DOI: 10.5061/dryad.xsj3tx9rh
title: Global seafloor connectivity over evolutionary time

description: Our knowledge of biogeographic patterns and processes in the deep sea has
 been limited by the lack of integrated datasets that cover its vast
 extent. Here we analyse a new global dataset of genomic DNA sequences,
 spanning an entire taxonomic class of benthic invertebrates (Ophiuroidea),
 to obtain a broad understanding of phylogenetic divergence and biotic
 movement across all oceans, from coastal margins down to the abyssal
 plains. We show that regional faunas on the continental shelf are
 phylogenetically divergent, particularly at temperate and tropical
 latitudes. In contrast, assemblages in the deep sea are much more
 connected. Many temperate deep-sea lineages have achieved distribution
 ranges across the planet, including over the Quaternary period. A close
 relationship exists between deep-sea faunas of the North Atlantic and
 Southern Australia, on the opposite sides of the globe. Bathymetric
 interchange is not only reliant on vertical migration through isothermal
 polar waters, but also occurs across the thermal depth gradients of
 tropical regions. The connected nature of deep-sea life should be an
 important consideration in marine conservation assessments.
description: Exon capture next-generation DNA sequence data, including
 mitochondrial genes, plus some COI-only samples
 Phylogenetic analysis, trees and sample descriptions
 Evolutionary biology and graphic scripts (R) and data
 tables
description: # Global marine connectivity over evolutionary time This dryad submission
 contains the aligned DNA nuclear and mitochondrial sequences, the
 phylogenetic trees, descriptive tables, spatial datasets, and r software
 code from our biogeographic study on marine benthic connectivity across
 the global oceans. Manuscript citation: O'Hara et al. (submitted)
 Global marine connectivity over evolutionary time. Nature ## Description
 of the data and file structure, Figure numbers refer to the submitted
 paper. osm9f.phy: phylip file with aligned nuclear (1487 exons, 260319 bp)
 and mitochondrial COI (1431 bp) sequence data from the 2699 samples used
 to create the OSM9f.nwk phylogeny for this study. OSM9f exon
 boundaries.txt: text file with a list of the exons (and COI) and the start
 and end positions in the OSM9f.phy file. OSM9f_p4.txt: partition file used
 in the maximum likelihood (RAxML v8.1.20) analysis of the OSM9f.phy file
 and the creation the OSM9f.nwk phylogenetic tree. OSM9f.nwk: the
 chronogram tree in NEWICK format used to create Fig. 1, Extended Data figs
 7 & 10, and input to the biogeographic analyses that result in the
 ordinations (Fig. 2-3, Extended Data fig. 9) and chord diagrams (Fig. 4,
 Extended Data Fig. 4). This tree was created by RAxML v8.1.20 and
 converted to a chronogram using the rate-smoothing software TreePL v1.0
 (see methods). Osm9f.csv: a table with sample, taxonomic, locality and
 environmental data corresponding to each DNA record in OSM9f.phy and each
 tip on the phylogenetic tree (OSM9f.nwk). The ID column indicates the
 order samples appear in the tree. Sample columns include Tip (full name of
 the sample), Sample code (unique sample code), Plate (sequencing plate
 run), Target (percentage of exon target captured by the sequencing) ,
 Heterozygosity (of the sites), COI_bp (the length of the COI fragment),
 Genbank COI code (code on Genbank). Taxonomic columns include Species
 (Genus and species name, including informal undescribed names), Family
 (taxonomic family), Order (taxonomic order), FamilyID (taxonomic family
 coded as an integer), FamilyFocalTaxa (label for display on
 fan-phylogenies). Locality columns include GlobBiome (the biome the sample
 belongs to, the main descriptor used in the biogeographic analyses),
 BiomeID (the biome coded as a integer), Region (one of 15 geographic
 regions), RegionID (the region coded as a integer), Strata (depth strata
 of the sample, S=0-200m, B=200-3500 m and A = &gt;3500 m), StrataID (depth
 strata coded as an integer), Locality (geographic description of
 collection), DepthLat (descriptor used in the 9 state chord diagrams,
 based on 3 latitude and 3 depth categories, DepthLatID (DepthLat
 descriptor encoded as an integer), Collection event code (survey and
 station code), Museum registration (museum acronym and registration code
 of original specimen), Lat (decimal latitude in degrees of collection
 site), Lon (decimal longitude in degrees of collection site), Depth (depth
 of collection site in meters). Environmental data includes Temp (seawater
 temperature in Celsius), Salinity (in PSU), and oxygen concentration
 (?mol/kg) derived from trilinear interpolation of World Ocean Atlas (2018)
 annual data from the sample latitude, longitude and depth. 'NA'
 in a cell indicates that there is no available data for this record field.
 BiomeID.csv: a table with the 37 biome codes and descriptors, including
 Biome (code), Biome ID (order of biomes according to depth strata and
 alphabetic region), Order (order of biomes resulting from the CorrHMM
 analysis), LatOrder (order of biomes according to depth strata and
 latitude), CountOfTips (number of samples in each biome), Col (colour
 pattern1), ColM (colour pattern2), Str (label of biome for figures),
 Lat_avg (mean latitude of all biome samples from data in OSM9f.csv),
 Lon_avg (mean longitude of all biome samples from data in OSM9f.csv),
 Depth_avg (mean depth of all biome samples from data in OSM9f.csv),
 Temp_avg (mean seawater temperature of all biome samples from data in
 OSM9f.csv), Salinity_avg (mean salinity of all biome samples from data in
 OSM9f.csv), O2_avg (mean oxygen content of all biome samples from data in
 OSM9f.csv), Region_str (descriptor for geographic region, for figure
 legends), Depth_str (descriptor for geographic region, for figure
 legends), DepthLatGroup (alphanumeric code for depth-latitudinal
 categories, the first letter indicating depth [A=abyssal, B=Bathyal, and
 S=Shelf] and the second letter indicating region [P=Polar, T=Temperate,
 and E=Equatorial], used to create Fig. ED4c-d), DepthLatID (integer code
 for depth-latitudinal categories), LatGroupOrder (Order for latitudinal
 groups: 3=Polar, 2=Temperate, and 1=Equatorial]), DepthOrder (Order for
 depth groups: 3=Shelf, 2=Bathyal, and 1=Abyssal]). DepthLatID.csv: a table
 with the 9 depth-latitude biome groups and descriptors with a subset of
 similar headings to BiomeID.csv. bl_x.csv: A comma-delimited text-based
 file containing known biome-species records that were not part of the
 genetic dataset. These tips are artifically added to the phylogeny at an
 appropriate taxonomic location to test whether missing data influences the
 ordination pattern (see Extended data Fig. 9g). Columns include: Var1=tip
 label, Code=unique code for each record, Taxonomy ID=unique species-level
 code, cat=code as to whether to include the tip or not (X=include, NA=dont
 include) modified in the R code, Biome1=code for the biome of the sample,
 BiomeID=integer factor of the Biome code, Depth1=average depth of this
 species in this biome, Family=taxonomic family of sample. OSM9f_RAxML.nwk:
 a phylogenetic tree in NEWICK format produced from a RAxML v8 maximum
 likelihood analysis with branch lengths reflecting genetic distance rather
 than time. This is used to test whether the ordination pattern is biased
 by the rate-smoothing algorithm that produces a chronogram (see Extended
 data Fig. 9h) biome-biome statistics.csv: a table with calculated
 biome-to-biome GUNN distance measures, including the number of unique
 nodes in the comparison, geometric mean and standard deviation, median,
 mean and standard deviation, harmonic mean, geometric mean of nodes &lt;
 65 MY, geometric mean of nodes between 3 and 65 MY, jackknifed dataset,
 dataset with added tips to represent unsampled (but known biome
 occurrences), geometric mean of node heights calculated from a
 non-ultrametric (RAxML) tree. GIS_transects_EDFig5.zip: archive containing
 ESRI shape and associated files for the 4 South to North transects used to
 create the latitude-depth plots on Extended Data Fig. 5. EA_buffer.* =
 East Atlantic, EP_buffer.* = East Pacific, WA_buffer.* = West Atlantic,
 and WP_buffer.* = West Pacific). Created using qGIS v3.28.3 software.
 OSM9e_LTT_ED8b.zip: archive with the 4 files used to create the Lineage
 Through Time plots, including: 1) OSM9e_DBv1.csv, a text file in comma
 delimnited format, with 5 columns: label=the sample's text label on
 the full phylogenetic tree, exon=binary on whether the sample contains
 nuclear exon data, order=integer facctor indicating which of the 6
 ophiuroid taxonomic orders the sample belongs to, family=integer factor
 indicating which of the 37 ophiuroid taxonomic families the sample belongs
 to, subord=integer factor indicating which of the 10 ophiuroid taxonomic
 suborders the sample belongs to. 2)
 OSM9e_RaxNGbbngg_pinct35_rr_tplo10b.nwk - text file with a representation
 of the full phylogenetic tree in Newick format. 3) OSM9e_tplo10b_sp3e.nwk
 - text file with a representation of a species-level tree (with duplicate
 within-species samples removed) in newick format. 4)
 OSM9e_tplo10b_sp3e_dlist.txt - a text file with the labels of the
 duplicate samples that have been removed in the creation of the species
 level phylogeny (OSM9e_tplo10b_sp3e.nwk) from the full phylogeny
 (OSM9e_RaxNGbbngg_pinct35_rr_tplo10b.nwk). World osm9 v3.jpeg: enlarged
 image of Fig. 1, a map with locations of sample-sites, encoded into
 genomic (exon capture and transcriptome) and barcode (COI) samples. ##
 Usage notes Comma-separated (*.csv) files can be read by a text editor, a
 spreadsheet program such as Microsoft Excel, or via the
 "read.csv()" function in the R programming language. Text
 (*.txt) files can be read by a text editor Shapefiles (*.shp) are a common
 format for vector-based geographic information system (GIS) data developed
 by the company esri. They can be opened and used in any GIS software and
 in R or Python. A shapefile consists of multiple file types beyond the
 .shp (specifically, .cpg, .dbf, .prj, .sbn, and .sbx). The user only
 interacts directly with the .shp file but the other files need to be in
 the same directory. NEWICK (*.nwk) are text-based files representing
 phylogenetic trees, which can be viewed by programs sich as FigTree v1.4.4
 (2006-2018) available on UNIX/Linux/Mac OS X/Windows, and can be read into
 the R computing environment using the function read.newick() in the
 phytools library. PHYLIP (*.phy) are text-based files representing DNA
 squence data, which can be viewed by many DNA sequence alignment editors
 and read into the R computing environment with the function read.phylip()
 in the library phylotools. JPEG (*.jpeg) is a common format for raster
 image files, which can be viewed by many public domain image viewing
 programs. ## Sharing/Access information Previous dryad submission(s) with
 the exon-capture methodology include
 [https://doi.org/10.5061/dryad.9jk90f6](https://doi.org/10.5061/dryad.9jk90f6). All data is included in this dryad submission ## Code/Software osm9fv3.r: The R code used to compute all the analyses and create all the figures in the manuscript.