Alan R. Rogers

GENETIC EVIDENCE FOR A PLEISTOCENE POPULATION EXPLOSION

Expansions of population size leave characteristic signatures in mitochondrial “mismatch distributions.” Consequently, these distributions can inform us about the history of changes in population size. Here, I study a simple model of population history that assumes that, t generations before the present, a population grows (or shrinks) suddenly from female size N0 to female size N1. Although this model is simple, it often provides an accurate description of data generated by complex population histories. I develop statistical methods that estimate θ0 = 2uN0, θ1 = 2uN1, and τ = 2ut (where u is the mutation rate), and place a confidence region around these estimates. These estimators are well behaved, and insensitive to simplifying assumptions. Finally, I apply these methods to published mitochondrial data, and infer that a major expansion of the human population occurred during the late Pleistocene.

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.

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.

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. BioEssays 20:126–136, 1998.

GROUP SELECTION BY SELECTIVE EMIGRATION: THE EFFECTS OF MIGRATION AND KIN STRUCTURE

Group selection may operate through selective emigration, as Sewall Wright envisioned, as well as through selective extinction. The discrete-generation model of selective emigration developed here yields the following conclusions. 1. The fitness benefit of altruism, bp̄, depends on the frequency of altruists. Consequently, selective emigration is more likely than kin selection or selective extinction to lead to polymorphic equilibria. 2. In contrast to selective extinction, selective emigration is facilitated (weakly) by high levels of mobility between groups. 3. Like selective extinction, selective emigration is facilitated (weakly) by kinstructured migration and by isolation by distance, particularly where the dimensionality of the migration pattern is low. 4. The only factor with any great effect on the strength of selective emigration is the size of the social group within which altruistic interactions occur. 5. Wright emphasized that selective emigration requires a delicate balance between the migration rate and population size, but this balance appears to be less delicate than Wright thought. For any conceivable migration pattern, migration rate, number of groups, and level of kin structure, an allele for altruism is favored only if its benefit-to-cost ratio exceeds a number of the same order as group size.

Sequence variations in the public human genome data reflect a bottlenecked population history

Single-nucleotide polymorphisms (SNPs) constitute the great majority of variations in the human genome, and as heritable variable landmarks they are useful markers for disease mapping and resolving population structure. Redundant coverage in overlaps of large-insert genomic clones, sequenced as part of the Human Genome Project, comprises a quarter of the genome, and it is representative in terms of base compositional and functional sequence features. We mined these regions to produce 500,000 high-confidence SNP candidates as a uniform resource for describing nucleotide diversity and its regional variation within the genome. Distributions of marker density observed at different overlap length scales under a model of recombination and population size change show that the history of the population represented by the public genome sequence is one of collapse followed by a recent phase of mild size recovery. The inferred times of collapse and recovery are Upper Paleolithic, in agreement with archaeological evidence of the initial modern human colonization of Europe.

When is technology worth the trouble

Human beings are unique in the degree to which they rely on technology to interface with their environment. Applications of biologically derived foraging models have typically taken this technology as a given when analyzing ethnographic and prehistoric subsistence practices. This paper departs from the standard approach by treating investment in technology as a decision variable and looking at how investment decisions might be expected to vary with changes in both the time available to forage and the nature of the local resource base. The study draws attention to the importance of understanding both the costs and the benefits of technological investment and how they relate to one another. We use ethnographic and hypothetical data to demonstrate how one might represent these relationships mathematically, discuss the importance for understanding investment decisions, and explore their implications in circumstances where resources are randomly and non-randomly encountered.

The male's dilemma: Increased offspring production is more paternity to steal

SummaryLarge potential effects of male care on the number of offspring females successfully raise are not sufficient to select for caring males because of the pervasive importance of mating competition. Males face a version of ‘the social dilemma’, in which increased production increases the pay-off for theft. Models of the allocation of male effort partitioned between caring for babies and competing for paternity show that the optimal allocation to care is very low under a wide range of conditions. Like sex allocation where the alternatives are male versus female function or sons versus daughters, the pay-offs to one alternative are always strongly frequency dependent. Because that alternative (male function, sons, male mating effort) pays so well when rare, it cannot remain rare under most conditions. Here we consider the consequences of partitioning mating effort into mate guarding and all other forms of mating conflict. If a male gets all his partners conceptions while guarding, gaining them at a constant rate, there are two possible regions of stability. The evolutionarily stable strategy (ESS) depends on a parameter scaling the decisiveness of (non-guarding) mating conflict. When marginal returns from conflict decrease with scale, almost all effort goes into guarding. When marginal returns increase, the ESS devotes all effort to mating. Even when the potential effect of care is large, male equilibrium strategies allocate little effort to it. We also report the results of computer simulations showing that care increases if gains from guarding saturate quickly, so that a male is assured of the paternity of most of his partners offspring with little guarding, and consequently the pool of unguarded conceptions open to competion shrinks sharply. But even when the males dilemma is very much reduced, it still substantially limits the allocation to care. The results of both computer simulations and mathematical analysis converge with other lines of evidence that mating has much stronger effects than parenting in shaping male strategies.

Conserving resources for children

Parents can benefit their offspring by conserving resources that the offspring stand to inherit. Thus, inheritance of resources should promote the evolution of propensities to conserve. But inheritance also has another, less obvious effect: it can reduce the fertility of the conserver’s grandchildren, thus reducing the expected number of great-grandchildren. Consequently, inheritance of resources promotes the evolution of conservation less than might be supposed.

On Wright's mechanism for intergroup selection

A haploid model of Wrights (1945) intergroup selection is described. Several approximate analyses as well as Monte Carlo simulation show that Wrights mechanism leads to powerful selection for group advantageous traits in the face of strong local selection against them. Intergroup selection is favored by small local subpopulation size and by high, not low, rates of immigration into local groups, although the dependence on migration rate is not strong. These results and others cast doubt on the primacy of genic selfishness as a tenet of Darwinian theory.