CSPs: Tree and shrub species allelic richness in the CSPs 2009-2012

Usage Rights

This data is Free within projects.

Data on Castanopsis eyrei from "Isolation by Elevation: Genetic Structure at Neutral and Putatively Non-Neutral Loci in a Dominant Tree of Subtropical Forests, Castanopsis eyrei By: MiaoMiao SHI; Stefan G. MICHALSKI; Xiao- Yong CHEN, Walter DURKA. Data on Ardisia crenata from " Species diversity and population density affect genetic structure and gene dispersal in a subtropical understory shrub
By:Zeng, XQ (Zeng, Xueqin) ; Michalski, SG (Michalski, Stefan G.); Fischer, M (Fischer, Markus); Durka, W (Durka, Walter)

Dataset Abstract

Genetic diversity parameters have been calculated for several species using molecular markers (Micorsatellites). The aim is to identify patterns of genetic diversity and answer if those are correlated to either species diversity and/or topographic parameters. Data where taken from existing, already published and unpublished studies. Samples where collected from the CSPs in the GNNR from 2008 to 2010. Species include Castanopsis eyrei, Castanopsis fargesii, Cyclobalanopsis glauca, Ardisia crenata, Daphniphyllum oldhamii, Lithocarpus glaber, Quercus serrata, Syzygium buxifolium, Vaccinium carlesii, Schima superba and Rhododendron simsii.

Dataset Design

Castanopsis eyrei, Castanopsis fargesii, Cyclobalanopsis glauca, Ardisia crenata, Daphniphyllum oldhamii,Lithocarpus glaber, Quercus serrata, Syzygium buxifolium, Vaccinium carlesii, Schima superba with at least 3 individuals per sampled CSP.

Spatial Extent

All 27 CSPs have been sampled with varying degrees of sampling density per species. Additionally, for Rhododendron simsii 50 individuals of a non- CSP population are available (not included in this data set)

Temporal Extent

samples have been collected between 2009 and 2012

Taxonomic Extent

individuals of 11 tree and shrub species

Measurement Circumstances

C. eyrei, D. oldhamii, L. glaber, Q. serrata, S. superba include loci potentially under positive selection.

Data Analysis

Leaf samples have been dried for transport and genomic DNA has been extracted using QIAGEN Plant 96 Kits. Specific microsatellite markers have been either developed newly or used from published studies (see publication for details). Multiplex PCR were run on Eppendorf cyclers and PCR fragments have been detected on an ABI 3130 capillary sequencer. Fragments binning and scoring were carried out in the Genemapper Software. Loci have been checked for Nullalleles using the Microchecker software which also provided adjusted genotypes. These adjusted genotypes have been used to check for candidate loci under positive selection (loci not behaving neutrally) with the lositan detection workbench. Loci under positive selection have been removed from further analysis. GenAlEx (Genetic Analysis in Excel) software was used to compute F statistics and PCoA for individuals and CSPs. The Fstat software was finally used to calculate allelic richness for all species.

Data columns available in the raw data part of this dataset

CSP
Number of the CSP
Data group: BEF research plot name
Keywords: plot
Values
CSP04
CSP03
CSP02
CSP05
CSP01
Ar_A.crenata
Mean allelic richness over all loci, Ardisia crenata
Data group: Intraspecific diversity
Keywords: allelic richness
Values
5.353199999999999
5.6
4.973599999999999
5.185999999999999
5.966
Ar_C.eyrei
Mean allelic richness over all loci, Castanopsis eyrei
Data group: Intraspecific diversity
Keywords: allelic richness
Values
5.5512500000000005
6.232
5.625
6.203874999999999
5.642
Ar_C.fargesii
Mean allelic richness over all loci, Castanopsis fargesii
Data group: Intraspecific diversity
Keywords: allelic richness
Values
5
4.99
5.413142857142857
4.714285714285714
5.353142857142856
Ar_C.glauca
Mean allelic richness over all loci, Cyclobalanopsis glauca
Data group: Intraspecific diversity
Keywords: allelic richness
Values
2.4285714285714284
2.184
1.927857142857143
2.3201428571428573
2.294714285714286
Ar_D.oldhamii
Mean, allelic richness over all loci, Daphniphyllum oldhamii
Data group: Intraspecific diversity
Keywords: allelic richness
Values
2.891166666666667
3.14125
2.9166666666666665
3.0353333333333334
3.231583333333333
Ar_L.glaber
Mean allelic richness over all loci, Lithocarpus glaber
Data group: Intraspecific diversity
Keywords: allelic richness
Values
2.80125
2.74125
2.883
2.75
2.47375
Ar_Q.serrata
Mean allelic richness over all loci, Quercus serrata
Data group: Intraspecific diversity
Keywords: allelic richness
Values
3.0515999999999996
3.5886000000000005
3.2
2.8
3.1686000000000005
Ar_R.simsii
Mean allelic richness over all loci, Rhododendron simsii
Data group: Intraspecific diversity
Keywords: allelic richness
Values
2
2.777
2.71875
2.73325
2.53325
Ar_S.superba
Mean allelic richness over all loci, Schima superba
Data group: Intraspecific diversity
Keywords: allelic richness
Values
3.6784545454545454
3.727272727272727
3.9426363636363635
3.539454545454545
4.008272727272728
Ar_S.buxifolium
Mean allelic richness over all loci, Syzygium buxifolium
Data group: Intraspecific diversity
Keywords: allelic richness
Values
5
4.06975
6.422
6.492750000000001
5.8469999999999995
Ar_V.carlesii
Mean allelic richness over all loci, Vaccinium carlesii
Data group: Intraspecific diversity
Keywords: allelic richness
Values
5.4104
4.827
5.5848
5
4.9138