Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)
dc.contributor.author | Yu, Lei | |
dc.contributor.author | Khachaturyan, Marina | |
dc.contributor.author | Matschiner, Michael | |
dc.contributor.author | Healey, Adam | |
dc.contributor.author | Bauer, Diane | |
dc.contributor.author | Cameron, Brenda | |
dc.contributor.author | Cusson, Mathieu | |
dc.contributor.author | Duffy, J. Emmett | |
dc.contributor.author | Fodrie, F. Joel | |
dc.contributor.author | Gill, Diana | |
dc.contributor.author | Grimwood, Jane | |
dc.contributor.author | Hori, Masakazu | |
dc.contributor.author | Hovel, Kevin | |
dc.contributor.author | Hughes, A. Randall | |
dc.contributor.author | Jahnke, Marlene | |
dc.contributor.author | Jenkins, Jerry | |
dc.contributor.author | Keymanesh, Keykhosrow | |
dc.contributor.author | Kruschel, Claudia | |
dc.contributor.author | Mamidi, Sujan | |
dc.contributor.author | Menning, Damian M. | |
dc.contributor.author | Moksnes, Per-Olav | |
dc.contributor.author | Nakaoka, Masahiro | |
dc.contributor.author | Pennacchio, Christa | |
dc.contributor.author | Reiss, Katrin | |
dc.contributor.author | Rossi, Francesca | |
dc.contributor.author | Ruesink, Jennifer L. | |
dc.contributor.author | Schultz, Stewart T. | |
dc.contributor.author | Talbot, Sandra | |
dc.contributor.author | Unsworth, Richard | |
dc.contributor.author | Ward, David H. | |
dc.contributor.author | Dagan, Tal | |
dc.contributor.author | Schmutz, Jeremy | |
dc.contributor.author | Eisen, Jonathan A. | |
dc.contributor.author | Stachowicz, John J. | |
dc.contributor.author | Van de Peer, Yves | |
dc.contributor.author | Olsen, Jeanine L. | |
dc.contributor.author | Reusch, Thorsten B.H. | |
dc.date.accessioned | 2024-02-14T10:09:31Z | |
dc.date.available | 2024-02-14T10:09:31Z | |
dc.date.issued | 2023-08 | |
dc.description | DATA AVAILABILITY : Genome data have been deposited in Genbank (short read archive, Supplementary Data Table 3). Coding sequences of Z. japonica and Z. marina for the ASTRAL analysis can be found on figshare (https://doi.org/10.6084/m9.figshare.21626327.v1). VCF files of the 11,705 core SNPs can be accessed at https://doi.org/10.6084/m9.figshare.21629471.v1. Source data for Fig. 1b,c are given, as well as statistics of sequencing coverage, mapping rate and further specifications of each sequenced library (Supplementary Tables 1–3). Source data are provided with this paper. | en_US |
dc.description | CODE AVAILABILITY : Custom-made scripts are deposited on GitHub for SNP filtering (github.com/leiyu37/populationGenomics_ZM.git), for clone mate detection (github.com/leiyu37/Detecting-clonemates.git), for heterozygote and nucleotide diversity quantification (github.com/leiyu37/populationGenomics_ZM.git) and to prepare SplitsTree input files (https://github.com/leiyu37/populationGenomics_ZM/blob/main/10_SplitsTree/vcf2alignment.py) and SNAPP input files (github.com/mmatschiner/snapp_prep). Scripts for calculating D-statistics are available at github.com/mmatschiner/tutorials/blob/master/analysis_of_introgression_with_snp_data/src/plot_d.rb. Scripts to prepare the gene presence/absence analysis are deposited on https://github.com/leiyu37/populationGenomics_ZM/tree/main/gene_presense_absence_analysis. Further software code for the MSMC analysis are found at http://lh3lh3.users.sourceforge.net/snpable.shtml (generation of mappability mask file for each of six chromosomes using SNPable) and at https://github.com/stschiff/msmc-tools (generation of ramet-specific mask file based on a bam file using bamCaller.py). | en_US |
dc.description | SUPPLEMENTARY MATERIAL : Supplementary Notes 1–8, Tables 1–6 and Figs. 1–12. | en_US |
dc.description | SUPPLEMENTARY DATA : Table 1: Sequence coverage. Supplementary Data Table 2: Mapping rate. Supplementary Data Table 3: Accession number of each library. | en_US |
dc.description | SOURCE DATA : Fig. 1b,c. | en_US |
dc.description.abstract | Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans. | en_US |
dc.description.department | Biochemistry | en_US |
dc.description.department | Genetics | en_US |
dc.description.department | Microbiology and Plant Pathology | en_US |
dc.description.librarian | hj2024 | en_US |
dc.description.sdg | Life below water | en_US |
dc.description.sponsorship | Open access funding provided by GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel. The China Scholarship Council, the Helmholtz School for Marine Data Science, the US Department of Energy Joint Genome Institute Community Sequencing Program, the Office of Science of the US Department of Energy and the National Science Foundation. | en_US |
dc.description.uri | http://www.nature.com/nplants | en_US |
dc.identifier.citation | Yu, L., Khachaturyan, M., Matschiner, M. et al. Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina). Nature Plants 9, 1207–1220 (2023). https://doi.org/10.1038/s41477-023-01464-3. | en_US |
dc.identifier.issn | 2055-026X (print) | |
dc.identifier.issn | 2055-0278 (online) | |
dc.identifier.other | 10.1038/s41477-023-01464-3 | |
dc.identifier.uri | http://hdl.handle.net/2263/94601 | |
dc.language.iso | en | en_US |
dc.publisher | Nature Research | en_US |
dc.rights | © The Author(s) 2023, corrected publication 2023. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License. | en_US |
dc.subject | Marine biology | en_US |
dc.subject | Plant evolution | en_US |
dc.subject | Population genetics | en_US |
dc.subject | SDG-14: Life below water | |
dc.title | Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina) | en_US |
dc.type | Article | en_US |
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