Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios

Even though human and chimpanzee gene sequences are nearly 99% identical, sequence comparisons can nevertheless be highly informative in identifying biologically important changes that have occurred since our ancestral lineages diverged. We analyzed alignments of 7645 chimpanzee gene sequences to their human and mouse orthologs. These three-species sequence alignments allowed us to identify genes undergoing natural selection along the human and chimp lineage by fitting models that include parameters specifying rates of synonymous and nonsynonymous nucleotide substitution. This evolutionary approach revealed an informative set of genes with significantly different patterns of substitution on the human lineage compared with the chimpanzee and mouse lineages. Partitions of genes into inferred biological classes identified accelerated evolution in several functional classes, including olfaction and nuclear transport. In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders.     

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees

The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.     

猪MSTN基因生物信息学分析

[目的]对猪MSTN基因进行生物信息学分析。[方法]以从GenBank中检索到的猪、大鼠、小鼠、狗、绵羊、山羊、牛、黑猩猩、人、马、鸡和斑马鱼的MSTN基因CDS序列为材料,将该12个物种的MSTN蛋白序列调入DNAStar软件的Megalign程序,进行系统进化分析;并对猪MSTN基因的基本信息、内切酶图谱、编码蛋白二级结构、信号肽、跨膜结构以及蛋白质亚细胞定位进行分析。[结果]猪MSTN基因与大鼠、小鼠、狗、绵羊、山羊、牛、黑猩猩、人、马亲缘关系很近;该基因包含多个酶切位点;其编码的蛋白是一个疏水性不稳定蛋白,分子量为42 791.3 u,等电点为6.98,包含375个氨基酸残基;蛋白二级结构上,含有20.53%的α-螺旋(Helix)、4%β-转角(Turn)、53.07%无规则卷曲(Coil)、22.4%伸展条(extenden strand)和1个跨膜结构区域;该蛋白定位于细胞外,作为信号肽的可能性很大。[结论]该研究为猪MSTN基因的进一步分析研究提供了参考依据。     

Human-specific gain of function in a developmental enhancer

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.     

猪MSTN基因生物信息学分析(英文)

[目的]对猪MSTN基因其进行生物信息学分析。[方法]以从GenBank中检索到的猪、大鼠、小鼠、狗、绵羊、山羊、牛、黑猩猩、人、马、鸡和斑马鱼的MSTN基因CDS序列为材料,将该12个物种的MSTN蛋白序列调入DNAStar软件的Megalign程序,进行系统进化分析;并对猪MSTN基因的基本信息、内切酶图谱、编码蛋白二级结构、信号肽、跨膜结构以及蛋白质亚细胞定位进行分析。[结果]猪MSTN基因与大鼠、小鼠、狗、绵羊、山羊、牛、黑猩猩、人、马亲缘关系很近;该基因包含多个酶切位点;其编码的蛋白是一个疏水性不稳定蛋白,分子量为42791.3u,等电点为6.98,包含375个氨基酸残基;蛋白二级结构上,含有20.53%的α-螺旋(Helix)、4%β-转角(Turn)、53.07%无规则卷曲(Coil)、22.4%伸展条(extendenstrand)和1个跨膜结构区域;该蛋白定位于细胞外,作为信号肽的可能性很大。[结论]该研究为猪MSTN基因的进一步分析研究提供了参考依据。     

Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons

Long-range regulatory elements are difficult to discover experimentally; however, they tend to be conserved among mammals, suggesting that cross-species sequence comparisons should identify them. To search for regulatory sequences, we examined about 1 megabase of orthologous human and mouse sequences for conserved noncoding elements with greater than or equal to 70% identity over at least 100 base pairs. Ninety noncoding sequences meeting these criteria were discovered, and the analysis of 15 of these elements found that about 70% were conserved across mammals. Characterization of the largest element in yeast artificial chromosome transgenic mice revealed it to be a coordinate regulator of three genes, interleukin-4, interleukin-13, and interleukin-5, spread over 120 kilobases.     

From genotype to phenotype: systems biology meets natural variation

The promise that came with genome sequencing was that we would soon know what genes do, particularly genes involved in human diseases and those of importance to agriculture. We now have the full genomic sequence of human, chimpanzee, mouse, chicken, dog, worm, fly, rice, and cress, as well as those for a wide variety of other species, and yet we still have a lot of trouble figuring out what genes do. Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered.     

African populations and the evolution of human mitochondrial DNA.

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.     

不同物种ATGL基因部分序列的生物信息学分析

[目的]深入了解ATGL基因的遗传多样性以及不同物种ATGL基因间的分子系统进化关系。[方法]应用比较基因组学和生物信息学方法分析了8个物种ATGL基因的遗传多样性和分子系统进化。[结果]32条基因序列共检测到77个多态位点,发现12种单倍型。各物种间核苷酸歧异度和净遗传距离分别在0.005 48~0.197 37和0.004 39~0.197 37。分子系统进化树结果显示,人、猕猴、黑猩猩之间以及挪威鼠和家鼠之间的亲缘关系较近,而狗、牛与家鼠间的亲缘关系较远。人、家鼠和猪的非同义替换位点数明显高于同义替换位点数。各同源ATGL基因的有效密码子数和密码子偏爱指数分别在27.618~38.016和0.643~0.807。[结论]该结果为进一步研究AT-GL基因的生物学功能和确定动物脂肪沉积及肉质性状的候选分子标记提供了基础资料。     

Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs)

Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and evolutionary depth of their conservation remain unanswered. We have quantified levels and patterns of conservation of 191 CNGs of human chromosome 21 in 14 mammalian species. We found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials. The pattern of substitutions in CNGs differed from that seen in protein-coding and ncRNA genes and resembled that of protein-binding regions. About 0.3% to 1% of the human genome corresponds to a previously unknown class of extremely constrained CNGs shared among mammals.     

A human-specific gene in microglia

Recent studies have shown multiple differences between humans and apes in sialic acid (Sia) biology, including Siglecs (Sia-recognizing-Ig-superfamily lectins). Comparisons with the chimpanzee genome indicate that human SIGLEC11 emerged through human-specific gene conversion by an adjacent pseudogene. Conversion involved 5 cent untranslated sequences and the Sia-recognition domain. This human protein shows reduced binding relative to the ancestral form but recognizes oligosialic acids, which are enriched in the brain. SIGLEC11 is expressed in human but not in chimpanzee brain microglia. Further studies will determine if this event was related to the evolution of Homo.     

A fine-scale chimpanzee genetic map from population sequencing

To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but with exceptions, particularly in regions of chromosomal rearrangements and around the site of ancestral fusion in human chromosome 2. At fine scales, chimpanzee recombination is dominated by hotspots, which show no overlap with those of humans even though rates are similarly elevated around CpG islands and decreased within genes. The hotspot-specifying protein PRDM9 shows extensive variation among Western chimpanzees, and there is little evidence that any sequence motifs are enriched in hotspots. The contrasting locations of hotspots provide a natural experiment, which demonstrates the impact of recombination on base composition.     

Evolutionarily assembled cis-regulatory module at a human ciliopathy locus

Neighboring genes are often coordinately expressed within cis-regulatory modules, but evidence that nonparalogous genes share functions in mammals is lacking. Here, we report that mutation of either TMEM138 or TMEM216 causes a phenotypically indistinguishable human ciliopathy, Joubert syndrome. Despite a lack of sequence homology, the genes are aligned in a head-to-tail configuration and joined by chromosomal rearrangement at the amphibian-to-reptile evolutionary transition. Expression of the two genes is mediated by a conserved regulatory element in the noncoding intergenic region. Coordinated expression is important for their interdependent cellular role in vesicular transport to primary cilia. Hence, during vertebrate evolution of genes involved in ciliogenesis, nonparalogous genes were arranged to a functional gene cluster with shared regulatory elements.     

Classic selective sweeps were rare in recent human evolution

Efforts to identify the genetic basis of human adaptations from polymorphism data have sought footprints of "classic selective sweeps" (in which a beneficial mutation arises and rapidly fixes in the population).Yet it remains unknown whether this form of natural selection was common in our evolution. We examined the evidence for classic sweeps in resequencing data from 179 human genomes. As expected under a recurrent-sweep model, we found that diversity levels decrease near exons and conserved noncoding regions. In contrast to expectation, however, the trough in diversity around human-specific amino acid substitutions is no more pronounced than around synonymous substitutions. Moreover, relative to the genome background, amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations. These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.     

Chromosomal speciation and molecular divergence--accelerated evolution in rearranged chromosomes

Humans and their closest evolutionary relatives, the chimpanzees, differ in approximately 1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.     

Conservation of RET regulatory function from human to zebrafish without sequence similarity

Evolutionary sequence conservation is an accepted criterion to identify noncoding regulatory sequences. We have used a transposon-based transgenic assay in zebrafish to evaluate noncoding sequences at the zebrafish ret locus, conserved among teleosts, and at the human RET locus, conserved among mammals. Most teleost sequences directed ret-specific reporter gene expression, with many displaying overlapping regulatory control. The majority of human RET noncoding sequences also directed ret-specific expression in zebrafish. Thus, vast amounts of functional sequence information may exist that would not be detected by sequence similarity approaches.     

The shared antibiotic resistome of soil bacteria and human pathogens

Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (β-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.     

Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region

Sequences from the upstream and downstream flanking DNA regions of the psi eta-globin locus in Pan troglodytes (common chimpanzee), Gorilla gorilla (gorilla), and Pongo pygmaeus (orangutan, the closest living relative to Homo, Pan, and Gorilla) provided further data for evaluating the phylogenetic relations of humans and African apes. These newly sequenced orthologs [an additional 4.9 kilobase pairs (kbp) for each species] were combined with published psi eta-gene sequences and then compared to the same orthologous stretch (a continuous 7.1-kbp region) available for humans. Phylogenetic analysis of these nucleotide sequences by the parsimony method indicated (i) that human and chimpanzee are more closely related to each other than either is to gorilla and (ii) that the slowdown in the rate of sequence evolution evident in higher primates is especially pronounced in humans. These results indicate that features (for example, knuckle-walking) unique to African apes (but not to humans) are primitive and that even local molecular clocks should be applied with caution.