This readme.txt file was generated on 2022-05-05 and updated on 2024-01-19 by Amy Waananen. Recommended citation for the data: Waananen, Amy; Richardson, Lea K; Thoen, Riley D; Nordstrom, Scott W; Eichenberger, Erin G; Kiefer, Gretel; Dykstra, Amy B; Shaw, Ruth G; Wagenius, Stuart. (2024). R code and data for “Offspring emergence, but not survival, increases with maternal mating opportunity." Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/b74k-7f48. ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: R code and data for “Offspring emergence, but not survival, increases with maternal mating opportunity 2. Author Information Principal Investigator Contact Information Name: Waananen, Amy Institution: University of Minnesota Email: waana001@umn.edu; ORCID: Associate or Co-investigator Contact Information Name: Richardson, Lea K Institution: Northwestern University; Chicago Botanic Garden Email: ORCID: Associate or Co-investigator Contact Information Name: Thoen, Riley D Institution: University of Georgia Email: ORCID: Associate or Co-investigator Contact Information Name: Nordstrom, Scott W Institution: University of Colorado, Boulder Email: ORCID: Associate or Co-investigator Contact Information Name: Eichenberger, Erin G Institution: North Carolina State University Email: ORCID: Associate or Co-investigator Contact Information Name: Kiefer, Gretel Institution: Chicago Botanic Garden Email: ORCID: Associate or Co-investigator Contact Information Name: Dykstra, Amy B Institution: Bethel University Email: a-b-dykstra@bethel.edu ORCID: Associate or Co-investigator Contact Information Name: Shaw, Ruth G Institution: University of Minnesota Email: shawx016@umn.edu ORCID: Associate or Co-investigator Contact Information Name: Wagenius, Stuart Institution: Chicago Botanic Garden Email: swagenius@chicagobotanic.org ORCID: 3. Date published or finalized for release: 2022-04-29 4. Date of data collection (single date, range, approximate date) 2006-05-01 to 2022-09-01 5. Geographic location of data collection: Grant County and Douglas County, Minnesota, USA. Most sites are located within Solem Township (45.804167, -95.683333). We have not provided exact coordinates here due to conservation concerns. However, we will share those locations with scientists who are conducting legitimate research on this species, on the grounds that the exact locations are not published in future studies. Please see contact information above. 6. Information about funding sources that supported the collection of the data: Sponsorship: NSF awards 2051562, 2050455, 1557075, 1555997, 1052165, 1051791, 0545072, and 0544970; Dayton Bell Museum Fund 7. Overview of the data (abstract): An individual’s fitness depends not only on its fecundity, but also on the viability of its offspring. Plant ecologists typically equate fecundity, or seed yield, with reproductive fitness, but fecundity might not correspond to offspring survival. Furthermore, individual fecundity and survival of the offspring might respond differently to external factors affecting fitness. One factor that may influence reproductive fitness through effects on both fecundity and offspring survival is mating opportunity, e.g., an individual’s access to potential mates. We investigated the relationship between maternal mating opportunity and both fecundity and offspring survival in populations of a long-lived herbaceous perennial, Echinacea angustifolia. Across seven years and 14 sites, we quantified the mating opportunity of 1279 plants and followed the progeny from these mating bouts over eight subsequent years. We used aster models to evaluate the relationship between mating opportunity and both the number of seedlings emerging and the number of progeny alive after 8 years. Seedling emergence increased strongly with mating opportunity, but we did not detect a significant relationship between progeny count after eight years and mating opportunity. These results show that mating opportunity increases fecundity, but its benefit to overall fitness may be weak. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: Waananen et al. Offspring emergence, but not survival, increases with maternal mating opportunity. Submitted to Ecology in April 2022. 3. Was data derived from another source? Yes If yes, list source(s): Echinacea Project demographic census in the remnants (http://echinaceaproject.org/category/experiments/ea-demo/) 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: seedling_demography.csv Short description: This file was cleaned and processed by team members between Fall 2019 and Summer 2020 and updated to include data from Summer 2021. This file contains one record per seedling per year. It houses information about seedling survival and plant status. There should exist data from the 2007 sling cohort through the current year of seedling re-finds, and the table is uploaded here in long format. B. Filename: mating_potential.csv Short description: This dataset contains information about focal circles and mating potential in the year prior to spring that we searched for seedlings. C. Filename: aster_analysis.R Short description: Contains code to perform aster analyses of the data to assess the relationship between maternal mating opportunity and progeny abundance at emergence and after eight years. 2. Relationship between files: The R code reads in and analyzes data from the two CSV files. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Flowering Surveys: Since 1995, the Echinacea Project has been mapping and collecting demographic information on Echinacea angustifolia to generate detailed, long-term records of individual fitness in prairie remnants. At each Echinacea plant, the team used handheld data collectors (visors) to record the flowering status, number of flowering heads, number of rosettes, and near neighbors of the plant. They then mapped the location of every flowering plant within each prairie remnant using a either a high-precision GPS unit or survey station. Seedling and Juvenile Surveys: Between 2007 and 2013, we surveyed for E. angustifolia seedlings at each of the 14 sites. We describe our seedling survey methods in detail elsewhere (Dykstra 2013; Nordstrom et al. 2021), and briefly here. To select our sampling locations at each site, we randomly selected up to 18 plants that had flowered in the previous year. We then searched for seedlings within a specified radius of each selected plant; we refer to this area as a ‘focal circle’ and to the plant at its center as the ‘maternal plant.’ Typically, we searched for seedlings within a focal circle with a 41 cm radius; in rare instances, we searched radii of 32, 50, or 80 cm. Although it is possible that the seedlings we found within a focal circle could result from seeds dispersing from other plants into the focal circle, we think this is unlikely. E. angustifolia achenes are gravity-dispersed, typically dropping directly below the seedhead. A relatively small percentage of our focal maternal plants were within 41 cm of another plant that had also flowered in the previous year (16%, 204 of 1278 focal circles). Searches for seedlings in 163 circles centered at random points within 4 meters but beyond 1.5 meters of any plant that had flowered in the previous year only yielded two seedlings, suggesting that dispersal within this range, and beyond the range of our focal circles, is rare. We searched for seedlings in May or early June, when seedling cotyledons remained easy to observe. To facilitate finding the individual progeny in later years, we mapped the location of each seedling relative to other seedlings, the focal plant, and other E. angustifolia within or near the search radius. In total, we searched for seedlings in 1279 focal circles, tracking cohorts that emerged across 7 years and at 14 sites. For each seedling cohort (one from each year 2007-2013), we tracked offspring outcomes for eight years (e.g., 2007-2014 for the 2007 cohort, 2013-2021 for the 2013 cohort). We searched each circle in the late summer following emergence to assess survival over the first growing season. Thereafter, we visited focal circles annually to assess the survival of the progeny identified in the seedling search. When we did not find one of the progeny in a given year, we noted this and searched again for at least two more years. If we found the individual in one of these years, we revised its demographic status in previous years to “alive.” If we did not find the juvenile in either of the subsequent two years, we no longer searched for it in following years and revised our records to “dead” in all years that we did not find it. Dykstra, A. B. 2013. Seedling recruitment in fragmented populations of Echinacea angustifolia. University of Minnesota. Nordstrom, S. W., A. B. Dykstra, and S. Wagenius. 2021. Fires slow population declines of a long-lived prairie plant through multiple vital rates. Oecologia 196:679–691. 2. Methods for processing the data: We quantified mating opportunity as “mating potential,” a weighted sum of the distances between a focal plant i and its seven nearest potential mates. Specifically, we took the sum of the distances between a focal maternal plant and its k = 1-7th nearest neighbors (i.e. its likely pollen sources), with each distance weighted by an exponential decay parameter γ = 0.13 that determines the strength of the relationship between distance and a neighbor’s contribution to mating potential. Previous studies in this study area found that γ = 0.13 best described patterns of reproduction in E. angustifolia (Wagenius et al. 2007). The relationship between 1-kth nearest neighbors and pollen limitation varies little between k=2 and k=18 (Wagenius 2006), suggesting that the results of this analysis should not be sensitive to this threshold. When fewer than seven individuals flowered within a site, we quantified mating potential with as many individuals as flowered in the site. For various historical reasons, there are some sites which we give distinct names in the field, but consider a single site for our analysis, e.g., indicating two adjacent units of a site separated by, for instance, a gravel road. We merged the following "sites" as indicated in 'seedling_demography.csv' for analysis: - Liatris Hill was included as part of North of Golf Course, - North of Northwest of Landfill was included with Northwest of Landfill, - Staffanson East and West were combined - Landfill East and West were combined - Loeffler's corner East and West were combined - RRXDC was combined with Loeffler's Corner Wagenius, S. 2006. Scale Dependence of reproductive failure in fragmented Echinacea populations. Ecology 87:931–941. Wagenius, S., E. Lonsdorf, and C. Neuhauser. 2007. Patch aging and the S‐Allee effect: breeding system effects on the demographic response of plants to habitat fragmentation. Am. Nat. 169:383–397. 3. Instrument- or software-specific information needed to interpret the data: The analyses we presented here were run in R version 4.0.3 (2020-10-10), Platform: x86_64-w64-mingw32/x64 (64-bit), Running under: Windows 10 x64 (build 19042). 4. Standards and calibration information, if appropriate: We measured distance between seedlings to the nearest centimeter. 5. Environmental/experimental conditions: We conducted this study in natural remnant populations of Echinacea angustifolia in western MN. 6. Describe any quality-assurance procedures performed on the data: We compared two independent datasets of flowering demography (survey records of flowering plants and demographic records of flowering plants) to create maps of flowering in remnant populations during the years that the maternal plants were flowering, which we used to calculate mating potential. 7. People involved with sample collection, processing, analysis and/or submission: Many interns with were involved in data collection. Please see the 'flog' (field blog) for entries related to the seedling search project over the years (http://echinaceaproject.org/category/experiments/seedling-establishment-aka-sling/). All co-authors were involved in data processing and curation. Amy was responsible for analysis and submission. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: mating_potential.csv ----------------------------------------- rows: 1278 cols: 9 A. Name: focalCd Description: identifier for the focal circle, denoted by site-searchYear-# (character) B. Name: year Description: this is the year prior to the seedling search year (i.e., the mating year) C. Name: site Description: this is the site where the focal maternal plant was located. See details above in 'Methods for processing data.' D. Name: hdCt.n Description: this number indicates the number of normal heads, i.e., heads that produced pollen and seeds normally (numeric) E. Name: hdCt.o Description: this indicates the number of "other" heads, i.e., heads that did not develop normally for some reason, such as abortion, mowing, disease, or herbivory. We use alphanumeric codes to indicate the fate of the head and the number of heads with that fate for each plant. Specifically, m = mowed, s = abortion or failure to develop due to internal processes of the plant, g = head is gone from plant, vd = vertical development of a stem, but no development of a flower head, d = diseased. So, m1 indicates a plant had one mowed head, m1s1 means that a plant had one head that was mowed and one that failed to develop due to internal processes, and so on. (character) F. Name: matingPotential1 Description: annual mating potential, calculated as a weighted average distance to all other flowering plants in the study area, including flowering plants that may not have developed normally (i.e., all plants where fl == 1, but hdCt.n may be 0) (numeric) G. Name: matingPotential2 Description: annual mating potential, calculated as a weighted average distance to all normally flowering plants in the study area (i.e., all plants for which hdCt.n > 0) (numeric) H. Name: slingCt Description: the number of seedlings initially found in each focal circle (numeric) I. Name: radius Description: radius of the focal circle in centimeters (numeric) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: seedling_demography.csv ----------------------------------------- rows: 11321 cols: 11 A. Name: focalCd Description: this is a unique identifier for each circle. It is unique to the year the maternal plant or random point was searched for seedlings. It is in the format, “siteName-searchYear-matPlant#” (character) B. Name: note Description: field and data wrangling note about record (character) C. Name: slingCd Description: this is a unique identifier for each sling. It is in the format, “siteName-searchYear-matPlant#-slingID” (character) This identifier remains unique for each plant (each sling) across the entire experiment–all years & all sites. D. Name: year Description: year that the former seedling was observed in annual demographic surveys (integer) E. Name: slingYr Description: year the seedling was originally found (i.e., its cohort) (integer) G. Name: site Description: name of the site (character). See details above in 'Methods for processing data.' J. Name: timeStamp Description: date, and sometimes time, of data collection. Many records have an incomplete or missing timeStamp becuase new records were generated based on data from subsequent years (date) K. Name: status Description: plant status in re-find year. Status is based on field observation OR was updated to reflect if a “missing” plant in one year was found alive in a subsequent year (character) L. Name: ld Description: living during observation year / 1 = yes, 0 = no, 1.1 = alive; record added for “basal based on subsequent yrs living”, 1.2 = alive; record changed from “can’t find” to “basal based on subsequent yrs living.” 1.1 and 1.2 statuses were added to indicate that these were changed from initial observations, whole 1 and 0 are based directly on field observations. In future iterations of the dataset, if slingCds with 0’s in the dataset are found to be alive in later years, change the 0 to 1.2; if there was no record in previous years, add an ld of 1.1 for missing years (numeric) AB. Name: newNote Description: note about records added due to subsequent years data (character) AF. Name: newLD Description: living during observation year / 1 = yes, 0 = no. Revised based on status described in 'ld' (numeric) ----------------------------------------- R SESSION INFORMATION FOR GENERATING RESULTS FROM: aster_analysis.R ----------------------------------------- R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631) Matrix products: default attached base packages: [1] stats graphics grDevices utils datasets methods [7] base loaded via a namespace (and not attached): [1] utf8_1.2.4 R6_2.5.1 tidyselect_1.2.0 [4] magrittr_2.0.3 gtable_0.3.4 glue_1.6.2 [7] tibble_3.2.1 pkgconfig_2.0.3 generics_0.1.3 [10] dplyr_1.1.3 lifecycle_1.0.3 ggplot2_3.4.4 [13] cli_3.6.1 fansi_1.0.5 scales_1.2.1 [16] rcartocolor_2.1.1 grid_4.3.1 vctrs_0.6.4 [19] compiler_4.3.1 rstudioapi_0.15.0 tools_4.3.1 [22] pillar_1.9.0 munsell_0.5.0 colorspace_2.1-0 [25] rlang_1.1.1