Molecular evolution of the psi eta-globin gene locus: gibbon phylogeny and the hominoid slowdown

An 8.4-kb genomic region spanning both the psi eta-globin gene locus and flanking DNA was sequenced from the common gibbon (Hylobates lar). In addition, sequencing of the entire orthologous region from galago (Galago crassicaudatus) was completed. The gibbon and galago sequences, along with published orthologous sequences from 10 other species, were aligned. These noncoding nucleotide sequences represented four human alleles, four apes (chimpanzee, gorilla, organgutan, and gibbon), an Old World monkey (rhesus monkey), two New World monkeys (spider and owl monkeys), tarsier, two strepsirhines (galago and lemur), and goat. Divergence and maximum parsimony analyses of the psi eta genomic region first groups humans and chimpanzees and then, at progressively more ancient branch points, successively joins gorillas, orangutans, gibbons, Old World monkeys, New World monkeys, tarsiers, and strepsirhines (the lemuriform-lorisiform branch of primates). This cladistic pattern supports the taxonomic grouping of all extant hominoids into family Hominidae, the division of Hominidae into subfamilies Hylobatinae (gibbons) and Homininae, the division of Homininae into tribes Pongini (orangutans) and Hominini, and the division of Hominini into subtribes Gorillina (gorillas) and Hominina (chimpanzees and humans). The additional gibbon and galago sequence data provide further support for the occurrence of a graded evolutionary-rate slowdown in the descent of simian primates, with the slowing rate being more pronounced in the great-ape and human lineages than in the gibbon or monkey lineages. A comparison of global versus local molecular clocks reveals that local clock predictions, when focused on a specific number of species within a narrow time frame, provide a more accurate estimate of divergence dates than do those of global clocks.     

Chromosomal phylogeny and evolution of gibbons (Hylobatidae)

Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to be picked up.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

A Shared Pattern of Postnatal Endocranial Development in Extant Hominoids

By comparing species-specific developmental patterns, we can approach the question of how development shapes adult morphology and contributes to the evolution of novel forms. Studies of evolutionary changes to brain development in primates can provide important clues about the emergence of human cognition, but are hindered by the lack of preserved neural tissue in the fossil record. As a proxy, we study the shape of endocasts, virtual imprints of the endocranial cavity, using 3D geometric morphometrics. We have previously demonstrated that the pattern of endocranial shape development is shared by modern humans, chimpanzees and Neanderthals after the first year of life until adulthood. However, whether this represents a common hominoid mode of development is unknown. Here, we present the first characterization and comparison of ontogenetic endocranial shape changes in a cross-sectional sample of modern humans, chimpanzees, gorillas, orangutans and gibbons. Using developmental simulations, we demonstrate that from late infancy to adulthood ontogenetic trajectories are similar among all hominoid species, but differ in the amount of shape change. Furthermore, we show that during early ontogeny gorillas undergo more pronounced shape changes along this shared trajectory than do chimpanzees, indicative of a dissociation of size and shape change. As shape differences between species are apparent in even our youngest samples, our results indicate that the ontogenetic trajectories of extant hominoids diverged at an earlier stage of ontogeny but subsequently converge following the eruption of the deciduous dentition.     

Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster.

Additional DNA sequence information from a range of primates, including 13.7 kb from pygmy chimpanzee (Pan paniscus), was added to data sets of beta-globin gene cluster sequence alignments that span the gamma 1, gamma 2, and psi eta loci and their flanking and intergenic regions. This enlarged body of data was used to address the issue of whether the ancestral separations of gorilla, chimpanzee, and human lineages resulted from only one trichotomous branching or from two dichotomous branching events. The degree of divergence, corrected for superimposed substitutions, seen in the beta-globin gene cluster between human alleles is about a third to a half that observed between two species of chimpanzee and about a fourth that between human and chimpanzee. The divergence either between chimpanzee and gorilla or between human and gorilla is slightly greater than that between human and chimpanzee, suggesting that the ancestral separations resulted from two closely spaced dichotomous branchings. Maximum parsimony analysis further strengthened the evidence that humans and chimpanzees share the longest common ancestry. Support for this human-chimpanzee clade is statistically significant at P = 0.002 over a human-gorilla clade or a chimpanzee-gorilla clade. An analysis of expected and observed homoplasy revealed that the number of sequence changes uniquely shared by human and chimpanzee lineages is too large to be attributed to homoplasy. Molecular clock calculations that accommodated lineage variations in rates of molecular evolution yielded hominoid branching times that ranged from 17-19 million years ago (MYA) for the separation of gibbon from the other hominoids to 5-7 MYA for the separation of chimpanzees from humans. Based on the relatively late dates and mounting corroborative evidence from unlinked nuclear genes and mitochondrial DNA for the close sister grouping of humans and chimpanzees, a cladistic classification would place all apes and humans in the same family. Within this family, gibbons would be placed in one subfamily and all other extant hominoids in another subfamily. The later subfamily would be divided into a tribe for orangutans and another tribe for gorillas, chimpanzees, and humans. Finally, gorillas would be placed in one subtribe with chimpanzees and humans in another, although this last division is not as strongly supported as the other divisions.     

The human SDF1 gene polymorphism is located on a mutational hot spot that was identified by the hominoid genome study.

Nucleotide sequences of a part of the stromal cell-derived factor-1 (SDF-1) gene 3' untranslated region were studied among hominoids (chimpanzees, gorillas, orangutans and gibbons). An identical sequence to the human SDF1-3'G allele was found in chimpanzees and gibbons, whereas that to the 3'A allele was found in gorillas. Based on the sequence data and the hominoid phylogenetic relation, it was suggested that an adenine nucleotide at nucleotide position (np) 801 in humans and gorillas was independently introduced into each lineage after the specific divergence and an ancestral hominoid sequence of this site (np 799-802) was deduced as CCGG. The present data showing a mutational hot spot on this site suggest the possible presence of multiple origins of the worldwide distribution of the SDF1-3'A allele in humans.     

Relative strength of the tibia and fibula and locomotor behavior in hominoids

The fibula has rarely been considered in comparative morphological studies, probably due to its relatively minor role in carrying mechanical loads. However, some differences in morphology (and inferred function) of the fibula between humans and apes, and within apes, have been noted and related to differences in positional behavior. Therefore, the study of tibiofibular relations may be useful in characterizing such differences. This study examines cross-sectional geometric (CSG) properties (cortical area and polar section modulus, Z(p)) of the tibia and fibula at mid-diaphysis across a sample (n=87) of humans, chimpanzees, gorillas, orangutans, and gibbons. The fibula is compared against the tibia in the different taxa. The results indicate that the robusticity of the fibula relative to that of the tibia can be explained in terms of differences in positional behavior. In particular, hominoids that are more arboreal (i.e., gibbons, orangutans, and chimpanzees) possess a relatively more robust fibula than do hominoids that are more terrestrial (i.e., gorillas and humans). The difference appears to be a consequence of the more mobile fibula and more adducted position of the hindlimb necessary in an arboreal environment. Apart from providing the first CSG data on the fibula, these results may be helpful in reconstructing the locomotor behavior of fossil hominoids.     

DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set

Summary The living hominoids are human, the two species of chimpanzees, gorilla, orangutan, and nine species of gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. A consensus about the phylogeny of the hominoids has been reached for the branching order of the gibbons (earliest) and the orangutan (next earliest), but the branching order among gorilla, chimpanzees, and human remains in contention. In 1984 we presented DNA-DNA hybridization data, based on 183 DNA hybrids, that we interpreted as evidence that the branching order, from oldest to most recent, was gibbons, orangutan, gorilla, chimpanzees, and human. In the present paper we report on an expanded data set totaling 514 DNA hybrids, which supports the branching order given above. The ranges for the datings of divergence nodes are Old World monkeys, 25–34 million years (Myr) ago; gibbons, 16.4–23 Myr ago; orangutan, 12.2–17 Myr ago; gorilla, 7.7–11 Myr ago; chimpanzees-human, 5.5–7.7 Myr ago. The possible effects of differences in age at first breeding are discussed, and some speculations about average genomic rates of evolution are presented.     

Molecular trajectories leading to the alternative fates of duplicate genes

Gene duplication generates extra gene copies in which mutations can accumulate without risking the function of pre-existing genes. Such mutations modify duplicates and contribute to evolutionary novelties. However, the vast majority of duplicates appear to be short-lived and experience duplicate silencing within a few million years. Little is known about the molecular mechanisms leading to these alternative fates. Here we delineate differing molecular trajectories of a relatively recent duplication event between humans and chimpanzees by investigating molecular properties of a single duplicate: DNA sequences, gene expression and promoter activities. The inverted duplication of the Glutathione S-transferase Theta 2 (GSTT2) gene had occurred at least 7 million years ago in the common ancestor of African great apes and is preserved in chimpanzees (Pan troglodytes), whereas a deletion polymorphism is prevalent in humans. The alternative fates are associated with expression divergence between these species, and reduced expression in humans is regulated by silencing mutations that have been propagated between duplicates by gene conversion. In contrast, selective constraint preserved duplicate divergence in chimpanzees. The difference in evolutionary processes left a unique DNA footprint in which dying duplicates are significantly more similar to each other (99.4%) than preserved ones. Such molecular trajectories could provide insights for the mechanisms underlying duplicate life and death in extant genomes.     

Genetic sex identification in orangutans

To date, no established protocol for genetic sex identification in orangutans (Pongo pygmaeus) exists. In nearly all apes (gibbons, gorillas, chimpanzees, and humans), genetic sex identification is possible using the amelogenin gene because copies located on X and Y chromosomes have different sizes. Here we report that orangutan sex identification can be resolved through multiplex polymerase chain reaction (PCR) of the Y-linked SRY locus and the amelogenin locus. PCR amplifications of orangutan amelogenin produces one fragment size in both sexes, while SRY amplifies only in males. This protocol will allow primatologists to identify the sex of orangutans through genetic analysis.     

Gene diversity patterns at 10 X-chromosomal loci in humans and chimpanzees

We have investigated the pattern and extent of nucleotide diversityin 10 X-chromosomal genes where mutations are known to causemental retardation in humans. For each gene, we sequenced theentire coding region from cDNA in humans, chimpanzees, and orangutans,as well as about 3 kb of genomic DNA in 20 humans sampled worldwideand in 10 chimpanzees representing two "subspecies." Overallnucleotide diversity in these genes is about twofold lower inhumans than in chimpanzees, and nucleotide diversity withinand between species is low, suggesting that a high level offunctional constraint acts on these genes. Strikingly, we findthat a summary of the allele frequency spectrum is significantlycorrelated in humans and chimpanzees, perhaps reflecting verysimilar levels of constraint at these genes in the two species.A possible exception is FMR2, which shows a higher number ofnonsynonymous than synonymous substitutions on the human lineage,suggesting the action of positive selection.     

Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus

Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts.     

Is culture a golden barrier between human and chimpanzee?

Culture pervades much of human existence. Its significance to human social interaction and cognitive development has convinced some researchers that the phenomenon and its underlying mechanisms represent a defining criterion for humankind. However, care should be taken not to make hasty conclusions in light of the growing number of observations on the cultural abilities of different species, ranging from chimpanzees and orangutans to whales and dolphins. The present review concentrates on wild chimpanzees and shows that they all possess an extensive cultural repertoire. In the light of what we know from humans, I evaluate the importance of social learning leading to acquisition of cultural traits, as well as of collective meaning of communicative traits. Taking into account cross‐cultural variations in humans, I argue that the cultural abilities we observe in wild chimpanzees present a broad level of similarity between the two species.     

Hypoglossal canal size in living hominoids and the evolution of human speech

The relative size of the hypoglossal canal has been proposed as a useful diagnostic tool for the identification of human-like speech capabilities in the hominid fossil record. Relatively large hypoglossal canals (standardized to oral cavity size) were observed in humans and assumed to correspond to relatively large hypoglossal nerves, the cranial nerve that controls motor function of the tongue. It was suggested that the human pattern of tongue motor innervation and associated speech potential are very different from those of African apes and australopithecines; the modern human condition apparently appeared by the time of Middle Pleistocene Homo. A broader interspecific analysis of hypoglossal canal size in primates conducted in 1999 has rejected this diagnostic and inferences based upon it. In an attempt to resolve these differences of opinion, which we believe are based in part on biased size-adjustments and/or unwarranted assumptions, a new data set was collected and analyzed from 298 extant hominoid skulls, including orangutans, gorillas, chimpanzees, bonobos, siamang, gibbons, and modern humans. Data on the absolute size of the hypoglossal nerve itself were also gathered from a small sample of humans and chimpanzee cadavers. A scale-free index of relative hypoglossal canal size (RHCS) was computed as 100 x (hypoglossal canal area(0.5)/oral cavity volume(0.333)). No significant sexual dimorphism in RHCS was discovered in any species of living hominoid, but there are significant interspecific differences in both absolute and relative sizes of the hypoglossal canal. In absolute terms, humans possess significantly larger canals than any other species except gorillas, but there is considerable overlap with chimpanzees. Humans are also characterized by large values of RHCS, but gibbons possess an even larger average mean for this index; siamang and bonobos overlap appreciably with humans in RHCS. The value of RHCS in Australopithecus afarensis is well within both human and gibbon ranges, as are the indices computed for selected representatives of fossil Homo. Furthermore, the size of the hypoglossal nerve itself, expressed as the mass of nerve per millimeter of length, does not distinguish chimpanzees from modern humans. We conclude, therefore, that the relative size of the hypoglossal canal is neither a reliable nor sufficient predictor of human-like speech capabilities, and paleoanthropology still lacks a quantifiable, morphological diagnostic for when this capability finally emerged in the human career.     

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth.     

Rotator cuff muscle function and its relation to scapular morphology in apes

It is widely held that many differences among primate species in scapular morphology can be functionally related to differing demands on the shoulder associated with particular locomotor habits. This perspective is largely based on broad scale studies, while more narrow comparisons of scapular form often fail to follow predictions based on inferred differences in shoulder function. For example, the ratio of supraspinous fossa/infraspinous fossa size in apes is commonly viewed as an indicator of the importance of overhead use of the forelimb, yet paradoxically, the African apes, the most terrestrial of the great apes, have higher scapular fossa ratios than the more suspensory orangutan. The recent discovery of several nearly complete early hominin scapular specimens, and their apparent morphological affinities to scapulae of orangutans and gorillas rather than chimpanzees, has led to renewed interest in the comparative analysis of human and extant ape scapular form. To facilitate the functional interpretation of differences in ape scapulae, particularly in regard to relative scapular fossa size, we used electromyography (EMG) to document the activity patterns in all four rotator cuff muscles in orangutans and gibbons, comparing the results with previously published data for chimpanzees.     

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution

DNA methylation is a pervasive epigenetic DNA modification that strongly affects chromatin regulation and gene expression. To date, it remains largely unknown how patterns of DNA methylation differ between closely related species and whether such differences contribute to species-specific phenotypes. To investigate these questions, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees. Levels and patterns of DNA methylation vary across individuals within species according to the age and the sex of the individuals. We also found extensive species-level divergence in patterns of DNA methylation and that hundreds of genes exhibit significantly lower levels of promoter methylation in the human brain than in the chimpanzee brain. Furthermore, we investigated the functional consequences of methylation differences in humans and chimpanzees by integrating data on gene expression generated with next-generation sequencing methods, and we found a strong relationship between differential methylation and gene expression. Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits.     

Ancestry of a human endogenous retrovirus family.

The human endogenous retrovirus type II (HERVII) family of HERV genomes has been found by Southern blot analysis to be characteristic of humans, apes, and Old World monkeys. New World monkeys and prosimians lack HERVII proviral genomes. Cellular DNAs of humans, common chimpanzees, gorillas, and orangutans, but not lesser ape lar gibbons, appear to contain the HERVII-related HLM-2 proviral genome integrated at the same site (HLM-2 maps to human chromosome 1). This suggests that the ancestral HERVII retrovirus(es) entered the genomes of Old World anthropoids by infection after the divergence of New World monkeys (platyrrhines) but before the evolutionary radiation of large hominoids.     

Ancestral Population Sizes and Species Divergence Times in the Primate Lineage on the Basis of Intron and BAC End Sequences

The effective sizes of ancestral populations and species divergence times of six primate species (humans, chimpanzees, gorillas, orangutans, and representatives of Old World monkeys and New World monkeys) are estimated by applying the two-species maximum likelihood (ML) method to intron sequences of 20 different loci. Examination of rate heterogeneity of nucleotide substitutions and intragenic recombination identifies five outrageous loci (ODC1, GHR, HBE, INS, and HBG). The estimated ancestral polymorphism ranges from 0.21 to 0.96% at major divergences in primate evolution. One exceptionally low polymorphism occurs when African and Asian apes diverged. However, taking into consideration the possible short generation times in primate ancestors, it is concluded that the ancestral population size in the primate lineage was no smaller than that of extant humans. Furthermore, under the assumption of 6 million years (myr) divergence between humans and chimpanzees, the divergence time of humans from gorillas, orangutans, Old World monkeys, and New World monkeys is estimated as 7.2, 18, 34, and 65 myr ago, respectively, which are generally older than traditional estimates. Beside the intron sequences, three other data sets of orthologous sequences are used between the human and the chimpanzee comparison. The ML application to these data sets including 58,156 random BAC end sequences (BES) shows that the nucleotide substitution rate is as low as 0.6–0.8 × 10^–9 per site per year and the extent of ancestral polymorphism is 0.33–0.51%. With such a low substitution rate and short generation time, the relatively high extent of polymorphism suggests a fairly large effective population size in the ancestral lineage common to humans and chimpanzees.[Reviewing Editor: Dr. Magnus Nordborg]