This codebook.txt file was generated on 2018-03-02 by wilsonkm ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides 2. Author Information Lead Author Contact Information Name: José A. Ramírez-Valiente Institution: University of Minnesota Email: josealberto.ramirezvaliente@gmail.com Co-Principal Investigator Contact Information Name: Julie Etterson Institution: University of Minnesota Principal Investigator Contact Information Name: Jeannine Cavender-Bares Institution: University of Minnesota Email: cavender@umn.edu Associate or Co-investigator Contact Information Name: Nicholas J Deacon Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Alyson Center Institution: St. Olaf's College Associate or Co-investigator Contact Information Name: Jed P. Sparks Institution: Cornell University Associate or Co-investigator Contact Information Name: Kimberlee L. Sparks Institution: Cornell University Associate or Co-investigator Contact Information Name: Timothy Longwell Institution: Zamorano University Associate or Co-investigator Contact Information Name: George Pilz Institution: Zamorano University 3. Date of data collection: 2009/01/01 - 2015/01/01 4. Geographic location of data collection: Field and greenhouse data were collected on plant populations collected from seed in Central America and Mexico; the field experiment was conducted in Zamorano, Honduras; the greenhouse experiment was conducted at the University of Minnesota 5. Information about funding sources that supported the collection of the data: Sponsorship: National Science Foundation IOS 0843665 2009-2014 to J.C.-B., J.R.E. and J.S. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-NoDerivs 3.0 United States 2. Links to publications that cite or use the data: Ramírez-Valiente, J; N Deacon; J Etterson; A Center; J Sparks; K Sparks; T Longwell; G Pilz; J Cavender-Bares. Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides, Molecular Ecology (in review) 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? N/A 6. Recommended citation for the data: Ramírez-Valiente, José A; Deacon, Nicholas J; Etterson, Julie; Center, Alyson; Sparks, Jed P.; Sparks, Kimberlee L; Longwell, Timothy; Pilz, George; Cavender-Bares, Jeannine. (2018). Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/D6D39K --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Field_garden_nSSR.csv Short description: Single sequence repeat data for nuclear microsatellites (QpZAG 1/2, QpZAG 1/5, QpZAG 9, QpZA15, QpZAG 16, QpZAG 36, QpZAG 46, QpZAG 102, QpZAG 110, QrZAG 11 and QrZAG 30) from Quercus oleoides individuals in six populations in Central America grown in the field common garden. B. Filename: Field_garden_Phenotypic_data.csv Short description: Phenotypic data on seedlings planted in the field garden in Zamorano, Honduras. Information is provided for each individual seedling. C. Filename: Greenhouse_garden_nSSR.csv Short description: Single sequence repeat data for nuclear microsatellites (QpZAG 1/2, QpZAG 1/5, QpZAG 9, QpZA15, QpZAG 16, QpZAG 36, QpZAG 46, QpZAG 102, QpZAG 110, QrZAG 11 and QrZAG 30) from Quercus oleoides individuals in five populations in Central America grown in the greenhouse experiment. D. Filename: Greenhouse_garden_Phenotypic_data.csv Short description: Phenotypic data on seedlings planted in the greenhouse common garden at the University of Minnesota. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Methodology documented in referenced publication: Ramirez-Valiente, J.A., Deacon, N.J., Etterson, J., Center, A., Sparks, J.P., Longwell, T... & Cavender-Bares, J. (2018). Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides. Molecular Ecology, 27(9), 2176-2192. httpsL//doi.org/10.1111/mec.14566 2. Methods for processing the data: See publication referenced above. 3. Instrument- or software-specific information needed to interpret the data: Microsoft Excel to view the data. 4. Standards and calibration information, if appropriate: N/A 5. Environmental/experimental conditions: See publication referenced above. 6. Describe any quality-assurance procedures performed on the data: See publication referenced above. 7. People involved with sample collection, processing, analysis and/or submission: J.C.-B. and J.R.E. conceived, designed and managed the common garden experiment in Honduras. J.A.R.-V. and J.C.-B. conceived, designed and implemented the greenhouse experiment established at the University of Minnesota. J.C.-B. and A.C. collected and transported seeds. T.L. and G.P. maintained and oversaw the experiment in Honduras and assisted in permit process. J.P.S. and K.L.S. peformed the stable carbon isotope and leaf nitrogen analyses. J.A.R.-V. performed the gas exchange, chlorophyll fluorescence and leaf morphology measurements. N.D. conducted the molecular analyses. J.A.R.-V. analysed the data. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Field_garden_nSSR.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 121 3. Missing data codes: Blank cells = data not collected 4. Variable List A. Name: No Description: Number of individual. B. Name: Populations Description: Six populations in Central America grown in the field common garden ZA = Zamorano, Honduras CH = Chagüite Maraita, Honduras BBA = Burrell Boom Belize MP = Mountain Pine Ridge, Belize LV = La Vigueta, Mexico SE = Santa Elena, Costa Rica C-I. Zag #-color Description: Nuclear micro satellite. J-M. Zag # Description: Nuclear micro satellite. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Field_garden_Phenotypic_data.csv ----------------------------------------- 1. Number of variables: 21 2. Number of cases/rows: 591 3. Missing data codes: Blank cells = data not collected 4. Variable List A. Name: Country Description: Country of origin BZ=Belize CR=Costa Rica HN=Honduras MX=Mexico B. Name: Pop Description: Population ZA = Zamorano, Honduras CH = Chagüite Maraita, Honduras BBA = Burrell Boom Belize MP = Mountain Pine Ridge, Belize LV = La Vigueta, Mexico SE = Santa Elena, Costa Rica C. Name: Mother Description: Source tree, i.e., number of parent tree of seedling D. Name: ID Description: Identification number of individual seedlings E. Name: Garden Description: Garden replicate in Zamorano Value labels: 1, 2 [There were two replicate gardens.] F. Name: Block Description: Block number within the garden replicate Value labels if appropriate G. Name: Finalblock Description: Block number used in analyses H. Name: Order in block Description: Row position in block I. Name: Treatment Description: Watering treatment NO_WATER = no water added BOTH = water added in wet and dry seasons H2O_DS = water added in dry season H2O_WS = water added in wet season J. Name: Stoma_density Description: Stomatal density K. Name: Stoma_length Description: Stomatal length (micromilimeter) L. Name: SPI Description: Stomatal Pore Index [stomatal density × (pore length)^2] M. Name: SPI100 Description: SPI x 100 N. Name: Area Description: lamina leaf area. (cm2) O. Name: SLA Description: Specific leaf area (cm2 g-1) P. Name: N Description: Percent nitrogen Q. Name: D13C Description: (mg g-1) stable carbon isotrope ratio (‰) value R. Name: VolCov Description: Initial plant size S. Name: AGR Description: Absolute growth rate T. Name: RGR Description: Relative growth rate ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Greenhouse_garden_nSSR.csv ----------------------------------------- 1. Number of variables: 13 2. Number of cases/rows: 122 3. Missing data codes: Blank cells = data not collected 4. Variable List A. Name: Sample No. Description: Sample number B. Name: Pop Description: Population C-I. Zag #-color Description: Nuclear micro satellite. J-M. Zag # Description: Nuclear micro satellite. Other variables in row 2 of .csv. Description: Quercus oleoides individuals in five populations in Central America grown in the greenhouse experiment. MZ = Macuelizo RI = Rincón de la Vieja SB = Sabana Grande SE = Santa Elena TA = Las Tablas. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Greenhouse_garden_Phenotypic_data.csv ----------------------------------------- 1. Number of variables: 36 2. Number of cases/rows: 1,323 3. Missing data codes: Blank cells = data not collected 4. Variable List A. Name: Bench Description: Bench number in the greenhouse B. Name: Row Description: Row position on the bench C. Name: Column Description: column position on the bench D. Name: Water Description: Watering treatment WW = 22-28% soil moisture (well-watered treatment) D = 8-12% soil moisture (dry treatment) E. Name: ID Description: individual seedling identification number F. Name: Country Description: Country of origin Honduras, Costa Rica G. Name: Pop Description: Population MZ = Macuelizo RI = Rincón de la Vieja SB = Sabana Grande SE = Santa Elena TA = Las Tablas H. Name: Mother Description: source tree, i.e., number of parent tree of all seedlings I. Name: Biomass_initial Description: Initial biomass at time of transplanting (g) J. Name: AGR Description: absolute growth rate (g day-1) K. Name: RGR Description: relative growth rate L. Name: RGR1000 Description: RGR x 1000 M. Name: Leaf_thickness Description: Leaf thickness (mm) N. Name: Leaf_area Description: lamina leaf area (cm2) O. Name: SLA Description: specific leaf area (cm2 g-1) P. Name: Stoma_Density Description: stomatal density (mm-2) Q. Name: Stoma_Length Description: stomatal length (μm) R. Name: SPI Description: stomatal pore index S. Name: SPI100 Description: SPI x 100 T. Name: Date_pre Description: date predawn Fv/FM measurement is taken U. Name: Time_pre Description: time predawn Fv/Fm measurement is taken V. Name: Fv/FM Description: maximum quantum yield W. Name: Date_mid Description: date midday quantum yield measurement is taken X. Name: Time_mid Description: time midday quantum yield measurement is taken Y. Name: Quantum_yield Description: quantum yield of photosynthesis measured using chlorophyll fluorescence Z. Name: ETR Description: = electron transport rate (μmol m-2 s-1) AA. Name: NPQ Description: non-photochemical quenching AB. Name: Soil_mois_fluoresc Description: soil moisture in the seedling pot at the time of the chlorophyll fluorescence measurement (%) **for columns AC-AJ, a subset of samples was measured** AC. Name: Date_LICOR Description: date of photosynthetic measurement AD. Name: Time_LICOR Description: time of photosynthetic measurement AE. Name: Photo Description: photosynthetic rate (μmolCO2 m-2 s-1) AF. Name: Cond Description: stomatal conductance rate (molH2O m-2 s-1) AG. Name: WUE Description: water use efficiency (μmolCO2 molH2O-1) AH. Name: Photo_mass Description: photosynthesis on a mass basis (μmolCO2 kg-1 s-1) AI. Cond_mass Description: stomatal conductance on a mass basis (molH2= kg-1 s-1) AJ. Name: Soil_mois_LICOR Description: soil moisture in the seedling pot at the time of gas exchange measurement (%)