CSPs: Genetic diversity of Castanopsis eyrei in CSPs

Usage Rights

This data is Free for public.

Permission is granted to anybody to access, use and publish all open for public data freely. The commercial use of any data is prohibited. The quality and completeness of data cannot be guaranteed. Users employ these data at their own risk. In order to make attribution of use for owners of the data possible, the identifier of ownership of data must be retained with every data record. Users must publicly acknowledge, in conjunction with the use of the data, the data owners. Cite the data as follows: Shi, M. and Durka, W. (2013): Genetic diversity of Castanopsis eyrei. BEF-China data portal (Accessed through URL http://china.befdata.biow.uni-leipzig.de/datasets/166)

Dataset Abstract

Plant populations growing along elevational gradients have been found to show inconsistent patterns in the distribution of genetic variation. Molecular markers used to study these patterns are usually targeting neutral processes, but may also be affected by selection. In this study, the effects of elevation and successional stage on genetic diversity of a dominant tree species were investigated controlling for neutrality of the microsatellite loci used. Diversity and differentiation among 24 populations of Castanopsis eyrei from different elevations (251-920m) and successional stages were analysed by eight microsatellite loci. One of the loci (Ccu97H18) deviated from a neutral model of differentiation among populations probably due to hitchhiking with an unknown locus under divergent selection. The analysis showed that C. eyrei populations had a high level of genetic diversity within populations (AR = 7.6, HE = 0.82). Genetic variation increased with elevation for both the putatively selected locus Ccu97H18 and the neutral loci. At locus Ccu97H18 one allele was dominant at low elevations, which was replaced at higher elevations by an increasing number of other alleles. The level of genetic differentiation at neutral loci was similar to that of other Fagaceae species (FST = 0.032, F'ST
= 0.15). Population differentiation followed a model of isolation by distance ,however, strongly significant isolation by elevation was found, both for all and the neutral loci and he putatively selected locus Ccu97H18..These patterns indicate higher gene flow among similar altitudinal levels than across different altitudinal levels. The study underlines the importance to check the selective neutrality of marker loci in analyses of population structure.

Dataset Design

we sampled 24 sites, including 20 CSP sites and additional 4 sites. 12 to 49 individuals (mean = 24) per sites were collected. Genomic DNA was extracted from leaf samples using the DNeasy Plant minikit (QIAGEN). Eight highly polymorphic microsatellite loci were used for genotyping (Ueno et al., 2000, 2003). Fragment analysis was performed on an ABI PRISM 3130 with GS600-LIZ (Applied Biosystems) as internal size standard and using GeneMapper v.3.7 software for genotyping.We used Micro-Checker 2.2.3 (Van Oosterhout et al. 2004), FDIST (Beaumont and Nichols, 1996), Fstat v. 2.9.3.2 (Goudet 2001) to analyse the data.

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.

Published

Shi, M. et al. ( 2010) Isolation by elevation in a subtropical dominant tree. 10.1371/journal.pone.0021302, PLoS ONE

Temporal Extent

Most of the data were collected in 2008, while some additional data were also collected in 2009.

Taxonomic Extent

Castanopsis eyrei

Data Analysis

This data can be used to assess the within species diversity of Castanopsis eyrei.

Data columns available in the raw data part of this dataset

date
year of sampling
Unit: year
Data group: Date time information
Keywords: date
Values
2008
2009
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. To increase the genetic diversity captured by BEF-China, addidtional individuals of the respective species were sampled. The "new" CSPs described in this dataset are labelled different from the general CSP nomenclature. The locations of these "new" CSPs is indicated in detail within the dataset.
Unit: id
Data group: BEF research plot name
Keywords: CSP
Values
CSP02
C
B
CSP03
A
N
number of leaf samples, all diversity statistics are based on these leaves genotyped
Data group: Sample size
Keywords: leaf
Values
12
19
17
15
18
A-neutral
number of alleles at neuteal loci; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Keywords: allelic richness
Values
10.6
10
10.7
11
10.1
Ar-neutral
allelic richness at neutral loci; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Values
5.4
6.3
6.2
6.1
5.7
He-neutral
expected heterozygosity at neutral loci; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Keywords: biodiversity, intraspecific diversity, genetic diversity
Values
0.69
0.76
0.74
0.77
0.68
A-selected
number of alleles at putatively selected locus; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Keywords: allelic richness
Values
11
1
12
15
10
Ar-selected
allelic richness at putatively selected locus; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Values
13.1
10.7
10.9
1
13.2
He-selected
expected heterozygosity at putatively selected locus; FDIST, Fstat v. 2.9.3.2
Data group: Intraspecific diversity
Keywords: biodiversity, intraspecific diversity, genetic diversity
Values
0.06
0.1
0.08
0
0.09