DOI: 10.5061/dryad.5qfttdzjj
title: Data from: Larval developmental histories, phenotypes, and stage-specific fitness of a temperate reef fish (<em>Forsterygion lapillum</em>)

description: Developmental histories shape individual fitness and demographic
 heterogeneity in many systems, yet the consequences of this variation
 across complex life histories remain relatively underexplored. We
 characterized variability in larval developmental histories of a temperate
 reef fish (the common triplefin, Forsterygion lapillum), and evaluated
 patterns and sources of variation in post-settlement selection that
 reshaped trait distributions in older life stages. More
 specifically, we sampled fish at successive life stages (larva, juvenile,
 adult) across six populations, evaluated microchemical profiles within
 their otoliths, and identified three distinct ‘larval developmental
 histories’ indicative of time spent in different nearshore coastal
 environments. Developmental histories showed contrasting survival
 advantages across different life stage transitions. Specifically,
 selection across the settlement transition favored a developmental history
 that was indicative of nearshore larval development, suggesting that
 larval retention (or early entrainment) in a coastal boundary layer
 enhances juvenile recruitment. In contrast, selection across the
 maturation transition favored a developmental history that was indicative
 of offshore larval development, suggesting trade-offs in fitness across
 life stages. Competitor density and habitat structure were
 significantly associated with per capita mortality rates, further shaping
 survival outcomes for favored developmental histories. Per capita
 mortality rates of the favored developmental history increased with
 conspecific density across the settlement transition and the maturation
 transition. This study highlights the importance of
 stage-specific selection and demographic heterogeneity (e.g., local
 patterns of phenotypic composition) on the dynamics of ecological systems.
description: # Data from: Larval developmental histories, phenotypes, and
 stage-specific fitness of a temperate reef fish (*Forsterygion lapillum*)
 Dataset DOI: [10.5061/dryad.5qfttdzjj](10.5061/dryad.5qfttdzjj) ##
 Description of the data and file structure Data consist of a set of files
 containing information about (1) collections of common triplefin
 (*Forsterygion lapillum*) from six sites within the Wellington region of
 New Zealand, (2) habitat and fish community data that characterize each
 site, and (3) otolith microchemistry and microstructure from a subset of
 collected fish. ### Files and variables #### File: analyses_v10.R
 **Description:** R code used to generate all analyses and figures for a
 manuscript submitted to Ecology #### File: fish_surveys.csv
 **Description:** Surveys of resident fish were conducted by a pair of
 divers (aided by SCUBA) swimming side-by-side along a 10 m × 4 m belt
 transect positioned near the center of each site (~ 2 - 4 m depth,
 oriented parallel to the shoreline). Censuses were completed on two
 separate occasions. ##### Variables * date: date of census * census: a
 numeric descriptor of each census (either 1 or 2) * site: name of the
 censused site; GPS locations for each site: Kau Bay
 (41°17'17.86"S, 174°49'53.35"E), Point Halswell
 (41°17'2.40"S, 174°49'30.89"E), and Shark Bay
 (41°18'7.57"S, 174°49'2.20"E), Island Bay
 (41°20'59.66"S, 174°46'9.02"E), Ohiro Bay
 (41°20'57.26"S, 174°45'30.80"E), and Yung Pen
 (41°20'53.20"S, 174°45'20.93"E) * diver: surname of
 the diver collecting the data * min depth: minimum depth (in meters) along
 the transect * max depth: maximum depth (in meters) along the transect *
 visibility: visibility in meters * n_celeidotus: counts of *Notolabrus
 celidotus* * blue_cod: counts of *Parapercis colias* * banded_wrasse:
 counts of *Notolabrus fucicola* * f_lapillum: counts of *Forsterygion
 lapillum* * f_varium: counts of *Forsterygion varium* *
 grahamina_bellpiscis: combined counts of *Grahamina sp.* and *Bellpiscis
 sp* * blue_moki: counts of *Latridopsis ciliaris* *
 banded_blue-eye_triplefin: counts of *Notoclinops segmentatus* *
 leatherjacket: counts of *Parika scaber* #### File: habitat_surveys.csv
 **Description:** Surveys of habitat attributes were conducted by a pair of
 divers (aided by SCUBA) swimming side-by-side along a 10 m × 4 m belt
 transect positioned near the center of each site (~ 2 - 4 m depth,
 oriented parallel to the shoreline). Censuses were completed on two
 separate occasions. Divers censused 2x2m squares (denoted by
 "transect position") along the transect (each diver did his/her
 own side) and counted all individual "plants" of macroalgae,
 identifying to genus/species. Divers estimated % cover of canopy at
 approximately 80-100cm off the substrate (imagining a plane through that
 depth). Lastly, divers estimated percent cover of substrate type (Rock,
 Boulder, Cobble, Shell/Pebble, or Sand). ##### Variables * date: date of
 census * census: a numeric descriptor of each census (either 1 or 2) *
 site: name of the censused site; GPS locations for each site: Kau Bay
 (41°17'17.86"S, 174°49'53.35"E), Point Halswell
 (41°17'2.40"S, 174°49'30.89"E), and Shark Bay
 (41°18'7.57"S, 174°49'2.20"E), Island Bay
 (41°20'59.66"S, 174°46'9.02"E), Ohiro Bay
 (41°20'57.26"S, 174°45'30.80"E), and Yung Pen
 (41°20'53.20"S, 174°45'20.93"E) * diver: surname of
 the diver collecting the data * transect position: start of the 2x2m
 censused area along either side of the transect * carpophyllum count:
 counts of individual "plants" of *Carpophyllum spp.* *
 cystophora count: counts of individual "plants" of *Cystophora
 spp.* * lessonia count: counts of individual "plants"
 of *Lessonia variegata* * ulva count: counts of individual
 "plants" of *Ulva spp.* * undaria count: counts of individual
 "plants" of *Undaria pinnatifida* * carpophyllum canopy: percent
 cover of canopies of *Carpophyllum spp.* * cystophora canopy: percent
 cover of canopies of *Cystophora spp.* * lessonia canopy: percent cover of
 canopies of *Lessonia variegata* * ulva canopy: percent cover of canopies
 of *Ulva spp.* * entromorpha canopy: percent cover of canopies of
 *Entromorpha spp.* * caulurpa canopy: percent cover of canopies of
 *Caulurpa spp.* * undaria canopy: percent cover of canopies of *Undaria
 pinnatifida* * percent_rock: percent cover of benthos by contiguous rocky
 reef * percent_boulder: percent cover of benthos by boulders *
 percent_cobble: percent cover of benthos by cobbles *
 percent_pebble_shell: percent cover of benthos by pebbles and/or shell *
 percent_sand: percent cover of benthos by sand * NOTES: a free-text field
 for any additional notes #### File: light_trap_and_smurf_collections.csv
 **Description:** Fish collections targeting common triplefin
 (*Forsterygion lapillum*) at two different life stages, using two
 different collector types: pre-settlement larvae were sampled by light
 traps deployed overnight, and settlement/early post-settlement stage
 juveniles were collected using "Standard Monitoring Units for
 Recruitment of Fishes" (i.e., "SMURFS") deployed for
 variable durations. Three replicate collectors were usually deployed at
 each site, but were not always recovered successfully (lost collectors or
 failure of light traps to activate yield missing values denoted by
 ".". Some observations also have missing data on taxonomic
 breakdown of triplefin assemblage (missing values indicated
 by"."). ##### Variables * deployment.date: date of collector
 deployment * collection.date: date of collector recovery * fishing_days:
 number of days (or nights) that collector was deployed (1 for light traps,
 variable durations for SMURFs) * sampler: either Light trap or SMURF *
 region: geographic description of an area (either Wellington harbour or
 Wellington south coast) * site: a specific location within each
 region: KB=Kau Bay (41°17'17.86"S, 174°49'53.35"E),
 PH=Point Halswell (41°17'2.40"S, 174°49'30.89"E), and
 SB=Shark Bay (41°18'7.57"S, 174°49'2.20"E) are located
 within the relatively sheltered Wellington harbour; IB=Island Bay
 (41°20'59.66"S, 174°46'9.02"E), OB=Ohiro Bay
 (41°20'57.26"S, 174°45'30.80"E), and YP=Yung Pen
 (41°20'53.20"S, 174°45'20.93"E), are located on
 Wellington south coast * site_detail: A desciptor of replicate collector
 position within each site (suffix E, M, W, S, N correspond to east,
 middle, west, south, and north respectively). * total_triplefins: counts
 of undifferentiated triplefins (mostly *Forsterygion lapillum*) *
 scaly_headed: combined counts of *Grahamina sp.* and *Bellpiscis sp* *
 variable: counts of *Forsterygion varium* * blue_eye: counts
 of *Notoclinops segmentatus* * common: counts of *Forsterygion lapillum* *
 unknown_triplefin: counts of unidentified triplefin * other: other species
 (identified in the "comments" field) * comments: a free text
 description, often used to identify other species found in collectors ####
 File: all_microchem_data.csv **Description:** Otolith microchemistry
 obtained from LA-ICP-MS sampling of a single sagittal otolith from common
 triplefin (*Forsterygion lapillum*). Data are ordered by fish.id (a unique
 identifier of individual fish) and LA-ICP-MS scans along a transect
 running from the otolith core to the postrostral otolith edge. Missing
 numeric values are indicated by "NA", and indicate cases where
 elemental counts were determined to be unreliable in pre-processing steps
 (i.e., below instrument detection limits, consistent with contamination,
 etc). Missing values within Notes fields are indicated as "N/A",
 and reflect no recorded note for the associated observation. #####
 Variables * : ordered, running count of rows containing data * fish.id: a
 unique identifier of subsampled fish * site: a specific location within
 each region: KB=Kau Bay (41°17'17.86"S,
 174°49'53.35"E), PH=Point Halswell (41°17'2.40"S,
 174°49'30.89"E), and SB=Shark Bay (41°18'7.57"S,
 174°49'2.20"E) are located within the relatively sheltered
 Wellington harbour; IB=Island Bay (41°20'59.66"S,
 174°46'9.02"E), OB=Ohiro Bay (41°20'57.26"S,
 174°45'30.80"E), and YP=Yung Pen (41°20'53.20"S,
 174°45'20.93"E), are located on Wellington south coast *
 region: geographic description of an area (either Wellington harbour or
 Wellington south coast) * site_detail: A descriptor of replicate collector
 position within each site (suffix E, M, W, S, N correspond to east,
 middle, west, south, and north respectively). * sampler: either Light
 trap, SMURF, or Hand net * wet_weight: wet weight of fish in g * tl: total
 length of fish in mm * sl: standard length of fish in mm * body_height:
 body height of fish in mm * body_width: body width of fish in mm * notes:
 free text field for notes * measured_by: first name of researcher
 conducting morphological measurements * collection.date: date of fish
 collection * ablation_time: time of LA-ICP-MS scan (seconds after first
 ablation) * Li: Lithium concentration (ratio of 7LI to 43Ca,
 units µmol/mol) * B: Boron concentration (ratio of 11B to 43Ca, units
 mmol/mol) * Mg: Magnesium concentration (ratio of 24Mgto 43Ca, units
 mmol/mol) * P: Phosphorus concentration (ratio of 41P to 43Ca, units
 mmol/mol) * S: Sulphur concentration (ratio of 34S to 43Ca, units
 mmol/mol) * K: Potassium concentration (ratio of 39K to 43Ca, units
 mmol/mol) * Mn: Manganese concentration (ratio of 55Mn to 43Ca,
 units µmol/mol) * Cu: Copper concentration (ratio of 63Cu to 43Ca,
 units µmol/mol) * Zn: Zinc concentration (ratio to 66Zn to 43Ca,
 units µmol/mol) * Sr: Strontium concentration (ratio to 88Sr to 43Ca,
 units mmol/mol) * Ba: Barium concentration (ratio of 138Ba to 43Ca,
 units µmol/mol) * Pb: Lead concentration (ratio of 208Pb to 43Ca,
 units µmol/mol) * block: an identifier of samples processed as a group on
 the same day * analysis_date: date of analysis * duplicate: qa/qc field *
 notes.x: additional notes field * analysis.date: date of analysis * plot:
 qa/qc field * mnminscan: scan_no corresponding to a local minima in Mn
 (used to infer start of period of pelagic larval development) *
 mn_max_scan: scan_no corresponding to a local maxima in Mn (used to infer
 end of period of pelagic larval development) * ba_breakpoint_scan: scan_no
 corresponding to a local minima (breakpoint) in Ba (used to infer start of
 period of pelagic larval development) * notes.y: additional notes field *
 scan_no: scan number, ordered from start of a given data series *
 inv_scan_no: inverse scan number, ordered from end of a given data series
 * scans_per_s: speed of acquisition * microns_from_start: an estimate of
 distance from start of transect (in microns) * microns_from_end: an
 estimate of distance from end of transect (in microns) #### File:
 metadata.csv **Description:** Information on collection location, date,
 mode, and body size of each sampled fish ##### Variables * fish.id: a
 unique identifier of subsampled fish * site: a specific location within
 each region: KB=Kau Bay (41°17'17.86"S,
 174°49'53.35"E), PH=Point Halswell (41°17'2.40"S,
 174°49'30.89"E), and SB=Shark Bay (41°18'7.57"S,
 174°49'2.20"E) are located within the relatively sheltered
 Wellington harbour; IB=Island Bay (41°20'59.66"S,
 174°46'9.02"E), OB=Ohiro Bay (41°20'57.26"S,
 174°45'30.80"E), and YP=Yung Pen (41°20'53.20"S,
 174°45'20.93"E), are located on Wellington south coast *
 region: geographic description of an area (either Wellington harbour or
 Wellington south coast) * site_detail: A descriptor of replicate collector
 position within each site (suffix E, M, W, S, N correspond to east,
 middle, west, south, and north respectively). * sampler: either Light
 trap, SMURF, or Hand net * wet_weight: wet weight of fish in g * tl: total
 length of fish in mm * sl: standard length of fish in mm *
 body_height: body height of fish in mm * body_width: body width of fish in
 mm * notes: free text field for notes * measured_by: first name of
 researcher conducting morphological measurements * collection.date: date
 of fish collection #### File: all_microstructure_data.csv
 **Description:** A subsample of otoliths were analyzed by Nuria Raventos
 (Barcelona Otolith Reading Service) to quantify microstructure. A
 sub-sample of sagittal otoliths from *Forsterygion lapillum* collected
 from light traps were randomly allocated to blocks (denoted
 "bag.id"). Otoliths were polished to expose a growth sequence,
 and daily growth increments were identified, counted and measured.  #####
 Variables * fish.id: a unique identifier of subsampled fish * bag.id: an
 identifier of "block" * hatch.1.1: distance from otolith core to
 an early putative "hatch check" that was evident in many
 otoliths (in microns) * hatch.1.2: distance from otolith core to an second
 putative "hatch check" that was evident in many otoliths (in
 microns) * set.1: distance from otolith core to edge * quality: a
 qualitative comment on the quality of the image * notes.x: an additional
 notes field * increment: daily increment number (starting from the second
 putative hatch check; i.e., inferred larval age of increment formation in
 days) * radius.width: distance from core to increment in microns *
 category: a qa/qc field * incr.width: width of daily growth increment in
 microns * site: a specific location within each region: KB=Kau Bay
 (41°17'17.86"S, 174°49'53.35"E), PH=Point Halswell
 (41°17'2.40"S, 174°49'30.89"E), and SB=Shark Bay
 (41°18'7.57"S, 174°49'2.20"E) are located within the
 relatively sheltered Wellington harbour; IB=Island Bay
 (41°20'59.66"S, 174°46'9.02"E), OB=Ohiro Bay
 (41°20'57.26"S, 174°45'30.80"E), and YP=Yung Pen
 (41°20'53.20"S, 174°45'20.93"E), are located on
 Wellington south coast * region: geographic description of an area (either
 Wellington harbour or Wellington south coast) * site_detail: A descriptor
 of replicate collector position within each site (suffix E, M, W, S, N
 correspond to east, middle, west, south, and north respectively). *
 sampler: either Light trap, SMURF, or Hand net * wet_weight: wet weight of
 fish in g * tl: total length of fish in mm * sl: standard length of fish
 in mm * body_height: body height of fish in mm * body_width: body width of
 fish in mm * notes.y: free text field for notes * measured_by: first name
 of researcher conducting morphological measurements *
 collection.date: date of fish collection * larval.age: putative larval age
 at increment formation in days * pld: putative pelagic larval duration
 (age at collection) * date: putative date of increment formation *
 date.hatch: putative date of hatch * Ri: radius width (distance from core
 to increment in microns) * lag.Ri: radius width lagged by 1d * delta.Ri:
 daily change in radius width * Ri.2: qa/qc field * estimated.lunar.day:
 estimated lunar day of increment formation * lunar.phase: estimated lunar
 phase of increment formation * LD.birth: estimated lunar day of hatch *
 lunar.phase.birth.centered: estimated lunar phase of hatch ##
 Code/software An R script containing all code used to import and analyze
 data (in support of manuscript entitled "Larval developmental
 histories shape phenotypes and stage-specific fitness of a reef
 fish", submitted to *Ecology*) has been uploaded.  This file
 (analysesv10.R) gives the required packages and code necessary to generate
 all figures and analyses presented in this manuscript