DOI: 10.5061/dryad.3r2280gkj
title: Mapping the correlations and gaps in studies of complex life histories

description: For species with complex life histories, phenotypic correlations between
 life-history stages constrain both ecological and evolutionary
 trajectories. Studies that seek to understand correlations across life
 history differ greatly in their experimental approach: some follow
 individuals (“individual longitudinal”), while others follow cohorts
 (“cohort longitudinal”). Cohort longitudinal studies risk confounding
 results through Simpson’s Paradox, where correlations observed at the
 cohort-level do not match that of the individual-level. Individual
 longitudinal studies are laborious in comparison, but provide a more
 reliable test of correlations across life-history stages. Our
 understanding of the prevalence, strength and direction of phenotypic
 correlations depends on the approaches that we use, but the relative
 representation of different approaches is unknown. Using marine
 invertebrates as a model group, we used a formal, systematic literature
 map to screen 17,000+ papers studying complex life histories, and
 characterized the study type (i.e. cohort longitudinal, individual
 longitudinal or single stage), as well as other factors. For 3,315
 experiments from 1,716 articles, most (67.4%) focused on a single stage,
 and just 1.7% used an individual longitudinal approach. While life-history
 stages have been studied extensively, we suggest that the field prioritize
 individual longitudinal studies to understand the phenotypic correlations
 among stages.
description: Mapping the correlations and gaps in studies of complex life histories
 This study is a literature map of marine invertebrate life histories. We
 have collated published articles and summarise their experimental methods
 as a means to evaluate the state of our field. This document includes a
 description of all data files: (1) FINAL_DATASET.xlsx--all data collected
 from over 3,000 published experiments in the literature \***light red
 shading is data summarised from main data source (within each tab these
 are labeled as Tables) \***light blue shading is data used in manuscript,
 tables or figures (2) species_list.csv--species names given in each
 article were put through GBIF database to find species synonyms (i.e. if a
 single species was referred to by more than one name in the literature)
 (3) simpons.csv--used to generate Figure1, a depiction of Simpson's
 Paradox, a central theme to the manuscript (4) search_articles.xlsx--all
 articles accepted and rejected through literature mapping process (1)
 FINAL_DATASET.xlsx Tabs * all data * Phylum * Class * Original species
 name * this is the species name found in the article * Gbif species name *
 this is the species name found in GBIF database, this may match the
 original species name, or may differ if a single species has a name
 synonym * Columns E to J * 'y' (stage present in experiment)/
 '-' (stage absent in experiment) * F0_adult * Embryo * Larvae *
 Metamorphosis * Post-metamorphosis/juvenile * F1_adult * Lab_field * where
 experiment was conducted * L = lab * F = field * Study type * S = Single
 stage (measure one stage) * CL = Cohort longitudinal (measure more than
 one stage, replication level is cohort) * IL = Individual longitudinal
 (measure more than one stage, replication level is individual) * Dev_mode
 * Development mode * P = planktotrophic (long-lived, feeding larvae) * L =
 lecithotrophic (short-lived, feeding larvae) * D = direct development
 (crawl-away juveniles) * Trait_measured * traits measured in experiment
 (Table A2 in Appendix lists accepted traits for this map) * Reference *
 Collected * Primary reviewer that collected data * Search (see Methods,
 Appendix Table A4) * 1conducted in 2014 * 2-conducted in 2014 * 3conducted
 in 2015 * 4conducted in 2021 * study type * Data used for Figure 2B *
 Number of studies for each study type * field vs. lab * Number of studies
 conducted in field vs laboratory * single stage * Data used for Figure 3A
 * number of single-stage studies that measured each stage * cohort
 longitudinal--counts for this experimental method * Table 1--light gray
 diagonal used in Figure 3B * Diagonal is number of studies that begin with
 each stage. * Rest of row is the number of studies that also measure other
 stages * Table 2--stages measured in each study * 'y' (stage
 present in experiment)/ '-' (stage absent in experiment) * Table
 3--summary of Table 2 * number of studies that measured each stage
 combination Middle is counts for every combination of stage transition *
 Table 4--Data used for Figure 4A * From Table 2, the number of studies
 that measure sequential stages * rows show studies that start at each
 stage and measure stages sequentially after * Table 5--Data used for
 Figure 4B * From Table 3, number of studies that measure stages that are
 not sequential * individual longitudinal--counts for this experimental
 method * Table 1--light gray diagonal used in Figure 3C * Diagonal is
 number of studies that begin with each stage. * Rest of row is the number
 of studies that also measure other stages * Table 2--stages measured in
 each study * 'y' (stage present in experiment)/ '-'
 (stage absent in experiment) * Table 3--summary of Table 2 * number of
 studies that measured each stage combination Middle is counts for every
 combination of stage transition * Table 4--Data used for Figure 4C * From
 Table 2, the number of studies that measure sequential stages * rows show
 studies that start at each stage and measure stages sequentially after *
 Table 5--Data used for Figure 4D * From Table 3, number of studies that
 measure stages that are not sequential * direct development-counts for
 species with direct development only (Appendix) * Table 1--Data used for
 Figure A2B * Number of studies for each study type * Table 2--Data used
 for Figure A3A * number of single-stage studies that measured each stage *
 Tables 3 - 7 cohort longitudinal counts * Table 3 light gray diagonal used
 in Figure A3B * Diagonal is number of studies that begin with each stage.
 * Rest of row is the number of studies that also measure other stages *
 Table 4--stages measured in each study * 'y' (stage present in
 experiment)/ '-' (stage absent in experiment) * Table 5--summary
 of Table 4 * number of studies that measured each stage combination Middle
 is counts for every combination of stage transition * Table 6--Data used
 for Figure A4A * From Table 4, the number of studies that measure
 sequential stages * rows show studies that start at each stage and measure
 stages sequentially after * Table 7--Data used for Figure A4B * From Table
 5, number of studies that measure stages that are not sequential * Tables
 8 - 11 individual longitudinal counts * Table 8 light gray diagonal used
 in Figure A3B * Diagonal is number of studies that begin with each stage.
 * Rest of row is the number of studies that also measure other stages *
 Table 9--stages measured in each study * 'y' (stage present in
 experiment)/ '-' (stage absent in experiment) * Table
 10--summary of Table 9 * number of studies that measured each stage
 combination Middle is counts for every combination of stage transition *
 Table 11--Data used for Figure A4C * From Table 9, the number of studies
 that measure sequential stages * rows show studies that start at each
 stage and measure stages sequentially after * taxonomy--data used for
 Figure 5 * Counts and percentages for phyla represented in study (Figure
 5A) and ten most common species (Figure 5B) * development mode * Table 1
 Development mode by number of experiments * A single study can have more
 than one experiment for one species (this map has 3315 experiments) *
 Table 2) Development mode and study type by number of experiments * Table
 3) Development mode by unique combinations of development mode, species
 and reference 'by study' * An article with multiple experiments
 on one species may inflate frequencies of development mode. * When
 accounting for articles that include multiple experiments on one species,
 there are 2944 unique studies * Table 4) Compare this map to Marshall et
 al. (2012), The biogeography of marine invertebrate life histories. Annual
 Review of Ecology, Evolution, and Systematics 43: 97-114. * Table 5) Table
 4 as percent * Percent misrepresentation is the percent difference between
 this map and the Marshall et al. (2012) estimates * resolved species *
 Original species name--species name taken from published study * Gbif
 species name--species name matched with each original name, using the Gbif
 database * Columns C and D of 'all data' tab (2)
 species_list.csv * Used to search GBIF database (see R file) * Phylum *
 Class * Species_name (3) simpsons.csv * Used to generate Figure 1 main
 text * Linepoints/lines shown in different colours in panels b and c;
 labelled as Cohorts 1, 2 and 3 in legend * xembryo size values * ylarval
 size values (4) search_articles.xlsx * List of articles accepted for
 literature map and articles rejected * Search (Year)corresponds with
 searches 1-4 described in methods * Articlefull citation