Polyploidy

Polyploidy is the state of a cell or organism having more than two paired (homologous) sets of chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two sets of chromosomes—one set inherited from each parent. However, some organisms are polyploid, and polyploidy is especially common in plants. In addition, polyploidy occurs in some tissues of animals that are otherwise diploid, such as human muscle tissues.[1] This is known as endopolyploidy. Species whose cells do not have nuclei, that is, prokaryotes, may be polyploid, as seen in the large bacterium Epulopiscium fishelsoni.[2] Hence ploidy is defined with respect to a cell. Most eukaryotes have diploid somatic cells, but produce haploid gametes (eggs and sperm) by meiosis. A monoploid has only one set of chromosomes, and the term is usually only applied to cells or organisms that are normally diploid. Males of bees and other Hymenoptera, for example, are monoploid. Unlike animals, plants and multicellular algae have life cycles with two alternating multicellular generations. The gametophyte generation is haploid, and produces gametes by mitosis, the sporophyte generation is diploid and produces spores by meiosis.

Polyploidy refers to a numerical change in a whole set of chromosomes. Organisms in which a particular chromosome, or chromosome segment, is under- or over-represented are said to be aneuploid (from the Greek words meaning "not", "good", and "fold"). Aneuploidy refers to a numerical change in part of the chromosome set, whereas polyploidy refers to a numerical change in the whole set of chromosomes.[3]

Polyploidy may occur due to abnormal cell division, either during mitosis, or commonly during metaphase I in meiosis. In addition, it can be induced in plants and cell cultures by some chemicals: the best known is colchicine, which can result in chromosome doubling, though its use may have other less obvious consequences as well. Oryzalin will also double the existing chromosome content.

Polyploidy occurs in highly differentiated human tissues in the liver, heart muscle, bone marrow and the placenta.[4] It occurs in the somatic cells of some animals, such as goldfish,[5] salmon, and salamanders, but is especially common among ferns and flowering plants (see Hibiscus rosa-sinensis), including both wild and cultivated species. Wheat, for example, after millennia of hybridization and modification by humans, has strains that are diploid (two sets of chromosomes), tetraploid (four sets of chromosomes) with the common name of durum or macaroni wheat, and hexaploid (six sets of chromosomes) with the common name of bread wheat. Many agriculturally important plants of the genus Brassica are also tetraploids.

Polyploidization is a mechanism of sympatric speciation because polyploids are usually unable to interbreed with their diploid ancestors. An example is the plant Erythranthe peregrina. Sequencing confirmed that this species originated from E. × robertsii, a sterile triploid hybrid between E. guttata and E. lutea, both of which have been introduced and naturalised in the United Kingdom. New populations of E. peregrina arose on the Scottish mainland and the Orkney Islands via genome duplication from local populations of E. × robertsii.[6] Because of a rare genetic mutation, E. peregrina is not sterile.[7]

Haploid, diploid ,triploid and tetraploid
This image shows haploid (single), diploid (double), triploid (triple), and tetraploid (quadruple) sets of chromosomes. Triploid and tetraploid chromosomes are examples of polyploidy.

Types

Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis - JHR-037-113-g001
Organ-specific patterns of endopolyploidy (from 2x to 64x) in the giant ant Dinoponera australis

Polyploid types are labeled according to the number of chromosome sets in the nucleus. The letter x is used to represent the number of chromosomes in a single set.

Animals

Examples in animals are more common in non-vertebrates[13] such as flatworms, leeches, and brine shrimp. Within vertebrates, examples of stable polyploidy include the salmonids and many cyprinids (i.e. carp).[14] Some fish have as many as 400 chromosomes.[14] Polyploidy also occurs commonly in amphibians; for example the biomedically-important genus Xenopus contains many different species with as many as 12 sets of chromosomes (dodecaploid).[15] Polyploid lizards are also quite common, but are sterile and must reproduce by parthenogenesis. Polyploid mole salamanders (mostly triploids) are all female and reproduce by kleptogenesis,[16] "stealing" spermatophores from diploid males of related species to trigger egg development but not incorporating the males' DNA into the offspring. While mammalian liver cells are polyploid, rare instances of polyploid mammals are known, but most often result in prenatal death.

An octodontid rodent of Argentina's harsh desert regions, known as the plains viscacha rat (Tympanoctomys barrerae) has been reported as an exception to this 'rule'.[17] However, careful analysis using chromosome paints shows that there are only two copies of each chromosome in T. barrerae, not the four expected if it were truly a tetraploid.[18] This rodent is not a rat, but kin to guinea pigs and chinchillas. Its "new" diploid (2n) number is 102 and so its cells are roughly twice normal size. Its closest living relation is Octomys mimax, the Andean Viscacha-Rat of the same family, whose 2n = 56. It was therefore surmised that an Octomys-like ancestor produced tetraploid (i.e., 2n = 4x = 112) offspring that were, by virtue of their doubled chromosomes, reproductively isolated from their parents.

Polyploidy was induced in fish by Har Swarup (1956) using a cold-shock treatment of the eggs close to the time of fertilization, which produced triploid embryos that successfully matured.[19][20] Cold or heat shock has also been shown to result in unreduced amphibian gametes, though this occurs more commonly in eggs than in sperm.[21] John Gurdon (1958) transplanted intact nuclei from somatic cells to produce diploid eggs in the frog, Xenopus (an extension of the work of Briggs and King in 1952) that were able to develop to the tadpole stage.[22] The British scientist J. B. S. Haldane hailed the work for its potential medical applications and, in describing the results, became one of the first to use the word "clone" in reference to animals. Later work by Shinya Yamanaka showed how mature cells can be reprogrammed to become pluripotent, extending the possibilities to non-stem cells. Gurdon and Yamanaka were jointly awarded the Nobel Prize in 2012 for this work.[22]

Humans

True polyploidy rarely occurs in humans, although polyploid cells occur in highly differentiated tissue, such as liver parenchyma, heart muscle, placenta and in bone marrow.[4][23] Aneuploidy is more common.

Polyploidy occurs in humans in the form of triploidy, with 69 chromosomes (sometimes called 69,XXX), and tetraploidy with 92 chromosomes (sometimes called 92,XXXX). Triploidy, usually due to polyspermy, occurs in about 2–3% of all human pregnancies and ~15% of miscarriages. The vast majority of triploid conceptions end as a miscarriage; those that do survive to term typically die shortly after birth. In some cases, survival past birth may be extended if there is mixoploidy with both a diploid and a triploid cell population present. There has been one report of a child surviving to the age of seven months with complete triploidy syndrome. He failed to exhibit normal mental or physical neonatal development, and died from a Pneumocystis carinii infection, which indicates a weak immune system.[24]

Triploidy may be the result of either digyny (the extra haploid set is from the mother) or diandry (the extra haploid set is from the father). Diandry is mostly caused by reduplication of the paternal haploid set from a single sperm, but may also be the consequence of dispermic (two sperm) fertilization of the egg.[25] Digyny is most commonly caused by either failure of one meiotic division during oogenesis leading to a diploid oocyte or failure to extrude one polar body from the oocyte. Diandry appears to predominate among early miscarriages, while digyny predominates among triploid zygotes that survive into the fetal period. However, among early miscarriages, digyny is also more common in those cases less than ​8 12 weeks gestational age or those in which an embryo is present. There are also two distinct phenotypes in triploid placentas and fetuses that are dependent on the origin of the extra haploid set. In digyny, there is typically an asymmetric poorly grown fetus, with marked adrenal hypoplasia and a very small placenta. In diandry, a partial hydatidiform mole develops.[25] These parent-of-origin effects reflect the effects of genomic imprinting.

Complete tetraploidy is more rarely diagnosed than triploidy, but is observed in 1–2% of early miscarriages. However, some tetraploid cells are commonly found in chromosome analysis at prenatal diagnosis and these are generally considered 'harmless'. It is not clear whether these tetraploid cells simply tend to arise during in vitro cell culture or whether they are also present in placental cells in vivo. There are, at any rate, very few clinical reports of fetuses/infants diagnosed with tetraploidy mosaicism.

Mixoploidy is quite commonly observed in human preimplantation embryos and includes haploid/diploid as well as diploid/tetraploid mixed cell populations. It is unknown whether these embryos fail to implant and are therefore rarely detected in ongoing pregnancies or if there is simply a selective process favoring the diploid cells.

Plants

Polyploidization
Speciation via polyploidy: A diploid cell undergoes failed meiosis, producing diploid gametes, which self-fertilize to produce a tetraploid zygote.

Polyploidy is pervasive in plants and some estimates suggest that 30–80% of living plant species are polyploid, and many lineages show evidence of ancient polyploidy (paleopolyploidy) in their genomes.[26][27][28][29] Huge explosions in angiosperm species diversity appear to have coincided with the timing of ancient genome duplications shared by many species.[30] It has been established that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase.[31]

Polyploid plants can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2n) gametes.[32] Both autopolyploids (e.g. potato[33]) and allopolyploids (such as canola, wheat and cotton) can be found among both wild and domesticated plant species.

Most polyploids display novel variation or morphologies relative to their parental species, that may contribute to the processes of speciation and eco-niche exploitation.[27][32] The mechanisms leading to novel variation in newly formed allopolyploids may include gene dosage effects (resulting from more numerous copies of genome content), the reunion of divergent gene regulatory hierarchies, chromosomal rearrangements, and epigenetic remodeling, all of which affect gene content and/or expression levels.[34][35][36][37] Many of these rapid changes may contribute to reproductive isolation and speciation. However seed generated from interploidy crosses, such as between polyploids and their parent species, usually suffer from aberrant endosperm development which impairs their viability,[38][39] thus contributing to polyploid speciation.

Some plants are triploid. As meiosis is disturbed, these plants are sterile, with all plants having the same genetic constitution: Among them, the exclusively vegetatively propagated saffron crocus (Crocus sativus). Also, the extremely rare Tasmanian shrub Lomatia tasmanica is a triploid sterile species.

There are few naturally occurring polyploid conifers. One example is the Coast Redwood Sequoia sempervirens, which is a hexaploid (6x) with 66 chromosomes (2n = 6x = 66), although the origin is unclear.[40]

Aquatic plants, especially the Monocotyledons, include a large number of polyploids.[41]

Crops

The induction of polyploidy is a common technique to overcome the sterility of a hybrid species during plant breeding. For example, triticale is the hybrid of wheat (Triticum turgidum) and rye (Secale cereale). It combines sought-after characteristics of the parents, but the initial hybrids are sterile. After polyploidization, the hybrid becomes fertile and can thus be further propagated to become triticale.

In some situations, polyploid crops are preferred because they are sterile. For example, many seedless fruit varieties are seedless as a result of polyploidy. Such crops are propagated using asexual techniques, such as grafting.

Polyploidy in crop plants is most commonly induced by treating seeds with the chemical colchicine.

Examples

Some crops are found in a variety of ploidies: tulips and lilies are commonly found as both diploid and triploid; daylilies (Hemerocallis cultivars) are available as either diploid or tetraploid; apples and kinnow mandarins can be diploid, triploid, or tetraploid.

Fungi

Polyploidy in fungi2.pdf
Schematic phylogeny of the fungi. Red circles indicate polyploidy, blue squares indicate hybridization. From Albertin and Marullo, 2012[45]

Besides plants and animals, the evolutionary history of various fungal species is dotted by past and recent whole-genome duplication events (see Albertin and Marullo 2012[45] for review). Several examples of polyploids are known:

In addition, polyploidy is frequently associated with hybridization and reticulate evolution that appear to be highly prevalent in several fungal taxa. Indeed, homoploid speciation (hybrid speciation without a change in chromosome number) has been evidenced for some fungal species (such as the basidiomycota Microbotryum violaceum[53]).

Polyploidy in fungi
Schematic phylogeny of the Chromalveolata. Red circles indicate polyploidy, blue squares indicate hybridization. From Albertin and Marullo, 2012[45]

As for plants and animals, fungal hybrids and polyploids display structural and functional modifications compared to their progenitors and diploid counterparts. In particular, the structural and functional outcomes of polyploid Saccharomyces genomes strikingly reflect the evolutionary fate of plant polyploid ones. Large chromosomal rearrangements[54] leading to chimeric chromosomes[55] have been described, as well as more punctual genetic modifications such as gene loss.[56] The homoealleles of the allotetraploid yeast S. pastorianus show unequal contribution to the transcriptome.[57] Phenotypic diversification is also observed following polyploidization and/or hybridization in fungi,[58] producing the fuel for natural selection and subsequent adaptation and speciation.

Chromalveolata

Other eukaryotic taxa have experienced one or more polyploidization events during their evolutionary history (see Albertin and Marullo, 2012[45] for review). The oomycetes, which are non-true fungi members, contain several examples of paleopolyploid and polyploid species, such as within the genus Phytophthora.[59] Some species of brown algae (Fucales, Laminariales[60] and diatoms[61]) contain apparent polyploid genomes. In the Alveolata group, the remarkable species Paramecium tetraurelia underwent three successive rounds of whole-genome duplication[62] and established itself as a major model for paleopolyploid studies.

Terminology

Autopolyploidy

Autopolyploids are polyploids with multiple chromosome sets derived from a single taxon. Two examples of natural autopolyploids are the piggyback plant, Tolmiea menzisii[63] and the white sturgeon, Acipenser transmontanum.[64] Most instances of autopolyploidy result from the fusion of unreduced (2n) gametes, which results in either triploid (n + 2n = 3n) or tetraploid (2n + 2n = 4n) offspring.[65] Triploid offspring are typically sterile (as in the phenomenon of 'triploid block'), but in some cases they may produce high proportions of unreduced gametes and thus aid the formation of tetraploids. This pathway to tetraploidy is referred to as the “triploid bridge”.[65] Triploids may also persist through asexual reproduction. In fact, stable autotriploidy in plants is often associated with apomictic mating systems.[66] In agricultural systems, autotriploidy can result in seedlessness, as in watermelons and bananas.[67] Triploidy is also utilized in salmon and trout farming to induce sterility.[68][69]

Rarely, autopolyploids arise from spontaneous, somatic genome doubling, which has been observed in apple (Malus domesticus) bud sports.[70] This is also the most common pathway of artificially induced polyploidy, where methods such as protoplast fusion or treatment with colchicine, oryzalin or mitotic inhibitors are used to disrupt normal mitotic division, which results in the production of polyploid cells. This process can be useful in plant breeding, especially when attempting to introgress germplasm across ploidal levels.[71]

Autopolyploids possess at least three homologous chromosome sets, which can lead to high rates of multivalent pairing during meiosis (particularly in recently formed autopolyploids, also known as neopolyploids) and an associated decrease in fertility due to the production of aneuploid gametes.[72] Natural or artificial selection for fertility can quickly stabilize meiosis in autopolyploids by restoring bivalent pairing during meiosis, but the high degree of homology among duplicated chromosomes causes autopolyploids to display polysomic inheritance.[73] This trait is often used as a diagnostic criterion to distinguish autopolyploids from allopolyploids, which commonly display disomic inheritance after they progress past the neopolyploid stage.[74] While most polyploid species are unambiguously characterized as either autopolyploid or allopolyploid, these categories represent the ends of a spectrum between of divergence between parental subgenomes. Polyploids that fall between these two extremes, which are often referred to as segmental allopolyploids, may display intermediate levels of polysomic inheritance that vary by locus.[75][76]

About half of all polyploids are thought to be the result of autopolyploidy,[77][78] although many factors make this proportion hard to estimate.[79]

Allopolyploidy

Allopolyploids or amphipolyploids or heteropolyploids are polyploids with chromosomes derived from two or more diverged taxa. As in autopolyploidy, this primarily occurs through the fusion of unreduced (2n) gametes, which can take place before or after hybridization. In the former case, unreduced gametes from each diploid taxa – or reduced gametes from two autotetraploid taxa – combine to form allopolyploid offspring. In the latter case, one or more diploid F1 hybrids produce unreduced gametes that fuse to form allopolyploid progeny.[80] Hybridization followed by genome duplication may be a more common path to allopolyploidy because F1 hybrids between taxa often have relatively high rates of unreduced gamete formation – divergence between the genomes of the two taxa result in abnormal pairing between homoeologous chromosomes or nondisjunction during meiosis.[80] In this case, allopolyploidy can actually restore normal, bivalent meiotic pairing by providing each homoeologous chromosome with its own homologue. If divergence between homoeologous chromosomes is even across the two subgenomes, this can theoretically result in rapid restoration of bivalent pairing and disomic inheritance following allopolyploidization. However multivalent pairing is common in many recently formed allopolyploids, so it is likely that the majority of meiotic stabilization occurs gradually through selection.[72][74]

Because pairing between homoeologous chromosomes is rare in established allopolyploids, they may benefit from fixed heterozygosity of homoeologous alleles.[81] In certain cases, such heterozygosity can have beneficial heterotic effects, either in terms of fitness in natural contexts or desirable traits in agricultural contexts. This could partially explain the prevalence of allopolyploidy among crop species. Both bread wheat and Triticale are examples of an allopolyploids with six chromosome sets. Cotton, peanut, or quinoa are allotetraploids with multiple origins. In Brassicaceous crops, the Triangle of U describes the relationships between the three common diploid Brassicas (B. oleracea, B. rapa, and B. nigra) and three allotetraploids (B. napus, B. juncea, and B. carinata) derived from hybridization among the diploid species. A similar relationship exists between three diploid species of Tragopogon (T. dubius, T. pratensis, and T. porrifolius) and two allotetraploid species (T. mirus and T. miscellus).[82] Complex patterns of allopolyploid evolution have also been observed in animals, as in the frog genus Xenopus.[83]

Paleopolyploidy

PaleopolyploidyTree
This phylogenetic tree shows the relationship between the best-documented instances of paleopolyploidy in eukaryotes.

Ancient genome duplications probably occurred in the evolutionary history of all life. Duplication events that occurred long ago in the history of various evolutionary lineages can be difficult to detect because of subsequent diploidization (such that a polyploid starts to behave cytogenetically as a diploid over time) as mutations and gene translations gradually make one copy of each chromosome unlike the other copy. Over time, it is also common for duplicated copies of genes to accumulate mutations and become inactive pseudogenes.[84]

In many cases, these events can be inferred only through comparing sequenced genomes. Examples of unexpected but recently confirmed ancient genome duplications include baker's yeast (Saccharomyces cerevisiae), mustard weed/thale cress (Arabidopsis thaliana), rice (Oryza sativa), and an early evolutionary ancestor of the vertebrates (which includes the human lineage) and another near the origin of the teleost fishes. Angiosperms (flowering plants) have paleopolyploidy in their ancestry. All eukaryotes probably have experienced a polyploidy event at some point in their evolutionary history.

Karyotype

A karyotype is the characteristic chromosome complement of a eukaryote species.[85][86] The preparation and study of karyotypes is part of cytology and, more specifically, cytogenetics.

Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karyotypes, which are highly variable between species in chromosome number and in detailed organization despite being constructed out of the same macromolecules. In some cases, there is even significant variation within species. This variation provides the basis for a range of studies in what might be called evolutionary cytology.

Homoeologous chromosomes

Homoeologous chromosomes are those brought together following inter-species hybridization and allopolyploidization, and whose relationship was completely homologous in an ancestral species. For example, durum wheat is the result of the inter-species hybridization of two diploid grass species Triticum urartu and Aegilops speltoides. Both diploid ancestors had two sets of 7 chromosomes, which were similar in terms of size and genes contained on them. Durum wheat contains two sets of chromosomes derived from Triticum urartu and two sets of chromosomes derived from Aegilops speltoides. Each chromosome pair derived from the Triticum urartu parent is homoeologous to the opposite chromosome pair derived from the Aegilops speltoides parent, though each chromosome pair unto itself is homologous.

Bacteria

Each Deinococcus radiodurans bacterium contains 4-8 copies of its chromosome.[87] Exposure of D. radiodurans to X-ray irradiation or desiccation can shatter its genomes into hundred of short random fragments. Nevertheless, D. radiodurans is highly resistant to such exposures. The mechanism by which the genome is accurately restored involves RecA-mediated homologous recombination and a process referred to as extended synthesis-dependent strand annealing (SDSA).[88]

Azotobacter vinelandii can contain up to 80 chromosome copies per cell.[89] However this is only observed in fast growing cultures, whereas cultures grown in synthetic minimal media are not polyploid.[90]

Archaea

The archaeon Halobacterium salinarium is polyploid[91] and, like Deinococcus radiodurans, is highly resistant to X-ray irradiation and desiccation, conditions that induce DNA double-strand breaks.[92] Although chromosomes are shattered into many fragments, complete chromosomes can be regenerated by making use of overlapping fragments. The mechanism employs single-stranded DNA binding protein and is likely homologous recombinational repair.[93]

See also

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Further reading

External links

Dryopteris

The moth genus Dryopteris is now considered a junior synonym of Oreta.

Dryopteris , commonly called the wood ferns, male ferns (referring in particular to Dryopteris filix-mas), or buckler ferns, is a genus of 300-350 (or possibly 400) species of ferns distributed in Asia, the Americas, Europe, Africa, and the Pacific islands, with the highest species diversity in eastern Asia. Many of the species have stout, slowly creeping rootstocks that form a crown, with a vase-like ring of fronds. The sori are round, with a peltate indusium. The stipes have prominent scales.

Hybridization and polyploidy are well-known phenomena in this group, with many species formed via these processes. The North American Dryopteris hybrid complex is a well-known example of speciation via allopolyploid hybridization.

Fragaria iturupensis

Fragaria iturupensis, the Iturup strawberry, is a species of wild strawberry, endemic to Iturup in the Kuril Islands. It is noted to have relatively large berries for a wild species, similar in appearance to those of Fragaria virginiana.

G. Ledyard Stebbins

George Ledyard Stebbins Jr. (January 6, 1906 – January 19, 2000) was an American botanist and geneticist who is widely regarded as one of the leading evolutionary biologists of the 20th century. Stebbins received his Ph.D. in botany from Harvard University in 1931. He went on to the University of California, Berkeley, where his work with E. B. Babcock on the genetic evolution of plant species, and his association with a group of evolutionary biologists known as the Bay Area Biosystematists, led him to develop a comprehensive synthesis of plant evolution incorporating genetics.

His most important publication was Variation and Evolution in Plants, which combined genetics and Darwin's theory of natural selection to describe plant speciation. It is regarded as one of the main publications which formed the core of the modern synthesis and still provides the conceptual framework for research in plant evolutionary biology; according to Ernst Mayr, "Few later works dealing with the evolutionary systematics of plants have not been very deeply affected by Stebbins' work." He also researched and wrote widely on the role of hybridization and polyploidy in speciation and plant evolution; his work in this area has had a lasting influence on research in the field.

From 1960, Stebbins was instrumental in the establishment of the Department of Genetics at the University of California, Davis, and was active in numerous organizations involved in the promotion of evolution, and of science in general. He was elected to the National Academy of Science, was awarded the National Medal of Science, and was involved in the development of evolution-based science programs for California high schools, as well as the conservation of rare plants in that state.

Gene duplication

Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

Genetic variation

Genetic variation is the difference in DNA among individuals. There are multiple sources of genetic variation, including mutation and genetic recombination.

Genetics and the Origin of Species

Genetics and the Origin of Species is a 1937 book by the Ukrainian-American evolutionary biologist Theodosius Dobzhansky. It is regarded as one of the most important works of the modern synthesis, and was one of the earliest. The book popularized the work of population genetics to other biologists, and influenced their appreciation for the genetic basis of evolution. In his book, Dobzhansky applied the theoretical work of Sewall Wright (1889-1988) to the study of natural populations, allowing him to address evolutionary problems in a novel way during his time. Dobzhansky implements theories of mutation, natural selection, and speciation throughout his book to explain habits of populations and the resulting effects on their genetic behavior. The book explains evolution in depth as a process over time that accounts for the diversity of all life on Earth. The study of evolution was present, but greatly neglected at the time. Dobzhansky illustrates that evolution regarding the origin and nature of species during this time in history was deemed mysterious, but had expanding potential for progress to be made in its field.

Inbreeding depression

Inbreeding depression is the reduced biological fitness in a given population as a result of inbreeding, or breeding of related individuals. Population biological fitness refers to an organism's ability to survive and perpetuate its genetic material. Inbreeding depression is often the result of a population bottleneck. In general, the higher the genetic variation or gene pool within a breeding population, the less likely it is to suffer from inbreeding depression.

Inbreeding depression seems to be present in most groups of organisms, but varies across mating systems. Hermaphroditic species often exhibit lower degrees of inbreeding depression than outcrossing species, as repeated generations of selfing is thought to purge deleterious alleles from populations. For example, the outcrossing nematode (roundworm) Caenorhabditis remanei has been demonstrated to suffer severely from inbreeding depression, unlike its hermaphroditic relative C. elegans, which experiences outbreeding depression.

Musa balbisiana

Musa balbisiana is a wild-type species of banana native to eastern South Asia, northern Southeast Asia, and southern China. It is one of the ancestors of modern cultivated bananas, along with Musa acuminata. It was first scientifically described in 1820 by the Italian botanist Luigi Aloysius Colla. It grows lush leaves in clumps with a more upright habit than most cultivated bananas. Flowers grow in inflorescences coloured red to maroon. The fruit are between blue and green. They are considered inedible because of the seeds they contain. It may be assumed that wild bananas were cooked and eaten or agriculturalists would not have developed the cultivated banana.

Seeded Musa balbisiana fruit are called butuhan ('with seeds') in the Philippines, and kluai tani (กล้วยตานี) in Thailand, where its leaves are used for packaging and crafts. Natural parthenocarpic clones occur through polyploidy and produce edible bananas, examples of which are wild saba bananas.

Musk strawberry

The musk strawberry or hautbois strawberry (Fragaria moschata), is a species of strawberry native to Europe. Its French name hautbois strawberry may be anglicised as hautboy strawberry. The plants are hardy and can survive in many weather conditions and are cultivated commercially on a small scale, particularly in Italy. The fruit are small and round; they are used in the gourmet community for their intense aroma and superb flavour, which has been compared to a mixture of regular strawberry, raspberry and pineapple. Popular cultivated varieties include 'Capron' and 'Profumata di Tortona'.

Octodontidae

Octodontidae is a family of rodents, restricted to southwestern South America. Thirteen species of octodontid are recognised, arranged in nine genera. The best known species is the common degu, Octodon degus.

Octodontids are medium-sized rodents, ranging from 12 to 20 cm (4.7 to 7.9 in) in body length. They have long, silky, fur, which is typically brownish in color, and often paler on the underside. The name 'octodont' derives from the wear pattern of their teeth, which resembles a figure 8. Most are nocturnal, social, burrowing animals, though the degu is largely diurnal. They are herbivorous, eating tubers, bulbs, and cactuses.Some authors have suggested that the octodontids should be reclassified in the order Lagomorpha, but this has not been supported by further analyses (e.g. Opazo, 2005). Older literature includes the tuco-tucos in the family, as the subfamily Ctenomyinae, but these animals are normally now treated as a separate family, Ctenomyidae. There is some evidence that evolution within the family may have resulted from polyploidy. The red viscacha rat, Tympanoctomys barrerae, is tetraploid, with 102 chromosomes, and the recently described golden viscacha rat Pipanacoctomys aureus has 92.

Members of the genus Aconaemys are referred to as rock rats, and members of genera Octodon and Octodontomys are called degus, though the name degu on its own historically implied O. degu. The single member of Spalacopus, S. cyanus, is called the coruro. Members of the other genera are called viscacha rats.

Paleopolyploidy

Paleopolyploidy is the result of genome duplications which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (autopolyploidy) or combine those of two species (allopolyploidy). Because of functional redundancy, genes are rapidly silenced or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids e.g. baker's yeast, Arabidopsis thaliana, and perhaps humans.Paleopolyploidy is extensively studied in plant lineages. It has been found that almost all flowering plants have undergone at least one round of genome duplication at some point during their evolutionary history. Ancient genome duplications are also found in the early ancestor of vertebrates (which includes the human lineage) and another near the origin of the bony fishes. Evidence suggests that baker's yeast (Saccharomyces cerevisiae), which has a compact genome, experienced polyploidization during its evolutionary history.

The term mesopolyploid is sometimes used for species that have undergone whole genome multiplication events (whole genome duplication, whole genome triplification, etc.) in more recent history, such as within the last 17 million years.

Plant evolution

Plant evolution is the subset of evolutionary phenomena that concern plants. Evolutionary phenomena are characteristics of populations that are described by averages, medians, distributions, and other statistical methods. This distinguishes plant evolution from plant development, a branch of developmental biology which concerns the changes that individuals go through in their lives. The study of plant evolution attempts to explain how the present diversity of plants arose over geologic time. It includes the study of genetic change and the consequent variation that often results in speciation, one of the most important types of radiation into taxonomic groups called clades. A description of radiation is called a phylogeny and is often represented by type of diagram called a phylogenetic tree.

Ploidy

Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Somatic cells, tissues, and individual organisms can be described according to the number of sets of chromosomes present (the "ploidy level"): monoploid (1 set), diploid (2 sets), triploid (3 sets), tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid or septaploid (7 sets), etc. The generic term polyploid is often used to describe cells with three or more chromosome sets.Virtually all sexually reproducing organisms are made up of somatic cells that are diploid or greater, but ploidy level may vary widely between different organisms, between different tissues within the same organism, and at different stages in an organism's life cycle. Half of all known plant genera contain polyploid species, and about two-thirds of all grasses are polyploid. Many animals are uniformly diploid, though polyploidy is common in invertebrates, reptiles, and amphibians. In some species, ploidy varies between individuals of the same species (as in the social insects), and in others entire tissues and organ systems may be polyploid despite the rest of the body being diploid (as in the mammalian liver). For many organisms, especially plants and fungi, changes in ploidy level between generations are major drivers of speciation. In mammals and birds, ploidy changes are typically fatal. There is, however, evidence of polyploidy in organisms now considered to be diploid, suggesting that polyploidy has contributed to evolutionary diversification in plants and animals through successive rounds of polyploidization and rediploidization.Humans are diploid organisms, carrying two complete sets of chromosomes in their somatic cells: one set of 23 chromosomes from their father and one set of 23 chromosomes from their mother. The two sets combined provide a full complement of 46 chromosomes. This total number of individual chromosomes (counting all complete sets) is called the chromosome number. The number of chromosomes found in a single complete set of chromosomes is called the monoploid number (x). The haploid number (n) refers to the total number of chromosomes found in a gamete (a sperm or egg cell produced by meiosis in preparation for sexual reproduction). Under normal conditions, the haploid number is exactly half the total number of chromosomes present in the organism's somatic cells. For diploid organisms, the monoploid number and haploid number are equal; in humans, both are equal to 23. When a human germ cell undergoes meiosis, the diploid 46-chromosome complement is split in half to form haploid gametes. After fusion of a male and a female gamete (each containing 1 set of 23 chromosomes) during fertilization, the resulting zygote again has the full complement of 46 chromosomes: 2 sets of 23 chromosomes.

Polyploid complex

A polyploid complex, also called a diploid-polyploid complex, is a group of interrelated and interbreeding species that also have differing levels of ploidy that can allow interbreeding.

A polyploid complex was described by E. B. Babcock and G. Ledyard Stebbins in their 1938 monograph The American Species of Crepis: their interrelationships and distribution as affected by polyploidy and apomixis. In Crepis and some other perennial plant species, a polyploid complex may arise where there are at least two genetically isolated diploid populations, in addition to auto- and allopolyploid derivatives that coexist and interbreed. Thus a complex network of interrelated forms may exist where the polyploid forms allow for intermediate forms between the diploid species that are otherwise unable to interbreed.This complex situation does not fit well within the biological species concept of Ernst Mayr which defines a species as "groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups".

In many diploid-polyploid complexes the polyploid hybrid members reproduce asexually while diploids reproduce sexually. Thus polyploidy is related to the phenomenon called "geographic parthenogenesis" by zoologist Albert Vandel, that asexual organisms often have greater geographic ranges than their sexual relatives. It is not known which of the associated factors is the major determiner of geographic parthenogenesis, hybridization, polyploidy, or asexual reproduction.

Rosa canina

Rosa canina, commonly known as the dog rose, is a variable climbing, wild rose species native to Europe, northwest Africa, and western Asia.

It is a deciduous shrub normally ranging in height from 1–5 metres (3.3–16.4 ft), though sometimes it can scramble higher into the crowns of taller trees. Its stems are covered with small, sharp, hooked prickles, which aid it in climbing. The leaves are pinnate, with 5–7 leaflets. The flowers are usually pale pink, but can vary between a deep pink and white. They are 4–6 centimetres (1.6–2.4 in) in diameter with five petals, and mature into an oval, 1.5–2-centimetre (0.59–0.79 in), red-orange fruit, or hip.

Saltation (biology)

In biology, saltation (from Latin, saltus, "leap") is a sudden and large mutational change from one generation to the next, potentially causing single-step speciation. This was historically offered as an alternative to Darwinism. Some forms of mutationism were effectively saltationist, implying large discontinuous jumps.

Speciation, such as by polyploidy in plants, can sometimes be achieved in a single and in evolutionary terms sudden step. Evidence exists for various forms of saltation in a variety of organisms.

Sequoioideae

Sequoioideae, popularly known as redwoods, is a subfamily of coniferous trees within the family Cupressaceae. It is most common in the coastal forests of Northern California and is known for being the largest tree in the world.

Speciation

Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within lineages. Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book On the Origin of Species. He also identified sexual selection as a likely mechanism, but found it problematic.

There are four geographic modes of speciation in nature, based on the extent to which speciating populations are isolated from one another: allopatric, peripatric, parapatric, and sympatric. Speciation may also be induced artificially, through animal husbandry, agriculture, or laboratory experiments. Whether genetic drift is a minor or major contributor to speciation is the subject matter of much ongoing discussion.

Rapid sympatric speciation can take place through polyploidy, such as by doubling of chromosome number; the result is progeny which are immediately reproductively isolated from the parent population. New species can also be created through hybridisation followed, if the hybrid is favoured by natural selection, by reproductive isolation.

Tapetum (botany)

The tapetum is a specialised layer of nutritive cells found within the anther, of flowering plants, where it is located between the sporangenous tissue and the anther wall.

Tapetum is important for the nutrition and development of pollen grains, as well as a source of precursors for the pollen coat. The cells are usually bigger and normally have more than one nucleus per cell. As the sporogenous cells undergo mitosis, the nuclei of tapetal cells also divide. Sometimes, this mitosis is not normal due to which many cells of mature tapetum become multinucleate. Sometimes polyploidy and polyteny can also be seen. The unusually large nuclear constitution of the tapetum helps it in providing nutrients and regulatory molecules to the forming pollen grains. The following processes are responsible for this:

Endomitosis

Normal mitosis not followed by cytokinesis

Formation of restitution nuclei

EndoreduplicationTapetum helps in pollenwall formation, transportation of nutrients to inner side of anther, synthesis of callase enzyme for separation of microspore tetrads.

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Basic concepts
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Hybridization
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