Genetic diversity of three donkey populations in the Croatian coastal region

Genetic variation in three Croatian donkey populations, Istrian (IS), North Adriatic (NA) and Littoral-Dinaric (LD), was analysed using eight microsatellite loci and by sequence and SSCP analysis of the proximal portion of the mtDNA D-loop region. The analysis of microsatellite loci revealed observed heterozygosities in the range of 0.37 (MPZ002 in LD) to 0.85 (AHT21 in LD) and polymorphic information content values in the range of 0.36 (MPZ002 in NA) to 0.78 (AHT21 in LD). The overall probability of exclusion was 0.991. Two populations (IS and NA) were closely related (Fst=0.0034), whereas genetic distances between IS and LD (Fst=0.021) and NA and LD (Fst=0.027) were higher. Using AMOVA, 97.6% of the total genetic variance was portioned within populations, while 2.7% was portioned between the Littoral-Dinaric population and the Istrian/North Adriatic population group. Sequencing of the proximal part of the mtDNA D-loop region revealed 36 polymorphic sites representing 19 haplotypes which clustered into three haplotype groups (Y, W, Ws). Only the Y haplotype was found in the IS population which is characterized by a large body size. Haplotypes W and Ws were found in the NA and LD populations which include smaller animals. All three haplotypes were found in the LD population, indicating sporadic migration events from the IS into LD donkey population.     

Time and biosequences: a contribution to the origin of modern man

The origin of modern man is still a highly debated problem. The new contributions of molecular biologists to paleontological data are numerous but discordant as these data obtained with biosequences are based on different methodologies. In order to obtain a more accurate measure of the genetic distance between extant humans and thus the deepest root of the human tree, we have reanalyzed the sequences of the regulatory region of mitochondrial DNA (D-loop) by using an improved version of the Markov Clock model devised in our laboratory. Our analysis, as well as other studies, supports the African origin of modern man. However the quantitative estimate of mtDNA evolution carried out with the corrected Markov Clock model pushes back irradiation time from Africa to 400±100 Kya. Thus according to our model there would be a genetic continuity betweenHomo erectus andHomo sapiens, who would therefore be the result of regional evolution differentiating himself under appropriate environmental pressures.     

Electron microscopic localization of replication origins in Oenothera chloroplast DNA

Summary The origins of chloroplast DNA (cpDNA) replication were mapped in two plastome types of Oenothera in order to determine whether variation in the origin of cpDNA replication could account for the different transmission abilities associated with these plastomes. Two pairs of displacement loop (D-loop) initiation sites were observed on closed circular cpDNA molecules by electron microscopy. Each pair of D-loops was mapped to the inverted repeats of the Oenothera cpDNA by the analysis of restriction fragments. The starting points of the two adjacent D-loops are approximately 4 kb apart, bracketing the 16S rRNA gene. Although there are small DNA length variations near one of the D-loop initiation sites, no apparent differences in the number and the location of replication origins were observed between plastomes with the highest (type I) and lowest (type IV) transmission efficiencies.     

动物mtDNA控制区及保守与异质

本文通过文献综述,对动物线粒体DNA控制区进行了阐述.从线粒体控制区（control region）基因组的研究出发,重点介绍了动物线粒体控制区基因组结构特点.主要结论：由于碱基替换、插入和缺失以及重复序列数目的变异致使D-loop成为mtDNA中变异最多的区域,但突变和结构重排并不是发生在整个D-loop区域,而是在高变区;大多研究集中在mtDNA D-loop保守区和异质方面：对D-loop序列分析,能较好地阐明动物的起源,在动物亲缘关系鉴定、系统进化和物种形成方式的研究等领域具有广阔的研究和应用前景.     

Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents

This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80 bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block (CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number, and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated; the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD, which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical support. Received: 26 February 2001 / Accepted: 6 June 2001     

Phylogenetic analysis of the Lacerta agilis subspecies complex

The Sand lizard Lacerta agilis inhabits a huge area across Eurasia with several subspecies. Nine subspecies are generally approved, L. a. agilis, L. a. argus, L. a. bosnica; L. a. chersonensis, L. a. exigua, L. a. grusinica, L. a. iorinensis, L. a. brevicaudata and L. a. boemica, but several more have been described. The emergence of this large number of subspecies is connected with the phylogeographic history of this species, defined by geographic and climatic processes. A study revealing phylogenetic relationships of this species was already conducted with a broad taxon sampling and coverage. However, the latter study was based solely on the cytochrome b gene and, furthermore, the Balkan Peninsula inhabited by the subspecies L. a. bosnica was underrepresented. This peninsula is a centre of European herpetofaunal endemism with high levels of phenotypic and genotypic variation. Therefore, the inclusion of the subspecies L. a. bosnica is important to clarify the overall view of the phylogenetic relations within the Lacerta agilis subspecies complex and to investigate the level of population differentiation within this highly diverse area. Thus, the aim of the present study was a more thorough analysis of the Balkan Peninsula with a broader taxon sampling. Furthermore, we extended the available datasets by adding the mitochondrial d-loop region and by further samples of different areas of the distribution range apart from the Balkan Peninsula. Our study reveals that the Balkan Peninsula is apparently inhabited by several differentiated lineages, whereby the Central Greek lineage might deserve subspecies status. Furthermore, the distribution area of the two subspecies L. a. agilis and L. a. argus should be revised, as the results of our study raise doubt about the commonly assumed distribution of both subspecies. As the most important outcome our results support that L. a. boemica deserves species status.     

简单重复DNA序列在哺乳动物mtDNA D-loop区的分布及进化特征

简单重复序列广泛分布于从原核到真核生物的基因组中, 其形成的分子机理目前尚不明确。对NCBI数据库中已有256种哺乳动物线粒体DNA (mtDNA) D-loop区进行序列比对分析, 根据其所含有的简单重复序列类型分为3组, 分别是53种哺乳动物含有六核苷酸重复序列; 104种哺乳动物含有非六核苷酸重复序列(＞6 bp); 99种哺乳动物不含有任何重复序列。通过碱基序列分析比对, 发现六核苷酸重复序列集中分布在CSB1-CSB2间隔区, 而非六核苷酸重复可以分布于终止区(TAS)、中央保守区(Central domain)以及CSB(Central sequence block)区。通过比较含有重复序列与不含重复序列的功能保守区发现, 简单重复序列的存在并不明确影响D-loop区内的中央保守区以及CSB1、CSB2、CSB3三个功能保守区的碱基序列保守性。在此基础上, 利用N-J法构建了256种哺乳动物的进化树, 分析了哺乳动物D-Loop区内重复序列在进化过程中的可能变化规律, 发现简单重复序列随着物种的进化地位的升高而呈现消失趋势。