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.     

Allelic variation of the serotonin transporter gene polymorphic region in apes

To assess the change of serotonin transporter (5-HTT) gene-linked polymorphic region that has occurred during the process of hominization, we examined the allelic variation of 5-HTT gene-linked polymorphic region (5-HTTLPR) in anthropoid apes such as chimpanzees, gorillas, orang-utans, and gibbons, and determined the DNA sequences of the alleles in each species. All chimpanzees examined shared only the 17.5 repeat allele, while polymorphism was observed in the other apes and the 16 and 20 repeat alleles were most frequent in gorillas and orang-utans, respectively. 5-HTTLPR was highly polymorphic in gibbons and the 17 and 23 repeat alleles were most common among 5 alleles. Alleles with extra-long repeated (22 and 23) sequences were found in orang-utans and gibbons, and the alleles of these Asian apes were similar to the rhesus monkey allele.     

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.     

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.     

Nucleotide diversity in gorillas

Comparison of the levels of nucleotide diversity in humans and apes may provide valuable information for inferring the demographic history of these species, the effect of social structure on genetic diversity, patterns of past migration, and signatures of past selection events. Previous DNA sequence data from both the mitochondrial and the nuclear genomes suggested a much higher level of nucleotide diversity in the African apes than in humans. Noting that the nuclear DNA data from the apes were very limited, we previously conducted a DNA polymorphism study in humans and another in chimpanzees and bonobos, using 50 DNA segments randomly chosen from the noncoding, nonrepetitive parts of the human genome. The data revealed that the nucleotide diversity (pi) in bonobos (0.077%) is actually lower than that in humans (0.087%) and that pi in chimpanzees (0.134%) is only 50% higher than that in humans. In the present study we sequenced the same 50 segments in 15 western lowland gorillas and estimated pi to be 0.158%. This is the highest value among the African apes but is only about two times higher than that in humans. Interestingly, available mtDNA sequence data also suggest a twofold higher nucleotide diversity in gorillas than in humans, but suggest a threefold higher nucleotide diversity in chimpanzees than in humans. The higher mtDNA diversity in chimpanzees might be due to the unique pattern in the evolution of chimpanzee mtDNA. From the nuclear DNA pi values, we estimated that the long-term effective population sizes of humans, bonobos, chimpanzees, and gorillas are, respectively, 10,400, 12,300, 21,300, and 25,200.     

Serum dopamine beta-hydroxylase activity in non-human primates: phylogenetic and genetic implications

1. Serum dopamine beta-hydroxylase (DBH) activity is one to two orders of magnitude higher in man than in any other species previously studied. The high levels of human serum DBH are associated with the inherited allele DBHH. 2. DBH activity was measured in serum from gorillas, chimpanzees, orangutans, gibbons, rhesus monkeys and squirrel monkeys in an attempt to determine how recently in the course of evolution the allele DBHH had originated. 3. Of the non-human primates tested, only gorillas had high levels of serum DBH activity comparable to those found in man. 4. The genetic polymorphism responsible for evaluated serum DBH in man is probably of very recent evolutionary origin.     

中国4个少数民族中SDF1多态性研究

研究与HIV 1感染相关的基质细胞衍生因子 (SDF1)等位基因突变频率和多态性在中国 4个少数民族的分布特征。应用PCR/ RFLP等方法检测回族 (5 7例 )、鄂伦春族 (71例 )、蒙古族 (30例 )及锡伯族 (2 6例 )共 184个个体中SDF1 -3’A基因突变频率。结果得出中国 4个民族中SDF1- 3’A基因的基因频率分别为 :蒙古族为 38 3%,锡伯族为 2 3 .1%,回族为 2 0 .2 %,鄂伦春族为 10 .6 %。中国 4个少数民族中SDF1- 3’A等位基因频率存在较大的差异 (χ2 =37 .82 6 ,P<0.01) , 提示这 4 个民族的遗传结构存在着一定的差异。 本研究 为评估中国不同民族对 HIV-1 的易感性及艾滋病的流行病学研究提供了基本数据。     

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.     

Apes and Tricksters: The Evolution and Diversification of Humans’ Closest Relatives

The evolutionary history of humans comprises an important but small branch on the larger tree of ape evolution. Today’s hominoids—gibbons, orangutans, gorillas, chimpanzees, and humans—are a meager representation of the ape diversity that characterized the Old World from 23–5 million years ago. In this paper, I briefly review this evolutionary history focusing on features important for understanding modern ape and human origins. As the full complexity of ape evolution is beyond this review, I characterize major geographic, temporal, and phylogenetic groups using a few flagship taxa. Improving our knowledge of hominoid evolution both complicates and clarifies studies of human origins. On one hand, features thought to be unique to the human lineage find parallels in some fossil ape species, reducing their usefulness for identifying fossil humans. On the other hand, the Miocene record of fossil apes provides an important source for generating hypotheses about the ancestral human condition; this is particularly true given the dearth of fossils representing our closest living relatives: chimpanzees and gorillas.     

中国傣族、景颇族人群中与艾滋病相关的CCR5△32、CCR2b-64I、SDF1-3′A等位基因多态性分布

为了调查HIV-1感染相关的等位基因CCR5△32、CCR2b-64I、SDF1-3′A在我国云南省德宏州傣族景颇族人群中的频率和多态性分布,此课题以101例傣族和113例景颇族人群为研究对象,应用PCR、PCR-RFLP(聚合酶链反应-限制性片段长度多态性)分析方法进行检测,计算突变基因频率;并对其群体分布、性别分布进行统计学分析。结果表明,中国傣族景颇族人群中未发现CCR5△32等位基因突变;傣族CCR2b-64I、SDF1-3′A基因突变频率分别为0.2130和0.2030,景颇族CCR2b-64I和SDF1-3′A基因突变频率分别为0.1637和0.1770;与中国汉族人群相比较,傣族和景颇族中SDF1-3′A突变频率较低（P值分别为0.0322和0.0021）;两个民族的CCR2b-64I和SDF1-3′A等位基因群体分布符合Hardy-Weinberg平衡,在性别之间分布无显著差异。中国傣族景颇族人群的CCR2b-64I等位基因的突变频率与汉族人相似,SDF1-3′A等位基因的突变频率比汉族人低,此两种突变基因在艾滋病发病过程中的影响值得进一步研究。由于未发现CCR5△32基因突变,中国傣族景颇族人群对HIV-1感染可能有较大的遗传易感性。 Abstract:The purpose of the work is to investigate the frequencies and polymorphisms of HIV-1 resistant CCR5delta32,CCR2b-64I,SDF1-3′A alleles in Chinese Dai and Chingpaw populations.Whole blood samples from 101 Dai subjects and 113 Chingpaw were collected randomly and their genomic DNA were extracted with QIAgen Blood Kits.Allelic frequencies were identified by PCR-RFLP analysis.Allelic polymorphisms in Dai population or Chingpaw population and both sexes in the samples were analyzed by χ2 test.The frequencies of CCR5delta32,CCR2b-64I,SDF1-3′A alleles in Dai population were 0.0000,0.2130,0.2030,respectively;The frequencies of CCR5delta32,CCR2b-64I,SDF1-3′A alleles in Chingpaw population were 0.000,0.1637,0.1770,respectively.Distributions of the CCR2b-64I,SDF1-3′A alleles among the both populations were in accordance with Hardy-Weinberg equilibrium.No statistical difference was found in the allelic frequencies of both CCR2b-64I and SDF1-3′A between male and female individuals.The frequencies of CCR5delta32,CCR2b-64I alleles in Chinese Dai and Chingpaw populations are similar to that in Chinese Han population,while the frequency of SDF1-3′A allele in Chinese Dai and Chingpaw populations are lower in contrast to that in Chinese Han population.The genotyping and polymorphism of CCR5delta32,CCR2b-64I,SDF1-3′A alleles in Chinese Dai and Chingpaw populations of Yunnan Province are the first time studied in China.The significance of the three mutant alleles conferring genetic resistance to HIV-1 and AIDS progression remains to be clarified.     

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.     

Scaling of postcranial joint size in hominoid primates

The scaling of sixteen articular dimensions in the locomotor skeleton of hominoid primates is examined with special reference to a recently proposed model of geometric similarity. Seven species are included in the analysis (gorillas, common chimpanzees, bonobos, orang-utans, siamang, lar gibbons, and modern humans of European descent); all specimens are adult individuals of known body mass (N=87). No significant sexual dimorphism in the scaling of joint size was observed. Overal results are compatible with the biomechanical model predictions of isometry, and lend additional support to the suggestion that joint stresses are of the same order of magnitude in animals differing vastly in body size and locomotor adaptations. The hindlimb and lumbosacral joints of humans, however, are consistently much larger than expected for their body mass. Full-time bipedality obviously precludes the sharing of weight support and propulsion with the forelimbs, and this fundamental difference is accurately reflected in the relative joint size of humans.     

Variation in anthropoid vertebral formulae: implications for homology and homoplasy in hominoid evolution

Variation in vertebral formulae within and among hominoid species has complicated our understanding of hominoid vertebral evolution. Here, variation is quantified using diversity and similarity indices derived from population genetics. These indices allow for testing models of hominoid vertebral evolution that call for disparate amounts of homoplasy, and by inference, different patterns of evolution. Results are interpreted in light of "short-backed" (J Exp Zool (Mol Dev Evol) 302B:241-267) and "long-backed" (J Exp Zool (Mol Dev Evol) 314B:123-134) ancestries proposed in different models of hominin vertebral evolution. Under the long-back model, we should expect reduced variation in vertebral formulae associated with adaptively driven homoplasy (independently and repeatedly reduced lumbar regions) and the relatively strong directional selection presumably associated with it, especially in closely related taxa that diverged relatively recently (e.g., Pan troglodytes and Pan paniscus). Instead, high amounts of intraspecific variation are observed among all hominoids except humans and eastern gorillas, taxa that have likely experienced strong stabilizing selection on vertebral formulae associated with locomotor and habitat specializations. Furthermore, analyses of interspecific similarity support an evolutionary scenario in which the vertebral formulae observed in western gorillas and chimpanzees represent a reasonable approximation of the ancestral condition for great apes and humans, from which eastern gorillas, humans, and bonobos derived their unique vertebral profiles. Therefore, these results support the short-back model and are compatible with a scenario of homology of reduced lumbar regions in hominoid primates. Fossil hominin vertebral columns are discussed and shown to support, rather than contradict, the short-back model.     

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.     

The phylogeny of the hominoid primates,as indicated by DNA-DNA hybridization

Summary The living hominoid primates are Man, the chimpanzees, the Gorilla, the Orangutan, and the gibbons. The cercopithecoids (Old World monkeys) are the sister group of the hominoids. The composition of the Hominoidea is not in dispute, but a consensus has not yet been reached concerning the phylogenetic branching pattern and the dating of divergence nodes. We have compared the single-copy nuclear DNA sequences of the hominoid genera using DNA-DNA hybridization to produce a complete matrix of delta T₅₀H values. The data show that the branching sequence of the lineages, from oldest to most recent, was: Old World monkeys, gibbons, Orangutan, Gorilla, chimpanzees, and Man. The calibration of the delta T₅₀H scale in absolute time needs further refinement, but the ranges of our estimates of the datings of the divergence nodes are: Cercopithecoidea, 27–33 million years ago (MYA); gibbons, 18–22 MYA; Orangutan, 13–16 MYA; Gorilla, 8–10 MYA; and chimpanzees-Man, 6.3–7.7 MYA.     

Sex differences in the relative lengths of metacarpals and metatarsals in gorillas and chimpanzees

Sex differences other than the simple dimorphism in size were documented for the metapodials of two primate species. Lengths of metacarpals and metatarsals were obtained from the skeletons of 64 gorillas and 42 chimpanzees. Length ratios were constructed for all possible pairings of the five bones in each individual hand and foot. For both species, several of these length ratios exhibited substantial differences between the sexes. Body size was not the basis for these sex differences; when specimens of similar size were compared, the sex differences remained. In humans, length ratios for the fingers and toes also have previously been demonstrated to exhibit sex differences, and the length ratio for the index and ring fingers (the 2D:4D ratio) has been shown to correlate with various medical conditions. Various facts suggest that length ratios in human digits are associated with androgen exposure, probably during prenatal development. For gorillas, the metacarpal length ratio showing the largest sex difference was 4Mc:5Mc in both hands, and the metatarsal length ratio showing the largest sex difference was 1Mt:2Mt in the left foot. Sex differences in length ratios also existed for chimpanzees, but they were generally smaller than for gorillas. Apparently, both gorillas and chimpanzees are affected by developmental mechanisms, possibly androgenic mechanisms, similar to those in humans. Analyses of previous measurements [Susman, R.L., 1979 Comparative and functional morphology of hominoid fingers. Am. J. Phys. Anthropol. 50, 215-236] revealed that all components of the rays are not affected equally by whatever mechanisms are responsible for the sex differences in length ratios.     

Characterization of human-specific DNA sequences obtained by genome subtraction

Recent studies on molecular evolution using nucleotide sequence data to clarify phylogenetic relationships among humans and the African great apes, have revealed that humans are more closely related to chimpanzees than to gorillas. However, the genetic basis of human uniqueness remains unclear. This is because phylogenetic studies have merely evaluated the degree of similarity by calculating the accumulation of nucleotide substitutions that have occurred in neutral DNA regions commonly present in all the species examined. In contrast, the genome subtraction method recently developed by us has revealed dissimilarity even among the genomes of the most closely related species. Here we describe the characteristics of the DNA sequences obtained by genome subtraction between humans and chimpanzees.     

Evolution of protamine P1 genes in primates

Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged group of primates these genes are clearly orthologous but very variable, both at the DNA level and in their expressed amino acid sequences. The rate of variation amongst the protamine Pls indicates that they are amongst the most rapidly diverging polypeptides studied. However, some regions are conserved both in primates and generally in other placental mammals. These are the 13 N-terminal residues (including a region of alternating serine and arginine residues (the motif SRSR, res. 10–13) susceptible to Ser phosphorylation), a tract of six Arg residues (res. 24–29) in the center of the molecule, and a six-residue region (RCCRRR, res. 39–44), consisting of a pair of cysteines flanked by arginines. Detailed consideration of nearest neighbor matrices and trees based on maximum parsimony indicates that PI genes from humans, gorillas, and chimpanzees are very similar. The amino acid and nucleotide differences between humans and gorillas. are fewer than those between humans and chimpanzees. This finding is at variance with data from DNA-DNA hybridization and extensive globin and mitochondrial DNA sequences which place human and chimpanzee as closest relatives in the super family, Hominoidea. This may be related to the fact that protamine Pls are expressed in germ line rather than somatic cells. In contrast to the variability of the exon regions of the protamine P1 genes, the sequence of the single intron is highly conserved.     

CCR5delta32, CCR2-64I, and SDF1-3'A polymorphisms related to resistance to HIV-1 infection and disease in the Ecuadorian population

The aim of this study was to determine the allele frequencies of genetic variants CCR5delta32, CCR2-64I, and SDF1-3'A (SDF1 801 A), which influence susceptibility to HIV-1 infection. We also investigated the effect of these variants on the general Ecuadoran population and on a group of HIV-infected individuals to determine the frequency of these genetics variants.