Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina)

dc.contributor.authorYu, Lei
dc.contributor.authorKhachaturyan, Marina
dc.contributor.authorMatschiner, Michael
dc.contributor.authorHealey, Adam
dc.contributor.authorBauer, Diane
dc.contributor.authorCameron, Brenda
dc.contributor.authorCusson, Mathieu
dc.contributor.authorDuffy, J. Emmett
dc.contributor.authorFodrie, F. Joel
dc.contributor.authorGill, Diana
dc.contributor.authorGrimwood, Jane
dc.contributor.authorHori, Masakazu
dc.contributor.authorHovel, Kevin
dc.contributor.authorHughes, A. Randall
dc.contributor.authorJahnke, Marlene
dc.contributor.authorJenkins, Jerry
dc.contributor.authorKeymanesh, Keykhosrow
dc.contributor.authorKruschel, Claudia
dc.contributor.authorMamidi, Sujan
dc.contributor.authorMenning, Damian M.
dc.contributor.authorMoksnes, Per-Olav
dc.contributor.authorNakaoka, Masahiro
dc.contributor.authorPennacchio, Christa
dc.contributor.authorReiss, Katrin
dc.contributor.authorRossi, Francesca
dc.contributor.authorRuesink, Jennifer L.
dc.contributor.authorSchultz, Stewart T.
dc.contributor.authorTalbot, Sandra
dc.contributor.authorUnsworth, Richard
dc.contributor.authorWard, David H.
dc.contributor.authorDagan, Tal
dc.contributor.authorSchmutz, Jeremy
dc.contributor.authorEisen, Jonathan A.
dc.contributor.authorStachowicz, John J.
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorOlsen, Jeanine L.
dc.contributor.authorReusch, Thorsten B.H.
dc.date.accessioned2024-02-14T10:09:31Z
dc.date.available2024-02-14T10:09:31Z
dc.date.issued2023-08
dc.descriptionDATA 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.descriptionCODE 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.descriptionSUPPLEMENTARY MATERIAL : Supplementary Notes 1–8, Tables 1–6 and Figs. 1–12.en_US
dc.descriptionSUPPLEMENTARY DATA : Table 1: Sequence coverage. Supplementary Data Table 2: Mapping rate. Supplementary Data Table 3: Accession number of each library.en_US
dc.descriptionSOURCE DATA : Fig. 1b,c.en_US
dc.description.abstractCurrents 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.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.librarianhj2024en_US
dc.description.sdgLife below wateren_US
dc.description.sponsorshipOpen 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.urihttp://www.nature.com/nplantsen_US
dc.identifier.citationYu, 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.issn2055-026X (print)
dc.identifier.issn2055-0278 (online)
dc.identifier.other10.1038/s41477-023-01464-3
dc.identifier.urihttp://hdl.handle.net/2263/94601
dc.language.isoenen_US
dc.publisherNature Researchen_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.subjectMarine biologyen_US
dc.subjectPlant evolutionen_US
dc.subjectPopulation geneticsen_US
dc.subjectSDG-14: Life below water
dc.titleOcean current patterns drive the worldwide colonization of eelgrass (Zostera marina)en_US
dc.typeArticleen_US

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