Sexual dimorphism in skeletal shape in voles (Arvicolinae): disparate selection on male bodies and female heads

Sexual dimorphism evolves as a response to different selective pressures on males and females. In mammals, sexual selection on traits that improve a male’s ability to compete for access to mates is a common cause of sexual dimorphism. In addition to body mass, adaptations in specific components of the musculoskeletal system that increase strength, stability, and agility, may improve male fighting performance. Here we test the hypotheses that males, when compared to females, are more specialized for physical competition in their skeletal anatomy and that the degree of this sexual dimorphism increases with the intensity of male–male competition. In three species of voles (Cricetidae: Arvicolinae: Microtus), we found partial support for these hypotheses. Male-biased sexual dimorphism in a set of functional indices associated with improved fighting performance was identified in the postcranial anatomy. This dimorphism was greatest in the polygynous Microtus californicus, absent in the monogamous M. ochrogaster, and intermediate in the promiscuous or socially flexible M. oeconomus. However, in the skull, we found results opposite to our predictions. Females had larger skulls relative to overall skeletal size than did males. This may be associated with selection for increased food processing efficiency, which should be highly important because of the compounding effects of increased caloric requirements during gestation and lactation, and the generally low-quality diet of voles. In addition, larger heads in females may be associated with selection for greater digging ability or for defending offspring. These results suggest disparate selective pressures on the postcranial skeletons and skulls of male and female voles.

Neanderthal-Denisovan ancestors interbred with a distantly related hominin

Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.

Legofit: estimating population history from genetic data

BACKGROUND

Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population histories also confront problems of statistical identifiability: different models or different combinations of parameter values may fit the data equally well. To deal with this problem, we need methods of model selection and model averaging, which are lacking from most existing software.

RESULTS

The Legofit software package allows simultaneous estimation of parameters describing admixture, and the sizes and separation times of ancestral populations. It includes facilities for data manipulation, estimation, analysis of residuals, model selection, and model averaging.

CONCLUSIONS

Legofit uses genetic data to study the history of a subdivided population. It is unaffected by recent history and can therefore focus on the deep history of population size, subdivision, and admixture. It outperforms several statistical methods that have been widely used to study population history and should be useful in any species for which DNA sequence data is available from several populations.

MIGRATION AND GENETIC DRIFT IN HUMAN POPULATIONS

In humans and many other species, mortality is concentrated early in the life cycle, and is low during the ages of dispersal and reproduction. Yet precisely the opposite is assumed by classical population-genetics models of migration and genetic drift. We introduce a model in which population regulation occurs before migration. In contrast to the conventional model, our model implies that geographic variation in the allele frequencies of newborns should exceed that of adults. Thus, it is important to distinguish genetic variation of adults from that of newborns in species with human-like life cycles. Classical models deal with the variance of group allele frequencies about the allele frequency of a hypothetical "continent" or "foundation stock." Empirical studies, however, can only measure "reduced" variance, i.e., variance about the current population mean. Our model deals with reduced variance, and should therefore be more relevant to field studies. We show that reduced variance converges faster, which implies that populations are more likely to be at equilibrium with respect to reduced than unreduced variance. To summarize the effect of migration on genetic population structure, we introduce a new parameter, the effective migration rate. Unlike most population structure statistics, it does not confound the effects of mobility and population size, and it should therefore be useful for comparisons between populations. Finally, we show that the difference between geographic variation of newborn and adult allele frequencies contains information about both effective population size and effective migration rate.

Evolutionary history of Tibetans inferred from whole-genome sequencing

The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.

Genetic relatedness to sisters' children has been underestimated

Males of many species help in the care and provisioning of offspring, and these investments often correlate with genetic relatedness. For example, many human males invest in the children of sisters, and this is especially so where men are less likely to share genes with children of wives. Although this makes qualitative sense, it has been difficult to support quantitatively. The prevailing model predicts investment in children of sisters only when paternity confidence falls below 0.268. This value is often seen as too low to be credible; so investment in sisters' children represents an unsolved problem. I show here that the prevailing model rests on a series of restrictive assumptions that underestimate relatedness to sisters' children. For this reason, it understates the fitness payoff to men who invest in these children. This effect can be substantial, especially in societies with low confidence in paternity. But this effect cannot be estimated solely from confidence in paternity. One must also estimate the probability that two siblings share the same father.

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10(-30)), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

Detecting positive selection from genome scans of linkage disequilibrium

BACKGROUND

Though a variety of linkage disequilibrium tests have recently been introduced to measure the signal of recent positive selection, the statistical properties of the various methods have not been directly compared. While most applications of these tests have suggested that positive selection has played an important role in recent human history, the results of these tests have varied dramatically.

RESULTS

Here, we evaluate the performance of three statistics designed to detect incomplete selective sweeps, LRH and iHS, and ALnLH. To analyze the properties of these tests, we introduce a new computational method that can model complex population histories with migration and changing population sizes to simulate gene trees influenced by recent positive selection. We demonstrate that iHS performs substantially better than the other two statistics, with power of up to 0.74 at the 0.01 level for the variation best suited for full genome scans and a power of over 0.8 at the 0.01 level for the variation best suited for candidate gene tests. The performance of the iHS statistic was robust to complex demographic histories and variable recombination rates. Genome scans involving the other two statistics suffer from low power and high false positive rates, with false discovery rates of up to 0.96 for ALnLH. The difference in performance between iHS and ALnLH, did not result from the properties of the statistics, but instead from the different methods for mitigating the multiple comparison problem inherent in full genome scans.

CONCLUSIONS

We introduce a new method for simulating genealogies influenced by positive selection with complex demographic scenarios. In a power analysis based on this method, iHS outperformed LRH and ALnLH in detecting incomplete selective sweeps. We also show that the single-site iHS statistic is more powerful in a candidate gene test than the multi-site statistic, but that the multi-site statistic maintains a low false discovery rate with only a minor loss of power when applied to a scan of the entire genome. Our results highlight the need for careful consideration of multiple comparison problems when evaluating and interpreting the results of full genome scans for positive selection.

Chronic hepatitis, hepatic dysplasia, fibrosis, and biliary hyperplasia in hamsters naturally infected with a novel Helicobacter classified in the H. bilis cluster

We recently described helicobacter-associated progressive, proliferative, and dysplastic typhlocolitis in aging (18- to 24-month-old) Syrian hamsters. Other pathogens associated with typhlocolitis in hamsters, Clostridium difficile, Lawsonia intracellularis, and Giardia spp., were not indentified. The presence of Helicobacter genus-specific DNA was noted by PCR in cecal and paraffin-embedded liver samples from aged hamsters by the use of Helicobacter-specific PCR primers. By 16S rRNA analysis, the Helicobacter sp. isolated from the liver tissue was identical to the cecal isolates from hamsters. The six hamster 16S rRNA sequences form a genotypic cluster most closely related to Helicobacter sp. Flexispira taxon 8, part of the Helicobacter bilis/H. cinaedi group. Livers from aged helicobacter-infected hamsters showed various stages of predominantly portocentric and, to a lesser extent, perivenular fibrosis. Within nodules, there was cellular atypia consistent with nodular dysplasia. The livers also exhibited a range of chronic active portal/interface and lobular inflammation, with significant portal hepatitis being present. The inflammation was composed of a mixture of lymphocytes, neutrophils, and macrophages, indicative of its chronic-active nature in these aged hamsters infected with Helicobacter spp. The isolation of novel Helicobacter spp., their identification by PCR from the diseased livers of aged hamsters, and their taxonomic classification as belonging to the Helicobacter bilis cluster strengthen the argument that H. bilis and closely related Helicobacter spp. play an etiological role in hepatobiliary disease in both animals and humans.

Effects of local anesthetic and a nonsteroidal antiinflammatory drug on pain responses of dairy calves to hot-iron dehorning

This study examined the effects of a nonsteroidal antiinflammatory agent (NSAID) on physiological responses of calves immediately after hot-iron dehorning (DH) and during the time that local anesthetic (LA) wears off (2 to 3 h) after this procedure. Forty-six calves (33 +/- 0.3 d of age) were randomly assigned to 6 treatments: hot-iron DH versus sham DH with either no pain mitigation, LA alone, or LA with NSAID (i.v. Meloxicam). Eye temperature (measured using infrared thermography) was recorded every 5 min for 3 h after treatments. Heart rate (HR) and heart rate variability (HRV) were recorded continuously; for analysis of HRV, short segments of 512 interbeat intervals were examined. After DH without LA or NSAID, HR increased by 35 +/- 3.0 beats/min in the first 5 min and remained elevated above baseline for 3 h. The HRV around the time of DH did not differ between treatments; however, the root mean square of successive differences decreased from 68 to 41 +/- 12.6 ms immediately following DH without pain relief, suggesting a decrease in vagal tone at this time. Between 2 and 3 h following DH with LA, there was a decrease in eye temperature (-0.6 +/- 0.1 degrees C), an increase in HR (8 +/- 3.0 beats per min) and changes in HRV. Changes in HRV at this time included a decreased high-frequency power and an increase in the low-frequency power and low-frequency/high-frequency ratio, indicating a change in sympatho-vagal balance. The changes in eye temperature, HR, and HRV between 2 and 3 h following DH with LA indicated the onset of pain coinciding with the time that the LA effects wear off. In addition, this study demonstrated that the combination of LA and NSAID mitigated the onset of pain responses when the LA wanes.

Estimating the age of retrotransposon subfamilies using maximum likelihood

We present a maximum likelihood model to estimate the age of retrotransposon subfamilies. This method is designed around a master gene model which assumes a constant retrotransposition rate. The statistical properties of this model and an ad hoc estimation procedure are compared using two simulated data sets. We also test whether each estimation procedure is robust to violation of the master gene model. According to our results, both estimation procedures are accurate under the master gene model. While both methods tend to overestimate ages under the intermediate model, the maximum likelihood estimate is significantly less inflated than the ad hoc estimate. We estimate the ages of two subfamilies of human-specific LINE-I insertions using both estimation procedures. By calculating confidence intervals around the maximum likelihood estimate, our model can both provide an estimate of retrotransposon subfamily age and describe the range of subfamily ages consistent with the data.

Genetic similarities within and between human populations

The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. Both findings can be obtained from the same data set, using the same number of polymorphic loci. This article explains why. Our analysis focuses on the frequency, omega, with which a pair of random individuals from two different populations is genetically more similar than a pair of individuals randomly selected from any single population. We compare omega to the error rates of several classification methods, using data sets that vary in number of loci, average allele frequency, populations sampled, and polymorphism ascertainment strategy. We demonstrate that classification methods achieve higher discriminatory power than omega because of their use of aggregate properties of populations. The number of loci analyzed is the most critical variable: with 100 polymorphisms, accurate classification is possible, but omega remains sizable, even when using populations as distinct as sub-Saharan Africans and Europeans. Phenotypes controlled by a dozen or fewer loci can therefore be expected to show substantial overlap between human populations. This provides empirical justification for caution when using population labels in biomedical settings, with broad implications for personalized medicine, pharmacogenetics, and the meaning of race.

Ancestral alleles and population origins: inferences depend on mutation rate

Previous studies have found that at most human loci, ancestral alleles are "African," in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans. This paper challenges that view by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in Alu insertion polymorphisms, and an even smaller bias in noncoding loci. Thus, the strong bias that was originally observed must reflect some factor that varies among data sets--something other than population history. This factor may be the per-locus mutation rate: the African bias is most pronounced in loci where this rate is high. The distribution of ancestral alleles among populations has been studied using 2 methods. One of these involves comparing the fractions of loci that reach maximal frequency in each population. The other compares the average frequencies of ancestral alleles. The first of these methods reflects history in a manner that depends on the mutation rate. When that rate is high, ancestral alleles at most loci reach their highest frequency in the ancestral population. When that rate is low, the reverse is true. The other method--comparing averages--is unresponsive. Average ancestral allele frequencies are affected neither by mutation rate nor by the history of population size and migration. In the absence of selection and ascertainment bias, they should be the same everywhere. This is true of one data set, but not of 2 others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies among data sets.

Brief communication: The Thule migration: Rejecting population histories using computer simulation

Locked within our genetic code are the histories of our genes and the genes of our ancestors. Deciphering a population's history from genetic data often involves lengthy investigations of many loci for many individuals. We test hypothetical population histories of the Thule expansion using a new coalescent simulation method that uses little more than mitochondrial haplogroup data. This new methodology rejects a severe bottleneck at expansion and reveals the range of probable population histories on which to focus future research.

Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions

BACKGROUND/AIMS

The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure.

METHODS

We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals.

RESULTS AND CONCLUSION

The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.

Genomics refutes an exclusively African origin of humans

Ten years ago, evidence from genetics gave strong support to the "recent African origin" view of the evolution of modern humans, which posits that Homo sapiens arose as a new species in Africa and subsequently spread, leading to the extinction of other archaic human species. Subsequent data from the nuclear genome not only fail to support this model, they do not support any simple model of human demographic history. In this paper, we study a process in which the modern human phenotype originates in Africa and then advances across the world by local demic diffusion, hybridization, and natural selection. While the multiregional model of human origins posits a number of independent single locus selective sweeps, and the "out of Africa" model posits a sweep of a new species, we study the intermediate case of a phenotypic sweep. Numerical simulations of this process replicate many of the seemingly contradictory features of the genetic data, and suggest that as much as 80% of nuclear loci have assimilated genetic material from non-African archaic humans.

Modeling the amplification dynamics of human Alu retrotransposons

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.

Nearly 50% of the human genome is composed of mobile elements. While much of this sequence consists of inactive “fossil” elements that are no longer actively moving or generating new copies, three families are currently proliferating in human genomes. Among these, the Alu lineage has reached a copy number of over 1 million and alone accounts for approximately 10% of the genome. While considerable evidence has been gathered concerning the underlying biological mechanisms of Alu mobilization and proliferation, a detailed understanding of Alu amplification history is currently lacking. Researchers are aware, for example, that several thousand Alu elements have inserted within the human genome since the divergence of humans and chimpanzees, but how those insertions were distributed over this ~6-million-year time period is currently unknown. In this work, the authors introduce a simulation framework that seeks to incorporate both sequence diversity and empirically gathered population data from human Alu elements, in order to provide a better understanding of the last several million years of human Alu evolution. The results suggest that a rapid explosion of Alu amplification at the time of the human–chimpanzee divergence is unlikely. Therefore, it is improbable that an increase in Alu retrotransposition activity was involved in the speciation of humans and chimpanzees.

Genetic analysis of lice supports direct contact between modern and archaic humans

Parasites can be used as unique markers to investigate host evolutionary history, independent of host data. Here we show that modern human head lice, Pediculus humanus, are composed of two ancient lineages, whose origin predates modern Homo sapiens by an order of magnitude (ca. 1.18 million years). One of the two louse lineages has a worldwide distribution and appears to have undergone a population bottleneck ca. 100,000 years ago along with its modern H. sapiens host. Phylogenetic and population genetic data suggest that the other lineage, found only in the New World, has remained isolated from the worldwide lineage for the last 1.18 million years. The ancient divergence between these two lice is contemporaneous with splits among early species of Homo, and cospeciation analyses suggest that the two louse lineages codiverged with a now extinct species of Homo and the lineage leading to modern H. sapiens. If these lice indeed codiverged with their hosts ca. 1.18 million years ago, then a recent host switch from an archaic species of Homo to modern H. sapiens is required to explain the occurrence of both lineages on modern H. sapiens. Such a host switch would require direct physical contact between modern and archaic forms of Homo.

Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms

We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). F(ST), the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that approximately 50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.

Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms

We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations.

Genetic traces of ancient demography

Patterns of gene differences among humans contain information about the demographic history of our species. Haploid loci like mitochondrial DNA and the nonrecombining part of the Y chromosome show a pattern indicating expansion from a population of only several thousand during the late middle or early upper Pleistocene. Nuclear short tandem repeat loci also show evidence of this expansion. Both mitochondrial DNA and the Y chromosome coalesce within the last several hundred thousand years, and they cannot provide information about the population before their coalescence. Several nuclear loci are informative about our ancestral population size during nearly the whole Pleistocene. They indicate a small effective size, on the order of 10,000 breeding individuals, throughout this time period. This genetic evidence denies any version of the multiregional model of modern human origins. It implies instead that our ancestors were effectively a separate species for most of the Pleistocene.

Using mitochondrial and nuclear DNA markers to reconstruct human evolution

Molecular genetic-data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection.

Evolution and human choice over time

This chapter reviews previous work on an evolutionary model describing the effect of time delays on human preferences. The model explains why the long-term real interest rate is usually near 3% and why rates of crime and driving accidents are highest among young adults. It does not succeed in explaining the phenomenon of preference reversal. The chapter reports new results on uncertainty and on a more comprehensive model allowing consumption to have simultaneous effects on mortality and fertility.

Microsatellite diversity and the demographic history of modern humans

We have examined differences in diversity at 60 microsatellite loci among human population samples from three major continental groups to evaluate the hypothesis of greater African diversity in this rapidly evolving class of loci. Application of a statistical test that assumes equal mutation rates at all loci fails to demonstrate differences in microsatellite diversity, while a randomization test that does not make this assumption finds that Africans have significantly greater microsatellite diversity (P < 10(-8)) than do Asians and Europeans. Greater African diversity is most apparent at loci with smaller overall variance in allele size, suggesting that the record of population history has been erased at repeat loci with higher mutation rates. A power analysis shows that only 35-40 microsatellites are needed to establish this difference statistically, demonstrating the considerable evolutionary information contained in these systems. On average, African populations have approximately 20% greater microsatellite diversity than do Asian and European populations. A comparison of continental diversity differences in microsatellites and mtDNA sequences suggests earlier demographic expansion of the ancestors of Africans.

Mitochondrial mismatch analysis is insensitive to the mutational process

Mismatch distributions are histograms showing the pattern of nucleotide (or restriction) site differences between pairs of individuals in a sample. They can be used to test hypotheses about the history of population size and subdivision (if selective neutrality is assumed) or about selection (if a constant population size is assumed). Previous work has assumed that mutations never strike the same site twice, an assumption that is called the model of infinite sites. Fortunately, the results are surprisingly robust even when this assumption is violated. We show here that (1) confidence regions inferred using the infinite-sites model differ little from those inferred using a model of finite sites with uniform site-specific mutation rates, and (2) even when site-specific mutation rates follow a gamma distribution, confidence regions are little changed until the gamma shape parameter falls well below its plausible range, to roughly 0.01. In addition, we evaluate and reject the proposition that mismatch waves are produced by pooling data from several subdivisions of a structured population.

Listeriolysin O production and pathogenicity of non-growing Listeria monocytogenes stored at refrigeration temperature

Three haemolytic, pathogenic strains of Listeria monocytogenes (a reference strain NCTC 7973, a food-derived strain L70 and a human strain L94) and a control strain of Listeria innocua L27 were held in phosphate-buffered saline (PBS) of pH 7.0 or 5.5 at 4 degrees C for 4 weeks. The number of viable cells did not change significantly during this storage (the cells were non-growing). Titers of Listeria listeriolysin O (LLO) activity against washed human erythrocytes and the pathogenicity of non-growing bacterial cells for 14-day-old chick embryos were determined before storage and after 1, 2, 3 and 4 weeks of storage. Prolonged storage at 4 degrees C affected both LLO production and pathogenicity of the non-growing cells, but effects were strain- and pH-dependent. At pH 7.0, all three L. monocytogenes strains had lost LLO activity after 2 weeks of storage. At pH 5.5, the reference and the food strains lost LLO activity 1 week later than when stored at neutral pH, and the human strain maintained LLO activity throughout the 4-week period. Pathogenicity of the reference strain stored at pH 7.0 and 5.5 and that of the food strain stored at pH 7.0 decreased during storage at 4 degrees C. However, the human strain stored at pH 7.0 and 5.5, and the food strain stored at pH 5.5, maintained their pathogenicity throughout the 4-week period. In all cases, non-growing L. monocytogenes cells that had ceased LLO production and/or had a reduced pathogenicity, recovered these characteristics after growth in media at 37 degrees C. This study indicates that prolonged storage of chilled-foods in which L. monocytogenes is present, but not growing may have the desirable result that the L. monocytogenes has a reduced ability to cause illness in humans. As well, pathogenicity testing involving growth of L. monocytogenes in laboratory media may not reflect the actual pathogenicity of the organism in the food as eaten.

Estimating sexual dimorphism by method-of-moments

Estimating the degree of sexual dimorphism is difficult in fossil species because most specimens lack indicators of sex. We present a procedure that estimates sexual dimorphism in samples of unknown sex using method-of-moments. We assume that the distribution of a metric trait is composed of two underlying normal distributions, one for males and one for females. We use three moments around the mean of the combined-sex distribution to estimate the means and the common standard deviation of the two underlying distributions. This procedure has advantages over previous methods: it is relatively simple to use, specimens need not be assigned to sex a priori, no reference to living species analogs is required, and the method provides conservative estimates of dimorphism under a variety of conditions. The method performs best when the male and female distributions overlap minimally but also works well when overlap is substantial. Simulations indicate that this relatively simple method is more accurate and reliable than previous methods for estimating dimorphism.

Genetic admixture in the late pleistocene

The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these "divergent" mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years.

Ascertainment bias in estimates of average heterozygosity

Population geneticists work with a nonrandom sample of the human genome. Conventional practice ensures that unusually variable loci are most likely to be discovered and thus included in the sample of loci. Consequently, estimates of average heterozygosity are biased upward. In what follows we describe a model of this bias. When the mutation rate varies among loci, bias is increased. This effect is only moderate, however, so that a model of invariant mutation rates provides a reasonable approximation. Bias is pronounced when estimated heterozygosity is < approximately 35% Consequently, it probably affects estimates from classical polymorphisms as well as from restriction-site polymorphisms. Estimates from short-tandem-repeat polymorphisms have negligible bias, because of their high heterozygosity. Bias should vary not only among categories of polymorphism but also among populations. It should be largest in European populations, since these are the populations in which most polymorphisms were discovered. As this argument predicts, European estimates exceed those of Africa and Asia at systems with large bias. The magnitude of this European excess is consistent with the version of our model in which mutation rates vary across loci.

Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data

To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating greater genetic diversity for African populations. This finding, which is consistent with previous mtDNA analyses, has been interpreted as evidence for an African origin of modern humans. Both sets of nuclear polymorphisms, as well as a third set of trinucleotide polymorphisms, are highly consistent with one another but fail to show deep branches for African populations. These results, which represent the first direct comparison of mtDNA and nuclear genetic data in major continental populations, undermine the genetic evidence for an African origin of modern humans.

Genetic evidence on modern human origins

A review of genetic evidence leads to the following conclusions concerning human population history: (1) Between 33,000 and 150,000 years ago the human population expanded from an initial size of perhaps 10,000 breeding individuals, reaching a size of at least 300,000. (2) Although the initial population was small, it contained at least 1000 breeding individuals. (3) The human races separated several tens of thousands of years before their separate expansions. (4) Before their expansions the separate racial populations were small. These inferences are inconsistent with both the multiregional and the replacement models of modern human origins. They support the "weak Garden of Eden" hypothesis, which holds that the human populations separated some 100,000 years ago but did not expand until tens of thousands of years later.

Genetic structure of the Utah Mormons: comparison of results based on RFLPs, blood groups, migration matrices, isonymy, and pedigrees

The genetic structure of the Utah Mormon population is examined using 25 blood group and 47 RFLP alleles obtained from 442 subjects living in 8 geographic subdivisions. Nei's GST was 0.013 (p < 0.002) for the RFLP data and 0.012 (p > 0.4) for the blood group data, showing that only 1% of the genetic variance in this population can be attributed to subdivision effects. A comparison of intersubdivision distance matrices based on blood groups, RFLPs, migration matrices, isonymy, and pedigrees shows that genetic distances have relatively low and nonsignificant correlations with the other three types of data. However, the correlations based on RFLPs are considerably higher than those based on blood groups. Relationship matrices based on interindividual allele sharing were compared with known genealogical kinship coefficients between each pair of individuals. The correlation between the blood group and RFLP relationship matrices was small but marginally significant using the Mantel test (r = 0.014, p < 0.06). The RFLP relationship matrix correlated more highly with genealogical kinship than did the blood group relationship matrix (r = 0.023, p < 0.0001 and r = 0.012, p < 0.001, respectively). These correlations increased by approximately one order of magnitude when pairs of subjects having zero kinship coefficients were excluded. These results show that genetic distances derived from RFLPs correlate more strongly with other types of kinship than do distances based on blood groups. This probably reflects the fact that RFLPs are more neutral, have frequencies that are more accurately estimated, and contain more information about DNA sequence variation.

Mismatch distributions of mtDNA reveal recent human population expansions

Although many genetic studies of human evolution have tried to make distinctions between the replacement and the multiregional evolution hypotheses, current methods and data have not resolved the issue. However, new advances in nucleotide divergence theory can complement these investigations with a description of human demographic behavior during the late Middle and Upper Paleolithic (approximately the last 250,000 years). Restriction fragment length polymorphism (RFLP) and DNA sequence analyses of human mitochondrial DNAs (mtDNAs) from 25 ethnic and racial groups indicate that significant expansions occurred during the late Middle and Upper Paleolithic in 23 of the 25 populations examined. Estimates for the individual group expansion times are consistently less than 100,000 years ago with a mean expansion time of approximately 40,000 years ago. The dramatic expansions suggested by these data occurred well after modern human anatomy appeared, approximately 100,000 years ago, but are concordant with archeological evidence for the expansion of modern human technology, approximately 50,000 years ago.

Founder effect: assessment of variation in genetic contributions among founders

We present a Monte Carlo method for determining the distribution of founders' genetic contributions to descendant cohorts. The simulation of genes through known pedigrees generates the probability distributions of contributed genes in recent cohorts of descendants, their means, and their variances. Genealogical data from three populations are analyzed: the Hutterite population of North America, the island population of Sottunga from the Aland archipelago, and the large Utah Mormon population. Two applications of the Monte Carlo method are presented. First we investigate the relative opportunity for founder effect in the three populations, which have dissimilar pedigree structures and dissimilar disease gene frequencies. Second, we measure the reproductive success of population founders in terms of the number of genes they contribute to a cohort some number of generations descendant and compare the effects of polygyny versus monogamy on reproductive success. The distribution of Hutterite founder contributions describes the context for a classic founder effect. Hutterite founders have a higher probability of leaving no genes in the population (72%) than Sottunga (48%) and Mormon (48%) founders. However, founder genes that survive among Hutterite descendants do so in larger numbers on average than founder genes in the other two populations. Greater variation among monogamous Hutterite founders compared with Mormon polygynous founders demonstrates that polygyny alone does not maximize the variance in reproductive success; other population characteristics are at least as important for determining variability among individuals in their genetic contributions to a gene pool. Our findings make it difficult to appreciate the reproductive advantage of polygyny in the Mormon population. Although the expected gene contributions and their variances were larger for polygynous founders compared with other Mormons, the main effect of polygyny was to increase the probability that any polygynist left a few genes among descendants. Furthermore, only 12% of the variation in the genetic contributions of Mormon founders is explained by their number of offspring. We conclude that shallow genealogical data (from one or a few generations) provide a poor measure of long-term reproductive success.

Is migration kin structured?

We estimate the strength of kin-structured migration in six human populations (five from New Guinea and one from Finland) and in one population of nonhuman primates. We also test the hypothesis that migration is not kin structured by generating a sampling distribution of the estimator under the null hypothesis of independent random migration. We are unable to detect a statistically significant level of kin-structured migration in any population. However, five of our six human populations were from Papua New Guinea, and we cannot dismiss the possibility that migration is kin structured in other parts of the world.

Population growth makes waves in the distribution of pairwise genetic differences

Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.

Doubts about isonymy

The method of isonymy, developed by Crow and Mange for estimating inbreeding from surname frequencies, requires an assumption that has not been appreciated: It is necessary to assume that all males in some ancestral generation, the founding stock, had unique surnames. Because this assumption is seldom justified in real populations, the applicability of the isonymy method is extremely limited. Even worse, the estimates it provides refer to an unspecified founding stock, and this implies that these estimates are devoid of information.