This README.txt file was generated on 07 May, 2021 ------------------- GENERAL INFORMATION ----------------- Title of Dataset: Data from: Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae) Author Information Principal Investigator: Joel H. Nitta Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan joelnitta@gmail.com Associate or Co-investigators: James E. Watkins, N. Michele Holbrook, Tristan W. Wang, Charles C. Davis Date of data collection: 2012–2014 Geographic location of data collection: Moorea, French Polynesia Information about funding sources or sponsorship that supported the collection of the data: Funding provided in part by the National Science Foundation (Doctoral Dissertation Improvement Grant DEB-1311169 to JHN and CCD), Setup Funds from Harvard University to CCD, American Society of Plant Taxonomists (Research Grant for Graduate Students to JHN), Garden Club of America (Award in Tropical Botany to JHN), Harvard University Herbaria (Fernald Fieldwork Fellowship to JHN), Society of Systematic Biologists (Graduate Student Research Award to JHN), and Systematics Association (Systematics Research Fund to JHN). -------------------------- SHARING/ACCESS INFORMATION -------------------------- Licenses/restrictions placed on the data, or limitations of reuse: CC0 1.0 Universal (CC0 1.0) Recommended citation for the data: Nitta JH, Watkins JE, Holbrook NM, Wang TW, Davis CC (2021) Data from: Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae) https://doi.org/10.6084/m9.figshare.14184572 Citation for and links to publications that cite or use the data: Nitta JH, Watkins JE, Holbrook NM, Wang TW, Davis CC (2021) Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae) (Hymenophyllaceae) <> Code for analyzing the data is available on github: https://github.com/joelnitta/moorea_filmies -------------------- DATA & FILE OVERVIEW -------------------- File list (filenames, directory structure (for zipped files) and brief description of all data files): • 2012_gameto_dt_times.csv: Start and end times of desiccation tolerance (DT) test on fern gametophytes during the 2012 field season. • 2012_sporo_dt_times.csv: Start and end times of desiccation tolerance (DT) test on fern sporophytes during the 2012 field season. • data_raw.tar.gz: Zipped raw data files. For a description, see README.md in the zipped archive. • fern_specimens.csv: Specimen data for ferns collected in French Polynesia primarily by Joel H. Nitta. • filmy_dt.csv: Data from desiccation tolerance test on filmy ferns from from Moorea, French Polynesia. • filmy_dt_chamber.csv: Temperature and humidity inside desiccation chambers during desiccation tolerance test. • filmy_growth_habit.csv: Growth habit of filmy ferns from Moorea, French Polynesia. • filmy_light_curves.csv: Light levels and chlorophyll fluorescence measured in filmy ferns from Moorea, French Polynesia with a chlorophyll fluorometer. Checksums are 32-byte MD5 hashes generated with tools::md5sum() in R. -------------------------- METHODOLOGICAL INFORMATION -------------------------- Description of methods used for collection/generation of data: Desiccation tolerance (DT) and light responses were measured in sporophytes and gametophytes of filmy ferns (family Hymenophyllaceae) on the island of Moorea, French Polynesia. Samples were collected in the field and stored in plastic bags with a small amount of water to keep them fresh during transport to the lab. To measure DT, pre-treatment maximum photochemical yield of photosystem II was measured in fresh plants after a 10 min period of dark-adaptation using a portable mini-PAM fluorometer (Walz Gmbh, Effeltrich, Germany). Samples were then transferred to desiccation chambers containing saturated salts at three different desiccation intensities or a control treatment with moist tissues (100% RH), and water withheld for either a short (2 d) or long (15 d) interval. Conditions inside the desiccation chambers were monitored during the experiment using Track-It RH/Temp dataloggers (Monarch Instrument, Amherst, NH) logging every 10 min or Hobo ProV2 dataloggers logging every 5 min. Salts used for desiccation and their corresponding mean water potentials and approximate relative humidity and VPD are as follows: LiCl (-282 MPa, 18% RH, 2.45 kPa), Mg(NO3)2 (-86 MPa, 58% RH, 1.25 kPa), and NaCl (-38 MPa, 80% RH, 0.60 kPa). Following the desiccation treatment, plants were rewetted and yield of photosystem II was again measured at 0.5 h, 24 h, and 48 h following rewetting. Eight individuals per treatment were used for sporophytes. No replication by species was possible for gametophytes due to their cryptic morphology. All gametophytes were subjected to the same treatment (2 d at -86 MPa). Gametophytes were later identified to species by DNA barcoding. Relative water content (RWC) was measured in a subset of samples by recording the mass of samples prior to the DT test (fresh mass), at each step of the DT test (turgid mass), then after drying them overnight in a drying oven at 65 °C following the DT test (dry mass). Relative water content was calculated as RWC = (TM - DM) / (FM - DM), where TM is turgid mass, DM is dry mass, and FM is fresh mass. Relative water content was not calculated for gametophytes, as these were too small to measure accurately with the balances available. To measure light responses, rapid light response curves were constructed for each species by measuring photosynthetic yield at gradually increasing levels of photosynthetically active actinic light (400 nm to 700 nm) with the Light Curve function of the mini-PAM portable chlorophyll fluorometer (Walz Gmbh, Effeltrich, Germany) as described by the manufacturer. Fieldwork was done under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (Protocole d’Accueil 2012–2014). fern_specimens.csv, filmy_dt.csv, filmy_dt_chamber.csv, and filmy_light_curves.csv were generated by processing the raw data files using scripts available at https://github.com/joelnitta/moorea_filmies (scripts beginning with “clean_” in the “R/” directory). For full methods, see Nitta JH, Watkins JE, Holbrook NM, Wang TW, Davis CC (2021) <> -------------------------- DATA-SPECIFIC INFORMATION -------------------------- 2012_gameto_dt_times.csv: Start and end times of desiccation tolerance (DT) experiment on fern gametophytes during the 2012 field season. All gametophytes were desiccated 2 d at -86 MPa. For other field seasons (2013, 2014), start and end times were recorded during each measurement, so are not included in this file. Number of variables: 4 Number of cases/rows: 4 Variable list: • date_time: Date and time, formatted YYYY-MM-DD HH-MM-SS. • event: Start or end of experiment. • group: Code corresponding to site and growth habit of samples. • cluster: Number assigned to each group of samples (gametophyte individuals) that were included together in a single experiment. Missing data codes: No missing data. Specialized formats or other abbreviations used: For ‘group’, ‘ter’ indicates terrestrial samples, ‘epi’ indicates epiphytic samples; number indicates site as follows: 1 = Three Pines 200m, 2 = Mt. Tohiea 400m, 3 = Mt. Tohiea 600m, 4 = Mt. Tohiea 800m, 5 = Mt. Tohiea 1000m, 6 = Mt. Tohiea 1170m. For a description of sites, see Nitta, Joel H.; Meyer, Jean-Yves; Taputuarai, Ravahere; Davis, Charles C. (2016), Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes, Dryad, Dataset, https://doi.org/10.5061/dryad.df59g MD5 checksum: a3b3f3198ec2d6a11d4103c8dce98834 -------------------------- 2012_sporo_dt_times.csv: Start and end times of desiccation tolerance (DT) test on fern sporophytes during the 2012 field season. For other field seasons (2013, 2014), start and end times were recorded during each measurement, so are not included in this file. Number of variables: 5 Number of cases/rows: 14 Variable list: • date_time: Date and time, formatted YYYY-MM-DD HH-MM-SS • event: Start or end of experiment. • salt: Name of salt used to maintain constant humidity in the desiccation chamber (see methods above for corresponding relative humidity). • dry_time: Length (d) of desiccation. • species: Species included in experiment. Missing data codes: No missing data. Specialized formats or other abbreviations used: None. MD5 checksum: e3f95794fe3f74227d4d9a9f1c3240dd -------------------------- data_raw.tar.gz: Zipped raw data files. For a description, see README.md in the zipped archive. These were used to generate the clean data files with code available at https://github.com/joelnitta/moorea_filmies (scripts starting with ‘clean_’ in the ‘R’ folder). MD5 checksum: 18b59b9aa52ca02862e733af94f2dc13 -------------------------- fern_specimens.csv: Specimen data for ferns collected in French Polynesia primarily by Joel H. Nitta. Number of variables: 27 Number of cases/rows: 2834 Variable list: • specimen_id: Unique key assigned to each specimen. • specimen: Specimen voucher (collector name and number). • collector: Name of primary collector. • coll_num: Collection number. • family: Family. • genus: Genus. • specific_epithet: Specific epithet. • infraspecific_rank: Infraspecific rank. • infraspecific_name: Infraspecific name. • certainty: Taxonomic certainty. • species: Genus and specific epithet. • taxon: Genus, specific epithet, and any infraspecific names. • country: Country. • county: County (or approximate political division). • locality: General locality. • site: Name of collection site. • elevation: Elevation (m). • latitude: Latitude (decimal degrees). • longitude: Longitude (decimal degrees). • observations: Observations about the specimen. • generation: Gametophyte or sporophyte. • gameto_net_location: Location of gametophyte sampling grid. • gameto_square: Grid square where gametophyte was sampled. • gameto_habit: Gametophyte growth habit. • date_collected: Collection date. • other_collectors: Names of other collectors present. • herbaria: Herbarium code where specimen is deposited. Missing data codes: Missing data entered as ‘NA’. Specialized formats or other abbreviations used: Herbarium codes follow Index Herbariorum (http://sweetgum.nybg.org/science/ih/) MD5 checksum: 87b9fc88d3daa56f4f0ea1d25e7e0f14 -------------------------- filmy_dt.csv: Data from desiccation tolerance test on filmy ferns from from Moorea, French Polynesia. Number of variables: 24 Number of cases/rows: 1159 Variable list: • species: Species. • salt: Name of salt used to maintain constant humidity in the desiccation chamber (see methods above for corresponding relative humidity). • dry_time: Length (d) of desiccation. • individual: Individual code assigned to each sample per species per treatment. (sporophytes) or collection number (gametophytes). • generation: Gametophyte or sporophyte. • dataset: Name of corresponding raw dataset file (sporophytes only). • yield_pre: Maximum photochemical yield of photosystem II (Fv/Fm) prior to desiccation treatment. • yield_30min: Fv/Fm 30 m after rewetting following desiccation treatment. • yield_24hr: Fv/Fm 24 h after rewetting. • yield_48hr: Fv/Fm 48 h after rewetting. • yield_72hr: Fv/Fm 72 h after rewetting (gametophytes only). • yield_dry: Fv/Fm in the desiccated state. • weight_pre: Mass (g) prior to desiccation treatment. • weight_desiccated: Mass (g) in the desiccated state. • weight_30min: Mass (g) 30 m after rewetting. • weight_24hr: Mass (g) 24 h after rewetting. • weight_48hr: Mass (g) 48 h after rewetting. • weight_dry: Mass (g) after drying overnight at 60 C. • time_pre: Date and time just before starting desiccation treatment, formatted YYYY-MM-DD HH-MM-SS. • time_30min: Date and time 30 m after rewetting. • time_24hr: Date and time 24 h after rewetting. • time_48hr: Date and time 48 h after rewetting. • time_72hr: Date and time 72 h after rewetting (gametophytes only). • time_dry: Date and time when yield was measured in the desiccated state. Missing data codes: Missing data entered as ‘NA’. Specialized formats or other abbreviations used: None. MD5 checksum: 909ca69af8e5e040441dd403473091fa -------------------------- filmy_dt_chamber.csv: Temperature and humidity inside desiccation chambers during desiccation tolerance test, measured using Track-It RH/Temp dataloggers (Monarch Instrument, Amherst, NH) logging every 10 min or Hobo ProV2 dataloggers logging every 5 min. Number of variables: 9 Number of cases/rows: 158994 Variable list: • date_time: Date and time, formatted YYYY-MM-DD HH-MM-SS. • temp: Temperature (degrees Celsius) • rh: Relative humidity (%) • salt: Name of salt used to maintain constant humidity in the desiccation chamber (see methods above for corresponding relative humidity). • generation: Gametophyte or sporophyte, or “mixed” if samples of both life stages were present in the growth chamber. • year: Year. • species: Species. • file: Name of file containing raw data. • serial_no: Serial number of datalogger. Missing data codes: Missing data entered as ‘NA’. Specialized formats or other abbreviations used: None. MD5 checksum: a4deca98c16d21f22d0775404a576f50 -------------------------- filmy_growth_habit.csv: Growth habit of filmy ferns from Moorea, French Polynesia. Growth habit determined by field observation. Species were categorized into one of four growth habits: terrestrial (growing in soil, with true roots), saxicolous (growing on rocks), low-elevation epiphyte (mostly occurring outside of cloud forest, i.e., below ca. 500 m), and high-elevation epiphyte (mostly occurring within cloud forest, i.e., above ca. 500 m). Crepidomanes bipunctatum and Crepidomanes humile were observed growing as both epiphytes and saxicoles, but are coded as epiphytes to distinguish them from exclusively saxicolous species. Number of variables: 2 Number of cases/rows: 22 Variable list: • species: Species. • habit: Growth habit. Missing data codes: None. Specialized formats or other abbreviations used: None. MD5 checksum: 23491d6f91d4b46fa8b307ad62e8b30e -------------------------- filmy_light_curves.csv: Light levels and chlorophyll fluorescence measured in filmy ferns from Moorea, French Polynesia with a chlorophyll fluorometer. Chlorophyll fluorescence measured with “light curve” function of mini-PAM chlorophyll fluorometer. Number of variables: 17 Number of cases/rows: 1960 Variable list: • type: Type of fluorescence measurement, from mini-PAM raw data. • no: Number of fluorescence measurement, from mini-PAM raw data (not unique, because this file includes measurements from multiple mini-PAM raw data files). • f: Momentary fluorescence level before application of saturation pulse. • fm: Maximum fluorescence level of the illuminated sample. • par: Level of photosynthetically active radiation during fluorescence measurement. • yield: Effective photochemical quantum yield of photosystem II. • etr: Relative electron transport rate. • date_time: Date and time of measurement, formatted YYYY-MM-DD HH-MM-SS. • species: Species. • individual: Individual code assigned to each sample per species per treatment. • generation: Gametophyte or sporophyte. • coll_num: J.H. Nitta collection number • sporo_site: Name of site where sporophyte sample was collected. • condition: Condition under which measurements were taken (lab or field). • date: Date of measurement, formatted YYYY-MM-DD. • outlier: “TRUE” or “FALSE”, indicating whether measurement should be excluded from light curve analysis. • light_id: Unique ID number corresponding to light curve measured from a single sample. Missing data codes: Missing data entered as ‘NA’. Specialized formats or other abbreviations used: For a description of sporophyte sites, see Nitta, Joel H.; Meyer, Jean-Yves; Taputuarai, Ravahere; Davis, Charles C. (2016), Data from: Life cycle matters: DNA barcoding reveals contrasting community structure between fern sporophytes and gametophytes, Dryad, Dataset, https://doi.org/10.5061/dryad.df59g MD5 checksum: 38633c4232b4ecc0b691707cf386f918 -------------------------- CHANGE LOG 2021-05-07 • Update specimens.csv in raw data. --- 2021-05-06 • Add MD5 checksums. • Correct missing values in ‘date_collected’ column of fern_specimens.csv from ‘NA-NA-NA’ to ‘NA’. • Change title of paper. • Change address of first author. • Change description of “generation” to “life stage”. --- 2021-03-13 Generate this README file.