The 9-bp deletion between the mitochondrial lysine tRNA and COII genes in tribal populations of India

A 9-base-pair (bp) deletion located between the lysine tRNA (MTTK) and COII (MTCOX*2) genes in the human mitochondrial genome is a valuable marker for tracing population relationships. Previous research has shown that the 9-bp deletion is associated with two major clusters of control region sequences; one occurs in sub-Saharan Africa, while the other is associated with Asian populations and populations of Asian origin. We surveyed 898 individuals from 16 tribal populations in India and found 6 individuals with the 9-bp deletion. Sequences of the first hypervariable segment (HV1) of the mtDNA control region from these 9-bp deletion-bearing mtDNAs were compared to those previously reported from Asian and African populations. Phylogenetic analysis indicates three distinct clusters of tribal Indian 9-bp deletion mtDNA types. One cluster, found in northeast India, includes southeast Asian and Indonesian mtDNA types. The remaining two clusters appear to have unique origins in southern India. These data provide further evidence of past migrations from Asia into the northeast corner of the Indian subcontinent.     

mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans.

The intergenic COII/tRNA(Lys) 9-bp deletion in human mtDNA, which is found at varying frequencies in Asia, Southeast Asia, Polynesia, and the New World, was also found in 81 of 919 sub-Saharan Africans. Using mtDNA control-region sequence data from a subset of 41 individuals with the deletion, we identified 22 unique mtDNA types associated with the deletion in Africa. A comparison of the unique mtDNA types from sub-Saharan Africans and Asians with the 9-bp deletion revealed that sub-Saharan Africans and Asians have sequence profiles that differ in the locations and frequencies of variant sites. Both phylogenetic and mismatch-distribution analysis suggest that 9-bp deletion arose independently in sub-Saharan Africa and Asia and that the deletion has arisen more than once in Africa. Within Africa, the deletion was not found among Khoisan peoples and was rare to absent in western and southwestern African populations, but it did occur in Pygmy and Negroid populations from central Africa and in Malawi and southern African Bantu-speakers. The distribution of the 9-bp deletion in Africa suggests that the deletion could have arisen in central Africa and was then introduced to southern Africa via the recent "Bantu expansion."     

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS 1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modern humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVSI diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.     

Multiple geographic sources of region V 9-bp deletion haplotypes in Brazilians

We investigated 245 white Brazilians for the presence of the 9-bp deletion in the intergenic COII/tRNALys region of the mitochondrial DNA (mtDNA) and found the deletion in 21 individuals (8.6% of the sample). Because white Brazilians are believed to be predominantly of European descent and this marker is rare in Europe, we established the geographic origin of these 21 mtDNA sequences by sequencing the hypervariable segment I of the mtDNA control region and by performing an RFLP analysis. Only 1 European mtDNA lineage was identified. On the other hand, 16 of the individuals had matrilineages of Amerindian origin and 4 had African mtDNA haplotypes. These results demonstrate that in the formation of the present-day white Brazilian population there was a significant contribution of Amerindian and African matrilineages. Although these data initially appear surprising, they agree well with the historical records of Brazilian colonization.     

Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations

Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA^lys) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.     

Frequency of a 9-bp deletion in the mitochondrial DNA among Asian populations.

Individuals of the following Asian populations were surveyed for the presence of a 9-base-pair deletion of mitochondrial DNA (mtDNA): Ainu, Japanese, Korean, Negrito, and Vedda. Although the variation was detected in every population except the Vedda, the frequencies of the variation differed widely among the populations, suggesting a geographic cline.     

Mitochondrial sequence variation in the Guahibo Amerindian population from Venezuela

New data were obtained on mitochondrial DNA (mtDNA) from Guahibo from Venezuela, a group so far not studied using molecular data. A population sample (n = 59) was analyzed for mtDNA variation in two control-region hypervariable segments (HV1 and HV2) by sequencing. The presence or absence of a 9-bp polymorphism in the COII/tRNA(Lys) region was studied by direct amplification and electrophoretic identification. Thirty-eight variable sites were detected in regions HV1 and HV2, defining 26 mtDNA lineages; 23.7% of these were present in a single individual. The 9-bp deletion was found in 3.39% of individuals. Nucleotide and haplotype diversities were relatively high compared with other New World populations. The identified sequence haplotypes were classified into four major haplogroups (A-D) according to previous studies, with high frequencies for A (47.46%) and C (49.15%), low frequency for B (3.39%), and an absence of D.     

The effect of the mtDNA4834 deletion on hearing

Mutations in mitochondrial DNA (mtDNA) are associated with diverse pathological states in humans, notably sensorineural deafness. In humans, mtDNA4977 deletion, known as common deletion, is thought to play a critical role in presbyacusis. A similar mtDNA deletion occurs in the naturally aging rats is mtDNA4834 deletion. Today, it is still obscure about the effect of common mtDNA deletion on the presbyacusis and hearing loss. We establish a model of rat associated with mtDNA4834 deletion in inner ear by d-galactose. It was found that the malondialdehyde (MDA) increased with superoxide dismutase (SOD) decreasing in the inner ear of the rat treated with d-galactose than of the control. However, there was no significant difference in elevation of ABR threshold between the rat with mtDNA4834 deletion induced by d-galactose and control. After aminoglycoside antibiotic injected, the hearing threshold of the rats carrying mtDNA4834 deletion increased significantly compared with the rats without mtDNA4834 deletion. The results show that resembled accelerated aging in the inner ear of the rat could be induced by injecting d-galactose. Moreover, those suggest that mtDNA4834 deletion can not directly induce the hearing loss, but acting as a predisposing factor which can greatly enhance the sensitivity of the inner ear to the aminoglycoside antibiotic.     

Absence of the 9-bp deletion of mitochondrial DNA in pre-Hispanic inhabitants of Argentina

We investigated the incidence of the Region V mitochondrial DNA 9-base-pair (bp) deletion from human remains recovered from several archaeological sites and contexts throughout Argentina. Of the 34 samples analyzed, 24 yielded DNA extractions that gave clear amplification results. All of the individuals carried two repeats of the 9 bp, one of which has been shown to be deleted in some individuals of Asian origin and defines mitochondrial lineage B. Although most of the modern Amerindian groups in the region exhibit the deletion in high frequencies, the absence of the 9-bp deletion among ancient populations of South America seems to be the rule rather than the exception, as was reported by several studies involving extinct populations. The evidence gathered until now suggests that the earliest settlers of this region of South America did not carry mitochondrial lineage B.     

Multiple origins of tetraploid taxa in the Eurasian Bufo viridis subgroup

We used Q-banding and analyzed nucleolar organizing regions (NORs) to study the cytogenetic evolution of tetraploids within the Palearctic Bufo viridis subgroup, the only known amphibian complex comprising di-, tri- and tetraploid bisexually reproducing taxa. We examined three diploid (2n) nominal taxa (Bufo viridis viridis, B. v. turanensis, B. v. kermanensis) from five Eurasian localities and six tetraploid (4n) nominal taxa (B. oblongus, B. o. danatensis, B. pewzowi pewzowi, B. p. taxkorensis, B. p. unicolor, B. p. strauchi) from eight Central Asian localities. Homeologous chromosomes of 2n and 4n toads exhibit a similar morphology. Silver-staining and in situ hybridization revealed terminal NORs in the long arms of chromosomes 6 in all 2n but in only two out of four chromosomes 6 in all 4n taxa. Q-banding and a rapidly evolving mitochondrial marker suggest at least two origination events for Asian 4n toads: “Western Central Asian tetraploids’’ (B. oblongus Nikolsky, 1896) exhibit distinct differences within some chromosome quartets, which are divisible into pairs of chromosomes and may be allopolyploid. In contrast, “Central Asian tetraploids” (B. pewzowi Bedriaga, 1898) showed homogenous Q-banding patterns within each quartet, suggesting autopolyploidy. In Northeastern Iran, we discovered a zone of either common ancestry or hybridization of 2n and Western Central Asian 4n toads. This raises intriguing questions about how diploid and tetraploid taxa may evolve by exchanging genetic material.     

Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases

Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist–selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.     

Large fragment deletion using a CRISPR/Cas9 system in Saccharomyces cerevisiae

Large chromosomal modifications have been performed in natural and laboratory evolution studies and hold tremendous potential for use in foundational research, medicine, and biotechnology applications. Recently, the type II bacterial Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR/Cas9) system has emerged as a powerful tool for genome editing in various organisms. In this study, we applied the CRISPR/Cas9 system to preform large fragment deletions in Saccharomyces cerevisiae and compared the performance activity to that of a traditional method that uses the Latour system. Here we report in S. Cerevisiae the CRIPR/Cas9 system has been used to delete fragments exceeding 30 kb. The use of the CRISPR/Cas9 system for generating chromosomal segment excision showed some potential advantages over the Latour system. All the results indicated that CRISPR/Cas9 system was a rapid, efficient, low-cost, and versatile method for genome editing and that it can be applied in further studies in the fields of biology, agriculture, and medicine.     

Multiple origins of the green-sensitive opsin genes in fish

Vertebrate opsins are divided into four major groups: RH1 (rhodopsins), RH2 (rhodopsinlike with various absorption sensitivities), SWS (short-wavelength sensitive), and LWS/MWS (long and middle-wavelength sensitive) groups. The green opsin genes (g101 _Af and g101 _Af ) in a Mexican characin Astyanax fasciatus belong to the LWS/MWS group, whereas those in goldfish belong to the RH2 group (Yokoyama 1994, Mol Biol Evol 11:32–39). A newly isolated opsin gene (rh11 _Af ) from A. fasciatus contains five exons and four introns, spanning 4.2 kilobases from start to stop codons. This gene is most closely related to the two green opsin genes of goldfish and belongs to the RH2 group. In the LWS/MWS group, gene duplication of the ancestral red and green opsin genes predates the speciation between A. fasciatus and goldfish, suggesting that goldfish also has an additional gene which is orthologous to g101 _Af and g103 _Af .Correspondence to: S. Yokoyama     

Molecular instability in the COII-tRNA(Lys) intergenic region of the human mitochondrial genome: multiple origins of the 9-bp deletion and heteroplasmy for expanded repeats.

We have identified two individuals from Glasgow in Scotland who have a deletion of one of two copies of the intergenic 9-bp sequence motif CCCCCTCTA, located between the cytochrome oxidase II (COII) and lysine tRNA (tRNA(Lys)) genes of the human mitochondrial genome. Although this polymorphism is common in Africa and Asia, it has not been reported in Northern Europe. Analysis of the mitochondrial DNA control region sequences of these two individuals suggests that they belong to a lineage that originated independently of the previously characterized African and Asian 9-bp deleted lineages. Among the Scottish population we have also identified a maternal lineage of three generations exhibiting heteroplasmy for two, three and four copies of the CCCCCTCTA motif. Polymerase chain reaction amplification across the COII-tRNA(Lys) intergenic region of these individuals gives different ratios of the three product lengths that are dependent on the concentration of the DNA-binding dye crystal violet. To investigate whether changes in repeat number were generated de novo, we constructed clones containing known numbers of the CCCCCTCTA motif. In the presence of high concentrations of crystal violet we obtained two, three and four copies of this motif when the amplification template contained only four copies. Various DNA-binding drugs are known to stabilize bulged structures in DNA and contribute to the process of slipped-strand mispairing during DNA replication. These results suggest that the COII-tRNA(Lys) intergenic region is unstable owing to slipped-strand mispairing. Although sequences containing four copies of the CCCCCTCTA motif are less stable in vitro, we observed an increase in the proportion of mitochondrial genomes with four repeats between-a mother and a daughter in the heteroplasmic lineage. From this we conclude that drift in the germ-line lineage is a main factor in the maintenance or loss of heteroplasmy.     

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。