Population bottleneck

(evolution) Genetic drift that occurs as a result of a drastic reduction in population by an event having little to do with the usual forces of natural selection.

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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.

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.

—Stanley Ambrose

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Population bottleneck followed by recovery or extinction

A population bottleneck (or genetic bottleneck) is an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.^[1]

A slightly different sort of genetic bottleneck can occur if a small group becomes reproductively separated from the main population. This is called a founder effect.

Population bottlenecks reduce the genetic variation and, therefore, the population's ability to adapt to new selective pressures, such as climatic change or shift in available resources. Genetic drift can eliminate alleles that could have been positively selected on by the environment if they had not already drifted out of the population.^[2]

Population bottlenecks increase genetic drift, as the rate of drift is inversely proportional to the population size. The reduction in a population's dispersal leads, over time, to increased genetic homogeneity. If severe, population bottlenecks can also markedly increase inbreeding due to the reduced pool of possible mates (see small population size).

Contents 1 Examples 1.1 Humans 1.2 Other animals 1.3 Plants 2 In evolutionary theory 3 Minimum viable population size 4 See also 5 References 6 External links

Examples

Humans

Richard Dawkins.

Evolutionary biologist Richard Dawkins has postulated that human mitochondrial DNA (inherited only from one's mother) and Y chromosome DNA (from one's father) show coalescence at around 140,000 and 60,000 years ago, respectively. In other words, all living humans' female line ancestry can be traced back to a single female (Mitochondrial Eve) at around 140,000 years ago. Via the male line, all humans can trace their ancestry back to a single male (Y-chromosomal Adam) at around 60,000 to 90,000 years ago.^[3]

This is consistent with the Toba catastrophe theory that suggests that a bottleneck of the human population occurred c. 70,000 years ago, proposing that the human population was reduced to perhaps 15,000 individuals^[4] when the Toba supervolcano in Indonesia erupted and triggered a major environmental change. The theory is based on geological evidences of sudden climate change and on coalescence evidences of some genes (including mitochondrial DNA, Y-chromosome and some nuclear genes)^[5] and the relatively low level of genetic variation with humans.^[4]

However, such coalescence is genetically expected and does not, in itself, indicate a population bottleneck, because mitochondrial DNA and Y-chromosome DNA are only a small part of the entire genome, and are atypical in that they are inherited exclusively through the mother or through the father, respectively. Most genes in the genome are inherited from either father or mother, and thus can be traced back in time via either matrilineal or patrilineal ancestry.^[6] Research on many genes finds different coalescence points from 2 million years ago to 60,000 years ago when different genes are considered, thus disproving the existence of more recent extreme bottlenecks (i.e., a single breeding pair).^[4][7]

On the other hand, in 2000, a Molecular Biology and Evolution paper suggested a transplanting model or a 'long bottleneck' to account for the limited genetic variation, rather than a catastrophic environmental change.^[8] This would be consistent with suggestions that in sub-Saharan Africa numbers could have dropped at times as low as 2,000, for perhaps as long as 100,000 years, before numbers began to expand again in the Late Stone Age.^[9]

Other animals

Year	American bison (est)
Before 1492	60,000,000
1890	750
2000	360,000

Wisent, also called European bison (Bison bonasus), faced extinction in the early 20th century. The animals living today are all descended from 12 individuals and they have extremely low genetic variation, which may be beginning to affect the reproductive ability of bulls (Luenser et al., 2005). The population of American bison (Bison bison) fell due to overhunting, nearly leading to extinction around the year 1890, though it has since begun to recover (see table).

Overhunting pushed the northern elephant seal to the brink of extinction by the late 19th century. Though they have made a comeback, the genetic variation within the population remains very low.

A classic example of a population bottleneck is that of the northern elephant seal, whose population fell to about 30 in the 1890s. Although it now numbers in the hundreds of thousands, the potential for bottlenecks within colonies remains. Dominant bulls are able to mate with the largest number of females — sometimes as many as 100. With so much of a colony's offspring descended from just one dominant male, genetic diversity is limited making the species more vulnerable to diseases and genetic mutations. The golden hamster is a similarly bottlenecked species, with the vast majority descended from a single litter found in the Syrian desert around 1930. And cheetahs are sufficiently closely related to one another that transplanted skin grafts do not provoke immune responses,^[10] thus suggesting an extreme population bottleneck in the past.

The genome of the giant panda shows evidence of a severe bottleneck that took place about 43,000 years ago.^[11] There is also evidence of at least one primate species, the golden snub-nosed monkey, that also suffered from a bottleneck around this time.

Further deductions can sometimes be inferred from an observed population bottleneck. Among the Galápagos Islands giant tortoises — themselves a prime example of a bottleneck — the comparatively large population on the slopes of Alcedo volcano is significantly less diverse than four other tortoise populations on the same island. DNA analyses date the bottleneck to around 88,000 years before present (YBP).^[12] About 100,000 YBP the volcano erupted violently, burying much of the tortoise habitat deep in pumice and ash.

Bottlenecks also exist among pure-bred animals (e.g., dogs and cats: pugs, Persian) because breeders limit their gene pools by breeding with close relatives for their looks and behaviors. The extensive use of desirable individual animals at the exclusion of others can result in a popular sire effect.

Before Europeans arrived in North America, prairies served as habitats to greater prairie chickens. In Illinois alone their numbers plummeted from over 100 million in 1900 to about 50 in 1990. These declines in population were the result of hunting and habitat destruction, but the random consequences have been a great loss in species diversity. DNA analysis comparing the birds from 1990 and mid-century shows a steep genetic decline in recent decades. The greater prairie chicken is currently experiencing low reproductive success.^[13]

Plants

Research showed that there is no genetic variability in the genome of the Wollemi Pine (Wollemia nobilis), indicating that the species (of which there are only around 100 specimens in the wild and tens of thousands cultivated) went through a severe population bottleneck.

In evolutionary theory

Further information: Evolutionary biology

As a population becomes smaller, genetic drift plays a bigger role in speciation. A land animal like a brown bear might find itself locally reduced to a few dozen pairs on an Arctic island. That likely happened as the last Ice Age came to an end, and the Bering land bridge receded into the sea. In that circumstance, a beneficial trait appearing in an alpha male or two may change the color, size, swimming ability, cold resistance, or aggressiveness of the group in just a few generations.

Minimum viable population size

In conservation biology, minimum viable population size (MVP) helps to determine the effective population size when a population is at risk for extinction (Gilpin and Soulé, 1986 and Soulé, 1987). There is considerable debate about the usefulness of the MVP.

See also

• Population boom
• Baby boom
• Small population size
• Effective population size
• Founder effect

References

1. ^ Population Bottleneck | Macmillan Genetics
2. ^ "Evolution 101". University of California Museum of Paleontology. http://evolution.berkeley.edu/evosite/evo101/IIID3Bottlenecks.shtml. Retrieved 2 February 2011. 
3. ^ Dawkins, Richard (2004). The Ancestor's Tale, A Pilgrimage to the Dawn of Life. Boston: Houghton Mifflin Company. ISBN 0297825038. ISBN. 
4. ^ ^{a b c} Dawkins, Richard (2004). "The Grasshopper's Tale". The Ancestor's Tale, A Pilgrimage to the Dawn of Life. Boston: Houghton Mifflin Company. pp. 416. ISBN 0297825038. ISBN. 
5. ^ Late Pleistocene human population bottlenecks, volcanic winter, and differentiation of modern humans by Stanley H. Ambrose
6. ^ See the chapter All Africa and her progenies in Dawkins, Richard (1995). River Out of Eden. New York: Basic Books. ISBN 0465016065. ISBN. 
7. ^ 'Templeton tree' showing coalescence points of different genes
8. ^ Population Bottlenecks and Pleistocene Human Evolution
9. ^ BBC news : Human line 'nearly split in two'
10. ^ HowStuffWorks "The Endangered Cheetah"
11. ^ Zhang, Ya-ping, et al. (2002). "Genetic diversity and conservation of endangered animal species" (PDF). Pure Appl. Chem. 74 (Vol. 74, No. 4): 575. doi:10.1351/pac200274040575. http://www.iupac.org/publications/pac/2002/pdf/7404x0575.pdf. 
12. ^ Luciano B. Beheregaray, Claudio Ciofi, Dennis Geist, James P. Gibbs, Adalgisa Caccone, and Jeffrey R. Powell (2003). "Genes Record a Prehistoric Volcano Eruption in the Galápagos" (PDF). Science 302 (5642): 75. doi:10.1126/science.1087486. PMID 14526072. http://www.sciencemag.org/content/302/5642/75.full.pdf?sid=f4e0c19b-a2c2-470a-b39f-a5bb82452ecd. 
13. ^ "Brain & Ecology Deep Structure Lab". Brain & Ecology Comparative Group. Brain & Ecology Deepstruc. System Co., Ltd.. 2010. http://www.brainecology.net/info/show.asp?bh=73. Retrieved March 13, 2011. 

• Gilpin, M.E., & Soulé, M.E. (1986). Minimum viable populations: The processes of species extinctions. In M. Soulé (Ed.). Conservation biology: The science of scarcity and diversity, pp. 13-34. Sunderland Mass: Sinauer Associates.
• Luenser, K., J. Fickel1, A. Lehnen, S. Speck and A. Ludwig. 2005. Low level of genetic variability in European bisons (Bison bonasus) from the Bialowieza National Park in Poland. European Journal of Wildlife Research 51 (2): 84-87.
• Soulé, M. (Ed.). (1987). Viable populations for conservation. Cambridge: Cambridge Univ. Press.

External links

• ScienceDaily: Big Bang Theory Of Human Evolution?
• Northern Elephant Seal History
• Masatoshi Nei (May 1, 2005). "Bottlenecks, Genetic Polymorphism and Speciation". Genetics (The Genetics Society of America) 170 (1): 1–4. PMC 1449701. PMID 15914771. http://www.genetics.org/cgi/content/full/170/1/1. Retrieved 2008-10-19. 

v d e Topics in population genetics Key concepts Hardy-Weinberg law · Genetic linkage · Linkage disequilibrium · Fisher's fundamental theorem · Neutral theory · Price equation Selection Natural · Sexual · Artificial · Ecological Effects of selection on genomic variation Genetic hitchhiking · Background selection Genetic drift Small population size · Population bottleneck · Founder effect · Coalescence · Balding–Nichols model Founders R. A. Fisher · J. B. S. Haldane · Sewall Wright Related topics Evolution · Microevolution · Evolutionary game theory · Fitness landscape · Genetic genealogy List of evolutionary biology topics

v d e Topics on human population Major articles World population · Family planning · Green revolution · Overpopulation · Over-consumption (water crisis) · Reproductive rights  · Sustainable development Biological topics Population biology · Population control (one-child policy · Immigration reduction) · Population decline · Population density (physiological density) · Population growth · Population pyramid · Projections of population growth · Zero population growth Population ecology Carrying capacity · Ecological footprint · I = P • A • T · Malthusian growth model · World3 model · Food security · World energy consumption · World energy resources · Habitat destruction · Optimum population  · Overshoot (ecology) Literary works A Modest Proposal · An Essay on the Principle of Population · Operating Manual for Spaceship Earth · How Much Land Does a Man Need? · The Limits to Growth · The Population Bomb · The Ultimate Resource · The Skeptical Environmentalist Lists Most highly populated countries · Metropolitan areas by population Events and organizations International Conference on Population and Development  · Optimum Population Trust  · United Nations Population Fund · World Population Foundation Related articles World Population Day · "The Day of Five Billion" · "The Day of Six Billion" · "Day of Seven Billion" · "Ecological Debt Day" · Easter Island downfall · Classic Maya collapse · Holocene extinction · Fertility and intelligence

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