Primary tables
sites
File name: BIO46_sample_sites.csv
Description:
Location and environmental data for Jasper Ridge survey sites.
Details:
Each row corresponds to one site that was sampled for lichens in the BIO46 class. Site numbers correspond to the same plant numbers used by the BIO47 course. Canopy cover variables are from Gap Light Analyzer (GLA) analysis of hemispherical digital photographs of taken at each site in April - May of 2017 (for the BIO 47 class).
| Column name | Description |
|---|---|
| Site | Unique site number. Corresponds to the same Plant numbers used in BIO 47. |
| Canopy_openness_pct | Percent canopy openness. 100 = 100% open sky. |
| LAI_75deg | Leaf area index within 75 degree zenith angle. |
| Group | Group number assigned to survey the site. |
| UTM_E & UTM_N | Location of the site in UTM coordinates (zone 10). |
| RH_site | Site whose humidity logger was used to estimate humidity at this site. |
lichens
File name: lichens.csv
Description:
Lichens collected at Jasper Ridge, including outcomes of growth and infection experiments.
Details:
Each row corresponds to a lichen collected at Jasper Ridge on January 11, 2018. Lichens were used in two experiments: 1) a growth experiment in which the change in mass and health of lichens was observed before and after growing in a growth chamber for 6 weeks (at 22 C with 14 / 10 hr light / dark cycle) and 2) an infection experiment in which lichens the health of lichens was observed after infection with different fungal isolates (see infection_experiment table).
| Column name | Description |
|---|---|
| Team | Team that collected the lichen. |
| LichenID | Unique code identifying a lichen individual. |
| Site | Site where lichen was collected. |
| Substrate_type | Whether lichen was collected from a tree or shrub. |
| Substrate_status | Whether the substrate from which the lichen was collected was alive or dead. |
| Ascomata | Number of ascomata of Unguiculariopsis lettaui observed present under a dissecting microscope. |
| Experiment | Which experiment the lichens was used for. |
| Mass_mg_init | Initial mass in mg. Recorded only for lichens in the growth experiment. |
| Mass_mg_6weeks | Mass after 6 weeks in the growth experiment. |
| Health | Categorical variable recording health status after 6 weeks. 1 = most healthy, 3 = least healthy. All lichens were initially at health status 1. |
fungal_isolates
File name: fungal_isolates.csv
Description:
Growth rates and identities of fungi isolated from lichens.
Details:
Lichens were surface steriled in falcon tubes ( 95% ethanol for 30 sec, 70% bleach for 2 min, 70% ethanol for 2 min) and then allowed to dry on sterile petri dishes before cutting into twelve 2x2 mm sections and plating on slants containing solid MEA media (in 1.5 mL eppendorf tubes). Each fungus that emerged was given a unique IsolateID and replated onto a petri dish with solid MEA media to measure growth. The radius was measured after 7 and 14 days of growth in three directions and then averaged.
After at least 7 days of growth mycelia from the growing edge of each culture were collected and DNA was extracted using Sigma Plant Extract-N-Amp kit. The ITS region of the rDNA gene was amplified with primers ITS1F and ITS4 and Sanger sequenced with ITS1F. TaxonIDs were then assigned using T-BAS (Carbone et al. 2016) and the RDP Classifier tool (Wang et al. 2007) with the Warcup fungal ITS training set (Deshpande et al. 2015). Sequences were inspected by eye to determine whether they should be assigned to the same TaxonID or Species. TaxonIDs with “gen1”, “gen2”, etc indicate that these sequences differ by only a couple few base pairs, whereas TaxonIDs assigned to different species differ by several based pairs.
Table updated on 2018-06-04 with 12 fungal isolates that emerged after the class concluded, of which only four were able to be assigned taxa from ITS sequences.
| Column name | Description |
|---|---|
| LichenID | Code identifying the lichen that the fungus was isolated from. |
| IsolateID | Unique code identifying a fungal isolate. |
| Date_emerged | Date that fungal isolate was transfered from a slant to a plate with solid media to measure growth. |
| Radius_mm_day7 | Radius after growing for 7 days. |
| Radius_mm_day14 | Radius after growing for 14 days. |
| TaxonID | Tentative taxon name. Corresponds to taxa table. |
| Notes | Additional information. |
taxa
File name: taxa.csv
Description:
Descriptions of TaxonIDs used to classify fungal isolates.
Details:
TaxonIDs were assigned to fungal isolates (see fungal_isolates table) according to differences in their rDNA ITS sequences. Names were tentatively assigned using T-BAS (Carbone et al. 2016) and the RDP Classifier tool (Wang et al. 2007) with the Warcup fungal ITS training set (Deshpande et al. 2015). T-BAS was primarily used to identify unique OTUS whereas the RDP Classifier was used to assign names. Sequences were inspected by eye to determine whether they should be assigned to the same TaxonID or Species. TaxonIDs with “gen1”, “gen2”, etc indicate that these sequences differ by only a couple base pairs, whereas TaxonIDs assigned to different species differ by several based pairs. Variation in bases on the ends of sequences were ignored since difference are likely due to errors in the sequencing process. Chromatograms were inspected to verify that single nucleotide differences between genotypes were actual substitutions and not errors in sequencing.
| Column name | Description |
|---|---|
| TaxonID | Unique name identifying a unique ITS sequence. |
| Class | Class assigned by RDP Classifier. If blank, the taxon could not be assigned to a Class with 80% confidence. |
| Order | Order assigned by RDP Classifier. If blank, the taxon could not be assigned to an Order with 80% confidence. |
| Family | Family assigned by RDP Classifier. If blank the taxon could not be assigned to a Family with 80% confidence. |
| Genus | Genus assigned by RDP Classified. If blank the taxon could not be assigned to a Genus with 80% confidence. |
| Species | The first two names in the TaxonID. These names do not correspond to actual fungal species. |
| Notes | Additional information including whether the sequence matched a particular taxon in the Warcup database. |
site_X_species_tables
Description:
These tables show whether different fungal taxa were present or absent in different lichens and at different sites. Each row is a lichen or a site and the columns are the different taxa. See 2018/Code/make_databases_tables.R for how the tables were generated. A 1 indicates that the taxon was isolated from a given lichen or from a lichen at a given site. Note tat different numbers of lichens were sampled at sites (see lichens and sites tables).
File names:
| File name | Description |
|---|---|
| taxaXlichen.csv | Presence / absence of TaxonIDs within lichens. |
| taxaXsite.csv | Presence / absence of TaxonIDs at sites. |
| speciesXlichen.csv | Presence / absence of species within lichens. |
| speciesXsite.csv | Presence / absence of species at sites. |
| classXlichen.csv | Presence / absence of fungal classes within lichens. |
| classXsite.csv | Presence / absence of fungal classes at sites. |
infection_prevalence
File name: infection_prevalence.csv
Description:
Abundance of E. prunastri and infection prevalence at survey sites.
Details:
Site were surveyed for Evernia prunastri abundance by searching for all E. prunastri present within a 1 x 3 meter plot centered on the station holding the ibutton. Lichens were not surveyed from branches that had fallen on the ground. The prevalence of Unguiculariopsis lettaui infecting E. prunastri was estimated by randomly choosing nine lichen thalli and inspecting them for ascomata with a 10x hand lens.
| Column name | Description |
|---|---|
| Site | Unique site number. |
| Date | Date when the site was surveyed. |
| Num_Eprunastri | Number of Evernia prunastri thalli. |
| Num_infected | Number of Evernia purnastri with ascomata from Unguiculariopsis lettaui. |
| Num_healthy | Number of Evernia prunastri that were not infected. |
interaction_experiment_byplate
File name: interaction_experiment_byplate.csv
Description:
Outcome of fungal isolate interaction experiment for each plate.
Details:
Fungal isolates were grown alone (“solo”) or in competition with one other isolate (“co-culture”) on 9 cm petri dishes filled with solid MEA media. To start te experiment, plugs of agar filled with fungal mycelia from the growing edge of a fresh culture were transfered with a plastic drinking straw to positions 3 cm apart from one another in the center of the plates. Culture grew for 1 - 2 weeks and the radius of each culture in the direction of the other culture was recorded each week. At the conclusion, the “winner” of the interaction was the isolate that was able to grow over the other isolate. If neither isolate grew over the other then the interaction was recorded as a “draw”.
IsolateIDs correspond to fungal isolates described in the BIO46_W2017_fungi.csv table which can be found in 2018/Data analysis exercises/data. See the taxa table for information on TaxonIDs.
This table has one row for each plate in the experiment.
| Column name | Description |
|---|---|
| PlateID | Unique code identifying a plate. |
| Culture_type | Whether the isolate grew aone (“solo”) or in competition with one other isolate (“co-culture”). |
| Isolate1_radius_mm_day7 | Radius of isolate 1 after 7 days in mm. |
| Isolate1_radius_mm_day14 | Radius of isolate 1 after 14 days in mm. |
| Isolate2_radius_mm_day7 | Radius of isolate 2 after 7 days in mm. Recorded only for co-culture plates. |
| Isolate2_radius_mm_day14 | Radius of isolate 2 after 14 days in mm. Recorded only for co-culture plates. |
| Isolate1_outcome and Isolate2_outcome | Whether isolate 1 or isolate 2 “won” or “lost” the interaction by growing over the other isolate. |
| IsolateID_1 and IsolateID_2 | Codes identifying isolates 1 and 2. |
| TaxonID_1 and TaxonID_2 | Tentative taxa assigned to isolates 1 and 2 based on ITS sequences. |
interaction_experiment_bycompetitor
File name: interaction_experiment_bycompetitor.csv
Description:
Outcome of fungal isolate interaction experiment for each competitor on a plate.
Details:
See the descriprion for the interaction_experiment_byplate table. Each row in this table corresponds to a single isolate on a plate.
| Column name | Description |
|---|---|
| IsolateID | Unique code identifying the isolate. |
| TaxonID | Tentative taxon assigned to the isolate based on ITS sequence. |
| Radius_mm_day7 | Radius after 7 days in mm. |
| Radius_mm_day14 | Radius after 14 days in mm. |
| Competitor_isolate | IsolateID of the fungal isolate that this isolate was plated with. Only reported for co-culture plates. |
| Competitor_taxon | TaxonID of the fungal isolate that this isolate was plated with. Only reported for co-culture plates. |
| Culture_type | Whether the isolate was grown alone (“solo”) or in competition with another isolate (“co-culture”) |
| PlateID | Code identifying which plate this data is from. |
env_logger_summary
File name: env_logger_summary.csv
Description:
Summaries of daily mean, min, max and range of temperature and vapor pressure deficit (VPD) for Nov 2017 - Feb 2018 at each site.
Details:
Daily mean, min, max and range values for temperature (C) and VPD are averaged for all time points measured (Time_period = “All”) and within each month and week. For example, Month1 = January, Month2 = February and Week1 = the first week of the year, Week2 = the second week of the year, etc.
Vapor pressure deficit difference between the vapor pressure of water in the air and the vapor pressure of water in air that is completely saturated. It is a measure of humidity and higher values correspond to drier air. Here we estimate VPD at each site using the Magnus equation to calculate VPD from actual temperature measured at each site and the the dewpoint temperature measured at three sites around Jasper Ridge. The humidity logger closest to the site was used to assign a dewpoint temperature, since this was only measured at three sites (see the sites table for which humidity loggers were assigned to each site). See 2018/Code/make_databases_tables.R for more information.
| Column name | Description |
|---|---|
| Time_period | Time period over which daily summary values were averaged. |
| Site | Site where temperature data was recorded. |
| Temp_mean | Average daily mean temperature in Celcius. |
| Temp_min | Average daily minimum temperature in Celcius. |
| Temp_max | Average daily maximum temperature in Celcius. |
| Temp_range | Average daily temperature range in Celcius. |
| VPD_mean | Average daily mean VPD in Pascals. |
| VPD_min | Average daily minimum VPD in Pascals. |
| VPD_max | Average daily maximum VPD in Pascals. |
| VPD_range | Average daily VPD range in Pascals. |