Data Package Metadata View Summary

Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities

General Information

Data Package:

Local Identifier:

edi.1370.3

Title:

Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

Experiments comparing diploids with polyploids and in single grassland sites show that nitrogen and/or phosphorus availability influences plant growth and community composition dependent on genome size; specifically plants with larger genomes grow faster under nutrient enrichments relative to those with smaller genomes. However, it is unknown if these effects are specific to particular site localities with speciifc plant assemblages, climates, and historical contingencies. To determine the generality of genome size dependent growth responses to nitrogen and phosphorus fertilisation, we combined genome size and species abundance data from 27 coordinated grassland nutrient addition experiments in the Nutrient Network that occur in the Northern Hemisphere across a range of climates and grassland communities. We found that after nitrogen treatment, species with larger genomes generally increased more in cover compared to those with smaller genomes, potentially due to a release from nutrient limitation. Responses were strongest for C3 grasses and in less seasonal, low precipitation environments, indicating that genome size effects on water-use-efficiency modulates genome size-nutrient interactions. Cumulatively the data suggest that genome size is informative and improves predictions of species’ success in grassland communities.

Publication Date:

2024-10-02

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2007

End:

2022

People and Organizations
Contact:	Hersch-Green, Erika (Michigan Technological University, Associate Professor) [ email ]
Contact:	Leitch, Ilia J (Royal Botanic Gardens Kew, Senior Reseach Leader) [ email ]
Contact:	Leitch, Andrew R (Queen Mary University of London, Professor of Plant Genetics) [ email ]
Creator:	Morton, Joseph A (Queen Mary University of London, PhD Student)
Creator:	Hersch-Green, Erika (Michigan Technological University, Associate Professor (corresponding author))
Creator:	Leitch, Ilia J (Royal Botanic Gardens Kew)
Creator:	Leitch, Andrew R (Queen Mary University of London)
Creator:	Arnillas, Carlos A (University of Toronto Scarborough)
Creator:	Biedermann, L (Iowa State University)
Creator:	Borer, Elizabeth T (University of Minnesota)
Creator:	Brudvig, Lars A (Michigan State University)
Creator:	Buckley, Yvonne M (Trinity College Dublin)
Creator:	Cadotte, Marc (University of Toronto Scarborough)
Creator:	Davies, Kendi (University of Colorado Boulder)
Creator:	Donohue, Ian (Trinity College Dublin)
Creator:	Anne, Ebeling (Friedrich Schiller University Jena)
Creator:	Eisenhauer, Nico (Universität Leipzig)
Creator:	Estrada, Catalina (Imperial College London)
Creator:	Haider, Sylvia (Leuphana University of Lüneburg)
Creator:	Hautier, Yann (University of Utrecht)
Creator:	Jentsch, Anke (University of Bayreuth)
Creator:	Martinson, Holly (McDaniel College Westminster)
Creator:	Rebecca, McCulley (Universiy of Kentucky)
Creator:	Raynaud, Xavier (Sorbonne Université, Paris)
Creator:	Roscher, Christian (Helmholtz Centre for Environmental Research)
Creator:	Seabloom, Eric (University of Minnesota)
Creator:	Stevens, Carly J (Lancaster University)
Creator:	Vesela, Katerina (Queen Mary University of London)
Creator:	Wallace, Alison (Minnesota State University Moorhead)

Data Entities
Data Table Name:	Genome Size Data (Figure 1A, 2, and S3 Figure)
Description:	GS data for analysis outlined in "Plot variation in GS across different groups" section of Key Analyses and Figure Plotting R script. Data used for Figures 1A, 2 And S3 Figure in the paper.
Data Table Name:	Cover proportion data (Figure 1B)
Description:	Data used to examine the proportion of total cover taken up by each functional group on a plot. This is used in the analysis outlined in "Quantifying variation in percent cover across functional groups" of the Key Analyses and Figure Plotting R script and used for Figure 1B
Data Table Name:	Cover-weighted genome size data (Figure 3, 4 and S4 Figure)
Description:	The cover-weighted genome size data used in "Analysis of cover-weighted genome size" of the Key Analyses and Figure Plotting R script to examine the effect of N and P treatment on the average genome size of a plot. Also used for Figure 3, 4 and S4 Figure.
Data Table Name:	27-site-background-data (S2 Figure)
Description:	Site specific data including climate, soil N, P and acidity, and the age of the plot. Used in "Climate variable selection and S2 Figure" of the Key Analyses and Figure Plotting R script, and in Figure S2 of the paper.
Data Table Name:	PCA Point Data (S2 Figure)
Description:	The data underlying the coordinates of each site in the climate principal component analysis. This summarises the key data used in Figure S2 and in the "Climate variable selection" section of the Key Analyses and Figure Plotting R script.
Data Table Name:	PCA variable data (S2 Figure)
Description:	The data underlying the direction of effect of each climate variable in the principal component analysss and the contribution of each variable to principal component 1 and 2 of the PCAs. This summarises the key data used in Figure S2 and in the "Climate variable selection" section of the Key Analyses and Figure Plotting R script.
Data Table Name:	Supplementary Cell Density Data (S5 Figure)
Description:	Mean cell density data for 63 species across 6 sites in the nutrient network (n = 81). Mean values are given, alongside the sample size used for the mean estimate. This is used in the "Cell Density Analysis" section of the Key Analyses and Figure Plotting R script E. Hersch Green is the author and owner of this dataset.
Data Table Name:	27-site-cover-data (Raw Data)
Description:	Raw cover data without genome size values for species, as used in "Loading in and formatting initial data" section of R script
Data Table Name:	27-site-plot-data (Raw Data)
Description:	Plot data made and used in "Analysis of cover-weighted genome size" and "Analysis of species richness" sections of the R script
Data Table Name:	27-site-species-final-data (Raw Data)
Description:	Dataset produced in "Loading in and formatting initial data" section of R script for use in later plot and species level analysis
Data Table Name:	27-site-phylo-data (Raw Data)
Description:	The subset of the cover and genome size data used in the phylogenetic analysis (Analysis of species cover responses to nutrients)
Other Name:	Key Analyses and Figure Plotting
Description:	This R script provides the code for the main analyses and plotting of figures, using data from "Genome size data", "Cover proportion data", "Cover-weighted genome size data", "27-site-background-data" and "Supplementary cell density data".
Other Name:	Full Data Processing and Analysis Script
Description:	This is the full code outlining the data processing, compiling and analysis, as well as all figure plotting. This uses the raw data (all beginning with "27-site-")
Other Name:	27_site_phylogeny
Description:	Phylogeny of species found on the 27 sites. Used in phylogenetic comparative models.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/c493a18b681d763c161d9ef3494d0a9d
Name:	Genome Size Data (Figure 1A, 2, and S3 Figure)
Description:	GS data for analysis outlined in "Plot variation in GS across different groups" section of Key Analyses and Figure Plotting R script. Data used for Figures 1A, 2 And S3 Figure in the paper.
Number of Records:	1507
Number of Columns:	10

Table Structure

Object Name:

Genome Size Data.csv

Size:

151304 byte

Authentication:

ff4aa6ca586ff65e3a8eb4d8701e78c6 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_code

taxon

family

lifeform

Photosynthetic_Pathway

species_GS_code

GS_2C

GS_1C

Source

Func_Group

Column Name:

site_code

taxon

family

lifeform

Photosynthetic_Pathway

species_GS_code

GS_2C

GS_1C

Source

Func_Group

Definition:

Name code of the Nutrient Network Site

Species name

Plant Family

Plant Functional Group

Photosynthetic pathway (mostly for grasses)

Unique code for each species on each site

Genome size value expressed as 2C-value

Genome size value expressed as 1C-value

Source for genome size measurement

Plantfunctional group, separating grasses by photosynthetic pathway

Storage Type:

string

float

string

Measurement Type:

nominal

ratio

nominal

Measurement Values Domain:

Definition

text

Definition

text

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual Forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass
Definition	Grass
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial Forb
Source

Code Definition

Code	Woody
Definition	Woody
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	C3
Definition	C3
Source

Code Definition

Code	C4
Definition	C4
Source

Definition

text

Unit	pg/2C
Type	real

Unit	pg/1C
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Database
Definition	From Kew Plant DNA C-values Database
Source

Code Definition

Code	Measured
Definition	Measured from collected sample by flow cytometry
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass (C3)
Definition	Grass with C3 photosynthetic pathway
Source

Code Definition

Code	Grass (C4)
Definition	Grass with C4 photosynthetic pathway
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial forb
Source

Code Definition

Code	Woody
Definition	Woody species
Source

Missing Value Code:

Code	NA
Expl	no DNA measurement

Code	NA
Expl	no DNA measurement

Code	NA
Expl	no DNA measurement

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/ab04a67afa2c5aa562d6001efa4cbe9e
Name:	Cover proportion data (Figure 1B)
Description:	Data used to examine the proportion of total cover taken up by each functional group on a plot. This is used in the analysis outlined in "Quantifying variation in percent cover across functional groups" of the Key Analyses and Figure Plotting R script and used for Figure 1B
Number of Records:	4434
Number of Columns:	10

Table Structure

Object Name:

Cover proportion data.csv

Size:

375189 byte

Authentication:

3ed61bf71a26e58ca06a21ad22498fd9 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

plotyear_code

plot_code

year

site_code

lifeform

Func_Group

Photosynthetic_Pathway

cover

total_cover

cover_pct

Column Name:

plotyear_code

plot_code

year

site_code

lifeform

Func_Group

Photosynthetic_Pathway

cover

total_cover

cover_pct

Definition:

Unique code for each plot within each site on each year

Unique code for each plot within each site

Pretreatment or 3 year mean values

Name code of the Nutrient Network Site

Plant Functional Group

Plantfunctional group, separating grasses by photosynthetic pathway

Photosynthetic pathway (mostly for grasses)

The cover taken up by all species in a functional group on a plot

The total percent cover taken up by all species on a plot

The percentage of the total cover on a plot taken up by all species in a functional group

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

text

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	initial
Definition	Pretreatment year
Source

Code Definition

Code	mean
Definition	3 year mean
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual Forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass
Definition	Grass
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial Forb
Source

Code Definition

Code	Woody
Definition	Woody
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass (C3)
Definition	Grass with C3 photosynthetic pathway
Source

Code Definition

Code	Grass (C4)
Definition	Grass with C4 photosynthetic pathway
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial forb
Source

Code Definition

Code	Woody
Definition	Woody species
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	C3
Definition	C3
Source

Code Definition

Code	C4
Definition	C4
Source

Unit	percent
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/93ad8dda28d6515d51fbf817227c9fb2
Name:	Cover-weighted genome size data (Figure 3, 4 and S4 Figure)
Description:	The cover-weighted genome size data used in "Analysis of cover-weighted genome size" of the Key Analyses and Figure Plotting R script to examine the effect of N and P treatment on the average genome size of a plot. Also used for Figure 3, 4 and S4 Figure.
Number of Records:	681
Number of Columns:	24

Table Structure

Object Name:

cwGS data.csv

Size:

114125 byte

Authentication:

f90928d0f4e0c6147e339a0c59d6f8b3 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_code

plotyear_code

site_name

block

plot

year

trt

plot_code

GS_rich

sp_rich

plot_cwGS

elevation

MAT

MAP

temp_seasonality

precip_seasonality

plot_age

initial_cwGS

control_cwGS

LRR_tp

LRR_tc

Column Name:

site_code

plotyear_code

site_name

block

plot

year

trt

plot_code

GS_rich

sp_rich

plot_cwGS

elevation

MAT

MAP

temp_seasonality

precip_seasonality

plot_age

initial_cwGS

control_cwGS

LRR_tp

LRR_tc

Definition:

Name code of the Nutrient Network Site

Unique code for each plot within each site on each year

Name of the Nutrient Network Site

Block number within site

Plot number within site

Pretreatment or 3 year mean values

Nutrient treatment applied to the plot

Indicates whether nitrogen was added

Indicates whether phosphorus was added

More detailed description of treatment added

Unique code for each plot within each site

Number of species with genome size measurments on plot

Species richness (number of species) of plot

Cover-weighted mean genome size of the plot

elevation of the site

Annual Mean Temperature

Mean annual precipitation

Seasonality in temperature

Seasonality in precipitation (Coefficient of variation)

Age of the plot at time of data collection

The cover-weighted genome size of a plot prior to nutrient treatment

The cover-weighted genome size of the control plot in the same block during the same time frame

The log response ratio of a plot's cover-weighted genome size relative to the same plot prior to nutrient treatment

The log response ratio of a plot's cover-weighted genome size relative to the average control plot in the block

Storage Type:

string

float

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

text

Definition

text

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	initial
Definition	Pretreatment year
Source

Code Definition

Code	mean
Definition	3 year mean
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No nitrogen added
Source

Code Definition

Code	1
Definition	Nitrogen added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No phosphorus added
Source

Code Definition

Code	1
Definition	Phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	K
Definition	Potassium added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	NK
Definition	Nitrogen and potassium added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Code Definition

Code	NPK
Definition	All nutrients added
Source

Code Definition

Code	Other
Definition	Lower nutrient concentrations added (specific to cereep.fr)
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	PK
Definition	Phosphorus and potassium added
Source

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Unit	pg/1C
Type	real

Unit	m (a.s.l)
Type	integer

Unit	celsius
Type	real

Unit	millimeter
Type	integer

Unit	standard deviation x 100
Type	real

Unit	Coefficient of Variation
Type	real

Definition

text

Unit	pg/1C
Type	real

Unit	pg/1C
Type	real

Unit	ratio (post vs pre)
Type	real

Unit	ratio (post vs control)
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/21d67ede0365e7f0e1ab0891389e4d76
Name:	27-site-background-data (S2 Figure)
Description:	Site specific data including climate, soil N, P and acidity, and the age of the plot. Used in "Climate variable selection and S2 Figure" of the Key Analyses and Figure Plotting R script, and in Figure S2 of the paper.
Number of Records:	27
Number of Columns:	36

Table Structure

Object Name:

27-site-background-data.csv

Size:

8009 byte

Authentication:

81d199d0cfb9fb2906fb84c088c7e868 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_code

continent

Country

habitat

site_name

elevation

latitude

longitude

RAIN_PET

MAT

MAT_range

isothermality

temp_seasonality

max_temp

min_temp

annual_temp_range

temp_wetq

temp_dryq

temp_warmq

temp_coldq

MAP

precip_wetm

precip_drym

precip_seasonality

precip_wetq

precip_dryq

precip_warmq

precip_coldq

pct_N

ppm_P

soil_pH

first_year

last_year

plot_age

blocks

GS_coverage

Column Name:

site_code

continent

Country

habitat

site_name

elevation

latitude

longitude

RAIN_PET

MAT

MAT_range

isothermality

temp_seasonality

max_temp

min_temp

annual_temp_range

temp_wetq

temp_dryq

temp_warmq

temp_coldq

MAP

precip_wetm

precip_drym

precip_seasonality

precip_wetq

precip_dryq

precip_warmq

precip_coldq

pct_N

ppm_P

soil_pH

first_year

last_year

plot_age

blocks

GS_coverage

Definition:

Name code of the Nutrient Network Site

Continent that the site is on

Country the site is found in

Habitat type

Name of the Nutrient Network Site

elevation of the site

Latitude of the site

longitude of the site

Potential evapotranspiration

Annual Mean Temperature

Range in mean diurnal temperature

Isothermality (BIO2/BIO7) (×100)

Seasonality in temperature

maxmimum temperature

minimum temperature

Range in annual mean temperature

Mean temperature of wettest quarter

Mean temperature of driest quarter

Mean temperature of warmest quarter

Mean temperature of coldest quarter

Mean annual precipitation

Mean precipitation of the wettest month

Mean precipitation of the driest month

Seasonality in precipitation (Coefficient of variation)

Mean precipitation of the wettest quarter

Mean precipitation of the driest quarter

Mean precipitation of the warmest quarter

Mean precipitation of the coldest quarter

Soil percent nitrogen

Soil phosphorus content

Soil pH

First year of nutrient treatment

most recent year of nutrient treatment

Age of the plot at time of data collection

Number of blocks on the site

Percent of species on site with available genome size data

Storage Type:

string

float

dateTime

string

float

Measurement Type:

nominal

ratio

dateTime

nominal

ratio

Measurement Values Domain:

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Unit	m (a.s.l)
Type	real

Unit	degree
Type	real

Unit	degree
Type	real

Unit	mm/month
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	none
Type	real

Unit	standard deviation x 100
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	celsius
Type	real

Unit	millimeter
Type	integer

Unit	millimeter
Type	integer

Unit	millimeter
Type	integer

Unit	Coefficient of Variation
Type	real

Unit	millimeter
Type	integer

Unit	millimeter
Type	integer

Unit	millimeter
Type	integer

Unit	millimeter
Type	integer

Unit	percent
Type	real

Unit	ppm
Type	real

Unit	number
Type	real

Format	YYYY
Precision

Format	YYYY
Precision

Definition

text

Unit	number
Type	real

Unit	percent
Type	real

Missing Value Code:

Code	NA
Expl	no measurement

Code	NA
Expl	no measurement

Code	NA
Expl	no measurement

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/bdf53d364639b3a09e303a23062bc575
Name:	PCA Point Data (S2 Figure)
Description:	The data underlying the coordinates of each site in the climate principal component analysis. This summarises the key data used in Figure S2 and in the "Climate variable selection" section of the Key Analyses and Figure Plotting R script.
Number of Records:	27
Number of Columns:	6

Table Structure

Object Name:

PCA Point Data.csv

Size:

1829 byte

Authentication:

bbcfad2c27c7076a51bad54a7a65febf Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_code

Country

Precipitation_PC1

Precipitation_PC2

Temperature_PC1

Temperature_PC2

Column Name:

site_code

Country

Precipitation_PC1

Precipitation_PC2

Temperature_PC1

Temperature_PC2

Definition:

The specific code for the site the data is collected on

The country in which the site is found

The coordinate for precipitation principal component 1

The coordinate for precipitation principal component 2

The coordinate for temperature principal component 1

The coordinate for temperature principal component 2

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

text

Definition

text

Unit	nominal
Type	real

Unit	nominal
Type	real

Unit	nominal
Type	real

Unit	nominal
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/2bca2c1796f51873307c5844f64a2330
Name:	PCA variable data (S2 Figure)
Description:	The data underlying the direction of effect of each climate variable in the principal component analysss and the contribution of each variable to principal component 1 and 2 of the PCAs. This summarises the key data used in Figure S2 and in the "Climate variable selection" section of the Key Analyses and Figure Plotting R script.
Number of Records:	19
Number of Columns:	5

Table Structure

Object Name:

PCA variable data.csv

Size:

1233 byte

Authentication:

2a98c0d51a3caf4f69f5bae39a75b72e Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Variable

rotation_PC1

rotation_PC2

contibution_PC1

contribution_PC2

Column Name:

Variable

rotation_PC1

rotation_PC2

contibution_PC1

contribution_PC2

Definition:

The climate variable (from Bioclim climate variables)

The direction of effect of the variable in principal component 1 of the PCA

The direction of effect of the variable in principal component 2 of the PCA

The contribution of the variable to principal component 1 of the PCA.

The contribution of the variable to principal component 2 of the PCA.

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

text

Unit	nominal
Type	real

Unit	nominal
Type	real

Unit	proportion
Type	real

Unit	proportion
Type	real

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/46b3361e3f9aaa4712ef7fc7071f2261
Name:	Supplementary Cell Density Data (S5 Figure)
Description:	Mean cell density data for 63 species across 6 sites in the nutrient network (n = 81). Mean values are given, alongside the sample size used for the mean estimate. This is used in the "Cell Density Analysis" section of the Key Analyses and Figure Plotting R script E. Hersch Green is the author and owner of this dataset.
Number of Records:	81
Number of Columns:	6

Table Structure

Object Name:

Supplementary Cell Size Data.csv

Size:

5006 byte

Authentication:

e556b0d3fdd6a837d66fc7c0df5af851 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Site

Taxa

LOG_GS

Mean_CellDensity_cm2

Column Name:

Site

Taxa

LOG_GS

Mean_CellDensity_cm2

Definition:

The site from which the sample was taken

Species name, with genus and species separated by underscores

Genome size value for the species, log-transformed.

Genome size value for the species sampled (per 2C)

Mean density of cells per square centimetre of fresh leaf tissue, measured by acid digestion and cell counting in a haemocytometer

Sample size

Storage Type:

string

float

integer

Measurement Type:

nominal

ratio

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	cbgb.us
Definition	Chichaqua Bottoms
Source

Code Definition

Code	cdcr.us
Definition	Cedar Creek
Source

Code Definition

Code	kbs.us
Definition	Kellogg Biological Station
Source

Code Definition

Code	konz.us
Definition	Konza LTER
Source

Code Definition

Code	spin.us
Definition	Spindletop
Source

Code Definition

Code	temple.us
Definition	Temple
Source

Definition

text

Unit	none
Type	real

Unit	picograms per 2C
Type	real

Unit	number per square centimetre
Type	real

Unit	number
Type	integer

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/b89fa33d7822c8e797f1d359b4c5e2f0
Name:	27-site-cover-data (Raw Data)
Description:	Raw cover data without genome size values for species, as used in "Loading in and formatting initial data" section of R script
Number of Records:	138148
Number of Columns:	14

Table Structure

Object Name:

27-site-cover-data.csv

Size:

12791922 byte

Authentication:

2f37cfca29c31b39468ec861681ea257 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_name

site_code

year

year_trt

block

plot

trt

taxon

Angiosperm

max_cover

plot_code

Column Name:

site_name

site_code

year

year_trt

block

plot

trt

taxon

Angiosperm

max_cover

plot_code

Definition:

Name of the Nutrient Network Site

Name code of the Nutrient Network Site

The year the data was collected

Age of the plot at time of data collection

Block number within site

Plot number within site

Nutrient treatment applied to the plot

Indicates whether nitrogen was added

Indicates whether phosphorus was added

More detailed description of treatment added

Species name

Whether species is an angiosperm or not

Maximum areal cover observed sampled for that species

Unique code for each plot within each site

Storage Type:

string

dateTime

string

float

string

Measurement Type:

nominal

dateTime

nominal

ratio

nominal

Measurement Values Domain:

Definition

text

Definition

text

Format	YYYY
Precision

Definition

text

Definition

text

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No nitrogen added
Source

Code Definition

Code	1
Definition	Nitrogen added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No phosphorus added
Source

Code Definition

Code	1
Definition	Phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	K
Definition	Potassium added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	NK
Definition	Nitrogen and potassium added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Code Definition

Code	NPK
Definition	All nutrients added
Source

Code Definition

Code	Other
Definition	Lower nutrient concentrations added (specific to cereep.fr)
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	PK
Definition	Phosphorus and potassium added
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Angiosperm
Definition	Angiosperm species
Source

Code Definition

Code	Non-Angiosperm
Definition	Not an angiosperm species
Source

Unit	percent
Type	real

Definition

text

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/164d232661edb1d1518ca958e0d30529
Name:	27-site-plot-data (Raw Data)
Description:	Plot data made and used in "Analysis of cover-weighted genome size" and "Analysis of species richness" sections of the R script
Number of Records:	1411
Number of Columns:	20

Table Structure

Object Name:

27-site-plot-data.csv

Size:

172302 byte

Authentication:

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Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_code

plotyear_code

site_name

block

plot

year

trt

plot_code

GS_rich

sp_rich

plot_cwGS

elevation

MAT

MAP

temp_seasonality

precip_seasonality

plot_age

Column Name:

site_code

plotyear_code

site_name

block

plot

year

trt

plot_code

GS_rich

sp_rich

plot_cwGS

elevation

MAT

MAP

temp_seasonality

precip_seasonality

plot_age

Definition:

Name code of the Nutrient Network Site

Unique code for each plot on each site for each year (initial vs 3 year mean)

Name of the Nutrient Network Site

Block number within site

Plot number within site

Pretreatment or 3 year mean values

Nutrient treatment applied to the plot

Indicates whether nitrogen was added

Indicates whether phosphorus was added

More detailed description of treatment added

Unique code for each plot within each site

Number of species with genome size measurments on plot

Species richness (number of species) of plot

Cover-weighted mean genome size of the plot

elevation of the site

Annual Mean Temperature

Mean annual precipitation

Seasonality in temperature

Seasonality in precipitation (Coefficient of variation)

Age of the plot at time of data collection

Storage Type:

string

float

string

float

Measurement Type:

nominal

ratio

nominal

ratio

Measurement Values Domain:

Definition

text

Definition

text

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	initial
Definition	Pretreatment year
Source

Code Definition

Code	mean
Definition	3 year mean
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No nitrogen added
Source

Code Definition

Code	1
Definition	Nitrogen added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No phosphorus added
Source

Code Definition

Code	1
Definition	Phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	K
Definition	Potassium added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	NK
Definition	Nitrogen and potassium added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Code Definition

Code	NPK
Definition	All nutrients added
Source

Code Definition

Code	Other
Definition	Lower nutrient concentrations added (specific to cereep.fr)
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	PK
Definition	Phosphorus and potassium added
Source

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Unit	pg/1C
Type	real

Unit	m (a.s.l)
Type	integer

Unit	celsius
Type	real

Unit	millimeter
Type	integer

Unit	standard deviation x 100
Type	real

Unit	Coefficient of Variation
Type	real

Unit	number
Type	integer

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/0cbe3b58121c03073d9967d2df128b7f
Name:	27-site-species-final-data (Raw Data)
Description:	Dataset produced in "Loading in and formatting initial data" section of R script for use in later plot and species level analysis
Number of Records:	71607
Number of Columns:	20

Table Structure

Object Name:

27-site-species-final-data.csv

Size:

11593003 byte

Authentication:

fd2171e0d2a1502d18146a32949b90da Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_name

site_code

block

plot

year

trt

taxon

Angiosperm

family

lifeform

Func_Group

Photosynthetic_Pathway

species_GS_code

GS_1C

Source

max_cover

plot_code

Column Name:

site_name

site_code

block

plot

year

trt

taxon

Angiosperm

family

lifeform

Func_Group

Photosynthetic_Pathway

species_GS_code

GS_1C

Source

max_cover

plot_code

Definition:

Name of the Nutrient Network Site

Name code of the Nutrient Network Site

Block number within site

Plot number within site

Pretreatment or 3 year mean values

Nutrient treatment applied to the plot

Indicates whether nitrogen was added

Indicates whether phosphorus was added

More detailed description of treatment added

Species name

Whether species is an angiosperm or not

Plant Family

Plant Functional Group

Plantfunctional group, separating grasses by photosynthetic pathway

Photosynthetic pathway (mostly for grasses)

Unique code for each species on each site

Genome size value expressed as 1C-value

Source for genome size measurement

Maximum areal cover observed sampled for that species

Unique code for each plot within each site

Storage Type:

string

float

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Definition

text

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	initial
Definition	Pretreatment year
Source

Code Definition

Code	mean
Definition	3 year mean
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No nitrogen added
Source

Code Definition

Code	1
Definition	Nitrogen added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No phosphorus added
Source

Code Definition

Code	1
Definition	Phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	K
Definition	Potassium added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	NK
Definition	Nitrogen and potassium added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Code Definition

Code	NPK
Definition	All nutrients added
Source

Code Definition

Code	Other
Definition	Lower nutrient concentrations added (specific to cereep.fr)
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	PK
Definition	Phosphorus and potassium added
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Angiosperm
Definition	Angiosperm
Source

Code Definition

Code	Non-Angiosperm
Definition	Not an angiosperm
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual Forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass
Definition	Grass
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial Forb
Source

Code Definition

Code	Woody
Definition	Woody
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass (C3)
Definition	Grass with C3 photosynthetic pathway
Source

Code Definition

Code	Grass (C4)
Definition	Grass with C4 photosynthetic pathway
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial forb
Source

Code Definition

Code	Woody
Definition	Woody species
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	C3
Definition	C3
Source

Code Definition

Code	C4
Definition	C4
Source

Definition

text

Unit	pg/1C
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Database
Definition	From Kew Plant DNA C-values Database
Source

Code Definition

Code	Measured
Definition	Measured from collected sample by flow cytometry
Source

Unit	percent
Type	real

Definition

text

Missing Value Code:

Code	NA
Expl	no DNA measurement

Code	NA
Expl	no DNA measurement

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/3cdd5a5e63a1bb0aacd1464bbb27fe07
Name:	27-site-phylo-data (Raw Data)
Description:	The subset of the cover and genome size data used in the phylogenetic analysis (Analysis of species cover responses to nutrients)
Number of Records:	71553
Number of Columns:	20

Table Structure

Object Name:

27-site-phylo-data.csv

Size:

11997899 byte

Authentication:

543971608675745603c505026cdd066d Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

site_name

site_code

block

plot

year

trt

taxon

Angiosperm

family

lifeform

Photosynthetic_Pathway

species_GS_code

GS_1C

Source

max_cover

plot_code

phylo

Column Name:

site_name

site_code

block

plot

year

trt

taxon

Angiosperm

family

lifeform

Photosynthetic_Pathway

species_GS_code

GS_1C

Source

max_cover

plot_code

phylo

Definition:

Name of the Nutrient Network Site

Name code of the Nutrient Network Site

Block number within site

Plot number within site

Pretreatment or 3 year mean values

Nutrient treatment applied to the plot

Indicates whether nitrogen was added

Indicates whether phosphorus was added

More detailed description of treatment added

Species name

Whether species is an angiosperm or not

Plant Family

Plant Functional Group

Photosynthetic pathway (mostly for grasses)

Unique code for each species on each site

Genome size value expressed as 1C-value

Source for genome size measurement

Maximum areal cover observed sampled for that species

Unique code for each plot within each site

The species name matching that on the phylogeny

Storage Type:

string

float

string

float

string

float

string

Measurement Type:

nominal

ratio

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Definition

text

Definition

text

Unit	number
Type	integer

Unit	number
Type	integer

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	initial
Definition	Pretreatment year
Source

Code Definition

Code	mean
Definition	3 year mean
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No nitrogen added
Source

Code Definition

Code	1
Definition	Nitrogen added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0
Definition	No phosphorus added
Source

Code Definition

Code	1
Definition	Phosphorus added
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Control
Definition	No nutrients added
Source

Code Definition

Code	K
Definition	Potassium added
Source

Code Definition

Code	N
Definition	Nitrogen added
Source

Code Definition

Code	NK
Definition	Nitrogen and potassium added
Source

Code Definition

Code	NP
Definition	Nitrogen and phosphorus added
Source

Code Definition

Code	NPK
Definition	All nutrients added
Source

Code Definition

Code	Other
Definition	Lower nutrient concentrations added (specific to cereep.fr)
Source

Code Definition

Code	P
Definition	Phosphorus added
Source

Code Definition

Code	PK
Definition	Phosphorus and potassium added
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Angiosperm
Definition	Angiosperm
Source

Code Definition

Code	Non-Angiosperm
Definition	Not an angiosperm
Source

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Annual Forb
Definition	Annual Forb
Source

Code Definition

Code	Geophyte
Definition	Geophyte
Source

Code Definition

Code	Grass
Definition	Grass
Source

Code Definition

Code	Legume
Definition	Legume
Source

Code Definition

Code	Perennial Forb
Definition	Perennial Forb
Source

Code Definition

Code	Woody
Definition	Woody
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	C3
Definition	C3
Source

Code Definition

Code	C4
Definition	C4
Source

Definition

text

Unit	pg/1C
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Database
Definition	From Kew Plant DNA C-values Database
Source

Code Definition

Code	Measured
Definition	Measured from collected sample by flow cytometry
Source

Unit	percent
Type	real

Definition

text

Definition

text

Missing Value Code:

Code	NA
Expl	no DNA measurement

Code	NA
Expl	no DNA measurement

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

Key Analyses and Figure Plotting

Entity Type:

Description:

This R script provides the code for the main analyses and plotting of figures, using data from "Genome size data", "Cover proportion data", "Cover-weighted genome size data", "27-site-background-data" and "Supplementary cell density data".

Physical Structure Description:

Object Name:

Key Analyses and Figure Plotting.R

Size:

40271 byte

Authentication:

920e018982f3b3babc9f33bf31cfc3bb Calculated By MD5

Externally Defined Format:

Format Name:

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/1d8cec9fff7dc3eb2a9d76cef7657600

Non-Categorized Data Resource

Name:

Full Data Processing and Analysis Script

Entity Type:

Description:

This is the full code outlining the data processing, compiling and analysis, as well as all figure plotting. This uses the raw data (all beginning with "27-site-")

Physical Structure Description:

Object Name:

Full Data Processing and Analysis Script.R

Size:

56064 byte

Authentication:

411119f7ddb4414ac75d307873d3f0a4 Calculated By MD5

Externally Defined Format:

Format Name:

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/4fbf992b2748b2161933edd63679b31a

Non-Categorized Data Resource

Name:

27_site_phylogeny

Entity Type:

.tre

Description:

Phylogeny of species found on the 27 sites. Used in phylogenetic comparative models.

Physical Structure Description:

Object Name:

27_site_phylogeny.tre

Size:

18871 byte

Authentication:

e1fec3fc58be1f7c162d01238a758b4e Calculated By MD5

Externally Defined Format:

Format Name:

.tre

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/1370/3/ab5b26ed97f5b8f655308d66b70aa4aa

Data Package Usage Rights

This data package is released to the "public domain" under Creative Commons CC0 1.0 "No Rights Reserved" (see: https://creativecommons.org/publicdomain/zero/1.0/). It is considered professional etiquette to provide attribution of the original work if this data package is shared in whole or by individual components. A generic citation is provided for this data package on the website https://portal.edirepository.org (herein "website") in the summary metadata page. Communication (and collaboration) with the creators of this data package is recommended to prevent duplicate research or publication. This data package (and its components) is made available "as is" and with no warranty of accuracy or fitness for use. The creators of this data package and the website shall not be liable for any damages resulting from misinterpretation or misuse of the data package or its components. Periodic updates of this data package may be available from the website. Thank you.

Keywords

By Thesaurus:
(No thesaurus)	Nutrients, Ecological Stoichiometry, Grassland Ecology, Climate, Genome Size

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package

Description:

Selection of climatic variables:

Files Required

"Selection of Climatic Variables" section of Full Data Processing and Analysis Script.R

27-site-background-data.csv

Twenty BioClim variables from WorldClim v.2 were extracted for each site at the 30 arc second scale. Principal component analysis of nine precipitation and eleven temperature variables was fitted across all sites. From contributions of each climatic variable to the principal components and a priori hypotheses, mean annual temperature (MAT; BIO1), mean annual precipitation (MAP; BIO12), the coefficient of variation of precipitation (BIO15) and the variability in temperature (BIO4) were chosen for use in our analysis.

Description:

Quantification of variation in genome size and percent cover between functional groups:

Files required:

GS-by-site.csv

27-site-species-final-data.csv

"Quantifying variation in genome size and percent cover across functional groups" section of Full Data Processing and Analysis Script.R

Genome size data for each species (Genome Size Data.csv) was used to calculate the mean genome size of each functional group (expressed as the log-transformed 1C-value to account for the non-normal distribution of residuals), and significant differences in genome size were tested using ANOVA.

For examining differences in plant cover between functional groups, percent cover data (27-site-species-final-data.csv) was total for each functional group at each site in the pretreatment year and used to calculate proportion of total percent cover taken up by each functional group.

Differences between functional groups were tested using linear mixed-effects ANOVA fitted using the lme4 R-package, with plot nested within site treated as a random effect. When significant differences were observed among functional groups, post-hoc Tukey tests were used to clarify patterns.

Description:

Calculation and analysis of cover-weighted mean genome size:

Files required

27-site-species-final-data.csv

27-site-background-data.csv

"Analysis of cover-weighted genome size" section from Full Data Processing and Analysis Script.R

To estimate average GS of each plot while accounting for differences in dominance of each species, weighted least squares models from the ‘nlme’ R package were used to calculate the cover-weighted genome size (cwGS), with the fraction of total plant cover taken up by a species used to weight its contribution to the “community mean GS value”.

Log response ratios were then used to calculate the change in cwGS value (ΔcwGS) in two ways:

1) Difference in cwGS between control and treated plots:

ΔcwGS(control vs treated )= ln((cwGS of nutrient treated plot)/(average cwGS of control plots))⁡

(2) Change in cwGS of plots from pretreatment cwGS,

ΔcwGS(pretreatment vs treatment). = ln((cwGS of plot)/(cwGS of plot the year before treatment))⁡

Linear mixed-effects ANOVAs were then used to fit ΔcwGS (both control vs treated and pretreatment vs treatment) against nutrient treatment, with site and block nested within site as random effects. ΔcwGS(control vs treated) was fitted against NP treatment and the four selected climate variables, including two-way interactions between NP treatment and each climate variable.

Description:

Analysis of species richness:

Files needed:

27-site-species-final-data.csv

27-site-background-data.csv

"Analysis of species richness" section from Full Data Processing and Analysis Script.R

Species presence absence data was used to tally numbers of species on each plot and, combined with genome size data, to tally numbers of species with genome size values larger and smaller than the average for that site.

Linear mixed-effects ANOVAs (from the lme4 R-package) were used to examine if diversity responses differed between species with larger versus smaller genomes, fitting the richness of species with a higher and lower than mean GS for the site against nutrient treatment, with site and block within site treated as random effects. Species richness of larger and smaller GS species was also fitted against NP treatment and the four selected climatic variables.

Description:

Compiling Phylogeny:

Files Required:

NutNet.tre (at https://github.com/JoeMorton44/Morton-NutNet)

"Compiling Phylogeny" Section of Full Data Processing and Analysis Script.R

To obtain a phylogeny of species at the sites studied, the phytools R package was used to prune an existing phylogeny. The tree was also further pruned to make smaller phylogenies for each plant functional group The phytools phylosig function was also used to measure the phylogenetic signal in GS within our data.

Description:

Phylogenetic analysis of species cover responses to nutrients:

Files required:

27-site-species-final-data.csv

27_site_phylogeny.tre

"Analysis of species cover responses to nutrients" Sections from Full Data Processing and Analysis Script.R

On each plot, the mean percent cover for the most recent 3 years was calculated, and used to calculate change in percent cover for each species (Δcover = mean percent cover of last 3 years – percent cover of pretreatment year).

Change in percent cover (Δcover ) was fitted against genome size (GS, expressed as log-transformed 1C-value) and N and P treatment in a phylogenetic mixed-effects model, using the brms R package and the pruned Nutrient Network phylogeny. This model was then repeated including the interactions between the GS, N, P and plant functional group, to test for differences in response among different functional groups. Lastly, a model was run for grass species only, with photosynthetic pathway included as an additional explanatory variable, allowing separation of responses of C3 and C4 grasses. For all models, weak priors were used where the slope of the regression b = normal (0,1), but models were also run with a wider range of priors, to test if prior choice impacted the convergence and output of the model. Models were run with three chains for 15,000 iterations, with a burn in of 5,000, and the model plots were used to examine posterior distributions and multiple chain convergence.

Description:

Relationship between cell density and genome size

Files required:

Supplementary Cell Density Data.csv - data owned by Erika Hersch-Green

"Cell Density Analysis" section from Full Data Processing and Analysis Script.R

To test correlations between cell density and GS, samples were collected from 63 species across 6 sites (Cedar Creek, Chichaqua Bottoms, Kellogg, Konza, Spindletop and Temple). Cell density per cm2 fresh material was measured by digestion in 100 µL of 10% chromic acid, followed by counting the number of cells in three 10 µL aliquots on a haemocytometer and averaged. The relationship between GS and cell density was tested using linear mixed-effects models as above, with site treated as a random effect.

People and Organizations

Publishers:

Organization:

Environmental Data Initiative

Email Address:

info@edirepository.org

Web Address:

https://edirepository.org

Id:

https://ror.org/0330j0z60

Creators:

Individual:

Joseph A Morton

Organization:

Queen Mary University of London

Position:

PhD Student

Email Address:

joe_amorton@yahoo.co.uk

Id:

https://orcid.org/0000-0003-4400-4575

Individual:

Erika Hersch-Green

Organization:

Michigan Technological University

Position:

Associate Professor (corresponding author)

Email Address:

eherschg@mtu.edu

Id:

https://orcid.org/0000-0003-3887-0768

Individual:

Ilia J Leitch

Organization:

Royal Botanic Gardens Kew

Email Address:

i.leitch@kew.org

Id:

https://orcid.org/0000-0002-3837-8186

Individual:

Andrew R Leitch

Organization:

Queen Mary University of London

Email Address:

a.r.leitch@qmul.ac.uk

Id:

https://orcid.org/0000-0001-8574-302X

Individual:

Carlos A Arnillas

Organization:

University of Toronto Scarborough

Email Address:

carlosalberto.arnillas@gmail.com

Individual:	L Biedermann
Organization:	Iowa State University
Id:	https://orcid.org/0000-0003-2171-7898

Individual:	Elizabeth T Borer
Organization:	University of Minnesota
Id:	https://orcid.org/0000-0003-2259-5853

Individual:	Lars A Brudvig
Organization:	Michigan State University
Id:	https://orcid.org/0000-0002-3857-2165

Individual:	Yvonne M Buckley
Organization:	Trinity College Dublin
Id:	https://orcid.org/0000-0001-7599-3201

Individual:

Marc Cadotte

Organization:

University of Toronto Scarborough

Email Address:

marc.cadotte@utoronto.ca

Individual:	Kendi Davies
Organization:	University of Colorado Boulder
Id:	https://orcid.org/0000-0001-7716-3359

Individual:	Ian Donohue
Organization:	Trinity College Dublin
Id:	https://orcid.org/0000-0002-4698-6448

Individual:	Ebeling Anne
Organization:	Friedrich Schiller University Jena
Id:	https://orcid.org/0000-0002-3221-4017

Individual:	Nico Eisenhauer
Organization:	Universität Leipzig
Id:	https://orcid.org/0000-0002-0371-6720

Individual:	Catalina Estrada
Organization:	Imperial College London
Id:	https://orcid.org/0000-0002-0074-0776

Individual:	Sylvia Haider
Organization:	Leuphana University of Lüneburg
Id:	https://orcid.org/0000-0002-2966-0534

Individual:

Yann Hautier

Organization:

University of Utrecht

Email Address:

y.hautier@uu.nl

Individual:	Anke Jentsch
Organization:	University of Bayreuth
Id:	https://orcid.org/0000-0002-2345-8300

Individual:	Holly Martinson
Organization:	McDaniel College Westminster
Id:	https://orcid.org/0000-0003-1462-0051

Individual:	McCulley Rebecca
Organization:	Universiy of Kentucky
Id:	https://orcid.org/0000-0002-2393-0599

Individual:	Xavier Raynaud
Organization:	Sorbonne Université, Paris
Id:	https://orcid.org/0000-0002-9065-2867

Individual:	Christian Roscher
Organization:	Helmholtz Centre for Environmental Research

Individual:	Eric Seabloom
Organization:	University of Minnesota
Id:	https://orcid.org/0000-0001-6780-9259

Individual:	Carly J Stevens
Organization:	Lancaster University
Id:	https://orcid.org/0000-0002-2390-1763

Individual:	Katerina Vesela
Organization:	Queen Mary University of London

Individual:	Alison Wallace
Organization:	Minnesota State University Moorhead

Contacts:

Individual:

Erika Hersch-Green

Organization:

Michigan Technological University

Position:

Associate Professor

Email Address:

eherschg@mtu.edu

Id:

https://orcid.org/0000-0003-3887-0768

Individual:

Ilia J Leitch

Organization:

Royal Botanic Gardens Kew

Position:

Senior Reseach Leader

Email Address:

i.leitch@kew.org

Id:

https://orcid.org/0000-0002-3837-8186

Individual:

Andrew R Leitch

Organization:

Queen Mary University of London

Position:

Professor of Plant Genetics

Email Address:

a.r.leitch@qmul.ac.uk

Id:

https://orcid.org/0000-0001-8574-302X

Metadata Providers:

Individual:

Joseph A Morton

Organization:

Queen Mary University of London

Position:

PhD Student

Email Address:

j.a.morton@qmul.ac.uk

Id:

https://orcid.org/0000-0003-4400-4575

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period

Begin:

2007

End:

2022

Geographic Region:

Description:

Sites included in this data are from across North America and Western Europe

Bounding Coordinates:

Northern:	53.99	Southern:	31.04
Western:	-123.63	Eastern:	11.88

Project

Parent Project Information:

Title:

Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities

Personnel:

Individual:

Joseph A Morton

Organization:

Queen Mary University of London

Position:

PhD Student

Email Address:

j.a.morton@qmul.ac.uk

Id:

https://orcid.org/0000-0003-4400-4575

Role:

PhD Student

Maintenance

Maintenance:

Description:	Dataset is maintained by JM and EHG as needed.
Frequency:	asNeeded

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'unitList' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unitList')
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'pg/2C'
        |     |     |     |  \___attribute 'name' = 'pg/2C'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'mass in picograms per 2C (DNA amount in a diploid nucleus)'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'pg/1C'
        |     |     |     |  \___attribute 'name' = 'pg/1C'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'm (a.s.l)'
        |     |     |     |  \___attribute 'name' = 'm (a.s.l)'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'Elevation in metres above sea level'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'mm/month'
        |     |     |     |  \___attribute 'name' = 'mm/month'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'mm rain per month'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'none'
        |     |     |     |  \___attribute 'name' = 'none'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'It is a log transformation of picograms, and is thus dimensionless'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'standard deviation x 100'
        |     |     |     |  \___attribute 'name' = 'standard deviation x 100'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'Coefficient of Variation'
        |     |     |     |  \___attribute 'name' = 'Coefficient of Variation'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'ppm'
        |     |     |     |  \___attribute 'name' = 'ppm'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'Parts per million'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'picograms per 2C'
        |     |     |     |  \___attribute 'name' = 'picograms per 2C'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'number per square centimetre'
        |     |     |     |  \___attribute 'name' = 'number per square centimetre'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'ratio (post vs control)'
        |     |     |     |  \___attribute 'name' = 'ratio (post vs control)'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'natural log of the cwGS (post treatment) divided by the cwGS (control)'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'ratio (post vs pre)'
        |     |     |     |  \___attribute 'name' = 'ratio (post vs pre)'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'natural log of the cwGS (post treatment) divided by the cwGS (pretreatment)'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'nominal'
        |     |     |     |  \___attribute 'name' = 'nominal'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:unit')
        |     |     |     |  \___attribute 'id' = 'proportion'
        |     |     |     |  \___attribute 'name' = 'proportion'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description' in ns 'http://www.xml-cml.org/schema/stmml-1.2' ('stmml:description')
        |     |     |     |     |___text 'Ranges 0-1'
        |     |     |     |___text '\n            '
        |     |     |___text '\n         '
        |     |___text '\n      '
        |___text '\n   '

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2024.09.18'
        |     |___text '\n      '
        |___text '\n   '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

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Data Package Metadata View Summary

Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

Data Package Usage Rights

Keywords

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Genome size influences plant growth and biodiversity responses to nutrient fertilization in diverse grassland communities

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Non-Categorized Data Resource

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata

Additional Metadata