Intragenomic conflict refers to the

evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

ary phenomenon where

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

s have phenotypic effects that promote their own transmission in detriment of the transmission of other genes that reside in the same

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

. The

selfish gene theory With gene defined as "not just one single physical bit of DNA utall replicas of a particular bit of DNA distributed throughout the world", the gene-centered view of evolution, gene's eye view, gene selection theory, or selfish gene theory hol ...

postulates that

natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Cha ...

will increase the frequency of those genes whose phenotypic effects cause their transmission to new organisms, and most genes achieve this by cooperating with other genes in the same genome to build an

organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fu ...

capable of reproducing and/or helping kin to reproduce. The assumption of the prevalence of intragenomic cooperation underlies the organism-centered concept of

inclusive fitness In evolutionary biology, inclusive fitness is one of two metrics of evolutionary success as defined by W. D. Hamilton in 1964: * Personal fitness is the number of offspring that an individual begets (regardless of who rescues/rears/supports th ...

. However, conflict among genes in the same genome may arise both in events related to reproduction (a selfish gene may "cheat" and increase its own presence in

gamete A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...

s or

offspring In biology, offspring are the young creation of living organisms, produced either by a single organism or, in the case of sexual reproduction, two organisms. Collective offspring may be known as a brood or progeny in a more general way. This ca ...

above the expected according to fair Mendelian segregation and fair

gametogenesis Gametogenesis is a biological process by which diploid or haploid precursor cells undergo cell division and differentiation to form mature haploid gametes. Depending on the biological life cycle of the organism, gametogenesis occurs by meiotic di ...

) and altruism (genes in the same genome may disagree on how to value other organisms in the context of helping kin because coefficients of relatedness diverge between genes in the same genome).

Nuclear genes

Autosomic genes usually have the same mode of transmission in sexually reproducing species due to the fairness of Mendelian segregation, but conflicts among

allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...

s of autosomic genes may arise when an allele cheats during

(segregation distortion) or eliminates

embryo An embryo is an initial stage of development of a multicellular organism. In organisms that reproduce sexually, embryonic development is the part of the life cycle that begins just after fertilization of the female egg cell by the male spe ...

s that don't contain it (lethal maternal effects). An allele may also directly convert its rival allele into a copy of itself (homing endonucleases). Finally, mobile genetic elements completely bypass Mendelian segregation, being able to insert new copies of themselves into new positions in the genome (transposons).

Segregation distortion

In principle, the two parental

s have equal probabilities of being present in the mature

. However, there are several mechanisms that lead to an unequal transmission of parental alleles from parents to offspring. One example is a gene, called a ''segregation distorter'', that "cheats" during meiosis or

and thus is present in more than half of the functional gametes. The most studied examples are ''sd'' in ''

Drosophila melanogaster ''Drosophila melanogaster'' is a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is often referred to as the fruit fly or lesser fruit fly, or less commonly the " vinegar fly" or "pomace fly". Starting with ...

'' ( fruit fly), ''t'' haplotype in ''

Mus musculus Mus or MUS may refer to: Abbreviations * MUS, the NATO country code for Mauritius * MUS, the IATA airport code for Minami Torishima Airport * MUS, abbreviation for the Centre for Modern Urban Studies on Campus The Hague, Leiden University, Net ...

'' (

mouse A mouse ( : mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus' ...

) and ''sk'' in ''

Neurospora ''Neurospora'' is a genus of Ascomycete fungi. The genus name, meaning "nerve spore" refers to the characteristic striations on the spores that resemble axons. The best known species in this genus is '' Neurospora crassa'', a common model organ ...

'' spp. (

fungus A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately fr ...

). Possible examples have also been reported in humans. Segregation distorters that are present in sexual chromosomes (as is the case with the X chromosome in several ''Drosophila'' species) are denominated sex-ratio distorters, as they induce a sex-ratio bias in the offspring of the carrier individual.

Killer and target

The simplest model of

meiotic drive Meiotic drive is a type of intragenomic conflict, whereby one or more loci within a genome will effect a manipulation of the meiotic process in such a way as to favor the transmission of one or more alleles over another, regardless of its phenoty ...

involves two tightly linked loci: a ''Killer'' locus and a ''Target'' locus. The segregation distorter set is composed by the allele ''Killer'' (in the ''Killer'' locus) and the allele ''Resistant'' (in the ''Target'' locus), while its rival set is composed by the alleles ''Non-killer'' and ''Non-resistant''. So, the segregation distorter set produces a toxin to which it is itself resistant, while its rival is not. Thus, it kills those gametes containing the rival set and increases in frequency. The tight linkage between these loci is crucial, so these genes usually lie on low-recombination regions of the genome.

True meiotic drive

Other systems do not involve gamete destruction, but rather use the asymmetry of

meiosis Meiosis (; , since it is a reductional division) is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, such as sperm or egg cells. It involves two rounds of division that ultimately ...

in females: the driving allele ends up in the

oocyte An oocyte (, ), oöcyte, or ovocyte is a female gametocyte or germ cell involved in reproduction. In other words, it is an immature ovum, or egg cell. An oocyte is produced in a female fetus in the ovary during female gametogenesis. The female ...

instead of in the

polar bodies A polar body is a small haploid cell that is formed at the same time as an egg cell during oogenesis, but generally does not have the ability to be fertilized. It is named from its polar position in the egg. When certain diploid cells in animals ...

with a probability greater than one half. This is termed true

, as it does not rely on a post-meiotic mechanism. The best-studied examples include the

neocentromere Neocentromeres are new centromeres that form at a place on the chromosome that is usually not centromeric. They typically arise due to disruption of the normal centromere. These neocentromeres should not be confused with “knobs”, which were al ...

s (knobs) of maize, as well as several chromosomal rearrangements in mammals. The general molecular evolution of

centromere The centromere links a pair of sister chromatids together during cell division. This constricted region of chromosome connects the sister chromatids, creating a short arm (p) and a long arm (q) on the chromatids. During mitosis, spindle fibers ...

s is likely to involve such mechanisms.

Lethal maternal effects

The Medea gene causes the death of progeny from a heterozygous mother that do not inherit it. It occurs in the

flour beetle Flour beetles are members of the darkling beetle genera '' Tribolium'' or '' Tenebrio''. They are pests of cereal silos and are widely used as laboratory animals, as they are easy to keep. The flour beetles consume wheat and other grains, are ad ...

(''Tribolium castaneum''). Maternal-effect selfish genes have been successfully synthesized in the lab.

Transposons

Transposons A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Tran ...

are autonomous replicating genes that encode the ability to move to new positions in the genome and therefore accumulate in the genomes. They replicate themselves in spite of being detrimental to the rest of the genome. They are often called 'jumping genes' or parasitic DNA and were discovered by

Barbara McClintock Barbara McClintock (June 16, 1902 – September 2, 1992) was an American scientist and cytogeneticist who was awarded the 1983 Nobel Prize in Physiology or Medicine. McClintock received her PhD in botany from Cornell University in 1927. There ...

in 1944.

Homing endonuclease genes

Homing endonuclease genes (HEG) convert their rival

into a copy of themselves, and are thus inherited by nearly all meiotic daughter cells of a

heterozygote Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. M ...

cell. They achieve this by encoding an endonuclease which breaks the rival allele. This break is repaired by using the sequence of the HEG as template. HEGs encode sequence-specific endonucleases. The recognition sequence (RS) is 15–30 bp long and usually occurs once in the genome. HEGs are located in the middle of their own recognition sequences. Most HEGs are encoded by self-splicing

intron An intron is any Nucleic acid sequence, nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e. a region inside a gene."The notion of ...

s (group I & II) and inteins. Inteins are internal protein fragments produced from protein splicing and usually contain endonuclease and splicing activities. The allele without the HEGs are cleaved by the homing endonuclease and the double-strand break are repaired by homologous recombination (gene conversion) using the allele containing HEGs as template. Both chromosomes will contain the HEGs after repair.

B-chromosome

B-chromosomes are nonessential

chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...

s; not homologous with any member of the normal (A) chromosome set; morphologically and structurally different from the A's; and they are transmitted at higher-than-expected frequencies, leading to their accumulation in progeny. In some cases, there is strong evidence to support the contention that they are simply ''selfish'' and that they exist as parasitic chromosomes. They are found in all major taxonomic groupings of both

plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...

s and

animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage ...

Cytoplasmic genes

Since nuclear and cytoplasmic genes usually have different modes of transmission, intragenomic conflicts between them may arise. Mitochondria and chloroplasts are two examples of sets of cytoplasmic genes that commonly have exclusive maternal inheritance, similar to endosymbiont parasites in arthropods, like ''Wolbachia''.

Males as dead-ends to cytoplasmic genes

Anisogamy Different forms of anisogamy: A) anisogamy of motile cells, B) egg_cell.html"_;"title="oogamy_(egg_cell">oogamy_(egg_cell_and_sperm_cell),_C)_anisogamy_of_non-motile_cells_(egg_cell_and_spermatia)..html" ;"title="egg_cell_and_sperm_cell.html" ;" ...

generally produces

zygotes A zygote (, ) is a eukaryotic cell formed by a fertilization event between two gametes. The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic information of a new individual organism. In multicellula ...

that inherit cytoplasmic elements exclusively from the female gamete. Thus, males represent dead-ends to these genes. Because of this fact, cytoplasmic genes have evolved a number of mechanisms to increase the production of female descendants and eliminate offspring not containing them.

Feminization

Male organisms are converted into females by cytoplasmic inherited protists (

Microsporidia Microsporidia are a group of spore-forming unicellular parasites. These spores contain an extrusion apparatus that has a coiled polar tube ending in an anchoring disc at the apical part of the spore. They were once considered protozoans or pr ...

) or bacteria (''

Wolbachia ''Wolbachia'' is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes, and is possibly the most common reproducti ...

''), regardless of nuclear sex-determining factors. This occurs in

amphipod Amphipoda is an order of malacostracan crustaceans with no carapace and generally with laterally compressed bodies. Amphipods range in size from and are mostly detritivores or scavengers. There are more than 9,900 amphipod species so far descri ...

and

isopod Isopoda is an order of crustaceans that includes woodlice and their relatives. Isopods live in the sea, in fresh water, or on land. All have rigid, segmented exoskeletons, two pairs of antennae, seven pairs of jointed limbs on the thorax, and ...

Crustacea Crustaceans (Crustacea, ) form a large, diverse arthropod taxon which includes such animals as decapods, seed shrimp, branchiopods, fish lice, krill, remipedes, isopods, barnacles, copepods, amphipods and mantis shrimp. The crustacean group c ...

and

Lepidoptera Lepidoptera ( ) is an order of insects that includes butterflies and moths (both are called lepidopterans). About 180,000 species of the Lepidoptera are described, in 126 families and 46 superfamilies, 10 percent of the total described speci ...

Male-killing

Male

embryos An embryo is an initial stage of development of a multicellular organism. In organisms that reproduce sexually, embryonic development is the part of the life cycle that begins just after fertilization of the female egg cell by the male spe ...

(in the case of cytoplasmic inherited bacteria) or male

larva A larva (; plural larvae ) is a distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. ...

e (in the case of Microsporidia) are killed. In the case of embryo death, this diverts investment from males to females who can transmit these cytoplasmic elements (for instance, in ladybird beetles, infected female hosts eat their dead male brothers, which is positive from the viewpoint of the bacterium). In the case of microsporidia-induced larval death, the agent is transmitted out of the male lineage (through which it cannot be transmitted) into the environment, where it may be taken up again infectiously by other individuals. Male-killing occurs in many

insects Insects (from Latin ') are pancrustacean hexapod invertebrates of the class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, thorax and abdomen), three pairs of j ...

. In the case of male embryo death, a variety of bacteria have been implicated, including ''Wolbachia''.

Male-sterility

In some cases

anther The stamen (plural ''stamina'' or ''stamens'') is the pollen-producing reproductive organ of a flower. Collectively the stamens form the androecium., p. 10 Morphology and terminology A stamen typically consists of a stalk called the filam ...

tissue (male

gametophyte A gametophyte () is one of the two alternating multicellular phases in the life cycles of plants and algae. It is a haploid multicellular organism that develops from a haploid spore that has one set of chromosomes. The gametophyte is the ...

) is killed by

mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...

monoecious Monoecy (; adj. monoecious ) is a sexual system in seed plants where separate male and female cones or flowers are present on the same plant. It is a monomorphic sexual system alongside gynomonoecy, andromonoecy and trimonoecy. Monoecy is ...

angiosperms Flowering plants are plants that bear flowers and fruits, and form the clade Angiospermae (), commonly called angiosperms. The term "angiosperm" is derived from the Greek words ('container, vessel') and ('seed'), and refers to those plants ...

, increasing energy and material spent in developing female gametophytes. This leads to a shift from monoecy to

gynodioecy Gynodioecy is a rare breeding system that is found in certain flowering plant species in which female and hermaphroditic plants coexist within a population. Gynodioecy is the evolutionary intermediate between hermaphroditism (exhibiting both fem ...

, where part of the plants in the population are male-sterile.

Parthenogenesis induction

In certain

haplodiploid Haplodiploidy is a sex-determination system in which males develop from unfertilized eggs and are haploid, and females develop from fertilized eggs and are diploid. Haplodiploidy is sometimes called arrhenotoky. Haplodiploidy determines the sex ...

Hymenoptera Hymenoptera is a large order of insects, comprising the sawflies, wasps, bees, and ants. Over 150,000 living species of Hymenoptera have been described, in addition to over 2,000 extinct ones. Many of the species are parasitic. Females typic ...

and

mites Mites are small arachnids (eight-legged arthropods). Mites span two large orders of arachnids, the Acariformes and the Parasitiformes, which were historically grouped together in the subclass Acari, but genetic analysis does not show clear e ...

, in which males are produced asexually, ''Wolbachia'' and ''

Cardinium "''Candidatus'' Cardinium" is a genus of Gram-negative parasitic bacteria that reside within cells of some arthropods and nematodes. Although they have not yet been isolated in pure culture (hence the designation ''Candidatus''), they are kno ...

'' can induce duplication of the

s and thus convert the organisms into females. The cytoplasmic bacterium forces

haploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respective ...

cells to go through incomplete mitosis to produce

diploid Ploidy () is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Sets of chromosomes refer to the number of maternal and paternal chromosome copies, respectiv ...

cells which therefore will be female. This produces an entirely female population. If antibiotics are administered to populations which have become asexual in this way, they revert to sexuality instantly, as the cytoplasmic bacteria forcing this behaviour upon them are removed.

Cytoplasmic incompatibility

In many

arthropods Arthropods (, (gen. ποδός)) are invertebrate animals with an exoskeleton, a segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and cuticle made of chitin, ...

, zygotes produced by sperm of infected males and ova of non-infected females can be killed by ''Wolbachia'' or ''Cardinium''.

Evolution of sex

Conflict between chromosomes has been proposed as an element in the evolution of sex. See als