Evolutionary biology. Twinned genes live life in the fast lane

On page 1151, researchers describe new insights into how genes arise and fuel evolution. By trolling through sequence data for nine very distinct organisms, they have uncovered evidence that genes are copied far more frequently--and the duplicates are lost from the genome far faster--than researchers had thought. What's more, the work suggests that some duplicate genes play a key role in the evolution of new traits and in speciation.     

New genes in Drosophila quickly become essential

To investigate the origin and evolution of essential genes, we identified and phenotyped 195 young protein-coding genes, which originated 3 to 35 million years ago in Drosophila. Knocking down expression with RNA interference showed that 30% of newly arisen genes are essential for viability. The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal stage and also found in the larval stages. Lethality was attributed to diverse cellular and developmental defects, such as organ formation and patterning defects. These data suggest that new genes frequently and rapidly evolve essential functions and participate in development.     

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.     

Very low gene duplication rate in the yeast genome

The gene duplication rate in the yeast genome is estimated without assuming the molecular clock model to be approximately 0.01 to 0.06 per gene per billion years; this rate is two orders of magnitude lower than a previous estimate based on the molecular clock model. This difference is explained by extensive concerted evolution via gene conversion between duplicated genes, which violates the assumption of the molecular clock in the analyses of duplicated genes. The average length of the period of concerted evolution and the gene conversion rate are estimated to be approximately 25 million years and approximately 28 times the mutation rate, respectively.     

正选择驱动褪黑激素受体MT1与MT2基因的分化

【目的】研究褪黑激素受体（melatonin receptor,MTNR）基因的进化模式,为褪黑激素受体基因相关功能的研究提供理论参考。【方法】利用生物信息学的方法和软件对来自11个物种的褪黑激素受体1a（MT1）和褪黑激素受体1b（MT2）基因的系统发生关系、基因相似性、选择压力、选择方向等进行系统地分析。【结果】MT1和MT2基因可能由共同祖先基因通过基因重复产生, MT1可能保持着源基因的功能,MT2为新产生的功能基因。MT1基因在物种间的相似性极显著高于MT2基因（P＜0.01）;MT1基因主要受纯化选择,MT2基因受到显著的正选择;MT1与MT2基因均承受着较强的选择压力,且选择压力在2基因间无显著差异（P＞0.05）。【结论】MT1基因主要受纯化选择可能是MT1基因与动物季节性繁殖关联研究结论不统一的原因,MT2基因受正选择提示正选择可能是驱动MT2与MT1发生分化的重要动力。     

Genome evolution following host jumps in the Irish potato famine pathogen lineage

Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.     

Evolution of a vertebrate social decision-making network

Animals evaluate and respond to their social environment with adaptive decisions. Revealing the neural mechanisms of such decisions is a major goal in biology. We analyzed expression profiles for 10 neurochemical genes across 12 brain regions important for decision-making in 88 species representing five vertebrate lineages. We found that behaviorally relevant brain regions are remarkably conserved over 450 million years of evolution. We also find evidence that different brain regions have experienced different selection pressures, because spatial distribution of neuroendocrine ligands are more flexible than their receptors across vertebrates. Our analysis suggests that the diversity of social behavior in vertebrates can be explained, in part, by variations on a theme of conserved neural and gene expression networks.     

开放核心群育种体系(ONBS)研究 I.ONBS群体遗传学特征的计算机模拟

通过计算机模拟研究了开放核心群育种体系的群体遗传学特征，结果表明：配子抽样导致群体遗传特性的随机波动是小群体育种的一个技术难点．ＯＮＢＳ中连续迁移的效应往往导致亚群和总体间基因频率、群体均值、群体方差更加接近，群体间同质性增加．与ＣＮＢＳ相比，ＯＮＢＳ以其特有的迁移同质化效应，可以缓冲小群体复制育种中突出的源于配子抽样的群体遗传特性随机波动和抽样偏差，从而以渐进方式与总体保持遗传同质性．迁移和选择的联合遗传效应往往使得ＯＮＢＳ的遗传进展远大于封闭体系．     

Directional selection and the evolution of breeding date in birds

In many bird species, those pairs that breed earlier in the season have higher reproductive success than those that breed later. Since breeding date is known to be heritable, it is unclear why it does not evolve to an earlier time. Under assumptions outlined by Fisher, a model is developed that shows how breeding date may have considerable additive genetic variance, appear to be under directional selection, and yet not evolve. These results provide a general explanation for a persistent correlation of fitness with a variety of traits in natural populations.     

Massive horizontal gene transfer in bdelloid rotifers

Horizontal gene transfer in metazoans has been documented in only a few species and is usually associated with endosymbiosis or parasitism. By contrast, in bdelloid rotifers we found many genes that appear to have originated in bacteria, fungi, and plants, concentrated in telomeric regions along with diverse mobile genetic elements. Bdelloid proximal gene-rich regions, however, appeared to lack foreign genes, thereby resembling those of model metazoan organisms. Some of the foreign genes were defective, whereas others were intact and transcribed; some of the latter contained functional spliceosomal introns. One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution.     

Paucity of genes on the Drosophila X chromosome showing male-biased expression

Sex chromosomes are primary determinants of sexual dimorphism in many organisms. These chromosomes are thought to arise via the divergence of an ancestral autosome pair and are almost certainly influenced by differing selection in males and females. Exploring how sex chromosomes differ from autosomes is highly amenable to genomic analysis. We examined global gene expression in Drosophila melanogaster and report a dramatic underrepresentation of X-chromosome genes showing high relative expression in males. Using comparative genomics, we find that these same X-chromosome genes are exceptionally poorly conserved in the mosquito Anopheles gambiae. These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males.     

稻草复种模式下水稻不同品种不同播种量秧苗素质分析

稻草复种是辽宁农业职业技术学院近几年来研究的一种提高复种指数、提高单位面积经济效益的一项新的栽培模式,分析了不同水稻品种适宜的育秧密度,为稻草复种技术的推广提供了一定的技术参考。     

High resolution of mouse chromosomes: banding conservation between man and mouse

A detailed schematic representation of high-resolution G-banding patterns was prepared from elongated and finely banded mitotic chromosomes of the mouse. Such chromosomes can be obtained from both animal tissue and cell lines by a simple protocol, facilitating precise demarcation of breakpoints in chromosome rearrangements and aiding in the sublocalization of genes. Regions of subbanding homology were observed between human and mouse chromosomal segments known to have conserved gene assignments, an indication that, at the cytogenetic level, extensive regions of the mammalian genome may remain intact after 60 million years of species divergence.     

Magnetic Anomalies over the Mid-Atlantic Ridge near 27{degrees}N

Ten magnetic profiles across the mid-Atlantic ridge near 27 degrees N show trends that are parallel to the ridge axis and symmetrical about the ridge axis. The configuration of magnetic bodies that could account for the pattern supports the Vine and Matthews hypothesis for the origin of magnetic anomalies over oceanic ridges. A polarity-reversal time scale inferred from models for sea-floor spreading in the Pacific-Antarctic ridge and radiometrically dated reversals of the geomagnetic field indicates a spreading rate of 1.25 centimeters per year during the last 6 million years and a rate of 1.65 centimeters per year between 6 and 10 million years ago. A similar analysis of more limited data over the mid-Atlantic ridge near 22 degrees N also indicates a change in the spreading rate. Here a rate of 1.4 centimeters per year appears to have been in effect during the last 5 million years; between 5 and 9 million years ago, an increased rate of 1.7 centimeters per year is indicated. The time of occurrence and relative magnitude of these changes in the spreading rate, about 5 to 6 million years ago and 18 to 27 percent, respectively, accords with the spreading rate change implied for the Juan de Fuca ridge in the northeast Pacific.     

Gene flow and the geographic structure of natural populations

There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity. Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods show that species differ widely in the gene flow that they experience. Of particular interest are those species for which direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent past. Such species probably have undergone large-scale demographic changes relatively frequently.     

Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci

Independent domestication of sorghum, rice, and maize involved convergent selection for large seeds, reduced disarticulation of the mature inflorescence, and daylength-insensitive flowering. These similar phenotypes are largely determined by a small number of quantitative trait loci (QTLs) that correspond closely in the three taxa. The correspondence of these QTLs transcends 65 million years of reproductive isolation. This finding supports models of quantitative inheritance that invoke relatively few genes, obviates difficulties in map-based cloning of QTLs, and impels the comparative mapping of complex pheno-types across large evolutionary distances, such as those that separate humans from rodents and domesticated mammals.     

Local selection and latitudinal variation in a marine predator-prey interaction

Although pairs of species often interact over broad geographic ranges, few studies have explored how interactions vary across these large spatial scales. Surveys along 1500 kilometers of the Pacific coast of North America documented marked variation in the frequency of predation by the snail Nucella canaliculata on the intertidal mussel Mytilus californianus. Laboratory rearing experiments suggest that regional differences in drilling behavior have a genetic basis, and mitochondrial sequence variation confirms that gene flow is low among these snail populations. Marine communities separated by hundreds of kilometers may have intrinsically different dynamics, with interactions shaped by restricted gene flow and spatially varying selection.     

Burial rates, growth rates, and size distributions of deep-sea manganese nodules

The size distributions of deep-sea manganese nodules are consistent with a simple model of uniform growth at a few millimeters per million years and with the same probability of burial for all nodules, regardless of size. The model suggests that most nodules spend 1 million years or less on the sea floor.