Microsatellite mutation models: insights from a comparison of humans and chimpanzees

Using genomic data from homologous microsatellite loci of pure AC repeats in humans and chimpanzees, several models of microsatellite evolution are tested and compared using likelihood-ratio tests and the Akaike information criterion. A proportional-rate, linear-biased, one-phase model emerges as the best model. A focal length toward which the mutational and/or substitutional process is linearly biased is a crucial feature of microsatellite evolution. We find that two-phase models do not lead to a significantly better fit than their one-phase counterparts. The performance of models based on the fit of their stationary distributions to the empirical distribution of microsatellite lengths in the human genome is consistent with that based on the human-chimp comparison. Microsatellites interrupted by even a single point mutation exhibit a twofold decrease in their mutation rate when compared to pure AC repeats. In general, models that allow chimps to have a larger per-repeat unit slippage rate and/or a shorter focal length compared to humans give a better fit to the human-chimp data as well as the human genomic data.     

Temporal changes in allele frequencies and low effective population size in greater prairie-chickens

The number of greater prairie-chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo-likelihood approach that accounted for migration, estimates of Ne (15-32 prairie-chickens within each management area) were 10 times lower than census numbers from booming-ground counts. These low estimates of Ne are consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reduced Ne, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie-chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.     

Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size

We evaluate some common simulation procedures as well as a recently developed likelihood method used for testing hypotheses regarding microsatellite evolution. Results from simulated data revealed that the tests for the detection of multi-step mutations in general have some power, whereas tests for the presence of constraints on the repeat number have only very limited power. The tests were applied to population data obtained from nine different baleen whale populations. High agreement was found between results obtained using the simulation-based approach and results obtained using a likelihood ratio test. In four of the nine population samples the tests rejected the one-step mutation model. In two instances the significant deviation was due to excess of heterozygosity and in two instances to a reduced level of heterozygosity relative to the expectations under the stepwise mutation model. The former significant deviation was consistent with occasional multi-step mutations, whereas the latter may indicate the presence of constraints on the number of repeats.     

The ontogeny of cranial base angulation in humans and chimpanzees and its implications for reconstructing pharyngeal dimensions

This paper examines differences in the processes by which the cranial base flexes in humans and extends in chimpanzees. In addition, we test the extent to which one can use comparisons of cranial base angles in humans and non-human primates to predict vocal tract dimensions. Four internal cranial base angles and one external cranial base angle were measured in a longitudinal sample of Homo sapiens and a cross-sectional sample of Pan troglodytes. These data show that the processes of cranial base angulation differ substantially in these species. While the human cranial base flexes postnatally in a rapid growth trajectory that is complete by two years, the cranial base in P. troglodytes extends postnatally in a more prolonged skeletal growth trajectory. These comparisons also demonstrate that the rate of cranial base angulation is comparable for different measures, but that angles which incorporate different anterior cranial base measurements correlate poorly. We also examined ontogenetic relationships between internal and external cranial base angles and vocal tract growth in humans to test the hypothesis that cranial base angulation influences pharyngeal dimensions and can, therefore, be used to estimate vocal tract proportions in fossil hominids. Our results indicate that internal and external cranial base angles are independent of the horizontal and vertical dimensions of the vocal tract. Instead, a combination of mandibular and palatal landmarks can be used to predict dimensions of the vocal tract in H. sapiens. The developmental contrasts in cranial base angulation between humans and non-human primates may have important implications for testing hypotheses about the relationship between cranial base flexion and other craniofacial dimensions in hominid evolution.     

Allometric constraints on stability and maximum size in flying fishes: implications for their evolution

Flying fish wing area and wing-loading both rise in strongly negative allometric fashion with increasing body length and mass. Evidence is presented to show that this occurs because: (1) the leading edge of the pectoral fin 'wing' is fixed at 24% of standard length (  L _S) from the snout, (2) the wing length cannot exceed 76% of L _S or the tips will interfere with propulsive tail beat and (3) increased mass demands faster flying and wings with better lift : drag ratios; this selects for tapered, higher aspect ratio wing shapes. A consequence of this situation is that larger flying fishes have centres of mass increasingly further behind the centre of wing pressure. Resultant longitudinal instability restricts the maximum size of the two-winged design and the pelvic fins of four-wingers act as a stabilizing tailplane. These data indicate that the accepted model of evolution of flight in flying fishes (by extension of ballistic leaps) is flawed; it is proposed that evolution of lift-supported surface taxiing in half-beaks with enlarged pectoral fins (enhanced by ground effect) was an essential preliminary; subsequent forward migration of the centre of mass to within the wing chord permitted effective gliding.     

Bone mineral density in chimpanzees,humans, and Japanese macaques

We performed a comparative study of bone mechanical properties in the radii of chimpanzees (Pan troglodytes), humans (Homo sapiens), and Japanese macaques (Macaca fuscata) using peripheral quantitative computed tomography. We investigated: (1)cortical bone area relative to the total periosteal area (PrA); (2) trabecular bone area relative to PrA; (3) cortical bone density; and (4) trabecular bone density. The cortical bone area index for chimpanzees was almost the same as that of Japanese macaques, whereas the equivalent value in humans was about the two-fifths that of the others. Values for the other three properties were constant among these three catarrhine species. Chimpanzees do not particularly resemble humans, but are more similar to digitigrade macaques in terms of bone properties. The constant trabecular bone area index and trabecular density value in these species may suggest that a certain amount of trabecular bone (20–30% of total bone area at the distal 4% level of the forearm) is necessary to achieve normal bone turnover. The physiological metabolism of bone, including cortical bone density, might be conserved in these catarrhines. Electronic Publication     

Duplication and divergence in humans and chimpanzees

It has become a truism that we humans are genetically about 99% identical to chimpanzees. The origins of this assertion are clear: among early studies of DNA sequences, nucleotide identity between humans and chimpanzees was found to average around 98.9%.(1) However, this figure is correct only with respect to regions of the genome that are shared between humans and chimpanzees. Often ignored are the many parts of their genomes that are not shared. Genomic rearrangements, including insertions, deletions, translocations and duplications, have long been recognized as potentially important sources of novel genomic material(2,3) and are known to account for major genomic differences between humans and chimpanzees.(4) Further, such changes have been implicated in a number of genetic disorders, such as DiGeorge, Angelman/Prader-Willi and Charcot-Marie-Tooth syndromes.(5)     

Using maximum likelihood to estimate population size from temporal changes in allele frequencies.

We develop a maximum-likelihood framework for using temporal changes in allele frequencies to estimate the number of breeding individuals in a population. We use simulations to compare the performance of this estimator to an F-statistic estimator of variance effective population size. The maximum-likelihood estimator had a lower variance and smaller bias. Taking advantage of the likelihood framework, we extend the model to include exponential growth and show that temporal allele frequency data from three or more sampling events can be used to test for population growth.     

Power for genetic association studies with random allele frequencies and genotype distributions

One of the first and most important steps in planning a genetic association study is the accurate estimation of the statistical power under a proposed study design and sample size. In association studies for candidate genes or in fine-mapping applications, allele and genotype frequencies are often assumed to be known when, in fact, they are unknown (i.e., random variables from some distribution). For example, if we consider a diallelic marker with allele frequencies of 0.5 and 0.5 and Hardy-Weinberg proportions, the three genotype frequencies are often assumed to be 0.25, 0.50, and 0.25, and the statistical power is calculated. Unfortunately, ignoring this source of variation can inflate the estimated power of the study. In the present article, we propose averaging the estimates of power over the distribution of the genotype frequencies to calculate the true estimate of power for a fixed allele frequency. For the usual situation, in which allele frequencies in a population are not known, we propose placing a prior distribution on the allele frequency, taking advantage of any available genotype information. This Bayesian approach provides a more accurate estimate of power. We present examples for quantitative and qualitative traits in cohort studies of unrelated individuals and results from an extensive series of examples that show that ignoring the uncertainty in allele frequencies can inflate the estimated power of the study. We also present the results from case-control studies and show that standard methods may also overestimate power. As discussed in this article, the approach of fixing allele frequencies even if they are not known is the common approach to power calculations. We show that ignoring the sources of variation in allele frequencies tends to result in overestimates of power and, consequently, in studies that are underpowered. Software in C is available at http://www.ambrosius.net/Power/.     

Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees

To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of humans and chimpanzees, we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan. The average sequence divergence was only 1.24% +/- 0.07% for the human-chimpanzee pair, 1.62% +/- 0.08% for the human-gorilla pair, and 1.63% +/- 0.08% for the chimpanzee-gorilla pair. These estimates, which were confirmed by additional data from GenBank, are substantially lower than previous ones, which included repetitive sequences and might have been based on less-accurate sequence data. The average sequence divergences between orangutans and humans, chimpanzees, and gorillas were 3.08% +/- 0.11%, 3.12% +/- 0.11%, and 3.09% +/- 0.11%, respectively, which also are substantially lower than previous estimates. The sequence divergences in other regions between hominoids were estimated from extensive data in GenBank and the literature, and Alus showed the highest divergence, followed in order by Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites. The neighbor-joining tree derived from the concatenated sequence of the 53 segments--24,234 bp in length--supports the Homo-Pan clade with a 100% bootstrap value. However, when each segment is analyzed separately, 22 of the 53 segments (approximately 42%) give a tree that is incongruent with the species tree, suggesting a large effective population size (N(e)) of the common ancestor of Homo and Pan. Indeed, a parsimony analysis of the 53 segments and 37 protein-coding genes leads to an estimate of N(e) = 52,000 to 96,000. As this estimate is 5 to 9 times larger than the long-term effective population size of humans (approximately 10,000) estimated from various genetic polymorphism data, the human lineage apparently had experienced a large reduction in effective population size after its separation from the chimpanzee lineage. Our analysis assumes a molecular clock, which is in fact supported by the sequence data used. Taking the orangutan speciation date as 12 to 16 million years ago, we obtain an estimate of 4.6 to 6.2 million years for the Homo-Pan divergence and an estimate of 6.2 to 8.4 million years for the gorilla speciation date, suggesting that the gorilla lineage branched off 1.6 to 2.2 million years earlier than did the human-chimpanzee divergence.     

Fusion of coccyx to sacrum in humans: prevalence, correlates, and effect on pelvic size, with obstetrical and evolutionary implications

Humans do not have a tail, but we have four rudimentary coccygeal vertebrae. This study considers several issues pertaining to fusion of the coccyx to the sacrum, including prevalence, sexual differences, effect on pelvic size, and obstetrical and evolutionary implications. Previous research on sacral-coccygeal fusion has reported: (1) lower prevalence in females than males, (2) prevalence increases with age, (3) range in prevalence among 13 samples from 0 to 72%, and (4) obstetrical complications. This study uses a sample of 2,354 American skeletons of known sex, age 20 years and older to ascertain prevalence of sacral-coccygeal fusion and to evaluate some of its correlates. Results show that the sexes do not differ in prevalence of sacral-coccygeal fusion for five of seven decades of life, but that prevalence does increase with advancing age-from 24 to 47% from the third to eighth decades of life in females. Pelvimetric analysis of 132 females shows that those with sacral-coccygeal fusion have a shorter posterior sagittal diameter of the outlet compared to those without fusion; more than half of those with sacral-coccygeal fusion have an obstetrically contracted posterior sagittal diameter. Shortening of the posterior sagittal diameter is important, because its conjoint occurrence with a narrow subpubic arch may result in an obstetrically inadequate outlet. This study concludes that sacral-coccygeal fusion is a principal contributor to the evolution of sexual dimorphism in sacral angulation, which is a determinant of the length of the posterior sagittal diameter of the outlet.     

Rates of genomic divergence in humans,chimpanzees and their lice

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.     

The scope of culture in chimpanzees, humans and ancestral apes

More studies have focused on aspects of chimpanzee behaviour and cognition relevant to the evolution of culture than on any other species except our own. Accordingly, analysis of the features shared by chimpanzees and humans is here used to infer the scope of cultural phenomena in our last common ancestor, at the same time clarifying the nature of the special characteristics that advanced further in the hominin line. To do this, culture is broken down into three major aspects: the large scale, population-level patterning of traditions; social learning mechanisms; and the behavioural and cognitive contents of culture. Each of these is further dissected into subcomponents. Shared features, as well as differences, are identified in as many as a dozen of these, offering a case study for the comparative analysis of culture across animal taxa and a deeper understanding of the roots of our own cultural capacities.     

Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys

We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan troglodytes; CERV-K). These sequences were compared with 55 human HERV-K and 20 CERV-K reported previously, producing a total data set of 106 full-length ERV-K genomes. Overall, 61% of the human elements compared to 21% of the chimpanzee and 47% of rhesus elements had estimated integration times less than 4.5 million years before present (MYBP), with an average integration times of 7.8 MYBP, 13.4 MYBP and 10.3 MYBP for HERV-K, CERV-K and RhERV-K, respectively. By excluding those ERV-K sequences generated by chromosomal duplication, we used 63 of the 106 elements to compare the population dynamics of ERV-K among species. This analysis indicated that both HERV-K and RhERV-K had similar demographic histories, including markedly smaller effective population sizes, compared to CERV-K. We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics.     

Functional evidence for differences in sperm competition in humans and chimpanzees

Sperm competition occurs when the gametes of or more males compete for opportunities to fertilize a given set of ova. Previous studies have demonstrated that certain morphological characteristics are affected by sperm competition intensity (e.g. relative testes size and sperm midpiece volume). This study examined whether aspects of sperm energetics may also be affected by sexual selection. We compared the membrane potential of mitochondria in live sperm between H. sapiens (single partner mating system) and P. troglodytes (multiple partner mating system). Flow cytometry of sperm stained with the carbocyanine fluorescent dye JC-1 (an assay for mitochondrial membrane potential) revealed marked differences in red fluorescence intensity. P. troglodytes sperm showed significantly higher mitochondrial membrane potential. Mitochondria provide a substantial part of the energy required for sperm motility. A higher mitochondrial loading may therefore be associated with enhanced sperm motility and/or longevity. Additionally, examination of JC-1 red fluorescence levels before and after in vitro capacitation revealed further differences. Whereas chimpanzee sperm showed maintenance of membrane potential after capacitation (in some cases even an increase), sperm from humans consistently showed reduction in membrane potential. These results indicate that the sperm of human beings and chimpanzees exhibit marked differences in mitochondrial function, which are affected by selection pressures relating to sperm competition and that these pressures differ significantly between humans and chimpanzees.     

Nut-like oil seeds: food for monkeys, chimpanzees, humans, and probably ape-men

The hypothetical hyperrobust australopithecine gnathic nutcracker adaptation is reexamined in light of ecobotanical information on edible wild nuts provided by the flora of tropical and subtropical Africa. The nut producing species are tree-forms. Those of the forest region do not as a rule produce fruits with edible mesocarps. In contrast, the woodland savanna species (particularly in the Zambezian region) characteristically provide an important whole fruit, i.e., a nutritious mesocarp in addition to edible oil-rich nut seeds. These fruits drop from the tree before they are fully mature and go through the final ripening phase on the ground. They are important seasonal foods for a variety of vertebrates, including primates, elephants, and antelope. Altogether the nuts exhibit a broad range of toughness values, measured here as strength under compression. The woodland nuts are not as tough (177-934 kg force, breaking load) as those of the tropical forest (192-1,673 kg force). The seed-predators of the woodland species include squirrels, baboons, warthogs, and parrots. Paleoecological analyses indicate that it was the woodland nuts that were probably available to Australopithecus boisei and A. robustus. Preliminary estimates of adult male gnathic nut-cracking capabilities suggest that A. boisei could have orally cracked a significant portion of the woodland nuts. In spite of this, ecobotanical data indicate that we can probably reject the hypothesis that these hominids were year-round gnathic nut-cracking specialists. Both the indirect and direct evidence support this conclusion.