnered with the University of Maryland Center for Environmental Science on an unprecedented collaboration between federal and jurisdictional/state agencies, academia, and non-governmental organizations to synthesize NCRMP data into a reporting format designed to be accessible and relevant to the public and policy makers. The process involved multi-year data analyses of key benthic, fish, and climate indicators. In populated jurisdictions, socioeconomic data were integrated to assess public support for management actions, participation in pro-environmental behaviors, and awareness of threats to coral reefs. Jurisdictions were scored using a report-card scale (0-100%) by establishing references for each indicator using best-available historical data or expert opinion where historical data did not exist or were not statistically comparable. Despite overall ecosystem scores of Fair for all combined Atlantic (70%) and Pacific (74%) jurisdictions, the current trend is downward with a majority of United States coral reefs declining and vulnerable to further degradation. Remote, uninhabited reefs had an advantage with respect to reef fish population scores, i.e., Flower Garden Banks (85%) and Pacific Remote Islands (93%), when compared to populated location scores, i.e., Puerto Rico (63%) and Main Hawaiian Islands (66%). All coral reefs are highly impacted by climate change, and climate impacts were more pronounced than expected on remote reefs, i.e., the Northwestern Hawaiian Islands (58%). Presenting results in a report-card style facilitates communication to the public and policy makers, and provides a useful mechanism to garner support for management actions such as expanding protected areas; enforcing existing regulations; increasing climate change education; reducing land-based sources of pollution; and other actions to improve the trajectory of coral reef ecosystem conditions