Ultimate fate of the universe

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

Physical cosmology

The ultimate fate of the universe is a topic in physical cosmology, whose theoretical restrictions allow possible scenarios for the evolution and ultimate fate of the universe to be described and evaluated. Based on available observational evidence, deciding the fate and evolution of the universe has become a valid cosmological question, being beyond the mostly untestable constraints of mythological or theological beliefs. Several possible futures have been predicted by different scientific hypotheses, including that the universe might have existed for a finite and infinite duration, or towards explaining the manner and circumstances of its beginning.

Observations made by Edwin Hubble during the 1920s–1950s found that galaxies appeared to be moving away from each other, leading to the currently accepted Big Bang theory. This suggests that the universe began – very small and very dense – about 13.82 billion years ago, and it has expanded and (on average) become less dense ever since. Confirmation of the Big Bang mostly depends on knowing the rate of expansion, average density of matter, and the physical properties of the mass–energy in the universe.

There is a strong consensus among cosmologists that the universe is considered "flat" and will continue to expand forever.

Factors that need to be considered in determining the universe's origin and ultimate fate include the average motions of galaxies, the shape and structure of the universe, and the amount of dark matter and dark energy that the universe contains.

Emerging scientific basis

Theory

The theoretical scientific exploration of the ultimate fate of the universe became possible with Albert Einstein's 1915 theory of general relativity. General relativity can be employed to describe the universe on the largest possible scale. There are several possible solutions to the equations of general relativity, and each solution implies a possible ultimate fate of the universe.

Alexander Friedmann proposed several solutions in 1922, as did Georges Lemaître in 1927. In some of these solutions, the universe has been expanding from an initial singularity which was, essentially, the Big Bang.

Observation

In 1929, Edwin Hubble published his conclusion, based on his observations of Cepheid variable stars in distant galaxies, that the universe was expanding. From then on, the beginning of the universe and its possible end have been the subjects of serious scientific investigation.

Big Bang and Steady State theories

In 1927, Georges Lemaître set out a theory that has since come to be called the Big Bang theory of the origin of the universe. In 1948, Fred Hoyle set out his opposing Steady State theory in which the universe continually expanded but remained statistically unchanged as new matter is constantly created. These two theories were active contenders until the 1965 discovery, by Arno Penzias and Robert Wilson, of the cosmic microwave background radiation, a fact that is a straightforward prediction of the Big Bang theory, and one that the original Steady State theory could not account for. As a result, the Big Bang theory quickly became the most widely held view of the origin of the universe.

Cosmological constant

Einstein and his contemporaries believed in a static universe. When Einstein found that his general relativity equations could easily be solved in such a way as to allow the universe to be expanding at the present and contracting in the far future, he added to those equations what he called a cosmological constant ⁠— ⁠essentially a constant energy density, unaffected by any expansion or contraction ⁠— ⁠whose role was to offset the effect of gravity on the universe as a whole in such a way that the universe would remain static. However, after Hubble announced his conclusion that the universe was expanding, Einstein would write that his cosmological constant was "the greatest blunder of my life."

Density parameter

An important parameter in fate of the universe theory is the density parameter, omega (${\displaystyle \Omega }$), defined as the average matter density of the universe divided by a critical value of that density. This selects one of three possible geometries depending on whether ${\displaystyle \Omega }$ is equal to, less than, or greater than ${\displaystyle 1}$. These are called, respectively, the flat, open and closed universes. These three adjectives refer to the overall geometry of the universe, and not to the local curving of spacetime caused by smaller clumps of mass (for example, galaxies and stars). If the primary content of the universe is inert matter, as in the dust models popular for much of the 20th century, there is a particular fate corresponding to each geometry. Hence cosmologists aimed to determine the fate of the universe by measuring ${\displaystyle \Omega }$, or equivalently the rate at which the expansion was decelerating.

Repulsive force

Starting in 1998, observations of supernovas in distant galaxies have been interpreted as consistent with a universe whose expansion is accelerating. Subsequent cosmological theorizing has been designed so as to allow for this possible acceleration, nearly always by invoking dark energy, which in its simplest form is just a positive cosmological constant. In general, dark energy is a catch-all term for any hypothesized field with negative pressure, usually with a density that changes as the universe expands.

Role of the shape of the universe

The ultimate fate of an expanding universe depends on the matter density ${\displaystyle \Omega _{M}}$ and the dark energy density ${\displaystyle \Omega _{\Lambda }}$

The current scientific consensus of most cosmologists is that the ultimate fate of the universe depends on its overall shape, how much dark energy it contains and on the equation of state which determines how the dark energy density responds to the expansion of the universe. Recent observations conclude, from 7.5 billion years after the Big Bang, that the expansion rate of the universe has likely been increasing, commensurate with the Open Universe theory. However, other recent measurements by Wilkinson Microwave Anisotropy Probe suggest that the universe is either flat or very close to flat.

Closed universe

If ${\displaystyle \Omega >1}$, the geometry of space is closed like the surface of a sphere. The sum of the angles of a triangle exceeds 180 degrees and there are no parallel lines; all lines eventually meet. The geometry of the universe is, at least on a very large scale, elliptic.

In a closed universe, gravity eventually stops the expansion of the universe, after which it starts to contract until all matter in the universe collapses to a point, a final singularity termed the "Big Crunch", the opposite of the Big Bang. Some new modern theories assume the universe may have a significant amount of dark energy, whose repulsive force may be sufficient to cause the expansion of the universe to continue forever—even if ${\displaystyle \Omega >1}$.

Open universe

If ${\displaystyle \Omega <1}$, the geometry of space is open, i.e., negatively curved like the surface of a saddle. The angles of a triangle sum to less than 180 degrees, and lines that do not meet are never equidistant; they have a point of least distance and otherwise grow apart. The geometry of such a universe is hyperbolic.

Even without dark energy, a negatively curved universe expands forever, with gravity negligibly slowing the rate of expansion. With dark energy, the expansion not only continues but accelerates. The ultimate fate of an open universe is either universal heat death, a "Big Freeze" (not to be confused with heat death, despite seemingly similar name interpretation ⁠— ⁠see §Theories about the end of the universe below), or a "Big Rip", where the acceleration caused by dark energy eventually becomes so strong that it completely overwhelms the effects of the gravitational, electromagnetic and strong binding forces.

Conversely, a negative cosmological constant, which would correspond to a negative energy density and positive pressure, would cause even an open universe to re-collapse to a big crunch.

Flat universe

If the average density of the universe exactly equals the critical density so that ${\displaystyle \Omega =1}$, then the geometry of the universe is flat: as in Euclidean geometry, the sum of the angles of a triangle is 180 degrees and parallel lines continuously maintain the same distance. Measurements from Wilkinson Microwave Anisotropy Probe have confirmed the universe is flat within a 0.4% margin of error.

In the absence of dark energy, a flat universe expands forever but at a continually decelerating rate, with expansion asymptotically approaching zero; with dark energy, the expansion rate of the universe initially slows down, due to the effects of gravity, but eventually increases, and the ultimate fate of the universe becomes the same as that of an open universe.

Theories about the end of the universe

The fate of the universe is determined by its density. The preponderance of evidence to date, based on measurements of the rate of expansion and the mass density, favors a universe that will continue to expand indefinitely, resulting in the "Big Freeze" scenario below. However, observations are not conclusive, and alternative models are still possible.

Big Freeze or Heat Death

The Big Freeze (or Big Chill) is a scenario under which continued expansion results in a universe that asymptotically approaches absolute zero temperature. This scenario, in combination with the Big Rip scenario, is gaining ground as the most important hypothesis. It could, in the absence of dark energy, occur only under a flat or hyperbolic geometry. With a positive cosmological constant, it could also occur in a closed universe. In this scenario, stars are expected to form normally for 10¹² to 10¹⁴ (1–100 trillion) years, but eventually the supply of gas needed for star formation will be exhausted. As existing stars run out of fuel and cease to shine, the universe will slowly and inexorably grow darker. Eventually black holes will dominate the universe, which themselves will disappear over time as they emit Hawking radiation. Over infinite time, there would be a spontaneous entropy decrease by the Poincaré recurrence theorem, thermal fluctuations, and the fluctuation theorem.

A related scenario is heat death, which states that the universe goes to a state of maximum entropy in which everything is evenly distributed and there are no gradients—which are needed to sustain information processing, one form of which is life. The heat death scenario is compatible with any of the three spatial models, but requires that the universe reach an eventual temperature minimum.

Big Rip

The current Hubble constant defines a rate of acceleration of the universe not large enough to destroy local structures like galaxies, which are held together by gravity, but large enough to increase the space between them. A steady increase in the Hubble constant to infinity would result in all material objects in the universe, starting with galaxies and eventually (in a finite time) all forms, no matter how small, disintegrating into unbound elementary particles, radiation and beyond. As the energy density, scale factor and expansion rate become infinite the universe ends as what is effectively a singularity.

In the special case of phantom dark energy, which has supposed negative kinetic energy that would result in a higher rate of acceleration than other cosmological constants predict, a more sudden big rip could occur.

Big Crunch

The Big Crunch. The vertical axis can be considered as expansion or contraction with time.

The Big Crunch hypothesis is a symmetric view of the ultimate fate of the universe. Just as the Big Bang started as a cosmological expansion, this theory assumes that the average density of the universe will be enough to stop its expansion and the universe will begin contracting. The end result is unknown; a simple estimation would have all the matter and space-time in the universe collapse into a dimensionless singularity back into how the universe started with the Big Bang, but at these scales unknown quantum effects need to be considered. Recent evidence suggests that this scenario is unlikely but has not been ruled out, as measurements have been available only over a short period of time, relatively speaking, and could reverse in the future.

This scenario allows the Big Bang to occur immediately after the Big Crunch of a preceding universe. If this happens repeatedly, it creates a cyclic model, which is also known as an oscillatory universe. The universe could then consist of an infinite sequence of finite universes, with each finite universe ending with a Big Crunch that is also the Big Bang of the next universe. A problem with the cyclic universe is that it does not reconcile with the second law of thermodynamics, as entropy would build up from oscillation to oscillation and cause the eventual heat death of the universe. Current evidence also indicates the universe is not closed. This has caused cosmologists to abandon the oscillating universe model. A somewhat similar idea is embraced by the cyclic model, but this idea evades heat death because of an expansion of the branes that dilutes entropy accumulated in the previous cycle.

Big Bounce

The Big Bounce is a theorized scientific model related to the beginning of the known universe. It derives from the oscillatory universe or cyclic repetition interpretation of the Big Bang where the first cosmological event was the result of the collapse of a previous universe.

According to one version of the Big Bang theory of cosmology, in the beginning the universe was infinitely dense. Such a description seems to be at odds with other more widely accepted theories, especially quantum mechanics and its uncertainty principle. It is not surprising, therefore, that quantum mechanics has given rise to an alternative version of the Big Bang theory. Also, if the universe is closed, this theory would predict that once this universe collapses it will spawn another universe in an event similar to the Big Bang after a universal singularity is reached or a repulsive quantum force causes re-expansion.

In simple terms, this theory states that the universe will continuously repeat the cycle of a Big Bang, followed up with a Big Crunch.

Big Slurp

This theory posits that the universe currently exists in a false vacuum and that it could become a true vacuum at any moment.

In order to best understand the false vacuum collapse theory, one must first understand the Higgs field which permeates the universe. Much like an electromagnetic field, it varies in strength based upon its potential. A true vacuum exists so long as the universe exists in its lowest energy state, in which case the false vacuum theory is irrelevant. However, if the vacuum is not in its lowest energy state (a false vacuum), it could tunnel into a lower energy state. This is called vacuum decay. This has the potential to fundamentally alter our universe; in more audacious scenarios even the various physical constants could have different values, severely affecting the foundations of matter, energy, and spacetime. It is also possible that all structures will be destroyed instantaneously, without any forewarning.

Cosmic uncertainty

Each possibility described so far is based on a very simple form for the dark energy equation of state. However, as the name is meant to imply, very little is currently known about the physics of dark energy. If the theory of inflation is true, the universe went through an episode dominated by a different form of dark energy in the first moments of the Big Bang, but inflation ended, indicating an equation of state far more complex than those assumed so far for present-day dark energy. It is possible that the dark energy equation of state could change again, resulting in an event that would have consequences which are extremely difficult to predict or parametrize. As the nature of dark energy and dark matter remain enigmatic, even hypothetical, the possibilities surrounding their coming role in the universe are currently unknown. None of these theoretic endings for the universe are certain.

Observational constraints on theories

Choosing among these rival scenarios is done by 'weighing' the universe, for example, measuring the relative contributions of matter, radiation, dark matter, and dark energy to the critical density. More concretely, competing scenarios are evaluated against data on galaxy clustering and distant supernovas, and on the anisotropies in the cosmic microwave background. 

Speculative evolution

From Wikipedia, the free encyclopedia

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

 

Surviving dinosaurs and Mesozoic creatures are a common theme in alternative evolution. One example is the 2001-2005 Speculative Dinosaur Project and its invention of many speculative animals.

Speculative evolution is a genre of speculative fiction and an artistic movement focused on hypothetical scenarios in the evolution of life, and a significant form of fictional biology. It is also known as speculative biology and it is referred to as speculative zoology in regards to hypothetical animals. Works incorporating speculative evolution may have entirely conceptual species that evolve on a planet other than Earth, or they may be an alternate history focused on an alternate evolution of terrestrial life. Speculative evolution is often considered hard science fiction because of its strong connection to and basis in science, particularly biology.

Speculative evolution is a long-standing trope within science fiction, often recognized as beginning as such with H. G. Wells's 1895 novel The Time Machine, which featured several imaginary future creatures. Although small-scale speculative faunas were a hallmark of science fiction throughout the 20th century, ideas were only rarely well-developed, with some exceptions such as Edgar Rice Burroughs's Barsoom, a fictional rendition of Mars and its ecosystem published through novels from 1912 to 1941, and Gerolf Steiner's Rhinogradentia, a fictional order of mammals created in 1957.

The modern speculative evolution movement is generally agreed to have begun with the publication of Dougal Dixon's 1981 book After Man, which explored a fully realized future Earth with a complete ecosystem of over a hundred hypothetical animals. The success of After Man spawned several "sequels" by Dixon, focusing on different alternate and future scenarios. Dixon's work, like most similar works that came after them, were created with real biological principles in mind and were aimed at exploring real life processes, such as evolution and climate change, through the use of fictional examples.

Speculative evolution's possible use as an educational and scientific tool has been noted and discussed through the decades following the publication of After Man. Speculative evolution can be useful in exploring and showcasing patterns present in the present and in the past. By extrapolating past trends into the future, scientists can research and predict the most likely scenarios of how certain organisms and lineages could respond to ecological changes. In some cases, creatures first imagined within speculative evolution have since been discovered, such as an imaginary filter-feeding anomalocarid illustrated by artist John Meszaros in the 2012 book All Yesterdays by John Conway, C. M. Kosemen and Darren Naish being proven as having existed through fossils discovered in 2014 of the real anomalocarid Tamisiocaris.

History

Early works

The Time Machine (1895) by H. G. Wells is seen by some as an early instance of speculative evolution and has been cited as an inspiration by later creators within the field.

Explorations of hypothetical worlds featuring future, alternate or alien lifeforms is a long-standing trope in science fiction. One of the earliest works usually recognized as representing one of speculative evolution is H. G. Wells's science fiction novel The Time Machine, published in 1895. The Time Machine, set over eight hundred thousand years in the future, features post-human descendants in the form of the beautiful but weak Eloi and the brutish Morlocks. Further into the future, the protagonist of the book finds large crab-monsters and huge butterflies. Science fiction authors who wrote after Wells often used fictional creatures in the same vein, but most such imaginary faunas were small and not very developed.

A four-armed "Green Martian" riding a "throat" from Edgar Rice Burroughs's Barsoom, a fictional version of the planet Mars. Illustration by James Allen St. John (1920).

Edgar Rice Burroughs, who wrote in the early 20th century, can like Wells be considered an early speculative evolution author. Although his fictional ecosystems were still relatively small in scope, they were the settings of many of his novels and as such quite well-developed. In particular, Burroughs's Barsoom, a fictional version of the planet Mars which appeared in ten novels published from 1912 to 1941, featured a Martian ecosystem with a variety of alien creatures and several distinct Martian cultures and ethnic groups.

A mock taxidermy of a rhinograde, using its nasorium to catch fish. Rhinogrades, created by Gerolf Steiner in 1957, are one of the earliest concrete examples of speculative zoology.

In 1930, Olaf Stapledon published a "future history", Last and First Men: A Story of the Near and Far Future, describing the history of humanity from the present onwards, across two billion years and eighteen human species, of which Homo sapiens is the first. The book anticipates the science of genetic engineering, and is an early instance of the fictional group mind idea. Published in 1957, German zoologist Gerolf Steiner's book Bau und Leben der Rhinogradentia (translated into English as The Snouters: The Form and Life of the Rhinogrades) described the fictional evolution, biology and behavior of an imaginary order of mammals, the Rhinogradentia or "rhinogrades". The Rhinogrades are characterized by a nose-like feature called a "nasorium", the form and function of which vary significantly between species, akin to Darwin's finches and their beak specialization. This diverse group of fictional animals inhabits a series of islands in which they have gradually evolved, radiating into most ecological niches. Satirical papers have been published continuing Steiner's imagined world. Although the work does feature an entire speculative ecosystem, its impact is dwarfed by the later works due to its limited scope, only exploring the life of an island archipelago.

In 1976, the Italian author and illustrator Leo Lionni published Parallel Botany, a "field guide to imaginary plants", presented with academic-style mentions of genuine people and places. Parallel Botany has been compared to the 1972 book Invisible Cities by Italo Calvino, in which Marco Polo in a dialogue with Kublai Khan describes 55 cities, which, like Lionni's "parallel" plants, are "only as real as the mind's ability to conceptualize them".

Movement

Author Dougal Dixon with a model of a "Strida", one of the creatures featured in his 2010 book Greenworld.

One of the significant "founding" works of speculative evolution is After Man by Dougal Dixon, published in 1981. To this day, After Man is recognized as the first truly large-scale speculative evolution project involving a whole world and a vast array of species. Furthering its significance is the fact that the book was made very accessible by being published by mainstream publishers and being fully illustrated with color images. As such, After Man is often seen as having firmly established the idea of creating entire speculative worlds. Through the decades following After Man's publication, Dixon remained one of the sole authors of speculative evolution, publishing two more books in the same vein as After Man; The New Dinosaurs in 1988 and Man After Man in 1990. Dixon cited The Time Machine as his primary inspiration, being unaware of Steiner's work, and devised After Man as a popular-level book on the processes of evolution that instead of using the past to tell the story projected the processes into the future. A central idea of After Man, besides a wave of extinction following humans, is convergent evolution as new species bear a close resemblance to their unrelated predecessors.

When designing the various animals of the book, Dixon looked at the different types of biomes on the planet and what adaptations animals living there have, designing new animals descended from modern day ones with the same set of adaptations. The success of After Man inspired Dixon to continue writing books that explained factual scientific processes through fictional examples. The New Dinosaurs was in essence a book about zoogeography, something the general public would be unfamiliar with, using a world in which the non-avian dinosaurs had not gone extinct. Man After Man, explored climate change over the course of the next few million years by showcasing its effects through the eyes of future human descendants.

Today, many artists and writers work on speculative evolution projects online, often in the same vein as Dixon's works. Speculative evolution continues to endure a somewhat mainstream presence through TV shows featuring hypothetical and imaginary creatures, such as The Future is Wild (2002), Primeval (2007–2011) and Terra Nova (2011) and films such as Avatar (2009) and After Earth (2013). The modern explosion of speculative evolution has been termed by British paleontologist Darren Naish as the "Speculative Zoology Movement".

As an educational and scientific tool

Reconstruction of Tamisiocaris (top), an anomalocarid from the Cambrian which was discovered to have been a filter-feeder in 2014. A hypothetical filter-feeding anomalocarid was featured in the book All Yesterdays (2012).

Although primarily characterized as entertainment, speculative evolution can be used as educational tool to explain and illustrate real natural processes through using fictional and imaginary examples. The worlds created are often built on ecological and biological principles inferred from the real evolutionary history of life on Earth and readers can learn from them as such. For example, all of Dixon's speculative works are aimed at exploring real processes, with After Man exploring evolution, The New Dinosaurs zoogeography and both Man After Man and Greenworld (2010) exploring climate change, offering an environmental message.

In some cases, speculative evolution artists have successfully predicted the existence of organisms that were later discovered to resemble something real. Many of the animals featured in Dixon's After Man are still considered plausible ideas, with some of them (such as specialized rodents and semi-aquatic primates) being reinforced with recent biology studies. A creature dubbed "Ceticaris", conceived by artist John Meszaros as a filter-feeding anomalocarid, was published in the 2012 book All Yesterdays and two years later, in 2014, the actual Cambrian anomalocarid Tamisiocaris was discovered to have been a filter-feeder. In honor of Meszaros's prediction, Tamisiocaris was included in a new clade named the Cetiocaridae.

Dougal Dixon's The New Dinosaurs was heavily influenced by paleontological ideas developing during its time, such as the ongoing dinosaur renaissance, and as such many of the dinosaurs in the book are energetic and active creatures rather than sluggish and lumbering. Dixon extrapolated on the ideas of paleontologists such as Robert Bakker and Gregory S. Paul when creating his creatures and also used patterns seen in the actual evolutionary history of the dinosaurs and pushing them to an extreme. Perhaps because of this, many of the animals in the book are similar to actual Mesozoic animals that were later discovered. Many of the dinosaurs in it are feathered, something not widely accepted at the time of its publication but seen as likely today. Similarly, After Man in 1981 represents a sort of time capsule of geological thought before global warming was fully discerned, but Dixon also portrays a sixth mass extinction or Anthropocene before it was commonplace to do so.

Hypothetical restoration of Dromaeosauroides bornholmensis, which is known from two teeth. Its appearance is inferred from related genera.

 

Speculative reconstruction of Sinopliosaurus fusuiensis with generalized spinosaurid morphology, and unique coloration pattern.

Speculative evolution can be useful in exploring and showcasing patterns present in the present and in the past, and there is a useful aspect to hypothesizing on the form of future and alien life. By extrapolating past trends into the future, scientists could research and predict the most likely scenarios of how certain organisms and lineages could respond to ecological changes. As such, speculative evolution facilitates authors and artists to develop realistic hypotheses of the future. In some scientific fields, speculation is essential in understanding what is being studied. Paleontologists apply their own understanding of natural processes and biology to understand the appearances and lifestyles of extinct organisms that are discovered, varying in how far their speculation goes. For instance, All Yesterdays and its sequel All Your Yesterdays (2017) explores highly speculative renditions of real (and in some cases hypothetical) prehistoric animals that do not explicitly contradict any of the recovered fossil material. The speculation undertaken for All Yesterdays and its sequel has been compared to that of Dixon's speculative evolution works, though its objective was to challenge modern conservative perceptions and ideas of how dinosaurs and other prehistoric creatures lived, rather than designing whole new ecosystems. The books have inspired a modern artistic movement of artists going beyond conventional paleoart tropes, expanding into increasingly speculative renditions of prehistoric life.

Additionally, the evolutionary history of fictional organisms has been used as a tool in biology education. Caminalcules, named after Joseph H. Camin, are a group of animal-like lifeforms, consisting of 77 purported extant and fossil species that were invented as a tool for understanding phylogenetics. The classification of Caminalcules, as well as other fictional creatures like dragons and aliens, have been used as analogies to teach concepts in evolution and systematics.

Speculative evolution is sometimes presented in museum exhibitions. For instance, both After Man and The Future is Wild has been presented in exhibition form, educating museum visitors on the principles of biology and evolution through using their own fictional future creatures.

Subsets

Alien life

The "Hellfire wasp", a wasp-like alien creature designed for James Cameron's film Avatar (2009).

A popular subset of speculative evolution is the exploration of possible realistic extraterrestrial life and ecosystems. Speculative evolution writings focusing on extraterrestrial life, like the blog Furahan Biology, use realistic scientific principles to describe the biomechanics of hypothetical alien life. Although commonly identified with terms such as "astrobiology", "xenobiology" or "exobiology", these terms designate actual scientific fields largely unrelated to speculative evolution. Though 20th century work in exobiology sometimes formulated "audacious" ideas about extraterrestrial forms of life. Astrophysicists Carl Sagan and Edwin Salpeter speculated that a "hunters, floaters and sinkers" ecosystem could populate the atmospheres of gas giant planets like Jupiter, and scientifically described it in a 1976 paper.

In extraterrestrial-focused speculative biology, lifeforms are often designed with the intention to populate planets wildly different from Earth, and in such cases concerns like chemistry, astronomy and the laws of physics become just as important to consider as the usual biological principles. Very exotic environments of physical extremes may be explored in such scenarios. For example, Robert Forward's 1980 Dragon's Egg develops a tale of life on a neutron star, and the resulting high-gravity, high-energy environment with an atmosphere of iron vapor and mountains 5-100 millimeters high. Once the star cools down and stable chemistry develops, life evolves extremely quickly, and Forward imagines a civilization of "cheela" that lives a million times faster than humans.

In some cases, artists and writers exploring possible alien life conjure similar ideas independent of each other, often attributed to studying the same biological processes and ideas. Such occasions can be called "convergent speculation", similar to the scientific idea of convergent evolution.

Perhaps the most famous speculative work on a hypothetical alien ecosystem is Wayne Barlowe's 1990 book Expedition, which explores the fictional planet Darwin IV. Expedition was written as a report of an 24th-century expedition that had been led to the planet by a team composed of both humans and intelligent aliens and used paintings and descriptive texts to create and describe a fully realized extraterrestrial ecosystem. Barlowe later served as an executive producer of a TV adaptation of the book, Alien Planet (2005) where exploration of Darwin IV is instead carried out by robotic probes and the segments detailing the ecosystems of the planet are intercut with interviews with scientists, such as Michio Kaku, Jack Horner and James B. Garvin.

Other examples of speculative evolution focused on extraterrestrial life include Dougal Dixon's 2010 book Greenworld, TV programmes such as 1997 the BBC2/Discovery Channel special Natural History of an Alien and the 2005 Channel 4/National Geographic programme Extraterrestrial as well as a variety of personal web-based artistic projects, such as C. M. Kosemen's "Snaiad" and Gert van Dijk's "Furaha", envisioning the biosphere of entire alien worlds.

Through science fiction, the speculative biology of extraterrestrial organisms has a strong presence in popular culture. The eponymous monster of Alien (1979), particularly its life cycle from egg to parasitoid larva to 'Xenomorph', is thought to be based on the real habits of parasitoid wasps in biology. Further, H. R. Giger's design of the Alien incorporated the features of insects, echinoderms and fossil crinoids, while concept artist John Cobb suggested acid blood as a biological defense mechanism. James Cameron's 2009 film Avatar constructed a fictional biosphere full of original, speculative alien species; a team of experts ensured that the lifeforms were scientifically plausible. The creatures of the movie took inspiration from Earth species as diverse as pterosaurs, microraptors, great white sharks, and panthers, and combined their traits to create an alien world.

Alternative evolution

Speculative zoology can examine sometimes overlooked prehistoric animals in an evolutionary context. The Speculative Dinosaur Project focused as much on mammals, squamates, and crocodylomorphs as on dinosaurs. Pictured are metatherian marsupials that have converged on our world's mustelids.

Similar to alternate history, alternative evolution is the exploration of possible alternate scenarios that could have played out in the Earth's past to give rise to alternate lifeforms and ecosystems, popularly the survival of non-avian dinosaurs to the present day. As humanity is often not a part of the worlds envisioned through alternative evolution, it has sometimes been characterized as non-anthropocentric.

Although dinosaurs surviving to the age of humans has been adapted as a plot point in numerous science fiction stories since at least 1912, beginning with Arthur Conan Doyle's The Lost World, the idea of exploring the fully fledged alternate ecosystems that would develop in such a scenario truly began with the publication of Dixon's The New Dinosaurs in 1988, in which dinosaurs were not some lone stragglers of known species that had survived more or less unchanged for the last 66 million years, but diverse animals that had continued to evolve beyond the Cretaceous. In the vein of Dixon's The New Dinosaurs imagination, a now largely defunct, but creatively significant collaborative online project the Speculative Dinosaur Project followed in the same zoological worldbuilding tradition.

Since 1988, alternative evolution has sometimes been applied in popular culture. The creatures in the 2005 film King Kong were fictitious descendants of real animals, with Skull Island being inhabited by dinosaurs and other prehistoric fauna. Inspired by Dougal Dixon's works, the designers imagined what 65 million years or more of isolated evolution might have done to dinosaurs. Concept art for the film was published in the book The World of Kong: A Natural History of Skull Island (2005), which explored the world of the film from a biological perspective, envisioning Skull Island as a surviving fragment of ancient Gondwana. Prehistoric creatures on a declining, eroding island had evolved into "a menagerie of nightmares".

A hypothetical natural history of dragons is a popular subject of speculative zoology, being explored in works such as Peter Dickinson's The Flight of Dragons (1979), the 2004 mockumentary The Last Dragon and the Dragonology series of books.

Future evolution

The evolution of organisms in the Earth's future is a popular subset of speculative evolution. A relatively common theme in future evolution is civilizational collapse and/or humans becoming extinct due to an anthropogenic extinction event caused by environmental degradation. After such a mass extinction event, the remaining non-human fauna and flora evolve into a variety of new forms. Although the foundations of this subset were laid by Wells's The Time Machine already in 1895, it is generally agreed to have been definitely founded through Dixon's After Man in 1981, which explored a fully realized future ecosystem set 50 million years from the present. Dixon's third work on speculative evolution, Man After Man (1990) is also an example of future evolution, this time exploring an imagined future evolutionary path of humanity.

Peter Ward's Future Evolution (2001) makes a scientifically accurate approach to the prediction of patterns of evolution in the future. Ward compares his predictions with those of Dixon and Wells. He tries to understand the mechanism of mass extinctions and the principles of recovery of ecosystems. A key point is that "champion supertaxa" who diversify and speciate at a greater rate, will inherit the world after mass extinctions. Ward quotes the paleontologist Simon Conway Morris, who points out that the fantastical or even whimsical creatures devised by Dougal Dixon's, echo nature's tendency to converge on the same body plans. While Ward calls Dixon's visions "semi-whimsical" and compares them to Wells' initial visions in The Time Machine, he nonetheless continues the use of analogous evolution, which is a larger trend in speculative zoology.

Future evolution has also been explored on TV, with the mockumentary series The Future is Wild in 2002, for which Dixon was a consultant (and author of the companion book), and the series Primeval (2007–2011), a drama series in which imagined future animals occasionally appeared. Ideas of future evolution are also frequently explored in science fiction novels, such as in Kurt Vonnegut's 1985 science fiction novel Galápagos, which imagines the evolution of a small surviving group of humans into a sea lion-like species. Stephen Baxter's 2002 science fiction novel Evolution follows 565 million years of human evolution, from shrewlike mammals 65 million years in the past to the ultimate fate of humanity (and its descendants, both biological and non-biological) 500 million years in the future. C. M. Kosemen's 2008 All Tomorrows similarly explores the future evolution of humanity. Speculative biology and the future evolution of the human species are significant in bio art.

Population genetics

From Wikipedia, the free encyclopedia

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

Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, laboratory, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept.

What sets population genetics apart from newer, more phenotypic approaches to modelling evolution, such as evolutionary game theory and adaptive dynamics, is its emphasis on such genetic phenomena as dominance, epistasis, the degree to which genetic recombination breaks linkage disequilibrium, and the random phenomena of mutation and genetic drift. This makes it appropriate for comparison to population genomics data.

History

Population genetics began as a reconciliation of Mendelian inheritance and biostatistics models. Natural selection will only cause evolution if there is enough genetic variation in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural or sexual selection implausible. The Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. According to this principle, the frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift.

The typical white-bodied form of the peppered moth.

 

Industrial melanism: the black-bodied form of the peppered moth appeared in polluted areas.

The next key step was the work of the British biologist and statistician Ronald Fisher. In a series of papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural Selection, Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection could change allele frequencies in a population, resulting in evolution. In a series of papers beginning in 1924, another British geneticist, J. B. S. Haldane, worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. Haldane also applied statistical analysis to real-world examples of natural selection, such as peppered moth evolution and industrial melanism, and showed that selection coefficients could be larger than Fisher assumed, leading to more rapid adaptive evolution as a camouflage strategy following increased pollution.

The American biologist Sewall Wright, who had a background in animal breeding experiments, focused on combinations of interacting genes, and the effects of inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932 Wright introduced the concept of an adaptive landscape and argued that genetic drift and inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks.

The work of Fisher, Haldane and Wright founded the discipline of population genetics. This integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. John Maynard Smith was Haldane's pupil, whilst W. D. Hamilton was influenced by the writings of Fisher. The American George R. Price worked with both Hamilton and Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were influenced by Wright and Haldane.

Gertrude Hauser and Heidi Danker–Hopfe have suggested that Hubert Walter also contributed to the creation of the subdiscipline population genetics.

Modern synthesis

The mathematics of population genetics were originally developed as the beginning of the modern synthesis. Authors such as Beatty have asserted that population genetics defines the core of the modern synthesis. For the first few decades of the 20th century, most field naturalists continued to believe that Lamarckism and orthogenesis provided the best explanation for the complexity they observed in the living world. During the modern synthesis, these ideas were purged, and only evolutionary causes that could be expressed in the mathematical framework of population genetics were retained. Consensus was reached as to which evolutionary factors might influence evolution, but not as to the relative importance of the various factors.

Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He helped to bridge the divide between the foundations of microevolution developed by the population geneticists and the patterns of macroevolution observed by field biologists, with his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic diversity of wild populations and showed that, contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity, with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into a more accessible form. Many more biologists were influenced by population genetics via Dobzhansky than were able to read the highly mathematical works in the original.

In Great Britain E. B. Ford, the pioneer of ecological genetics, continued throughout the 1930s and 1940s to empirically demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic polymorphisms such as human blood types. Ford's work, in collaboration with Fisher, contributed to a shift in emphasis during the modern synthesis towards natural selection as the dominant force.

Neutral theory and origin-fixation dynamics

The original, modern synthesis view of population genetics assumes that mutations provide ample raw material, and focuses only on the change in frequency of alleles within populations. The main processes influencing allele frequencies are natural selection, genetic drift, gene flow and recurrent mutation. Fisher and Wright had some fundamental disagreements about the relative roles of selection and drift. The availability of molecular data on all genetic differences led to the neutral theory of molecular evolution. In this view, many mutations are deleterious and so never observed, and most of the remainder are neutral, i.e. are not under selection. With the fate of each neutral mutation left to chance (genetic drift), the direction of evolutionary change is driven by which mutations occur, and so cannot be captured by models of change in the frequency of (existing) alleles alone.

The origin-fixation view of population genetics generalizes this approach beyond strictly neutral mutations, and sees the rate at which a particular change happens as the product of the mutation rate and the fixation probability.

Four processes

Selection

Natural selection, which includes sexual selection, is the fact that some traits make it more likely for an organism to survive and reproduce. Population genetics describes natural selection by defining fitness as a propensity or probability of survival and reproduction in a particular environment. The fitness is normally given by the symbol w=1-s where s is the selection coefficient. Natural selection acts on phenotypes, so population genetic models assume relatively simple relationships to predict the phenotype and hence fitness from the allele at one or a small number of loci. In this way, natural selection converts differences in the fitness of individuals with different phenotypes into changes in allele frequency in a population over successive generations.

Before the advent of population genetics, many biologists doubted that small differences in fitness were sufficient to make a large difference to evolution. Population geneticists addressed this concern in part by comparing selection to genetic drift. Selection can overcome genetic drift when s is greater than 1 divided by the effective population size. When this criterion is met, the probability that a new advantageous mutant becomes fixed is approximately equal to 2s. The time until fixation of such an allele depends little on genetic drift, and is approximately proportional to log(sN)/s.

Dominance

Dominance means that the phenotypic and/or fitness effect of one allele at a locus depends on which allele is present in the second copy for that locus. Consider three genotypes at one locus, with the following fitness values

Genotype:	A1A1	A1A2	A2A2
Relative fitness:	1	1-hs	1-s

s is the selection coefficient and h is the dominance coefficient. The value of h yields the following information:

h=0	A1 dominant, A2 recessive
h=1	A2 dominant, A1 recessive
0<h<1	incomplete dominance
h<0	overdominance
h>1	Underdominance

Epistasis

The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.

Epistasis means that the phenotypic and/or fitness effect of an allele at one locus depends on which alleles are present at other loci. Selection does not act on a single locus, but on a phenotype that arises through development from a complete genotype. However, many population genetics models of sexual species are "single locus" models, where the fitness of an individual is calculated as the product of the contributions from each of its loci—effectively assuming no epistasis.

In fact, the genotype to fitness landscape is more complex. Population genetics must either model this complexity in detail, or capture it by some simpler average rule. Empirically, beneficial mutations tend to have a smaller fitness benefit when added to a genetic background that already has high fitness: this is known as diminishing returns epistasis. When deleterious mutations also have a smaller fitness effect on high fitness backgrounds, this is known as "synergistic epistasis". However, the effect of deleterious mutations tends on average to be very close to multiplicative, or can even show the opposite pattern, known as "antagonistic epistasis".

Synergistic epistasis is central to some theories of the purging of mutation load and to the evolution of sexual reproduction.

Mutation

Drosophila melanogaster

Mutation is the ultimate source of genetic variation in the form of new alleles. In addition, mutation may influence the direction of evolution when there is mutation bias, i.e. different probabilities for different mutations to occur. For example, recurrent mutation that tends to be in the opposite direction to selection can lead to mutation–selection balance. At the molecular level, if mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes. Developmental or mutational biases have also been observed in morphological evolution. For example, according to the phenotype-first theory of evolution, mutations can eventually cause the genetic assimilation of traits that were previously induced by the environment.

Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population.

Mutation can have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example, pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation ability in a bacterium during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size, indicating that it is driven more by mutation bias than by genetic drift.

Mutations can involve large sections of DNA becoming duplicated, usually through genetic recombination. This leads to copy-number variation within a population. Duplications are a major source of raw material for evolving new genes. Other types of mutation occasionally create new genes from previously noncoding DNA.

Genetic drift

Genetic drift is a change in allele frequencies caused by random sampling. That is, the alleles in the offspring are a random sample of those in the parents. Genetic drift may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection, which makes gene variants more common or less common depending on their reproductive success, the changes due to genetic drift are not driven by environmental or adaptive pressures, and are equally likely to make an allele more common as less common.

The effect of genetic drift is larger for alleles present in few copies than when an allele is present in many copies. The population genetics of genetic drift are described using either branching processes or a diffusion equation describing changes in allele frequency. These approaches are usually applied to the Wright-Fisher and Moran models of population genetics. Assuming genetic drift is the only evolutionary force acting on an allele, after t generations in many replicated populations, starting with allele frequencies of p and q, the variance in allele frequency across those populations is

${\displaystyle V_{t}\approx pq\left(1-\exp \left\{-{\frac {t}{2N_{e}}}\right\}\right).}$

Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. No population genetics perspective have ever given genetic drift a central role by itself, but some have made genetic drift important in combination with another non-selective force. The shifting balance theory of Sewall Wright held that the combination of population structure and genetic drift was important. Motoo Kimura's neutral theory of molecular evolution claims that most genetic differences within and between populations are caused by the combination of neutral mutations and genetic drift.

The role of genetic drift by means of sampling error in evolution has been criticized by John H Gillespie and Will Provine, who argue that selection on linked sites is a more important stochastic force, doing the work traditionally ascribed to genetic drift by means of sampling error. The mathematical properties of genetic draft are different from those of genetic drift. The direction of the random change in allele frequency is autocorrelated across generations.

Gene flow

Gene flow is the transfer of alleles from one population to another population through immigration of individuals. In this example, one of the birds from population A immigrates to population B, which has fewer of the dominant alleles, and through mating incorporates its alleles into the other population.

Because of physical barriers to migration, along with the limited tendency for individuals to move or spread (vagility), and tendency to remain or come back to natal place (philopatry), natural populations rarely all interbreed as may be assumed in theoretical random models (panmixy). There is usually a geographic range within which individuals are more closely related to one another than those randomly selected from the general population. This is described as the extent to which a population is genetically structured.

The Great Wall of China is an obstacle to gene flow of some terrestrial species.

Genetic structuring can be caused by migration due to historical climate change, species range expansion or current availability of habitat. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China, which has hindered the flow of plant genes.

Gene flow is the exchange of genes between populations or species, breaking down the structure. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer. Population genetic models can be used to identify which populations show significant genetic isolation from one another, and to reconstruct their history.

Subjecting a population to isolation leads to inbreeding depression. Migration into a population can introduce new genetic variants, potentially contributing to evolutionary rescue. If a significant proportion of individuals or gametes migrate, it can also change allele frequencies, e.g. giving rise to migration load.

In the presence of gene flow, other barriers to hybridization between two diverging populations of an outcrossing species are required for the populations to become new species.

Horizontal gene transfer

Current tree of life showing vertical and horizontal gene transfers.

Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among prokaryotes. In medicine, this contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle Callosobruchus chinensis may also have occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants. Viruses can also carry DNA between organisms, allowing transfer of genes even across biological domains. Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and mitochondria.

Linkage

If all genes are in linkage equilibrium, the effect of an allele at one locus can be averaged across the gene pool at other loci. In reality, one allele is frequently found in linkage disequilibrium with genes at other loci, especially with genes located nearby on the same chromosome. Recombination breaks up this linkage disequilibrium too slowly to avoid genetic hitchhiking, where an allele at one locus rises to high frequency because it is linked to an allele under selection at a nearby locus. Linkage also slows down the rate of adaptation, even in sexual populations. The effect of linkage disequilibrium in slowing down the rate of adaptive evolution arises from a combination of the Hill–Robertson effect (delays in bringing beneficial mutations together) and background selection (delays in separating beneficial mutations from deleterious hitchhikers).

Linkage is a problem for population genetic models that treat one gene locus at a time. It can, however, be exploited as a method for detecting the action of natural selection via selective sweeps.

In the extreme case of an asexual population, linkage is complete, and population genetic equations can be derived and solved in terms of a travelling wave of genotype frequencies along a simple fitness landscape. Most microbes, such as bacteria, are asexual. The population genetics of their adaptation have two contrasting regimes. When the product of the beneficial mutation rate and population size is small, asexual populations follow a "successional regime" of origin-fixation dynamics, with adaptation rate strongly dependent on this product. When the product is much larger, asexual populations follow a "concurrent mutations" regime with adaptation rate less dependent on the product, characterized by clonal interference and the appearance of a new beneficial mutation before the last one has fixed.

Applications

Explaining levels of genetic variation

Neutral theory predicts that the level of nucleotide diversity in a population will be proportional to the product of the population size and the neutral mutation rate. The fact that levels of genetic diversity vary much less than population sizes do is known as the "paradox of variation". While high levels of genetic diversity were one of the original arguments in favor of neutral theory, the paradox of variation has been one of the strongest arguments against neutral theory.

It is clear that levels of genetic diversity vary greatly within a species as a function of local recombination rate, due to both genetic hitchhiking and background selection. Most current solutions to the paradox of variation invoke some level of selection at linked sites. For example, one analysis suggests that larger populations have more selective sweeps, which remove more neutral genetic diversity. A negative correlation between mutation rate and population size may also contribute.

Life history affects genetic diversity more than population history does, e.g. r-strategists have more genetic diversity.

Detecting selection

Population genetics models are used to infer which genes are undergoing selection. One common approach is to look for regions of high linkage disequilibrium and low genetic variance along the chromosome, to detect recent selective sweeps.

A second common approach is the McDonald–Kreitman test. The McDonald–Kreitman test compares the amount of variation within a species (polymorphism) to the divergence between species (substitutions) at two types of sites, one assumed to be neutral. Typically, synonymous sites are assumed to be neutral. Genes undergoing positive selection have an excess of divergent sites relative to polymorphic sites. The test can also be used to obtain a genome-wide estimate of the proportion of substitutions that are fixed by positive selection, α. According to the neutral theory of molecular evolution, this number should be near zero. High numbers have therefore been interpreted as a genome-wide falsification of neutral theory.

Demographic inference

The simplest test for population structure in a sexually reproducing, diploid species, is to see whether genotype frequencies follow Hardy-Weinberg proportions as a function of allele frequencies. For example, in the simplest case of a single locus with two alleles denoted A and a at frequencies p and q, random mating predicts freq(AA) = p² for the AA homozygotes, freq(aa) = q² for the aa homozygotes, and freq(Aa) = 2pq for the heterozygotes. In the absence of population structure, Hardy-Weinberg proportions are reached within 1-2 generations of random mating. More typically, there is an excess of homozygotes, indicative of population structure. The extent of this excess can be quantified as the inbreeding coefficient, F.

Individuals can be clustered into K subpopulations. The degree of population structure can then be calculated using F_ST, which is a measure of the proportion of genetic variance that can be explained by population structure. Genetic population structure can then be related to geographic structure, and genetic admixture can be detected.

Coalescent theory relates genetic diversity in a sample to demographic history of the population from which it was taken. It normally assumes neutrality, and so sequences from more neutrally-evolving portions of genomes are therefore selected for such analyses. It can be used to infer the relationships between species (phylogenetics), as well as the population structure, demographic history (e.g. population bottlenecks, population growth), biological dispersal, source–sink dynamics and introgression within a species.

Another approach to demographic inference relies on the allele frequency spectrum.

Evolution of genetic systems

By assuming that there are loci that control the genetic system itself, population genetic models are created to describe the evolution of dominance and other forms of robustness, the evolution of sexual reproduction and recombination rates, the evolution of mutation rates, the evolution of evolutionary capacitors, the evolution of costly signalling traits, the evolution of ageing, and the evolution of co-operation. For example, most mutations are deleterious, so the optimal mutation rate for a species may be a trade-off between the damage from a high deleterious mutation rate and the metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.

One important aspect of such models is that selection is only strong enough to purge deleterious mutations and hence overpower mutational bias towards degradation if the selection coefficient s is greater than the inverse of the effective population size. This is known as the drift barrier and is related to the nearly neutral theory of molecular evolution. Drift barrier theory predicts that species with large effective population sizes will have highly streamlined, efficient genetic systems, while those with small population sizes will have bloated and complex genomes containing for example introns and transposable elements. However, somewhat paradoxically, species with large population sizes might be so tolerant to the consequences of certain types of errors that they evolve higher error rates, e.g. in transcription and translation, than small populations.