DNA and recent human evolution

The study of recent human evolution, or the origin of modern humans, is currently dominated by two theories. The recent African origin hypothesis holds that there was a single origin of modern humans in Africa about 100,000 years ago, after which these humans dispersed throughout the rest of the world, mixing little or not at all with nonmodern populations. The multiregional evolution hypothesis holds that there was no single origin of modern humans but, instead, that the mutations and other traits that led to modern humans were spread in concert throughout the old world by gene flow, leading to genetic continuity among old world populations during the past million years. Although both of these theories are based on observations stemming from the fossil record, much discussion and controversy during the past six years has focused on the application and interpretation of studies of DNA variation, particularly mitochondrial DNA (mtDNA). The past year, especially, has brought new data, interpretations, and controversies. Indeed, I initially resisted writing this review, on the grounds that new information would be likely to render it obsolete by the time it was published. However, now that the dust is starting to settle, it seems timely to review various investigations and interpretations and where they are likely to lead. While the focus of this review is the mtDNA story, brief mention is made of studies of nuclear DNA variation (both autosomal and Y-chromosome DNA) and the implications of the genetic data with regard to the fossil record and our understanding of recent human evolution.     

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia)

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage.     

Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae)

Exceptionally high levels of intraspecific variation of mitochondrial DNA (mtDNA) sequences encoding 16S ribosomal RNA (16SrRNA) were detected in populations of the land snail Euhadra peliomphala from the eastern part of Japan. Geographical isolation has occurred within small areas and has created many genetically distinct local populations. These are morphologically segregated into two groups: the first consists of populations from the southern part of the Izu Peninsula, and the second of populations from other areas within the peninsula. They are separated by mountains in the middle of the peninsula. Sequence divergences between these two groups were 7.6–9.5%. The sequence divergences and geological ages of the Izu peninsula and its mountains suggest that the divergence rate of mitochondrial 16SrRNA sequences of this species is extremely rapid, approximately 10% per million years. This rapid evolutional")' rate of mtDNA and vicariance events due to tectonic events and sea level changes has also contributed to creating exceptional geographical variation in the mtDNA of this species.     

Cophylogenetic analysis of the relationship between anemonefish Amphiprion (Perciformes: Pomacentridae) and their symbiotic host anemones (Anthozoa: Actiniaria)

ABSTRACT

The association between anemonefish and anemone is a classical example of mutualism in coral reefs. Although mutualism is probably the key innovation that triggered the adaptive radiation of anemonefish into a wide range of habitats, the coevolutionary history between the groups has not been thoroughly tested in a phylogenetic framework. We examined the evolutionary history of the association via distance-based (Parafit and PACo) and event-based methods (Core-PA, Jane). Mitochondrial DNA sequences (COI mtDNA, Cytb, 16S rDNA and 12S rDNA) were used to reconstruct the phylogenies of tropical Amphiprion species and their host anemones by using maximum likelihood with best-fit models selected. Neither distance-based analyses nor event-based analyses revealed global significant congruence between the phylogenies of the hosts and the symbionts, and thus no evidence for coevolution between anemone-anemonefish. However, at the individual pair level, the fish showed some dependence on anemone hosts. Even though living in close association and benefiting from each other, the change of genetic composition of one species (anemonefish) does not always evolve in response to changes in the other (anemones). These findings expand our understanding of the pattern and the role of evolutionary events to allow a better prediction of the future of the anemonefish-anemone relationship.     

褐马鸡圈养种群的mtDNA控制区多态性

褐马鸡(Crossoptilon mantchuricum)是我国特有的濒危鸟类,国家一级保护动物。为了保护褐马鸡的种质资源,从分子水平上评价褐马鸡的遗传多样性,对山西省庞泉沟自然保护区、太原市动物园的褐马鸡种群20个个体,线粒体DNA D-loop区全序列进行了克隆和测定,使用Clustal X、DnaSP4.0、Mega3.1等生物信息学软件,对全部20条序列开展了比对分析,确定了多态位点与单倍型数目,计算了核苷酸多样性和单倍型多样性;比较了两个种群的遗传变异,初步探讨了褐马鸡种群的遗传多样性和遗传结构。结果表明:20条褐马鸡线粒体DNA D-loop区全序列长度在1236 1237bp之间,其中A、T、G和C 4种核苷酸的平均含量分别为31.0%、26.8%、27.5%和14.8%,A+T含量(57.8%)高于G+C含量(42.3%)。排除1处核苷酸的插入或缺失后,共检测出26个突变位点,占分析序列总长度的2.1%,其中包括25处单一多态位点和1处简约信息位点。20个个体检测出13个单倍型,其中11个个体具有独特的单倍型,2个共享单倍型。褐马鸡两个种群的单倍型多样性(h)为0.911 0.933,核苷酸多样性(π)为0.002 0.003,单倍型间的遗传距离为0.003 0.002。根据单倍型构建了褐马鸡两个种群的NJ分子系统树。聚类表明,2个种群的个体并没有按相应的地理位置进行聚类。揭示褐马鸡具有较高的单倍型多样性和较低的核苷酸多样性,种群的遗传变异较低;两个种群单倍型间的遗传距离较近,遗传多样性参数接近,统计分析无显著差异,两个种群尚未表现出明显的遗传分化,且两个种群间有基因流存在。     

Concerted evolution of sequence repeats inDrosophila mitochondrial DNA

Summary In the eightDrosophila species of themelanogaster subgroup, the mitochondrial DNA (mtDNA) contains an A+T-rich region in which replication originates. The length of this region, in contrast with that of the coding part of the genome, varies extensively among these species. The A+T-rich region ranges from about 1kbp inD. yakuba, D. teissieri, D. erecta, andD. orena to 5 kbp inD. melanogaster, D. simulans, D. mauritiana, andD. sechellia. The difference in size is due in part to the amplification, in the species with long genomes, of a 470-bp sequence that is present only once in each of the four species with short genomes.Usually three to six repeats of this sequence occur in direct tandem repetition in the species with long genomes. The sequence is characterized by the relative positions of the Hpa I and Acc I cleavage sites. Comparative study of the genomes found in the species with long mtDNA molecules reveals relative homogeneity of the repeat units within a given genome, which contrasts with the variability found among the repeats of different genomes. This result is suggestive of a process of a concerted evolution.The examination of heteroplasmic flies of three species (D. simulans, D. mauritiana, andD. sechellia) has shed light on this process. In most cases the molecular types of mtDNA present in a heteroplasmic individual differ by one repeat unit. Addition or deletion of this sequence appears to be the original mutational event generating transient heteroplasmy. Cycles of addition or deletion may consequently maintain the intragenomic homogeneity of the repeats.Finally, we have analyzed an exceptional isofemale line in which three molecular lengths of mtDNA are found (molecules with four, five, and six repeats, respectively). Individual offspring of this line carry from one to three of the molecular types, in all combinations. This indicates that the remodeling of the mitochondrial genome occurs through a mechanism that is at present unknown, but that is site specific and rather frequent.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports classification of antipatharians within the subclass Hexacorallia

Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.     

Phylogeography of the canyon treefrog, Hyla arenicolor (Cope) based on mitochondrial DNA sequence data

Patterns of phylogeography and gene flow were examined in the canyon treefrog, Hyla arenicolor. A total of 973 bp of mitochondrial cytochrome b sequence data were obtained for 65 individuals from 53 populations, yielding 50 unique haplotypes. Interpopulation sequence variation ranged from 0 to 13.7%. Phylogenetic analysis revealed three deeply divergent mtDNA lineages. These three Clades were mapped onto geography and found to represent completely concordant, nonoverlapping, geographical regions. Levels of sequence divergence between the three Clades were equal to or greater than published levels of divergence found in other vertebrate species and genera. Furthermore, one Clade of H. arenicolor was found to be more closely related to the outgroup H. eximia than to other H. arenicolor, suggesting that the taxonomy of this species may require revision.     

Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation

Swamp and river buffalo mitochondrial DNA (mtDNA) was sequenced for 303 bp of the cytochrome b gene for 54 animals from 14 populations, and for 158 bp of the D-loop region for 80 animals from 11 populations. Only one cytochrome b haplotype was found in river buffalo. Of the four haplotypes identified in swamp buffalo, one found in all populations is apparently ancestral both to the other swamp haplotypes and to the river haplotype. The phylogenetic relationships among the 33 D-loop haplotypes, with a cluster of 11 found in swamp buffalo only, also support the evolution of domesticated swamp and river buffalo from an ancestral swamp-like animal, most likely represented today by the wild Asian buffalo ( Bubalus arnee ). The time of divergence of the swamp and river types, estimated from the D-loop data, is 28 000 to 87 000 years ago. We hypothesise that the species originated in mainland south-east Asia, and that it spread north to China and west to the Indian subcontinent, where the rive type evolved and was domesticated. Following domestication in China, the domesticated swamp buffalo spread through two separate routes, through Taiwan and the Philippines to the eastern islands of Borneo and Sulawesi, and south through mainland southeast Asia and then to the western islands of Indonesia.     

Find structural aspects of anthozoan desmocyte development (phylum Cnidaria)

The fine structural changes associated with the differentiation of skeletogenic cells into cells specialized in binding soft tissues onto skeletal structures are described in the gorgonian coral, Leptogorgia virgulata (Lam.). These binding cells are called desmocytes. The sequence of events in desmocyte development includes: growth of the plasma membrane, invagination of the mesoglea-end of the cell, expansion of the axis-end of the cell, loss of organelles involved in skeletogenesis, proliferation of double vesicles and transformation of double vesicles into cytoskeletal rods. Double vesicles appear either cup-shaped or as a vesicle within a vesicle in sectioned material. These observations of desmocyte development are compared to previous light microscopical observations desmocyte development in diverse forms of anthozoans. Similarities in desmocyte development throughout the class include invagination of the differentiating cell, formation of a pectinate mesogleal margin and formation of an array of cytoskeletal rods at the axis-end of the cell. Comparison with available information on the development and fine structure of desmocytes in the cnidarian classes Scyphozoa and Hydrozoa shows these similarities do not extend across class boundaries and, therefore, common ancestry between the three classes of cnidarian desmocytes seems remote if, indeed, such an ancestral cell existed at all.     

西藏牦牛线粒体DNA 的遗传多样性及系统进化分析

为从分子水平上探究西藏牦牛类群的遗传多样性、亲缘关系,本研究测定了日多牦牛、类乌齐牦牛、丁青牦牛、错那牦牛、隆子牦牛、仲巴牦牛、聂荣牦牛、申札牦牛等8 个西藏牦牛类群共328 头牦牛mtDNAD-loop区序列,分析其多态性,构建系统进化树。结果表明:本次测定的西藏牦牛mtDNA D-loop 区序列长度为 887 - 895 bp,共检测到135 个变异位点,其中单态突变位点52 个,简约信息位点83 个。在328 个个体中共检测出91 种单倍型,平均单倍型多样性(Hd)、平均核苷酸多样性(π)分别为0. 884、0.010 27,显示西藏牦牛具有丰富的遗传多样性。8 个类群间平均遗传距离为0.011;日多牦牛与错那牦牛间遗传距离最小(0. 006);类乌 齐牦牛与隆子牦牛间遗传距离最大(0.015)。系统进化分析显示西藏牦牛可分为两大类,错那牦牛是较纯的牦牛类群,其它牦牛类群在进化过程中出现相互交流的情况。     

蚕类昆虫线粒体DNA研究及其在起源与进化研究中的应用

线粒体DNA(mtDNA)属母系遗传,进化速率较核基因快且基因组结构相对简单,已作为理想的分子标记广泛应用于昆虫群体遗传学及分子系统学等研究。本文对蚕类昆虫线粒体DNA在分子水平上的最新研究进展进行了较详细的阐述,重点介绍了蚕类昆虫线粒体基因组的组成及特征、mtDNA克隆与多态性及在蚕类昆虫分子系统学研究中的应用等。     

DNA sequence variation in the mitochondrial control region of subterranean mole rats,Spalax ehrenbergi superspecies,in Israel

The complete mitochondrial control region was sequenced for 60 individuals representing different populations for each of the four species of the subterranean mole rat Spalax ehrenbergi superspecies in Israel: Spalax galili (2n = 52), S. golani (2n = 54), S. carmeli (2n = 58), and S. judaei (2n = 60). The control region of all species and populations is very similar both in length (979 to 983 bp) and in base composition. As in agreement with previous surveys on mitochondrial control regions on mammals, the mole rat control region can be divided into a central domain and two flanking domains, ETAS (extended termination associated sequences) and CSB (conserved sequence blocks). Along with the common conserved blocks found in these domains (ETAS1, ETAS2, CSB1, CSB2, and CSB3), we have also detected in all individuals an ETAS1-like and a CSB1-like element, both in the ETAS domain. The most conserved region was the central domain, followed by the CSB and ETAS domains, showing important differences in the four species analyzed. Phylogenetic analysis supported the existence of two clades. One clade contained individuals belonging to Spalax galili (2n = 52) and S. golani (2n = 54), separated in two different branches depending on the species. The other clade contained individuals belonging to S. carmeli (2n = 58) and S. judaei (2n = 60) mixed together, suggesting a more recent event of speciation. Within species we have observed a southward trend of increasing variability. These results have been explained as a consequence of the adaptation of the species to ecological factors such as aridity and temperature stresses.     

Comparisons of mitochondrial DNA (mtDNA) sequences (16S rRNA gene) between oviparous and viviparous strains of Lacerta vivipara: a preliminary study

The lizard Lacerta vivipara has allopatric oviparous and viviparous populations. The mitochondrial DNA (mtDNA) gene coding for the 16S rRNA was sequenced for several viviparous lizard populations from France, Switzerland, Bulgaria, Czech Republic, The Netherlands, Sweden, and for oviparous lizard populations from the Pyrenean and Cantabric Mountains. Seven distinct groups (three oviparous and four viviparous) were identified. The net nucleotide divergence between oviparous and viviparous haplotypes was 1.3% +/- 0.5 (mean +/- standard deviation). These results on mtDNA, together with other data obtained previously, led us to formulate a biogeographical scenario that could be tested by further research.     

Nuclear and mitochondrial DNA have sequence homology with a chloroplast gene

Summary A PstI 7.7 kbp fragment from chloroplast (ct) DNA of spinach shows homology to an EcoRI 8.3 kbp fragment of mitochondrial (mt) DNA and in turn, both are homologous to a number of common regions of nuclear (n) DNA. The common area of homology between the chloroplast and mitochondrial fragments is between a KpnI 1.8 segment internal to the PstI sites in the ctDNA and an EcoRI/BamHI 2.9 kbp fragment at one end of the mitochondrial 8.3 kbp fragment. The KpnI 1.8 kbp ctDNA fragment is within a structural gene for the P₇₀₀ chlorophyll a apoprotein. Further analysis of this KpnI 1.8 kbp fragment confined the homologous region in mtDNA to a ct 0.8 kbp HpaII fragment. These smaller pieces of the organellar genomes share homologies with nuclear DNA as well as displaying unique hybridization sites. The observations reported here demonstrate that there is a common or closely related sequence in all three genetic compartments of the cell.     

Analysis of sequence homology between human and mouse mitochondrial DNA

The base sequence homology between human and mouse mitochondrial DNA has been investigated by hybridization of highly labelled mitochondrial DNA probes with restriction fragments of mitochondrial DNA blotted according to the Southern technique. By this analysis, the homologous regions have been found to be widely distributed along the mitochondrial genome. Competition hybridization experiments with unlabelled HeLa mitochondrial RNAs have shown that most of the cross-hybridization involves the ribosomal and 4 S RNA genes.