Population Bottleneck

A population bottleneck is a significant reduction in the size of a population that causes the extinction of many genetic lineages within that population, thus decreasing genetic diversity. Population bottlenecks have occurred in the evolutionary history of many species, including humans. Present-day bottlenecks are seen in endangered species such as the Yangtze River dolphin, whose numbers have dwindled to less than 100. Endangered species that do not become extinct may expand their numbers later on, but with a limited amount of genetic diversity with which to adapt to changing conditions. The genomes of future populations will reflect the narrowing of genetic possibility for thousands of years.

Reconstructing Genealogies

The genomes of living organisms record both genealogical and population histories. Our own genome tells a remarkable story of events in recent human evolution. Relatedness of individuals within and between populations and species can be determined by measuring the number of genetic differences between two individuals. When applied to segments of the genome that accumulate mutations at relatively constant rates over time, they can provide information about the time that has elapsed since the existence of their last common ancestor. Research shows that human and chimpanzee lineages diverged about six million years ago, that neanderthals and anatomically modern humans diverged 500 thousand years ago, and that all living humans can trace their ancestry to a maternal lineage that lived in Africa about 130 thousand years ago. Figure 2 illustrates differentiation of lineages and the effects of bottlenecks on diversity.

Reconstructing Ancient Population Sizes

Knowledge of mutation rates also permits reconstruction of past population sizes. A small number of genetic differences between individuals in a population or species may indicate either a recent origin, or a population bottleneck. Which of these two possible causes is responsible can be determined by measuring the number of so-called pairwise differences (mismatch distributions) in the DNA sequences that occur between individuals. Population expansion times are earlier for populations with higher average pairwise differences. Irregular mismatch distributions indicate long-term populations that have been stable for long times.

As shown in Figure 3, humans have remarkably little genetic diversity, especially in comparison to our closest living relative, the chimpanzee. Indeed, there is substantially more genetic difference among individuals within chimpanzee troops in West Africa than among all living humans on earth. As shown in Figure 1, this is due to a series of bottlenecks in human evolutionary history. Geneticists studying many different parts of the human genome have concluded that the past effective population size (that is, the number of reproducing females) averaged only 10,000 individuals over the last one million years, and was as low as 5,000 around 70,000 years ago. Compare this to the approximately one billion reproducing females alive today, and it becomes clear just how narrow these bottlenecks were.

Population Bottlenecks and Expansions in Human Evolution

The genetic structure of human populations suggests four bottlenecks in our lineage. Stanley Ambrose has proposed that two bottlenecks may be related to past environmental changes. Marta Lahr has attributed bottlenecks to migrations of small populations across geographic barriers, a phenomenon variously referred to as the founder effect or colonization bottlenecks.

Bottleneck 1.

When traced backward in time, all human lineages coalesce to an ancestral lineage that lived in Africa about 130 thousand years ago. This date coincides with the end of the penultimate glacial period (190 to 130 thousand years ago). Populations were probably very small during this ice age. Expansion (bottleneck release) occurred during the last interglacial (130 to 71 thousand years ago), when warm climates and higher rainfall returned. Other lineages probably existed at that time, but they left no modern descendants.

Bottleneck 2.

A severe bottleneck around 70,000 years ago may have reduced the effective population size in Africa to only 5,000 females. This date coincides with the super-eruption of Toba, a volcano located in northern Sumatra. Toba blasted over 800 cubic kilometers of volcanic ash and millions of tons of sulfur gas into the atmosphere. The volcanic ash settled relatively quickly, but the sulfur formed a long-lasting stratospheric haze that reflected sunlight and may have caused rapid global cooling. Annual layers of ice in the Greenland ice sheet suggest that this haze lasted six years, causing a "volcanic winter." This was followed by 1,000 years of the coldest temperatures of the last ice age. Analysis of air trapped in these ice layers suggests that temperatures dropped 16 °C over Greenland during this "instant ice age." Drought and famine during this cataclysmic event undoubtedly decimated populations in most parts of Africa.

Bottleneck 3.

Analysis of Y chromosomes shows that all modern populations in southern Australasia can trace their ancestry to a small founding population from the Horn of northeast Africa (Ethiopia and Somalia) around 60,000 to 70,000 years ago. Increases in windblown dust in Greenland ice indicate a rapid drop in sea level to more than 100 meters lower than at present. This would have greatly facilitated dispersal from Africa to the Arabian Peninsula. Expansion around the perimeter of the Indian Ocean culminated in the colonization of Australia about 60,000 years ago.

Bottleneck 4.

Analyses of gene sequences provide evidence of a possible second exodus from Africa by a small founding population that traveled overland via the shoreline of the Red Sea. This colonization bottleneck occurred during a period of milder climate about 50,000 years ago, and also coincides with the appearance of advanced stone tool technologies. Expansion continued into Europe and northern Asia. All living humans outside of Africa can thus trace their ancestry to these colonizing populations.

Technological and Social Influences on Past Population Size

Social and technological innovations in Africa during the later Middle Stone Age and early Later Stone Age (50,000 to 70,000 years ago) may have facilitated population expansions and colonizations by enhancing survival in arid, unpredictable ice age environments. New stone tool technologies may have increased foraging efficiency and food supply. A system of mutual reliance and cooperation between distant foraging groups, mediated by reciprocal gift exchange, may have also increased humans' ability to survive in unpredictable environments. Further social and technological innovations may have facilitated population expansion within Africa, dispersals out of Africa, and the replacement of archaic populations, including Neanderthals, by anatomically modern humans outside of Africa.

Low levels of modern human diversity thus reflect our recent African ancestry and the effects of several population bottlenecks. In a similar fashion, colonization bottlenecks promoted rapid differentiation of northwestern Eurasians and southeastern Australasians.

see also Conservation Biology:Genetic Approaches;Founder Effect; Hardy-Weinberg Equilibrium; Molecular Anthropology; Population Genetics; Y Chromosome.

Stanley Ambrose

Bibliography

Ambrose, Stanley H. "Late Pleistocene Human Population Bottlenecks, VolcanicWinter, and the Differentiation of Modern Humans." Journal of Human Evolution 34 (1998): 623-651.

Harpending, Henry, and Alan R. Rogers. "Genetic Perspectives on Human Origins and Differentiation." Annual Review of Genomics and Human Genetics 1 (2000): 361-385.

Harpending, Henry C., et al. "The Genetic Structure of Ancient Human Populations." Current Anthropology 34 (1993): 483-496.

Jorde, Lynn B., Michael Bamshad, and Alan R. Rogers. "Using Mitochondrial and Nuclear DNA Markers to Reconstruct Human Evolution." BioEssays 20 (1998): 126-136.

Ke, Yuehai, et al. "African Origin of Modern Humans in East Asia: A Tale of 12,000Y Chromosomes." Science (2001): 1151-1153.

Lahr, Marta. The Evolution of Modern Human Diversity. Cambridge, U.K.: Cambridge University Press, 1996.

Underhill, Peter A., et al. "Y Chromosome Sequence Variation and the History of Human Populations." Nature Genetics 26 (2000): 358-361.