The paleodemographic history of humanity has classically been studied as a problem of archaeology with largely theoretical contributions from mathematical modeling. However, in the past several years, an increased availability of data on human genetic variation, coupled with advances in theoretical population biology, have allowed us to further examine human demographic history from a genetic perspective. These data have addressed some of the earlier problems but have also created others, because genetic hypotheses about the past are largely a reflection of the paleodemographic models assumed.
Large-scale genetic studies have assessed the worldwide pattern of variation in human mtDNA, Y chromosomes, ß-globin, and HLA alleles. Other studies have analyzed systems comprising multiple loci interspersed throughout the genome, including microsatellites, single-nucleotide polymorphisms, and human-specific Alu insertions. When these sources of data have been compared, they have sometimes yielded contradictory results. Methods of population genetic analysis have begun to address these contradictions in the context of testing hypotheses of past demographic change.
Contradictions also occur between genetic and other, more traditional, sources of data addressing past human evolution. Unlike indirect methods based on population genetics, archaeological and paleontological sources provide direct evidence about the past that can be independently compared with genetic inferences. Recent debates have pitted such evidence against genetic interpretations, simplifying the controversy to dueling slogans about which source of evidence is “better”: e.g., “fossils are the only direct evidence of evolution,” and “all of the living have ancestors while it may be that no fossils have descendants.” This is not a useful way to proceed, and the use of simulations provides the possibility of using such evidence quite differently, to test models of demographic evolution rather than to emphasize the incompatibilities of different data sources.
Here, we provide a broad application of the simulation approach to examine both genetic and nongenetic sources of information concerning the most fundamental demographic issues—the population size of the human lineage in the past, and how it has changed during the last 2 Myr. The different reconciliations of paleoanthropological data and recombining genetic systems, nonrecombining systems, or systems with low rates of recombination all have one thing in common: the expectation that small population size bottlenecks (reductions in population size followed by population size increases) played an important role in the Plio-Pleistocene evolution of our lineage. No evidence contradicts the contention that one of these bottlenecks took place at the time of the speciation at the beginning of our lineage, at the end of the Pliocene some 2 MYA. This early population size bottleneck has great explanatory power and important implications for understanding genetic variation and its relationship with past population size. The question we address is whether this bottleneck is compatible with any other more recent ones.
In this paper, we review the anatomical and archaeological evidence for an early population size bottleneck and bracket the time when it could have occurred. We outline the subsequent demographic changes that the archaeological evidence of range expansions and contractions address, and we examine how estimates of inbreeding effective population size from genetic data may provide an alternative view of past population size change. We discuss the possibility of more recent population size bottlenecks, and we review nonrecombining and recombining genetic systems that may reflect them. We examine the constraints that these genetic data place on the possibility of significant population size bottlenecks (i.e., of sufficiently small size and/or long duration to minimize genetic variation in autosomal and haploid systems) at several different critical times in human history. Different constraints appear in nonrecombining and recombining systems, and among autosomal loci most are incompatible with any Pleistocene population size expansions. Microsatellite data can be construed as showing Pleistocene population size expansions but are difficult to interpret because different microsatellite studies do not show the same expansion. The archaeological data are only compatible with a few of these analyses, most prominently with data from Alu elements, and we use these facts to question whether the view of the past from analysis of inbreeding effective population size is valid. Finally, we examine the conditions under which inbreeding effective population size can be expected to provide any reasonable measure of the actual past size of the human species.
Source: Hawks J, Hunley K, Lee SH, Wolpoff M (January 2000). “Population bottlenecks and Pleistocene human evolution”. Molecular Biology and Evolution. 17 (1): 2–22.