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Good place

1.Stanford Medical School:斯坦福医学院

（http://med.stanford.edu/: logo encrypted）

2.harvard medical school: 哈佛医学院

Purcell lab: in Department of Psychiatry at Brigham & Women’s Hospital, an affiliate of Harvard Medical School.(plink)

3.Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh: 匹兹堡大学，人类遗传学院，统计遗传所

4.ecole polytechnique federale de lausanne: 洛桑联邦理工学院

5.Stowers Institute for Medical Research: 斯托瓦斯医学研究所

 

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eigensoft 7.2.1

1.vcf样例

2.genotype

3.smartpca 结果

PC1 PC2
eigenvector1 eigenvector2
eigenvalue 9 0
YC1.YC_snp -0.3162 -0.3162
YC2.YC_snp -0.3162 -0.3162
YC3.YC_snp -0.3162 -0.3162
YC4.YC_snp -0.3162 -0.3162
YC5.YC_snp -0.3162 -0.3162
ZC1.ZC_snp 0.3162 0.3162
ZC2.ZC_snp 0.3162 0.3162
ZC3.ZC_snp 0.3162 0.3162
ZC4.ZC_snp 0.3162 0.3162
ZC5.ZC_snp 0.3162 0.3162

4.PCA图

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PCA summary

方法：

1. 使用的population scale SNPs

2. EIGENSOFT 4.2

结果解读：

亚洲的野猪和家猪聚类在一起；欧洲的野猪和家猪以及巴克夏猪聚类在一起；非洲的疣猪和四种野生猪聚在一起（另外这四种野生猪是否也是非洲的？）；

引文：

2014 – Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

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BMC genomics – 2017 – Oreochromis niloticus (Nile Tilapia) – sex determination regions

Sex determination regions

The new O_niloticus_UMD1 assembly was used to study sequence differentiation across two sex-determining regions in tilapias. The first region is an XX/XY sex-determination region on LG1 found in many strains of til-apia [9, 34, 44–47]. We previously characterized this region by whole genome Illumina re-sequencing of pooled DNA from males and females [48]. We realigned these sequences to the new O_niloticus_UMD1 assembly and searched for variants that were fixed in the XX female pool and poly-morphic in the XY male pool. Figure 4 shows the FST and the sex-patterned variant alle le frequencies for the XX/XY O. niloticus comparison across the complete Orenil1.1 and O_niloticus_UMD1 assemblies, while Fig. 5 focuses on the highly differentiated ~9Mbp region on LG1 with a substantial number of sex-patterned variants, indicative of a reduction in recombination in a sex determination region that hasexistedforsometime[48].

The second sex comparison is for an ZZ/WZ sex-determination region on LG3 in a strain of O. aureus [11,49]. This region has not previously been characterized using whole genome sequencing. For this comparison we identified variant alleles fixed in the ZZ male pool and polymorphic in the WZ female pool. Figure 6 shows the FST and the sex-patterned variant allele frequencies for this comparison across the whole O_niloticus_UMD1 assembly, while Fig. 7 focuses on the differentiated region on LG3. O. aureus LG3 contains a large ~50Mbp region of differentiated sex-patterned variants, also indicative of a reduction in recombination in the sex determination region. Figure 6 also shows this differentiation pattern on several other LGs (LG7, LG9, LG14, LG16, LG18, LG22 and LG23). It is possible that these smaller regions of sex-patterned differentiation are actually translocations in O.aureus relative to the O. niloticus genome assembly.

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summary of phylogenetic tree

Tools:

2014-RAxML version 8  ->  2006-RAxML-VI-HPC  ->  2005-RAxML-III

Methods:

=>  1981-Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach

Theories:

=>  Maximum Likelihood Approach ->  statistics

一种概率论在统计学的应用，它是参数估计的方法之一。

 

进化模型=替换矩阵

concatenation: 将关心的基因连在一起做

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Beavis effect

In a simulation study, William D. Beavis showed that the average estimates of phenotypic variances associated with correctly identified QTL were greatly overestimated if only 100 progeny were evaluated, slightly overestimated if 500 progeny were evaluated, and fairly close to the actual magnitude when 1000 progeny were evaluated.

(http://www.genetics.org/content/165/4/2259)