Data from: Larval developmental histories, phenotypes, and stage-specific fitness of a temperate reef fish (Forsterygion lapillum)
Data files
Oct 18, 2025 version files 75.03 MB
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all_microchem_data.csv
73.70 MB
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all_microstructure_data.csv
1.11 MB
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analyses_v10.R
71.66 KB
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fish_surveys.csv
1.52 KB
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habitat_surveys.csv
8.67 KB
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light_trap_and_smurf_collections.csv
13.74 KB
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metadata.csv
106.66 KB
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README.md
15.44 KB
Abstract
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.
Dataset DOI: 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