The huntingtingene, also called the HTT or HD (Huntington disease) gene, is the IT15 ("interesting transcript 15") gene, which codes for a protein called the huntingtin protein. The gene and its product are under heavy investigation as part of Huntington's disease clinical research and the suggested role for huntingtin in long-term memory storage.
It is variable in its structure, as the many polymorphisms of the gene can lead to variable numbers of glutamine residues present in the protein. In its wild-type (normal) form, it contains 6-35 glutamine residues. However, in individuals affected by Huntington's disease (an autosomal dominantgenetic disorder), it contains more than 36 glutamine residues (highest reported repeat length is about 250). Its commonly used name is derived from this disease; previously, the IT15 label was commonly used.
The mass of huntingtin protein is dependent largely on the number
of glutamine residues it has, the predicted mass is around 350 kDa.
Normal huntingtin is generally accepted to be 3144 amino acids in size.
The exact function of this protein is not known, but it plays an
important role in nerve cells.
Within cells, huntingtin may or may not be involved in signaling,
transporting materials, binding proteins and other structures, and
protecting against programmed cell death (apoptosis). The huntingtin protein is required for normal development before birth. It is expressed in many tissues in the body, with the highest levels of expression seen in the brain.
Gene
The 5' end of the HD gene has a sequence of three DNA bases, cytosine-adenine-guanine (CAG), coding for the amino acid glutamine, that is repeated multiple times. This region is called a trinucleotide repeat. Normal persons have a CAG repeat count of between seven and 35 repeats.
The HD gene is located on the short (p) arm of chromosome 4 at position 16.3, from base pair 3,074,510 to base pair 3,243,960.
Protein
Function
The function of huntingtin is unclear. It is essential for development, and absence of huntingtin is lethal in mice. The protein has no sequence homology with other proteins and is highly expressed in neurons and testes in humans and rodents. Huntingtin upregulates the expression of Brain Derived Neurotrophic Factor (BDNF) at the transcription level, but the mechanism by which huntingtin regulates gene expression has not been determined. From immunohistochemistry, electron microscopy, and subcellular fractionation studies of the molecule, it has been found that huntingtin is primarily associated with vesicles and microtubules. These appear to indicate a functional role in cytoskeletal anchoring or transport of mitochondria. The Htt protein is involved in vesicle trafficking as it interacts with HIP1, a clathrin-binding protein, to mediate endocytosis, the trafficking of materials into a cell. Huntingtin has also been shown to have a role in the establishment in epithelial polarity through its interaction with RAB11A.
Interactions
Huntingtin has been found to interact directly with at least 19 other proteins,
of which six are used for transcription, four for transport, three for
cell signalling, and six others of unknown function (HIP5, HIP11, HIP13,
HIP15, HIP16, and CGI-125). Over 100 interacting proteins have been found, such as huntingtin-associated protein 1 (HAP1) and huntingtin interacting protein 1 (HIP1), these were typically found using two-hybrid screening and confirmed using immunoprecipitation.
Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CAG repeats
Repeat count
Classification
Disease status
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Normal
Unaffected
27–35
Intermediate
Unaffected
36–40
Reduced penetrance
+/- Affected
>40
Full penetrance
Affected
Huntington's disease
(HD) is caused by a mutated form of the huntingtin gene, where
excessive (more than 36) CAG repeats result in formation of an unstable
protein. These expanded repeats lead to production of a huntingtin protein that contains an abnormally long polyglutamine tract at the N-terminus. This makes it part of a class of neurodegenerative disorders known as trinucleotide repeat disorders or polyglutamine disorders. The key sequence which is found in Huntington's disease is a trinucleotide repeat expansion of glutamine
residues beginning at the 18th amino acid. In unaffected individuals,
this contains between 9 and 35 glutamine residues with no adverse
effects. However, 36 or more residues produce an erroneous form of Htt, "mHtt" (standing for mutant Htt). Reduced penetrance is found in counts 36-39.
Enzymes in the cell often cut this elongated protein into
fragments. The protein fragments form abnormal clumps, known as neuronal
intranuclear inclusions (NIIs), inside nerve cells, and may attract
other, normal proteins into the clumps. The presence of these clumps was
once thought to play a causal role in Huntington disease.
Further research undermined this conclusion by showing the presence of
NIIs actually extended the life of neurons and acted to reduce
intracellular mutant huntingtin in neighboring neurons.
Thus, the likelihood of neuronal death can be predicted by accounting
for two factors: (1) the length of CAG repeats in the Huntingtin gene
and (2) the neuron's exposure to diffuse intracellular mutant huntingtin
protein. NIIs (protein clumping) can thereby be construed as a coping
mechanism—as opposed to a pathogenic mechanism—to stem neuronal death by
decreasing the amount of diffuse huntingtin. This process is particularly likely to occur in the striatum (a part of the brain that coordinates movement) primarily, and the frontal cortex (a part of the brain that controls thinking and emotions).
People with 36 to 40 CAG repeats may or may not develop the signs
and symptoms of Huntington disease, while people with more than 40
repeats will develop the disorder during a normal lifetime. When there
are more than 60 CAG repeats, the person develops a severe form of HD
known as juvenile HD.
Therefore, the number of CAG (the sequence coding for the amino acid
glutamine) repeats influences the age of onset of the disease. No case
of HD has been diagnosed with a count less than 36.
As the altered gene is passed from one generation to the next,
the size of the CAG repeat expansion can change; it often increases in
size, especially when it is inherited from the father. People with 28 to
35 CAG repeats have not been reported to develop the disorder, but
their children are at risk of having the disease if the repeat expansion
increases.
The Golden toad of Monteverde, Costa Rica, was among the first casualties of amphibian declines. Formerly abundant, it was last seen in 1989.
The decline in amphibian populations is an ongoing mass extinction of amphibian species worldwide. Since the 1980s, decreases in amphibian populations, including population crashes and mass localized extinctions, have been observed in locations all over the world. These declines are known as one of the most critical threats to global biodiversity, and several causes are believed to be involved, including disease, habitat destruction and modification, exploitation, pollution, pesticide use, introduced species, and ultraviolet-B
radiation (UV-B). However, many of the causes of amphibian declines are
still poorly understood, and the topic is currently a subject of much
ongoing research. Calculations based on extinction rates suggest that
the current extinction rate of amphibians could be 211 times greater
than the background extinction rate and the estimate goes up to 25,000–45,000 times if endangered species are also included in the computation.
Although scientists began observing reduced populations of
several European amphibian species already in the 1950s, awareness of
the phenomenon as a global problem and its subsequent classification as a
modern-day mass extinction only dates from the 1980s. By 1993, more
than 500 species of frogs and salamanders present on all five continents
were in decline. Today, the phenomenon of declining amphibian
populations affects thousands of species in all types of ecosystems and
is thus recognized as one of the most severe examples of the Holocene extinction, with severe implications for global biodiversity.
Background
In the past three decades, declines in populations of amphibians (the class of organisms that includes frogs, toads, salamanders, newts, and caecilians)
have occurred worldwide. In 2004, the results were published of the
first worldwide assessment of amphibian populations, the Global
Amphibian Assessment. This found that 32% of species were globally
threatened, at least 43% were experiencing some form of population
decrease, and that between 9 and 122 species have become extinct since
1980. As of 2010, the IUCN Red List, which incorporates the Global Amphibian Assessment and subsequent updates, lists 486 amphibian species as "Critically Endangered".
Despite the high risk this group faces, recent evidence suggests the
public is growing largely indifferent to this and other environmental
problems, posing serious problems for conservationists and environmental
workers alike.
Habitat loss, disease and climate change are thought to be responsible for the drastic decline in populations in recent years.
Declines have been particularly intense in the western United States, Central America, South America, eastern Australia and Fiji
(although cases of amphibian extinctions have appeared worldwide).
While human activities are causing a loss of much of the world's
biodiversity, amphibians appear to be suffering much greater effects
than other classes of organism. Because amphibians generally have a
two-staged life cycle consisting of both aquatic (larvae) and terrestrial (adult) phases, they are sensitive to both terrestrial and aquatic environmental effects. Because their skins are highly permeable, they may be more susceptible to toxins in the environment than other organisms such as birds or mammals. Many scientists believe that amphibians serve as "canaries in a coal mine," and that declines in amphibian populations and species indicate that other groups of animals and plants will soon be at risk.
Declines in amphibian populations were first widely recognized in the late 1980s, when a large gathering of herpetologists reported noticing declines in populations in amphibians across the globe. Among these species, the Golden toad (Bufo periglenes) endemic to Monteverde, Costa Rica,
featured prominently. It was the subject of scientific research until
populations suddenly crashed in 1987 and it had disappeared completely
by 1989. Other species at Monteverde, including the Monteverde Harlequin Frog (Atelopus varius),
also disappeared at the same time. Because these species were located
in the pristine Monteverde Cloud Forest Reserve, and these extinctions
could not be related to local human activities, they raised particular
concern among biologists.
Initial skepticism
When
amphibian declines were first presented as a conservation issue in the
late 1980s, some scientists remained unconvinced of the reality and
gravity of the conservation issue.
Some biologists argued that populations of most organisms, amphibians
included, naturally vary through time. They argued that the lack of
long-term data on amphibian populations made it difficult to determine
whether the anecdotal declines reported by biologists were worth the
(often limited) time and money of conservation efforts.
However, since this initial skepticism, biologists have come to a
consensus that declines in amphibian populations are a real and severe
threat to biodiversity.
This consensus emerged with an increase in the number of studies that
monitored amphibian populations, direct observation of mass mortality in
pristine sites that lacked apparent cause, and an awareness that
declines in amphibian populations are truly global in nature.
Potential causes
Numerous
potential explanations for amphibian declines have been proposed. Most
or all of these causes have been associated with some population
declines, so each cause is likely to affect in certain circumstances but
not others. Many of the causes of amphibian declines are well
understood, and appear to affect other groups of organisms as well as
amphibians. These causes include habitat modification and
fragmentation, introduced predators or competitors, introduced species,
pollution, pesticide use, or over-harvesting. However, many amphibian
declines or extinctions have occurred in pristine habitats where the
above effects are not likely to occur. The causes of these declines are
complex, but many can be attributed to emerging diseases, climate
change, increased ultraviolet-B radiation, or long-distance transmission
of chemical contaminants by wind.
Artificial lighting has been suggested as another potential
cause. Insects are attracted to lights making them scarcer within the
amphibian habitats.
Habitat modification
Habitat
modification or destruction is one of the most dramatic issues
affecting amphibian species worldwide. As amphibians generally need
aquatic and terrestrial habitats to survive, threats to either habitat
can affect populations. Hence, amphibians may be more vulnerable to
habitat modification than organisms that only require one habitat type.
Large scale climate changes may further be modifying aquatic habitats,
preventing amphibians from spawning altogether.
Habitat fragmentation
Habitat fragmentation occurs when habitats are isolated by habitat
modification, such as when a small area of forest is completely
surrounded by agricultural fields. Small populations that survive
within such fragments are often susceptible to inbreeding, genetic drift, or extinction due to small fluctuations in the environment.
Pollution and chemical contaminants
There is evidence of chemical pollutants causing frog developmental deformities (extra limbs, or malformed eyes). Pollutants have varying effects on frogs. Some alter the central nervous system; others like atrazine
cause a disruption in the production and secretion of hormones.
Experimental studies have also shown that exposure to commonly used
herbicides such as glyphosate (Tradename Roundup) or insecticides such as malathion or carbaryl greatly increase mortality of tadpoles.
Additional studies have indicated that terrestrial adult stages of
amphibians are also susceptible to non-active ingredients in Roundup,
particularly POEA, which is a surfactant.
Atrazine has been shown to cause male tadpoles of African clawed frogs
to become hermaphroditic with development of both male and female
organs. Such feminization has been reported in many parts of the world.
In a study conducted in a laboratory at Uppsala University in Sweden,
more than 50% of frogs exposed to levels of estrogen-like pollutants
existing in natural bodies of water in Europe and the United States
became females. Tadpoles exposed even to the weakest concentration of
estrogen were twice as likely to become females while almost all of the
control group given the heaviest dose became female.
While most pesticide effects are likely to be local and restricted to areas near agriculture, there is evidence from the Sierra Nevada mountains of the western United States that pesticides are traveling long distances into pristine areas, including Yosemite National Park in California.
Some recent evidence points to ozone as a possible contributing factor to the worldwide decline of amphibians.
Ozone depletion, ultraviolet radiation and cloud cover
Like many other organisms, increasing ultraviolet-B (UVB) radiation due to stratospheric ozone depletion and other factors may harm the DNA of amphibians, particularly their eggs.
The amount of damage depends upon the life stage, the species type and
other environmental parameters. Salamanders and frogs that produce less photolyase,
an enzyme that counteracts DNA damage from UVB, are more susceptible to
the effects of loss of the ozone layer. Exposure to ultraviolet
radiation may not kill a particular species or life stage but may cause
sublethal damage.
More than three dozen species of amphibians have been studied,
with severe effects reported in more than 40 publications in
peer-reviewed journals representing authors from North America, Europe
and Australia. Experimental enclosure approaches to determine UVB
effects on egg stages have been criticized; for example, egg masses were
placed at water depths much shallower than is typical for natural
oviposition sites. While UVB radiation is an important stressor for
amphibians, its effect on the egg stage may have been overstated.
Anthropogenic climate change has likely exerted a major effect on
amphibian declines. For example, in the Monteverde Cloud Forest, a
series of unusually warm years led to the mass disappearances of the
Monteverde Harlequin frog and the Golden Toad. An increased level of cloud cover, a result of geoengineering
and global warming, which has warmed the nights and cooled daytime
temperatures, has been blamed for facilitating the growth and
proliferation of the fungus Batrachochytrium dendrobatidis (the causative agent of the fungal infection chytridiomycosis).
Although the immediate cause of the die offs was the chytrid, climate
change played a pivotal role in the extinctions. Researchers included
this subtle connection in their inclusive climate-linked epidemic
hypothesis, which acknowledged climatic change as a key factor in
amphibian extinctions both in Costa Rica and elsewhere.
New evidence has shown global warming to also be capable of directly degrading toads' body condition and survivorship.
Additionally, the phenomenon often colludes with landscape
alteration, pollution, and species invasions to effect amphibian
extinctions.
Disease
A number of diseases have been related to mass die-offs or declines in populations of amphibians, including "red-leg" disease (Aeromonas hydrophila), Ranavirus (family Iridoviridae), Anuraperkinsus, and chytridiomycosis.
It is not entirely clear why these diseases have suddenly begun to
affect amphibian populations, but some evidence suggests that these
diseases may have been spread by humans, or may be more virulent when
combined with other environmental factors.
Trematodes
Trematode cyst-infected Pacific Tree Frog (Hyla regilla)
with supernumerary limbs, from La Pine, Deschutes County, Oregon,
1998-9. This 'category I' deformity (polymelia) is believed to be caused
by the trematode cyst infection. The cartilage is stained blue and
calcified bones in red.
There is considerable evidence that parasitic trematodeplatyhelminths (a type of fluke) have contributed to developmental abnormalities and population declines of amphibians in some regions. These trematodes of the genus Ribeiroia
have a complex life cycle with three host species. The first host
includes a number of species of aquatic snails. The early larval stages
of the trematodes then are transmitted into aquatic tadpoles, where the
metacercariae (larvae) encyst in developing limb buds. These encysted
life stages produce developmental abnormalities in post-metamorphic
frogs, including additional or missing limbs. These abnormalities increase frog predation by aquatic birds, the final host of the trematode.
A study showed that high levels of nutrients used in farming and
ranching activities fuel parasite infections that have caused frog
deformities in ponds and lakes across North America. The study showed
increased levels of nitrogen and phosphorus cause sharp hikes in the
abundance of trematodes, and that the parasites subsequently form cysts
in the developing limbs of tadpoles causing missing limbs, extra limbs
and other severe malformations including five or six extra or even no
limbs.
Chytridiomycosis
A chytrid-infected frog
In 1998, following large-scale frog deaths in Australia and Central
America, research teams in both areas came up with identical results: a
previously undescribed species of pathogenic fungus, Batrachochytrium dendrobatidis. It is now clear that many recent extinctions of amphibians in Australia and the Americas are linked to this fungus. This fungus belongs to a family of saprobes known as chytrids that are not generally pathogenic.
The disease caused by Batrachochytrium dendrobatidis is called chytridiomycosis. Frogs infected by this disease generally show skin lesions and hyperkeratosis,
and it is believed that death occurs because of interference with skin
functions including maintenance of fluid balance, electrolyte homeostasis, respiration and role as a barrier to infections. The time from infection to death has been found to be 1–2 weeks in experimental tests, but infected animals can carry the fungus as long as 220 days. There are several hypotheses on the transmission and vectors of the fungus.
Subsequent research has established that the fungus has been
present in Australia since at least 1978, and present in North America
since at least the 1970s. The first known record of chytrid infection
in frogs is in the African Clawed Frog, Xenopus laevis.
Because Xenopus are sold in pet shops and used in laboratories
around the world, it is possible that the chytrid fungus may have been
exported from Africa.
Introduced predators
Non-native predators and competitors have also been found to affect the viability of frogs in their habitats. The mountain yellow-legged frog which typically inhabits the Sierra Nevada lakes have seen a decline in numbers due to stocking of non-native fish (trout) for recreational fishing. The developing tadpoles and froglets fall prey to the fish in large numbers. This interference in the frog's three-year metamorphosis is causing a decline that is manifest throughout their ecosystem.
Increased noise levels
Frogs
and toads are highly vocal, and their reproductive behaviour often
involves the use of vocalizations. There have been suggestions that
increased noise levels caused by human activities may be contributing to
their declines. In a study in Thailand, increased ambient noise levels were shown to decrease calling in some species and to cause an increase in others. This has, however, not been shown to be a cause for the widespread decline.
Symptoms of stressed populations
Amphibian
populations in the beginning stages of decline often exude a number of
signs, which may potentially be used to identify at-risk segments in
conservation efforts. One such sign is developmental instability, which
has been proven as evidence of environmental stress.
This environmental stress can potentially raise susceptibility to
diseases such as chytridiomycosis, and thus lead to amphibian declines.
In a study conducted in Queensland, Australia, for example, populations of two amphibian species, Litoria nannotis and Litoria genimaculata,
were found to exhibit far greater levels of limb asymmetry in
pre-decline years than in control years, the latter of which preceded
die offs by an average of 16 years.
Learning to identify such signals in the critical period before
population declines occur might greatly improve conservation efforts.
Conservation measures
The first response to reports of declining amphibian populations was
the formation of the Declining Amphibian Population Task Force (DAPTF)
in 1990. DAPFT led efforts for increased amphibian population monitoring
in order to establish the extent of the problem, and established
working groups to look at different issues. Results were communicated through the newsletter Froglog.
Much of this research went into the production of the first
Global Amphibian Assessment (GAA), which was published in 2004 and
assessed every known amphibian species against the IUCN Red List
criteria. This found that approximately one third of amphibian species
were threatened with extinction.
As a result of these shocking findings an Amphibian Conservation Summit
was held in 2005, because it was considered "morally irresponsible to
document amphibian declines and extinctions without also designing and
promoting a response to this global crisis".
Outputs from the Amphibian Conservation Summit included the first Amphibian Conservation Action Plan (ACAP) and to merge the DAPTF and the Global Amphibian Specialist Group into the IUCN SSC Amphibian Specialist Group (ASG).
The ACAP established the elements required to respond to the crisis,
including priority actions on a variety of thematic areas. The ASG is a
global volunteer network of dedicated experts who work to provide the
scientific foundation for effective amphibian conservation action around
the world.
On 16 February 2007, scientists worldwide met in Atlanta, U.S., to form a group called the Amphibian Ark to help save more than 6,000 species of amphibians from disappearing by starting captive breeding programmes.
Areas with noticed frog extinctions, like Australia, have few
policies that have been created to prevent the extinction of these
species. However, local initiatives have been placed where conscious
efforts to decrease global warming will also turn into a conscious
effort towards saving the frogs. In South America, where there is also
an increased decline of amphibian populations, there is no set policy to
try to save frogs. Some suggestions would include getting entire
governments to place a set of rules and institutions as a source of
guidelines that local governments have to abide by.
A critical issue is how to design protected areas for amphibians
which will provide suitable conditions for their survival. Conservation
efforts through the use of protected areas have shown to generally be a
temporary solution to population decline and extinction because the
amphibians become inbred. It is crucial for most amphibians to maintain a high level of genetic variation through large and more diverse environments.
Education of local people to protect amphibians is crucial, along
with legislation for local protection and limiting the use of toxic
chemicals, including some fertilizers and pesticides in sensitive
amphibian areas.
Founder effect: The original population (left) could give rise to different founder populations (right).
In population genetics, the founder effect
is the loss of genetic variation that occurs when a new population is
established by a very small number of individuals from a larger
population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.
In the figure shown, the original population has nearly equal
numbers of blue and red individuals. The three smaller founder
populations show that one or the other color may predominate (founder
effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect, though it is not strictly a new population.
The founder effect occurs when a small group of migrants that is
not genetically representative of the population from which they came
establish in a new area. In addition to founder effects, the new population is often a very small population, so shows increased sensitivity to genetic drift, an increase in inbreeding, and relatively low genetic variation.
Founder mutation
In genetics, a founder mutation is a mutation that appears in the DNA
of one or more individuals which are founders of a distinct population.
Founder mutations initiate with changes that occur in the DNA and can
be passed down to other generations.
Any organism—from a simple virus to something complex like a
mammal—whose progeny carry its mutation has the potential to express the
founder effect, for instance a goat or a human.
Founder mutations originate in long stretches of DNA on a single chromosome; indeed, the original haplotype
is the whole chromosome. As the generations progress, the proportion of
the haplotype that is common to all carriers of the mutation is
shortened (due to genetic recombination). This shortening allows scientists to roughly estimate the age of the mutation.
General
The founder effect is a special case of genetic drift,
occurring when a small group in a population splinters off from the
original population and forms a new one. The new colony may have less
genetic variation than the original population, and through the random
sampling of alleles during reproduction of subsequent generations, continue rapidly towards fixation. This consequence of inbreeding makes the colony more vulnerable to extinction.
When a newly formed colony is small, its founders can strongly
affect the population's genetic makeup far into the future. In humans,
who have a slow reproduction rate, the population will remain small for
many generations, effectively amplifying the drift effect generation
after generation until the population reaches a certain size. Alleles
which were present but relatively rare in the original population can
move to one of two extremes. The most common one is that the allele is
soon lost altogether, but the other possibility is that the allele
survives and within a few generations has become much more dispersed
throughout the population. The new colony can experience an increase in
the frequency of recessive alleles, as well, and as a result, an increased number who are homozygous for certain recessive traits.
The variation in gene frequency between the original population and colony may also trigger the two groups to diverge significantly over the course of many generations. As the variance, or genetic distance, increases, the two separated populations may become distinctively different, both genetically and phenotypically,
although not only genetic drift, but also natural selection, gene flow
and mutation all contribute to this divergence. This potential for
relatively rapid changes in the colony's gene frequency led most
scientists to consider the founder effect (and by extension, genetic
drift) a significant driving force in the evolution of new species. Sewall Wright was the first to attach this significance to random drift and small, newly isolated populations with his shifting balance theory of speciation. Following behind Wright, Ernst Mayr
created many persuasive models to show that the decline in genetic
variation and small population size accompanying the founder effect were
critically important for new species to develop.
However, much less support for this view is shown today, since the
hypothesis has been tested repeatedly through experimental research, and
the results have been equivocal at best. Speciation by genetic drift is a specific case of peripatric speciation which in itself occurs in rare instances.
It takes place when a random change in genetic frequency of population
favours the survival of a few organisms of the species with rare genes
which cause reproductive mutation. These surviving organisms then breed
among themselves over a long period of time to create a whole new
species whose reproductive systems or behaviors are no longer compatible
with the original population.
Serial founder effect
Serial
founder effects have occurred when populations migrate over long
distances. Such long-distance migrations typically involve relatively
rapid movements followed by periods of settlement. The populations in
each migration carry only a subset of the genetic diversity carried from
previous migrations. As a result, genetic differentiation tends to
increase with geographic distance as described by the "isolation by
distance" model. The migration of humans out of Africa is characterized by serial founder effects.
Africa has the highest degree of genetic diversity of any continent,
which is consistent with an African origin of modern humans. After the
initial migration from Africa, the Indian subcontinent was the first
major settling point for modern humans. Consequently, India has the
second-highest genetic diversity in the world. In general, the genetic
diversity of the Indian subcontinent is a subset of Africa, and the
genetic diversity outside Africa is a subset of India.
In island ecology
Founder populations are essential to the study of island biogeography and island ecology.
A natural "blank slate" is not easily found, but a classic series of
studies on founder population effects was done following the
catastrophic 1883 eruption of Krakatoa, which erased all life on the island. Another continuing study has been following the biocolonization of Surtsey, Iceland, a new volcanic island that erupted offshore between 1963 and 1967. An earlier event, the Toba eruption in Sumatra about 73,000 years ago, covered some parts of India with 3–6 m (10–20 ft) of ash, and must have coated the Nicobar Islands and Andaman Islands, much nearer in the ash fallout cone, with life-smothering layers, forcing the restart of their biodiversity.
However, not all founder effect studies are initiated after a
natural disaster; some scientists study the reinstatement of a species
that became locally extinct. Hajji and others, and Hundertmark & Van
Daele, studied the current population statuses of past founder effects
in Corsican red deer and Alaskan elk, respectively. Corsican red deer are still listed as an endangered
species, decades after a severe bottleneck. They inhabit the Tyrrhenian
islands and surrounding mainlands currently, and before the bottleneck,
but Hajji and others wanted to know how the deer originally got to the
islands, and from what parent population or species they were derived.
Through molecular analysis, they were able to determine a possible
lineage, with red deer from the islands of Corsica and Sardinia
being the most related to one another. These results are promising, as
the island of Corsica was repopulated with red deer from the Sardinian
island after the original Corsican red deer population became extinct,
and the deer now inhabiting the island of Corsica are diverging from
those inhabiting Sardinia.
Kolbe and others set up a pair of genetically sequenced and morphologically examined lizards
on seven small islands to watch each new population's growth and
adaptation to its new environment. Specifically, they were looking at
the effects on limb length and perch width, both widely varying
phenotypic ranges in the parent population. Unfortunately, immigration
did occur, but the founder effect and adaptive differentiation, which
could eventually lead to peripatric speciation, were statistically and
biologically significant between the island populations after a few
years. The authors also point out that although adaptive differentiation
is significant, the differences between island populations best reflect
the differences between founders and their genetic diversity that has
been passed down through the generations.
Founder effects can affect complex traits, such as song diversity. In the Common Myna (Acridotheres tristis),
the percentage of unique songs within a repertoire and within‐song
complexity were significantly lower in birds from founder populations.
Among human populations
Due
to various migrations throughout human history, founder effects are
somewhat common among humans in different times and places. The French Canadians of Quebec
are a classical example of founder population. Over 150 years of French
colonization, between 1608 and 1760, an estimated 8,500 pioneers
married and left at least one descendant on the territory.
Following the takeover of the colony by the British crown in 1760,
immigration from France effectively stopped, but descendants of French
settlers continued to grow in number mainly because of high fertility
rate. Intermarriage occurred mostly with the deported Acadians
and migrants coming from the British Isles. Since the 20th century,
immigration in Quebec and mixing of French Canadians involve people from
all over the world. While the French Canadians of Quebec today may be
partly of other ancestries, the genetic contribution of the original
French founders is predominant, explaining about 90% of regional gene
pools, while Acadians (descended from other French settlers in eastern
Canada) explain4% and British 2%, with Native American and other groups contributing less.
In humans, founder effects can arise from cultural isolation, and inevitably, endogamy. For example, the Amish
populations in the United States exhibit founder effects because they
have grown from a very few founders, have not recruited newcomers, and
tend to marry within the community. Though still rare, phenomena such as
polydactyly (extra fingers and toes, a symptom of a condition such as Weyers acrodental dysostosis or Ellis-van Creveld syndrome) are more common in Amish communities than in the American population at large. Maple syrup urine disease affects about one out of 180,000 infants in the general population. Due in part to the founder effect, however, the disease has a much higher prevalence in children of Amish, Mennonite, and Jewish descent. Similarly, a high frequency of fumarase deficiency exists among the 10,000 members of the Fundamentalist Church of Jesus Christ of Latter Day Saints, a community which practices both endogamy and polygyny, where an estimated 75-80% of the community are blood relatives of just two men—founders John Y. Barlow and Joseph Smith Jessop.
The island of Pingelap
also suffered a population bottleneck in 1775 following a typhoon that
had reduced the population to only 20 people. As a result complete achromatopsia with a rate of occurrence of roughly 10% with an additional 30% being carriers of this recessive condition.
Around 1814, a small group of British colonists founded a settlement on Tristan da Cunha,
a group of small islands in the Atlantic Ocean, midway between Africa
and South America. One of the early colonists apparently carried a rare,
recessive allele for retinitis pigmentosa, a progressive form of blindness that afflicts homozygous
individuals. As late as 1961, the majority of the genes in the gene
pool on Tristan were still derived from 15 original ancestors; as a
consequence of the inbreeding, of 232 people tested in 1961, four were
suffering from retinitis pigmentosa. This represents a prevalence of 1
in 58, compared with a worldwide prevalence of around 1 in 4,000.
The abnormally high rate of twin births in Cândido Godói could be explained by the founder effect.
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