README

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