Decline in amphibian populations

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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). 

An adult male Ecnomiohyla rabborum in the Atlanta Botanical Garden, a species ravaged by Batrachochytrium dendrobatidis in its native habitat. It was the last known surviving member of its species, and with its death on Sept 28, 2016, the species is believed to be extinct.

 

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 trematode platyhelminths (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. 

Pacific Tree Frog with limb malformation induced by Ribeiroia ondatrae

 

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

From Wikipedia, the free encyclopedia

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) explain 4% 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.

Population bottleneck

From Wikipedia, the free encyclopedia

 

Population bottleneck followed by recovery or extinction

 

A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events (such as famines, earthquakes, floods, fires, disease, or droughts) or human activities (such as genocide). Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring through sexual reproduction. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the frequency of the fitter genes within the gene pool is increased, while the pool itself is reduced. 

The genetic drift caused by a population bottleneck can change the proportional random distribution of alleles and even lead to loss of alleles. The chances of inbreeding and genetic homogeneity can increase, possibly leading to inbreeding depression. Smaller population size can also cause deleterious mutations to accumulate.

A slightly different form of bottleneck can occur if a small group becomes reproductively (e.g. geographically) separated from the main population, such as through a founder event, e.g. if a few members of a species successfully colonize a new isolated island, or from small captive breeding programs such as animals at a zoo. Alternatively, invasive species can undergo population bottlenecks through founder events when introduced into their invaded range.

Population bottlenecks play an important role in conservation biology and in the context of agriculture (biological and pest control).

Examples

Humans

According to a 1999 model, a severe population bottleneck, or more specifically a full-fledged speciation, occurred among a group of Australopithecina as they transitioned into the species known as Homo erectus two million years ago. It is believed that additional bottlenecks must have occurred since Homo erectus started walking the Earth, but current archaeological, paleontological, and genetic data is inadequate to give much reliable information about such conjectured bottlenecks. That said, the possibility of a severe recent species-wide bottleneck cannot be ruled out.

A 2005 study from Rutgers University theorized that the pre-1492 native populations of the Americas are the descendants of only 70 individuals who crossed the land bridge between Asia and North America.

Toba catastrophe theory

The controversial Toba catastrophe theory, presented in the late 1990s to early 2000s, suggested that a bottleneck of the human population occurred c. 70,000 years ago, proposing that the human population was reduced to perhaps 10,000–30,000 individuals when the Toba supervolcano in Indonesia erupted and triggered a major environmental change. Parallel bottlenecks were proposed to exist among chimpanzees, gorillas, rhesus macaques, orangutans and tigers. The hypothesis was based on geological evidence of sudden climate change and on coalescence evidence of some genes (including mitochondrial DNA, Y-chromosome DNA and some nuclear genes) and the relatively low level of genetic variation in humans.

However, subsequent research, especially in the 2010s, appeared to refute both the climate argument and the genetic argument. Recent research shows the extent of climate change was much smaller than believed by proponents of the theory. In addition, coalescence times for Y-chromosomal and mitochondrial DNA have been revised to well above 100,000 years since 2011. Finally, such coalescence would 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. Genetic material inherited exclusively from either father or mother can be traced back in time via either matrilineal or patrilineal ancestry.

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. 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.

Other animals

European bison, also called wisent (Bison bonasus), faced extinction in the early 20th century. The animals living today are all descended (except those in South Dakota at the time), from 12 individuals and they have extremely low genetic variation, which may be beginning to affect the reproductive ability of bulls. 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.

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 of domesticated hamsters descended from a single litter found in the Syrian desert around 1930, and very few wild golden hamsters remaining. 

An extreme example of a population bottleneck is the New Zealand Black Robin, of which every specimen today is a descendant of a single female, called Old Blue. The Black Robin population is still recovering from its low point of only five individuals in 1980.

The genome of the giant panda shows evidence of a severe bottleneck about 43,000 years ago. There is also evidence of at least one primate species, the golden snub-nosed monkey, that also suffered from a bottleneck around this time. An unknown environmental event is suspected to have caused the bottlenecks observed in both of these species. The bottlenecks likely caused the low genetic diversity observed in both species.

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 the 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). About 100,000 YBP the volcano erupted violently, deeply burying much of the tortoise habitat in pumice and ash. 

Before Europeans arrived in North America, prairies served as habitats to greater prairie chickens. In Illinois alone, the number of greater prairie chickens 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 also caused 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.

Population bottlenecking poses a major threat to the stability of species populations as well. Papilio homerus is the largest butterfly in the Americas and is endangered according to the IUCN. The disappearance of a central population poses a major threat of population bottleneck. The remaining two populations are now geographically isolated and the populations face an unstable future with limited remaining opportunity for gene flow.

Genetic bottlenecks exist in cheetahs.

Selective breeding

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

Selective breeding for dog breeds caused constricting breed-specific bottlenecks. These bottlenecks have led to dogs having an average of 2-3% more genetic loading than gray wolves. The strict breeding programs and population bottlenecks have led to the prevalence of diseases such as heart disease, blindness, cancers, hip dysplasia, cataracts, and more.

Selective breeding to produce high-yielding crops has caused genetic bottlenecks in these crops and has led to genetic homogeneity. This reduced genetic diversity in many crops could lead to broader susceptibility to new diseases or pests, which threatens global food security.

Plants

Research showed that there is incredibly low, nearly undetectable amounts of genetic diversity in the genome of the Wollemi pine (Wollemia nobilis). The IUCN found a population count of 80 mature individuals and about 300 seedlings and juveniles in 2011, and previously, the Wollemi pine had fewer than 50 individuals in the wild. The low population size and low genetic diversity indicates that the Wollemi pine went through a severe population bottleneck.

A population bottleneck was created in the 1970s through the conservation efforts of the endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense). The small natural population of silversword was augmented through the 1970s with outplanted individuals. All of the outplanted silversword plants were found to be first or subsequent generation offspring of just two maternal founders. The low amount of polymorphic loci in the outplanted individuals led to the population bottleneck, causing the loss of the marker allele at eight of the loci.

Minimum viable population size

In conservation biology, minimum viable population (MVP) size helps to determine the effective population size when a population is at risk for extinction. The effects of a population bottleneck often depend on the number of individuals remaining after the bottleneck and how that compares to the minimum viable population size. There is considerable debate about the usefulness of the MVP.

Metatranscriptomics

From Wikipedia, the free encyclopedia

 

Metatranscriptomics is the science that studies gene expression of microbes within natural environments. It also allows to obtain whole gene expression profiling of complex microbial communities.

While metagenomics focuses on studying the genomic content and on identifying which microbes are present within a community, metatranscriptomics can be used to study the diversity of the active genes within such community, to quantify their expression levels and to monitor how these levels change in different conditions (e.g., physiological vs. pathological conditions in an organism). The advantage of metatranscriptomics is that it can provide information about differences in the active functions of microbial communities which appear to be the same in terms of microbe composition.

Introduction

The microbiome has been defined as a microbial community occupying a well-defined habitat. They are ubiquitous and extremely relevant for the maintenance of” the characteristic of the environment in which they reside and an imbalance in these communities can affect negatively the activity of the setting in which they reside. To study these communities, and to then determine their impact and correlation with their niche, different omics- approaches have been used. While metagenomics allows to obtain a taxonomic profile of the sample, metatrascriptomics provides a functional profile by analysing which genes are expressed by the community. It is possible to infer what genes are expressed under specific conditions, and this can be done using functional annotations of expressed genes.

Function

Since metatranscriptomics focuses on what genes are expressed, it allows to understand the active functional profile of the entire microbial community. The overview of the gene expression in a given sample is obtained by capturing the total mRNA of the microbiome and by performing a whole metatranscriptomics shotgun sequencing.

Tools and techniques

Although microarrays can be exploited to determine the gene expression profiles of some model organisms, NGS is the preferred technique in metatranscriptomics. The protocol that is used to perform a metatranscriptome analysis may vary depending on the type of sample that needs to be analysed. Indeed, many different protocols have been developed for studying the metatranscriptome of microbial samples. Generally, the steps include sample harvesting, RNA extraction (different extraction methods for different kinds of samples have been reported in the literature), mRNA enrichment, cDNA synthesis and preparation of metatranscriptomic libraries, sequencing and data processing and analysis. mRNA enrichment is one of the trickiest parts. Different strategies have been proposed:

• removing rRNA through Ribosomal RNA capture
• using a 5-3 exonuclease to degrade processed RNAs (mostly rRNA and tRNA
• adding poly(A) to mRNAs by using a polyA polymerase (in E. coli)
• using antibodies to capture mRNAs that bind to specific proteins

The last two strategies are not recommended as they have been reported to be highly biased. 

Computational analysis

A typical metatranscriptome analysis pipeline:

• maps reads to a reference genome or
• performs de novo assembly of the reads into transcript contigs and supercontigs

The first strategy maps reads to reference genomes in databases, to collect information that is useful to deduce the relative expression of the single genes. Metatranscriptomic reads are mapped against databases using alignment tools, such as Bowtie2, BWA, and BLAST. Then, the results are annotated using resources, such as GO, KEGG, COG, and Swiss-Prot. The final analysis of the results is carried out depending on the aim of the study. One of the latest metatranscriptomics techniques is stable isotope probing (SIP), which has been used to retrieve specific targeted transcriptomes of aerobic microbes in lake sediment. The limitation of this strategy is its reliance on the information of reference genomes in databases. The second strategy retrieves the abundance in the expression of the different genes by assembling metatranscriptomic reads into longer fragments called contigs using different softwares. So, its limits depend on the software that is used for the assembly. The Trinity software for RNA-seq, in comparison with other de novo transcriptome assemblers, was reported to recover more full-length transcripts over a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. This is particularly important in the absence of a reference genome. A quantitative pipeline for transcriptomic analysis was developed by Li and Dewey and called RSEM (RNA-Seq by Expectation Maximization). It can work as stand-alone software or as a plug-in for Trinity. RSEM starts with a reference transcriptome or assembly along with RNA-Seq reads generated from the sample and calculates normalized transcript abundance (meaning the number of RNA-Seq reads cor-responding to each reference transcriptome or assembly). Although both Trinity and RSEM were designed for transcriptomic datasets (i.e., obtained from a single organism), it may be possible to apply them to metatranscriptomic data (i.e., obtained from a whole microbial community). 

Bioinformatics

Given the huge amount of data obtained from metagenomic and metatranscriptomic analysis, the use of bioinformatic tools have become of greater importance in the last decades. In order to achieve so, many different bioinformatic pipelines have been developed, often as open source platforms, such as HUMAnN and the most recent HUMAnN2, MetaTrans, SAMSA, Leimena-2013 and mOTUs2.

HUMAnN2

HUMAnN2 is a bioinformatic pipeline designed from the latter HUMAnN developed during the Human Microbiome Project (HMP), implementing a “tiered search” approach. In the first tier, HUMAnN2 screens DNA or RNA reads with MetaPhlAn2 in order to identify already known microbes and constructing a sample-specific database by merging pangenomes of annotated species; in the second tier the algorithm performs a mapping of the reads against the assembled pangenome database; in the third tier, non-aligned reads are used for a translated search against a protein database 

MetaTrans

MetaTrans is a pipeline that exploits multi-threading computers to improve metagenomic and metatranscriptomic analysis. Data is obtained from paired-end RNA-Seq, mainly from 16S RNA for taxonomy and mRNA for gene expression levels. The pipeline is divided in 4 major steps. Firstly, paired-end reads are filtered for quality control purposes, to be thereafter sorted for taxonomic analysis (by removal of tRNA sequences) or functional analysis (by removal of both tRNA and rRNA sequencing). For the taxonomic analysis, sequences are mapped against 16S rRNA Greengenes v13.5 database using SOAP2, while for functional analysis sequences are mapped against a functional database such as MetaHIT-2014 always by using SOAP2 tool. This pipeline is highly flexible, since it offers the possibility to use third-party tools and improve single modules as long as the general structure is preserved.

SAMSA

This pipeline is designed specifically for metatranscriptomics data analysis, by working in conjunction with the MG-RAST server for metagenomics. This pipeline is simple to use, requires low technical preparation and computational power and can be applied to a wide range of microbes. The algorithm is divided in 4 steps. At first, sequences from raw sequencing data are selected on quality basis and are then submitted to MG-RAST (which foresee different steps such as quality control check, gene calling, clustering of amino acid sequences and use of sBLAT on each cluster to detect the best matches). Matches are then aggregated for taxonomic and functional analysis purposes, that usually follow up as last steps of the process.

Leimena-2013

This pipeline actually does not have a name so that it is usually reckoned with the first name of the author of the article in which it is described. This algorithm foresees the implementation of alignment tools such as BLAST and MegaBLAST. Reads, usually obtained by Illumina sequencing, are clustered in identical-reads clusters and are then processed for in-silico removal of t-RNA and r-RNA sequences. Remaining reads are then mapped on NCBI databases by using BLAST and MegaBLAST tools and classified by their bitscore. Higher bitscore sequences are thereby interpreted to predict phylogenetic origin and function. Lower score reads instead are aligned with BLASTX (higher sensitivity) and eventually can be aligned in protein databases so that their function can be characterized.

mOTUs2

The mOTUs2 profiler, which is based on essential housekeeping genes, is demonstrably well-suited for quantification of basal transcriptional activity of microbial community members. Depending on environmental conditions, the number of transcripts per cell varies for most genes. An exception to this are housekeeping genes that are expressed constitutively and with low variability under different conditions. Thus, the abundance of transcripts from such genes strongly correlate with the abundance of active cells in a community.

Microarray

Another method that can be exploited for metatranscriptomic purposes is Tiling Microarrays. In particular, microarrays have been used to measure microbial transcription levels, to detect new transcripts and to obtain information about the structure of mRNAs (for instance, the UTR boundaries). Recently, it has also been used to find new regulatory ncRNA. However, microarrays are affected by some pitfalls:

• requirement of probe design
• low sensitivity
• prior knowledge of gene targets.

RNA-Seq can overcome these limitations: it does not require any previous knowledge about the genomes that have to be analysed and it provides high throughput validation of genes prediction, structure, expression. Thus, by combining the two approaches it is possible to have a more complete representation of bacterial transcriptome.

Limits of the metatranscriptomic techniques

• With its dominating abundance, ribosomal RNA strongly reduces the coverage of mRNA (main focus of transcriptomic studies) in the total collected RNA.
• Extraction of high-quality RNA from some biological or environmental samples (such as feces) can be difficult
• Instability of mRNA that compromises sample integrity even before sequencing.
• Experimental issues can affect the quantification of differences in expression among multiple samples: They can influence integrity and input RNA, as well as the amount of rRNA remaining in the samples, size section and gene models. Moreover, molecular base techniques are very prone to artefacts.
• Difficulties in differentiating between host and microbial RNA, although commercial kits for the microbial enrichment are available. This may also be done in silico if a reference genome is available for the host.
• Transcriptome reference databases are limited in their coverage.
• Generally, large populations of cells are exploited in metatranscriptomic analysis, so it is difficult to resolve important variances that can exist between subpopulations. Actually, high variability in pathogen populations was demonstrated to affect disease progression and virulence.
• Both for microarray and RNA-Seq, it is difficult to set a real “cut off” in order to consider the genes as “express”, due to the high dynamic range in gene expression.
• The presence of mRNA is not always associated with the actual presence of the respective protein.

Metatrascriptomics and Gut Microbiome

The gut microbiome has emerged in recent years as an important player in human health. Its prevalent functions are related to the fermentation of indigestible food components, competitions with pathogen, strengthening of the intestinal barrier, stimulation and regulation of the immune system. Although much has been learnt about the microbiome community in the last years, the wide diversity of microorganisms and molecules in the gut requires new tools to enable new discoveries. By focusing on the changes in the expression of the genes, metatrascriptomics allows to take a more dynamic picture of the state and activity of the microbiome than metagenomics. It has been observed that metatranscriptomic functional profiles are more variable than what might have been reckoned only by metagenomic information. This suggests that non-housekeeping genes are not stably expressed in situ. One example of metatranscriptomic application is in the study of the gut microbiome in inflammatory bowel disease. Inflammatory bowel disease (IBD) is a group of chronic diseases of the digestive tract that affects millions of people worldwide. Several human genetic mutations have been linked to an increased susceptibility to IBD, but additional factors are needed for the full development of the disease. Regarding the relationship between IBD and gut microbiome, it is known that there is a dysbiosis in patients with IBD but microbial taxonomic profiles can be highly different among patients, making it difficult to implicate specific microbial species or strains in disease onset and progression. In addition, the gut microbiome composition presents a high variability over time among people, with more pronounced variations in patient with IBD. The functional potential of an organism, meaning the genes and pathways encoded in its genome, provides only indirect information about the level or extent of activation of such functions. So, the measurement of functional activity (gene expression) is critical to understand the mechanism of the gut microbiome dysbiosis. Alterations in transcriptional activity in IBD, established on the rRNA expression, indicate that some bacterial populations are active in patients with IBD, while other groups are inactive or latent. A metatranscriptomics analysis measuring the functional activity of the gut microbiome reveals insights only partially observable in metagenomic functional potential, including disease-linked observations for IBD. It has been reported that many IBD-specific signals are either more pronounced or only detectable on the RNA level. These altered expression profiles are potentially the result of changes in the gut environment in patients with IBD, which include increased levels of inflammation, higher concentrations of oxygen and a diminished mucous layer. Metatranscriptomics has the advantage of allowing to skip the assaying of biochemical products in situ (like mucus or oxygen) and allows to study the effects of environmental changes on microbial expression patterns in vivo for large human populations. In addition, it can be coupled with longitudinal sampling to associate modulation of activity with the disease progression. Indeed, it has been shown that while a particular path may remain stable over time at the genomic level, the corresponding expression varies with the disease severity. This suggests that microbial dysbiosis affect the gut health through changing in the transcriptional programmes in a stable community. In this way, metatracriptomic profiling emerges as an important tool for understanding the mechanisms of that relationship. Some technical limitations of the RNA measurements in stool are related to the fact that the extracted RNA can be degraded and, if not, it still represents only the organisms presents in the stool sample. Other applications of metagenomics:

• Directed culturing: it was used to understand nutritional preferences of organisms in order to allow the preparation of a proper culture medium, resulting in a successful isolation of microbes in vitro.
• Identify potential virulence factors: through comparative transcriptomics, in order to compare different transcriptional responses of related strains or species after specific stimuli.
• Identify host-specific biological processes and interactions For this purpose, it’s important to develop new technologies which allow the detection, at the same time, of changes in the expression levels of some genes.

Examples of techniques applied: Microarrays: allow the monitoring of changes in the expression levels of many genes in parallel for both host and pathogen. First microarray approaches have shown the first global analysis of gene expression changes in pathogens such as Vibrio cholerae, Borrelia burgdorferi, Chlamydia trachomatis, Chlamydia pneumoniae and Salmonella enterica, revealing the strategies that are used by these microorganisms to adapt to the host. In addition, microarrays only provide the first global insights about the host innate immune response to PAMPs, as the effects of bacterial infection on the expression of various host factor. Anyway, the detection through microarrays of both organisms at the same time could be problematic. Problems:

• Probe selection (hundreds of millions of different probes)
• Cross-hybridization
• Need of expensive chips (with the proper design; high-density arrays)
• Require the pathogen and host cells to be physically separated before gene expression analysis (eukaryotic cells’ transcriptomes are larger in comparison to the pathogens’ ones, so could happen that the signal from pathogens’ RNAs is hidden).
• Loss of RNA molecules during the eukaryotic cells lysis.

Dual RNA-Seq: this technique allows the simultaneous study of both host and pathogen transcriptomes as well. It is possible to monitor the expression of genes at different time points of the infection process; in this way could it be possible to study the changes in cellular networks in both organisms starting from the initial contact until the manipulation of the host (interplay host-patogen).

• Potential: No need of expensive chips
• Probe-independent approach (RNA-seq provides transcript information without prior knowledge of mRNA sequences)
• High sensitivity.
• Possibility of studying the expression levels of even unknown genes under different conditions

Moreover, RNA-Seq is an important approach for identifying coregulated genes, enabling the organization of pathogen genomes into operons. Indeed, genome annotation has been done for some eukaryotic pathogens, such as Candida albicans, Trypanosoma brucei and Plasmodium falciparum. Despite the increasing sensitivity and depth of sequencing now available, there are still few published RNA-Seq studies concerning the response of the mammalian host cell to the infection.

Genetic diversity

From Wikipedia, the free encyclopedia

 

Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary. 

Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals.

The academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions. Diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large range relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common, they become more vulnerable. This occurs in host–pathogen interactions, where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele.

Within Species Diversity

Varieties of maize in the office of the Russian plant geneticist Nikolai Vavilov

 

A study conducted by the National Science Foundation in 2007 found that genetic diversity ( within species diversity) and biodiversity are dependent upon each other — i.e. that diversity within a species is necessary to maintain diversity among species, and vice versa. According to the lead researcher in the study, Dr. Richard Lankau, "If any one type is removed from the system, the cycle can break down, and the community becomes dominated by a single species." Genotypic and phenotypic diversity have been found in all species at the protein, DNA, and organismal levels; in nature, this diversity is nonrandom, heavily structured, and correlated with environmental variation and stress.

The interdependence between genetic and species diversity is delicate. Changes in species diversity lead to changes in the environment, leading to adaptation of the remaining species. Changes in genetic diversity, such as in loss of species, leads to a loss of biological diversity. Loss of genetic diversity in domestic animal populations has also been studied and attributed to the extension of markets and economic globalization.

Evolutionary importance of Genetic Diversity

Adaptation

Variation in the populations gene pool allows natural selection to act upon traits that allow the population to adapt to changing environments. Selection for or against a trait can occur with changing environment – resulting in an increase in genetic diversity (if a new mutation is selected for and maintained) or a decrease in genetic diversity (if a disadvantageous allele is selected against). Hence, genetic diversity plays an important role in the survival and adaptability of a species. The capability of the population to adapt to the changing environment will depend on the presence of the necessary genetic diversity The more genetic diversity a population has, the more likelihood the population will be able to adapt and survive. Conversely, the vulnerability of a population to changes, such as climate change or novel diseases will increase with reduction in genetic diversity. For example, the inability of koalas to adapt to fight Chlamydia and the koala retrovirus (KoRV) has been linked to the koala’s low genetic diversity. This low genetic diversity also has geneticists concerned for the koalas ability to adapt to climate change and human-induced environmental changes in the future.

Small populations

Large populations are more likely to maintain genetic material and thus generally have higher genetic diversity. Small populations are more likely to experience the loss of diversity over time by random chance, which is called genetic drift. When an allele (variant of a gene) drifts to fixation, the other allele at the same locus is lost, resulting in a loss in genetic diversity. In small population sizes, inbreeding, or mating between individuals with similar genetic makeup, is more likely to occur, thus perpetuating more common alleles to the point of fixation, thus decreasing genetic diversity. Concerns about genetic diversity are therefore especially important with large mammals due to their small population size and high levels of human-caused population effects.

A genetic bottleneck can occur when a population goes through a period of low number of individuals, resulting in a rapid decrease in genetic diversity. Even with an increase in population size, the genetic diversity often continues to be low if the entire species began with a small population, since beneficial mutations (see below) are rare, and the gene pool is limited by the small starting population. This is an important consideration in the area of conservation genetics, when working toward a rescued population or species that is genetically-healthy.

Mutation

Random mutations consistently generate genetic variation. A mutation will increase genetic diversity in the short term, as a new gene is introduced to the gene pool. However, the persistence of this gene is dependent of drift and selection (see above). Most new mutations either have a neutral or negative effect on fitness, while some have a positive effect. A beneficial mutation is more likely to persist and thus have a long-term positive effect on genetic diversity. Mutation rates differ across the genome, and larger populations have greater mutation rates. In smaller populations a mutation is less likely to persist because it is more likely to be eliminated by drift. 

Gene Flow

Gene flow, often by migration, is the movement of genetic material (for example by pollen in the wind, or the migration of a bird). Gene flow can introduce novel alleles to a population. These alleles can be integrated into the population, thus increasing genetic diversity.

For example, an insecticide-resistant mutation arose in Anopheles gambiae African mosquitoes. Migration of some A. gambiae mosquitoes to a population of Anopheles coluzziin mosquitoes resulted in a transfer of the beneficial resistance gene from one species to the other. The genetic diversity was increased in A. gambiae by mutation and in A. coluzziin by gene flow.

In agriculture

In crops

When humans initially started farming, they used selective breeding to pass on desirable traits of the crops while omitting the undesirable ones. Selective breeding leads to monocultures: entire farms of nearly genetically identical plants. Little to no genetic diversity makes crops extremely susceptible to widespread disease; bacteria morph and change constantly and when a disease-causing bacterium changes to attack a specific genetic variation, it can easily wipe out vast quantities of the species. If the genetic variation that the bacterium is best at attacking happens to be that which humans have selectively bred to use for harvest, the entire crop will be wiped out.

The nineteenth-century Potato Famine in Ireland was in part caused by lack of biodiversity. Since new potato plants do not come as a result of reproduction, but rather from pieces of the parent plant, no genetic diversity is developed, and the entire crop is essentially a clone of one potato, it is especially susceptible to an epidemic. In the 1840s, much of Ireland's population depended on potatoes for food. They planted namely the "lumper" variety of potato, which was susceptible to a rot-causing oomycete called Phytophthora infestans. The fungus destroyed the vast majority of the potato crop, and left one million people to starve to death. 

Genetic diversity in agriculture does not only relate to disease, but also herbivores. Similarly, to the above example, monoculture agriculture selects for traits that are uniform throughout the plot. If this genotype is susceptible to certain herbivores, this could result in the loss of a large portion of the crop. One way farmers get around this is through inter-cropping. By planting rows of unrelated, or genetically distinct crops as barriers between herbivores and their preferred host plant, the farmer effectively reduces the ability of the herbivore to spread throughout the entire plot.

In livestock

The genetic diversity of livestock species permits animal husbandry in a range of environments and with a range of different objectives. It provides the raw material for selective breeding programmes and allows livestock populations to adapt as environmental conditions change.

Livestock biodiversity can be lost as a result of breed extinctions and other forms of genetic erosion. As of June 2014, among the 8,774 breeds recorded in the Domestic Animal Diversity Information System (DAD-IS), operated by the Food and Agriculture Organization of the United Nations (FAO), 17 percent were classified as being at risk of extinction and 7 percent already extinct. There is now a Global Plan of Action for Animal Genetic Resources that was developed under the auspices of the Commission on Genetic Resources for Food and Agriculture in 2007, that provides a framework and guidelines for the management of animal genetic resources. 

Awareness of the importance of maintaining animal genetic resources has increased over time. FAO has published two reports on the state of the world's animal genetic resources for food and agriculture, which cover detailed analyses of our global livestock diversity and ability to manage and conserve them.

Viral Implications

High genetic diversity in viruses must be considered when designing vaccinations. High genetic diversity results in difficulty in designing targeted vaccines, and allows for viruses to quickly evolve to resist vaccination lethality. For example, malaria vaccinations are impacted by high levels of genetic diversity in the protein antigens. In addition, HIV-1 genetic diversity limits the use of currently available viral load and resistance tests.

Coping with low genetic diversity

Photomontage of planktonic organisms.

 

A Tanzanian cheetah.

Natural

The natural world has several ways of preserving or increasing genetic diversity. Among oceanic plankton, viruses aid in the genetic shifting process. Ocean viruses, which infect the plankton, carry genes of other organisms in addition to their own. When a virus containing the genes of one cell infects another, the genetic makeup of the latter changes. This constant shift of genetic makeup helps to maintain a healthy population of plankton despite complex and unpredictable environmental changes.

Cheetahs are a threatened species. Low genetic diversity and resulting poor sperm quality has made breeding and survivorship difficult for cheetahs. Moreover, only about 5% of cheetahs survive to adulthood However, it has been recently discovered that female cheetahs can mate with more than one male per litter of cubs. They undergo induced ovulation, which means that a new egg is produced every time a female mates. By mating with multiple males, the mother increases the genetic diversity within a single litter of cubs.

Human Intervention

Attempts to increase the viability of a species by increasing genetic diversity is called genetic rescue. For example, eight panthers from Texas were introduced to the Florida panther population, which was declining and suffering from inbreeding depression. Genetic variation was thus increased and resulted in a significant increase in population growth of the Florida Panther. Creating or maintaining high genetic diversity is an important consideration in species rescue efforts, in order to ensure the longevity of a population.

Measures

Genetic diversity of a population can be assessed by some simple measures.

• Gene diversity is the proportion of polymorphic loci across the genome.
• Heterozygosity is the fraction of individuals in a population that are heterozygous for a particular locus.
• Alleles per locus is also used to demonstrate variability.
• Nucleotide diversity is the extent of nucleotide polymorphisms within a population, and is commonly measured through molecular markers such as micro- and minisatellite sequences, mitochondrial DNA, and single-nucleotide polymorphisms (SNPs).

Furthermore, stochastic simulation software is commonly used to predict the future of a population given measures such as allele frequency and population size.