Comparison of human and chimpanzee ξ1 blobin genes

Summary The DNA base sequences of the entire chimpanzee 1 globin gene and an additional 1 kb of DNA flanking both the human and chimpanzee genes have been determined. Whereas the human 1 gene contains a termination codon in the sixth position, the chimpanzee gene appears to be functional. This finding confirms Proudfoot et al.'s suggestion that the human 1 gene was recently inactivated. Like the corresponding human 1 and 2 genes, the first and second introns of the chimpanzee 1 gene are occupied largely by tandem repeats of short oligonucleotides. These tandem repeats have undergone several rearrangements since the divergence of the human and chimpanzee 1 genes.     

Measuring pad-pad pinch strength in a non-human primate: Macaca fascicularis.

The primary purpose of this study was to establish a methodology for determining and perhaps predicting (via regression analysis of anthropometric measures) Macaca fascicularis isometric pinch strength for a specific task. The larger purpose of this work was to properly scale a pinching task for the monkeys in order to study dose-response relationships in a non-human primate model for carpal tunnel syndrome. Three female and one male macaque (n = 4) of varying size and age were trained to perform a left-handed pad–pad pinch. The task required 60° of wrist flexion at a static pinching distance of 3 cm between the thumb and fingers. Subjects were trained for a period of 20-weeks. After that time, an analysis of performance gradients found that they had each reached a plateau in their force output. Pinch strength for the four animals ranged from 29.4 to 59.8 N. Regression analysis revealed that body mass (kg) and wrist circumference (cm) were both predictive of pinch strength, exhibiting adjusted R² values of 0.93 (p = 0.024) and 0.96 (p = 0.015), respectively. Thus, the results suggest that maximal pinch strength could be acceptably estimated in future subjects using either the wrist circumference or the body mass measures, as both were strong predictors of pad–pad pinch strength.     

Speed modulation in hylobatid bipedalism: a kinematic analysis

Gibbons are highly arboreal apes, and it is expected that their bipedal locomotion will show some particularities related to the arboreal environment. Previous research has shown that, during hylobatid bipedalism, unsupported phases are rare and stride frequencies are relatively low. This study confirms previous findings, and we suggest that low stride frequencies and the absence of unsupported phases are ways to reduce disadvantageous branch oscillations during arboreal travel. Despite these restrictions, gibbons are able to locomote at a wide range of speeds, implying that they likely exploit other mechanisms to modulate their locomotor speed. To investigate this possibility, we collected video images of a large number of spontaneous bipedal bouts of four untrained white-handed gibbons by using an instrumented walkway with four synchronized cameras. These video images were digitized to obtain a quantification of the 3D kinematics of hylobatid bipedalism. We defined a large number of spatiotemporal and kinematic gait variables, and the relationship between these gait variables and (dimensionless) speed was statistically tested. It was found that gibbons mainly increase stride length to increase their locomotor speed; the main speed-modulating mechanisms are hip and ankle excursion and coupled knee and ankle extension at toe-off. Although aerial phases are rare, gibbons generally adopt a bipedal bouncing gait at most speeds and a clear-cut gait transition, as seen in human locomotion, is absent. Comparison with human and bonobo bipedalism showed that the variability of the 3D joint angles of the hind limb are comparable during human and gibbon bipedalism, and much lower than during bonobo bipedalism. The low variability found in gibbons might be related to constraints imposed by the arboreal environment. These arboreal constraints clearly affect the bipedal gait characteristics of gibbons, but do not constrain the ability to adopt a bipedal bouncing gait during terrestrial locomotion.     

Severe wear and tooth loss in wild ring-tailed lemurs (Lemur catta): a function of feeding ecology, dental structure, and individual life history

The ring-tailed lemurs at Beza Mahafaly Special Reserve, Madagascar, exhibit a high frequency of severe wear and antemortem tooth loss. As part of a long-term study, we collected dental data on 83 living adult ring-tailed lemurs during 2003 and 2004. Among these individuals, 192 teeth were scored as absent. The most frequently missing tooth position is M1 (24%). As M1 is the first tooth to erupt, its high frequency of absence (primarily a result of wear) is not remarkable. However, the remaining pattern of tooth loss does not correlate with the sequence of eruption. We suggest that this pattern is a function of 1) feeding ecology, as hard, tough tamarind fruit is a key fallback food of ring-tailed lemurs living in gallery forests; 2) food processing, as tamarind fruit is primarily processed in the P3-M1 region of the mouth; and 3) tooth structure, as ring-tailed lemurs possess thin dental enamel. The incongruity between thin enamel and use of a hard, tough fallback food suggests that ring-tailed lemurs living in riverine gallery forests may rely on resources not used in the past. When comparing dental health in the same individuals (n=50) between 2003 and 2004, we found that individual tooth loss can show a rapid increase over the span of one year, increasing by as much as 20%. Despite this rapid loss, individuals are able to survive, sometimes benefiting from unintentional assistance from conspecifics, from which partially processed tamarind fruit is obtained. Although less frequent in this population, these longitudinal data also illustrate that ring-tailed lemurs lose teeth due to damage and disease, similar to other nonhuman primates. The relationship between tooth loss, feeding ecology, dental structure, and individual life history in this population has implications for interpreting behavior based on tooth loss in the hominid fossil record.     

Counting primates for conservation: primate surveys in Uganda

Primate census techniques have been developed over the past 35–40 years yet there is still some confusion and great variation in the methods used. This precludes comparisons between sites where different techniques have been used. This paper discusses the variations between the methods that seem to be practiced currently and then describes a census of primates in the forests of western Uganda. Primate density and biomass varied greatly between forests as well as within forests and this is probably related to food availability. Chimpanzee (Pan troglodytes) density was strongly correlated with nest encounter rates from reconnaissance walks in the forest. This result can be used to estimate chimpanzee density in forests where it is difficult to survey this species (e.g., due to security reasons). A total of 4,980 chimpanzee was estimated for Uganda which is higher than previously guessed, but still of conservation concern. Only four forests had more than 500 individuals which gives concern for long-term population viability.     

Recent duplication and positive selection of the <Emphasis Type="Italic">GAGE</Emphasis> gene family

We report that the GAGE gene family of human Cancer/testis antigen (CTA) genes is likely to be in an early stage of its evolution. Members of this gene family are tandemly arranged on the X chromosome only in human, chimpanzee and macaque genomes and share a very high similarity. Phylogenetic trees show that the GAGE gene family began to duplicate after the split of human and chimpanzee. The estimated ages of the duplication events range from 4 million years ago to the present. The Ka/Ks values between the duplicates are significantly greater than 1, indicating that the mutation rate is higher in coding regions than non-coding regions of the genes, which suggests that the GAGE gene family is under positive selection. These findings indicate that the GAGE gene family may be a newly formed gene family undergoing rapid functional evolution. Yang Liu and Qiyun Zhu contributed equally to this work.     

Relief index of second mandibular molars is a correlate of diet among prosimian primates and other euarchontan mammals

This study describes and tests a new method of calculating a shape metric known as the relief index (RFI) on lower second molars of extant euarchontan mammals, including scandentians (treeshrews), dermopterans (flying lemurs), and prosimian primates (strepsirhines and tarsiers). RFI is the ratio of the tooth crown three-dimensional area to two-dimensional planar area. It essentially expresses hypsodonty and complexity of tooth shape. Like other measurements of complexity, RFI ignores taxon-specific features, such as certain cusps and crests, which are usually considered in more traditional studies of tooth function. Traditional statistical analyses of the study sample show that RFI distinguishes taxa with differing amounts of structural carbohydrates in their diets, with frugivore/gramnivores being significantly lower in RFI than omnivores, and insectivores/folivores being significantly higher in RFI than the other two. Information on absolute size, or body mass, is needed to reliably parse out insectivores and folivores; however, if the study sample is limited to Primates, RFI alone distinguishes many folivores (lower) from insectivores (higher). Finally, phylogenetically independent contrasts of RFI and dietary preference are strongly correlated with one another, indicating that variance in RFI is better explained by dietary diversity than phylogenetic affinity in this sample. Because of the accuracy and phylogenetic insensitivity of the RFI among Euarchonta, this method can be applied to fossil primates and stem-primates (plesiadapiforms) and used to elucidate and compare their dietary preferences. Such comparisons are important for developing a more detailed view of primate evolution.     

Density compensation in neotropical primate communities: evidence from 56 hunted and nonhunted Amazonian forests of varying productivity

Density compensation is a community-level phenomenon in which increases in the abundance of some species may offset the population decline, extirpation, or absence of other potentially interacting competitors. In this paper we examine the evidence for density compensation in neotropical primate assemblages using data from 56 hunted and nonhunted, but otherwise undisturbed, forest sites of Amazonia and the Guianan shields from which population density estimates are available for all diurnal primate species. We found good evidence of density compensation of the residual assemblage of nonhunted mid-sized species where the large-bodied (ateline) species had been severely reduced in numbers or driven to local extinction by subsistence hunters. Only weak evidence for density compensation, however, was detected in small-bodied species. These conclusions are based on the effects of ordinal measures of hunting pressure on the aggregate primate biomass across different size classes after controlling for the effects of forest type and productivity. These results are interpreted primarily in relation to patterns of niche partitioning between different primate functional groups or ecospecies. This study suggests that while overhunting drastically reduces the average body size in multi-species assemblages of forest vertebrates, depletion of large-bodied species is only partially offset (i.e. undercompensated) by smaller taxa. Received: 2 November 1998 / Accepted: 8 September 1999     

Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence

Accurate divergence date estimates improve scenarios of primate evolutionary history and aid in interpretation of the natural history of disease-causing agents. While molecule-based estimates of divergence dates of taxa within the superfamily Hominoidea (apes and humans) are common in the literature, few such estimates are available for the Cercopithecoidea (Old World monkeys), the sister taxon of the hominoids in the primate infraorder Catarrhini. To help fill this gap, we have sequenced the entire mitochondrial DNA (mtDNA) genomes from a representative of three cercopithecoid tribes, Cercopithecini (Chlorocebus aethiops), Colobini (Colobus guereza), and Presbytini (Trachypithecus obscurus), and analyzed these new data together with other catarrhine mtDNA genomes available in public databases. Molecular divergence date estimates are dependent on calibration points gleaned from the paleontological record. We defined criteria for the selection of good calibration points and identified three points meeting these criteria: Homo-Pan, 6.0 Ma; Pongo-hominines, 14.0 Ma; hominoid/cercopithecoid, 23.0 Ma. Because a uniform molecular clock does not fit the catarrhine mtDNA data, we estimated divergence dates using a penalized likelihood and a Bayesian method, both of which take into account the effects of rate differences on lineages, phylogenetic tree structure, and multiple calibration points. The penalized likelihood method applied to the coding regions of the mtDNA genome yielded the following divergence date estimates, with approximate 95% confidence intervals: cercopithecine-colobine, 16.2 (14.4-17.9) Ma; colobin-presbytin, 10.9 (9.6-12.3) Ma; cercopithecin-papionin, 11.6 (10.3-12.9) Ma; and Macaca-Papio, 9.8 (8.6-10.9) Ma. Within the hominoids, the following dates were inferred: hylobatid-hominid, 16.8 (15.0-18.5) Ma; Gorilla-Homo+Pan, 8.1 (7.1-9.0) Ma; Pongo pygmaeus pygmaeus-P. p. abelii, 4.1 (3.5-4.7) Ma; and Pan troglodytes-P. paniscus, 2.4 (2.0-2.7) Ma. These dates were similar to those found using penalized likelihood on other subsets of the data, but slightly younger than several of the Bayesian estimates.