Origin and impacts of ploidy variation in the coral Pocillopora acuta in Hawai‘i
Data files
Jul 31, 2026 version files 27.47 MB
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coast_n83.dbf
1.05 KB
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coast_n83.met
18.90 KB
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coast_n83.prj
424 B
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coast_n83.shp
1.47 MB
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coast_n83.shx
204 B
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coast_n83.txt
1.36 KB
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DAPC.R
3.36 KB
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dhw_data.csv
1.72 KB
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dip_trip_pdam.txt
818 B
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Figure_1.R
2.91 KB
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Figure_2.R
4.37 KB
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Figure_3.R
11.43 KB
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Figure_5.R
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Figure_6.R
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Fringing_Reef.dbf
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Fringing_Reef.prj
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Fringing_Reef.qpj
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Fringing_Reef.shp
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Fringing_Reef.shx
188 B
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growth.csv
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haw_benthic_habitat.CPG
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haw_benthic_habitat.dbf
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haw_benthic_habitat.prj
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haw_benthic_habitat.qix
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haw_benthic_habitat.shp
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haw_benthic_habitat.shp.xml
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haw_benthic_habitat.shx
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Historical_clone_year.csv
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Patches2.cpg
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Patches2.dbf
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Patches2.prj
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Patches2.qpj
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Patches2.shp
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Patches2.shx
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Percent_shared_SNPs.csv
2.32 MB
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Ploidy_polyVCF.txt
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Pocilloploidy_collection_site_GPS_-_all_studies.csv
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Pocilloploidy_dp10miss0.05_SNPs_thin1000.vcf
2.33 MB
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Pocilloploidy_historical_and_2024_metadata.csv
14.36 KB
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Pocilloploidy_spawning_metadata.csv
4.85 KB
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Pocilloploidy.ibsMat
1.35 MB
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README.md
8.56 KB
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sample_metadata.txt
6.73 KB
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samples.txt
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StAMPP.R
5.86 KB
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str_K7_plot.csv
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str_K8_plot.csv
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str_K9_plot.csv
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STRUCTURE.R
3.82 KB
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surv_data.csv
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surv_SA.csv
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weight.csv
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Abstract
Differences in ploidy impact fitness, shaping adaptation and evolutionary trajectories. Although polyploidy has been documented in corals, the mechanisms that give rise to polyploidy and the phenotypic consequences of this variation are unknown. We established a model population of 326 Pocillopora acuta colonies in Kāneʻohe Bay, Hawai‘i, and used RAD sequencing of these samples and historical collections to define clonal lineages, ploidy state, and mechanistic origin of polyploidy in each colony. We also measured growth, morphometrics, thermal tolerance, and fecundity in common-gardened corals. Here we show that triploidy in P. acuta likely originated via allopolyploidy via hybridization between P. acuta and its sister species, P. damicornis. Triploids were present in this population before and after the 2014/2015 bleaching events, becoming the dominant ploidy on contemporary reefs (>60% of genotypes). These bleaching events did not select for triploid genotypes; however, relative triploid abundance may have increased in part due to higher growth rates compared to diploids. Both ploidies released larvae on the same lunar cycle and there was no difference in photosynthetic efficiency during heat stress, but triploid colonies experienced greater mortality at lower levels of stress, suggesting a host-derived fitness consequence influenced by ploidy state. This work highlights a cryptic source of variance in coral fitness, with important implications for understanding their ecology and evolution.
Dataset DOI: 10.5061/dryad.vx0k6dk7m
Description of the data and file structure
Files and variables
File: Figure_1.R
Description: R code to produce Figure 1, the map of collection site locations of colonies.
Files: coast_n83
Description: This set of files (.dbf, .met, .prj, .shp, .shx, .txt) is used to generate the map of O'ahu, Hawai'i, in Figure 1.
Files: Fringing_Reef
Description: This set of files (.dbf, .prj, .qpg, .shp, .shx) is used to generate the map of fringing reef in Kāne'ohe Bay in Figure 1.
Files: haw_benthic_habitat
Description: This set of files (.CPG, .dbf, .prj, .qix, .shp, .shp.xml, .shx) is used to generate the map of the back reef and reef flat in Kāne'ohe Bay in Figure 1.
Files: Patches2
Description: This set of files (.cpg, .dbf, .prj, .qpg, .shp, .shx) is used to generate the map of the patch reefs in Kāne'ohe Bay in Figure 1.
File: Pocilloploidy_collection_site_GPS_-_all_studies.csv
Description: dataset of Pocillopora collection sites from Gorospe and Karl (2013), Stephens et al. (2023), and this study used to make Figure 1.
Variables
- Reef: Patch or back reef identification in Kāne'ohe Bay
- GPS: GPS coordinates for that reef
- Study: The study for which each reef was sampled
File: Figure_2.R
Description: R code to produce Figure 2, the identity by state matrix and % shared SNPs used to identify unique genotypes of Pocillopora acuta and P. damicornis.
File: Percent_shared_SNPs.csv
Description: Percent of Shared SNPs dataset used to make Figure 2.
Variables
- ind1: Sample ID of colony
- ind2: Sample ID of colony
- match_perc: Percent of Shared SNPs between ind1 and ind2
File: Pocilloploidy.ibsMat
Description: dataset used to make identity by state matrix Figure 2.
File: sample_metadata.txt
Description: metadata used to make Figure 2.
Variables
- Sample_IDs: Sample ID of colony
- Ploidy: Either Diploid, Triploid, Diploid: P. damicornis mtORF, or Ploidy unknown: P. damicornis mtORF
- New_Clade: Genotype ID
File: Figure_3.R
Description: R code to produce Figure 3, the change in ploidy frequency and genotypes of P. acuta over time, and the accompanying analyses presented in the text.
File: Historical_clone_year.csv
Description: dataset of colonies collected by Gorospe and Karl (2013) used to make Figure 3.
Variables
- Reef: Reef identification in Kāne'ohe Bay
- Clone: Clonal lineage identified by Gorospe and Karl (2013) using microsatellites
- Year: Year that colony was sampled by Gorospe and Karl (2013)
- tot_colonies: Total number of colonies that were sampled of that clonal lineage from a specific reef and year
File: Pocilloploidy_historical_and_2024_metadata.csv
Description: dataset of historically collected colonies and colonies collected in 2024 used to make Figure 3A - 3D.
Variables
- Reef: Reef identification in Kāne'ohe Bay. Letters identify locations in Kāne'ohe Bay that are not numbered reefs
- Plug ID: Sample ID of colony
- Sample date: Year that colony was collected
- Species: Mitochondrial identification
- Ploidy: Diploid, Triploid, or Unknown
- New Clade: Genotype ID
- Clone: Clonal lineage identified by Gorospe and Karl (2013) using microsatellites
File: DAPC.R
Description: R code to produce Discriminant Analysis of Principal Components in Figure 4A showing the genomic relationships between unique diploid and triploid P. acuta genotypes and P. damicornis.
File: Pocilloploidy_dp10miss0.05_SNPs_thin1000.vcf
Description: filtered mixed ploidy VCF file that was used to make Figures 4A, 4B, 4D, and 4E.
File: dip_trip_pdam.txt
Description: metadata used to make Figure 4A.
Variables
- sample.id: Sample ID of colony
- ploidy: diploid, triploid, P. damicornis diploid, and P. damicornis ploidy unknown
- ploidy_n: Numeric code of ploidy
File: STRUCTURE.R
Description: R code to produce STRUCTURE plot in Figure 4B showing the genomic relationships between unique diploid and triploid P. acuta genotypes and P. damicornis.
File: str_K7_plot.csv
Description: dataset used to make Figure 4B.
Variables
- id: Sample ID of colony
- cluster_1 - 7: STRUCTURE assignment of sample to various groups
- ploidy: diploid, triploid, and P. damicornis
File: str_K8_plot.csv
Description: dataset used to make Figure 4B.
Variables
- id: Sample ID of colony
- cluster_1 - 8: STRUCTURE assignment of sample to various groups
- ploidy: diploid, triploid, and P. damicornis
File: str_K9_plot.csv
Description: dataset used to make Figure 4B.
Variables
- id: Sample ID of colony
- cluster_1 - 9: STRUCTURE assignment of sample to various groups
- ploidy: diploid, triploid, and P. damicornis
File: StAMPP.R
Description: R code to produce PCoA analysis and neighbor-joining network of Nei's D genetic distances in Figures 4D and 4E showing the genomic relationships between unique diploid and triploid P. acuta genotypes and P. damicornis.
File: Ploidy_polyVCF.txt
Description: metadata used to make Figure 4D and 4E.
Variables
- Sample: Sample ID of colony
- Pop: Diploid, Triploid, P. damicornis mt genome diploid, and P. damicornis mt genome ploidy unknown
- Ploidy: Numeric code of ploidy
- color: Color code for column "Pop"
File: Figure_5.R
Description: R code to produce Figure 5 showing the relationships between ploidy and growth metrics and survival of P. acuta under thermal stress, and the accompanying analyses presented in the text.
File: growth.csv
Description: dataset used to make Figures 5A, 5B, 5D, and 5E.
Variables
- Sample_ID: Sample ID of colony
- New.Genotype: Genotype ID
- Ploidy: Diploid or Triploid
- Time.point: Either July or October (2024)
- Surface.Area.cm2: Surface Area of colony
- Volume.cm3: Volume of colony
- fractal_dimension: Fractal dimension of colony
File: weight.csv
Description: dataset of buoyant and dry weight used to make Figure 5C.
Variables
- Plug.id: Sample ID of colony
- New.Genotype: Genotype ID
- Ploidy: Diploid or Triploid
- Date: Calendar day buoyant weight data was collected
- Time_point: July or October
- bw_weight: Buoyant weight in grams
- dry_weight: Dry weight in grams
File: dhw_data.csv
Description: dataset of temperature in the aquarium during thermal stress experiment used to make Figure 5F.
Variables
- date: Date of thermal stress experiment
- mean_temp: Mean temperature of aquaria
- edhw: Experimental Degree Heating Week
- Days: Day of thermal stress experiment
File: surv_data.csv
Description: dataset of survival of P. acuta under thermal stress used to make Figure 5G.
Variables
- Colony.ID: Sample ID of colony
- Ploidy: Diploid or Triploid
- New.Genotype: Genotype ID
- day: Day of thermal stress experiment
- measurement: Survival measurement (0 = alive, 1 = dead)
- date: Calendar day data was recorded
- mean_temp: Mean temperature of aquaria
- edhw: Experimental Degree Heating Week
File: surv_SA.csv
Description: dataset of P. acuta survival under thermal stress and change in surface area used to make Figure 5H.
Variables
- colony: Sample ID of colony
- ploidy: Diploid or Triploid
- genotype: Genotype ID
- days.alive: Number of days that a colony survived in the thermal stress experiment
- July: Surface area (cm2) of colony in July 2024
- October: Surface area (cm2) of colony in October 2024
- delta_SA: (Surface Area in October - Surface Area in July) / Surface Area in July
- delta_SA_n: Square-root of delta_SA
File: Figure_6.R
Description: R code to produce Figure 6, larval release by P. acuta ploidy over the course of four months.
File: Pocilloploidy_spawning_metadata.csv
Description: dataset of larval release used to make Figure 6.
Variables
- Plug ID: Sample ID of colony
- Ploidy: Diploid or Triploid
- New Clade: Genotype ID
- Full moon: Date of full moon in that respective month
- Month: Month larval release occurred
- Date: Calendar day larvae were collected
- Larvae released: number of larvae released per day by each colony
