CSPs: Diversity measures based on tree and shrub species of the CSPs

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BEF-China intern

Dataset Abstract

Updated 2011-11-14: Different diversity measures, including richness, Shannon, Simpson, Eveness, rarefaction and phylogenetic diversity based on the tree and shrub species in the CSPs. Comparative Study Plots (CSP) of the Biodiversity - Ecosystem Functioning Experiment (BEF-China) were selected according to gradients in successive age and woody species diversity. Diversity indices are based on the dataset "Abundance of Tree and Shrub species in the Comparative Study Plots (CSP)" from Z1, SP3

Spatial Extent

The Gutianshan National Nature Reserve (NNR) is located in the western part of Zhejiang Province (29º8'18" – 29º17'29" N, 118º2'14" – 118º11'12" E, Fig. 1). The Gutianshan NNR has an area of approximately 81 km2 and was initially established as a National Forest Reserve in 1975 and became a National Nature Reserve in 2001. The NNR comprises a large portion of broad-leaved forests of advanced successional stages (Hu & Yu 2008), which have not been managed since the beginning of the 1990ies, as well as young successional stages and conifer plantations, mainly of Cunninghamia lanceolata and Pinus massoniana. --- The vegetation is composed of different types of subtropical evergreen and mixed broad-leaved forests (Yu et al. 2001). Most of the stands are secondary forests, evidenced by maximum tree ages of 180 years, by agricultural terraces in almost all plots and by the presence of charcoal in almost all soil profiles. Around the Gutianshan NRR extensive deforestation has occurred during the Great Leap Forward in the 1950s, as in most parts of Southeast China. However, due to prevailing steep slopes, the Gutianshan area was only marginally usable for agricultural activities, and thus an exceptionally intact forest cover has been preserved. --- The climate at Gutianshan NNR is warm and temperate with a short dry season in November and December and with warm summers (Fig. 2). The climatic conditions are characteristic for the subtropics with an annual average temperature of 15.1°C, January minimum temperatures of -6.8°C, July maximum temperatures of 38.1°C and an accumulated temperature sum (≥ 5°C) of 5221.5 degree days.

Temporal Extent

2007-2009

Data columns available in the raw data part of this dataset

CSP
name of the CSP in the Nature ReserveBEF research plot nameReasearch plots of the Biodiversity - Ecosystem functioning experiment (BEF-China). There are three main sites for research plots in the BEF Experiment: Comparative Study Plots (CSP) in the Gutianshan Nature Reserve, having a size of 30x30m^2, measured on the ground.
Unit: id
Data group: BEF research plot name
Keywords: CSP
Values
CSP02
CSP05
CSP04
CSP03
CSP01
rarefy_100
estimate of species number by randomly drawing 100 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.
Unit: count
Data group: Taxonomic biodiversity
Keywords: biodiversity, rarefied diversity
Values
18.11426524
16.77861972
15.25412562
16.70766334
14.1498851
* Bruelheide, H. also contributed to this column.
rarefy_150
estimate of species number by randomly drawing 150 individuals (rarefaction) Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. To compare different plots, the number of individuals should be smaller than the minimum number of individuals.
Unit: count
Data group: Taxonomic biodiversity
Keywords: biodiversity, rarefied diversity
Values
19.9003489513211
21.4050395995021
17.9835641625816
18.9879178142534
16.3495699866678
rar_se_150
standard error of the rarefaction estimate of species number given 150 , individuals, Rarefaction curves show the increase in species number with an increase of sampled individuals. R uses rarefy() from the package vegan to estimated species number for a given number of individuals. This is done by randomly drawing individuals from the specified set of individuals. Since this is done several times, a standard error of the estimate can be given.
Unit: count
Data group: Taxonomic biodiversity
Values
1.76623888700344
1.74980648752147
1.85777405018676
1.57248411592856
1.288955006708
shannon
Shannon diversity, The Shannon diversity is given by H = -sum (p_i log(p_i)), p_i is the relative abundance of the ith species. R provides this through the vegan package: diversity(x).
Data group: Taxonomic biodiversity
Keywords: biodiversity, shannon diversity
Values
1.80135260900934
2.20757996553768
2.15652761556872
2.00100657919975
2.33790930497816
simpson
Simpson diversity, The Simpson diversity is given by D = sum p_i^2, with p_i representing the relative abundance of the ith species. R provides this through the vegan package: diversity(x, index="simpson")
Data group: Taxonomic biodiversity
Keywords: simpson diversity
Values
0.771700211449605
0.716691365917927
0.855971684531093
0.820868211625887
0.776980957748114
rich
Species richness of trees and shrubs, Trees were counted when they exceeded 1m height. This data is aggregated from the raw data provided by Martin Böhnke and Martin Baruffol; in R with vegan: specnumber()
Unit: count
Data group: Taxonomic biodiversity
Keywords: species richness
Values
27
32
30
25
29
even_shan
Evenness based on Shannon diversity and species richness, Eveness as defined by Ricotta, C. A semantic taxonomy for diversity measures Acta Biotheoretica, 2007, 55, 23-33: shannon/log(rich)
Data group: Taxonomic biodiversity
Keywords: eveness
Values
0.687756486697894
0.606558789258259
0.606880460998821
0.529623072957036
0.572287216321793
gen_fam_div
Phylogenetic diversity based on genus and familiy, Phylogenetic diversity is calculated using Rao's Q. This is basically the mean distance of all pairswise distances between individuals in phylogenetic space. I used genus and family name to calculate phylogenetic distances between species. R provides Rao's Q and tools for calculating phylogenetic distances in the package ade4. Commands: as.taxo(), divc()
Data group: Taxonomic biodiversity
Keywords: phylogenetic diversity
Values
2.27015665777399
2.43757701491914
2.08312498478908
2.41848821766954
2.23792309499569