When initially developed, the GBS approach was tested and validated in recombinant inbred lines (RILs) from a high-resolution maize mapping population (IBM) and doubled haploid (DH) barley lines from the Oregon Wolfe Barley (OWB) mapping population. Up to 96 RE (ApeKI)-digested DNA samples were pooled and processed simultaneously during the GBS library construction, which was checked on a Genome Analyzer II (Illumina, Inc.). Overall, 25,185 biallelic tags were mapped in maize, while 24,186 sequence tags were mapped in barley. Barley GBS marker validation using a single DH line (OWB003) showed 99% agreement between the reference markers and the mapped GBS reads. Although barley lacks a complete genome sequence, GBS does not require a reference genome for sequence tag mapping, the reference is developed during the process of sampling genotyping. Tags can also be treated as dominant markers for alternative genetic analysis in the absence of a reference genome. Other than the multiplex GBS skimming, imputation of missing SNPs has the potential to further reduce GBS costs. GBS is a versatile and cost-effective procedure that will allow
mining genomes of any species without prior knowledge of its genome structure.  [ 1 ]


Germline mosaicism , also called  gonadal mosaicism , is a type of  genetic mosaicism  where more than one set of genetic information is found specifically within the  gamete  cells; conversely,  somatic mosaicism  is a type of genetic mosaicism found in  somatic cells .  Germline  mosaicism can be present at the same time as somatic mosaicism or individually, depending on when the conditions occur. Pure germline mosaicism refers to mosaicism found exclusively in the gametes and not in any somatic cells. Germline mosaicism can be caused either by a mutation that occurs after conception, [ 1 ] [ 2 ]  or by  epigenetic regulation , [ 3 ]  alterations to DNA such as  methylation  that do not involve changes in the DNA coding sequence.


A mutation in an  allele  acquired by a somatic cell early in its development can be passed on to its daughter cells, including those that later specialize to gametes. With such mutation within the gamete cells, a pair of medically typical individuals may have repeated succession of children who suffer from certain genetic disorders such as  Duchenne muscular dystrophy  and  osteogenesis imperfecta  because of germline mosaicism. It is possible for parents unaffected by  germline mutations  to produce an offspring with an  autosomal dominant  (AD) disorder due to a random new mutation within one’s gamete cells known as  sporadic mutation ; however, if these parents produce more than one child with an AD disorder, germline mosaicism is more likely the cause than a sporadic mutation. [ 4 ] [ unreliable source? ]  In the first documented case of its kind, two offspring of a French woman who had no phenotypic expression of the AD disorder  hypertrophic cardiomyopathy , inherited the disease. [ 5 ]


Germline mosaicism disorders are usually inherited in a pattern that suggests that the condition is dominant in either or both of the parents. That said, diverging from Mendelian gene inheritance patterns, a parent with a recessive allele can produce offspring expressing the phenotype as dominant through germline mosaicism. A situation may also arise in which the parents have milder phenotypic expression of a mutation yet produce offspring with more expressive phenotypic variance and a more frequent sibling recurrences of the mutation. [ 6 ] [ 7 ] [ 8 ]


Diseases caused by germline mosaicism can be difficult to diagnose as genetically-inherited because the  mutant   alleles  are not likely to be present in the somatic cells. Somatic cells are more commonly used for  genetic analysis  because they are easier to obtain than gametes. If the disease is a result of pure germline mosaicism, then the disease causing mutant allele would never be present in the somatic cells. This is a source of uncertainty for  genetic counselling . An individual may still be a carrier for a certain disease even if the disease causing mutant allele is not present in the cells that were analyzed because the causative mutation could still exist in some of the individual's gametes. [ 9 ]


Germline mosaicism may contribute to the inheritance of many genetic conditions. Conditions that are inherited by means of germline mosaicism are often mistaken as being the result of  de novo mutations . Various diseases are now being re-examined for presence of mutant alleles in the germline of the parents in order to further our understanding of how they can be passed on. [ 10 ]  The frequency of germline mosaicism is not known due to the sporadic nature of the mutations causing it and the difficulty in obtaining the gametes that must be tested to diagnose it.


Autosomal dominant or X-linked familial disorders often prompt prenatal testing for germline mosaicism. This diagnosis may involve minimally invasive procedures, such as blood sampling or amniotic fluid sampling. [ 9 ] [ 11 ] [ 12 ] [ 13 ] [ 14 ]  Collected samples can be sequenced via common DNA testing methods, such as  Sanger Sequencing ,  MLPA , or  Southern Blot  analysis, to look for variations on relevant genes connected to the disorder. [ 14 ] [ 15 ]


The recurrence rate of conditions caused by germline mosaicism varies greatly between subjects. Recurrence is proportional to the number of gamete cells that carry the particular mutation with the condition. If the mutation occurred earlier on in the development of the gamete cells, then the recurrence rate would be higher because a greater number of cells would carry the mutant allele. [ 11 ]


A Moroccan family consisting of two healthy unrelated parents and three offspring—including two with Noonan syndrome, a rare autosomal dominant disorder with varying expression and genetic heterogeneity—underwent  genetic testing  revealing that both of the siblings with NS share the same PTPN11 haplotype from both parents, while a distinct paternal and maternal haplotype was inherited by the unaffected sibling.  [ 16 ]
In the paper Germline and somatic mosaicism in transgenic mice published in 1986, Thomas M.Wilkie, Ralph L.Brinster, and Richard D.Palmiter analyzed a germline mosaicism experiment done on 262 transgenic mice and concluded that 30% of founder transgenic mice are mosaic in the germline.  [ 17 ]


The  GNC hypothesis  or  GNC-SNS primeval genetic code hypothesis  refers to a hypothesis about the  origin of genes .  It suggests the universal genetic code originated not from a three-amino acid system, but from a four-amino acid system. It is this GNC code encoding [GADV]-proteins which is the most primitive genetic code. This hypothesis was first proposed by Kenji Ikehara at Nara Women's University.


While almost all of the  organisms  on Earth share the universal  genetic code , in the GNC hypothesis it is argued that two primeval genetic codes preceded the present genetic code as follows:


The GNC hypothesis is based on the following facts:


Ikehara, Kenji; Omori, Yoko; Arai, Rieko; Hirose, Akiko (2002). "A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis".  Journal of Molecular Evolution .  54  (4):  530– 538.  Bibcode : 2002JMolE..54..530I .  doi : 10.1007/s00239-001-0053-6 .  PMID   11956691 .


Haploidisation  is the process of halving the chromosomal content of a cell, producing a  haploid  cell. Within the normal reproductive cycle, haploidisation is one of the major functional consequences of  meiosis , the other being a process of  chromosomal crossover  that mingles the genetic content of the parental chromosomes. [ 1 ]  Usually, haploidisation creates a monoploid cell from a diploid progenitor, or it can involve halving of a polyploid cell, for example to make a diploid potato plant from a tetraploid lineage of potato plants.


If haploidisation is not followed by  fertilisation , the result is a haploid lineage of cells. For example, experimental haploidisation may be used to recover a strain of haploid  Dictyostelium  from a diploid strain. [ 2 ]  It sometimes occurs naturally in plants when meiotically reduced cells (usually egg cells) develop by  parthenogenesis .


Haploidisation was one of the procedures used by  Japanese  researchers to produce  Kaguya , a  mouse  which had  same-sex  parents; two haploids were then combined to make the diploid mouse.


Haploidisation commitment is a checkpoint in meiosis which follows the successful completion of premeiotic DNA replication and recombination commitment. [ 3 ]


Haploinsufficiency  in  genetics  describes a model of  dominant  gene action in  diploid  organisms, in which a single copy of the  wild-type   allele  at a  locus  in  heterozygous  combination with a variant allele is insufficient to produce the wild-type  phenotype . Haploinsufficiency may arise from a  de novo  or inherited  loss-of-function mutation  in the variant allele, such that it yields little or no gene product (often a  protein ). Although the other, standard allele still produces the standard amount of product, the total product is insufficient to produce the standard phenotype. This  heterozygous   genotype  may result in a non- or sub-standard, deleterious, and (or) disease phenotype. Haploinsufficiency is the standard explanation for dominant deleterious alleles. [ clarification needed ]


In the alternative case of  haplosufficiency , the loss-of-function allele behaves as above, but the single standard allele in the  heterozygous  genotype produces sufficient gene product to produce the same, standard phenotype as seen in the  homozygote . Haplosufficiency accounts for the typical dominance of the "standard" allele over variant alleles, where the phenotypic identity of genotypes heterozygous and homozygous for the allele defines it as dominant,  versus  a variant phenotype produced only by the genotype homozygous for the alternative allele, which defines it as recessive.


The alteration in the  gene dosage , which is caused by the loss of a functional allele, is also called allelic insufficiency.


About 3,000 human genes cannot tolerate loss of one of the two alleles. [ 1 ]


An example of this is seen in the case of  Williams syndrome , a neurodevelopmental disorder caused by the haploinsufficiency of genes at 7q11.23. The haploinsufficiency is caused by the  copy-number variation  (CNV) of 28 genes led by the deletion of ~1.6 Mb. These dosage-sensitive genes are vital for human language and constructive cognition. [ 2 ]


Another example is the haploinsufficiency of  telomerase reverse transcriptase  which leads to anticipation in autosomal dominant  dyskeratosis congenita . It is a rare inherited disorder characterized by abnormal skin manifestations, which results in  bone marrow failure ,  pulmonary fibrosis  and an increased predisposition to cancer. A  null mutation  in motif D of the reverse transcriptase domain of the telomerase protein, hTERT, leads to this phenotype. Thus telomerase dosage is important for maintaining tissue proliferation. [ 3 ]


A variation of haploinsufficiency exists for mutations in the gene  PRPF31 , a known cause of  autosomal dominant   retinitis pigmentosa . There are two wild-type alleles of this gene—a high- expressivity  allele and a low-expressivity allele. When the mutant gene is inherited with a high-expressivity allele, there is no disease phenotype. However, if a mutant allele and a low-expressivity allele are inherited, the residual protein levels falls below that required for normal function, and disease phenotype is present. [ 4 ]


Copy number variation  (CNV) refers to the differences in the number of copies of a particular region of the genome. This leads to too many or too few of the dosage sensitive genes. The genomic rearrangements, that is, deletions or duplications, are caused by the mechanism of  non-allelic homologous recombination  (NAHR). In the case of the Williams Syndrome, the microdeletion includes the  ELN  gene. The hemizygosity of the elastin is responsible for  supravalvular aortic stenosis , the obstruction in the left ventricular outflow of blood in the heart. [ 5 ] [ 6 ]


Other examples include:


The most direct method to detect haploinsufficiency is the  heterozygous  deletion of one  allele  in a model organism. This can be done in  tissue culture cells  or in single-celled organisms such as yeast ( Saccharomyces cerevisiae ). [ 11 ]


The  haplotype-relative-risk  ( HRR ) method is a family-based method for determining gene  allele   association  to a disease in the presence of actual  genetic linkage .  Nuclear families  with one affected child are sampled using the parental  haplotypes  not transmitted as a control.  While similar to the  genotype   relative risk  (RR), the HRR provides a solution to the problem of  population stratification  by only sampling within family trios. The HRR method was first proposed by Rubinstein in 1981 then detailed in 1987 by Rubinstein and Falk [ 1 ]  and is an important tool in  genetic association  studies.


The original method proposed by Falk and Rubinstien fell under scrutiny in 1989, when Ott showed the equivalence of HRR to the classical RR method [ 2 ]  demonstrating that the HRR holds only when there is zero chance of  recombination  between a disease  locus  and its markers. [ 3 ]  Yet, even when the recombination factor for a locus and its genetic markers is >0 HRR estimates are still more conservative than RR estimates. [ 4 ]


While the HRR method has proven an effective means of avoiding population stratification biases, another family-based association test known as the  transmission disequilibrium test , [ 5 ]  or TDT, is more commonly used. Some research uses both HRR and TDT for their ability to complement each other since one result may give no association while the other will. A positive association result from both TDT and HRR means there is strong evidence that a link exists and vice versa. For example, both HRR and TDT methods were used in a study looking for polymorphism in D2 and D3  dopamine receptor  in association with  schizophrenia  and neither found any evidence for linkage, [ 6 ]  making an actual role of those genes in the etiology of the mental disorder all the more unlikely.


This model represents a case which there is a single locus where all genotypes may lead to expression of the allele in its most simplified definition. Under these parameters a  linkage disequilibrium  of more than 50% means there is a possible link to the gene allele and inheritance.


H
 R
 R
 =

 P

 1

 1
 −

 P

 1

 ∗

 1
 −

 P

 2

 P

 2

 {\displaystyle HRR={\frac {P_{1}}{1-P_{1}}}*{\frac {1-P_{2}}{P_{2}}}}


Gives the HHR which can be estimated by


H
 R
 R
 =

 a

 ′

 b

 ′

 ∗

 d

 ′

 c

 ′

 {\displaystyle HRR={\frac {a^{'}}{b^{'}}}*{\frac {d^{'}}{c^{'}}}}


a '  denotes the observed frequency of children who are positive for the gene allele H.


b '  denotes the observed frequency of children who are negative for the gene allele H.


c '  is the observed frequency of families with at least one transmitted parental marker allele H.


d '  is the observed frequency of families with no transmitted parental marker allele H.


P 1  is the probability this child is positive for the allele of interest H.


P 2  is the probability that at least one of the nontransmitted parental marker alleles equals the allele of interest H.


H is the allele of interest. [ 7 ]


The  Hayflick limit , or  Hayflick phenomenon , is the number of times a normal  somatic ,  differentiated  human cell population will divide before  cell division  stops. [ 1 ] [ 2 ]


The concept of the Hayflick limit was advanced by American anatomist  Leonard Hayflick  in 1961, [ 3 ]  at the  Wistar Institute  in  Philadelphia , Pennsylvania. Hayflick demonstrated that a normal  human   fetal  cell population will divide between 40 and 60 times in  cell culture  before entering a  senescence  phase. This finding refuted the contention by  Alexis Carrel  that normal cells are  immortal .


Hayflick interpreted his discovery to be aging at the cellular level. The aging of cell populations appears to correlate with the overall physical aging of an organism. [ 3 ] [ 4 ]


Macfarlane Burnet  coined the name "Hayflick limit" in his book  Intrinsic Mutagenesis: A Genetic Approach to Ageing , published in 1974. [ 5 ]


Prior to Leonard Hayflick's discovery, it was believed that  vertebrate  cells had an unlimited potential to replicate.  Alexis Carrel , a  Nobel Prize -winning surgeon, had stated "that all cells explanted in  tissue culture  are immortal, and that the lack of continuous cell replication was due to ignorance on how best to cultivate the cells". [ 5 ]  He claimed to have cultivated  fibroblasts  from the hearts of  chickens  (which typically live 5 to 10 years) and to have kept the culture growing for 34 years. [ 6 ]


However, other scientists have been unable to replicate Carrel's results, [ 5 ]  and they are suspected to be due to an error in experimental procedure. To provide required nutrients,  embryonic stem cells  of chickens may have been re-added to the culture daily. This would have easily allowed the cultivation of new, fresh cells in the culture, so there was not an infinite reproduction of the original cells. [ 3 ]  It has been speculated that Carrel knew about this error, but he never admitted it. [ 7 ] [ 8 ]


Also, it has been theorized [ by whom? ]  that the cells Carrel used were young enough to contain  pluripotent stem cells , which, if supplied with a supporting  telomerase -activation nutrient, would have been capable of staving off replicative senescence, or even possibly reversing it. Cultures not containing telomerase-active pluripotent stem cells would have been populated with telomerase-inactive cells, which would have been subject to the 50 ± 10 mitosis event limit until  cellular senescence  occurs as described in Hayflick's findings. [ 4 ]


Hayflick first became suspicious of Carrel's claims while working in a lab at the Wistar Institute. Hayflick noticed that one of his cultures of embryonic human  fibroblasts  had developed an unusual appearance and that cell division had slowed. Initially, he brushed this aside as an anomaly caused by contamination or technical error. However, he later observed other cell cultures exhibiting similar manifestations. Hayflick checked his research notebook and was surprised to find that the atypical cell cultures had all been cultured to approximately their 40th doubling while younger cultures never exhibited the same problems. Furthermore, conditions were similar between the younger and older cultures he observed—same culture medium, culture containers, and technician. This led him to doubt that the manifestations were due to contamination or technical error. [ 9 ]


Hayflick next set out to prove that the cessation of normal cell replicative capacity that he observed was not the result of viral contamination, poor culture conditions or some unknown artifact. Hayflick teamed with  Paul Moorhead  for the definitive experiment to eliminate these as causative factors. As a skilled  cytogeneticist , Moorhead was able to distinguish between male and female cells in culture. The experiment proceeded as follows: Hayflick mixed equal numbers of normal human male fibroblasts that had divided many times (cells at the 40th population doubling) with female fibroblasts that had divided fewer times (cells at the 15th population doubling). Unmixed cell populations were kept as controls. After 20 doublings of the mixed culture, only female cells remained.  Cell division  ceased in the unmixed control cultures at the anticipated times; when the male control culture stopped dividing, only female cells remained in the mixed culture. This suggested that technical errors or contaminating  viruses  were unlikely explanations as to why cell division ceased in the older cells, and proved that unless the virus or artifact could distinguish between male and female cells (which it could not) then the cessation of normal cell replication was governed by an internal counting mechanism. [ 3 ] [ 5 ] [ 9 ]


These results disproved Carrel's immortality claims and established the Hayflick limit as a credible biological theory. Unlike Carrel's experiment, Hayflick's have been successfully repeated by other scientists. [ citation needed ]


Hayflick describes three phases in the life of normal cultured cells. At the start of his experiment he named the primary culture "phase one". Phase two is defined as the period when cells are proliferating; Hayflick called this the time of "luxuriant growth". After months of doubling the cells eventually reach phase three, a phenomenon he named " senescence ", where cell replication rate slows before halting altogether. [ citation needed ]


The Hayflick limit has been found to correlate with the length of the telomeric region at the end of chromosomes. During the process of  DNA replication  of a chromosome, small segments of DNA within each  telomere  are unable to be copied and are lost. [ 10 ]  This occurs due to the uneven nature of DNA replication, where leading and lagging strands are not replicated symmetrically. [ 11 ]  The telomeric region of DNA does not code for any protein; it is simply a repeated code on the end region of linear eukaryotic chromosomes. After many divisions, the telomeres reach a critical length and the cell becomes senescent. It is at this point that a cell has reached its Hayflick limit. [ 12 ] [ 13 ]


Hayflick was the first to report that only cancer cells are immortal. This could not have been demonstrated until he had demonstrated that normal cells are mortal. [ 3 ] [ 4 ]   Cellular senescence  does not occur in most  cancer cells  due to expression of an  enzyme  called  telomerase . This enzyme extends telomeres, preventing the telomeres of cancer cells from shortening and giving them infinite replicative potential. [ 14 ]  A proposed  treatment for cancer  is the usage of telomerase  inhibitors  that would prevent the restoration of the telomere, allowing the cell to die like other body cells. [ 15 ]


Hayflick suggested that his results in which normal cells have a limited replicative capacity may have significance for understanding human aging at the cellular level. [ 4 ]


It has been reported that the limited replicative capability of human  fibroblasts  observed in  cell culture  is far greater than the number of replication events experienced by non-stem cells  in vivo  during a normal postnatal lifespan. [ 16 ]  In addition, it has been suggested that no inverse correlation exists between the replicative capacity of normal human cell strains and the age of the human donor from which the cells were derived, as previously argued. It is now clear that at least some of these variable results are attributable to the mosaicism of cell replication numbers at different body sites where cells were taken. [ 16 ]


Comparisons of different species indicate that cellular replicative capacity may correlate primarily with species body mass, but more likely to species lifespan. [ clarification needed ]   Thus, the limited capacity of cells to replicate in culture may be directly relevant to the overall physical aging of an organism. [ 3 ] [ 4 ]


A  hereditary carrier  ( genetic carrier  or just  carrier ), is a person or other organism that has  inherited  a recessive allele for a genetic trait or mutation but usually does not display that  trait  or show symptoms of the  disease . Carriers are, however, able to  pass  the  allele  onto their offspring, who may then express the genetic trait.


Autosomal  dominant-recessive  inheritance  is made possible by the fact that the individuals of most species (including all higher animals and plants) have two  alleles  of most hereditary predispositions because the  chromosomes  in the  cell nucleus  are usually present in pairs ( diploid ). Carriers can be female or male as the autosomes are homologous independently from the sex.


In carriers the expression of a certain characteristic is recessive. The individual has both a genetic predisposition for the  dominant  trait and a genetic predisposition for the recessive trait, and the dominant expression prevails in the  phenotype . In an individual which is  heterozygous  regarding a certain allele, it is not externally recognisable that it also has the recessive allele. But if the carrier has a child, the recessive trait appears in the phenotype, in case the descendant receives the recessive  allele  from both parents and therefore does not possess the dominant allele that would cover the recessive trait. According to  Mendelian Law of Segregation of genes  an average of 25% of the offspring become  homozygous  and express the recessive trait. Carriers can either pass on normal autosomal recessive hereditary traits or an autosomal recessive  hereditary disease .


Gonosomal  recessive genes are also passed on by carriers. The term is used in  human genetics  in cases of hereditary traits in which the observed trait lies on the female  sex chromosome , the  X chromosome . These are  sex-linked  genes. The carriers are always  women . Women have two homologous sex chromosomes (XX).  Men  cannot be carriers because they only have one X chromosome. If a man has a certain recessive genetic disposition on his X chromosome, this is called  hemizygous  and it gets phenotypically expressed.


Although the Y chromosome is not a really homologous chromosome and carries relatively little genetic information compared to X chromosomes, a genetic component on the Y chromosome can come to expression because there is no homologous chromosome with an allele which could overlay it.


Examples of traits inherited via the X chromosome are  color blindness  and the most common hereditary form of  haemophilia  which therefore affect men much more often than women. [ 1 ] [ 2 ]


Queen Victoria , and her daughters Princesses Alice and Beatrix, were carriers of the   hemophilia  gene (an abnormal allele of a gene, necessary to produce one of the blood clotting factors). Both had children who continued to pass on the gene to succeeding generations of the royal houses of  Spain  and  Russia , into which they married. [ 3 ]  Since males only have one X chromosome, males who carried the altered gene had hemophilia B. Those female children who inherited the altered gene were asymptomatic carriers who also would have passed it to half of their children.


Gonosomal dominant inheritances are also known. There are  no  carriers since owners of a dominant hereditary disposition phenotypically express the trait in each case.


Heredity , also called  inheritance  or  biological inheritance , is the passing on of  traits  from parents to their offspring; either through  asexual reproduction  or  sexual reproduction , the offspring  cells  or  organisms  acquire the  genetic information  of their parents. Through heredity, variations between individuals can accumulate and cause  species  to  evolve  by  natural selection . The study of heredity in  biology  is  genetics .


In humans,  eye color  is an example of an inherited characteristic: an individual might inherit the "brown-eye trait" from one of the parents. [ 1 ]  Inherited traits are controlled by  genes  and the complete set of genes within an organism's  genome  is called its  genotype . [ 2 ]


The complete set of observable traits of the structure and behavior of an organism is called its  phenotype . These traits arise from the interaction of the organism's genotype with the  environment . [ 3 ]  As a result, many aspects of an organism's phenotype are not inherited. For example,  suntanned  skin derives from the interaction between a person's genotype and sunlight; [ 4 ]  thus, suntans are not passed on to people's children. However, some people tan more easily than others, due to differences in their genotype: [ 5 ]  a striking example is people with the inherited trait of  albinism , who do not tan at all and are very sensitive to  sunburn . [ 6 ]


Heritable traits are known to be passed from one generation to the next via  DNA , a  molecule  that encodes genetic information. [ 2 ]  DNA is a long  polymer  that incorporates four types of  bases , which are interchangeable. The  Nucleic acid sequence  (the sequence of bases along a particular DNA molecule) specifies the genetic information: this is comparable to a sequence of letters spelling out a passage of text. [ 7 ]  Before a cell divides through  mitosis , the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. A portion of a DNA molecule that specifies a single functional unit is called a  gene ; different genes have different sequences of bases. Within  cells , the long strands of DNA form condensed structures called  chromosomes . Organisms inherit genetic material from their parents in the form of  homologous chromosomes , containing a unique combination of DNA sequences that code for genes. The specific location of a DNA sequence within a chromosome is known as a  locus . If the DNA sequence at a particular locus varies between individuals, the different forms of this sequence are called  alleles . DNA sequences can change through  mutations , producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. [ 8 ]


However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by  multiple interacting genes  within and among organisms. [ 9 ] [ 10 ]  Developmental biologists suggest that complex interactions in genetic networks and communication among cells can lead to heritable variations that may underlie some of the mechanics in  developmental plasticity  and  canalization . [ 11 ]


Recent findings have confirmed important examples of heritable changes that cannot be explained by direct agency of the DNA molecule. These phenomena are classed as  epigenetic  inheritance systems that are causally or independently evolving over genes. Research into modes and mechanisms of epigenetic inheritance is still in its scientific infancy, but this area of research has attracted much recent activity as it broadens the scope of  heritability  and evolutionary biology in general. [ 12 ]   DNA methylation  marking  chromatin , self-sustaining  metabolic loops , gene silencing by  RNA interference , and the three dimensional  conformation  of proteins (such as  prions ) are areas where epigenetic inheritance systems have been discovered at the organismic level. [ 13 ] [ 14 ]  Heritability may also occur at even larger scales. For example, ecological inheritance through the process of  niche construction  is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effect that modifies and feeds back into the selection regime of subsequent generations. Descendants inherit genes plus environmental characteristics generated by the ecological actions of ancestors. [ 15 ]  Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of  cultural traits ,  group heritability , and  symbiogenesis . [ 16 ] [ 17 ] [ 18 ]  These examples of heritability that operate above the gene are covered broadly under the title of  multilevel or hierarchical selection , which has been a subject of intense debate in the history of evolutionary science. [ 17 ] [ 19 ]


When  Charles Darwin  proposed his theory of  evolution  in 1859, one of its major problems was the lack of an underlying mechanism for heredity. [ 20 ]  Darwin believed in a mix of blending inheritance and the inheritance of acquired  traits  ( pangenesis ). Blending inheritance would lead to uniformity across populations in only a few generations and then would remove variation from a population on which natural selection could act. [ 21 ]  This led to Darwin adopting some  Lamarckian  ideas in later editions of  On the Origin of Species  and his later biological works. [ 22 ]  Darwin's primary approach to heredity was to outline how it appeared to work (noticing that traits that were not expressed explicitly in the parent at the time of reproduction could be inherited, that certain traits could be  sex-linked , etc.) rather than suggesting mechanisms. [ citation needed ]


Darwin's initial model of heredity was adopted by, and then heavily modified by, his cousin  Francis Galton , who laid the framework for the  biometric  school of heredity. [ 23 ]  Galton found no evidence to support the aspects of Darwin's pangenesis model, which relied on acquired traits. [ 24 ]


The  inheritance of acquired traits  was shown to have little basis in the 1880s when  August Weismann  cut the  tails  off many generations of  mice  and found that their offspring continued to develop tails. [ 25 ]


Scientists in  Antiquity  had a variety of ideas about heredity:  Theophrastus  proposed that male flowers caused female flowers to ripen; [ 26 ]   Hippocrates  speculated that "seeds" were produced by various body parts and transmitted to offspring at the time of conception; [ 27 ]  and  Aristotle  thought that male and female fluids mixed at conception. [ 28 ]   Aeschylus , in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sown within her". [ 29 ]


Ancient understandings of heredity transitioned to two debated doctrines in the 18th century. The Doctrine of Epigenesis and the Doctrine of Preformation were two distinct views of the understanding of heredity. The Doctrine of Epigenesis, originated by  Aristotle , claimed that an embryo continually develops. The modifications of the parent's traits are passed off to an embryo during its lifetime. The foundation of this doctrine was based on the theory of  inheritance of acquired traits . In direct opposition, the Doctrine of Preformation claimed that "like generates like" where the germ would evolve to yield offspring similar to the parents. The Preformationist view believed procreation was an act of revealing what had been created long before. However, this was disputed by the creation of the  cell theory  in the 19th century, where the fundamental unit of life is the cell, and not some preformed parts of an organism. Various hereditary mechanisms, including  blending inheritance  were also envisaged without being properly tested or quantified, and were later disputed. Nevertheless, people were able to develop domestic breeds of animals as well as crops through artificial selection. The inheritance of acquired traits also formed a part of early Lamarckian ideas on evolution. [ citation needed ]


During the 18th century, Dutch microscopist  Antonie van Leeuwenhoek  (1632–1723) discovered "animalcules" in the sperm of humans and other animals. [ 30 ]  Some scientists speculated they saw a "little man" ( homunculus ) inside each  sperm . These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. [ 31 ]  An opposing school of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception. [ 32 ]


An early research initiative emerged in 1878 when  Alpheus Hyatt  led an investigation to study the laws of heredity through compiling data on family phenotypes (nose size, ear shape, etc.) and expression of pathological conditions and abnormal characteristics, particularly with respect to the age of appearance. One of the projects aims was to tabulate data to better understand why certain traits are consistently expressed while others are highly irregular. [ 33 ]


The idea of particulate inheritance of genes can be attributed to the  Moravian [ 34 ]  monk  Gregor Mendel  who published his work on pea plants in 1865. However, his work was not widely known and was rediscovered in 1901. It was initially assumed that  Mendelian inheritance  only accounted for large (qualitative) differences, such as those seen by Mendel in his pea plants – and the idea of additive effect of (quantitative) genes was not realised until  R.A. Fisher 's (1918) paper, " The Correlation Between Relatives on the Supposition of Mendelian Inheritance " Mendel's overall contribution gave scientists a useful overview that traits were inheritable. His pea plant demonstration became the foundation of the study of Mendelian Traits. These traits can be traced on a single locus. [ 35 ]


In the 1930s, work by Fisher and others resulted in a combination of Mendelian and biometric schools into the  modern evolutionary synthesis . The modern synthesis bridged the gap between experimental geneticists and naturalists; and between both and palaeontologists, stating that: [ 36 ] [ 37 ]


The idea that  speciation  occurs after populations are reproductively isolated has been much debated. [ 38 ]  In plants, polyploidy must be included in any view of speciation. Formulations such as 'evolution consists primarily of changes in the  frequencies of alleles  between one generation and another' were proposed rather later. The traditional view is that developmental biology (' evo-devo ') played little part in the synthesis, but an account of  Gavin de Beer 's work by  Stephen Jay Gould  suggests he may be an exception. [ 39 ]


Almost all aspects of the synthesis have been challenged at times, with varying degrees of success. There is no doubt, however, that the synthesis was a great landmark in evolutionary biology. [ 40 ]  It cleared up many confusions, and was directly responsible for stimulating a great deal of research in the post- World War II  era.


Trofim Lysenko  however caused a backlash of what is now called  Lysenkoism  in the  Soviet Union  when he emphasised  Lamarckian  ideas on the  inheritance of acquired traits . This movement affected agricultural research and led to food shortages in the 1960s and seriously affected the USSR. [ 41 ]


There is growing evidence that there is transgenerational inheritance of epigenetic changes in humans [ 42 ]  and other animals. [ 43 ]


The description of a mode of biological inheritance consists of three main categories:


These three categories are part of every exact description of a mode of inheritance in the above order. In addition, more specifications may be added as follows:


Determination and description of a mode of inheritance is also achieved primarily through statistical analysis of pedigree data. In case the involved loci are known, methods of  molecular genetics  can also be employed.


An  allele  is said to be dominant if it is always expressed in the appearance of an organism (phenotype) provided that at least one copy of it is present. For example, in peas the allele for green pods,  G , is dominant to that for yellow pods,  g . Thus pea plants with the pair of alleles  either   GG  (homozygote)  or   Gg  (heterozygote) will have green pods. The allele for yellow pods is recessive. The effects of this allele are only seen when it is present in both chromosomes,  gg  (homozygote). This derives from  Zygosity , the degree to which both copies of a chromosome or gene have the same genetic sequence, in other words, the degree of similarity of the alleles in an organism.


Heterogamy  is a term applied to a variety of distinct phenomena in different scientific domains. Usually having to do with some kind of difference, "hetero", in reproduction, "gamy". See below for more specific senses.


In reproductive biology, heterogamy is the alternation of differently organized generations, applied to the alternation between  parthenogenetic  and a  sexual  generation. [ 1 ] [ 2 ]  This type of heterogamy occurs for example in some  aphids .


Alternately,  heterogamy  or  heterogamous  is often used as a synonym of  heterogametic , meaning the presence of two unlike chromosomes in a sex. [ 3 ] [ 4 ]  For example,  XY males  and  ZW  females are called the heterogamous sex.


In  cell biology , heterogamy is a synonym of  anisogamy , the condition of having differently sized male and female  gametes  produced by different sexes or mating types in a species.


In  botany , a plant is heterogamous when it carries at least two different types of flowers in regard to their reproductive structures, for example male and female flowers or bisexual and female flowers.  Stamens  and  carpels  are not regularly present in each flower or floret.


In  sociology , heterogamy refers to a  marriage  between two individuals that differ in a certain criterion, and is contrasted with  homogamy  for a marriage or union between partners that match according to that criterion. For example, ethnic heterogamy refers to marriages involving individuals of different ethnic groups. Age heterogamy refers to marriages involving partners of significantly different ages. Heterogamy and homogamy are also used to describe marriage or union between people of unlike and like sex (or gender) respectively.


Hypoxia inducible lipid droplet-associated  ( Hilpda , also known as  C7orf68  and  HIG-2 ) is a protein that in humans is encoded by the HILPDA gene.


HILPDA was originally discovered in a screen to identify new genes that are activated by low oxygen pressure (hypoxia) in human cervical cancer cells. [ 1 ]  The protein consists of 63 amino acids in humans and 64 amino acids in mice.


HILPDA is produced by numerous cells and tissues, including cancer cells, immune cells, fat cells, and liver cells. [ 2 ] [ 3 ] [ 4 ] [ 5 ]  Low oxygen pressure ( hypoxia ),  fatty acids , and beta-adrenergic agonists stimulate HILPDA expression.


Nearly all cells have the ability to store excess energy as fat in special structures in the cell called lipid droplets. The formation and breakdown of lipid droplets is controlled by various enzymes and lipid droplet-associated proteins. One of the lipid droplet-associated proteins is HILPDA. HILPDA acts as a regulatory signal that blocks the breakdown of the fat stores in cells when the external fat supply is high or the availability of oxygen is low. In cells, HILPDA is located in the  endoplasmic reticulum  and around  lipid droplets . [ 2 ] [ 4 ]  Gain and loss-of-function studies have shown that HILPDA promotes fat storage in cancer cells,  macrophages  and liver cells. [ 5 ] [ 3 ] [ 6 ] [ 7 ] [ 8 ]  This effect is at least partly achieved by suppressing triglyceride breakdown by inhibiting the enzyme  adipose triglyceride lipase . The binding of HILPDA to adipose triglyceride lipase occurs via the conserved N-terminal portion of HILPDA, which is similar to a region in the G0S2 protein. [ 9 ] [ 7 ]


The deficiency of HILPDA in mice that are prone to develop  atherosclerosis  led to a reduction in atherosclerotic plaques, suggesting that HILPDA may be a potential therapeutic target for atherosclerosis. [ 5 ]  In addition, HILPDA may be targeted for the treatment of  non-alcoholic fatty liver disease .


Horizontal gene transfer  ( HGT ) refers to the transfer of genes between distant branches on the  tree of life . In  evolution , it can scramble the information needed to reconstruct the phylogeny of  organisms , how they are related to one another.


HGT can also help scientists to reconstruct and date the tree of life, as a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.


HGT happens very infrequently – at the individual organism level, it is highly improbable for any such event to take place. However, on the grander scale of evolutionary history, these events occur with some regularity. On one hand, this forces biologists to abandon the use of individual genes as good markers for the history of life. On the other hand, this provides an almost unexploited large source of information about the past.


The three main early branches of the  tree of life  have been intensively studied by  microbiologists  because the first organisms were microorganisms. Microbiologists (led by  Carl Woese ) have introduced the term  domain  for the three main branches of this tree, where  domain  is a phylogenetic term similar in meaning to biological  kingdom . To reconstruct this tree of life, the gene sequence encoding the small subunit of  ribosomal   RNA  (SSU rRNA,  16s rRNA ) has proven useful, and the tree (as shown in the picture) relies heavily on information from this single gene.


These three domains of life represent the main evolutionary lineages of early cellular life and currently include  Bacteria ,  Archaea  (single-celled organisms superficially similar to bacteria), and  Eukarya . Eukarya includes only organisms having a well-defined nucleus, such as  fungi ,  protists , and all organisms in the plant and animals kingdoms (see figure).


The gene most commonly used for constructing phylogenetic relationships in  microorganisms  is the small subunit ribosomal RNA gene, as its sequences tend to be conserved among members with close phylogenetic distances, yet variable enough that differences can be measured.
 [ 1 ]
The  SSU rRNA  as a measure of evolutionary distances was pioneered by  Carl Woese  when formulating the first modern "tree of life", and his results led him to propose the  Archaea  as a third domain of  life . However, recently it has been argued that SSU rRNA genes can also be horizontally transferred. [ 2 ]   Although this may be rare, this possibility is forcing scrutiny of the validity of phylogenetic trees based on SSU rRNAs.


Recent discoveries of "rampant" HGT in microorganisms, and the detection of horizontal movement of even genes for the small subunit of ribosomal RNA, have forced biologists to question the accuracy of at least the early branches in the tree, and even question the validity of trees as useful models of how early evolution occurs. [ 3 ]  In fact, early evolution is considered to have occurred starting from a community of  progenotes , able to exchange large molecules when HGT was the standard. This lateral gene transfer occurred also beyond the  Darwinian threshold , after heredity or vertical gene transfer was established. [ 4 ] [ 5 ]
"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." [ 6 ]  HGT is thus a potential  confounding factor  in inferring  phylogenetic trees  from the  sequence  of one  gene . For example, if two distantly related bacteria have exchanged a gene, a  phylogenetic tree  including those species will show them to be closely related even though most other genes have diverged substantially. For this reason it is important to use other information to infer phylogenies, such as the presence or absence of genes, or, more commonly, to include as wide a range of genes for analysis as possible. [ 6 ]


Earlier HGTs are thought to have happened. The  first universal common ancestor  (FUCA), earliest ancestor of the  last common ancestor to all life  (LUCA), is thought to have had other descendants that had their own lineages. [ 7 ] [ 8 ]  These now-extinct sister lineages of LUCA descending from FUCA are thought to have horizontally transferred some of their genes into the genome of early descendants of LUCA. [ 8 ]


In his article  Uprooting the Tree of Life , W.  Ford Doolittle  discusses the  Last Universal Common Ancestor  – the root of the Tree of Life – and the problems with that concept posed by HGT. [ 9 ]  He describes the microorganism  Archaeoglobus fulgidus  as an anomaly with respect to a  phylogenetic  tree based upon the code for the  enzyme   HMGCoA reductase  – the organism is definitely an archaean, with all the cell lipids and transcription machinery expected of an archaean, but its HMGCoA genes are of bacterial origin. In the article, Doolittle says that while it is now widely accepted that  mitochondria  in eukaryotes derived from alpha-proteobacterial cells and that  chloroplasts  came from ingested  cyanobacteria , [ 9 ]


".. it is no longer safe to assume that those were the only lateral gene transfers that occurred after the first eukaryotes arose. Only in later, multicellular eukaryotes do we know of definite restrictions on horizontal gene exchange, such as the advent of separated (and protected)  germ cells ...


If there had never been any lateral gene transfer, all these individual gene trees would have the same topology (the same branching order), and the ancestral genes at the root of each tree would have all been present in the last universal common ancestor, a single ancient cell. But extensive transfer means that neither is the case: gene trees will differ (although many will have regions of similar topology)  and  there would never have been a single cell that could be called the last universal common ancestor..." [ 9 ]


Doolittle suggested that the universal common ancestor cannot have been one particular organism, but must have been a loose, diverse conglomeration of primitive cells that evolved together. These early cells, each with relatively few genes, differed in many ways, and swapped their  genes  freely. Eventually, from these eclectic cells came the three domains of life as we know them today:  bacteria ,  archaea  and  eukaryote . These domains are now recognizably distinct because much of the gene transfer that still occurs is within these domains, rather than between them. Biologist  Peter Gogarten  reinforced these arguments, and suggested that the metaphor of a tree does not fit the data from recent genome research, and that biologists should now instead use "the metaphor of a mosaic to describe the different histories combined in individual genomes and use [the] metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes." [ 10 ]


Despite the uncertainties in reconstructing phylogenies back to the beginnings of life, progress is being made in reconstructing the tree of life in the face of uncertainties raised by HGT. The uncertainty of any inferred phylogenetic tree based on a single gene can be resolved by using several common genes or even evidence from whole genomes. [ 12 ]  One such approach, sometimes called 'multi-locus typing', has been used to deduce phylogenic trees for organisms that exchange genes, such as meningitis bacteria. [ 13 ]


Jonathan Eisen  and  Claire Fraser  have pointed out that:


"In building the tree of life, analysis of whole genomes has begun to supplement, and in some cases to improve upon, studies previously done with one or a few genes. For example, recent studies of complete bacterial genomes have suggested that the  hyperthermophilic  species are not deeply branching; if this is true, it casts doubt on the idea that the first forms of life were thermophiles. Analysis of the genome of the eukaryotic parasite  Encephalitozoon cuniculi  supports suggestions that the group  Microsporidia  are not deep branching protists but are in fact members of the fungal kingdom. Genome analysis can even help resolve relationships within species, such as by providing new genetic markers for population genetics studies in the bacteria causing anthrax or tuberculosis. In all these studies, it is the additional data provided by a complete genome sequence that allows one to separate the phylogenetic signal from the noise. This is not to say the tree of life is now resolved – we only have sampled a smattering of genomes, and many groups are not yet touched" [ 14 ]


These approaches are enabling estimates of the relative frequency of HGT; the relatively low values that have been observed suggests that the 'tree' is still a valid metaphor for evolution – but the tree is adorned with 'cobwebs' of horizontally transferred genes. This is the main conclusion of a 2005 study of more than 40 complete microbial genomic sequences by Fan Ge, Li-San Wang, and  Junhyong Kim . They estimate the frequency of HGT events at about 2% of core genes per genome. [ 15 ]  Similar whole genome approaches to assessing evolution are also enabling progress in identifying very early events in the tree of life, such as a proposal that eukaryotes arose by fusion of two complete but very diverse prokaryote genomes: one from a bacterium and one from an archaeal cell. [ 3 ]


Such a fusion of organisms  hypothesis  for the origin of complex nucleated cells has been put forward by  Lynn Margulis  using quite different reasoning about  symbiosis  between a bacterium and an archaen arising in an ancient consortium of microbes. [ 16 ]


While HGT is often seen as a challenge for the reconstruction of the tree of life, an alternative view is that oppositely it provides additional valuable information for its reconstruction.


First, for the recipient organism, HGT is a  DNA mutation  like others, and as such, it can be modeled and used in tree reconstruction and rooting. [ 17 ]


Second, it is necessary that the recipient of a gene acquisition by HGT lives at the same time, or at an ulterior time, as the donor. [ 18 ]  In consequence there is an information on the timing of diversification in HGT. [ 19 ]  This is all the more remarkable since the principal usual source for dating in the living world, the fossil record, is absent precisely where HGT is abundant, in the microbial world.


Third, it provides information about the extinct biodiversity, because transfers are likely from extinct species. [ 20 ]


Human germline engineering  (HGE) is the process by which the  genome  of an individual is modified in such a way that the change is heritable. This is achieved by altering the genes of the  germ cells , which mature into eggs and sperm. For safety, ethical, and social reasons, the scientific community and the public have concluded that germline editing for reproduction is inappropriate. [ 1 ] [ 2 ]  HGE is prohibited by law in more than 70 countries [ 3 ]  and by a binding international treaty of the  Council of Europe .


In November 2015, a group of Chinese researchers used  CRISPR / Cas9  to edit single-celled, non-viable embryos to assess its effectiveness. This attempt was unsuccessful; only a small fraction of the embryos successfully incorporated the genetic material and many of the embryos contained a large number of random mutations. The non-viable embryos that were used contained an extra set of chromosomes, which may have been problematic. In 2016, a similar study was performed in China on non-viable embryos with extra sets of chromosomes. This study showed similar results to the first; except that no embryos adopted the desired gene.


In November 2018, researcher  He Jiankui  created the first human babies from genetically edited embryos, known by their pseudonyms,  Lulu and Nana . In May 2019, lawyers in China reported that regulations had been drafted that anyone manipulating the human genome would be held responsible for any related adverse consequences. [ 4 ]


The CRISPR-Cas9 system consists of an enzyme called  Cas9  and a special piece of  guide RNA  (gRNA). Cas9 acts as a pair of ‘molecular scissors’ that can cut the DNA at a specific location in the genome so that genes can be added or removed. The guide RNA has complementary bases to those at the target location, so it binds only there. Once bound Cas9 makes a cut across both DNA strands allowing base pairs to inserted/removed. Afterwards, the cell recognizes that the DNA is damaged and tries to repair it. [ 5 ]


Although CRISPR/Cas9 can be used in humans, [ 6 ]  it is more commonly used in other species or cell culture systems, including in experiments to study genes potentially involved in human diseases.


Genetic engineering is in widespread use, particularly in agriculture. Human germline engineering has two potential applications: prevent genetic disorders from passing to descendants, and to modify traits such as height that are not disease related. For example, the  Berlin Patient  has a genetic mutation in the  CCR5  gene that suppresses the expression of CCR5. This confers  innate resistance to HIV . Modifying human embryos to give the CCR5 Δ32 allele protects them from the disease.


An other use would be to cure genetic disorders. In the first study published regarding human germline engineering, the researchers attempted to edit the  HBB  gene which codes for the human  β-globin  protein.  HBB  mutations produce  β-thalassaemia , which can be fatal. [ 7 ]  Genome editing in patients who have these  HBB  mutations would leave copies of the unmutated gene, effectively curing the disease. If the germline could be edited, this normal copy of the  HBB  genes could be passed on to future generations.


Eugenic  modifications to humans yield " designer babies ", with deliberately-selected traits, possibly extending to its entire genome. [ 8 ]  HGE potentially allows for enhancement of these traits. [ 8 ]  The concept has produced strong objections, particularly among bioethicists. [ 9 ]


In a 2019 animal study with Liang Guang small spotted pigs, precise editing of the  myostatin  signal peptide yielded increased muscle mass. Myostatin is a negative regulator of muscle growth, so by mutating the gene's signal peptide regions could be promoted. One study mutated myostatin genes in 955 embryos at several locations with CRISPR/cas9 and implanted them into five surrogates, resulting in 16 piglets. Only specific mutations to the myostatin signal peptide increased muscle mass, mainly due to an increase in muscle fibers. [ 10 ]  A similar mice study knoced out the myostatin gene, which also increased their muscle mass. [ 11 ]  This showed that muscle mass could be increased with germline editing, which is likely applicable to humans because the myostatin gene regulates human muscle growth. [ 12 ]


HGE is widely debated, and more than 40 countries formally outlaw it. [ 13 ]  No legislation explicitly prohibits germline engineering in the United States. The  Consolidated Appropriation Act of 2016  bans the use of  US FDA  funds to engage in human germline modification research. [ 14 ]  In April 2015, a research team published an unsuccessful experiment in which they used CRISPR to edit a gene that is associated with blood disease in non-living human embryos.


researchers using CRISPR/Cas9 have run into issues when it comes to mammals due to their complex  diploid cells . Studies in microorganisms have examined loss of function genetic screening. Some studies used mice as a subject. Because RNA processes differ between bacteria and mammalian cells, researchers have had difficulties coding for mRNA's translated data without RNA interference. Studies have successfully used a Cas9 nuclease with a single guide RNA to allow for larger knockout regions in mice. [ 15 ]


The lack of international regulation led researchers to attempt to create an international framework of ethical guidelines. The framework lacks the requisite international treaties for enforcement. At the first International Summit on Human Gene Editing in December 2015 researchers issued the first international guidelines. [ 16 ]  These guidelines allowed pre-clinical research into gene editing in human cells as long as the embryos were not used to implant pregnancy. Genetic alteration of somatic cells for therapeutic proposes was considered ethically acceptable in part because somatic cells cannot pass modifications to subsequent generations. However the lack of consensus and the risks of inaccurate editing led the conference to call for restraint on germline modifications.


On March 13, 2019 researchers  Eric Lander ,  Françoise Baylis ,  Feng Zhang ,  Emmanuelle Charpentier , Paul Bergfrom and others called for a framework that did not foreclose any outcome, but included a voluntary pledge and a call for a coordinating body to monitor the HGE moratorium with an attempt to reach social consensus before furthering research. [ 17 ]   The World Health Organization  announced on December 18, 2018 plans to convene an intentional committee on the topic. [ 18 ]


The  He Jiankui genome editing incident  is a scientific and  bioethical  controversy concerning the use of  genome editing  following its first use on humans by Chinese scientist  He Jiankui , who edited the genomes of  human embryos  in 2018. [ 19 ] [ 20 ]  He became widely known on 26 November 2018 [ 21 ]  after he announced that he had created the first human genetically edited babies. He was listed in  Time  magazine's  100 most influential people  of 2019. [ 22 ]  The affair led to ethical and legal controversies, resulting in the indictment of He and two of his collaborators, Zhang Renli and Qin Jinzhou. He eventually received widespread international condemnation.


He Jiankui, working at the  Southern University of Science and Technology  (SUSTech) in  Shenzhen , China, started a project to help people with  HIV-related fertility problems , specifically involving  HIV-positive  fathers and HIV-negative mothers. The subjects were offered standard  in vitro  fertilisation  services and in addition, use of  CRISPR gene editing  ( CRISPR/Cas9 ), a technology for modifying  DNA . The embryos' genomes were edited to remove the  CCR5  gene in an attempt to confer  genetic resistance to HIV . [ 23 ]  The clinical project was conducted secretly until 25 November 2018, when  MIT Technology Review  broke the story of the human experiment based on information from the Chinese clinical trials registry. Compelled by the situation, he immediately announced the birth of genome-edited babies in a series of five  YouTube  videos the same day. [ 24 ] [ 25 ]  The first babies, known by their pseudonyms Lulu ( Chinese :  露露 ) and Nana ( 娜娜 ), are twin girls born in October 2018, and the second birth or the third baby born was in 2019, [ 26 ] [ 27 ]  named Amy. [ 28 ]  He reported that the babies were born healthy. [ 29 ]


His actions received widespread criticism, [ 30 ] [ 31 ]  and included concern for the girls' well-being. [ 23 ] [ 32 ] [ 33 ]  After his presentation on the research at the Second International Summit on Human Genome Editing at the  University of Hong Kong  on 28 November 2018, Chinese authorities suspended his research activities the following day. [ 34 ]  On 30 December 2019, a Chinese district court found He Jiankui guilty of illegal practice of medicine, sentencing him to three years in prison with a fine of 3 million yuan. [ 35 ] [ 36 ]  Zhang Renli and Qin Jinzhou received an 18-month prison sentence and a 500,000-yuan fine, and were banned from working in assisted reproductive technology for life. [ 37 ]


As early in the history of biotechnology as 1990, there have been researchers opposed to attempts to modify the human  germline  using these new tools, [ 50 ]  and such concerns have continued as technology progressed. [ 51 ] [ 52 ]  In March 2015, with the advent of new techniques like  CRISPR , researchers urged a worldwide moratorium on clinical use of gene editing technologies to edit the human genome in a way that can be inherited. [ 53 ]   In April 2015, researchers reported results of basic research to edit the DNA of non-viable human embryos using CRISPR, creating controversy. [ 54 ]


A committee of the American  National Academy of Sciences  and  National Academy of Medicine  gave support to human genome editing in 2017 [ 55 ] [ 56 ]  once answers have been found to safety and efficiency problems "but only for serious conditions under stringent oversight." [ 57 ]  The  American Medical Association 's Council on Ethical and Judicial Affairs stated that "genetic interventions to enhance traits should be considered permissible only in severely restricted situations: (1) clear and meaningful benefits to the fetus or child; (2) no trade-off with other characteristics or traits; and (3) equal access to the genetic technology, irrespective of income or other socioeconomic characteristics." [ 58 ]


Several religious positions have been published with regards to human germline engineering. According to them, many see germline modification as being more moral than the alternative, which would be either discarding of the embryo, or birth of a diseased human. The main conditions when it comes to whether or not it is morally and ethically acceptable lie within the intent of the modification, and the conditions in which the engineering is done. [ 59 ]


Ethical claims about germline engineering include beliefs that every  fetus  has a right to remain genetically unmodified, that parents hold the right to genetically modify their offspring, and that every child has the right to be born free of preventable diseases. [ 60 ] [ 61 ] [ 62 ]  For parents, genetic engineering could be seen as another child enhancement technique to add to diet, exercise, education, training, cosmetics, and plastic surgery. [ 63 ] [ 64 ]  Another theorist claims that moral concerns limit but do not prohibit germline engineering. [ 65 ]


One issue related to human genome editing relates to the impact of the technology on future individuals whose genes are modified without their consent. Clinical ethics accepts the idea that parents are, almost always, the most appropriate surrogate medical decision makers for their children until the children develop their own autonomy and decision-making capacity. This is based on the assumption that, except under rare circumstances, parents have the most to lose or gain from a decision and will ultimately make decisions that reflects the future values and beliefs of their children. According to this assumption, it could be assumed that parents are the most appropriate decision makers for their future children as well. However, there are anecdotal reports of children and adults who disagree with the medical decisions made by a parent during pregnancy or early childhood, such as when death was a possible outcome. There are also published patient stories by individuals who feel that they would not wish to change or remove their own medical condition if given the choice and individuals who disagree with medical decisions made by their parents during childhood. [ 66 ]


Other researchers and philosophers have noted that the issue of the lack of prior consent applies as well to individuals born via traditional sexual reproduction. [ 67 ] [ 68 ]  Philosopher  David Pearce  further argues that “old-fashioned sexual reproduction is itself an untested genetic experiment”, often compromising a child's wellbeing and pro-social capacities even if the child grows in a healthy environment. According to Pearce, “the question of [human germline engineering] comes down to an analysis of risk-reward ratios – and our basic ethical values, themselves shaped by our evolutionary past.” [ 69 ]  Bioethicist  Julian Savulescu  in turn proposes the principle of  procreative beneficence , according to which “couples (or single reproducers) should select the child, of the possible children they could have, who is expected to have the best life, or at least as good a life as the others, based on the relevant, available information”. [ 70 ]  Some ethicists argue that the principle of procreative beneficence would justify or even require  genetically enhancing  one's children. [ 71 ] [ 72 ]


A relevant issue concerns “off target effects”, large genomes may contain identical or homologous DNA sequences, and the enzyme complex CRISPR/Cas9 may unintentionally cleave these DNA sequences causing mutations that may lead to cell death. The mutations can cause important genes to be turned on or off, such as genetic anti-cancer mechanisms, that could speed up disease exasperation. [ 66 ] [ 73 ] [ 74 ] [ 75 ] [ 76 ]


The other ethical concern is the potential for “designer babies”, or the creation of humans with "perfect", or "desirable" traits. There is a debate as to if this is morally acceptable as well. Such debate ranges from the ethical obligation to use safe and efficient technology to prevent disease to seeing some actual benefit in genetic disabilities.


There are concerns that the introduction of desirable traits in a certain part of the population (instead of the entire population) could cause economic inequalities (“positional” good) [ clarification needed ] . [ 77 ]  However, this is not the case if a same desirable trait would be  introduced over the entire population  (similar to vaccines). [ citation needed ]


Another ethical concern pertains to potential unequal distribution of benefits, even in the case of genome editing being inexpensive. For example, corporations may be able to take unfair advantage of patent law or other ways of restricting access to genome editing and thereby may increase the inequalities. There are already disputes in the courts where CRISPR-Cas9 patents and access issues are being negotiated. [ 78 ]


There remains debate on if the permissibility of human germline engineering for reproduction is dependent on the use, being either a therapeutic or non-therapeutic application. In a survey by the UK's Royal Society, 76% of participants in the UK supported therapeutic human germline engineering to prevent or correct disease, however for non-therapeutic edits such as enhancing intelligence or altering eye or hair color in embryos, there was only 40% and 31% support, respectively. [ 1 ]  There was a similar result in a study at the  University of Bogota , Colombia, where students as well as professors generally agreed that therapeutic genome editing is acceptable, while non-therapeutic genome editing is not. [ 2 ]


There is also debate on if there can be a defined distinction between therapeutic and non-therapeutic germline editing. An example would be if two embryos are predicted to grow up to be very short in height. Boy 1 will be short because of a mutation in his Human Growth Hormone gene, while boy 2 will be short because his parents are very short. Editing the embryo of boy 1 to make him of average height would be a therapeutic germline edit, while editing the embryo of boy 2 to be of average height would be a non-therapeutic germline edit. In both cases with no editing of the boys' genomes they would both grow up to be very short, which would decrease their wellbeing in life. Likewise editing both of the boys' genomes would allow them to grow up to be of average height. In this scenario, editing for the same phenotype for being of average height falls under both therapeutic and non-therapeutic germline engineering. [ 79 ]


There is distinction in some country policies, including but not limited to official regulation and legislation, between human germline engineering for reproductive use and for laboratory research. As of October 2020, there are 96 countries that have policies involving the use of germline engineering in human cells. [ 3 ]


Reproductive use of human germline engineering involves implanting the edited embryo to be born. 70 countries currently explicitly prohibit the use of human germline engineering for use in reproduction, while 5 countries prohibit it for reproduction with exceptions. No countries permit the use of human germline engineering for reproduction. [ 3 ]


Countries that explicitly prohibit any use of human germline engineering for reproduction are:  Albania ,  Argentina ,  Australia ,  Austria ,  Bahrain ,  Belarus ,  Benin ,  Bosnia and Herzegovina ,  Brazil ,  Bulgaria ,  Burundi ,  Canada ,  Chile ,  China ,  Congo ,  Costa Rica ,  Croatia ,  Cyprus ,  Czech Republic ,  Denmark ,  Estonia ,  Finland ,  France ,  Georgia ,  Germany ,  Greece ,  Hungary ,  Iceland ,  India ,  Iran ,  Ireland ,  Israel ,  Japan ,  Kenya ,  Latvia ,  Lebanon ,  Lithuania ,  Malaysia ,  Malta ,  Mexico ,  Moldova ,  Montenegro ,  Netherlands ,  New Zealand ,  Nigeria ,  North Macedonia ,  Norway ,  Oman ,  Pakistan ,  Poland ,  Portugal ,  Qatar ,  Romania ,  Russia ,  San Marino ,  Saudi Arabia ,  Serbia ,  Slovakia ,  Slovenia ,  South Korea ,  Spain ,  Sweden ,  Switzerland ,  Thailand ,  Tunisia ,  Turkey , the  United Kingdom , the  United States ,  Uruguay , and the  Vatican [ 3 ]


Countries that explicitly prohibit (with exceptions) the use of human germline engineering for reproduction are:  Belgium ,  Colombia ,  Italy ,  Panama , and the  United Arab Emirates [ 3 ]


Laboratory research use involves human germline engineering restricted to  in vitro  use, where edited cells will not be implanted to be born. 19 countries currently explicitly prohibit any use of human germline engineering for  in vitro  use, while 4 prohibit it with exceptions, and 11 permit it. [ 3 ]


Countries that explicitly prohibit any use of germline engineering for  in vitro  use are:  Albania ,  Austria ,  Bahrain ,  Belarus ,  Brazil ,  Canada ,  Costa Rica ,  Croatia ,  Germany ,  Greece ,  Lebanon ,  Malaysia ,  Malta ,  Pakistan ,  Saudi Arabia ,  Sweden ,  Switzerland ,  Uruguay , and the  Vatican [ 3 ]


Countries that explicitly prohibit (with exceptions) the use of germline engineering for  in vitro  use are:  Colombia ,  Finland ,  Italy , and  Panama [ 3 ]


Countries that explicitly permit the use of germline engineering for  in vitro  use are:  Burundi ,  China ,  Congo ,  India ,  Iran ,  Ireland ,  Japan ,  Norway ,  Thailand , the  United Kingdom , and the  United States [ 3 ]


Hybrid speciation  is a form of  speciation  where  hybridization  between two different  species  leads to a new species, reproductively isolated from the parent species. Previously, reproductive isolation between two species and their parents was thought to be particularly difficult to achieve, and thus hybrid species were thought to be very rare. With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a somewhat common phenomenon, particularly in plants. [ 1 ] [ 2 ]  In  botanical nomenclature , a hybrid species is also called a  nothospecies . [ 3 ]  Hybrid species are by their nature  polyphyletic . [ 4 ]


A hybrid may occasionally be better fitted to the local environment than the parental lineage, and as such,  natural selection  may favor these individuals. If  reproductive isolation  is subsequently achieved, a separate species may arise. Reproductive isolation may be genetic,  ecological , [ 5 ]  behavioral, spatial, or a combination of these.


If reproductive isolation fails to establish, the hybrid population may merge with either or both parent species. This will lead to an influx of foreign genes into the parent population, a situation called an  introgression . Introgression is a source of genetic variation, and can in itself facilitate speciation. There is evidence that introgression is a ubiquitous phenomenon in plants and animals, [ 6 ] [ 7 ]  even in humans, [ 8 ]  where genetic material from  Neanderthals  and  Denisovans  is responsible for much of the  immune genes  in non-African populations. [ 9 ] [ 10 ]


For a hybrid form to persist, it must be able to exploit the available resources  better  than either parent species, which, in most cases, it will have to compete with.  For example : while  grizzly bears  and  polar bears  may be able to mate and produce offspring, a  grizzly–polar bear hybrid  is apparently less- suited in either of the parents' ecological niches than the original parent species themselves. So: although the hybrid is fertile  (i.e. capable of reproduction and thus theoretically could propagate) , this poor adaptation would be unlikely to support the establishment of a permanent population. [ 11 ]


Likewise,  lions  and  tigers  have historically overlapped in a portion of their range and can theoretically produce wild hybrids:  ligers , which are a cross between a male lion and female tiger, and  tigons , which are a cross between a male tiger and a female lion; however, tigers and lions have thus far only hybridized in captivity. [ 12 ]  In both ligers and tigons, the females are fertile and the males are sterile. [ 12 ]  One of these hybrids (the tigon) carries growth-inhibitor genes from both parents and thus is smaller than either parent species [ 12 ]  and might in the wild come into competition with smaller carnivores, e.g. the  leopard . The other hybrid, the liger, ends up larger than either of its parents: about a thousand pounds (450 kilograms) fully grown. [ 12 ]   No tiger-lion hybrids are known from the wild, and the ranges of the two species no longer overlap (tigers are not found in Africa, and while there was formerly overlap in the distribution of the two species in Asia, both have been extirpated from much of their respective historic ranges, and the  Asiatic lion  is now restricted to the  Gir Forest National Park , where tigers are mostly absent). [ 13 ]


Some situations may favor hybrid population. One example is rapid turnover of available environment types, like the historical fluctuation of water level in  Lake Malawi , a situation that generally favors speciation. [ 14 ]   A similar situation can be found where closely related species occupy a  chain of islands . This will allow any present hybrid population to move into new, unoccupied habitats, avoiding direct competition with parent species and giving a hybrid population time and space to establish. [ 15 ] [ 5 ]  Genetics, too, can occasionally favor hybrids. In the  Amboseli National Park  in Kenya,  yellow baboons  and  anubis baboons  regularly interbreed. The hybrid males reach maturity earlier than their pure-bred cousins, setting up a situation where the hybrid population may over time replace one or both of the parent species in the area. [ 16 ]


Genetics are more variable and malleable in plants than in animals, probably reflecting the higher activity level in animals. [ citation needed ]  Hybrids' genetics will necessarily be less stable than those of species evolving through isolation, which explains why hybrid species appear more common in plants than in animals. [ citation needed ]  Many agricultural crops are hybrids with double or even triple chromosome sets. Having multiple sets of chromosomes is called  polyploidy . Polyploidy is usually fatal in animals where extra chromosome sets upset  fetal development , but is often found in plants. [ 17 ]  A form of hybrid speciation that is relatively common in plants occurs when an infertile hybrid becomes fertile after doubling of the  chromosome  number.


Hybridization without change in chromosome number is called  homoploid  hybrid speciation. [ 1 ]  This is the situation found in most animal hybrids. For a hybrid to be viable, the chromosomes of the two organisms will have to be very similar, i.e., the parent species must be closely related, or else the difference in chromosome arrangement will make  mitosis  problematic. With polyploid hybridization, this constraint is less acute. [ citation needed ]


Super-numerary chromosome numbers can be unstable, which can lead to instability in the genetics of the hybrid. The European  edible frog  appears to be a species, but is actually a triploid semi-permanent hybrid between  pool frogs  and  marsh frogs . [ 18 ]  In most populations, the edible frog population is dependent on the presence of at least one of the parent species to be maintained, as each individual need two gene sets from one parent species and one from the other. Also, the male sex determination gene in the hybrids is only found in the genome of the pool frog, further undermining stability. [ 19 ]  Such instability can also lead to rapid reduction of chromosome numbers, creating reproductive barriers and thus allowing speciation. [ citation needed ]


Hybrid speciation in animals is primarily  homoploid . While thought not to be very common, a few animal species are the result of hybridization, mostly  insects  such as  tephritid  fruitflies that inhabit   Lonicera  plants [ 20 ]  and  Heliconius  butterflies, [ 21 ] [ 22 ]  as well as some  fish , [ 15 ]  one marine mammal, the  clymene dolphin , [ 23 ]  a few birds. [ 24 ]  and certain  Bufotes  toads. [ 25 ]


One bird is an  unnamed form  of  Darwin's finch  from the Galapagos island of Daphne Major, described in 2017 and likely founded in the early 1980s by a male  Española cactus finch  from Española Island and a female  medium ground finch  from Daphne Major. [ 26 ]  Another is the  great skua , which has a surprising genetic similarity to the physically very different  pomarine skua ; most ornithologists [ who? ]  now assume it to be a hybrid between the pomarine skua and one of the southern skuas. [ 27 ]  The  golden-crowned manakin  was formed 180,000 years ago by hybridization between  snow-capped  and  opal-crowned manakins . [ 28 ]


A 2021 DNA study determined that the  Columbian mammoth  of North America was a hybrid species between  woolly mammoths  and another lineage, discovered in  Krestovka , descended from  steppe mammoths . The two populations had diverged from the ancestral steppe mammoth earlier in the Pleistocene. Analysis of genetic material recovered from their remains showed that half of the ancestry of the Columbian mammoths originated from the Krestovka lineage and the other half from woolly mammoths, with the hybridization happening more than 420,000 years ago, during the  Middle Pleistocene . This is the first evidence of hybrid speciation obtained from prehistoric DNA. [ 29 ] [ 30 ]


Rapidly diverging species can sometimes form multiple hybrid species, giving rise to a  species complex , like several physically divergent but closely related genera of  cichlid  fishes in  Lake Malawi . [ 14 ]  The duck genus  Anas  (mallards and teals) has a very recent divergence history, many of the species are inter-fertile, and quite a few of them are thought to be hybrids. [ 31 ] [ 32 ]  While hybrid species generally appear rare in mammals, [ 15 ]  the American  red wolf  appears to be a hybrid species of the  Canis  species complex, between  gray wolf  and  coyote . [ 33 ]  Hybridization may have led to the species-rich  Heliconius   butterflies , [ 34 ]  though this conclusion has been criticized. [ 35 ]


Hybrid speciation occurs when two divergent lineages (e.g., species) with independent evolutionary histories come into contact and interbreed. Hybridization can result in speciation when hybrid populations become isolated from the parental lineages, leading to divergence from the parent populations.


In cases where the first-generation hybrids are viable but infertile, fertility can be restored by whole genome duplication (polyploidy), resulting in reproductive isolation and polyploid speciation.  Polyploid  speciation is commonly observed in plants because their nature allows them to support genome duplications. Polyploids are considered a new species because the occurrence of a whole genome duplication imposes post-zygotic barriers, which enable reproductive isolation between parent populations and hybrid offspring. Polyploids can arise through single step mutations or through triploid bridges. In single step mutations,  allopolyploids  are the result of unreduced gametes in crosses between divergent lineages. The F1 hybrids produced from these mutations are infertile due to failure of bivalent pairing of chromosomes and segregation into gametes which leads to the production of unreduced gametes by single division meiosis, which results in unreduced, diploid (2N) gametes. Triploid bridges occur in low frequencies in populations and are produced when unreduced gametes combine with haploid (1N) gametes to produce a triploid offspring that can function as a bridge to the formation of tetraploids. [ 36 ]  In both paths, the polyploid hybrids are reproductively isolated from the parents due to the difference in ploidy. Polyploids manage to remain in populations because they generally experience less  inbreeding depression  and have higher self-fertility. [ 36 ] [ 37 ]


Homoploid  (diploid) speciation is another result of hybridization, but the hybrids remain diploid. It is less common in plants than polyploid speciation because, without genome duplication, genetic isolation must develop through other mechanisms. Studies on diploid hybrid populations of  Louisiana irises  show how these populations occur in Hybrid zones created by disturbances and  ecotones  (Anderson 1949). Novel niches can allow for the persistence of hybrid lineages. For example, established sunflower ( Helianthus ) hybrid species show  transgressive  phenotypes and display genomic divergence separating them from the parent species. [ 38 ]


Hybrizyme  is a term coined to indicate novel or normally rare  gene  variants (or  alleles ) that are associated with  hybrid zones , geographic areas where two related taxa (e.g.  species  or  subspecies ) meet, mate, and produce hybrid offspring. [ 1 ]  The hybrizyme phenomenon is widespread and these alleles occur commonly, if not in all hybrid zones. [ 2 ]  Initially considered to be caused by elevated rates of mutation in hybrids, the most probable hypothesis infers that they are the result of  negative (purifying) selection . Namely, in the center of the hybrid zone, negative selection purges alleles against hybrid disadvantage (e.g.  hybrid inviability  or infertility). Stated differently, any allele that will decrease reproductive isolation is favored and any linked alleles (genetic markers) also increase their frequency by  genetic hitchhiking . If the linked alleles used to be rare variants in the parental taxa, they will become more common in the area where the hybrids are formed. [ 3 ]


Originally hybrizymes were defined as "unexpected allelic electromorphs associated with hybrid zones", a formal term proposed by renowned conservation geneticist and biogeographer David S. Woodruff in 1988. [ 1 ]  By suggesting a new definition for a phenomenon that had been previously widely observed Woodruff's interpretation bypasses the etiological connotation of alternative terms and avoids inappropriate context. Namely, previous studies referred to  allozymes  that were observed at high frequency in hybrid zones, but are absent or rare in parental taxa as "the rare allele phenomenon". [ 2 ] [ 4 ] [ 5 ]  These alleles can have increased frequencies up to a point of the allele becoming the most common one in the hybrid zone, rendering the term "the rare allele phenomenon" deceptive. Despite this, these two terms have been used interchangeably in literature.


Hybrid populations display the hybrizyme phenomenon by having increased frequencies of certain alleles that are rare or non-existent outside of the hybrid zone. The hybrizyme phenomenon is widespread in hybrid zones of species of snails, crickets, lizards, salamanders, rodents, fish and birds. [ 1 ]  Intriguingly, the increased frequency of some of these alleles can have a pronounced effect making them 3-20 times more common in hybrids than in non-hybrid populations. [ 6 ]


Early studies focused on detecting electromorphs for loci that code regulatory and non-regulatory enzymes from several functional classes using allozyme electrophoresis and usually involved loci that were polymorphic in parental populations. The phenomenon has also been detected in a broad range of genetic markers such as intron haplotypes, [ 3 ]  microsatellites, [ 7 ]  ribosomal DNA spacer variants, [ 8 ]  and anonymous SNPs. [ 9 ]


Multiple hypotheses have been proposed to explain the mutational (molecular) origin of hybrizymes. They include gene conversion, [ 10 ]  transposable element activity, [ 11 ]  post-translational modification, mutations. [ 12 ] [ 13 ] [ 14 ] [ 1 ]  and intragenic recombination. Some of these hypotheses are rejected by research in the past couple of years, but there is an unambiguous explanation for the mutational origin of hybrizymes. The two hypotheses most often discussed are increased mutation rates and intragenic recombination.


Under the mutational hypothesis, hybrizymes likely arise due to simple point mutations. Sequencing data have indicated this and imply low likelihood that hybrizymes arise as a result of transposition or recombination. Research on  pocket gophers  and Japanese freshwater crabs confirms that the phenomenon is possibly caused by simple  nucleotide substitutions . [ 13 ] [ 12 ] [ 15 ] [ 16 ]  However, the hypothesis has several weaknesses. It does not explain why normally rare alleles are restricted to a hybrid zone, why polymorphic loci are affected more or offers a mechanism that explains the high frequency of even the rarest variants. [ 1 ]


Intragenic recombination, under certain circumstances, might create new allelic variants at rates higher than the ones associated with regular mutational processes. Under this hypothesis the variant allele would be a mosaic of the parental alleles. The likelihood of this hypothesis was disputed, through sequencing studies. [ 14 ] [ 13 ] [ 17 ]  Although there is yet no specific explanation for hybrizymes, it is not excluded that hybrizymes are generated by the combined effect of recombination and mutation events, with any recombination trace concealed by succeeding mutations. However, research on  Acer  species implies that high recombination rates are possible due to acceleration of genetic variation after hybridization. [ 8 ]  Furthermore, results are found that indicate that recurrent mutation is unlikely and that support the hypothesis of recombination. [ 18 ]


Several hypotheses have been proposed to account the high frequency of hybrizymes in hybrid zones such as genetic drift, elevated rates of nucleotide substitutions. [ 1 ] [ 2 ] [ 19 ] [ 20 ]  or positive selection on alleles which are mildly deleterious in parental taxa. Still, some faced a certain degree of unpredictability; specifically under the mutational hypothesis the overall substitution rates are elevated and many variants are expected versus having only one allele reaching high frequency and, at the same time, positive selection on deleterious alleles seems ambiguous.


Selection does not need to be directed to the hybrizyme, but to other genes with which the hybrizyme is linked, placing genetic hitchhiking in perspective. In other words, hybrid zones are maintained primarily by balance between  gene flow  and hybrid inferiority. In the centre of hybrid zones, the process of constant creation of low-fitness recombinant genotypes will favor any allele that will decrease reproductive isolation, consequently elevating the hybrid fitness. So, a likely mechanism would be negative or purifying selection against poorly fit multilocus genotypes. Therefore, the hybrizymes that increase in frequency could be modifier alleles or genetic markers that increase via hitchhiking. [ 21 ]  It is not excluded that the targets of selection are the barrier loci, loci that resist homogenization with the other genome during gene flow among diverging species, making them the most different parts of the  genome  between divergent populations. [ 22 ]


If allelic variation at these loci is considered, there might be alleles that have differential effect on reproductive isolation or hybrid disadvantage, leading to selection of those who have lower severity. [ 21 ]  The exact origin and mechanism that maintains these alleles at a high frequency is still a subject of debate and additional studies, such as  Next Generation Sequencing  analysis of the genomic regions involved in the phenomenon as a more trustworthy pathway to identify genes that impact the level of reproductive isolation. [ 9 ]


Hybridization might expand the prospect of adaptive radiation to the point where positive selection on recombinant hybrid genotypes surpasses the intrinsic selection against them. Therefore, the selection schemes in  hybrid swarms  ensures that relatively strong endogenous selection would not quench such potential. [ 23 ]  Additionally, partial postzygotic reproductive isolation usually involves multiple genes and segregation and recombination of genes creates broadly varying reproductive compatibility in hybrid populations. Consequently, there will be recurrent removal of disadvantageous alleles for reproductive isolation and relative stabilization of hybrid zones, possibly slowing down the path of complete  speciation  by reinforcement. [ 24 ] [ 25 ]


With the continual selection against hybrid disadvantage, crossing-over might, over time, interrupt existing linkages and establish new. This generates a shift in selection pressure on loci which are in linkage with these genes and will contribute to further changes in allele frequencies on a genome scale. [ 9 ]  The "rare allele phenomenon" might be an indication of this process. Even with the continuous effect of relatively strong endogenous selection against hybrids, a hybrid population might be an example where selection against reproductive isolation results in creating variable recombinant genotypes. [ 24 ]  Sometimes, this phenomenon might assist in creating a complex of adaptive traits that lead to adaptive novelty.


In  genetics  a  hypersensitive site  is a short region of  chromatin  and is detected by its super sensitivity to cleavage by  DNase I  and other various  nucleases  ( DNase II  and  micrococcal nucleases ).  In a hypersensitive site, the nucleosomal structure is less compacted, increasing the availability of the DNA to binding by proteins, such as  transcription factors  and DNase I. These sites account for many inherited tendencies. [ 2 ]


Hypersensitive sites are found on every active gene, and many of these genes often have more than one hypersensitive site.  Most often, hypersensitive sites are found only in chromatin of cells in which the associated gene is being expressed, and do not occur when the gene is inactive.


In DNA being transcribed, 5'hypersensitive sites appear before transcription begins, and the DNA sequences within the hypersensitive sites are required for  gene expression .  Note: hypersensitive sites precede active  promoters .


Hypersensitive sites are generated as a result of the binding of  transcription factors  that displace  histone octamers .


They can also be located by indirect end labelling. A fragment of DNA is cut once at the hypersensitive site with  DNase  and at another site with a  restriction enzyme . The distance from the known restriction site to the DNase cut is then measured to give the location.


Hypervariable  may refer to:


Imaging genetics  refers to the use of anatomical or physiological imaging technologies as  phenotypic   assays  to evaluate  genetic  variation. Scientists that first used the term imaging genetics were interested in how genes influence  psychopathology  and used  functional neuroimaging  to investigate genes that are expressed in the  brain  (neuroimaging genetics). [ 1 ]


Imaging genetics uses research approaches in which genetic information and  fMRI  data in the same subjects are combined to define neuro-mechanisms linked to genetic variation. [ 2 ]  With the images and genetic information, it can be determined how individual differences in  single nucleotide polymorphisms , or SNPs, lead to differences in brain wiring structure, and intellectual function. [ 3 ]  Imaging genetics allows the direct observation of the link between genes and brain activity in which the overall idea is that common variants in SNPs lead to common diseases. [ 4 ]  A neuroimaging  phenotype  is attractive because it is closer to the biology of genetic function than illnesses or cognitive phenotypes. [ 5 ]


By combining the outputs of the polygenic and neuro-imaging within a linear model, it has been shown that genetic information provides additive value in the task of predicting  Alzheimer's disease  (AD). [ 6 ]   AD traditionally has been considered a disease marked by neuronal cell loss and widespread gray matter atrophy and the apolipoprotein E allele ( APOE4 ) is a widely confirmed genetic risk factor for late-onset AD. [ 7 ]


Another gene risk variant is associated with Alzheimer's, which is known as the  CLU gene  risk variant.  The CLU gene risk variant showed a distinct profile of lower white matter integrity that may increase vulnerability to developing AD later in life. [ 7 ]  Each CLU-C allele was associated with lower FA in frontal, temporal, parietal, occipital, and subcortical white matter. [ 7 ]   Brain regions with lower FA included corticocortical pathways previously demonstrated to have lower FA in AD patients and APOE4 carriers. [ 7 ]  CLU-C related variability found here might create a local vulnerability important for disease onset. [ 7 ]   These effects are remarkable as they already exist early in life and are associated with a risk gene that is very prevalent (~36% of Caucasians carry two copies of the risk conferring genetic variant CLU-C.)  [ 7 ]
Quantitative mapping of structural brain differences in those at genetic risk of AD is crucial for evaluating treatment and prevention strategies.  If the risk for AD is identified, appropriate changes in lifestyle may limit the apprehension of AD; exercise and body mass index-have an effect on brain structure and the level of brain atrophy  [ 7 ]


If suitable biomarkers are found and applied in clinical use, we will be able to give the diagnosis of the AD spectrum at an even earlier stage. [ 8 ]  In the proposal, the AD spectrum is divided into the three stages (i) the preclinical stage; (ii) mild cognitive impairment; and (iii) clinical AD. [ 8 ]   In the preclinical stage, only changes in a specific biomarker are observed with neither cognitive impairment nor clinical signs of AD.  The mild cognitive impairment stage may include those showing biomarker changes as well as mild cognitive decline but no clinical signs and symptoms of AD. AD is diagnosed in patients with biomarker changes and clinical signs and symptoms of AD.  This concept will promote understanding of the continuous transition from preclinical stage to AD via mild cognitive impairment, in which biomarkers can be utilized to discriminate and clearly define each stage of the AD spectrum.  The new criteria will promote earlier detection of the subjects who will develop AD in later life, and also to initiate intervention aiming for the prevention of AD.


Imaging genetics must develop methods that will allow relating the effects of a large number of genetic variants on equally multi-dimensional neuroimaging phenotypes. [ 9 ]   Additionally, the field of imaging epigenetics is emerging with particular relevance, for example, to the understanding of intergenerational transmission of trauma-related psychopathology and related disturbances of maternal care. [ 10 ]


Medication, hospitalization history, or associated behaviors ranging such as smoking can affect imaging. [ 9 ]