DOI: 10.5061/dryad.8gtht76wn
title: Global patterns of nuclear and mitochondrial genetic diversity in marine fishes

description: Genetic diversity is a fundamental component of biodiversity. Examination
 of global patterns of genetic diversity can help highlight mechanisms
 underlying species diversity, though a recurring challenge has been that
 patterns may vary by molecular marker. Here, we compiled 6862 observations
 of genetic diversity from 492 species of marine fish and tested among
 hypotheses for diversity gradients: the founder effect hypothesis, the
 kinetic energy hypothesis, and the productivity-diversity hypothesis. We
 fit generalized linear mixed effect models (GLMMs) and explored the extent
 to which various macroecological drivers (latitude, longitude, temperature
 (SST), and chlorophyll-a concentration) explained variation in genetic
 diversity. We found that mitochondrial genetic diversity followed
 geographic gradients similar to those of species diversity, being highest
 near the Equator, particularly in the Coral Triangle, while nuclear
 genetic diversity did not follow clear geographic patterns. Despite these
 differences, all genetic diversity metrics were correlated with
 chlorophyll-a concentration, while mitochondrial diversity was also
 positively associated with SST. Our results provide support for the
 kinetic energy hypothesis, which predicts that elevated mutation rates at
 higher temperatures increase mitochondrial but not necessarily nuclear
 diversity, and the productivity-diversity hypothesis, which posits that
 resource-rich regions support larger populations with greater genetic
 diversity. Overall, these findings reveal how environmental variables can
 influence mutation rates and genetic drift in the ocean, caution against
 using mitochondrial macro-genetic patterns as proxies for whole-genome
 diversity, and aid in defining global gradients of genetic diversity.
description: This dataset was collected via a literature search in Web of
 Science with the following keywords: <em>fish microsatellite (marine
 OR ocean OR sea) </em>and <em>fish mtDNA (marine OR ocean OR
 sea)</em>. Only studies published before January 5, 2020, were
 included. We retained studies that recorded genetic
 diversity (mitochondrial or nuclear) from wild marine fish populations. To
 do this, we first conducted a title/abstract filter by hand and then
 recorded data for each paper, following the guidelines listed in
 either <em><strong>msat_data_entry_instructions.md</strong></em> or <em><strong>mtDNA_data_entry_instructions.md</strong></em>.
description: # Global patterns of nuclear and mitochondrial genetic diversity in marine
 fishes --- This repository provides the data and scripts for all analyses
 in the associated paper. Data was gathered from a literature search in the
 Web of Science. A complete list of all necessary software and packages
 (with version numbers) can be found at the bottom of this README. --- ##
 Data A list of the files read into R scripts for analyses. These include
 the CSV files where data from the literature search was originally
 recorded. Cells with missing information are infilled with *NA*. * To
 respect the licenses and conditions of data reuse outlined by the data
 creators and managers of the primary data publications, as well as limit
 data reduplication, we have excluded the genetic diversity estimates (He,
 Hd, and pi) in each of the following datasets. All genetic diversity
 estimates are provided and freely accessible in the original publications
 (cited within each dataset), or upon request. Associated metadata are
 reported. * To reduce the potential to introduce unintended risk, we have
 masked the location information for vulnerable, endangered, or otherwise
 threatened species in our dataset. We have followed Dryad's
 guidelines for species data. A summary of each species' IUCN status
 can be found in ***spp_combined_info.csv***. *Files generated by scripts
 are not included, with 1 exception.* ### *Fishery lat msats .csv*,
 *msat\_2011-2020*.csv These files are where microsatellite data were
 originally recorded. In these spreadsheets, studies are assigned to rows.
 If a study recorded data from more than one species, location, and/or
 microsatellite marker, it was given more than one row (e.g., each row
 represented data from a unique study/species/location/marker combination).
 These files are all read into ***assemble_data_msat.R***. Information in
 the columns is as follows: * Column 1: Species scientific name * Column 2:
 Species common name * Column 3: Study (paper) the data were recorded from
 * Column 4: Indicates whether the study is a primer note or not (1 for
 yes, 0 for no) * Column 5: Country where the sample was taken * Column 6:
 Site where the sample was taken, as named by the paper author * Column 7:
 Degrees latitude (may be decimal degrees) * Column 8: Minutes latitude *
 Column 9: Seconds latitude * Column 10: Degrees longitude (may be decimal
 degrees) * Column 11: Minutes longitude * Column 12: Seconds longitude *
 Column 13: Year in which the samples were taken * Column 14: Number of
 microsatellite markers * Column 15: Name of the microsatellite marker, as
 listed in the paper * Column 16: Indicates whether the microsatellite was
 originally developed in a different species (1 if yes, 0 if no) * Column
 17: Number of individuals sampled * Column 18: Length of the
 microsatellite repeat, in bases * Column 19 (for the
 ***msat_2011-2020_data.csv**** files only): A "Notes" column,
 that contains any notes made by the recorder during the data collection
 process. ### **ppdat\_2016-03-04wLL.csv** This file contains the raw data
 used in Pinsky & Palumbi (2014). It is also read into
 ***assemble_data_msat.R***. Information in the columns is as follows: *
 Columns 1-8: Match columns 1-8 in ***Fishery lat msats.csv*** and
 ***msat_2011-2020_data.csv*** * Column 9: Degrees longitude (may be
 decimal degrees) * Column 10: Minutes longitude * Columns 11-16: Match
 columns 13-18 in ***Fishery lat msats.csv*** and
 ***msat_2011-2020_data.csv*** ### **Fishery lat mtDNA Complete
 Database.csv**, **mtdna\_2013-2020\_data.csv**,
 **mtdna\_2013-2020\_data\_1site.csv** These files are where mitochondrial
 DNA (mtDNA) data were originally recorded. In these spreadsheets, studies
 are assigned to rows. If a study recorded data from more than one species,
 location, and/or mtDNA locus, it was given more than one row (e.g., each
 row represented data from a unique study/species/location/locus
 combination). These files are all read into ***assemble_data_mtDNA.R***.
 Information in the columns is as follows: * Column 1: Species scientific
 name * Column 2: Species common name * Column 3: Study (paper) the data
 were recorded from * Column 4: Country where the sample was taken * Column
 5: Site where the sample was taken, as named by the paper author * Column
 6: Degrees latitude (may be decimal degrees) * Column 7: Minutes latitude
 * Column 8: Seconds latitude * Column 9: Degrees longitude (may be decimal
 degrees) * Column 10: Minutes longitude * Column 11: Seconds longitude *
 Column 12: Year in which the sample was taken * Column 13: Name of the
 mtDNA locus, as listed in the paper * Column 14: Number of individuals
 sampled * Column 15: Length of the mtDNA locus, in bases * Column 16: Any
 notes made by the recorder during the data collection process ###
 **msat\_to\_match.csv** This file contains information on matching stock
 IDS (RAM Legacy fishery stocks) for some of the microsatellite data. This
 file is read into ***assemble_data_msat.R***. Information in the columns
 is as follows: * Column 1: Species scientific name (of matching stock from
 the RAM database) * Column 2: Country of the matching stock from RAM
 database * Column 3: Name of the location of the matching stock from the
 RAM database * Column 4: Name of the stock from the RAM database * Column
 5: Species scientific name * Column 6: Species common name * Column 7:
 Study (paper) the data were recorded from * Column 8: Indicates whether
 the study is a primer note or not (1 for yes, 0 for no) * Column 9: Year
 in which the samples were taken * Column 10: Number of microsatellite
 markers * Column 11: Name of the microsatellite marker, as listed in the
 paper * Column 12: Indicates whether the microsatellite was originally
 developed in a different species (1 if yes, 0 if no) * Column 13: Number
 of individuals sampled * Column 14: Length of the microsatellite repeat,
 in bases * Column 15: Name of the data file that contains data from the
 matching population * Column 16: Latitude of the sample (in decimal
 degrees) * Column 17: Longitude of the sample (in decimal degrees) ###
 **mtDNA\_to\_match.csv** This file contains information on matching stock
 IDS (RAM Legacy fishery stocks) for some of the mtDNA data. This file is
 read into ***assemble_data_mtDNA.R***. Information in the columns is as
 follows: * Column 1: Species scientific name (of matching stock from the
 RAM database) * Column 2: Country of the matching stock from RAM database
 * Column 3: Name of the location of the matching stock from the RAM
 database * Column 4: Name of the stock from the RAM database * Column 5:
 Species scientific name * Column 6: Species common name * Column 7: Study
 (paper) the data were recorded from * Column 8: Year in which the samples
 were taken * Column 9: Name of the mtDNA locus, as listed in the paper *
 Column 10: Number of individuals sampled * Column 11: Length of the mtDNA
 locus, in bases * Column 12: Latitude of the sample (in decimal degrees) *
 Column 13: Longitude of the sample (in decimal degrees) ###
 **spp\_combined\_info.csv** This file contains the taxonomic information,
 IUCN status, and range extent information for all species in either (or
 both) the microsatellite and mitochondrial datasets. This file is read
 into ***bootstrap_hd.R***, ***bootstrap_he.R***, ***bootstrap_pi.R***,
 ***msat_he_family_trends.R***, ***msat_he_models.R***,
 ***msat_he_predict.R***, ***mtdna_hd_family_trends.R***,
 ***mtdna_hd_models.R***, ***mtdna_hd_predict.R***,
 ***mtdna_pi_family_trends.R***, ***mtdna_pi_models.R***, and
 ***mtdna_pi_predict.R***. Information in the columns is as follows: *
 Column 1: Species scientific name * Column 2: Species common name * Column
 3: The genus the species belongs to * Column 4: The family the species
 belongs to * Column 5: The order the species belongs to * Column 6: The
 IUCN red list status of the species * Column 7: Whether the species is
 pelagic or coastal * Column 8: The latitude of the northernmost extent of
 the species range * Column 9: The latitude of the southernmost extent of
 the species range * Column 10: The longitude of the westernmost extent of
 the species range * Column 11: The longitude of the easternmost extent of
 the species range * Column 12: The total latitudinal breadth of the
 species range * Column 13: Half of the total latitudinal breadth of the
 species * Column 14: The latitude of the central point (centroid) of the
 species range ### **sharedstudies.csv** This file contains the
 microsatellite and mtDNA genetic diversity observations for populations
 where both nuclear & mitochondrial genetic diversity were recorded.
 This file is both read into (and created by) ***ID_shared_species.R***. *
 Column 1: Species scientific name * Column 2: Species common name * Column
 3: Study (paper) the data were recorded from * Column 4: Country where the
 samples were taken * Column 5: Site where the samples were taken, as named
 by the paper author * Column 6: Latitude of the samples (in decimal
 degrees) * Column 7: Longitude of the samples (in decimal degrees) --- ##
 Code A list of the R scripts used for analyses. **assemble_data_msat.R**
 Cleans and assembles ***Fishery lat msats.csv***,
 ***msat_2011-2020.csv***, and ***ppdat_2016-03-04wLL.csv*** into one
 cohesive data frame. **assemble_data_mtDNA.R** Cleans and assembles
 ***Fishery lat mtDNA Complete Database.csv***,
 ***mtdna_2013-2020_data.csv***, and ***mtdna_2013-2020_data_1site.csv***
 into one cohesive data frame. **bootstrap_hd.R** Bootstraps mtDNA Hd
 models to calculate 95% confidence intervals for model coefficients.
 **bootstrap_he.R** Bootstraps nuclear microsatellite He models to
 calculate 95% confidence intervals for model coefficients.
 **bootstrap_pi.R** Bootstraps mtDNA pi models to calculate 95% confidence
 intervals for model coefficients. **coefficient_bootstrap_cis.R** Reads in
 output from the ***bootstrap.R*** files to create supplemental figures
 summarizing results. **ID_shared_species.R** Identifies
 populations/species where both mtDNA and nuclear (microsatellite) genetic
 diversity was measured. **maps.R** Creates maps of the global distribution
 of all genetic diversity estimates, as well as mean chlorophyll-a
 concentration and SST (and a correlation plot between the two).
 **msat_he_family_trends.R** Plots marginal effects (relationship between
 microsatellite He and a given predictor variable) for a subset of 10
 families for all nuclear (microsatellite) He models. **msat_he_models.R**
 Code for all nuclear (microsatellite) He models. **msat_he_predict.R**
 Plots marginal effects (relationship between microsatellite He and a given
 predictor variable) for all nuclear (microsatellite) He models.
 **mtdna_hd_family_trends.R** Plots marginal effects (relationship between
 mtDNA Hd and a given predictor variable) for a subset of 10 families for
 all mtDNA Hd models. **mtdna_hd_models.R** Code for all mtDNA Hd models.
 **mtdna_hd_predict.R** Plots marginal effects (relationship between mtDNA
 Hd and a given predictor variable) for all mtDNA Hd models.
 **mtdna_pi_family_trends.R** Plots marginal effects (relationship between
 mtDNA pi and a given predictor variable) for a subset of 10 families for
 all mtDNA pi models. **mtdna_pi_models.R** Code for all mtDNA pi models.
 **mtdna_pi_predict.R** Plots marginal effects (relationship between mtDNA
 pi and a given predictor variable) for all mtDNA pi models.
 **pull_env_data.R** Pulls corresponding environmental data from Bio-ORACLE
 for populations in either (or both) the nuclear (microsatellite) and mtDNA
 datasets. **pull_range_data.R** Pulls range extent data from FishBase
 (i.e., AquaMaps) for all species in either (or both) the nuclear
 (microsatellite) and mtDNA datasets --- ## Software **Necessary Software**
 1. R (v.4.2.2 or above) 2. RStudio (v.2022.12.0 or above) **Necessary R
 Packages** 1. data.table (v.1.14.8) 2. DHARMa (v.0.4.6) 3. glmmTMB
 (v.1.1.7) 4. here (v.1.0.1) 5. leaflet (v.2.1.2) 6. lme4 (v.1.1-31) 7.
 MuMIn (v.1.47.5) 8. performance (v.0.10.4) 9. raster (v.3.6-20) 10.
 rfishbase (v.4.1.1) 11. scales (v.1.2.1) 12. sdmpredictors (v.0.2.14) 13.
 sf (v.1.0.13) 14. sjplot (v.2.8.12) 15. splines (v.4.2.2) 16. tidyverse
 (v.2.0.0) 17. tmap (v.3.3.4) --- ## Data Filtering Steps Documents that
 catalog all of the filtering steps and decisions that the studies included
 in the literature search went through. General outline of the steps: 1.
 Microsatellite Web of Science search (conducted on 2011.12.11 &
 2020.01.05) with the following keywords: fish, microsatellite, marine OR
 ocean OR sea. mtDNA Web of Science search (conducted on 2013.01.29 &
 2020.01.05) with the following keywords: fish, mtDNA, marine OR ocean OR
 sea. 2. Filtered title/abstract by hand and recorded data from each study
 following the guidelines listed in ***msat_data_entry_instructions.md***
 or ***mtDNA_data_entry_instructions.md***. Notes on filtering can be found
 in (1) ***undergrad_data_entry_notes_2012-2015.md***,
 ***rene_data_entry_notes_2019-2020.md***, or (3)
 ***marial_data_entry_notes_2020.md***. * A complete list of references for
 all studies included in our datasets can be found
 in ***Data_Sources.pdf***.