1、生命起源
Surface Origin Hypothesis和Subsurface Origin Hypothesis
2、An RNA world &Protein synthesis
LUCA (last universal common ancestor)
3、生命起源的过程
Organic matters有机物质—first macromolecules大分子 –proteins蛋白--lipid membranes脂膜--metabolism (autotrophic)新陈代谢
4、Stromatolite层叠石: fossilized microbial mat微生物菌席形成的化石
5、Phototrophic bacteria光合细菌 (cyanobacteria and the green nonsulfur bacterium) play a central role in the formation of modern stromatolites层叠石
经历从不产氧光合细菌到产氧光合细菌的进化
6、内共生假说Endosymbiosis: Mitochondria and chloroplasts arose from the stable incorporation of a chemoorganotrophic bacterium and a cyanobacterium
两个假说：serial endosymbiosis hypothesis系列内共生假说、symbiogenesis hypothesis共生假说。
区别就是共生是发生在Eukarya分化前还是分化后
7、
8、进化的因素
Mutations：replication error，UV radiation，other factors，etc
Gene duplication
Horizontal Gene Transfer水平基因转移
Gene loss
Recombination of homologous DNA同源DNA重组
Genetic Drift遗传漂变：a random process 随机过程that can cause gene frequencies基因频率 in a population to change over time, causing evolution without natural selection.导致没有自然选择的进化
9、Molecular clocks (chronometers)分子钟理论
– Certain genes and proteins that are measures of evolutionary change
- 某些基因和蛋白质是进化变化的衡量标准。
– Major assumptions of this approach are that nucleotide changes occur at a constant rate, are generally neutral, and are random
- 这种方法的主要假设是核苷酸变化以恒定的速度发生，通常是中性的，并且是随机的
- Microbial genomes are highly dynamic. 微生物基因组是高度动态的
- Prokaryotic cells regularly sample genes from other microbes in their environment through HGTs. 原核细胞通过HGT定期从其环境中的其他微生物中提取基因。
- Variations between genomes then arise through the forces of mutation and recombination, with the evolutionary dynamics of genomes being governed by selection and genetic drift. 基因组之间的变异随后通过突变和重组的力量产生，基因组的进化动态受选择和遗传漂移的支配。
Pan Genome泛基因组不断增加，Core Genome核心基因稳定不变甚至稳定下降
10、黑皇后假说：不同物种争相“堕落”，尽可能多地摆脱那些代价高昂的生理功能
11、分子系统学Molecular Phylogeny: Making Sense of Molecular sequences
用于系统发育分析的基因，需要有以下几个特点：
·普遍分布Universally distributed
·功能稳定Functionally constant
·足够保守Sufficiently conserved
·足够长度Adequate length
- Small subunit ribosomal RNA (SSU rRNA)
16SrRNA九个可变区Variable regions，十个保守区Conserved regions
设计引物是在保守区域，比对是用可变区
除了小亚基核糖体RNA，还有：
- Large subunit rRNA (LSU rRNA)
Salmonella typhimurium 2994-3094 bp
- Protein synthesis elongation factor Tu 蛋白质合成的延伸因子
- Heat-shock protein Hsp60
- Several tRNA synthetases
- Recombinase enzyme (recA), only for Bacteria重组酶RecA
12、分子系统发育分析过程
双峰：污染、16srRNA可能不只有一个拷贝
13、系统发育树的限制因素
·频发突变recurrent mutation回复表型
·水平基因转移违反了基因垂直遗传的假设The horizontal exchange of genes between unrelated organisms violates the assumption that the gene is inherited in a vertical fashion
14、系统发育分析Phylogenetic Analyses
– Should be monophyletic (sharing a recent common ancestor excluding other species)
应该是单系进化的(共享最近的共同祖先，不包括其他物种)
– Phylogenetic relationships determined by analyzing SSU rRNA gene sequences
通过分析SSU rRNA基因序列确定的系统发育关系
- SSU rRNA genes from other strains of the same species have >98.6% sequence similarity
来自同一物种其他菌株的SSU rRNA基因的序列相似性>98.6%
- From different species have <97% similarity
来自不同物种的相似性<97%
– SSU rRNA can also help classify higher ranks
SSU rRNA还可以帮助对更高的级别进行分类
与标准菌株进行比对
疑似新种如何判断？小于97% 16srRNA相似性以及小于93%ANI
15、比较相近的亲缘关系鉴别，用多基因分析或全系列分析Multilocus sequence analysis (MLSA)
- Highly conserved genes (e.g., recA and gyrB candistinguish bacteria at species level)
高度保守的基因(例如，recA和gyrB可以在物种一级区分细菌)。
- DNA sequences of protein-encoding genes accumulate mutations faster than rRNA genes, thus distinguishing species that cannot be resolved by rRNA sequences
蛋白质编码基因的DNA序列积累突变的速度比rRNA基因快，从而区分不能由rRNA序列解析的物种。
- Usually use at least 4, up to 1000+ genes
16、其他分类技术
Ribotyping核糖分型
rep-PCR (repetitive extragenic palindromic)重复性基因外回文
AFLP (amplified fragment length polymorphism)扩增片段长度多态性
Phenotypic Analysis表型分析：FAME (Fatty Acid Methyl Ester) analysis脂肪酸甲酯分析
鉴定：Biolog、VITEK Test Card