Significance of enamel thickness in hominoid evolution

Enamel thickness has assumed unique importance in the debate about the hominid status of Ramapithecus, despite the fact that there is little agreement about the meaning of 'thick enamel' or the significance of enamel thickness for hominoid taxonomy. My aim here is to evaluate the usefulness of enamel thickness and microstructure as characteristics for determining the relationships of the later Miocene hominoids, based both on a quantitative study of enamel thickness in extant hominoids and four species of later Miocene Sivapithecus (including 'Ramapithecus') and on scanning electron microscope analysis of enamel microstructure. Four categories of enamel thickness are defined metrically here and have been related to enamel microstructure and developmental rates. Thin fast-formed (pattern 3) enamel represents the ancestral condition in hominoids; it increased developmentally to thick pattern 3 enamel in the great ape and human clade and that condition is primitively retained in Homo and in the fossil hominoid Sivapithecus (including 'Ramapithecus'). Enamel thickness has been secondarily reduced in the African apes and also, although at a different rate and extent, in the orang-utan. Thick enamel, previously the most important characteristic in arguments about the earliest hominid, does not therefore identify a hominid.     

Sequence organization and genomic complexity of primate theta 1 globin gene, a novel alpha-globin-like gene

The alpha-like and beta-like globin genes have provided a paradigm for the study of molecular evolution and regulation of multigene families in eukaryotes. The human alpha-globin gene cluster, which is on chromosome 16 (ref. 1), consists of six genes arranged in the order 5'-zeta(embryonic)-psi zeta-psi alpha 2-psi alpha 1-alpha 2(adult)-alpha 1(adult)-3'. DNA sequencing data have demonstrated that zeta (ref. 6) and alpha 2 (or alpha 1, refs 7-9) are the embryonic and adult genes, respectively, while psi zeta (ref. 6), psi alpha 2 (ref. 5) psi alpha 1 (ref. 10) are all inactive pseudogenes. Restriction mapping analysis has shown that the structure of this locus in several anthropoid primates is nearly identical to that of the human. Recently, we have isolated the adult alpha-globin gene region from orang-utan, olive baboon and rhesus macaque by molecular cloning. We report here the complete nucleotide sequence of a gene located immediately downstream from the adult alpha 1-globin gene of the orang-utan, along with its flanking DNA. We designate this gene as theta 1, and show that it contains the essential sequence elements required for an expressive gene. The putative polypeptide is 141 amino acids long, identical to that of the alpha- or zeta-globin, but its predicted amino-acid sequence is nearly as different from the orang-utan alpha-globin (55 differences) as the human zeta-globin is from the human alpha-globin (59 differences), suggesting an ancient history for the theta 1-globin gene. Results of blot hybridization experiments using the cloned orang-utan theta 1 gene sequence as probe demonstrate a similar alpha 2-alpha 1-theta 1 linkage map existing in the human genome. Furthermore, multiple copies of sequences homologous to the theta 1 gene are detected in both human and orang-utan. These results cast a new light on the primate alpha-globin gene family, and have intriguing implications for the existence of previously unreported, functional globin-like gene(s) in the primate genomes.     

Insights into hominid evolution from the gorilla genome sequence

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.     

The bonobo genome compared with the chimpanzee and human genomes

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.     

Evolution and environment in the Hominoidea.

Between 10 and 20 million years ago, a variety of hominoid primates lived in Africa, Europe and Asia. The question of which of these, if any, lie closest to the ancestries of humans and modern apes remains a lively source of debate. Recent fossil discoveries, though, shed light on the environments in which the various groups of hominoid emerged and, it is hoped, on their evolution. But the lack of a hominid fossil record before about 5 million years ago--and any fossil record for the African apes--is still a frustrating barrier.     

Ramapithecines from China: evidence from tooth dimensions

Data obtained from ramapithecine specimens found in Asia, Africa and Europe have suggested the existence of two major subgroups, Ramapithecus and Sivapithecus, with Ramapithecus having pre-human status. Recently, however, it has been proposed that the fossils all belong to a single group, Sivapithecus, which is more closely related to the apes, in particular the orang-utan. Here we analyse data from a series of similar fossils which have been found in late Miocene coalfields in Lufeng, Yunnan Province, China. These include a number of almost complete jaws and five partial skulls which are more complete than any others so far known. A statistical analysis of the overall dimensions of the large number of teeth included in these finds shows that the differences between the groups previously assigned to Ramapithecus and Sivapithecus are greater than those found between the sexes in the most sexually dimorphic of the living great apes. Within the groups the distribution is bimodal and we suggest each group contains sex subgroups.     

Unexpectedly similar rates of nucleotide substitution found in male and female hominids

In 1947, it was suggested that, in humans, the mutation rate is dramatically higher in the male germ line than in the female germ line. This hypothesis has been supported by the observation that, among primates, Y-linked genes evolved more rapidly than homologous X-linked genes. Based on these evolutionary studies, the ratio (alpha(m)) of male to female mutation rates in primates was estimated to be about 5. However, selection could have skewed sequence evolution in introns and exons. In addition, some of the X-Y gene pairs studied lie within chromosomal regions with substantially divergent nucleotide sequences. Here we directly compare human X and Y sequences within a large region with no known genes. Here the two chromosomes are 99% identical, and X-Y divergence began only three or four million years ago, during hominid evolution. In apes, homologous sequences exist only on the X chromosome. We sequenced and compared 38.6 kb of this region from human X, human Y, chimpanzee X and gorilla X chromosomes. We calculated alpha(m) to be 1.7 (95% confidence interval 1.15-2.87), significantly lower than previous estimates in primates. We infer that, in humans and their immediate ancestors, male and female mutation rates were far more similar than previously supposed.     

Evidence that the recently discovered theta 1-globin gene is functional in higher primates

A new subfamily of the alpha-globin-like family has recently been identified in higher primates, rabbit, galago and possibly the horse. One member of this subfamily, theta 1, is downstream from the adult alpha 1-globin gene. In orang-utan, but not in rabbit or galago, the theta 1-gene appears to be structurally intact, suggesting that it may be functional in this species. The orang-utan theta 1-gene possesses initiation and termination codons, and the predicted polypeptide differs from the orang-utan alpha 1-globin by 55 amino acids. The upstream promoter boxes CCAAT and ATA are present, although approximately 150 base pairs (bp) farther upstream than in the alpha 1-gene. This structural difference in the promoter between the orang-utan theta 1- and alpha 1-genes has led Proudfoot to speculate that the theta 1-gene may be inactive. We have now cloned the theta 1- and alpha 1-globin genes from the olive baboon, and have compared their sequences with those of orang-utan. The unique promoter structure of the orang-utan theta 1-gene is highly conserved in baboon, although the orang-utan and baboon diverged nearly 30 million years ago. The coding sequences of the two theta 1-genes differ by only 6.3% with 22 out of 27 nucleotide substitutions being codon third position silent changes. These data support the view that the theta 1-gene has been functional in the baboon, orang-utan, and by implication, in man. We also estimate that the duplication event generating the theta 1- and alpha-globin-like subfamilies may have occurred as much as 260 million years ago.     

Genetic evidence for complex speciation of humans and chimpanzees

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human-chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.     

Evolution of type C viral genes: evidence for an Asian origin of man.

Old World monkeys and apes, including man, possess, as a normal component of their cellular DNA, gene sequences (virogenes) related to the RNA of a virus isolated from baboons. A comparison of the viral gene sequences and the other cellular sequences distinguishes those Old World monkeys and apes that have evolved in Africa from those that have evolved in Asia. Among the apes, only gorilla and chimpanzee seem by these criteria to be African, whereas gibbon, orang-utan and man are identified as Asian, leading us to conclude that most of man's evolution has occurred outside Africa.     

Engineering evolution to study speciation in yeasts

The Saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids. A retrospective analysis of their genomes revealed that translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation). However, that analysis was unable to infer what contribution such rearrangements make to reproductive isolation between these organisms. Here, we report experiments that take an interventionist, rather than a retrospective approach to studying speciation, by reconfiguring the Saccharomyces cerevisiae genome so that it is collinear with that of Saccharomyces mikatae. We demonstrate that this imposed genomic collinearity allows the generation of interspecific hybrids that produce a large proportion of spores that are viable, but extensively aneuploid. We obtained similar results in crosses between wild-type S. cerevisiae and the naturally collinear species Saccharomyces paradoxus, but not with non-collinear crosses. This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism for the generation of redundancy in the S. cerevisiae genome.     

Ancient co-speciation of simian foamy viruses and primates

Although parasite-host co-speciation is a long-held hypothesis, convincing evidence for long-term co-speciation remains elusive, largely because of small numbers of hosts and parasites studied and uncertainty over rates of evolutionary change. Co-speciation is especially rare in RNA viruses, in which cross-species transfer is the dominant mode of evolution. Simian foamy viruses (SFVs) are ubiquitous, non-pathogenic retroviruses that infect all primates. Here we test the co-speciation hypothesis in SFVs and their primate hosts by comparing the phylogenies of SFV polymerase and mitochondrial cytochrome oxidase subunit II from African and Asian monkeys and apes. The phylogenetic trees were remarkably congruent in both branching order and divergence times, strongly supporting co-speciation. Molecular clock calibrations revealed an extremely low rate of SFV evolution, 1.7 x 10(-8) substitutions per site per year, making it the slowest-evolving RNA virus documented so far. These results indicate that SFVs might have co-speciated with Old World primates for at least 30 million years, making them the oldest known vertebrate RNA viruses.     

Periodicity of Retzius lines in fossil <Emphasis Type="Italic">Pongo</Emphasis> from South China

Periodicity of Retzius lines is a key factor in dental development. In this study, we examined the periodicity of Retzius lines in fossil Pongo from South China using polarized light microscope observation of dental ground sections. The periodicities all of the 15 teeth were 9 d. Comparisons of periodicity were made with extant primates, fossil apes and hominins. Periodicity of fossil Pongo from South China was relatively long but fell within the variation of extant Pongo, Gorilla and modern human, and longer than periodicity of Pan and other extant primates. Fossil Pongo from South China was similar to Lufengpithecus and Sivapithecus, shorter than Gigantopithecus and longer than European and African fossil apes and most early hominins in periodicity. Generally, the periodicities of Asian large-body fossil apes were longer than the periodicities of European and African large-body fossil apes in Miocene. Difference among species and trend of evolution in periodicity were analyzed and discussed. We found that periodicity might gradually increase from Proconsul in early Miocene to several fossil apes in Miocene and then Gigantopithecus in Pleistocene. In addition, this study made correlate analysis between periodicity and body mass respectively in males and females of six extant apes and five fossil apes, and found that periodicity positively correlated with body mass.     

Virtual cranial reconstruction of Sahelanthropus tchadensis

Previous research in Chad at the Toros-Menalla 266 fossiliferous locality (about 7 million years old) uncovered a nearly complete cranium (TM 266-01-60-1), three mandibular fragments and several isolated teeth attributed to Sahelanthropus tchadensis. Of this material, the cranium is especially important for testing hypotheses about the systematics and behavioural characteristics of this species, but is partly distorted from fracturing, displacement and plastic deformation. Here we present a detailed virtual reconstruction of the TM 266 cranium that corrects these distortions. The reconstruction confirms that S. tchadensis is a hominid and is not more closely related to the African great apes. Analysis of the basicranium further indicates that S. tchadensis might have been an upright biped, suggesting that bipedalism was present in the earliest known hominids, and probably arose soon after the divergence of the chimpanzee and human lineages.     

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.     

Chromosomal evolution in Saccharomyces

The chromosomal speciation model invokes chromosomal rearrangements as the primary cause of reproductive isolation. In a heterozygous carrier, chromosomes bearing reciprocal translocations mis-segregate at meiosis, resulting in reduced fertility or complete sterility. Thus, chromosomal rearrangements act as a post-zygotic isolating mechanism. Reproductive isolation in yeast is due to post-zygotic barriers, as many species mate successfully but the hybrids are sterile. Reciprocal translocations are thought to be the main form of large-scale rearrangement since the hypothesized duplication of the whole yeast genome 10(8) years ago. To test the chromosomal speciation model in yeast, we have characterized chromosomal translocations among the genomes of six closely related species in the Saccharomyces 'sensu stricto' complex. Here we show that rearrangements have occurred between closely related species, whereas more distant ones have colinear genomes. Thus, chromosomal rearrangements are not a prerequisite for speciation in yeast and the rate of formation of translocations is not constant. These rearrangements appear to result from ectopic recombination between Ty elements or other repeated sequences.     

The oldest known anthropoid postcranial fossils and the early evolution of higher primates

The middle Eocene primate family Eosimiidae, which is known from sites in central and eastern China and Myanmar, is central to efforts to reconstruct the origin and early evolution of anthropoid or 'higher' primates (monkeys, apes and humans). Previous knowledge of eosimiid anatomy has been restricted to the dentition and an isolated petrosal bone, and this limited anatomical information has led to conflicting interpretations of early anthropoid phylogeny. Here we describe foot bones of Eosimias from the same middle Eocene sites in China that yield abundant dental remains of this primate. Tarsals of Eosimias show derived anatomical traits that are otherwise restricted to living and fossil anthropoids. These new fossils substantiate the anthropoid status of Eosimias and clarify the phylogenetic position of anthropoids with respect to other major primate clades. Early anthropoids possessed a mosaic of primitive and derived traits in their postcranial skeletons, reflecting their derivation from haplorhine ancestors that retained many prosimian-like features.     

A new orang-utan relative from the Late Miocene of Thailand

The fossil record of the living great apes is poor. New fossils from undocumented areas, particularly the equatorial forested habitats of extant hominoids, are therefore crucial for understanding their origins and evolution. Two main competing hypotheses have been proposed for orang-utan origins: dental similarities support an origin from Lufengpithecus, a South Chinese and Thai Middle Miocene hominoid; facial and palatal similarities support an origin from Sivapithecus, a Miocene hominoid from the Siwaliks of Indo-Pakistan. However, materials other than teeth and faces do not support these hypotheses. Here we describe the lower jaw of a new hominoid from the Late Miocene of Thailand, Khoratpithecus piriyai gen. et sp. nov., which shares unique derived characters with orang-utans and supports a hypothesis of closer relationships with orang-utans than other known Miocene hominoids. It can therefore be considered as the closest known relative of orang-utans. Ancestors of this great ape were therefore evolving in Thailand under tropical conditions similar to those of today, in contrast with Southern China and Pakistan, where temperate or more seasonal climates appeared during the Late Miocene.     

Comparative analyses of multi-species sequences from targeted genomic regions

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.     

Juvenile hominoid cranium from the terminal Miocene of Yunnan, China

Fossil apes are known from several late Miocene localities in Yunnan Province, southwestern China, principally from Shihuiba (Lufeng) and the Yuanmou Basin, and represent three species of Lufengpithecus. They mostly comprise large samples of isolated teeth, but there are also several partial or complete adult crania from Shihuiba and a single juvenile cranium from Yuanmou. Here we describe a new, relatively complete and largely undistorted juvenile cranium from the terminal Miocene locality of Shuitangba, also in Yunnan. It is only the second ape juvenile cranium recovered from the Miocene of Eurasia and it is provisionally assigned to the species present at Shihuiba, Lufengpithecus lufengensis. Lufengpithecus has most often been linked to the extant orangutan, Pongo pygmaeus, but recent studies of the crania from Shihuiba and Yuanmou have demonstrated that this is unlikely. The new cranium reinforces the view that Lufengpithecus represents a distinct, late surviving lineage of large apes in the late Miocene of East Asia that does not appear to be closely affiliated with any extant ape lineage. It substantially increases knowledge of cranial morphology in Lufengpithecus and demonstrates that species of this genus represent a morphologically diverse radiation of apes, which is consistent with the dynamic tectonic and biotic milieu of southwestern China in the late Miocene.