Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.     

植物居群的基因流动态及其相关适应进化的研究进展

生物自然居群间的基因流不但可以阻止遗传分化以维持物种的完整性,而且也能积极响应生物多样化的进程。理解与基因流相关的适应性进化及其内在机理将有助于我们更好地认识生物物种形成和多样化的原始动力以及真正原因。该文通过对植物种内和种间居群基因流动态进行讨论,阐述了近年来有关植物基因流动态的一些重要理论观念和研究进展,以期为相关领域动态及趋势研究提供参考。     

Sequence Similarity in Nuclear and Mitochondrial Gene Regions in Plants

A 114-basepair fragment at 5′-upstream of the gene oee2-A from Nicotiana tabacum encoding the 23kD polypeptide of oxygen-evolving complex of photosystem II was found, through database search, to have high sequence similarity with segments in the mitochondrial genome of Oenothera, watermelon and wheat. This observation is supported by the Southern hybridization data. Repeated sequences were also found in the nuclear-mitochondrial homologous region, However, the function of these repeats is yet to be determined.     

Dynamics of Introduced Populations of Phragmidium violaceum and Implications for Biological Control of European Blackberry in Australia

Phragmidium violaceum causes leaf rust on the European blackberry (Rubus fruticosus L. aggregate). Multiple strains of this pathogen have been introduced into southern Australia for the biological control of at least 15 taxa of European blackberry, a nonindigenous, invasive plant. In climates conducive to leaf rust, the intensity of disease varies within and among infestations of the genetically variable host. Genetic markers developed from the selective amplification of microsatellite polymorphic loci were used to assess the population genetic structure and reproductive biology of P. violaceum within and among four geographically isolated and diseased infestations of the European blackberry in Victoria, Australia. Despite the potential for long-distance aerial dispersal of urediniospores, there was significant genetic differentiation among all populations, which was not associated with geographic separation. An assessment of multilocus linkage disequilibrium revealed temporal and geographic variation in the occurrence of random mating among the four populations. The presence of sexual spore states and the results of genetic analyses indicated that recombination, and potentially random migration and genetic drift, played an important role in maintaining genotypic variation within populations. Recombination and genetic differentiation in P. violaceum, as well as the potential for metapopulation structure, suggest the need to release additional, genetically diverse strains of the biocontrol agent at numerous sites across the distribution of the Australian blackberry infestation for maximum establishment and persistence.     

Dynamics of Foliage and Thatch Populations of Introduced Pseudomonas fluorescens and Streptomyces sp. on a Fairway Turf

Populations of bacteria (Pseudomonas fluorescens A506 and Streptomyces sp. strain 93) applied to a creeping bentgrass/annual bluegrass fairway turf were followed over time on leaves and thatch. While introduced populations remained at detectable levels over a period of 11–25 days, they usually declined gradually and did not increase after their application to turf. Streptomyces rapidly disappeared from leaves while P. fluorescens was able to maintain similar population sizes on both thatch and leaves, after an initial decline of about 1-log unit, showing that it was actively colonizing the foliage despite loss of biomass from lawn mowing. Throughout these experiments, populations of indigenous microbes on foliage and thatch remained stable, about 10⁶ and 10⁸ cfu g⁻¹ for fungi and bacteria, respectively, and were not affected by the application of bacterial antagonists. Niche-clearing with hydrogen peroxide, which temporarily reduced the population size of indigenous microorganisms two-fold, caused population size of P. fluorescens to increase approximately ten-fold within 24 h, while it declined by about one log unit on untreated turf. It is concluded that the indigenous microflora competes with introduced bacterial antagonists and interferes with their establishment and persistence on turf. Additional studies with P. fluorescens revealed that its population size was inoculum dose-dependent and that solid top dressing was slightly more efficient than spraying liquid suspension in establishing the antagonist. It was possible to maintain P. fluorescens populations above 10⁵ cfu/g of thatch and leaves for 2 weeks or more with both top-dressing or spraying with about 1 to 3 × 10¹⁰ cfu m⁻².     

Mitochondrial and Nuclear Genes of Mitochondrial Components in Cancer

Although the observation of aerobic glycolysis of tumor cells by Otto v. Warburg had demonstrated abnormalities of mitochondrial energy metabolism in cancer decades ago, there was no clear evidence for a functional role of mutant mitochondrial proteins in cancer development until the early years of the 21^st century. In the year 2000, a major breakthrough was achieved by the observation, that several genes coding for subunits of the respiratory chain (ETC) complex II, succinate dehydrogenase (SDH) are tumor suppressor genes in heritable paragangliomas, fulfilling Knudson’s classical two-hit hypothesis. A functional inactivation of both alleles by germline mutations and chromosomal losses in the tumor tissue was found in the patients. Later, SDH mutations were also identified in sporadic paragangliomas and pheochromocytomas. Genes of the mitochondrial ATP-synthase and of mitochondrial iron homeostasis have been implicated in cancer development at the level of cell culture and mouse experiments. In contrast to the well established role of some nuclear SDH genes, a functional impact of the mitochondrial genome itself (mtDNA) in cancer development remains unclear. Nevertheless, the extremely high frequency of mtDNA mutations in solid tumors raises the question, whether this small circular genome might be applicable to early cancer detection. This is a meaningful approach, especially in cancers, which tend to spread tumor cells early into bodily fluids or faeces, which can be screened by non-invasive methods.     

Mitochondrial genome sequence of the bluegill sunfish (Lepomis macrochirus)

The bluegill sunfish (Lepomis macrochirus) belongs to Lepomis genera of the family Centrarchidae, which is an economically important freshwater species in China. This study presents the complete mitochondrial genome of L. macrochirus, which is the first complete sequence from sunfish species. L. macrochirus mitochondrial DNA is 16,489 bp long, with the genome organization and gene order being identical to that of the typical vertebrate.     

Analyses of Nuclear ldhA Gene and mtDNA Control Region Sequences of Atlantic Northern Bluefin Tuna Populations

There has been considerable debate about whether the Atlantic northern bluefin tuna exist as a single panmictic unit. We have addressed this issue by examining both mitochondrial DNA control region nucleotide sequences and nuclear gene ldhA allele frequencies in replicate size or year class samples of northern bluefin tuna from the Mediterranean Sea and the northwestern Atlantic Ocean. Pairwise comparisons of multiple year class samples from the 2 regions provided no evidence for population subdivision. Similarly, analyses of molecular variance of both mitochondrial and ldhA data revealed no significant differences among or between samples from the 2 regions. These results demonstrate the importance of analyzing multiple year classes and large sample sizes to obtain accurate estimates when using allele frequencies to characterize a population. It is important to note that the absence of genetic evidence for population substructure does not unilaterally constitute evidence of a single panmictic population, as genetic differentiation can be prevented by large population sizes and by migration.     

A Biogeographic View of Apodemus in Asia and Europe Inferred From Nuclear and Mitochondrial Gene Sequences

Sequences of the mitochondrial cyt b gene and nuclear IRBP, RAGI, I7, and vWF genes were used to assess the evolutionary history of major lineages of Apodemus, in particular to better understand dispersal between Asia and Europe. Our data show eight extant lineages of Late Tertiary origin: Apodemus agrarius, A. semotus, A. peninsulae, A. speciosus, A. argenteus, A. gurkha, A. mystacinus, and A. sylvaticus. Monophyly of two European lineages (A. mystacinus and A. sylvaticus) and four Asian lineages (A. agrarius, A. semotus, A. peninsulae, and A. speciosus) was confirmed with high bootstrap support. Together with literature data, the available molecular data depict three crucial evolutionary events: (1) initial wide dispersal and subsequent radiation around 6 million years ago, (2) region-specific radiations in Europe and southern China around 2 million years ago, and (3) westward dispersal of A. agrarius to Europe in the Late Quaternary.     

Mitochondrial Genome Dynamics in Plants and Animals: Convergent Gene Fusions of a MutS Homologue

Mitochondrial processes influence a broad spectrum of physiological and developmental events in higher eukaryotes, and their aberrant function can lead to several familiar disease phenotypes in mammals. In plants, mitochondrial genes directly influence pollen development and the occurrence of male sterility in natural plant populations. Likewise, in animal systems evidence accumulates to suggest important mitochondrial functions in spermatogenesis and reproduction. Here we present evidence for a convergent gene fusion involving a MutS-homologous gene functioning within the mitochondrion and designated Msh1. In only plants and soft corals, the MutS homologue has fused with a homing endonuclease sequence at the carboxy terminus of the protein. However, the endonuclease domains in the plants and the soft corals are members of different groups. In plants, Msh1 can influence mitochondrial genome organization and male sterility expression. Based on parallels in Msh1 gene structure shared by plants and corals, and their similarities in reproductive behavior, we postulate that this convergent gene fusion might have occurred in response to coincident adaptive pressures on reproduction. [Reviewing Editor: Dr. Deborah Charlesworth]     

基于线粒体ND4基因和核c-mos基因初步探讨广西拟水龟和艾氏拟水龟的系统发生

广西拟水龟和艾氏拟水龟的分类和系统发生多年来存在争议。通过测定广西拟水龟、艾氏拟水龟和黄喉拟水龟线粒体ND4基因和核c-mos基因部分序列,合并GenBank中拟水龟属其他物种的ND4基因和c-mos基因部分序列进行分析,从分子水平探讨广西拟水龟和艾氏拟水龟的系统发生。ND4基因数据分析发现NJ、MP和BI树中广西拟水龟与安南拟水龟的聚类分支相互交织聚为一支,二者种内遗传距离均为0.002～0.017,种间遗传距离为0.000～0.035,种间遗传距离明显小于同属内其他种间0.056～0.109的遗传距离,表明广西拟水龟与安南拟水龟可能为同一物种,可能是安南拟水龟的同种异名,或是作为安南拟水龟的一个亚种;NJ树、MP树和BI树均显示,艾氏拟水龟与黄喉拟水龟的位置和关系最为相近,二者间的遗传距离为0.020～0.035,明显小于拟水龟属其他物种间遗传距离,而明显大于同属各物种内遗传距离,艾氏拟水龟与黄喉拟水龟之间系统分类关系是介于种内与种间之间;乌龟、中华花龟、安南拟水龟等物种都是与拟水龟属中其他物种先聚成一支后再与同科的地龟属的地龟形成姐妹支,支持将乌龟属、花龟属和安南龟属并入拟水龟属的分类。c-mos基因数据分析发现,拟水龟属各物种间不存在明显的遗传距离,NJ树和MP树也未能对属中各物种的分子系统发生位置进行有效的界定,但在属及属以上阶元的分子分类系统中c-mos基因可以作为分类依据,并与线粒体基因数据有较好的一致性。     

Contrasting Evolutionary Dynamics and Information Content of the Avian Mitochondrial Control Region and ND2 Gene

Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (Agelaius phoeniceus) and its close relative the tricolored blackbird (A. tricolor). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for A. phoeniceus. However, individual Sanger-read-length fragments (∼600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.     

Mitochondrial Ribosomal Protein L11 Gene of Dictyostelium discoideum Resides not in the Nuclear Genome but in the Mitochondrial Genome

During the course of analysis of the mitochondrial genome ofthe cellular slime mold, Dictyostelium discoideum, we founda gene (rpl11) for mitochondrial ribosomal protein L11 (RPL11),having 172 amino acid residues. Southern blot analysis revealedthat the gene resided in the mitochondrial DNA as a singlecopybut not in the nuclear DNA. From Northern blot experiments,one major mRNA (about 27 kb) and two minor mRNAs (about 4 and5 kb) for the gene were detected in the mitochondria. This isthe first report showing that the active gene for RPL11 stillresides in the mitochondrial genome and has not been transferredto the nuclear genome in D. discoideum.     

Ribosomal and Mitochondrial DNA Analyses of Xiphinema americanum-Group Populations

The 18S ribosomal DNA (rDNA) and cytochrome oxidase I region of mitochondrial DNA (mtDNA) were sequenced for 24 Xiphinema americanum-group populations sourced from a number of geographically disparate locations. Sequences were subjected to phylogenetic analysis and compared. 18S rDNA strongly suggested that only X. pachtaicum, X. simile (two populations) and a X. americanum s.l. population from Portugal were different from the other 20 populations studied, whereas mtDNA indicated some heterogeneity between populations. Phylogenetically, based on mtDNA, an apparent dichotomy existed amongst X. americanum-group populations from North America and those from Asia, South America and Oceania. Analyses of 18S rDNA and mtDNA sequences underpin the classical taxonomic issues of the X. americanum-group and cast doubt on the degree of speciation within the X. americanum-group.     

Modeling the Dynamics of a Non-Limited and a Self-Limited Gene Drive System in Structured Aedes aegypti Populations

Recently there have been significant advances in research on genetic strategies to control populations of disease-vectoring insects. Some of these strategies use the gene drive properties of selfish genetic elements to spread physically linked anti-pathogen genes into local vector populations. Because of the potential of these selfish elements to spread through populations, control approaches based on these strategies must be carefully evaluated to ensure a balance between the desirable spread of the refractoriness-conferring genetic cargo and the avoidance of potentially unwanted outcomes such as spread to non-target populations. There is also a need to develop better estimates of the economics of such releases. We present here an evaluation of two such strategies using a biologically realistic mathematical model that simulates the resident Aedes aegypti mosquito population of Iquitos, Peru. One strategy uses the selfish element Medea, a non-limited element that could permanently spread over a large geographic area; the other strategy relies on Killer-Rescue genetic constructs, and has been predicted to have limited spatial and temporal spread. We simulate various operational approaches for deploying these genetic strategies, and quantify the optimal number of released transgenic mosquitoes needed to achieve definitive spread of Medea-linked genes and/or high frequencies of Killer-Rescue-associated elements. We show that for both strategies the most efficient approach for achieving spread of anti-pathogen genes within three years is generally to release adults of both sexes in multiple releases over time. Even though females in these releases should not transmit disease, there could be public concern over such releases, making the less efficient male-only release more practical. This study provides guidelines for operational approaches to population replacement genetic strategies, as well as illustrates the use of detailed spatial models to assist in safe and efficient implementation of such novel genetic strategies.     

Mitochondrial Portraits of Human Populations Using Median Networks

Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< ~50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.     

Diversity and Dynamics of Indigenous Rhizobium japonicum Populations

A simple method, based upon the separation of cellular proteins by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, has been devised for distinguishing between isolates of Rhizobium japonicum. Eleven laboratory strains, previously classified into five serogroups, were analyzed by gel electrophoresis. Groups determined subjectively according to protein patterns matched the serogroups, with one exception. Most strains within serogroups could be distinguished from one another. For studying the ecology of Rhizobium, an important advantage of this technique compared with serology or phage typing is that it discriminates among previously unencountered indigenous bacterial isolates as well as among known laboratory strains. SDS-gels were used to analyze the Rhizobium population of 500 nodules, sampled throughout the growing season, from soybeans at two different Wisconsin localities. Although the soybeans had been inoculated with laboratory strains of R. japonicum, indigenous R. japonicum predominated. At one location, 19 indigenous gel types were distinguished and classified mainly into four groups. At the other location, 18 gel types, falling mainly into three groups, were detected. The predominance of a particular group varied, in some cases dramatically, depending upon the time and depth of nodule formation.     

Forty Million Years of Independent Evolution: A Mitochondrial Gene and Its Corresponding Nuclear Pseudogene in Primates

Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model — the nucleotide composition — is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the “common ancestor” of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.[Reviewing Editor: Dr. Rafael Zardoya]     

Variability of Fragments of Nuclear Brca1 Gene,Exon 11, and Mitochondrial Cox1 Gene in House Mice Mus musculus

Molecular Biology - To clarify genetic differences between subspecies of the house mouse Mus musculus, their distribution, and hybridization, we first conducted a comparative analysis of...