Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia

Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution.  A recent molecular systematics study has revealed there might be some geographic structuring among the N. lloydii populations. Therefore, we undertook a genome wide Single Nucleotide Polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south-eastern Queensland (SE-QLD). Furthermore, as the reproductive phase of a plant’s life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two con..., Genomic DNA of 123 individuals were sent to DArT analysis facility (DArT Pty Ltd., Canberra, Australia) for DArTseq high-density genotyping and the results of the SNP calling were obtained as a matrix., Data set can be opened and analysed using the DArTR package in the R platform., # SNP Data: N-lloydii Manawaduge et. al.

This is the SNP data set that was used in the manuscript \"Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia \"

## Description of the data and file structure

File Format: SNP 1 Row Mapping Format: \"0\" = Reference allele homozygote, \"1\" = SNP allele homozygote, \"2\"= heterozygote and \"-\" = double null/null allele homozygote (absence of fragment with SNP in genomic representation)

Metadata columns:
AlleleID:Unique identifier for the sequence in which the SNP marker occurs
SNP:In 1 row format: contains the base position and base variant details
SnpPosition:The position (zero indexed) in the sequence tag at which the defined SNP variant base occurs
CallRate:The proportion of samples for which the genotype call is either \"1\" or \"0\", rather than \"-\"
AvgPIC:The average of the polymorphism information content (PIC) of the Reference and SNP allele rows
RepAvg:The proportion of technical replicate assay pairs for ...

生境破碎化会提升种群瓶颈与近交发生的概率，并最终可能导致适合度下降及局地灭绝。劳氏李榄（Notelaea lloydii）是澳大利亚特有本土橄榄树种，因分布范围狭窄而被列为易危物种。近期一项分子系统学研究显示，该物种种群间可能存在一定的地理遗传结构。为此，我们开展了全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分析，以探明澳大利亚昆士兰州东南部（SE-QLD）劳氏李榄种群内部及种群间的遗传多样性水平、遗传模式、近交程度与基因流情况。此外，由于植物生活史中的生殖阶段对遗传多样性具有深远影响，本研究同时对其生活史生殖性状展开了调查。本研究的SNP分析结果显示，即使是邻近种群间，劳氏李榄也存在较低的遗传多样性、近交现象以及显著的遗传结构。两项花与果实套袋实验的结果[原文未完整表述]。我们将123个个体的基因组DNA送至澳大利亚堪培拉的DArT分析机构（DArT Pty Ltd.）进行DArTseq高密度基因分型，最终获得了SNP基因型矩阵格式的结果。本数据集可通过R语言平台的DArTR包进行读取与分析。# SNP数据集：N-lloydii Manawaduge等人
本数据集为论文《澳大利亚昆士兰州东南部劳氏李榄（木犀科）的保护遗传学研究》中所使用的SNP数据集。

## 数据与文件结构说明
文件格式：SNP单行映射格式："0" = 参考等位基因纯合子，"1" = SNP等位基因纯合子，"2" = 杂合子，"-" = 双无效/无效等位基因纯合子（即基因组表征中无含SNP的片段）
元数据列：
AlleleID：SNP标记所在序列的唯一标识符
SNP：采用单行格式，包含碱基位点与碱基变异详情
SnpPosition：序列标签上指定SNP变异碱基所在的位置（以0为起始索引）
CallRate：基因型结果为"1"或"0"而非"-"的样本占总样本的比例
AvgPIC：参考等位基因行与SNP等位基因行的多态性信息含量（Polymorphism Information Content, PIC）平均值
RepAvg：技术重复实验配对的比例……