The role of natural selection in the evolution of mitochondrial haplogroups in Northeastern Eurasia

The role of natural selection in the evolution of the mitochondrial genome in human populations from Northeastern Eurasia was studied. Selection for the regions-specific haplogroup C was demonstrated.

     

The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection

South American tuco-tucos (Ctenomys) and the related coruro (Spalacopus) are two rodent lineages that have independently colonised the subterranean niche. The energetically demanding lifestyles of these species, coupled with the hypoxic atmospheres characteristic of subterranean environments, may have altered the selective regimes on genes encoding proteins related to cellular respiration. Here, we examined the molecular evolution of 13 protein-coding genes in the mitochondrial genome of seven caviomorph rodents, including these two subterranean genera and their above-ground relatives. Using maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (dS) and nonsynonymous (dN) substitutions. We found a significantly higher ω ratio (dN/dS) in subterranean groups as compared to their non-subterranean counterparts in 11 of 13 genes, although no ω ratio was larger than 1. Additionally, we applied a method based on quantitative physicochemical properties to test for positive selection. Amino acid changes implicated in radical structural or functional shifts in the protein property were found to be ubiquitous across the phylogeny, but concentrated in the subterranean lineages. Convergent changes were also found between the subterranean genera used in this study and other mammals adapted to hypoxia. The results of this study suggest a link between niche shifts and weak directional (or episodic) selection at the molecular level against a background of purifying selection.     

The evolution of mitochondrial genomes in modern frogs (Neobatrachia): nonadaptive evolution of mitochondrial genome reorganization

Background

Although mitochondrial (mt) gene order is highly conserved among vertebrates, widespread gene rearrangements occur in anurans, especially in neobatrachians. Protein coding genes in the mitogenome experience adaptive or purifying selection, yet the role that selection plays on genomic reorganization remains unclear. We sequence the mitogenomes of three species of Glandirana and hot spots of gene rearrangements of 20 frog species to investigate the diversity of mitogenomic reorganization in the Neobatrachia. By combing these data with other mitogenomes in GenBank, we evaluate if selective pressures or functional constraints act on mitogenomic reorganization in the Neobatrachia. We also look for correlations between tRNA positions and codon usage.

Results

Gene organization in Glandirana was typical of neobatrachian mitogenomes except for the presence of pseudogene trnS (AGY). Surveyed ranids largely exhibited gene arrangements typical of neobatrachian mtDNA although some gene rearrangements occurred. The correlation between codon usage and tRNA positions in neobatrachians was weak, and did not increase after identifying recurrent rearrangements as revealed by basal neobatrachians. Codon usage and tRNA positions were not significantly correlated when considering tRNA gene duplications or losses. Change in number of tRNA gene copies, which was driven by genomic reorganization, did not influence codon usage bias. Nucleotide substitution rates and d_N/d_S ratios were higher in neobatrachian mitogenomes than in archaeobatrachians, but the rates of mitogenomic reorganization and mt nucleotide diversity were not significantly correlated.

Conclusions

No evidence suggests that adaptive selection drove the reorganization of neobatrachian mitogenomes. In contrast, protein-coding genes that function in metabolism showed evidence for purifying selection, and some functional constraints appear to act on the organization of rRNA and tRNA genes. As important nonadaptive forces, genetic drift and mutation pressure may drive the fixation and evolution of mitogenomic reorganizations.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-691) contains supplementary material, which is available to authorized users.     

Parallel evolution of the genetic code in arthropod mitochondrial genomes

The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.     

The role of climate in human mitochondrial DNA evolution: a reappraisal

Previous studies have proposed that selection has been involved in the differentiation of human mitochondrial DNA (mtDNA) and climate was the main driving force. This viewpoint, however, gets no support from the subsequent studies and remains controversial thus far. To clarify this issue, a total of 237 complete mtDNA sequences belonging to autochthonous lineages from South Asia, Oceania, and East Asia were collected to seek for the imprint of selection. Based on nonsynonymous (N) and synonymous (S) substitutions analysis, our results confirmed that purifying selection was the predominant force during the evolution of human mtDNA. However, no significant and extensive difference was detected among these three regions, which did not support the climate adaptation hypothesis but preferred random genetic drift to be the main factor in shaping the current landscape of human mtDNA, at least those from Asian and Oceanian regions.     

The role of natural selection in evolution

To evaluate properly a role of natural selection, its effect should be considered in relation to different phases of the evolutionary cycle postulated earlier by the author. At the first stage of the cycle natural selection is directed towards organism's persistence to detrimental external factors and leads to an increased fitness (that is viability and fecundity) in every generation. At the next stage of the cycle natural selection occurs under conditions of intraspecific competition and is directed towards a more efficient utilization of food resources. At this stage natural selection leads to formation and divergence of intraspecific races and is carried out by "single" selection actions occurring now and then and consisting of the survival of rare mutants with an altered ecological potential. Such a strict selection for certain mutants occurs again during the periods of acute competition for food, the selected mutants being characterized by a decrease of fitness, the latter to have been restored by means of the "ordinary" selection within the intervals between crises. According to the model suggested, homozygotes for "detrimental" recessive alleles could be selected in diploids, as the mutants mentioned with altered ecological potential. At the end of the cycle, there is a kind of selection for hybrids in which ecological potential of specialized intraspecific races is combined. The genetic drift is considered as an inevitable consequence of the postulated mechanism of natural selection.     

The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genomes in bilateral animals

Booklice (order Psocoptera) in the genus Liposcelis are major pests to stored grains worldwide and are closely related to parasitic lice (order Phthiraptera). We sequenced the mitochondrial (mt) genome of Liposcelis bostrychophila and found that the typical single mt chromosome of bilateral animals has fragmented into and been replaced by two medium-sized chromosomes in this booklouse; each of these chromosomes has about half of the genes of the typical mt chromosome of bilateral animals. These mt chromosomes are 8,530 bp (mt chromosome I) and 7,933 bp (mt chromosome II) in size. Intriguingly, mt chromosome I is twice as abundant as chromosome II. It appears that the selection pressure for compact mt genomes in bilateral animals favors small mt chromosomes when small mt chromosomes co-exist with the typical large mt chromosomes. Thus, small mt chromosomes may have selective advantages over large mt chromosomes in bilateral animals. Phylogenetic analyses of mt genome sequences of Psocodea (i.e. Psocoptera plus Phthiraptera) indicate that: 1) the order Psocoptera (booklice and barklice) is paraphyletic; and 2) the order Phthiraptera (the parasitic lice) is monophyletic. Within parasitic lice, however, the suborder Ischnocera is paraphyletic; this differs from the traditional view that each suborder of parasitic lice is monophyletic.     

Changes in the number of mitochondrial genomes during human development

Using a cDNA probe for the mitochondrially encoded third subunit of cytochrome c oxidase (COIII) we found a progressive increase in the number of mitochondrial DNA molecules in specific human tissues during normal fetal development. The data indicate that the tissue, rather than the final number of mitochondrial genomes, apparently plays a dominant role in determining the gestational stage at which the adult complement of this DNA is established.     

Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes

The cloverleaf secondary structure of transfer RNA (tRNA) is highly conserved across all forms of life. Here, we provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders. These data show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from many of the 22 tRNAs in the genomes of 4 out of 7 orders of arachnids. Additionally, all opisthothele spiders possess some tRNA genes that lack sequences that could form well-paired aminoacyl acceptor stems. We trace the evolution of T-arm loss onto phylogenies of arachnids and show that a genome-wide propensity to lose sequences that encode canonical cloverleaf structures likely evolved multiple times within arachnids. Mapping of structural characters also shows that certain tRNA genes appear more evolutionarily prone to lose the sequence coding for the T-arm and that once a T-arm is lost, it is not regained. We use tRNA structural data to construct a phylogeny of arachnids and find high bootstrap support for a clade that is not supported in phylogenies that are based on more traditional morphological characters. Together, our data demonstrate variability in structural evolution among different tRNAs as well as evidence for parallel evolution of the loss of sequence coding for tRNA arms within an ancient and diverse group of animals.     

Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes

The H-strand of vertebrate mitochondrial DNA is left single-stranded for hours during the slow DNA replication. This facilitates C-->U mutations on the H-strand (and consequently G-->A mutations on the L-strand) via spontaneous deamination which occurs much more frequently on single-stranded than on double-stranded DNA. For the 12 coding sequences (CDS) collinear with the L-strand, NNY synonymous codon families (where N stands for any of the four nucleotides and Y stands for either C or U) end mostly with C, and NNR and NNN codon families (where R stands for either A or G) end mostly with A. For the lone ND6 gene on the other strand, the codon bias is the opposite, with NNY codon families ending mostly with U and NNR and NNN codon families ending mostly with G. These patterns are consistent with the strand-specific mutation bias. The codon usage biased towards C-ending and A-ending in the 12 CDS sequences affects the codon-anticodon adaptation. The wobble site of the anticodon is always G for NNY codon families dominated by C-ending codons and U for NNR and NNN codon families dominated by A-ending codons. The only, but consistent, exception is the anticodon of tRNA-Met which consistently has a 5'-CAU-3' anticodon base-pairing with the AUG codon (the translation initiation codon) instead of the more frequent AUA. The observed CAU anticodon (matching AUG) would increase the rate of translation initiation but would reduce the rate of peptide elongation because most methionine codons are AUA, whereas the unobserved UAU anticodon (matching AUA) would increase the elongation rate at the cost of translation initiation rate. The consistent CAU anticodon in tRNA-Met suggests the importance of maximizing the rate of translation initiation.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Concordant evolution of mitochondrial and nuclear genomes in the wheat pathogen Phaeosphaeria nodorum

We compared patterns of mitochondrial restriction fragment length polymorphism (RFLP) diversity with patterns of nuclear RFLP diversity to investigate the effects of selection, gene flow, and sexual reproduction on the population genetic structure and evolutionary history of the wheat pathogen Phaeosphaeria nodorum. A total of 315 fungal isolates from Texas, Oregon, and Switzerland were analyzed using seven nuclear RFLP probes that hybridized to discrete loci and purified mitochondrial DNA that hybridized to the entire mtDNA genome. Forty-two different mitochondrial haplotypes and 298 different nuclear haplotypes were detected. The two most frequent mtDNA haplotypes were present in every population and represented 32% of all isolates. High levels of gene flow, low levels of population subdivision, no evidence for either host specificity or cyto-nuclear disequilibrium were inferred from the analysis of both genomes. The concordance in estimates of these population genetic parameters from both genomes suggests that the two genomes experienced similar degrees of migration, genetic drift and selection.     

Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection

This article provides evidence that selection has been a significant force during the evolution of the human mitochondrial genome. Both gene-by-gene and whole-genome approaches were used here to assess selection in the 560 mitochondrial DNA (mtDNA) coding-region sequences that were used previously for reduced-median-network analysis. The results of the present analyses were complex, in that the action of selection was not indicated by all tests, but this is not surprising, in view of the characteristics and limitations of the different analytical methods. Despite these limitations, there is evidence for both gene-specific and lineage-specific variation in selection. Whole-genome sliding-window approaches indicated a lack of selection in large-scale segments of the coding region. In other tests, we analyzed the ratio of nonsynonymous-to-synonymous substitutions in the 13 protein-encoding mtDNA genes. The most straightforward interpretation of those results is that negative selection has acted on the mtDNA during evolution. Single-gene analyses indicated significant departures from neutrality in the CO1, ND4, and ND6 genes, although the data also suggested the possible operation of positive selection on the AT6 gene. Finally, our results and those of other investigators do not support a simple model in which climatic adaptation has been a major force during human mtDNA evolution.     

Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution

Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition, and distribution of short repetitive sequences we observed among green algal mitochondrial genomes on the other. It is conceivable that the accumulation of GC- rich short repeated sequences in the Chlamydomonas-like but not Prototheca-like mitochondrial genomes might have triggered evolutionary events responsible for the distinct series of evolutionary changes undergone by the two green algal mitochondrial lineages. The similarity in base composition, nucleotide sequence, abundance, and mode of organization we observed between the short repetitive sequences present in Chlamydomonas-like mitochondrial genomes on one hand and fungal and vertebrate homologs on the other might extend to some of the roles that the short repetitive sequences have been shown to have in the latter. Potential involvements we propose for the short repetitive sequences in the evolution of Chlamydomonas-like mitochondrial genomes include fragmentation and scrambling of the ribosomal-RNA-coding regions, extensive gene rearrangements, coding-region deletions, surrogate origins of replication, and chromosomal linearization.      

制作工具在人类演化中的地位与作用

制作工具曾经被视作人类独有的行为能力,"人类"曾经据此而定义。但目前学术界将直立行走作为人类区别于其他灵长类最重要的体质与行为特征。少量其他动物种类,尤其是非人高等灵长类,也能使用工具乃至简单制作工具。如何认识制作工具在人类演化中的作用?人类制作工具的能力与其他动物有何区别?考古学是否有能力分辨人类的工具和其他灵长类的产品?本文通过对现代巴西猴群敲砸石头的行为及其产品、4300年前黑猩猩的"石制品"和早期人类石制品的比较研究,指出人类的工具与其他动物制作和使用的工具存在根本的区别;工具制作和使用对确定人类的演化方向,增强人类的适应生存能力,塑造人类的大脑与心智及行为方式,提升语言和交流能力,形成现代人类的身心和社会,至关重要,不可或缺。考古工作者一方面需要谨慎分辨、研究人类工具制作初期的产品,不使其与自然的产物和其他动作的作品相混淆,另一方面应该认识到人类工具制作在计划性、目的性、预见性、规范性和精美度上具有唯一性,有内在的智能控制、思维逻辑和规律可循。学科发展的积累和现代科技的支撑使考古学者具有多方面的利器,能够把人类工具制作的历史挖掘、复原出来,能够破译特定的石器技术和功能,进而将人类演化的历史画卷描绘得更加精细,更加完整。     

Rearranged mitochondrial genomes are present in human oocytes.

Using quantitative PCR, we have determined that a human oocyte contains approximately 100,000 mitochondrial genomes (mtDNAs). We have also found that some oocytes harbor measurable levels (up to 0.1%) of the so-called common deletion, an mtDNA molecule containing a 4,977-bp rearrangement that is present in high amounts in many patients with "sporadic" Kearns-Sayre syndrome (KSS) and progressive external ophthalmoplegia (PEO). This is the first demonstration that rearranged mtDNAs are present in human oocytes, and it provides experimental support for the supposition that pathogenic deletions associated with the ontogeny of sporadic KSS and PEO can be transmitted in the female germ line, from mother to child. The relevance of these finding to the accumulation of extremely low levels of deleted mtDNAs in both somatic and germ-line tissues during normal human aging is also discussed.