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    A regulatory hydrogenase gene cluster observed in the thioautotrophic symbiont of Bathymodiolus mussel in the East Pacific Rise

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    Galápagos tortoise stable isotope ecology and the 1850s Floreana Island Chelonoidis niger niger extinction

    Sample procurement and data analysisTo establish a diachronic dataset of Galápagos tortoise dietary stable isotope ecology, we selected samples from five sources (see Supplemental Text): the American Museum of Natural History, New York, New York, (2) the California Academy of Sciences, San Francisco, California, (3) the Natural History Museum, London, England, (4) the National Museum of Natural History, Smithsonian Institution, Washington, D.C., and (5) the Thompson’s Cove (CA-SFR-186H) archaeological site in San Francisco, California. We provide details regarding sample provenience information and date-of-death as supplemental information. From these collections, we obtained single or multiple isotope samples from a total of 57 individual tortoises representing the following subspecies (n = 10) and islands: five C. n. abingdonii (Pinta Island), one C. n. becki (Volcán Wolf, Isabela Island), five C. n. chathamensis (San Cristóbal Island), four C. n. darwini (Santiago Island), thirteen C. n. duncanensis (Pinzón Island), four C. n. guentheri (Sierra Nega, Isabela Island), six C. n. hoodensis (Española Island), one C. n. microphyes (Volcán Darwin, Isabela Island), four C. n. niger (Floreana Island), nine C. n. porteri (Western Santa Cruz Island), one C. n. vicina (Cerro Azul, Isabela Island), one unknown Isabela Island tortoise, two C. n. vicina tortoises which were transported, lived and collected on Rabida Island, and one unknown tortoise (Chelonoidis niger ssp.; unknown Island—the San Francisco Gold Rush sample). The two earliest collected tortoises in our sample date to1833 and the latest tortoise is from 1967, representing a period of 134 years.To understand tissue-specific isotopic variation and fractionation for the purposes of reconstructing long-term dietary ecology, we sampled tortoise bone collagen (n = 57), bone apatite (n = 23), scute keratin (n = 8) and skin (n = 2) for carbon (δ13Ccollagen and δ13Capatite), nitrogen (δ15N), hydrogen (δD) and oxygen (δ18Oapatite) stable isotopes. All samples were drilled or cut using a Dremel rotary tool with either a blade or diamond spherical bit attachment and were transported to the University of New Mexico, Center for Stable Isotopes (UNM-CSI), Albuquerque, NM, for preparation and analysis. All statistical and metric data analysis and visualization occurred in R (4.0.4) and RStudio (2022.02.4). We provide reproducible source code supplemental to the text35.Bone collagen δ13C, δ15N and δDAnalysis of bone collagen, skin and scute keratin for carbon, nitrogen and hydrogen stable isotopes followed standardized protocols (e.g., see36). For bone collagen, we cut and demineralized a small portion of bulk bone in 0.5 N hydrochloric acid (HCl) at 5 °C for 24 h prior to rinsing all samples to neutrality using deionized water. For lipid extraction, we immersed the samples in a solution of 2:1 chloroform:methanol (C2H5Cl3) for 24 h (repeated three times) while also sonicating samples for 15 min to ensure complete chemical saturation. Preparation of skin and scute keratin samples was only included this during the later lipid extraction step (i.e., no demineralization required). After 72 h we rinsed all samples to neutrality and lyophilized the tortoise samples for another 24 h. We then measured approximately 0.5–0.6 mg of bone collagen/skin/scute tissue into tin capsules for carbon (δ13Ccollagen) and nitrogen (δ15N) stable isotope analysis. We also measured approximately 0.2–0.3 mg of bone collagen/skin/scute tissue into silver capsules for hydrogen (δD) isotope analysis. We report isotope values in delta (δ) notation, calculated as: ((Rsample/Rstandard) − 1) × 1000, where Rsample and Rstandard are the ratios (e.g., 13C/12C, 15N/14N) of the unknown and standard material, respectively. Delta values are reported as parts per thousand (‰).Carbon and nitrogen samples were measured on a Costech 4010 elemental analyzer (Valencia, California, USA) coupled to a Scientific Delta V Plus isotope ratio mass spectrometer by a Conflo IV, and hydrogen samples were measured on a Finnigan high-temperature conversion elemental analyzer (TC/EA) coupled to a Thermo Scientific Delta V Plus mass spectrometer by a Conflo IV at UNM-CSI (see37 for details on the high temperature conversion method for hydrogen analysis). All nitrogen and carbon isotope data are reported relative to atmospheric N2 and V-PDB, respectively. The data were corrected using lab standards with values of δ15 N = 6.4‰ and δ13C =  − 26.5‰ (casein protein), and of δ15N = 13.3‰ and δ13C =  − 16.7‰ (tuna muscle) that have been calibrated relative to the universally accepted standards: IAEA-N1, USGS 24, IAEA 600, USGS 63, and USGS 40.To ensure equilibrium between the exchangeable hydrogen in tissue samples and local atmosphere38, we weighed hydrogen standards and samples into silver capsules and allowed both to sit in the laboratory for at least 2 weeks before analysis. Hydrogen data were corrected using three UNM-CSI laboratory keratin standards (δDnon-ex =  − 174‰, − 93‰, and − 54‰) of which the δDnon-ex values were previously determined through a series of atmospheric exchange experiments. These standards were also calibrated to USGS standards CBS and KHS values of − 178.8‰ and − 47.5‰, respectively (see39,40 for details and updated values). To quantitate any error imparted to our collagen data through correction with keratin standards, a UNM-CSI cow (Bos taurus) bone collagen standard was analyzed in every run over a 6-month period (July 2017–January 2018) and gave an inter-run standard deviation of 3.9‰, suggesting the difference in percent exchangeable hydrogen between collagen and keratin tissues did not significantly impact our results. All hydrogen isotope data are reported relative to Vienna-Standard Mean Ocean Water (V-SMOW). The H3 factor was between 8 and 8.5 for all runs.Collagen precision (standard deviation; SD) for within-run analyses is  More

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    Author Correction: The hidden land use cost of upscaling cover crops

    Correction to: Communications Biology https://doi.org/10.1038/s42003-020-1022-1, published online 11 June 2020.In the original version of the Perspective, a unit conversion error affected calculations for cereal rye, triticale, barley, and oats. Further, berseem clover yield estimates were mistranscribed from the original source. These mistakes led to errors in Supplementary Data 1, Figure 2 and in the presentation of the data in the text.Supplementary Data 1 has now been replaced with a file containing the correct numbers.Figure 2 has been corrected:Original figure 2New figure 2The Abstract stated: “In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 3.8% (median 2.0%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.5% and 11.9%, respectively”.The text should read: “In this Perspective, we estimate land use requirements to supply the United States maize production area with cover crop seed, finding that across 18 cover crops, on average 2.4% (median 2.1%) of current production area would be required, with the popular cover crops rye and hairy vetch requiring as much as 4.8% and 11.9%, respectively”.In the 1st paragraph of the right hand column on page 2, the text said: “(…), we find that the land requirements for production of cover crop seed would be on average 1.4 million hectares (median 746,000 ha), which is equivalent to 3.8% (median 2.0%) of the U.S. maize farmland. Rye (Secale cereale L.) – a midrange seed yielding cover crop and one of the most commonly used in the corn belt, would require as much as 1,661,000 hectares (4.5% of maize farmland), (…)”The text should read: “(…) we find that the land requirements for production of cover crop seed would be on average 892,526 hectares (median 774,417 ha), which is equivalent to 2.4% (median 2.1%) of the U.S. maize farmland. Rye (Secale cereale L.) – a midrange seed yielding cover crop and one of the most commonly used in the corn belt, would require as much as 1,779,770 hectares (4.8% of maize farmland), (…)”On page 3, second paragraph the text said: “Cover cropping the entire U.S. maize area would require the equivalent of as much as 18% (rye) to 49% (hairy vetch) (…)”The text should read: “Cover cropping the entire U.S. maize area would require the equivalent of as much as 19% (rye) to 49% (hairy vetch) (…)”This errors have now been corrected in the Perspective Article. More

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    Simultaneous invasion decouples zebra mussels and water clarity

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