Data Package Metadata View Summary

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

General Information

Data Package:

Local Identifier:

edi.1370.2

Title:

Genome size influences plant growth and biodiversity responses to nutrient fertilisations 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:

2024-09-03

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 (and corresponding author))
Creator:	Arnillas, Carlos A (University of Toronto Scarborough)
Creator:	Cadotte, Marc (University of Toronto Scarborough)
Creator:	Hautier, Yann (University of Utrecht)
Creator:	Leitch, Ilia J (Royal Botanic Gardens Kew)
Creator:	Leitch, Andrew R (Queen Mary University of London)

Data Entities
Data Table Name:	27-site-cover-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:	GS-by-site
Description:	Raw GS data for analysis for incorporation into data ("Loading in and formatting initial data" in R script) and variation in GS between functional groups ("Quantifying variation in genome size and percent cover across functional groups" in R script)
Data Table Name:	27-site-background-data
Description:	Site specific data including climate, soil N, P and acidity, and the age of the plot. Used in "Selection of climate variables" of R script and the plot level analysis ("Analysis of cover-weighted genome size"; "Analysis of species richness" in R script)
Data Table Name:	27-site-species-final-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-plot-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:	Supplementary Cell Density Data
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. E. Hersch Green is the author of this dataset.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/1370/2/8a791d7c241346f22c971f90b9f31d48
Name:	27-site-cover-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/1370/2/6d582e6563e5ddcac975e729bcd62bb4
Name:	GS-by-site
Description:	Raw GS data for analysis for incorporation into data ("Loading in and formatting initial data" in R script) and variation in GS between functional groups ("Quantifying variation in genome size and percent cover across functional groups" in R script)
Number of Records:	1507
Number of Columns:	9

Table Structure

Object Name:

GS-by-site.csv

Size:

133153 byte

Authentication:

05b048230b447d3b63fd599afeaceddb 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

Column Name:

site_code

taxon

family

lifeform

Photosynthetic_Pathway

species_GS_code

GS_2C

GS_1C

Source

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

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

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/1370/2/0cc2932fda98bf68062c2cf4097975e9
Name:	27-site-background-data
Description:	Site specific data including climate, soil N, P and acidity, and the age of the plot. Used in "Selection of climate variables" of R script and the plot level analysis ("Analysis of cover-weighted genome size"; "Analysis of species richness" in R script)
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/1370/2/387607c26cde925480d79d5e64fd75d6
Name:	27-site-species-final-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:	71553
Number of Columns:	19

Table Structure

Object Name:

27-site-species-final-data.csv

Size:

10710381 byte

Authentication:

c6747c0ebfdf9b3ce693223b0ab97ce5 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

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

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

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 species
Source

Code Definition

Code	Non-Angiosperm
Definition	Not an angiosperm species
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

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/1370/2/4bb365e8ad324a8d6ea5bbf6df884ae5
Name:	27-site-plot-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:

02160e14a3faea7df8dfb07f54e14c37 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

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/1370/2/97cfd8e9afbb5ae3351154437f812189
Name:	Supplementary Cell Density Data
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. E. Hersch Green is the author 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 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 Data Processing R Script at https://github.com/JoeMorton44/Morton-NutNet

ggbiplot2 function.R https://github.com/JoeMorton44/Morton-NutNet

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 Data Processing R Script at https://github.com/JoeMorton44/Morton-NutNet

Genome size data for each species (GS-by-site.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 Data Processing R script at https://github.com/JoeMorton44/Morton-NutNet

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) Change 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

"Analysis of species richness" section from Data Processing R Script at https://github.com/JoeMorton44/Morton-NutNet

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 Data Processing R Script (https://github.com/JoeMorton44/Morton-NutNet)

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

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

"Compiling phylogeny" and "Analysis of species cover responses to nutrients" Sections from Data Processing R-script at https://github.com/JoeMorton44/Morton-NutNet

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"

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 (and corresponding author)

Email Address:

eherschg@mtu.edu

Id:

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

Individual:

Carlos A Arnillas

Organization:

University of Toronto Scarborough

Email Address:

carlosalberto.arnillas@gmail.com

Individual:

Marc Cadotte

Organization:

University of Toronto Scarborough

Email Address:

marc.cadotte@utoronto.ca

Individual:

Yann Hautier

Organization:

University of Utrecht

Email Address:

y.hautier@uu.nl

Individual:

Ilia J Leitch

Organization:

Royal Botanic Gardens Kew

Email Address:

i.leitch@kew.org

Individual:

Andrew R Leitch

Organization:

Queen Mary University of London

Email Address:

a.r.leitch@qmul.ac.uk

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

Individual:

Andrew R Leitch

Organization:

Queen Mary University of London

Position:

Professor of Plant Genetics

Email Address:

a.r.leitch@qmul.ac.uk

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 grassland plant community responses to nutrients across diverse climate and species assemblages of the Northern hemisphere.

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            '
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        |     |     |___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 'picograms per 1C (DNA amount in an unreplicated monoploid nucleus)'
        |     |     |     |___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            '
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        |     |     |___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               '
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        |     |     |___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         '
        |     |___text '\n      '
        |___text '\n   '

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2024.08.06'
        |     |___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.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

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

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

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 fertilisations in diverse grassland communities

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

+/- 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