This Mazer et al., Madrono, readme.txt file was generated on 2021-09-13 by Susan Mazer


GENERAL INFORMATION

1. Title of Dataset: Data used in: Phenological sensitivities to climate are similar in two Clarkia congeners: Indirect evidence for facilitation, convergence, niche conservatism, or genetic constraints

2. Author Information
    A. Principal Investigator Contact Information
        Name: Susan J. Mazer
        Institution: University of California, Santa Barbara
        Address: Department of Ecology, Evolution & Marine Biology
        Email: sjmazer@ucsb.edu

    B. Associate or Co-investigator Contact Information
        Name: Natalie L. Love
        Institution: University of California, Santa Barbara
        Address: Department of Ecology, Evolution & Marine Biology
        Email: nllove@calpoly.edu
    C. Alternate Contact Information
        Name: Tadeo Ramirez-Parada
        Institution: University of California, Santa Barbara
        Address: Department of Ecology, Evolution & Marine Biology
        Email: tadeo@ucsb.edu
    D. Alternate Contact Information
        Name: Isaac Park
        Institution: University of California, Santa Barbara
        Address: Department of Ecology, Evolution & Marine Biology
        Email: isaac_park@ucsb.edu
    E. Alternate Contact Information
        Name: Elizabeth Matthews
        Institution: National Park Service, National Capital Region Network
        Email: elizabeth_matthews@nps.gov

3. Date of data collection (single date, range, approximate date):  Data extracted from physical herbarium specimens borrowed from herbaria described in manuscript.  Specimens examined and floral organs counted in 2012-2013. 


SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: None 

2. Links to publications that cite or use the data: Madroño, Special issue on Phenology, 2022

3. Links to other publicly accessible locations of the data: N/A

4. Links/relationships to ancillary data sets: N/A

5. Was data derived from another source? No
    A. If yes, list source(s): 

6. Recommended citation for this dataset: 


DATA & FILE OVERVIEW

1. File List:   Clarkia_n_514_copy.csv

Each record (row) in this data set represents a single herbarium specimen and includes its:

a) phenotypic attributes (the numbers of buds, open flowers, developing fruits, and ripe fruits; and its phenological index, a quantitative metric reflecting the weighted proportions of each of these reproductive organ types), 

b) date of specimen collection

c) geographic information (latitude, longitude, elevation), 

d) long-term, mean climatic conditions (climate "Normals"), 

e) climatic conditions in the year of specimen collection or in the previous autumn (climate in the year-of-collection), and

f) the deviation between the two types of climatic conditions (long-term vs. year-of-collection) at the specimen's site of collection.


2. Relationship between files, if important: N/A

3. Additional related data collected that was not included in the current data package: None

4. Are there multiple versions of the dataset? 24 numerical values in this data set were updated because dryad required that they be converted to integers from real numbers.  These edits resulted in rounding the real numbers to integers and should not materially affect the results.


METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: See published paper that used these data.

Mazer, S. J., N. R. Love, I M. Park, T. Ramirez-Parada, and E. R. Matthews.  2022.  Phenological sensitivities to climate are similar in two Clarkia congeners: Indirect evidence for facilitation, convergence, niche conservatism, or genetic constraints. Madrono, in press.

2. Methods for processing the data: See Methods section of paper cited above.

3. Instrument- or software-specific information needed to interpret the data: N/A

4. Standards and calibration information, if appropriate: N/A

5. Environmental/experimental conditions: N/A

6. Describe any quality-assurance procedures performed on the data: See Methods section of published paper.

7. People involved with sample collection, processing, analysis and/or submission.  

The authors gratefully acknowledge the many UCSB students who invested much time and effort in the scoring and georeferencing of hundreds of specimens, including Adam Lota, Adam Monahan, Allison White, Dana Hoffenberg, Elizabeth Cannon, Emmanuel Lopez, Jazmine Brownlee, Joel Kirksey, Kimberly Crispin, Louis Lin, Laurel Schmalz, Marco Marquez, Melissa Mckiddy, Robert Ottolia, Tahirany Diaz, and Tiffany Thaphasouk. We also thank Danica Taber for her assistance in managing students and data. We are very grateful to the staff of the JEPS, RAS, SBBG, UC, and UCR herbaria who managed the loans for this project, and particularly to Dr. Jennifer Thorsch and the herbarium of UCSB’s Cheadle Center for Biodiversity and Ecological Restoration for hosting the borrowed specimens and for providing workspace. The authors acknowledge funding from NSF (DBI-1802181) to SJM, from the National Park Service Climate Change Response Program (Cooperative Agreement H8C07080001), and from UCSB, which provided a generous Chancellor’s Fellowship to TRP. SJM is indebted to the Yale Institute for Biospheric Studies, which provided support and camaraderie during the sabbatical year in which this manuscript was prepared. Finally, this work would not have been possible without the generosity and time of the many collectors and systematists who collected and identified the specimens analyzed here.


DATA-SPECIFIC INFORMATION FOR: 

1. Number of variables: 125 variables are included in the dataset provided here, but only some of them were used in the analyses published in this paper.

2. Number of cases/rows: 514

3. Variable List and brief definition

Species:  Clarkia cylindrical or Clarkia unguiculata, the two species analyzed in the current manuscript

WarmOrCool: Category indicating whether the specimen was collected from a site for which the mean annual temperature normal (from 1921-2010) was above (Warm) or below (Cool)the mean value of all of the specimens

DryOrWet: Category indicating whether the specimen was collected from a site for which the mean cumulative precipitation normal (from 1921-2010) was above (Wet) or below (Dry) the mean value of all of the specimens

Temp-MoistureCombination: Category indicating whether, based on the categories in "WarmOrCool" and "DryOrWet", the specimen was collected from a site that was relatively Warm/Dry, Warm/Wet, Cool/Dry, or Cool Wet


Log10_PI: Log-transformed value of the Phenology Index (see article and definition of "Phono-Index", below

MAT_Norm: Mean Annual Temperature (1921-2010) at the site of specimen collection

MAP_Norm: Mean Cumulative Annual Precipitation (1921-2010) at the site of specimen collection

Year: Year of specimen collection

DOY: Day of year (1-365, or 366 in a leap year) on which the specimen was collected

Latitude: the latitude of the herbarium specimen's site of collection, expressed in decimal degrees

Longitude: the longitude of the herbarium specimen's site of collection, expressed in decimal degrees

N_Rows: the number of individual plants pressed on a given herbarium sheet; these were pooled to count the number of reproductive organs on the sheet when calculating the specimen's phenological index

Buds: the number of closed buds present on the specimen

Flowers: the number of open flowers present on the specimen

Fruits: the number of developing ovaries/fruits present on the specimen

Ripe_Fruits: the number of ripe (full-sized, dry, and beginning to split) fruits borne by the specimen

Pheno_Index: This is the phenological index described in the paper; it is a quantitative metric describing the phenological status of an herbarium specimen, based on the proportions of buds, open flowers, developing ovaries, and ripe fruits.

Longitude2: A repeat of the Longitude column, above

Latitude2: A repeat of the Latitude column, above

Elevation_m: The elevation at which the specimen was collected, either recorded by the collector or estimated during georeferencing.

Day: Day of the month (1-31) on which the specimen was collected

Month: Month (1-12) on which the specimen was collected

Year2: Year in which the specimen was collected

DOY2: Day of year (1-365, or 366 in a leap year) on which the specimen was collected

The following climatic parameters represent conditions at the site of specimen collection. Data were extracted from the database, ClimateNA. See methods in published paper for details.

Where the variable name ends with the letters "Norm", the climatic parameter represents the long-term normals (or the mean value) from 1921-2010. 

Where the variable name ends with the letters "Ann", the climatic parameter represents the long-term normals (or the mean value) in the year of specimen collection.

Where the variable name ends with the letters "at_Prior" or "PriorDev", the climatic parameter represents the conditions during the autumn PRIOR to the year of collection. 

Where the variable name ends with the letter Ann_Dev, the climatic parameter represents the climate anomaly, or the difference between long-term climatic conditions (the normal) and the conditions in the year of specimen collection.

Where the variable name includes the letters "wt", the climatic parameter refers to winter conditions (December, January, and February)

Where the variable name includes the letters "sp", the climatic parameter refers to spring conditions (March, April and May).

Where the variable name includes the letters "sm", the climatic parameter refers to summer conditions (June, July, and August).

Where the variable name includes the letters "at", the climatic parameter refers to autumn conditions (September, October, November).


MWMT_Norm: Mean temperature of the warmest month  (°C), normals (1921-2010)

MCMT_Norm: Mean temperature of the warmest month  (°C), normals (1921-2010)

PAS_Norm: Precipitation as snow, normals

RH_Norm: Relative humidity, normals

Tave_wt_Norm: Mean average daily temperature (°C)
Tave_sp_Norm: Mean average daily temperature (°C)
Tave_sm_Norm: Mean average daily temperature (°C)
Tave_at_Norm: Mean average daily temperature (°C)

Tmin_wt_Norm: Mean minimum daily temperature (°C)
Tmin_sp_Norm: Mean minimum daily temperature (°C)
Tmin_sm_Norm: Mean minimum daily temperature (°C)
Tmin_at_Norm: Mean minimum daily temperature (°C)

Tmax_wt_Norm: Mean maximum daily temperature (°C)
Tmax_sp_Norm: Mean maximum daily temperature (°C)
Tmax_sm_Norm: Mean maximum daily temperature (°C)
Tmax_at_Norm: Mean maximum daily temperature (°C)

NFFD_wt_Norm: Number of frost-free days
NFFD_sp_Norm: Number of frost-free days
NFFD_sm_Norm: Number of frost-free days
NFFD_at_Norm: Number of frost-free days

CMD_wt_Norm: Hargreaves climatic moisture deficit (mm)
CMD_sp_Norm: Hargreaves climatic moisture deficit (mm)
CMD_sm_Norm: Hargreaves climatic moisture deficit (mm)
CMD_at_Norm: Hargreaves climatic moisture deficit (mm)

RH_wt_Norm: Mean relative humidity (%)
RH_sp_Norm: Mean relative humidity (%)
RH_sm_Norm: Mean relative humidity (%)
RH_at_Norm: Mean relative humidity (%)

MAR_Norm: Mean annual solar radiation (MJ m-2 d-1)

Rad_wt_Norm: Mean solar radiation (MJ m-2 d-1)
Rad_sp_Norm: Mean solar radiation (MJ m-2 d-1)
Rad_sm_Norm: Mean solar radiation (MJ m-2 d-1)
Rad_at_Norm: Mean solar radiation (MJ m-2 d-1)

MAT_Ann: Mean annual temperature (°C)

MWMT_Ann: Mean warmest month temperature (°C)
MCMT_Ann: Mean coldest month temperature (°C)
MAP_Ann: Mean annual precipitation (mm)
PAS_Ann: Precipitation as snow (mm). For individual years, it covers the period between August in previous year and July in current year.

RH_Ann: Mean annual relative humidity (%)

Tave_wt_Ann: Mean average daily temperature (°C)
Tave_sp_Ann: Mean average daily temperature (°C)
Tave_sm_Ann: Mean average daily temperature (°C)

Tmin_wt_Ann: Mean minimum daily temperature (°C)
Tmin_sp_Ann: Mean minimum daily temperature (°C)
Tmin_sm_Ann: Mean minimum daily temperature (°C)

Tmax_wt_Ann: Mean maximum daily temperature (°C)
Tmax_sp_Ann: Mean maximum daily temperature (°C)
Tmax_sm_Ann: Mean maximum daily temperature (°C)

NFFD_wt_Ann: Number of frost-free days
NFFD_sp_Ann: Number of frost-free days
NFFD_sm_Ann: Number of frost-free days

CMD_wt_Ann: Hargreaves climatic moisture deficit (mm)
CMD_sp_Ann: Hargreaves climatic moisture deficit (mm)
CMD_sm_Ann: Hargreaves climatic moisture deficit (mm)

RH_wt_Ann: Mean relative humidity (%)
RH_sp_Ann: Mean relative humidity (%)
RH_sm_Ann: Mean relative humidity (%)

PAS_wt_Ann: Precipitation as snow (mm)
PAS_sp_Ann: Precipitation as snow (mm)
PAS_sm_Ann: Precipitation as snow (mm)

PPT_wt_Ann: Cumulative winter precipitation (mm)
PPT_sp_Ann: Cumulative spring precipitation (mm)
PPT_sm_Ann: Cumulative summer precipitation (mm)

Tave_at_Prior: Mean average daily temperature (°C) during the autumn prior to specimen collection
Tmin_at_Prior: Minimum average daily temperature (°C) during the autumn prior to specimen collection
Tmax_at_Prior: Maximum average daily temperature (°C) during the autumn prior to specimen collection

NFFD_at_Prior: Number of frost free days during the autumn prior to specimen collection

CMD_at_Prior: Hargreaves climatic moisture deficit (mm) during the autumn prior to specimen collection

RH_at_Prior: Mean relative humidity (%) during the autumn prior to specimen collection

PPT_at_Prior: Cumulative autumn precipition (mm) during the autumn prior to specimen collection

PAS_at_Prior: Cumulative precipitation as snow (mm) during the autumn prior to specimen collection

MAT_AnnDev:  Difference between the mean annual temperature Normal and the mean annual temperature in the year of collection (=MAT anomaly)

MWMT_AnnDev: Mean warmest month temperature (°C), anomaly

MCMT_AnnDev: Mean coldest month temperature (°C), anomaly

MAP_AnnDev: Cumulative annual precipitation (mm), anomaly

PAS_AnnDev: Precipitation as snow (mm), anomaly

RH_AnnDev: Relative Humidity (%), anomaly

Tave_wt_AnnDev: Mean average daily temperature (°C), winter anomaly
Tave_sp_AnnDev: Mean average daily temperature (°C), spring anomaly
Tave_sm_AnnDev: Mean average daily temperature (°C), summer anomaly

Tave_at_PriorDev: Mean average daily temperature (°C), anomaly for the autumn prior to year of specimen collection

Tmin_wt_AnnDev: Mean minimum daily temperature (°C), winter anomaly
Tmin_sp_AnnDev: Mean minimum daily temperature (°C), spring anomaly
Tmin_sm_AnnDev: Mean minimum daily temperature (°C), summer anomaly

Tmin_at_PriorDev: Mean minimum daily temperature (°C), anomaly for the autumn prior to year of specimen collection

Tmax_wt_AnnDev: Mean maximum daily temperature (°C), winter anomaly
Tmax_sp_AnnDev: Mean maximum daily temperature (°C), spring anomaly
Tmax_sm_AnnDev: Mean maximum daily temperature (°C), summer anomaly

Tmax_at_PriorDev: Mean maximum daily temperature (°C), anomaly for the autumn prior to year of specimen collection

NFFD_wt_AnnDev: Number of frost-free days, winter anomaly
NFFD_sp_AnnDev: Number of frost-free days, spring anomaly
NFFD_sm_AnnDev: Number of frost-free days, summer anomaly

NFFD_at_PriorDev: Number of frost-free days, anomaly for the autumn prior to year of specimen collection

CMD_wt_AnnDev: Hargreaves climatic moisture deficit (mm), winter anomaly
CMD_sp_AnnDev: Hargreaves climatic moisture deficit (mm), spring anomaly
CMD_sm_AnnDev: Hargreaves climatic moisture deficit (mm), summer anomaly

CMD_at_PriorDev: Hargreaves climatic moisture deficit (mm), anomaly for the autumn prior to year of specimen collection

RH_wt_AnnDev: Relative humidity (%), winter anomaly
RH_sp_AnnDev: Relative humidity (%), spring anomaly
RH_sm_AnnDev: Relative humidity (%), summer anomaly

RH_at_PriorDev: Relative humidity (%), anomaly for the autumn prior to year of specimen collection


4. Missing data codes: In the csv file, missing data are reflected in empty cells


5. Specialized formats or other abbreviations used: N/A