Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences

Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review

Body fluid identification in crime scene investigations aids in reconstruction of crime scenes. Several studies have identified and reported differentially methylated sites (DMSs) and regions (DMRs) which differ between forensically relevant tissues (tDMRs) and body fluids. Diverse factors affect methylation patterns such as the environment, diets, lifestyle, disease, ethnicity, genetic variation, amongst others. Thus, it is important to analyse the stability of markers employed for forensic identification. Furthermore, even though epigenetic modifications are described as stable and heritable, epigenetic inheritance of potential markers for body fluid identification needs to be assessed in the long term. Here, we discuss the current status of reported DNA methylation-based markers and their verification studies. Such thorough investigation is crucial to develop a stable panel of DNA methylation-based markers for accurate body fluid identification.

Molecular discrimination of tall fescue morphotypes in association with Festuca relatives

Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute's core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. F. pratensis and F. arundinacea var. glaucescens, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and F. mairei (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both F. pratensis and F. mairei formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity.

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture

HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV's most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV's replication in cell culture. We compare our experimental measurements of each site's preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. Our data enable us to quantify the inherent mutational tolerance of each site in Env. We show that the epitopes of broadly neutralizing antibodies have a significantly reduced inherent capacity to tolerate mutations, rigorously validating a pervasive idea in the field. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env's evolution.

Sequence diversity and molecular evolutionary rates between buffalo and cattle

Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow. The cross-species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study, gene diversity between buffalo and cattle was determined using 86 gene orthologues. There was approximately 3% difference in all genes in terms of nucleotide diversity and 0.267 ± 0.134 in amino acids, indicating the possibility for successfully using cross-species strategies for genomic studies. There were significantly higher non-synonymous substitutions both in cattle and buffalo; however, there was similar difference in terms of dN- dS (4.414 versus 4.745) in buffalo and cattle, respectively. Higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure. Results for relative rate test were assessed with the chi-squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non-synonymous sites, indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes

Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.

Molecular adaptation of telomere associated genes in mammals

BACKGROUND

Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these traits, there are exceptions that warrant further investigation. Species such as naked mole rat, human and certain bat species all exhibit extreme longevity with respect to body size. It has long been established that telomeres and telomere maintenance have a clear role in ageing but it has not yet been established whether there is evidence for adaptation in telomere maintenance proteins that could account for increased longevity in these species.

RESULTS

Here we carry out a molecular investigation of selective pressure variation, specifically focusing on telomere associated genes across placental mammals. In general we observe a large number of instances of positive selection acting on telomere genes. Although these signatures of selection overall are not significantly correlated with either longevity or body size we do identify positive selection in the microbat species Myotis lucifugus in functionally important regions of the telomere maintenance genes DKC1 and TERT, and in naked mole rat in the DNA repair gene BRCA1.

CONCLUSION

These results demonstrate the multifarious selective pressures acting across the mammal phylogeny driving lineage-specific adaptations of telomere associated genes. Our results show that regardless of the longevity of a species, these proteins have evolved under positive selection thereby removing increased longevity as the single selective force driving this rapid rate of evolution. However, evidence of molecular adaptations specific to naked mole rat and Myotis lucifugus highlight functionally significant regions in genes that may alter the way in which telomeres are regulated and maintained in these longer-lived species.

Global patterns of diversity and selection in human tyrosinase gene

Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.

More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting

When speciation events occur in rapid succession, incomplete lineage sorting (ILS) can cause disagreement among individual gene trees. The probability that ILS affects a given locus is directly related to its effective population size (Ne ), which in turn is proportional to the recombination rate if there is strong selection across the genome. Based on these expectations, we hypothesized that low-recombination regions of the genome, as well as sex chromosomes and nonrecombining chromosomes, should exhibit lower levels of ILS. We tested this hypothesis in phylogenomic datasets from primates, the Drosophila melanogaster clade, and the Drosophila simulans clade. In all three cases, regions of the genome with low or no recombination showed significantly stronger support for the putative species tree, although results from the X chromosome differed among clades. Our results suggest that recurrent selection is acting in these low-recombination regions, such that current levels of diversity also reflect past decreases in the effective population size at these same loci. The results also demonstrate how considering the genomic context of a gene tree can assist in more accurate determination of the true species phylogeny, especially in cases where a whole-genome phylogeny appears to be an unresolvable polytomy.

Neurochemical organization of the vestibular brainstem in the common chimpanzee (Pan troglodytes)

Chimpanzees are one of the closest living relatives of humans. However, the cognitive and motor abilities of chimpanzees and humans are quite different. The fact that humans are habitually bipedal and chimpanzees are not implies different uses of vestibular information in the control of posture and balance. Furthermore, bipedal locomotion permits the development of fine motor skills of the hand and tool use in humans, suggesting differences between species in the structures and circuitry for manual control. Much motor behavior is mediated via cerebro-cerebellar circuits that depend on brainstem relays. In this study, we investigated the organization of the vestibular brainstem in chimpanzees to gain insight into whether these structures differ in their anatomy from humans. We identified the four nuclei of vestibular nuclear complex in the chimpanzee and also looked at several other precerebellar structures. The size and arrangement of some of these nuclei differed between chimpanzees and humans, and also displayed considerable inter-individual variation. We identified regions within the cytoarchitectonically defined medial vestibular nucleus visualized by immunoreactivity to the calcium-binding proteins calretinin and calbindin as previously shown in other species including human. We have found that the nucleus paramedianus dorsalis, which is identified in the human but not in macaque monkeys, is present in the chimpanzee brainstem. However, the arcuate nucleus, which is present in humans, was not found in chimpanzees. The present study reveals major differences in the organization of the vestibular brainstem among Old World anthropoid primate species. Furthermore, in chimpanzees, as well as humans, there is individual variability in the organization of brainstem nuclei.

Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds

Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.

Comparative genetic approaches to the evolution of human brain and behavior

With advances in genomic technologies, the amount of genetic data available to scientists today is vast. Genomes are now available or planned for 14 different primate species and complete resequencing of numerous human individuals from numerous populations is underway. Moreover, high-throughput deep sequencing is quickly making whole genome efforts within the reach of single laboratories allowing for unprecedented studies. Comparative genetic approaches to the identification of the underlying basis of human brain, behavior, and cognitive ability are moving to the forefront. Two approaches predominate: inter-species divergence comparisons and intra-species polymorphism studies. These methodological differences are useful for different time scales of evolution and necessarily focus on different evolutionary events in the history of primate and hominin evolution. Inter-species divergence is more useful in studying large scale primate, or hominoid, evolution whereas intra-species polymorphism can be more illuminating of recent hominin evolution. These differences in methodological utility also extend to studies of differing genetic substrates; current divergence studies focus primarily on protein evolution whereas polymorphism studies are substrate ambivalent. Some of the issues inherent in these studies can be ameliorated by current sequencing capabilities whereas others remain intractable. New avenues are also being opened that allow for the incorporation of novel substrates and approaches. In the post-genomic era, the study of human evolution, specifically as it relates to the brain, is becoming more complete focusing increasingly on the totality of the system and better conceptualizing the entirety of the genetic changes that have lead to the human phenotype today.

Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships

Non-human primate genetic research defines itself through comparisons to humans; few other species require the implicit comparative genomics approaches. Because of this, errors in the identification of non-human primate orthologs can have profound effects. Gene prediction algorithms can and have produced false transcripts that have become incorporated into commonly used databases and genomics portals. These false transcripts can arise from deficiencies in the algorithms themselves as well as through gaps and other problems in the genome assembly. Putative genes generated can not only miss microexons, but improperly incorporate non-coding sequence resulting in pseudogenes or other transcripts without biological relevance. False transcripts then become identified as orthologs to established human genes and are too often taken as gospel by unwary researchers. Here, the processes through which these errors propagate are isolated and methods are described for identifying false orthologs in databases with several representative errors illustrated. Through these steps any researcher seeking to make use of non-human primate genetic information will have the tools at their disposal to ascertain where errors exist and to remedy them once encountered.

Sequence assembly

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html.

High divergence in primate-specific duplicated regions: human and chimpanzee chorionic gonadotropin beta genes

Background

Low nucleotide divergence between human and chimpanzee does not sufficiently explain the species-specific morphological, physiological and behavioral traits. As gene duplication is a major prerequisite for the emergence of new genes and novel biological processes, comparative studies of human and chimpanzee duplicated genes may assist in understanding the mechanisms behind primate evolution. We addressed the divergence between human and chimpanzee duplicated genomic regions by using Luteinizing Hormone Beta (LHB)/Chorionic Gonadotropin Beta (CGB) gene cluster as a model. The placental CGB genes that are essential for implantation have evolved from an ancestral pituitary LHB gene by duplications in the primate lineage.

Results

We shotgun sequenced and compared the human (45,165 bp) and chimpanzee (39,876 bp) LHB/CGB regions and hereby present evidence for structural variation resulting in discordant number of CGB genes (6 in human, 5 in chimpanzee). The scenario of species-specific parallel duplications was supported (i) as the most parsimonious solution requiring the least rearrangement events to explain the interspecies structural differences; (ii) by the phylogenetic trees constructed with fragments of intergenic regions; (iii) by the sequence similarity calculations. Across the orthologous regions of LHB/CGB cluster, substitutions and indels contributed approximately equally to the interspecies divergence and the distribution of nucleotide identity was correlated with the regional repeat content. Intraspecies gene conversion may have shaped the LHB/CGB gene cluster. The substitution divergence (1.8–2.59%) exceeded two-three fold the estimates for single-copy loci and the fraction of transversional mutations was increased compared to the unique sequences (43% versus ~30%). Despite the high sequence identity among LHB/CGB genes, there are signs of functional differentiation among the gene copies. Estimates for d_n/d_s rate ratio suggested a purifying selection on LHB and CGB8, and a positive evolution of CGB1.

Conclusion

If generalized, our data suggests that in addition to species-specific deletions and duplications, parallel duplication events may have contributed to genetic differences separating humans from their closest relatives. Compared to unique genomic segments, duplicated regions are characterized by high divergence promoted by intraspecies gene conversion and species-specific chromosomal rearrangements, including the alterations in gene copy number.

Rate of recombinational deletion among human endogenous retroviruses

The fate of most human endogenous retroviruses (HERVs) has been to undergo recombinational deletion. This process involves homologous recombination between the flanking long terminal repeats (LTRs) of a full-length element, leaving a relic structure in the genome termed a solo LTR. We examined loci in one family, HERV-K(HML2), and found that the deletion rate decreased markedly with age: the rate among recently integrated loci was almost 200-fold higher than that among loci whose insertion predated the divergence of humans and chimpanzees (8 x 10(-5) and 4 x 10(-7) recombinational deletion events per locus per generation, respectively). One hypothesis for this finding is that increasing mutational divergence between the flanking LTRs reduces the probability of homologous recombination and thus the rate of solo LTR formation. Consistent with this idea, we were able to replicate the observed rates by a simulation in which the probability of recombinational deletion was reduced 10-fold by a single mutation and 100-fold by any additional mutations. We also discuss the evidence for other factors that may influence the relationship between locus age and the rate of deletion, for example, host recombination rates and selection, and highlight the consequences of recombinational deletion for dating recent HERV integrations.

Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata

Background

There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution.

Results

We generated a set of 66 intergenic sequences in Arabidopsis lyrata, a close relative of Arabidopsis thaliana. The intergenic regions included transposable element (TE) remnants and regions flanking the TEs. We verified orthology of these amplified regions both by comparison of existing A. lyrata – A. thaliana genetic maps and by using molecular features. We compared substitution rates among the 66 intergenic loci, which exhibit ~5-fold rate variation, and compared intergenic rates to a set of 64 orthologous coding sequences. Our chief observations were that the average rate of nucleotide substitution is slower in intergenic regions than in synonymous sites, that rate variation in both intergenic and coding regions correlate with GC content, that GC content alone is not sufficient to explain differences in rates between intergenic and coding regions, and that rates of evolution in intergenic regions correlate negatively with gene density.

Conclusion

Our observations indicated that mutation rates vary among genomics regions as a function of base composition, suggesting that previous observations of "selective constraint" on non-coding regions could more accurately be attributed to a GC effect instead of selection. The negative correlation between nucleotide substitution rate and gene density provides a potential neutral explanation for a previously documented correlation between gene density and polymorphism levels within A. thaliana. Finally, we discuss potential forces that could contribute to rapid synonymous rates, and provide evidence to suggest that transcription-related mutation contributes to rate differences between intergenic and synonymous sites.

Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome

The genetic basis of the phenotypic difference between human and chimpanzee is one of the most actively pursued issues in current genomics. Although the genomic divergence between the two species has been described, the transcriptomic divergence has not been well documented. Thus, we newly sequenced and analyzed chimpanzee full-length cDNAs (FLcDNAs) representing 87 protein-coding genes. The number of nucleotide substitutions and sites of insertions/deletions (indels) was counted as a measure of sequence divergence between the chimpanzee FLcDNAs and the human genome onto which the FLcDNAs were mapped. Difference in transcription start/termination sites (TSSs/TTSs) and alternative splicing (AS) exons was also counted as a measure of structural divergence between the chimpanzee FLcDNAs and their orthologous human transcripts (NCBI RefSeq). As a result, we found that transposons (Alu) and repetitive segments caused large indels, which strikingly increased the average amount of sequence divergence up to more than 2% in the 3'-UTRs. Moreover, 20 out of the 87 transcripts contained more than 10% structural divergence in length. In particular, two-thirds of the structural divergence was found in the 3'-UTRs, and variable transcription start sites were conspicuous in the 5'-UTRs. As both transcriptional and translational efficiency were supposed to be related to 5'- and 3'-UTR sequences, these results lead to the idea that the difference in gene regulation can be a major cause of the difference in phenotype between human and chimpanzee.

Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories

Sequencing of the human and chimpanzee genomes has revealed approximately 99% similarity in the coding sequence between both the species, which in no way parallels the observable phenotypic differences. Contribution of the non-coding sequences which comprise a bulk of the genome, in functional divergence between human and chimpanzee, is largely understudied. In this context, we have compared extents of divergence in the non-coding repetitive DNA in a data set of well-classified neuronal and housekeeping genes between human and chimpanzee. The coding regions of these genes have earlier been extensively compared between the two species. It was revealed that the neurodevelopmental genes show accelerated evolution compared to neurophysiology and housekeeping genes in human. In this study, comparative analysis in terms of repeat spectrum, divergence in dinucleotide content density, JC divergence and its partitioning in repeats versus unique regions and transcription factor binding sites indicate different extents of functional constraints associated with the non-coding repeat regions. The constraints are also different when the upstream and downstream genic regions are compared across the functional categories. The neurodevelopmental genes seem to diverge more in the genic regions, whereas the neurophysiology genes show higher divergence in the upstream 2 kb region. Most of the divergence observed in the housekeeping genes is contributed by repeats. We also observe an accumulation of function-specific transcription factor profiles in the human lineage. Interestingly, a major fraction of the regulatory sites in these regions is differently partitioned in the repetitive sequences which in turn is dependant upon the relative distribution of the repeats across the functional categories. Thus, differential distribution of repeats across the various functional categories could have substantial effects on genome wide regulation and structure. The insights obtained from this study further add a new facet to the contribution of non-coding factors especially repeats in divergence of human and chimpanzee.

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.

What makes us human: revisiting an age-old question in the genomic era

In 1970, Karl Pribram took on the immense challenge of asking the question, what makes us human? Nearly four decades later, the most significant finding has been the undeniable realization of how incredibly subtle and fine-scaled the unique biological features of our species must be. The recent explosion in the availability of large-scale sequence data, however, and the consequent emergence of comparative genomics, are rapidly transforming the study of human evolution. The field of comparative genomics is allowing us to reach unparalleled resolution, reframing our questions in reference to DNA sequence--the very unit that evolution operates on. But like any reductionist approach, it comes at a price. Comparative genomics may provide the necessary resolution for identifying rare DNA sequence differences in a vast sea of conservation, but ultimately we will have to face the challenge of figuring out how DNA sequence divergence translates into phenotypic divergence. Our goal here is to provide a brief outline of the major findings made in the study of human brain evolution since the Pribram lecture, focusing specifically on the field of comparative genomics. We then discuss the broader implications of these findings and the future challenges that are in store.

Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution

Sequence comparison of humans and chimpanzees is of interest to understand the mechanisms behind primate evolution. Here we present an independent analysis of human chromosome 21 and the high-quality BAC clone sequences of the homologous chimpanzee chromosome 22. In contrast to previous studies, we have used global alignment methods and Ensembl predictions of protein coding genes (n = 224) for the analysis. Divergence due to insertions and deletions (indels) along with substitutions was examined separately for different genomic features (coding, noncoding genic, and intergenic sequence). The major part of the genomic divergence could be attributed to indels (5.07%), while the nucleotide divergence was estimated as 1.52%. Thus the total divergence was estimated as 6.58%. When excluding repeats and low-complexity DNA the total divergence decreased to 2.37%. The chromosomal distribution of nucleotide substitutions and indel events was significantly correlated. To further examine the role of indels in primate evolution we focused on coding sequences. Indels were found within the coding sequence of 13% of the genes and approximately half of the indels have not been reported previously. In 5% of the chimpanzee genes, indels or substitutions caused premature stop codons that rendered the affected transcripts nonfunctional. Taken together, our findings demonstrate that indels comprise the majority of the genomic divergence. Furthermore, indels occur frequently in coding sequences. Our results thereby support the hypothesis that indels may have a key role in primate evolution.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences

BACKGROUND

Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages.

RESULTS

Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic sequence) were constructed using the human and dog genome assemblies as references. Genomic divergences and substitution rates were examined for each clone and for various sequence classes under different functional constraints. Analysis of these alignments revealed that the overall genomic divergences are relatively constant (0.32-0.37 change/site) for pairwise comparisons among cattle, dog and human; however substitution rates vary across genomic regions and among different sequence classes. A neutral mutation rate (2.0-2.2 x 10(-9) change/site/year) was derived from ancestral repetitive sequences, whereas the substitution rate in coding sequences (1.1 x 10(-9) change/site/year) was approximately half of the overall rate (1.9-2.0 x 10(-9) change/site/year). Relative rate tests also indicated that cattle have a significantly faster rate of substitution as compared to dog and that this difference is about 6%.

CONCLUSION

This analysis provides a large-scale and unbiased assessment of genomic divergences and regional variation of substitution rates among cattle, dog and human. It is expected that these data will serve as a baseline for future mammalian molecular evolution studies.

Hearing silence: non-neutral evolution at synonymous sites in mammals

Although the assumption of the neutral theory of molecular evolution - that some classes of mutation have too small an effect on fitness to be affected by natural selection - seems intuitively reasonable, over the past few decades the theory has been in retreat. At least in species with large populations, even synonymous mutations in exons are not neutral. By contrast, in mammals, neutrality of these mutations is still commonly assumed. However, new evidence indicates that even some synonymous mutations are subject to constraint, often because they affect splicing and/or mRNA stability. This has implications for understanding disease, optimizing transgene design, detecting positive selection and estimating the mutation rate.

Sequence diversity and rates of molecular evolution between sheep and cattle genes

Experiments that aim to identify genes of importance in sheep are currently inhibited by a paucity of genomic resources. One approach, therefore, is to exploit the wealth of data and associated capabilities becoming available for the bovine genome. Cross-species application of microarrays and comparative sequencing to identify single nucleotide polymorphisms are two possibilities; however, both are dependant on the level of nucleotide sequence similarity between the two species. This study used 120 gene orthologues consisting of over 60 kb of aligned sequence to estimate the gene diversity between cattle and sheep. Less than 3% of protein-coding nucleotide positions were found to be different, indicating that the prospect for successfully using cross-species strategies is high. Substitution at synonymous sites ranged between 6.9 and 7.7% (+/- 0.3%), and was higher than at non-synonymous sites (1.4-1.7 +/- 0.1%). The relative rate test was used to determine whether the observed mutation rates were constant between the two lineages. While the rate at synonymous sites appeared constant, the rate at non-synonymous sites was significantly higher within the caprinae lineage (sheep) when compared with bovinae (cattle; chi2 = 10.03; d.f. = 1, P < 0.01). This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae.

Variable molecular clocks in hominoids

Generation time is an important determinant of a neutral molecular clock. There are several human-specific life history traits that led to a substantially longer generation time in humans than in other hominoids. Indeed, a long generation time is considered an important trait that distinguishes humans from their closest relatives. Therefore, humans may exhibit a significantly slower molecular clock as compared to other hominoids. To investigate this hypothesis, we performed a large-scale analysis of lineage-specific rates of single-nucleotide substitutions among hominoids. We found that humans indeed exhibit a significant slowdown of molecular evolution compared to chimpanzees and other hominoids. However, the amount of fixed differences between humans and chimpanzees appears extremely small, suggesting a very recent evolution of human-specific life history traits. Notably, chimpanzees also exhibit a slower rate of molecular evolution compared to gorillas and orangutans in the regions analyzed.

Placing confidence limits on the molecular age of the human-chimpanzee divergence

Molecular clocks have been used to date the divergence of humans and chimpanzees for nearly four decades. Nonetheless, this date and its confidence interval remain to be firmly established. In an effort to generate a genomic view of the human-chimpanzee divergence, we have analyzed 167 nuclear protein-coding genes and built a reliable confidence interval around the calculated time by applying a multifactor bootstrap-resampling approach. Bayesian and maximum likelihood analyses of neutral DNA substitutions show that the human-chimpanzee divergence is close to 20% of the ape-Old World monkey (OWM) divergence. Therefore, the generally accepted range of 23.8-35 millions of years ago for the ape-OWM divergence yields a range of 4.98-7.02 millions of years ago for human-chimpanzee divergence. Thus, the older time estimates for the human-chimpanzee divergence, from molecular and paleontological studies, are unlikely to be correct. For a given the ape-OWM divergence time, the 95% confidence interval of the human-chimpanzee divergence ranges from -12% to 19% of the estimated time. Computer simulations suggest that the 95% confidence intervals obtained by using a multifactor bootstrap-resampling approach contain the true value with >95% probability, whether deviations from the molecular clock are random or correlated among lineages. Analyses revealed that the use of amino acid sequence differences is not optimal for dating human-chimpanzee divergence and that the inclusion of additional genes is unlikely to narrow the confidence interval significantly. We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations.

Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites

The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is approximately 10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is approximately 30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s approximately 0.25/Ne approximately 10(-5), where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries approximately 10(7) suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them.

A molecular cytogenetic study of chromosome evolution in chimpanzee

We applied multitude multicolor banding (mMCB) in combination with a novel FISH DNA probe set including subcentromeric, subtelomeric and whole chromosome painting probes (subCTM) to characterize a Pan paniscus (PPA) cell line. These powerful techniques allowed us to refine the breakpoints of a pericentric inversion on chimpanzee chromosome 4, and discovered a novel cryptic pericentric inversion in chimpanzee chromosome 11. mMCB provided a starting point for mapping and high resolution analysis of breakpoints on PPA chromosome 4, which are within a long terminal repeat (LTR) and surrounded by segmental duplications, as well as the integration/expansion sites of the interstitial heterochromatin on chimpanzee chromosomes 6 and 14. Moreover, we found evidence at hand for different types of heterochromatin in the chimpanzee genome. Finally, shedding new light on the human/chimpanzee speciation, karyotypes of three members of the genus Pan were studied by mMCB and no cytogenetic differences were found although the phylogenetic distance between these subspecies is suggested to be 2.5 million years.

Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals

Evolutionary rates are not uniformly distributed across the genome. Knowledge about the biological causes of this observation is still incomplete, but its exploration has provided valuable insight into the genomical, historical and demographical variables that influence rates of genetic divergence. Recent studies suggest a possible association between chromosomal rearrangements and regions of greater divergence, but evidence is limited and contradictory. Here, we test the hypothesis of a relationship between chromosomal rearrangements and higher rates of molecular evolution by studying the genomic distribution of divergence between 12,000 human-mouse orthologous genes. Our results clearly show that genes located in genomic regions that have been highly rearranged between the two species present higher rates of synonymous (0.7686 vs. 0.7076) and non-synonymous substitution (0.1014 vs. 0.0871), and that synonymous substitution rates are higher in genes close to the breakpoints of individual rearrangements. The many potential causes of such striking are discussed, particularly in the light of speciation models suggesting that chromosomal rearrangements may have contributed to some of the speciation processes along the human and mouse lineages. Still, there are other possible causes and further research is needed to properly explore them.

The scale of mutational variation in the murid genome

Mutation rates vary across mammalian genomes, but little is known about the scale over which this variation occurs. Knowledge of the magnitude and scale of mutational variation is required to understand the processes that drive mutation, and is essential in formulating a robust null hypothesis for comparative genomics studies. Here we estimate the scale of mutational variation in the murid genome by calculating the spatial autocorrelation of nucleotide substitution rates in ancestral repeats. Such transposable elements are good candidates for neutrally evolving sequence and therefore well suited for the study of mutation rate variation. We find that the autocorrelation coefficient decays to a value close to zero by approximately 15 Mb, with little apparent variation in mutation rate under 100 kb. We conclude that the primary scale over which mutation rates vary is subchromosomal. Furthermore, our analysis shows that within-chromosome mutational variability exceeds variation among chromosomes by approximately one order of magnitude. Thus, differences in mutation rate between different regions of the same chromosome frequently exceed differences both between whole autosomes and between autosomes and the X-chromosome. Our results indicate that factors other than the time spent in the male germ line are important in driving mutation rates. This raises questions about the biological mechanism(s) that produce new mutations and has implications for the study of male-driven evolution.

Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Interspecies comparisons of gene expression levels will increase our understanding of the evolution of transcriptional mechanisms and help to identify targets of natural selection. This approach holds particular promise for apes, as many human-specific adaptations are thought to result from differences in gene expression rather than in coding sequence. To date, however, all studies directly comparing interspecies gene expression have been performed on single-species arrays, so that it has been impossible to distinguish differential hybridization due to sequence mismatches from underlying expression differences. To evaluate the severity of this potential problem, we constructed a new multiprimate cDNA array using probes from human, chimpanzee, orangutan, and rhesus. We find a large effect of sequence divergence on hybridization signal, even in the closest pair of species, human and chimpanzee. By comparing single-species array analyses with results from multispecies arrays, we examine how estimates of differential gene expression are affected by sequence divergence. Our results indicate that naive use of single-species arrays in direct interspecies comparisons can yield spurious results.

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Olfactory receptor (OR) genes constitute the basis of the sense of smell and are encoded by the largest mammalian gene superfamily, with >1000 members. In humans, but not in mice or dogs, the majority of OR genes have become pseudogenes, suggesting that OR genes in humans evolve under different selection pressures than in other mammals. To explore this further, we compare the OR gene repertoire of human with its closest living evolutionary relative, by taking advantage of the recently sequenced genome of the chimpanzee. In agreement with previous reports based on a small number of ORs, we find that humans have a significantly higher proportion of OR pseudogenes than chimpanzees. Moreover, we can reject the possibility that humans have been accumulating OR pseudogenes at a constant neutral rate since the divergence of human and chimpanzee. The comparison of the two repertoires reveals two chimpanzee-specific OR subfamily expansions and three expansions specific to humans. It also suggests that a subset of OR genes are under positive selection in either the human or the chimpanzee lineage. Thus, although overall there is relaxed constraint on human olfaction relative to chimpanzee, species-specific sensory requirements appear to have shaped the evolution of the functional OR gene repertoires in both species.

Evolutionary Conservation of 5' upstream Sequence of Nine Genes between Human and Great Apes

Nucleotide sequences of nine 5' upstream gene regions for human, chimpanzee, gorilla, and orangutan were determined. We estimated nucleotide differences (d) for each region between human and great apes. The overall d was 0.027 (ranged from 0.004 to 0.052). Rates of nucleotide substitution were estimated by using d and divergence times of human, chimpanzee, gorilla, and orangutan. The overall rate of nucleotide substitution between human and other hominoids was estimated to be 0.52-0.85 x 10(-9). This rate in 5' upstream regions was lower than that of synonymous sites, suggesting that 5' upstream regions have evolved under some functional constraints. Because lower rates have been reported for coding sequences in primates compared to rodents, we also estimated the rate (1.17-1.76 x 10(-9)) of nucleotide substitutions for the corresponding 5' upstream regions in rodents (mouse/rat comparison). Thus the primate rate was lower than rodent rate also for the 5' upstream regions.

Accelerated Evolution of Nervous System Genes in the Origin of Homo sapiens

Human evolution is characterized by a dramatic increase in brain size and complexity. To probe its genetic basis, we examined the evolution of genes involved in diverse aspects of nervous system biology. We found that these genes display significantly higher rates of protein evolution in primates than in rodents. Importantly, this trend is most pronounced for the subset of genes implicated in nervous system development. Moreover, within primates, the acceleration of protein evolution is most prominent in the lineage leading from ancestral primates to humans. Thus, the remarkable phenotypic evolution of the human nervous system has a salient molecular correlate, i.e., accelerated evolution of the underlying genes, particularly those linked to nervous system development. In addition to uncovering broad evolutionary trends, our study also identified many candidate genes--most of which are implicated in regulating brain size and behavior--that might have played important roles in the evolution of the human brain.

Relaxation of selective constraint and loss of function in the evolution of human bitter taste receptor genes

Bitter taste perception prevents mammals from ingesting poisonous substances because many toxins taste bitter and cause aversion. We hypothesize that human bitter taste receptor (TAS2R) genes might be relaxed from selective constraints because of the change in diet, use of fire and reliance on other means of toxin avoidance that emerged in human evolution. Here, we examine the intra-specific variations of all 25 genes of the human TAS2R repertoire. Our data show hallmarks of neutral evolution, including similar rates of synonymous (d(S)) and non-synonymous (d(N)) nucleotide changes among rare polymorphisms, common polymorphisms and substitutions; no variation in d(N)/d(S) among functional domains; segregation of pseudogene alleles within species and fixation of loss-of-function mutations. These results, together with previous findings of large numbers of loss-of-function mutations in olfactory, pheromonal and visual sensory genes in humans, suggest surprisingly reduced sensory capabilities of humans in comparison with many other mammals.

Continued colonization of the human genome by mitochondrial DNA

Integration of mitochondrial DNA fragments into nuclear chromosomes (giving rise to nuclear DNA sequences of mitochondrial origin, or NUMTs) is an ongoing process that shapes nuclear genomes. In yeast this process depends on double-strand-break repair. Since NUMTs lack amplification and specific integration mechanisms, they represent the prototype of exogenous insertions in the nucleus. From sequence analysis of the genome of Homo sapiens, followed by sampling humans from different ethnic backgrounds, and chimpanzees, we have identified 27 NUMTs that are specific to humans and must have colonized human chromosomes in the last 4–6 million years. Thus, we measured the fixation rate of NUMTs in the human genome. Six such NUMTs show insertion polymorphism and provide a useful set of DNA markers for human population genetics. We also found that during recent human evolution, Chromosomes 18 and Y have been more susceptible to colonization by NUMTs. Surprisingly, 23 out of 27 human-specific NUMTs are inserted in known or predicted genes, mainly in introns. Some individuals carry a NUMT insertion in a tumor-suppressor gene and in a putative angiogenesis inhibitor. Therefore in humans, but not in yeast, NUMT integrations preferentially target coding or regulatory sequences. This is indeed the case for novel insertions associated with human diseases and those driven by environmental insults. We thus propose a mutagenic phenomenon that may be responsible for a variety of genetic diseases in humans and suggest that genetic or environmental factors that increase the frequency of chromosome breaks provide the impetus for the continued colonization of the human genome by mitochondrial DNA.

DNA from mitochondria has regularly inserted into the human nuclear genome. Some insertions are polymorphic, revealing that the invasion of the human genome is an ongoing process

Mutation rate variation in the mammalian genome

Recent advances in the large-scale sequencing of mammalian genomes have provided a means to study divergence in not only genic sequences but also in the non-coding bulk of DNA. There is evidence of significant variation in the levels of divergence between presumably neutral regions, pointing at an underlying variation in the rate of mutation across the genome. Apparently, such variation occurs on different scales, including sequence context effects (the influence of neighboring nucleotides on the rate of mutation at individual sites), variation within chromosomes (on the scales of kilobases as well as megabases), and between chromosomes (among autosomes as well as between autosomes and sex chromosomes). An important aspect for further research in this area is to study whether there is an ultimate evolutionary explanation for mutation rate variation within mammalian genomes.

Reduced polymorphism in the chimpanzee semen coagulating protein, semenogelin I

The semen of many primate species coagulates into a mating plug believed to prevent the sperm of subsequent mating events from accessing the ova. The texture of the coagulum varies among species: from a semisoft mass in humans to a firm plug in chimpanzees. In humans, a component of the coagulum, semenogelin I, also inhibits sperm motility. We tested the hypothesis that polymorphism and divergence at semenogelin I differ among hominoid species with different mating systems. Sequence data for the semenogelin I locus were obtained from 12 humans, 10 chimpanzees, 7 gorillas, and 1 bonobo. Mitochondrial D-loop data were collected from a subset of individuals to assess levels of variation at an unlinked locus. HKA tests using D-loop sequence data revealed a significant reduction of polymorphism at semenogelin I in chimpanzees, consistent with predictions of a selective sweep at this locus. This result was supported by independent HKA tests using polymorphism data from a putatively neutral locus from the literature. Humans show a similar trend toward reduced polymorphism, although HKA tests were only marginally significant. Gorilla sequence data show evidence of functional loss at the semenogelin I locus, indicated by stop codons within the putative open reading frame as well as high levels of polymorphism. Elevated Ka/Ks ratios within the Pan-Homo clade suggest a history of positive selection at semenogelin I. Our results suggest that there is a positive relationship between the intensity of sperm competition in a species and the strength of positive Darwinian selection on the seminal protein semenogelin I.

Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution

Human chromosome 18 differs from its homologues in the great apes by a pericentric inversion. We have identified a chimpanzee bacterial artificial chromosome that spans a region where a break is likely to have occurred in a human progenitor and have characterized the corresponding regions in both chimpanzees and humans. Interspecies sequence comparisons indicate that the ancestral break occurred between the genes ROCK1 and USP14. In humans, the inversion places ROCK1 near centromeric heterochromatin and USP14 adjacent to highly repetitive subtelomeric repeats. In addition, we provide evidence for a human segmental duplication that may have provided a mechanism for the inversion.

Natural selection on the olfactory receptor gene family in humans and chimpanzees

The olfactory receptor (OR) genes constitute the largest gene family in mammalian genomes. Humans have >1,000 OR genes, of which only approximately 40% have an intact coding region and are therefore putatively functional. In contrast, the fraction of intact OR genes in the genomes of the great apes is significantly greater (68%-72%), suggesting that selective pressures on the OR repertoire vary among these species. We have examined the evolutionary forces that shaped the OR gene family in humans and chimpanzees by resequencing 20 OR genes in 16 humans, 16 chimpanzees, and one orangutan. We compared the variation at the OR genes with that at intergenic regions. In both humans and chimpanzees, OR pseudogenes seem to evolve neutrally. In chimpanzees, patterns of variability are consistent with purifying selection acting on intact OR genes, whereas, in humans, there is suggestive evidence for positive selection acting on intact OR genes. These observations are likely due to differences in lifestyle, between humans and great apes, that have led to distinct sensory needs.

Low nucleotide diversity in chimpanzees and bonobos

Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (pi) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the pi value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The pi values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (N(e)) in the human lineage after the human-chimpanzee divergence, because a reduction in N(e) has a stronger effect on mtDNA diversity than on nuclear DNA diversity. Sequence data from this article have been deposited with the GenBank Data libraries under accession nos. AY 275957-AY 277244.

Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: enlarging genus Homo

What do functionally important DNA sites, those scrutinized and shaped by natural selection, tell us about the place of humans in evolution? Here we compare approximately 90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. On a time scale, the coding DNA divergencies separate the human-chimpanzee clade from the gorilla clade at between 6 and 7 million years ago and place the most recent common ancestor of humans and chimpanzees at between 5 and 6 million years ago. The evolutionary rate of coding DNA in the catarrhine clade (Old World monkey and ape, including human) is much slower than in the lineage to mouse. Among the genes examined, 30 show evidence of positive selection during descent of catarrhines. Nonsynonymous substitutions by themselves, in this subset of positively selected genes, group humans and chimpanzees closest to each other and have chimpanzees diverge about as much from the common human-chimpanzee ancestor as humans do. This functional DNA evidence supports two previously offered taxonomic proposals: family Hominidae should include all extant apes; and genus Homo should include three extant species and two subgenera, Homo (Homo) sapiens (humankind), Homo (Pan) troglodytes (common chimpanzee), and Homo (Pan) paniscus (bonobo chimpanzee).

Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes

Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%-60% higher mutation rate in exons than in noncoding DNA. We propose a differential CpG content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. We find that the increased exonic rate is the result of the relative overabundance of synonymous sites involved in CpG dinucleotides, as the evolutionary divergence in non-CpG sites is similar in noncoding DNA and synonymous sites of exons. Expectations and predictions of our hypothesis are confirmed in comparisons involving more distantly related species, including human-orangutan, human-baboon, and human-macaque. Our results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms (SNPs) in the synonymous sites of exons compared to the noncoding regions.

Analysis of 5'-end sequences of chimpanzee cDNAs

We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. Randomly selected clones from the libraries were subjected to one-pass sequencing from their 5'-ends. As a result, we collected 6813 chimpanzee cDNA sequences longer than 400 bp. Homology search against human mRNA sequences (RefSeq mRNAs) revealed that our collection included sequences of 1652 putative chimpanzee genes. In order to calculate the sequence identity between human and chimpanzee homologs, we constructed 5'-end consensus sequences of 226 chimpanzee genes by aligning at least three sequences for individual genes. Sequence identity was estimated by comparing these consensus sequences and the corresponding sequences of their human homologs. The average sequence identity of the 5'-end cDNAs was 99.30%. Those of the 5'-UTRs and CDSs were 98.79% and 99.42%, respectively. The results confirmed that human and chimpanzee genes are highly conserved at the nucleotide level. As for amino acids, the average sequence identity was 99.44%. The average synonymous (K(S)) and nonsynonymous (K(A)) divergences were estimated to be 1.33% and 0.28%, respectively.

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1-2 x 10(-9) substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%-20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.

The mosaic that is our genome

The discovery of the basis of genetic variation has opened inroads to understanding our history as a species. It has revealed the remarkable genetic similarity we share with other individuals as well as with our closest primate relatives. To understand what make us unique, both as individuals and as a species, we need to consider the genome as a mosaic of discrete segments, each with its own unique history and relatedness to different contemporary and ancestral individuals.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements active only before the human-mouse speciation, and (3) the nonaligning fraction of human DNA that is nonrepetitive or in ancestral repeats; and three derived from human genome data alone, consisting of (4) SNP density, (5) frequency of insertion of transposable elements, and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of "neutral" sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary significantly in megabase-sized regions genome-wide, and many vary together. This indicates that some regions of a genome change slowly by all processes that alter DNA, and others change faster. Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse.