Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus

As the only remainder type of phycobiliproteins in Prochlorococcus, the actual role of phycoerythrin still remains unknown. Previous studies revealed that two different forms of phycoerythrin gene were found in two ecotypes of Prochlorococcus that are specifically adapted to either high light (HL) or low light (LL) conditions. Here we analyze patterns of phycoerythrin nucleotide variation in the HL- and LL-Prochlorococcus populations. Our analyses reveal a significantly greater number of non-synonymous fixed substitutions in peB and peA than expected based on interspecific comparisons. This pattern of excess non-synonymous fixed substitutions is not seen in other five phycoerythrin-related genes (peZ/V/Y/T/S). Several neutrality statistical tests indicate an excess of rare frequency polymorphisms in the LL-Prochlorococcus data, but an excess of intermediate frequency polymorphisms in the HL-Prochlorococcus data. Distributions of the positively selected sites identified using the likelihood ratio test, when mapped onto the phycoerythrin tertiary structure, reveal that HL- and LL-phycoerythrin should be under different selective patterns. These findings may provide insights into the likely role of selection at the phycoerythrin locus and motivate further research to unveil the function of phycoerythrin in Prochlorococcus.

Population genetics of Crassostrea ariakensis in Asia inferred from microsatellite markers

Crassostrea ariakensis is an important aquacultured oyster species in Asia, its native region. During the past decade, consideration was given to introducing C. ariakensis into Chesapeake Bay, in the United States, to help revive the declining native oyster industry and bolster the local ecosystem. Little is known about the ecology and biology of this species in Asia due to confusion with nomenclature and difficulty in accurately identifying the species of wild populations in their natural environment. Even less research has been done on the population genetics of native populations of C. ariakensis in Asia. We examined the magnitude and pattern of genetic differentiation among 10 wild populations of C. ariakensis from its confirmed distribution range using eight polymorphic microsatellite markers. Results showed a small but significant global theta (ST) (0.018), indicating genetic heterogeneity among populations. Eight genetically distinct populations were further distinguished based on population pairwise theta (ST) comparisons, including one in Japan, four in China, and three populations along the coast of South Korea. A significant positive association was detected between genetic and geographic distances among populations, suggesting a genetic pattern of isolation by distance. This research represents a novel observation on wild genetic population structuring in a coastal bivalve species along the coast of the northwest Pacific.

盐渍条件下野大豆群体的DNA变异

当前分子生物学的方法以惊人的速度渗透到生命科学研究的各个领域。植物对不断变化的环境逐步适应的过程中，积累了丰富的遗传多样性。与此同时，人类活动空间的不断扩大已经严重威胁到其他生命的生存和繁衍，越来越多的物种以越来越快的速度在我们还没有来得及认识它们时就已经永远地消失了。加快物种鉴定和保护的步伐就必须发展更多能充分揭示物种遗传多样性的实验技术，从具有丰富遗传多样性的野生资源中寻找到更多能够服务于人类可持续发展的基因资源。本文以杨树杂交后代过氧化物同工酶和RAPD分析为基础，论证了我们改进的RAPD方法用于遗传分析的可行性。在前期工作的基础上，进一步测定了野大豆自然群体的耐盐性变异，并且用微卫星和RAPD分析的方法研究分子标记与DXA变异、植株耐盐性之间的关系。对四个可能与抗盐性有关的RAPD片段进行克隆、测序，并进行序列比较。由此得出以下结论： 1、在本文的实验条件下，杨树同工酶和RAPD分析均表明，RAPD标记在亲本及其杂交后代中性状比例符合孟德尔遗传规律，尽管有时也会出现遗传负载等机制引起的基因分布扭曲现象。 2、初步研究了个体发育阶段和环境条件对植株耐盐性的影响。结果表明，植物耐盐性不仅仅与外界的盐度有关，而且受发育阶段和其它环境条件（如，温度）的影响。但也发现了某些个体在各种条件下都具有较高的耐盐性，而且，不易受到其它环境条件的影响。 3、微卫星标记的结果表明，10对引物中的8对引物共检测到时17个等位基因，平均每对引物2.125个等位基因。本文的实验条件下，双核苷酸和三核苷酸的引物对扩增产物都没有出现“ghosts"条带或“打滑”现象。 4、有4个RAPD标记可能与野大豆群体的耐盐性有关，分别是OPCO8460bp、OPCO8213bp、OPCO2690bp、以及OPCO5270bp。测序结果与GenBank中的序列作同源性比较，结果显示，OPCO2_(690bp)与小麦、松树等植物的吉普赛性的逆转录转座子的部分区域（24－－53）有很高的同源性（86－89％）。此外，OPCO2690bp与栽培大豆胞质谷氨酰胺合成酶（gs15）基因的启动子有高达95％的同源性。 5、本文实验条件下，RAPD扩增产物在限制性内切酶消化后，消化产物的多态性未见增大，也没有发现与耐盐性相关的多态位点。 6、野大豆自然群体DNA变异的研究中也可以应用SWAPP方法。

MULTIPLE GENOTYPES OF MITOCHONDRIAL-DNA WITHIN A HORSE POPULATION FROM A SMALL REGION IN YUNNAN PROVINCE OF CHINA

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km(2) in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with restriction endonucleases which recognize 6-bp sequences. An average of fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.

A common SNP of MCPH1 is associated with cranial volume variation in Chinese population

Microcephaly (MCPH) genes are informative in understanding the genetics and evolution of human brain volume. MCPH1 and abnormal spindle-like MCPH associated (ASPM) are the two known MCPH causing genes that were suggested undergone recent positive selectio

Positive selection drives population differentiation in the skeletal genes in modern humans

During the course of evolution, the human skeletal system has evolved rapidly leading to an incredible array of phenotypic diversity, including variations in height and bone mineral density. However, the genetic basis of this phenotypic diversity and the relatively rapid tempo of evolution have remained largely undocumented. Here, we discover that skeletal genes exhibit a significantly greater level of population differentiation among humans compared with other genes in the genome. The pattern is exceptionally evident at amino acid-altering sites within these genes. Divergence is greater between Africans and both Europeans and East Asians. In contrast, relatively weak differentiation is observed between Europeans and East Asians. SNPs with higher levels of differentiation have correspondingly higher derived allele frequencies in Europeans and East Asians. Thus, it appears that positive selection has operated on skeletal genes in the non-African populations and this may have been initiated with the human colonization of Eurasia. In conclusion, we provide genetic evidence supporting the rapid evolution of the human skeletal system and the associated diversity of phenotypes.

Population genetic structure of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis): Implications for management and conservation

Understanding the population genetic structure is a prerequisite for conservation of a species. The degree of genetic variability characteristic of the mitochondrial DNA control region has been widely exploited in studies of population genetic structure and can be useful in identifying meaningful population subdivisions. To estimate the genetic profile of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), an endangered freshwater population endemic to China, the complete mtDNA control region was examined in 39 individuals belonging to seven different stocks inhabiting the middle and lower reaches of the Yangtze River. Very low genetic diversity was found (nucleotide diversity 0.0011 +/- 0.0002 and haplotypic diversity 0.65 +/- 0.05). The mtDNA genetic pattern of the Yangtze population appears to indicate a founder event in its evolutionary history and to support the marine origin for this population. Analyses by F-st and Phi(st) yielded statistically significant population genetic structure (F-st = 0.44, P < 0.05; phi(st) = 0.36, P < 0.05). These results may have significant implications for the management and conservation of the Yangtze finless porpoise in the future.

稻属A基因组的分子系统发育--兼论亚洲栽培稻的起源

稻属Oryza隶属禾本科Poaceae，包括20多个野生种和2个栽培种(亚洲栽培稻O. sativa L和非洲栽培稻O. glaberrima Steud) ，广泛分布于全球热带和亚热带。稻属物种可划分为10个基因组(又称染色体组)类型：A, B, C, BC, CD, E, F, G, HJ 和 HK。栽培稻所属的A基因组是稻属中物种数目最多、地理分布最广的基因组类型，由8个种组成。由于栽培稻属于A基因组，故A基因组物种是栽培稻遗传改良的巨大基因源。数十年来，国际上许多学者对A基因组类群开展了大量涉及形态、细胞、同工酶和分子标记方面的研究，但由于A基因组物种间遗传关系十分接近，形态上差异小且地理分布重叠，使得A基因组物种的系统发育、物种起源和生物地理学等方面存在诸多悬而未决的问题，是稻属中分类和鉴定困难较多的类群。本文利用核基因内含子序列，结合转座子插入分析，重建了A基因组的系统发育，估测了各类群的分化时间;与此同时，基于多克隆测序和基因谱系分析，探讨了O. rufipogon和O. nivara遗传关系以及亚洲栽培稻起源。主要研究结果如下： 1. A基因组的系统发育 在水稻全基因组数据库搜索的基础上，测定了4个单拷贝核基因（Adh1 及3个未注释基因）的内含子序列，构建了稻属A基因组8个种的系统发育关系。基于最大简约法和贝叶斯法的系统发育分析表明：1）澳大利亚的O. meridionalis为A基因组的基部类群;2）亚洲栽培稻两个亚种O. sativa ssp. japonica 和 O. sativa ssp. indica分别和不同的野生类群聚为独立的两个分支，支持japonica 和 indica为多次起源;3）O. rufipogon和O. nivara在系统发育树上完全混在一起，显示出二者间不存在遗传分化;4）非洲一年生野生种O. barthii是非洲栽培稻O. glaberrima的祖先，而非洲多年生野生种O. longistaminata与O. glaberrima/O. barthii.亲缘关系较远;5）分子钟方法估测A基因组类群约在2百万年前（2.0MYA）开始分化，亚洲栽培稻和非洲栽培稻，以及亚洲栽培稻的两个亚种则分别在0.7和 0.4 MYA左右开始分化。此外，通过核基因内含子序列与其它常用片段如ITS，matK等对比分析表明，进化速率相对较快的核基因内含子序列可以有效地用于近缘类群的系统发育研究。 2. Oryza rufipogon 和O. nivara群体遗传研究及亚洲栽培稻起源 对于亚洲野生类群O. rufipogon和O. nivara是合并为一个种还是处理为两个独立的种一直存在争议。在系统发育研究基础上，我们选取4个核基因内含子或5’-UTR区（Waxy, LHS，CatA和1个未注释基因），对采自整个分布区的群体样品进行了多克隆测序，结果表明：1）检测到O. rufipogon和O. nivara均有较高的核苷酸多态性，4个位点上π值和θw值平均分别为0.011和0.014;2）且二者在遗传上没有明显分化，两个类群在4个核基因位点上均检测到大量共享多态（shared polymorphism），未发现固有差异(fixed difference)，表明它们历史上可能属于一个大群体，支持将二者作为种内不同生态型或亚种处理;3）基因谱系树表明亚洲栽培稻的两个亚种indica和japonica分别和不同的O. rufipogon (包括O. nivara)群体聚在一起，进一步从基因谱系角度支持亚洲栽培稻多次起源假说。 3．转座子在群体遗传与系统发育研究中的应用 鉴于目前植物谱系地理学研究中缺乏具有足够信息量的分子标记用于检测种内遗传变异，我们选取3个核基因中的转座子，通过对取自O. rufipogon和O. nivara整个分布区的37份样品的克隆测序，探讨了进化速率快、信息含量丰富的转座子序列在群体遗传上的应用。结果表明：1）无论在物种水平还是群体水平，转座子能检测到比包括内含子在内的其它DNA区域高得多的遗传变异;2）在物种水平上，异交多年生的O. rufipogon和自交一年生的O. nivara多样性均较高，且2个种间相差很小，二者在3个位点上平均核苷酸多样性π值均为0.013，差别主要表现在O. rufipogon杂合位点比例（46.1%）明显高于O. nivara（9.1%），说明交配系统不同并不一定和物种多样性水平相关;3）是否发生转座子序列插入是有价值的系统发育信息，发生在不同染色体上3个基因中的转座子插入进一步证实A基因组基部类群是O. meridionalis;通过叶绿体中3个转座子的插入现象推断了稻族一些四倍体物种，如稻属BC基因组的一些类群的母本来源。

Molecular evolution of microcephalin, a gene determining human brain size

Microcephalin gene is one of the major players in regulating human brain development. It was reported that truncated mutations in this gene can cause primary microcephaly in humans with a brain size comparable with that of early hominids. We studied the m

Genetic diversity and divergence in Chinese yak (Bos grunniens) populations inferred from blood protein electrophoresis

In 6 Chinese yak (Bos. grunniens) populations including 177 yaks, 34 blood protein loci were studied by horizontal starch gel electrophoresis, four of these loci (AKP: ALB, LDH-1, TF) were found to be polymorphic. The percentage of polymorphic loci(P) is 0.118, the mean individual heterozygosity(H) is 0.015, which means a low level of genetic diversity in the whole Chinese yak population. The coefficient of gene differentiation (G(ST)) is 0.0625, which indicated an almost-indistinguishable divergence among different populations at the level of blood protein electrophoresis.

Genetic diversity of cattle in South China as revealed by blood protein electrophoresis

Genetic variation of 31 blood protein loci in 236 cattle from eight South China populations (including mithan, Bos frontalis) and a Holstein population was investigated by means of horizontal starch gel electrophoresis. Thirteen loci (ALB, CAR, Hb-b, Np, PGM, Amy-I, PEP-B, AKP, 6PGD, Cp, Pa, EsD, and TF) were found to be polymorphic. The comparison of average heterozygosities (H) shows that all the native cattle embrace a rich genetic diversity Our results on protein polymorphism suggest that cattle in China originated mainly from Bos indicus and Bos taurus; Xuwen, Hainan, Wenshan, and Dehong cattle and the Dehong zebu are close to zebu-type cattle, and Diqing and Zhaotong cattle are close to the taurine. The mithan was very different from other native cattle, and we suggest that its origin was complicated and may be influenced by other cattle species.

Genetic diversity and taxonomic implication of Cordyceps sinensis as revealed by RAPD markers

Random amplified polymorphic DNA (RAPD) markers are used to investigate genetic variation and evolutionary relationships of 29 samples of Cordyceps sinensis from different geographical populations on the Qinghai-Tibet plateau. Out of 137 RAPD bands scored, 100 are polymorphic. A correlation is revealed between geographical distance and genetic distance. The molecular phylogenetic tree suggests that the 29 samples are divided into three notable clusters, corresponding to the geographical populations, i.e., the north population (NP), middle population (MP), and south population (SP). The NP consists of 7 northern samples from Menyuan, Maqu, and Luqu, the MP consists of 8 samples from Yushu and Chengduo, and the SP consists of 14 samples from Byma Snow Mountain, Renzhi Snow Moutain, Chongcaoxiwa, and Dacaodi. It is demonstrated that extensive genetic diversity is found among different geographical populations of C. sinensis. The genetic diversity pattern of C. sinensis may be caused by the founder effects. The taxonomic status of NP, MP, and SP populations should be that they are different subspecies rather than different species.