Evolvability

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Evolvability

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

In order for a biological organism to evolve by natural selection, there must be a certain minimum probability that new, heritable variants are beneficial. Random mutations, unless they occur in DNA sequences with no function, are expected to be mostly detrimental. Beneficial mutations are always rare, but if they are too rare, then adaptation cannot occur. Early failed efforts to evolve computer programs by random mutation and selection showed that evolvability is not a given, but depends on the representation of the program as a data structure, because this determines how changes in the program map to changes in its behavior. Analogously, the evolvability of organisms depends on their genotype–phenotype map. This means that genomes are structured in ways that make beneficial changes more likely. This has been taken as evidence that evolution has created fitter populations of organisms that are better able to evolve.

Alternative definitions

Andreas Wagner describes two definitions of evolvability. According to the first definition, a biological system is evolvable:

• if its properties show heritable genetic variation, and
• if natural selection can thus change these properties.

According to the second definition, a biological system is evolvable:

• if it can acquire novel functions through genetic change, functions that help the organism survive and reproduce.

For example, consider an enzyme with multiple alleles in the population. Each allele catalyzes the same reaction, but with a different level of activity. However, even after millions of years of evolution, exploring many sequences with similar function, no mutation might exist that gives this enzyme the ability to catalyze a different reaction. Thus, although the enzyme's activity is evolvable in the first sense, that does not mean that the enzyme's function is evolvable in the second sense. However, every system evolvable in the second sense must also be evolvable in the first.

Massimo Pigliucci recognizes three classes of definition, depending on timescale. The first corresponds to Wagner's first, and represents the very short timescales that are described by quantitative genetics. He divides Wagner's second definition into two categories, one representing the intermediate timescales that can be studied using population genetics, and one representing exceedingly rare long-term innovations of form.

Pigliucci's second definition of evolvability includes Altenberg's quantitative concept of evolvability, being not a single number, but the entire upper tail of the fitness distribution of the offspring produced by the population. This quantity was considered a "local" property of the instantaneous state of a population, and its integration over the population's evolutionary trajectory, and over many possible populations, would be necessary to give a more global measure of evolvability.

Generating more variation

More heritable phenotypic variation means more evolvability. While mutation is the ultimate source of heritable variation, its permutations and combinations also make a big difference. Sexual reproduction generates more variation (and thereby evolvability) relative to asexual reproduction (see evolution of sexual reproduction). Evolvability is further increased by generating more variation when an organism is stressed, and thus likely to be less well adapted, but less variation when an organism is doing well. The amount of variation generated can be adjusted in many different ways, for example via the mutation rate, via the probability of sexual vs. asexual reproduction, via the probability of outcrossing vs. inbreeding, via dispersal, and via access to previously cryptic variants through the switching of an evolutionary capacitor. A large population size increases the influx of novel mutations in each generation.

Enhancement of selection

Rather than creating more phenotypic variation, some mechanisms increase the intensity and effectiveness with which selection acts on existing phenotypic variation. For example:

• Mating rituals that allow sexual selection on "good genes", and so intensify natural selection.
• Large effective population size increasing the threshold value of the selection coefficient above which selection becomes an important player. This could happen through an increase in the census population size, decreasing genetic drift, through an increase in the recombination rate, decreasing genetic draft, or through changes in the probability distribution of the numbers of offspring.
• Recombination decreasing the importance of the Hill-Robertson effect, where different genotypes contain different adaptive mutations. Recombination brings the two alleles together, creating a super-genotype in place of two competing lineages.
• Shorter generation time.

Robustness and evolvability

Further information: Mutational robustness

The relationship between robustness and evolvability depends on whether recombination can be ignored. Recombination can generally be ignored in asexual populations and for traits affected by single genes.

Without recombination

Robustness in the face of mutation does not increase evolvability in the first sense. In organisms with a high level of robustness, mutations have smaller phenotypic effects than in organisms with a low level of robustness. Thus, robustness reduces the amount of heritable genetic variation on which selection can act. However, robustness may allow exploration of large regions of genotype space, increasing evolvability according to the second sense. Even without genetic diversity, some genotypes have higher evolvability than others, and selection for robustness can increase the "neighborhood richness" of phenotypes that can be accessed from the same starting genotype by mutation. For example, one reason many proteins are less robust to mutation is that they have marginal thermodynamic stability, and most mutations reduce this stability further. Proteins that are more thermostable can tolerate a wider range of mutations and are more evolvable. For polygenic traits, neighborhood richness contributes more to evolvability than does genetic diversity or "spread" across genotype space.

With recombination

Temporary robustness, or canalisation, may lead to the accumulation of significant quantities of cryptic genetic variation. In a new environment or genetic background, this variation may be revealed and sometimes be adaptive.

Factors affecting evolvability via robustness

Different genetic codes have the potential to change robustness and evolvability by changing the effect of single-base mutational changes.

Exploration ahead of time

When mutational robustness exists, many mutants will persist in a cryptic state. Mutations tend to fall into two categories, having either a very bad effect or very little effect: few mutations fall somewhere in between. Sometimes, these mutations will not be completely invisible, but still have rare effects, with very low penetrance. When this happens, natural selection weeds out the very bad mutations, while leaving the others relatively unaffected. While evolution has no "foresight" to know which environment will be encountered in the future, some mutations cause major disruption to a basic biological process, and will never be adaptive in any environment. Screening these out in advance leads to preadapted stocks of cryptic genetic variation.

Another way that phenotypes can be explored, prior to strong genetic commitment, is through learning. An organism that learns gets to "sample" several different phenotypes during its early development, and later sticks to whatever worked best. Later in evolution, the optimal phenotype can be genetically assimilated so it becomes the default behavior rather than a rare behavior. This is known as the Baldwin effect, and it can increase evolvability.

Learning biases phenotypes in a beneficial direction. But an exploratory flattening of the fitness landscape can also increase evolvability even when it has no direction, for example when the flattening is a result of random errors in molecular and/or developmental processes. This increase in evolvability can happen when evolution is faced with crossing a "valley" in an adaptive landscape. This means that two mutations exist that are deleterious by themselves, but beneficial in combination. These combinations can evolve more easily when the landscape is first flattened, and the discovered phenotype is then fixed by genetic assimilation.

Modularity

If every mutation affected every trait, then a mutation that was an improvement for one trait would be a disadvantage for other traits. This means that almost no mutations would be beneficial overall. But if pleiotropy is restricted to within functional modules, then mutations affect only one trait at a time, and adaptation is much less constrained. In a modular gene network, for example, a gene that induces a limited set of other genes that control a specific trait under selection may evolve more readily than one that also induces other gene pathways controlling traits not under selection. Individual genes also exhibit modularity. A mutation in one cis-regulatory element of a gene's promoter region may allow the expression of the gene to be altered only in specific tissues, developmental stages, or environmental conditions rather than changing gene activity in the entire organism simultaneously.

Evolution of evolvability

While variation yielding high evolvability could be useful in the long term, in the short term most of that variation is likely to be a disadvantage. For example, naively it would seem that increasing the mutation rate via a mutator allele would increase evolvability. But as an extreme example, if the mutation rate is too high then all individuals will be dead or at least carry a heavy mutation load. Short-term selection for low variation most of the time is usually thought likely to be more powerful than long-term selection for evolvability, making it difficult for natural selection to cause the evolution of evolvability. Other forces of selection also affect the generation of variation; for example, mutation and recombination may in part be byproducts of mechanisms to cope with DNA damage.

When recombination is low, mutator alleles may still sometimes hitchhike on the success of adaptive mutations that they cause. In this case, selection can take place at the level of the lineage. This may explain why mutators are often seen during experimental evolution of microbes. Mutator alleles can also evolve more easily when they only increase mutation rates in nearby DNA sequences, not across the whole genome: this is known as a contingency locus.

The evolution of evolvability is less controversial if it occurs via the evolution of sexual reproduction, or via the tendency of variation-generating mechanisms to become more active when an organism is stressed. The yeast prion [PSI+] may also be an example of the evolution of evolvability through evolutionary capacitance. An evolutionary capacitor is a switch that turns genetic variation on and off. This is very much like bet-hedging the risk that a future environment will be similar or different. Theoretical models also predict the evolution of evolvability via modularity. When the costs of evolvability are sufficiently short-lived, more evolvable lineages may be the most successful in the long-term. However, the hypothesis that evolvability is an adaptation is often rejected in favor of alternative hypotheses, e.g. minimization of costs.

Applications

Evolvability phenomena have practical applications. For protein engineering we wish to increase evolvability, and in medicine and agriculture we wish to decrease it. Protein evolvability is defined as the ability of the protein to acquire sequence diversity and conformational flexibility which can enable it to evolve toward a new function.

In protein engineering, both rational design and directed evolution approaches aim to create changes rapidly through mutations with large effects. Such mutations, however, commonly destroy enzyme function or at least reduce tolerance to further mutations. Identifying evolvable proteins and manipulating their evolvability is becoming increasingly necessary in order to achieve ever larger functional modification of enzymes. Proteins are also often studied as part of the basic science of evolvability, because the biophysical properties and chemical functions can be easily changed by a few mutations. More evolvable proteins can tolerate a broader range of amino acid changes and allow them to evolve toward new functions. The study of evolvability has fundamental importance for understanding very long term evolution of protein superfamilies.

Many human diseases are capable of evolution. Viruses, bacteria, fungi and cancers evolve to be resistant to host immune defences, as well as pharmaceutical drugs. These same problems occur in agriculture with pesticide and herbicide resistance. It is possible that we are facing the end of the effective life of most of available antibiotics. Predicting the evolution and evolvability of our pathogens, and devising strategies to slow or circumvent the development of resistance, demands deeper knowledge of the complex forces driving evolution at the molecular level.

A better understanding of evolvability is proposed to be part of an Extended Evolutionary Synthesis.

Mars habitability analogue environments on Earth

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Mars_habitability_analogue_environments_on_Earth

Mars habitability analogue environments on Earth are environments that share potentially relevant astrobiological conditions with Mars. These include sites that are analogues of potential subsurface habitats, and deep subsurface habitats.

A few places on Earth, such as the hyper-arid core of the high Atacama Desert and the McMurdo Dry Valleys in Antarctica approach the dryness of current Mars surface conditions. In some parts of Antarctica, the only water available is in films of brine on salt / ice interfaces. There is life there, but it is rare, in low numbers, and often hidden below the surface of rocks (endoliths), making the life hard to detect. Indeed, these sites are used for testing sensitivity of future life detection instruments for Mars, furthering the study of astrobiology, for instance, as a location to test microbes for their ability to survive on Mars, and as a way to study how Earth life copes in conditions that resemble conditions on Mars.

Other analogues duplicate some of the conditions that may occur in particular locations on Mars. These include ice caves, the icy fumaroles of Mount Erebus, hot springs, or the sulfur rich mineral deposits of the Rio Tinto region in Spain. Other analogues include regions of deep permafrost and high alpine regions with plants and microbes adapted to aridity, cold and UV radiation with similarities to Mars conditions.

Precision of analogues

Mars surface conditions are not reproduced anywhere on Earth, so Earth surface analogues for Mars are necessarily partial analogues. Laboratory simulations show that whenever multiple lethal factors are combined, the survival rates plummet quickly. There are no full-Mars simulations published yet that include all of the biocidal factors combined.

• Ionizing radiation. Curiosity rover measured levels on Mars similar to the interior of the International Space Station (ISS), which is far higher than surface Earth levels.
• Atmosphere. The Martian atmosphere is a near vacuum while Earth's is not. Through desiccation resistance, some life forms can withstand the vacuum of space in dormant state.
• UV levels. UV levels on Mars are much higher than on Earth. Experiments show that a thin layer of dust is enough to protect microorganisms from UV radiation.
• Oxidizing surface. Mars has a surface layer which is highly oxidizing (toxic) because it contains salts such as perchlorates, chlorates, cholorites, and sulfates pervasive in the soil and dust, and hydrogen peroxide throughout the atmosphere. Earth does have some areas that are highly oxidizing, such as the soda lakes, and though not direct analogues, they have conditions that may be duplicated in thin films of brines on Mars.
• Temperature. Nowhere on Earth reproduces the extreme changes in temperature that happen within a single day on Mars.
• Dry ice. The Mars surface consists of dry ice (CO₂ ice) in many areas. Even in equatorial regions, dry ice mixed with water forms frosts for about 100 days of the year. On Earth, although temperatures on Earth briefly get cold enough for dry ice to form in the Antarctic interior at high altitudes, the partial pressure of carbon dioxide in Earth's atmosphere is too low for dry ice to form because the depositional temperature for dry ice on Earth under 1 bar of pressure is −140 °C (−220 °F) and the lowest temperature recorded in Antarctica is −94.7 °C (−138.5 °F), recorded in 2010 by satellite.

These partial analogues are useful, for instance for:

• Testing life detection equipment which may one day be sent to Mars
• Studying conditions for preservation of past life on Mars (biosignatures)
• Studying adaptations to conditions similar to those that may occur on Mars
• As a source of microbes, lichens etc. that can be studied as they may exhibit resistance to some conditions present on Mars.

Atacama Desert

The Atacama Desert plateau lies at an altitude of 3,000 meters and lies between the Pacific and the Andes mountains. Its Mars-like features include

• Hyper arid conditions
• Cold compared to most arid deserts because of the altitude
• High levels of UV light (because it is relatively cloudless, also the higher altitude means less air to filter the UV out, and the ozone layer is somewhat thinner above sites in the southern hemisphere than above corresponding sites in the northern hemisphere)
• Salt basins, which also include perchlorates making them the closest analogues to Martian salts on Earth.

Yungay area

Atacama Desert

Atacama Desert (South America)

The Yungay area at the core of the Atacama Desert used to be considered the driest area on Earth for more than a decade, until the discovery in 2015 that Maria Elena South is drier. It can go centuries without rainfall, and parts of it have been hyper-arid for 150 million years. The older regions in this area have salts that are amongst the closest analogues of salts on Mars because these regions have nitrate deposits that contain not only the usual chlorides, but also sulfates, chlorates, chromates, iodates, and perchlorates. The infrared spectra are similar to the spectra of bright soil regions of Mars.

The Yungay area has been used for testing instruments intended for future life detection missions on Mars, such as the Sample Analysis at Mars instruments for Curiosity, the Mars Organic Analyzer for ExoMars, and Solid3 for Icebreaker Life, which in 2011, in a test of its capabilities, was able to find a new "microbial oasis" for life two meters below the surface of the Atacama desert. It is the current testing site for the Atacama Rover Astrobiology Drilling Studies (ARADS) project to improve technology and strategies for life detection on Mars.

Experiments conducted on Mars have also been successfully repeated in this region. In 2003, a group led by Chris McKay repeated the Viking Lander experiments in this region and got the same results as those of the Viking landers on Mars: decomposition of the organics by non-biological processes. The samples had trace elements of organics, no DNA was recovered, and extremely low levels of culturable bacteria. This led to increased interest in the site as a Mars analogue.

Although hardly any life, including plant or animal life, exists in this area, the Yungay area does have some microbial life, including cyanobacteria, both in salt pillars, as a green layer below the surface of rocks, and beneath translucent rocks such as quartz. The cyanobacteria in the salt pillars have the ability to take advantage of the moisture in the air at low relative humidities. They begin to photosynthesize when the relative humidity rises above the deliquescence relative humidity of salt, at 75%, presumably making use of deliquescence of the salts. Researchers have also found that cyanobacteria in these salt pillars can photosynthesize when the external relative humidity is well below this level, taking advantage of micropores in the salt pillars which raise the internal relative humidity above the external levels^.

Maria Elena South

This site is even drier than the Yungay area. It was found through a systematic search for drier regions than Yungay in the Atacama Desert, using relative humidity data loggers set up from 2008 to 2012, with the results published in 2015. The relative humidity is the same as the lowest relative humidity measured by Curiosity rover.

A 2015 paper reported  an average atmospheric relative humidity 17.3%, and soils relative humidity a constant 14% at depth of 1 meter, which corresponds to the lowest humidity measured by Curiosity rover on Mars. This region's maximum atmospheric relative humidity is 54.7% compared with 86.8% for the Yungay region.

The following living organisms were also found in this region:

• Actinomycetota: Actinobacterium, Aciditerrmonas, and Geodermatophilus
• Pseudomonadota: Caulobacter and Sphingomonas
• Bacillota: Clostridiales
• Acidobacteriota: Acidobacterium
• 16 new species of Streptomyces, 5 of Bacillus and 1 of Geodermatophilus.

There was no decrease in the numbers of species as the soil depth increased down to a depth of one meter, although different microbes inhabited different soil depths. There was no colonization of gypsum, showing the extreme dryness of the site.

No archaea was detected in this region using the same methods that detected archaea in other regions of the Atacama Desert. The researchers said that if this is confirmed in studies of similarly dry sites, it could mean that "there may be a dry limit for this domain of life on Earth."

McMurdo Dry Valleys in Antarctica

Researchers scout out field sites in Antarctica's Beacon Valley, one of McMurdo Dry Valleys, is one of the most Mars-like places on Earth in terms of cold and dryness.

These valleys lie on the edge of the Antarctic plateau. They are kept clear of ice and snow by fast katabatic winds that blow from the plateau down through the valleys. As a result, they are amongst the coldest and driest areas in the world.

The central region of Beacon Valley is considered to be one of the best terrestrial analogues for the current conditions on Mars. There is snowdrift and limited melting around the edges and occasionally in the central region, but for the most part, moisture is only found as thin films of brine around permafrost structures. It has slightly alkaline salt rich soil.

Don Juan Pond

Don Juan Pond is a small pond in Antarctica, 100 meters by 300 meters, and 10 cm deep, that is of great interest for studying the limits of habitability in general. Research using a time-lapse camera shows that it is partly fed by deliquescing salts. The salts absorb water by deliquescence only, at times of high humidity, then flows down the slope as salty brines. These then mix with snow melt, which feeds the lake. The first part of this process may be related to the processes that form the Recurring Slope Lineae (RSLs) on Mars.

This valley has an exceptionally low water activity (a_w) of 0.3 to 0.6. Though microbes have been retrieved from it, they have not been shown to be able to reproduce in the salty conditions present in the lake, and it is possible that they only got there through being washed in by the rare occasions of snow melt feeding the lake.

Blood Falls

Blood Falls seeps from the end of the Taylor Glacier into Lake Bonney. The tent at left provides a sense of scale

A schematic cross-section of Blood Falls showing how subglacial microbial communities have survived in cold, darkness, and absence of oxygen for a million years in brine water below Taylor Glacier.

This unusual flow of melt water from below the glacier gives scientists access to an environment they could otherwise only explore by drilling (which would also risk contaminating it). The melt water source is a subglacial pool of unknown size which sometimes overflows. Biogeochemical analysis shows that the water is marine in source originally. One hypothesis is that the source may be the remains of an ancient fjord that occupied the Taylor valley in the tertiary period. The ferrous iron dissolved in the water oxidizes as the water reaches the surface, turning the water red.

Its autotrophic bacteria metabolize sulfate and ferric ions. According to geomicrobiologist Jill Mikucki at the University of Tennessee, water samples from Blood Falls contained at least 17 different types of microbes and almost no oxygen. An explanation may be that the microbes use sulfate as a catalyst to respire with ferric ions and metabolize the trace levels of organic matter trapped with them. Such a metabolic process had never before been observed in nature. This process is of astrobiological importance as an analogue for environments below the Glaciers on Mars, if there is any liquid water there, for instance through hydrothermal melting (though none such has been discovered yet). This process is also an analogue for cryovolcanism in icy moons such as Enceladus.

Subglacial environments in Antarctica need similar protection protocols to interplanetary missions.

"7. Exploration protocols should also assume that the subglacial aquatic environments contain living organisms, and precautions should be adopted to prevent any permanent alteration of the biology (including introduction of alien species) or habitat properties of these environments.

28. Drilling fluids and equipment that will enter the subglacial aquatic environment should be cleaned to the extent practicable, and records should be maintained of sterility tests (e.g., bacterial counts by fluorescence microscopy at the drilling site). As a provisional guideline for general cleanliness, these objects should not contain more microbes than are present in an equivalent volume of the ice that is being drilled through to reach the subglacial environment. This standard should be re-evaluated when new data on subglacial aquatic microbial populations become available".

Blood Falls was used as the target for testing IceMole in November 2014. This is being developed in connection with the Enceladus Explorer (EnEx) project by a team from the FH Aachen in Germany. The test returned a clean subglacial sample from the outflow channel from Blood Falls. Ice Mole navigates through the ice by melting it, also using a driving ice screw, and using differential melting to navigate and for hazard avoidance. It is designed for autonomous navigation to avoid obstacles such as cavities and embedded meteorites, so that it can be deployed remotely on Encladus. It uses no drilling fluids, and can be sterilized to suit the planetary protection requirements as well as the requirements for subglacial exploration. The probe was sterilized to these protocols using hydrogen peroxide and UV sterilization. Also, only the tip of the probe samples the liquid water directly.

Qaidam Basin

David Rubin of the USGS Pacific Coastal and Marine Science Center at Qaidam Basin

At 4,500 metres (14,800 ft), Qaidam Basin is the plateau with highest average elevation on the Earth. The atmospheric pressure is 50% - 60% of sea level pressures, and as a result of the thin atmosphere it has high levels of UV radiation, and large temperature swings from day to night. Also, the Himalayas to the South block humid air from India, making it hyper arid.

In the most ancient playas (Da Langtang) at the north west of the plateau, the evaporated salts are magnesium sulfates (sulfates are common on Mars). This, combined with the cold and dryness conditions make it an interesting analogue of the Martian salts and salty regolith. An expedition found eight strains of Haloarchaea inhabiting the salts, similar to some species of Virgibacillus, Oceanobacillus, Halobacillus, and Ter-ribacillus.

Mojave Desert

Mojave Desert map

The Mojave Desert is a desert within the United States that is often used for testing Mars rovers. It also has useful biological analogues for Mars.

• Some arid conditions and chemical processes are similar to Mars.
• Has extremophiles within the soils.
• Desert varnish similar to Mars.
• Carbonate rocks with iron oxide coatings similar to Mars - niche for microbes inside and underneath the rocks, protected from the sun by the iron oxide coating, if microbes existed or exist on Mars they could be protected similarly by the iron oxide coating of rocks there.

Other analogue deserts

• Namib Desert - oldest desert, life with limited water and high temperatures, large dunes and wind features
• Ibn Battuta Centre Sites, Morocco - several sites in the Sahara desert that are analogues of some of the conditions on present day Mars, and used for testing of ESA rovers and astrobiological studies.

Axel Heiberg Island (Canada)

Two sites of special interest: Colour Peak and Gypsum Hill, two sets of cold saline springs on Axel Heiberg Island that flow with almost constant temperature and flow rate throughout the year. The air temperatures are comparable to the McMurdo Dry Valleys, range -15 °C to -20 °C (for the McMurdo Dry Valleys -15 °C to -40 °C). The island is an area of thick permafrost with low precipitation, leading to desert conditions. The water from the springs has a temperature of between -4 °C and 7 °C. A variety of minerals precipitate out of the springs including gypsum, and at Colour Peak crystals of the metastable mineral ikaite (CaCO
₃·6H
₂O) which decomposes rapidly when removed from freezing water.

"At these sites permafrost, frigid winter temperatures, and arid atmospheric conditions approximate conditions of present-day, as well as past, Mars. Mineralogy of the three springs is dominated by halite (NaCl), calcite (CaCO
₃), gypsum (CaSO
₄·2 H₂O), thenardite (Na
₂SO
₄), mirabilite (Na
₂SO
₄·10H
₂O), and elemental sulfur (S°).

Some of the extremophiles from these two sites have been cultured in simulated Martian environment, and it is thought that they may be able to survive in a Martian cold saline spring, if such exist.

Colour Lake Fen

This is another Mars analogue habitat in Axel Heiberg Island close to Colour Peak and Gypsum Hill. The frozen soil and permafrost hosts many microbial communities that are tolerant of anoxic, acid, saline and cold conditions. Most are in survival rather than colony forming mode. Colour Lake Fen is a good terrestrial analogue of the saline acidic brines that once existed in the Meridani Planum region of Mars and may possibly still exist on the martian surface. Some of the microbes found there are able to survive in Mars-like conditions.

"A martian soil survey in the Meridiani Planum region found minerals indicative of saline acidic brines. Therefore acidic cryosol/permafrost habitats may have once existed and are perhaps still extant on the martian surface. This site comprises a terrestrial analogue for these environments and hosts microbes capable of survival under these Mars-like conditions"

Rio Tinto, Spain

Rio Tinto is the largest known sulfide deposit in the world, and it is located in the Iberian Pyrite Belt. (IPB).

Riotintoagua

Many of the extremophiles that live in these deposits are thought to survive independently of the Sun. This area is rich in iron and sulfur minerals such as

• hematite (Fe
  ₂O
  ₃) which is common in the Meridiani Planum area of Mars explored by Opportunity rover and thought to be signs of ancient hot springs on Mars.

Jarosite, on quartz

• jarosite (KFe³⁺
  ₃(OH)
  ₆(SO
  ₄)
  ₂), discovered on Mars by Opportunity and on Earth forms either in acid mine drainage, during oxidation of sulphide minerals, and during alteration of volcanic rocks by acidic, sulphur-rich fluids near volcanic vents.

Permafrost soils

Much of the water on Mars is permanently frozen, mixed with the rocks. So terrestrial permafrosts are a good analogue. And some of the Carnobacterium species isolated from permafrosts have the ability to survive under the conditions of the low atmospheric pressures, low temperatures and CO
₂ dominated anoxic atmosphere of Mars.

Ice caves

Ice caves, or ice preserved under the surface in cave systems protected from the surface conditions, may exist on Mars. The ice caves near the summit of Mount Erebus in Antarctica, are associated with fumaroles in a polar alpine environments starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock.

Cave systems

Mines on Earth give access to deep subsurface environments which turn out to be inhabited, and deep caves may possibly exist on Mars, although without the benefits of an atmosphere.

Basaltic lava tubes

The only caves found so far on Mars are lava tubes. These are insulated to some extent from surface conditions and may retain ice also when there is none left on the surface, and may have access to chemicals such as hydrogen from serpentization to fuel chemosynthetic life. Lava tubes on Earth have microbial mats, and mineral deposits inhabited by microbes. These are being studied to help with identification of life on Mars if any of the lava tubes there are inhabited.

Lechuguilla Cave

Further information: Lechuguilla Cave

First of the terrestrial sulfur caves to be investigated as a Mars analogue for sulfur based ecosystems that could possibly exist underground also on Mars. On Earth, these form when hydrogen sulfide from below the cave meets the surface oxygenated zone. As it does so, sulfuric acid forms, and microbes accelerate the process.

The high abundance of sulfur on Mars combined with presence of ice, and trace detection of methane suggest the possibility of sulfur caves below the surface of Mars like this.

Cueva de Villa Luz

The Snottites in the toxic sulfur cave Cueva de Villa Luz flourish on Hydrogen Sulfide gas and though some are aerobes (though only needing low levels of oxygen), some of these species (e.g. Acidianus), like those that live around hydrothermal vents, are able to survive independent of a source of oxygen. So the caves may give insight into subsurface thermal systems on Mars, where caves similar to the Cueva de Villa Luz could occur.

Movile Cave

Further information: Movile Cave

• Movile Cave is thought to have been isolated from the atmosphere and sunlight for 5.5 million years.
• Atmosphere rich in H
  ₂S and CO
  ₂ with 1% - 2% CH
  ₄ (methane)
• It does have some oxygen, 7-10% O
  ₂ in the cave atmosphere, compared to 21% O
  ₂ in the air
• Microbes rely mainly on sulfide and methane oxidation.
• Has 33 vertebrates and a wide range of indigenous microbes.

Magnesium sulfate lakes

Spotted Lake in British Columbia, Canada. Its sulfate concentrations are amongst the highest in the world. Every summer the water evaporated to form this pattern of interconnected brine pools separated by salt crusts.

Crystals of Meridianiite, formula Magnesium sulfate 11 hydrate MgSO
₄·11H
₂O. Evidence from orbital measurements show that this is the phase of Magnesium sulfate which would be in equilibrium with the ice in the Martian polar and sub polar regions It also occurs on the Earth, for instance in Basque Lake 2 in Western Columbia, which may give an analogue for Mars habitats.

Vugs on Mars which may be voids left by Meridianiite when it dissolved or dehydrated

Opportunity found evidence for magnesium sulfates on Mars (one form of it is epsomite, or "Epsom salts"), in 2004. Curiosity rover has detected calcium sulfates on Mars. Orbital maps also suggest that hydrated sulfates may be common on Mars. The orbital observations are consistent with iron sulfate or a mixture of calcium and magnesium sulfate.

Magnesium sulfate is a likely component of cold brines on Mars, especially with the limited availability of subsurface ice. Terrestrial magnesium sulfate lakes have similar chemical and physical properties. They also have a wide range of halophilic organisms, in all the three Kingdoms of life (Archaea, Bacteria and Eukaryota), in the surface and near subsurface. With the abundance of algae and bacteria, in alkaline hypersaline conditions, they are of astrobiological interest for both past and present life on Mars.

These lakes are most common in western Canada, and the northern part of Washington state, USA. One of the examples, is Basque Lake 2 in Western Canada, which is highly concentrated in magnesium sulfate. In summer it deposits epsomite ("Epsom salts"). In winter, it deposits meridianiite. This is named after Meridiani Planum where Opportunity rover found crystal molds in sulfate deposits (Vugs) which are thought to be remains of this mineral which have since been dissolved or dehydrated. It is preferentially formed at subzero temperatures, and is only stable below 2 °C, while Epsomite (MgSO
₄·7H
₂O) is favored at higher temperatures.

Another example is Spotted Lake, which shows a wide variety of minerals, most of them sulfates, with sodium, magnesium and calcium as cations.

"Dominant minerals included blöedite Na
₂Mg(SO
₄)
₂·4H
₂O, konyaite Na
₂Mg(SO
₄)
₂·5H
₂O, epsomite MgSO
₄·7H
₂O, and gypsumCaSO
₄·2H
₂O, with minor eugsterite, picromerite, syngenite, halite, and sylvite",

Some of the microbes isolated have been able to survive the high concentrations of magnesium sulfates found in Martian soils, also at low temperatures that may be found on Mars.

Sulfates (for instance of sodium, magnesium and calcium) are also common in other continental evaporates (such as the salars of the Atacama Desert), as distinct from salt beds associated with marine deposits which tend to consist mainly of halites (chlorides).

Subglacial lakes

Lake Vostok drill 2011

Subglacial lakes such as Lake Vostok may give analogues of Mars habitats beneath ice sheets. Sub glacial lakes are kept liquid partly by the pressure of the depth of ice, but that contributes only a few degrees of temperature rise. The main effect that keeps them liquid is the insulation of the ice blocking escape of heat from the interior of the Earth, similarly to the insulating effect of deep layers of rock. As for deep rock layers, they don't require extra geothermal heating below a certain depth.

In the case of Mars, the depth needed for geothermal melting of the basal area of a sheet of ice is 4-6 kilometers. The ice layers are probably only 3.4 to 4.2 km in thickness for the north polar cap. However, it was shown that the situation is different when considering a lake that is already melted. When they applied their model to Mars, they showed that a liquid layer, once melted (initially open to the surface of the ice), could remain stable at any depth over 600 meters even in absence of extra geothermal heating. According to their model, if the polar regions had a subsurface lake perhaps formed originally through friction as a subglacial lake at times of favourable axial tilt, then supplied by accumulating layers of snow on top as the ice sheets thickened, they suggest that it could still be there. If so, it could be occupied by similar life forms to those that could survive in Lake Vostok.

Ground penetrating radar could detect these lakes because of the high radar contrast between water and ice or rock. MARSIS, the ground penetrating radar on ESA's Mars Express detected a subglacial lake in Mars near the south pole.

Subsurface life kilometers below the surface

Investigations of life in deep mines, and drilling beneath the ocean depths may give an insight into possibilities for life in the Mars hydrosphere and other deep subsurface habitats, if they exist.

Mponeng gold mine in South Africa

Further information: Mponeng

• bacteria obtain their energy from hydrogen oxidation linked to sulfate reduction, living independent of the surface
• nematodes feeding on those bacteria, again living independent of the surface.
• 3 to 4 km depth

Boulby Mine on the edge of the Yorkshire moors

Further information: Boulby Mine

• 250 million year halite (chloride) and sulfate salts
• High salinity and low water activity
• 1.1. km depth
• Anaerobic microbes that could survive cut off from the atmosphere

Alpine and permafrost lichens

In high alpine and polar regions, lichens have to cope with conditions of high UV fluxes low temperatures and arid environments. This is especially so when the two factors, polar regions and high altitudes are combined. These conditions occur in the high mountains of Antarctica, where lichens grow at altitudes up to 2,000 meters with no liquid water, just snow and ice. Researchers described this as the most Mars-like environment on the Earth.

Genetic diversity

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Genetic_diversity 

A graphical representation of the typical human karyotype.

Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for 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.

Neutral and adaptive genetic diversity

Neutral genetic diversity consists of genes that do not increase fitness and are not responsible for adaptability. Natural selection does not act on these neutral genes. Adaptive genetic diversity consists of genes that increase fitness and are responsible for adaptability to changes in the environment. Adaptive genes are responsible for ecological, morphological, and behavioral traits. Natural selection acts on adaptive genes which allows the organisms to evolve. The rate of evolution on adaptive genes is greater than on neutral genes due to the influence of selection. However, it has been difficult to identify alleles for adaptive genes and thus adaptive genetic diversity is most often measured indirectly. For example, heritability can be measured as ${\displaystyle h^2=V_A/V_P}$ or adaptive population differentiation can be measured as ${\displaystyle Q_{ST}=V_G/(V_G+2V_A)}$. It may be possible to identify adaptive genes through genome-wide association studies by analyzing genomic data at the population level.

Identifying adaptive genetic diversity is important for conservation because the adaptive potential of a species may dictate whether it survives or becomes extinct, especially as the climate changes. This is magnified by a lack of understanding whether low neutral genetic diversity is correlated with high genetic drift and high mutation load. In a review of current research, Teixeira and Huber (2021), discovered some species, such as those in the genus Arabidopsis, appear to have high adaptive potential despite suffering from low genetic diversity overall due to severe bottlenecks. Therefore species with low neutral genetic diversity may possess high adaptive genetic diversity, but since it is difficult to identify adaptive genes, a measurement of overall genetic diversity is important for planning conservation efforts and a species that has experienced a rapid decline in genetic diversity may be highly susceptible to extinction.

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 an example of 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 Great Famine in Ireland was caused in part by a 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.

Coronavirus populations have considerable evolutionary diversity due to mutation and homologous recombination. For example, the sequencing of 86 SARS-CoV-2 coronavirus samples obtained from infected patients revealed 93 mutations indicating the presence of considerable genetic diversity. Replication of the coronavirus RNA genome is catalyzed by an RNA-dependent RNA polymerase. During replication this polymerase may undergo template switching, a form of homologous recombination. This process which also generates genetic diversity appears to be an adaptation for coping with RNA genome damage.

Coping with low genetic diversity

A Tanzanian cheetah.

Natural

Photomontage of planktonic organisms.

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.

Genetic diversity can also be measured. The various recorded ways of measuring genetic diversity include:

• Species richness is a measure of the number of species
• Species abundance a relative measure of the abundance of species
• Species density an evaluation of the total number of species per unit area