http://lod.bco-dmo.org/id/dataset/958640 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2025-04-10 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Summary data for whole genome sequencing on Lottia samples collected from Northern California to Baja from Nov 2020 to Jan 2022 2026-03-17 publication 2026-03-17 revision Woods Hole Oceanographic Institution (WHOI BCO-DMO) 2026-03-18 publication https://doi.org/10.26008/1912/bco-dmo.958640.1 Rachael Bay University of California-Davis principalInvestigator Richard K. Grosberg University of California-Davis principalInvestigator Eric Sanford University of California-Davis principalInvestigator Brenda Cameron University of California-Davis principalInvestigator Philip Fenberg University of Southampton principalInvestigator Erica Nielsen University of California-Davis principalInvestigator David A. Paz-García Center for Biological Research of the Northwest, SC principalInvestigator Jacqueline Sones University of California-Davis principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Nielsen, E., Walkes, S., Sones, J., Fenberg, P., Paz-García, D. A., Cameron, B., Grosberg, R. K., Sanford, E., Bay, R. (2026) Summary data for whole genome sequencing on Lottia samples collected from Northern California to Baja from Nov 2020 to Jan 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-03-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.958640.1 [access date] Sample data for Lottia genomic samples Dataset Description: Methods and Sampling: &lt;p&gt;We sampled 19 sites on the Pacific coast of North America, spanning most of the contemporary range of&amp;nbsp;&lt;em&gt;Lottia&amp;nbsp;gigantea &lt;/em&gt;(urn:lsid:marinespecies.org:taxname:456593)&lt;em&gt;.&amp;nbsp;&lt;/em&gt;We non-lethally excised a small piece of foot muscle tissue. For all locations except the four northern sites, we collected tissue from roughly 30 individuals per site, comprised of 10 individuals within each of the following size ranges: 10–25 mm (small), 30–40 mm (medium), and &amp;gt;40 mm (large). Sampling of the four northern sites (i.e., expanded range) also consisted of roughly 10 small, medium, and large individuals per site. However, as individual limpets at these four sites have been closely monitored over the past 8 years, these sites had known cohorts based on the estimated year of settlement. Size classes at sites for which we do not have monitoring data were chosen based on our data and previous growth curves (Kido &amp;amp; Murray,&amp;nbsp;2003) to approximately group individuals into those that settled during the marine heatwaves (MHWs), soon after the MHWs (late 2016 or late 2017), or well after the MHWs (late 2018 or late 2019).&amp;nbsp;Tissue was stored in 90% ethanol at −20°C. We used the Qiagen DNeasy extraction kit to perform DNA extractions following the manufacturer's protocols. DNA quantity and quality were assessed with NanoDrop, Qubit, and gel electrophoresis. Library preparation followed the Nextera Lite protocol, with adaptations following Rowan et&amp;nbsp;al.&amp;nbsp;(2019). Briefly, this consisted of normalizing samples, tagmentation, PCR, pooling samples, and bead size selection. The purified samples were run on a High Sensitivity DNA Bioanalyzer chip and then sent to BGI Genomics for whole-genome sequencing on the DNBSEQ-T7 PE150 platform on four lanes of sequencing.&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023297 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023297 completed Rachael Bay University of California-Davis 530-754-1439 Dept of Evolution and Ecology University of California Davis CA 95616 US rbay@ucdavis.edu pointOfContact Richard K. Grosberg University of California-Davis Department of Ecology and Evolution 1 Shields Ave Davis CA 95616 USA rkgrosberg@ucdavis.edu pointOfContact Eric Sanford University of California-Davis P.O. Box 247 2099 Westshore Road Bodega Bay CA 94923 USA edsanford@ucdavis.edu pointOfContact Brenda Cameron University of California-Davis bbcameron@ucdavis.edu pointOfContact Philip Fenberg University of Southampton pfenberg@gmail.com pointOfContact Erica Nielsen University of California-Davis erica.nielsen@tnc.org pointOfContact David A. Paz-García Center for Biological Research of the Northwest, SC dpaz@cibnor.mx pointOfContact Jacqueline Sones University of California-Davis jlsones@ucdavis.edu pointOfContact asNeeded Dataset Version: 1 Unknown Library_Name Sample_ID Percent_Dups Percent_GC Average_read_length M_Seqs mill num_reads sequencer_read_length read_X_read_length genome_size Cov site date latitude longitude size size_group DNBSEQ-T7 PE150 platform High Sensitivity DNA Bioanalyzer chip Qubit scalpel NanoDrop theme None, User defined seq_descrip sample identification No BCO-DMO term site date latitude longitude length sample description featureType BCO-DMO Standard Parameters Automated DNA Sequencer Bioanalyzer Fluorometer scalpel Thermo Scientific NanoDrop spectrophotometer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Evolutionary and ecological dynamics of a contemporary climate-driven range expansion https://osprey.bco-dmo.org/project/867543 Evolutionary and ecological dynamics of a contemporary climate-driven range expansion <p><em>NSF abstract:</em><br /> Anthropogenic climate change is shifting the distributions of species across the globe. Such contemporary shifts in species’ ranges may have cascading effects on entire ecosystems. This project disentangles the mechanisms underlying climate-driven species range shifts in marine systems using the intertidal owl limpet as a case study. During the recent marine heatwaves off the Pacific coast of North America, populations at the northern range limit in northern California have expanded, with ongoing reproduction even after termination of the heatwave events. This is therefore an ideal system to explore the dynamics of natural selection that occur as species occupy new regions. Broadly, this project deepens understanding of how range shifts occur in marine systems and furthers the ability to predict future species distributions in response to climate change. The project provides research experiences for high school and undergraduate students from historically underrepresented groups by engaging with existing, demonstrably-effective programs. The investigators host leadership and skill-building workshops for senior female graduate students and engage the public in partnership with the California Academy of Sciences, Bodega Marine Lab, and San Francisco Exploratorium. Finally, the project provides training for a postdoctoral scholar and two graduate students.</p> <p>Although phenomenological studies suggest that climate-associated range shifts are common in marine systems, to date, mechanistic studies of the climate-organism interactions that alter geographic distributions have largely focused on terrestrial systems. However, dispersal dynamics greatly differ in many marine systems, as currents may frequently transport planktonic larvae into new environmental regimes. This project integrates detailed demographic observations of the recent range expansion of the intertidal owl limpet, Lottia gigantea, with ecological, phenotypic, and genomic measurements of divergence across its range. Specifically, the work 1) documents phenotypic divergence in larval and juvenile traits across the zone of range expansion, 2) uses whole genome sequencing to estimate gene flow across the entire range, 3) identifies genomic patterns of selection across the zone of range expansion and through time, and 4) identifies drivers of variation in performance over latitudinal and microgeographic scales. The ability to monitor this range shift in real time, along with the suitability of this system for tracking individuals across multiple years, allows the investigators to examine the impact of selection in novel range-edge conditions at the phenotypic and genomic levels, and scale from individuals to species-level responses to ongoing environmental change.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> LottiaRangeExp largerWorkCitation project eng; USA biota oceans -123.34527765215 -114.245933 27.128191 38.591004548812 2020-11-12 2022-01-13 Coastal California intertidal 0 BCO-DMO catalogue of parameters from Summary data for whole genome sequencing on Lottia samples collected from Northern California to Baja from Nov 2020 to Jan 2022 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/995054.rdf Name: Library_Name Units: unitless Description: <p>Library Name</p> http://lod.bco-dmo.org/id/dataset-parameter/995055.rdf Name: Sample_ID Units: unitless Description: <p>Sample ID</p> http://lod.bco-dmo.org/id/dataset-parameter/995056.rdf Name: Percent_Dups Units: percent Description: <p>Percent of reads that are PCR duplicates</p> http://lod.bco-dmo.org/id/dataset-parameter/995057.rdf Name: Percent_GC Units: percent Description: <p>GC content (%) for DNA sequences</p> http://lod.bco-dmo.org/id/dataset-parameter/995058.rdf Name: Average_read_length Units: base pairs (bp) Description: <p>Average realized read length</p> http://lod.bco-dmo.org/id/dataset-parameter/995059.rdf Name: M_Seqs Units: million reads (10^6 reads) Description: <p>Number of reads (in millions)</p> http://lod.bco-dmo.org/id/dataset-parameter/995060.rdf Name: mill Units: unitless Description: <p>Constant value (1,000,000) used to scale read counts during processing</p> http://lod.bco-dmo.org/id/dataset-parameter/995061.rdf Name: num_reads Units: unitless Description: <p>Total number of reads (e.g., M_Seqs × 1,000,000).</p> http://lod.bco-dmo.org/id/dataset-parameter/995062.rdf Name: sequencer_read_length Units: base pairs (bp) Description: <p>Read length of flow cell (150 bp)</p> http://lod.bco-dmo.org/id/dataset-parameter/995063.rdf Name: read_X_read_length Units: base pairs (bp) Description: <p>Number of base pairs sequenced (num_reads × read_length)</p> http://lod.bco-dmo.org/id/dataset-parameter/995064.rdf Name: genome_size Units: base pairs (bp) Description: <p>Total length of L. gigantea genome measured in base pairs (bp)</p> http://lod.bco-dmo.org/id/dataset-parameter/995065.rdf Name: Cov Units: unitless Description: <p>Estimated mean sequencing depth (× coverage) across the genome for the sample/library (total bases / genome size)</p> http://lod.bco-dmo.org/id/dataset-parameter/995066.rdf Name: site Units: unitless Description: <p>Site name of sampling</p> http://lod.bco-dmo.org/id/dataset-parameter/995067.rdf Name: date Units: unitless Description: <p>Date of sampling</p> http://lod.bco-dmo.org/id/dataset-parameter/995068.rdf Name: latitude Units: decimal degrees Description: <p>Latitude of sampling, South is negative</p> http://lod.bco-dmo.org/id/dataset-parameter/995070.rdf Name: longitude Units: decimal degrees Description: <p>Longitude of sampling, East is positive</p> http://lod.bco-dmo.org/id/dataset-parameter/995072.rdf Name: size Units: mm Description: <p>Shell length/size (mm) measured</p> http://lod.bco-dmo.org/id/dataset-parameter/995073.rdf Name: size_group Units: unitless Description: <p>Binned sizes used to infer settlement time relative to the 2014–2016 marine heatwaves (e.g., small 10–25 mm, medium 30–40 mm, large &gt;40 mm)</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact https://doi.org/10.26008/1912/bco-dmo.958640.1 download onLine dataset &lt;p&gt;We sampled 19 sites on the Pacific coast of North America, spanning most of the contemporary range of&amp;nbsp;&lt;em&gt;Lottia&amp;nbsp;gigantea &lt;/em&gt;(urn:lsid:marinespecies.org:taxname:456593)&lt;em&gt;.&amp;nbsp;&lt;/em&gt;We non-lethally excised a small piece of foot muscle tissue. For all locations except the four northern sites, we collected tissue from roughly 30 individuals per site, comprised of 10 individuals within each of the following size ranges: 10–25 mm (small), 30–40 mm (medium), and &amp;gt;40 mm (large). Sampling of the four northern sites (i.e., expanded range) also consisted of roughly 10 small, medium, and large individuals per site. However, as individual limpets at these four sites have been closely monitored over the past 8 years, these sites had known cohorts based on the estimated year of settlement. Size classes at sites for which we do not have monitoring data were chosen based on our data and previous growth curves (Kido &amp;amp; Murray,&amp;nbsp;2003) to approximately group individuals into those that settled during the marine heatwaves (MHWs), soon after the MHWs (late 2016 or late 2017), or well after the MHWs (late 2018 or late 2019).&amp;nbsp;Tissue was stored in 90% ethanol at −20°C. We used the Qiagen DNeasy extraction kit to perform DNA extractions following the manufacturer's protocols. DNA quantity and quality were assessed with NanoDrop, Qubit, and gel electrophoresis. Library preparation followed the Nextera Lite protocol, with adaptations following Rowan et&amp;nbsp;al.&amp;nbsp;(2019). Briefly, this consisted of normalizing samples, tagmentation, PCR, pooling samples, and bead size selection. The purified samples were run on a High Sensitivity DNA Bioanalyzer chip and then sent to BGI Genomics for whole-genome sequencing on the DNBSEQ-T7 PE150 platform on four lanes of sequencing.&lt;/p&gt; Specified by the Principal Investigator(s) &lt;p&gt;The data included here are sample data taken directly in the field and summary data for whole genome data, before any processing or analysis.&lt;/p&gt; Specified by the Principal Investigator(s) - Loaded Lottia_metadata.xlsx into BCO-DMO system - Loaded Lottia_reads.cov.xlsx into BCO-DMO system - Converted lottia_metadata-1 field date from %m/%d/%y to %Y-%m-%d - Inner-joined lottia_reads.cov-1 (target) with lottia_metadata-1 (source) on key Library Name - Set data types in lottia_reads.cov-1: % Dups number; % GC integer; Read Length number; M Seqs number; mill integer; #reads number (scientific notation output); read length integer; read X read length number (scientific notation output); genome size number (scientific notation output); Cov number; latitude number; longitude number; size number; size_group string; date date with format %Y-%m-%d - Renamed multiple fields: &quot;Library Name&quot; → Library_Name, &quot;Sample ID&quot; → Sample_ID, &quot;% Dups&quot; → Percent_Dups, &quot;% GC&quot; → Percent_GC, &quot;Read_Length&quot; → Average_read_length, &quot;M Seqs&quot; → M_Seqs, &quot;#reads&quot; → num_reads, &quot;read_length&quot; → sequencer_read_length , &quot;read X read length&quot; → read_X_read_length, &quot;genome size&quot; → genome_size - Standardized site text in lottia_reads.cov-1 via find/replace to comply with BCO-DMO character guidance: “Bahía Asunción”→“Bahia Asuncion”; then “Bahía”→“Bahia” - Renamed resource lottia_reads.cov-1 to 958640_v1_lottia_genome. - Exported final output as CSV named 958640_v1_lottia_genome.csv Accepted species identifier confirmed on 2026-03-17. Specified by BCO-DMO Data Managers asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact DNBSEQ-T7 PE150 platform DNBSEQ-T7 PE150 platform PI Supplied Instrument Name: DNBSEQ-T7 PE150 platform PI Supplied Instrument Description:Whole genome samples were sequenced at BGI Genomics on a DNBSEQ-T7. The purified samples were run on a High Sensitivity DNA Bioanalyzer chip and then sent to BGI Genomics for whole-genome sequencing on the DNBSEQ-T7 PE150 platform on four lanes of sequencing. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. High Sensitivity DNA Bioanalyzer chip High Sensitivity DNA Bioanalyzer chip PI Supplied Instrument Name: High Sensitivity DNA Bioanalyzer chip PI Supplied Instrument Description:The purified samples were run on a High Sensitivity DNA Bioanalyzer chip and then sent to BGI Genomics for whole-genome sequencing on the DNBSEQ-T7 PE150 platform on four lanes of sequencing. Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument Description: A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100. Qubit Qubit PI Supplied Instrument Name: Qubit PI Supplied Instrument Description:DNA quantity and quality were assessed with Nanodrop, Qubit, and gel electrophoresis. Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/ scalpel scalpel PI Supplied Instrument Name: scalpel PI Supplied Instrument Description:Samples were collected with a small scalpel. Instrument Name: scalpel Instrument Short Name: Instrument Description: A scalpel, or lancet, or bistoury, is a small and extremely sharp bladed instrument used for dissection and surgery. NanoDrop NanoDrop PI Supplied Instrument Name: NanoDrop PI Supplied Instrument Description:DNA quantity and quality were assessed with Nanodrop, Qubit, and gel electrophoresis. Instrument Name: Thermo Scientific NanoDrop spectrophotometer Instrument Short Name:NanoDrop spectrophotometer Instrument Description: Thermo Scientific NanoDrop spectrophotometers provide microvolume quantification and purity assessments of DNA, RNA, and protein samples. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. The range consists of the NanoDrop One/OneC UV-Vis Spectrophotometers, NanoDrop Eight UV-Vis Spectrophotometer and NanoDrop Lite Plus UV Spectrophotometer.