Gene flow

In population genetics, gene flow (also known as gene migration or allele flow) is the transfer of genetic variation from one population to another. If the rate of gene flow is high enough, then two populations are considered to have equivalent allele frequencies and therefore effectively be a single population. It has been shown that it takes only "One migrant per generation" to prevent populations from diverging due to drift.[1] Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity within the populations, by modifying the allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to full speciation.[2] In some cases migration may also result in the addition of novel genetic variants to the gene pool of a species or population.

There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there is long distances between populations, and when there are small population sizes.[3][4] Mobility plays an important role in the migration rate, as highly mobile individuals tend to have greater migratory prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.[5]

Gene flow final
Gene flow is the transfer of alleles from one population to another population through immigration of individuals.

Measuring gene flow

Decrease in population size leads to increased divergence due to drift, while migration reduces divergence and inbreeding. Gene flow can be measured by using the effective population size () and the net migration rate per generation (m). Using the approximation based on the Island model, the effect of migration can be calculated for a population in terms of the degree of genetic differentiation().[6] This formula accounts for the proportion of total molecular marker variation among populations, averaged over loci.[7] When there is one migrant per generation, the inbreeding coefficient () equals 0.2. However, when there is less than 1 migrant per generation (no migration), the inbreeding coefficient rises rapidly resulting in fixation and complete divergence ( = 1). The most common is < 0.25. This means there is some migration happening. Measures of population structure range from 0 to 1. When gene flow occurs via migration the deleterious effects of inbreeding can be ameliorated[1].

The formula can be modified to solve for the migration rate when is known: , Nm = number of migrants [1].

Barriers to gene flow

Allopatric speciation

Speciation modes edit
Examples of speciation affecting gene flow.

When gene flow is blocked by physical barriers, this results in Allopatric speciation or a geographical isolation that does not allow populations of the same species to exchange genetic material. Physical barriers to gene flow are usually, but not always, natural. They may include impassable mountain ranges, oceans, or vast deserts. In some cases, they can be artificial, man-made barriers, such as the Great Wall of China, which has hindered the gene flow of native plant populations.[8] One of these native plants, Ulmus pumila, demonstrated a lower prevalence of genetic differentiation than the plants Vitex negundo, Ziziphus jujuba, Heteropappus hispidus, and Prunus armeniaca whose habitat is located on the opposite side of the Great Wall of China where Ulmus pumila grows.[8] This is because Ulmus pumila has wind-pollination as its primary means of propagation and the latter-plants carry out pollination through insects.[8] Samples of the same species which grow on either side have been shown to have developed genetic differences, because there is little to no gene flow to provide recombination of the gene pools.

Sympatric speciation

Barriers to gene flow need not always be physical. Sympatric speciation happens when new species from the same ancestral species arise along the same range. This is often a result of a reproductive barrier. For example, two palm species of Howea found on Lord Howe Island were found to have substantially different flowering times correlated with soil preference, resulting in a reproductive barrier inhibiting gene flow.[9] Species can live in the same environment, yet show very limited gene flow due to reproductive barriers, fragmentation, specialist pollinators, or limited hybridization or hybridization yielding unfit hybrids. A cryptic species is a species that humans cannot tell is different without the use of genetics. Moreover, gene flow between hybrid and wild populations can result in loss of genetic diversity via genetic pollution, assortative mating and outbreeding. In human populations, genetic differentiation can also result from endogamy, due to differences in caste, ethnicity, customs and religion.

Human assisted gene-flow

Genetic rescue

Gene flow can also be used to assist species which are threatened with extinction. When a species exist in small populations there is an increased risk of inbreeding and greater susceptibility to loss of diversity due to drift. These populations can benefit greatly from the introduction of unrelated individuals who can increase diversity and reduce the amount of inbreeding, and thus increase overall fitness. This was demonstrated in the lab with two bottleneck strains of drosophila melanogaster, in which crosses between the two populations reversed the effects of inbreeding and led to greater chances of survival in not only one generation but two.[10]

Genetic pollution

Human activities such as movement of species and modification of landscape can result in genetic pollution, hybridization, introgression and genetic swamping. These processes can lead to homogenization or replacement of local genotypes as a result of either a numerical and/or fitness advantage of introduced plant or animal.[11] Nonnative species can threaten native plants and animals with extinction by hybridization and introgression either through purposeful introduction by humans or through habitat modification, bringing previously isolated species into contact. These phenomena can be especially detrimental for rare species coming into contact with more abundant ones which can occur between island and mainland species. Interbreeding between the species can cause a 'swamping' of the rarer species' gene pool, creating hybrids that supplant the native stock. This is a direct result of evolutionary forces such as natural selection, as well as genetic drift, which lead to the increasing prevalence of advantageous traits and homogenization. The extent of this phenomenon is not always apparent from outward appearance alone. While some degree of gene flow occurs in the course of normal evolution, hybridization with or without introgression may threaten a rare species' existence.[12][13] For example, the Mallard is an abundant species of duck that interbreeds readily with a wide range of other ducks and poses a threat to the integrity of some species.[14]

Gene flow between species

Horizontal gene transfer

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction, either through transformation (direct uptake of genetic material by a cell from its surroundings), conjugation (transfer of genetic material between two bacterial cells in direct contact), transduction (injection of foreign DNA by a bacteriophage virus into the host cell) or GTA-mediated transduction (transfer by a virus-like element produced by a bacterium) .[15][16]

Viruses can transfer genes between species.[17] Bacteria can incorporate genes from dead bacteria, exchange genes with living bacteria, and can exchange plasmids across species boundaries.[18] "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."[19]

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research". Biologists [should] instead use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of an intertwined net to visualize the rich exchange and cooperative effects of horizontal gene transfer.[20]

"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT. Combining the simple coalescence model of cladogenesis with rare HGT events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."[21]

Hybridization

In some instances, when a species has a sister species and breeding capabilities are possible due to the removal of previous barriers or through introduction due to human intervention, species can hybridize and exchange genes and corresponding traits. This exchange is not always clear-cut, for sometimes the hybrids may look identical to the original species phenotypically but upon testing the mtDNA it is apparent that hybridization has occurred. Differential hybridization also occurs because some traits and DNA are more readily exchanged than others, and this is a result of selective pressure or the absence thereof that allows for easier transaction. In instances in which the introduced species begins to replace the native species, the native species becomes threatened and the biodiversity is reduced, thus making this phenomenon negative rather than a positive case of gene flow that augments genetic diversity. Introgression is the replacement of the native species genes with that of the invader species. It is important to note that hybrids are generally deemed less "fit" than their parental generation, and as a result is a closely monitored genetic issue as the ultimate goal in conservation genetics is to maintain the genetic integrity of a species and preserve biodiversity.

Examples

Marineiguana03
Marine iguana of the Galapagos Islands evolved via allopatric speciation, through limited gene flow and geographic isolation.

While gene flow can greatly enhance the fitness of a population, it can also have negative consequences depending on the population and the environment in which they reside. The effects of gene flow are context-dependent.

  • Fragmented Population: fragmented landscapes such as the Galapagos Islands are an ideal place for adaptive radiation to occur as a result of differing geography. Darwin's Finches likely experienced allopatric speciation in some part due to differing geography, but that doesn't explain why we see so many different kinds of finches on the same island. This is due to adaptive radiation, or the evolution of varying traits in light of competition for resources. Gene flow moves in the direction of what resources are abundant at a given time.[22]
  • Island Population: The Marine Iguana is an endemic species of the Galapagos Islands, but it evolved from a mainland ancestor of land iguana. Due to geographic isolation gene flow between the two species was limited and differing environments caused the Marine Iguana to evolve in order to adapt to the island environment. For instance, they are the only iguana that has evolved the ability to swim.
  • Human Populations: Two theories exist for the human evolution throughout the world. The first is known as the multiregional model in which modern human variation is seen as a product of radiation of Homo erectus out of Africa after which local differentiation led to the establishment of regional population as we see them now.[23][24] Gene flow plays an important role in maintaining a grade of similarities and preventing speciation. In contrast the single origin theory assumes that there was a common ancestral population originating in Africa of Homo sapiens which already displayed the anatomical characteristics we see today. This theory minimizes the amount of parallel evolution that is needed.[24]
  • Butterflies: Comparisons between sympatric and allopatric populations of Heliconius melpomeneH. cydno, and H. timareta revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow.[25] 
  • Human-mediated gene flow: The captive genetic management of threatened species is the only way in which humans attempt to induce gene flow in ex situ situation. One example is the Giant Panda which is part of an international breeding program in which genetic materials are shared between zoological organizations in order to increase genetic diversity in the small populations. As a result of low reproductive success, artificial insemination with fresh/frozen-thawed sperm was developed which increased cub survival rate. A 2014 study found that high levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers.[26]
  • Plants: Two species of Monkeyflowers, mimulus lewsii and mimulus cardinalis, were found to have highly specialized pollinators that acted on major genes resulting in a contribution to the floral evolution and reproductive isolation of these two species.[27] The specialized pollination limited gene flow between the two species, eventually resulting in two different species.
  • Sika deer: Sika deer were introduced into Western Europe, and they reproduce easily with the native red deer. This translocation of Sika deer has led to introgression and there are no longer "pure" red deer in the region, and all can be classified as hybrids.[28]
  • Bobwhite quail: Bobwhite quail were translocated from the southern part of the United States to Ontario in order to increase population numbers and game for hunting.The hybrids that resulted from this translocation was less fit than the native population and were not adapted to survived the Northern Winters. [29]

See also

References

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  2. ^ Daniel I. Bolnick and Patrik Nosil (2007). "NATURAL SELECTION IN POPULATIONS SUBJECT TO A MIGRATION LOAD". Evolution. 61 (9): 2229–2243. doi:10.1111/j.1558-5646.2007.00179.x. PMID 17767592.
  3. ^ A Hastings; Harrison, and S. (1994). "Metapopulation Dynamics and Genetics". Annual Review of Ecology and Systematics. 25 (1): 167–188. doi:10.1146/annurev.es.25.110194.001123.
  4. ^ Hamrick, J. L.; Godt, M. J. W. (1996-09-30). "Effects of Life History Traits on Genetic Diversity in Plant Species". Philosophical Transactions of the Royal Society of London B: Biological Sciences. 351 (1345): 1291–1298. doi:10.1098/rstb.1996.0112. ISSN 0962-8436.
  5. ^ Eldridge, Mark D. B.; King, Juliet M.; Loupis, Anne K.; Spencer, Peter B. S.; Taylor, Andrea C.; Pope, Lisa C.; Hall, Graham P. (1999). "Unprecedented Low Levels of Genetic Variation and Inbreeding Depression in an Island Population of the Black-Footed Rock-Wallaby". Conservation Biology. 13 (3): 531–541. doi:10.1046/j.1523-1739.1999.98115.x. ISSN 0888-8892.
  6. ^ Neigel, J. E. (1996). Estimation of effective population size and migration parameters from genetic data. Molecular genetic approaches in conservation, 329-346.
  7. ^ Rogers, D. L., & Montalvo, A. M. (2004). Genetically appropriate choices for plant materials to maintain biological diversity. University of California. Report to the USDA Forest Service, Rocky Mountain Region, Lakewood, CO. www. f s I ed. u s/ r2.
  8. ^ a b c Su H, Qu LJ, He K, Zhang Z, Wang J, Chen Z, Gu H (March 2003). "The Great Wall of China: a physical barrier to gene flow?". Heredity. 90 (3): 212–9. doi:10.1038/sj.hdy.6800237. PMID 12634804.
  9. ^ Savolainen, Vincent; Anstett, Marie-Charlotte; Lexer, Christian; Hutton, Ian; Clarkson, James J.; Norup, Maria V.; Powell, Martyn P.; Springate, David; Salamin, Nicolas (2006-05-11). "Sympatric speciation in palms on an oceanic island". Nature. 441 (7090): 210–213. doi:10.1038/nature04566. ISSN 0028-0836. PMID 16467788.
  10. ^ Heber, Sol, et al. “A Test of the ‘Genetic Rescue’ Technique Using Bottlenecked Donor Populations of Drosophila Melanogaster.” National Center for Biotechnology Information, U.S. National Library of Medicine, 2012, www.ncbi.nlm.nih.gov/pmc/articles/PMC3418252/.
  11. ^ Aubry, C.; Shoal, R.; Erickson, V. (2005). "Glossary". Grass cultivars: their origins, development, and use on national forests and grasslands in the Pacific Northwest. Corvallis, OR: USDA Forest Service; Native Seed Network (NSN), Institute for Applied Ecology. Archived from the original on 2006-02-22.
  12. ^ Rhymer, Judith M.; Simberloff, Daniel (1996). "Extinction by Hybridization and Introgression". Annual Review of Ecology and Systematics. 27 (1): 83–109. doi:10.1146/annurev.ecolsys.27.1.83. JSTOR 2097230.
  13. ^ Potts, Brad M.; Barbour, Robert C.; Hingston, Andrew B. (September 2001). Genetic Pollution from Farm Forestry using eucalypt species and hybrids; A report for the RIRDC/L&WA/FWPRDC; Joint Venture Agroforestry Program (PDF). RIRDC Publication No 01/114; RIRDC Project No CPF - 3A. Australian Government, Rural Industrial Research and Development Corporation. ISBN 978-0-642-58336-9. ISSN 1440-6845. Archived from the original (PDF) on 2004-01-02.
  14. ^ "Hybrid Mallards-they're everywhere". Archived from the original on February 21, 2013. Retrieved January 23, 2013.
  15. ^ Johnston C, Martin B, Fichant G, Polard P, Claverys JP (March 2014). "Bacterial transformation: distribution, shared mechanisms and divergent control". Nature Reviews. Microbiology. 12 (3): 181–96. doi:10.1038/nrmicro3199. PMID 24509783.
  16. ^ Lang, A. S.; Zhaxybayeva, O.; Beatty, J. T. (2012). "Gene transfer agents: Phage-like elements of genetic exchange". Nature Reviews Microbiology. 10 (7): 472–82. doi:10.1038/nrmicro2802. PMC 3626599. PMID 22683880.
  17. ^ https://non.fiction.org/lj/community/ref_courses/3484/enmicro.pdf
  18. ^ "Archived copy" (PDF). Archived from the original (PDF) on 2006-02-18. Retrieved 2005-12-31.CS1 maint: Archived copy as title (link)
  19. ^ "Archived copy". Archived from the original on 2005-10-16. Retrieved 2005-12-31.CS1 maint: Archived copy as title (link)
  20. ^ Horizontal Gene Transfer - A New Paradigm for Biology (from Evolutionary Theory Conference Summary), Esalen Center for Theory & Research
  21. ^ http://web.uconn.edu/gogarten/articles/TIG2004_cladogenesis_paper.pdf
  22. ^ Grant, Peter R.; Grant, B. Rosemary (2002-04-26). "Unpredictable Evolution in a 30-Year Study of Darwin's Finches". Science. 296 (5568): 707–711. doi:10.1126/science.1070315. PMID 11976447.
  23. ^ Tobias, P. V., Strong, V., & White, H. (1985). Hominid Evolution: Past, Present, and Future: Proceedings of the Taung Diamond Jubilee International Symposium, Johannesburg and Mmabatho, Southern Africa, 27th January-4th February 1985. Alan R. Liss.
  24. ^ a b Stringer, C., & Andrews, P. (1988). Genetic and Fossil Evidence for the Origin of Modern Humans. Science,239(4845), 1263-1268. Retrieved from http://www.jstor.org/stable/1700885
  25. ^ Martin, S. H.; Dasmahapatra, K. K.; Nadeau, N. J.; Salazar, C.; Walters, J. R.; Simpson, F.; Jiggins, C. D. (2013). "Genome-wide evidence for speciation with gene flow in Heliconius butterflies". Genome Research. 23 (11): 1817–1828. doi:10.1101/gr.159426.113. PMC 3814882. PMID 24045163.
  26. ^ Shan, Lei; Hu, Yibo; Zhu, Lifeng; Yan, Li; Wang, Chengdong; Li, Desheng; Jin, Xuelin; Zhang, Chenglin; Wei, Fuwen (2014-10-01). "Large-Scale Genetic Survey Provides Insights into the Captive Management and Reintroduction of Giant Pandas". Molecular Biology and Evolution. 31 (10): 2663–2671. doi:10.1093/molbev/msu210. PMID 25015646.
  27. ^ Schemske, Douglas W.; Bradshaw, H. D. (1999-10-12). "Pollinator preference and the evolution of floral traits in monkeyflowers (Mimulus)". Proceedings of the National Academy of Sciences. 96 (21): 11910–11915. doi:10.1073/pnas.96.21.11910. PMC 18386. PMID 10518550.
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External links

Ancient Beringian

The Ancient Beringians (AB) is a specific archaeogenetic lineage, based on the genome of an infant found at the Upward Sun River site (dubbed USR1), dated to 11,500 years ago. The AB lineage diverged from the Ancestral Native American (ANA) lineage about 20,000 years ago. The ANA lineage was estimated as having been formed between 20,000 and 25,000 years ago by

a mixture of Proto-Mongoloid and used to be thought to have Ancient North Eurasian lineage, consistent with the model of the peopling of the Americas via Beringia during the Last Glacial Maximum. The Ancient Beringian lineage is extinct, and is not found as a contribution to modern indigenous lineages in Alaska. The 2018 study suggests that the AB lineage was replaced by or absorbed in a back-migration of NNA (see below) to Alaska. The modern Athabaskan populations are derived from an admixture of this NNA back-migration and a Paleo-Siberian (Early Paleo-Eskimo) lineage before about 2,500 years ago.The discovery was made from archaeogenetic analyses on the remains of two female infants discovered in 2013 at the Upward Sun River site (USR). The USR site is affiliated with the Denali Complex, a dispersed archaeological culture of the American Arctic. The genomic analysis of nuclear DNA of the older of the two infants (USR1) was done at the Centre for Geogenetics at the University of Copenhagen's Natural History Museum of Denmark. Results from the team's genetic analysis were published in January 2018 in the scientific journal Nature.

The analysis compared the infant's genomes with both ancient and contemporary genomes. The results suggested that the pre-"Ancestral Native American" lineage derived from the proto-Mongoloid lineage after 36 kya, with gene flow until about 25 kya. During 25–20 kya, this lineage was substantially mixed with the Ancient North Eurasian lineage, to form the "Ancestral Native American" lineage by 20 kya.

The "Ancient Beringian" (AB) lineage derived from ANA and persisted without significant admixture in Alaska until the time of USR1, some 8,000 years later. The lineage of other Paleo-Indians diverged form AB at ca. 20–18 kya, and further divided into "North Native American" (NNA) and "South Native American" lineages between 17.5 kya and 14.6 kya, reflecting the dispersal associated with the early peopling of the Americas.

Biological dispersal

Biological dispersal refers to both the movement of individuals (animals, plants, fungi, bacteria, etc.) from their birth site to their breeding site ('natal dispersal'), as well as the movement from one breeding site to another ('breeding dispersal').

Dispersal is also used to describe the movement of propagules such as seeds and spores.

Technically, dispersal is defined as any movement that has the potential to lead to gene flow.

The act of dispersal involves three phases: departure, transfer, settlement and there are different fitness costs and benefits associated with each of these phases.

Through simply moving from one habitat patch to another, the dispersal of an individual has consequences not only for individual fitness, but also for population dynamics, population genetics, and species distribution. Understanding dispersal and the consequences both for evolutionary strategies at a species level, and for processes at an ecosystem level, requires understanding on the type of dispersal, the dispersal range of a given species, and the dispersal mechanisms involved.

Biological dispersal may be contrasted with geodispersal, which is the mixing of previously isolated populations (or whole biotas) following the erosion of geographic barriers to dispersal or gene flow (Lieberman, 2005; Albert and Reis, 2011).

Dispersal can be distinguished from animal migration (typically round-trip seasonal movement), although within the population genetics literature, the terms 'migration' and 'dispersal' are often used interchangeably.

Cleistogamy

Cleistogamy is a type of automatic self-pollination of certain plants that can propagate by using non-opening, self-pollinating flowers. Especially well known in peanuts, peas, and pansy this behavior is most widespread in the grass family. However, the largest genus of cleistogamous plants is Viola.

The more common opposite of cleistogamy, or "closed marriage", is called chasmogamy, or "open marriage". Virtually all plants that produce cleistogamous flowers also produce chasmogamous ones. The principal advantage of cleistogamy is that it requires fewer plant resources to produce seeds than does chasmogamy, because development of petals, nectar and large amounts of pollen is not required. This efficiency makes cleistogamy particularly useful for seed production on unfavorable sites or adverse conditions. Impatiens capensis, for example, has been observed to produce only cleistogamous flowers after being severely damaged by grazing and to maintain populations on unfavorable sites with only cleistogamous flowers. The obvious disadvantage of cleistogamy is that self-fertilization occurs, which may suppress the creation of genetically superior plants.For genetically modified (GM) rapeseed, researchers hoping to minimise the admixture of GM and non-GM crops are attempting to use cleistogamy to prevent gene flow. However, preliminary results from Co-Extra, a current project within the EU research program, show that although cleistogamy reduces gene flow, it is not at the moment a consistently reliable tool for biocontainment; due to a certain instability of the cleistogamous trait, some flowers may open and release genetically modified pollen.

Cline (biology)

In biology, a cline (from the Greek “klinein”, meaning “to lean”) is a measurable gradient in a single character (or biological trait) of a species across its geographical range. First coined by Julian Huxley in 1938, the “character” of the cline referred to is usually genetic (e.g allele frequency, blood type), or phenotypic (e.g. body size, skin pigmentation). Clines can show smooth, continuous gradation in a character, or they may show more abrupt changes in the trait from one geographic region to the next.A cline refers to a spatial gradient in a specific, singular trait, rather than a gradient in a population as a whole. A single population can therefore theoretically have as many clines as it has traits. Additionally, Huxley recognised that these multiple independent clines may not act in concordance with each other. For example, it has been observed that in Australia, birds generally become smaller the further towards the north of the country they are found. In contrast, the intensity of their plumage colouration follows a different geographical trajectory, being most vibrant where humidity is highest and becoming less vibrant further into the arid centre of the country.

Because of this, clines were defined by Huxley as being an “auxiliary taxonomic principle”; that is, clinal variation in a species is not awarded taxonomic recognition in the way subspecies or species are.While the terms “ecotype” and “cline” are sometimes used interchangeably, they do in fact differ in that “ecotype” refers to a population which differs from other populations in a number of characters, rather than the single character that varies amongst populations in a cline.

Domestication of animals

The domestication of animals is the mutual relationship between animals and the humans who have influence on their care and reproduction. Charles Darwin recognized a small number of traits that made domesticated species different from their wild ancestors. He was also the first to recognize the difference between conscious selective breeding in which humans directly select for desirable traits, and unconscious selection where traits evolve as a by-product of natural selection or from selection on other traits. There is a genetic difference between domestic and wild populations. There is also such a difference between the domestication traits that researchers believe to have been essential at the early stages of domestication, and the improvement traits that have appeared since the split between wild and domestic populations. Domestication traits are generally fixed within all domesticates, and were selected during the initial episode of domestication of that animal or plant, whereas improvement traits are present only in a proportion of domesticates, though they may be fixed in individual breeds or regional populations.Domestication should not be confused with taming. Taming is the conditioned behavioral modification of a wild-born animal when its natural avoidance of humans is reduced and it accepts the presence of humans, but domestication is the permanent genetic modification of a bred lineage that leads to an inherited predisposition toward humans. Certain animal species, and certain individuals within those species, make better candidates for domestication than others because they exhibit certain behavioral characteristics: (1) the size and organization of their social structure; (2) the availability and the degree of selectivity in their choice of mates; (3) the ease and speed with which the parents bond with their young, and the maturity and mobility of the young at birth; (4) the degree of flexibility in diet and habitat tolerance; and (5) responses to humans and new environments, including flight responses and reactivity to external stimuli.It is proposed that there were three major pathways that most animal domesticates followed into domestication: (1) commensals, adapted to a human niche (e.g., dogs, cats, fowl, possibly pigs); (2) prey animals sought for food (e.g., sheep, goats, cattle, water buffalo, yak, pig, reindeer, llama, alpaca, and turkey); and (3) targeted animals for draft and nonfood resources (e.g., horse, donkey, camel). The dog was the first to be domesticated, and was established across Eurasia before the end of the Late Pleistocene era, well before cultivation and before the domestication of other animals. Unlike other domestic species which were primarily selected for production-related traits, dogs were initially selected for their behaviors. The archaeological and genetic data suggest that long-term bidirectional gene flow between wild and domestic stocks – including donkeys, horses, New and Old World camelids, goats, sheep, and pigs – was common. One study has concluded that human selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars into pigs and created domestication islands in the genome. The same process may also apply to other domesticated animals.

Ecological corridor (Brazil)

An ecological corridor (Portuguese: Corredor ecológico) in Brazil is a collection of natural or semi-natural areas that link protected areas and allow gene flow between them.

Evolutionarily significant unit

An evolutionarily significant unit (ESU) is a population of organisms that is considered distinct for purposes of conservation. Delineating ESUs is important when considering conservation action.

This term can apply to any species, subspecies, geographic race, or population. Often the term "species" is used rather than ESU, even when an ESU is more technically considered a subspecies or variety rather than a biological species proper. In marine animals the term "stock" is often used as well.

Genetic diversity

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

Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals.The academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions. Diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large range relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common, they become more vulnerable. This occurs in host–pathogen interactions, where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele.

Genetic pollution

Genetic pollution is a controversial term for uncontrolled gene flow into wild populations. It is defined as “the dispersal of contaminated altered genes from genetically engineered organisms to natural organisms, esp. by cross-pollination”, but has come to be used in some broader ways. It is related to the population genetics concept of gene flow, and genetic rescue, which is genetic material intentionally introduced to increase the fitness of a population. It is called genetic pollution when it negatively impacts on the fitness of a population, such as through outbreeding depression and the introduction of unwanted phenotypes which can lead to extinction.

Conservation biologists and conservationists have used the term to describe gene flow from domestic, feral, and non-native species into wild indigenous species, which they consider undesirable. They promote awareness of the effects of introduced invasive species that may "hybridize with native species, causing genetic pollution". In the fields of agriculture, agroforestry and animal husbandry, genetic pollution is used to describe gene flows between genetically engineered species and wild relatives. The use of the word “pollution” is meant to convey the idea that mixing genetic information is bad for the environment, but because the mixing of genetic information can lead to a variety of outcomes, “pollution” may not always be the most accurate descriptor.

Genus

A genus (, pl. genera ) is a taxonomic rank used in the biological classification of living and fossil organisms, as well as viruses, in biology. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomenclature, the genus name forms the first part of the binomial species name for each species within the genus.

E.g. Panthera leo (lion) and Panthera onca (jaguar) are two species within the genus Panthera. Panthera is a genus within the family Felidae.The composition of a genus is determined by a taxonomist. The standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. There are some general practices used, however, including the idea that a newly defined genus should fulfill these three criteria to be descriptively useful:

monophyly – all descendants of an ancestral taxon are grouped together (i.e. phylogenetic analysis should clearly demonstrate both monophyly and validity as a separate lineage).

reasonable compactness – a genus should not be expanded needlessly; and

distinctness – with respect to evolutionarily relevant criteria, i.e. ecology, morphology, or biogeography; DNA sequences are a consequence rather than a condition of diverging evolutionary lineages except in cases where they directly inhibit gene flow (e.g. postzygotic barriers).Moreover, genera should be composed of phylogenetic units of the same kind as other (analogous) genera.

Habitat fragmentation

Habitat fragmentation describes the emergence of discontinuities (fragmentation) in an organism's preferred environment (habitat), causing population fragmentation and ecosystem decay. Causes of habitat fragmentation include geological processes that slowly alter the layout of the physical environment

(suspected of being one of the major causes of speciation),and human activity such as land conversion, which can alter the environment much faster and causes the extinction of many species.

History of speciation

The scientific study of speciation — how species evolve to become new species — began around the time of Charles Darwin in the middle of the 19th century. Many naturalists at the time recognized the relationship between biogeography (the way species are distributed) and the evolution of species. The 20th century saw the growth of the field of speciation, with major contributors such as Ernst Mayr researching and documenting species' geographic patterns and relationships. The field grew in prominence with the modern evolutionary synthesis in the early part of that century. Since then, research on speciation has expanded immensely.

The language of speciation has grown more complex. Debate over classification schemes on the mechanisms of speciation and reproductive isolation continue. The 21st century has seen a resurgence in the study of speciation, with new techniques such as molecular phylogenetics and systematics. Speciation has largely been divided into discrete modes that correspond to rates of gene flow between two incipient populations. Today however, research has driven the development of alternative schemes and the discovery of new processes of speciation.

Horizontal gene transfer

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms.Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the LGT of antibiotic resistant genes. It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.Gene delivery can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering.

Microevolution

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow and genetic drift. This change happens over a relatively short (in evolutionary terms) amount of time compared to the changes termed macroevolution which is where greater differences in the population occur.

Population genetics is the branch of biology that provides the mathematical structure for the study of the process of microevolution. Ecological genetics concerns itself with observing microevolution in the wild. Typically, observable instances of evolution are examples of microevolution; for example, bacterial strains that have antibiotic resistance.

Microevolution over time leads to speciation or the appearance of novel structure, sometimes classified as macroevolution. Macro and microevolution describe fundamentally identical processes on different scales.

Parapatric speciation

In parapatric speciation, two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes. This mode of speciation has three distinguishing characteristics: 1) mating occurs non-randomly, 2) gene flow occurs unequally, and 3) populations exist in either continuous or discontinuous geographic ranges. This distribution pattern may be the result of unequal dispersal, incomplete geographical barriers, or divergent expressions of behavior, among other things. Parapatric speciation predicts that hybrid zones will often exist at the junction between the two populations.

In biogeography, the terms parapatric and parapatry are often used to describe the relationship between organisms whose ranges do not significantly overlap but are immediately adjacent to each other; they do not occur together except in a narrow contact zone. Parapatry is a geographical distribution opposed to sympatry (same area) and allopatry or peripatry (two similar cases of distinct areas).

Various "forms" of parapatry have been proposed and are discussed below. Coyne and Orr in Speciation categorise these forms into three groups: clinal (environmental gradients), "stepping-stone" (discrete populations), and stasipatric speciation in concordance with most of the parapatric speciation literature. Henceforth, the models are subdivided following a similar format.

Charles Darwin was the first to propose this mode of speciation. It was not until 1930 when Ronald Fisher published The Genetical Theory of Natural Selection where he outlined a verbal theoretical model of clinal speciation. In 1981, Joseph Felsenstein proposed an alternative, "discrete population" model (the "stepping-stone model). Since Darwin, a great deal of research has been conducted on parapatric speciation—concluding that its mechanisms are theoretically plausible, "and has most certainly occurred in nature".

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, lab, 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 today from newer, more phenotypic approaches to modelling evolution, such as evolutionary game theory and adaptive dynamics, is its emphasis on genetic phenomena as dominance, epistasis, and the degree to which genetic recombination breaks up linkage disequilibrium. This makes it appropriate for comparison to population genomics data.

Reinforcement (speciation)

Reinforcement is a process of speciation where natural selection increases the reproductive isolation between two populations of species. This occurs as a result of selection acting against the production of hybrid individuals of low fitness. The idea was originally developed by Alfred Russel Wallace and is sometimes referred to as the Wallace effect. The modern concept of reinforcement originates from Theodosius Dobzhansky. He envisioned a species separated allopatrically, where secondary contact of the two populations mate, producing hybrids with lower fitness. Natural selection results from the hybrid's inability to produce viable offspring; thus members of one species who do not mate with members of the other have greater reproductive success. This favors the evolution of greater prezygotic isolation (differences in behavior or biology that inhibit formation of hybrid zygotes). Reinforcement is one of the few cases in which selection can favor an increase in prezygotic isolation, influencing the process of speciation directly. This aspect has been particularly appealing among evolutionary biologists.The support for reinforcement has fluctuated since its inception, and terminological confusion and differences in usage over history have led to multiple meanings and complications. Various objections have been raised by evolutionary biologists as to the plausibility of its occurrence. Since the 1990s, data from theory, experiments, and nature have overcome many of the past objections, rendering reinforcement widely accepted, though its prevalence in nature remains unknown.Numerous models have been developed to understand its operation in nature, most relying on several facets: genetics, population structures, influences of selection, and mating behaviors. Empirical support for reinforcement exists, both in the laboratory and in nature. Documented examples are found in a wide range of organisms: both vertebrates and invertebrates, fungi, and plants. The secondary contact of originally separated incipient species (the initial stage of speciation) is increasing due to human activities such as the introduction of invasive species or the modification of natural habitats. This has implications for measures of biodiversity and may become more relevant in the future.

Ring species

In biology, a ring species is a connected series of neighbouring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" population. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region (sympatry) thus closing a "ring". The German term Rassenkreis, meaning a ring of populations, is also used.

Ring species represent speciation and have been cited as evidence of evolution. They illustrate what happens over time as populations genetically diverge, specifically because they represent, in living populations, what normally happens over time between long-deceased ancestor populations and living populations, in which the intermediates have become extinct. The evolutionary biologist Richard Dawkins remarks that ring species "are only showing us in the spatial dimension something that must always happen in the time dimension".Formally, the issue is that interfertility (ability to interbreed) is not a transitive relation; if A can breed with B, and B can breed with C, it does not mean that A can breed with C, and therefore does not define an equivalence relation. A ring species is a species with a counterexample to the transitivity of interbreeding. However, it is unclear whether any of the examples of ring species cited by scientists actually permit gene flow from end to end, with many being debated and contested.

Sympatric speciation

Sympatric speciation is the evolution of a new species from a surviving ancestral species while both continue to inhabit the same geographic region. In evolutionary biology and biogeography, sympatric and sympatry are terms referring to organisms whose ranges overlap so that they occur together at least in some places. If these organisms are closely related (e.g. sister species), such a distribution may be the result of sympatric speciation. Etymologically, sympatry is derived from the Greek roots συν ("together") and πατρίς ("homeland"). The term was invented by Edward Bagnall Poulton in 1904, who explains the derivation.Sympatric speciation is one of three traditional geographic modes of speciation. Allopatric speciation is the evolution of species caused by the geographic isolation of two or more populations of a species. In this case, divergence is facilitated by the absence of gene flow. Parapatric speciation is the evolution of geographically adjacent populations into distinct species. In this case, divergence occurs despite limited interbreeding where the two diverging groups come into contact. In sympatric speciation, there is no geographic constraint to interbreeding. These categories are special cases of a continuum from zero (sympatric) to complete (allopatric) spatial segregation of diverging groups.In multicellular eukaryotic organisms, sympatric speciation is a plausible process that is known to occur, but the frequency with which it occurs is not known.

In bacteria, however, the analogous process (defined as "the origin of new bacterial species that occupy definable ecological niches") might be more common because bacteria are less constrained by the homogenizing effects of sexual reproduction and are prone to comparatively dramatic and rapid genetic change through horizontal gene transfer.

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