Neanderthal genome project

From Wikipedia, the free encyclopedia

The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006.

It was initiated by 454 Life Sciences, a biotechnology company based in Branford, Connecticut in the United States and is coordinated by the Max Planck Institute for Evolutionary Anthropology in Germany. In May 2010 the project published their initial draft of the Neanderthal genome (Vi33.16, Vi33.25, Vi33.26) based on the analysis of four billion base pairs of Neanderthal DNA. The study determined that some mixture of genes occurred between Neanderthals and anatomically modern humans and presented evidence that elements of their genome remain in modern humans outside Africa.

In December 2013, a high coverage genome of a Neanderthal was reported for the first time. DNA was extracted from a toe fragment from a female Neanderthal researchers have dubbed the "Altai Neandertal". It was found in Denisova Cave in the Altai Mountains of Siberia and is estimated to be 50,000 years old.

Findings

The researchers recovered ancient DNA of Neanderthals by extracting the DNA from the femur bones of three 38,000 year-old female Neanderthal specimens from Vindija Cave, Croatia, and other bones found in Spain, Russia, and Germany. Only about half a gram of the bone samples (or 21 samples each 50–100 mg) was required for the sequencing, but the project faced many difficulties, including the contamination of the samples by the bacteria that had colonized the Neanderthal's body and humans who handled the bones at the excavation site and at the laboratory.

Svante Pääbo, director of the Department of Genetics at the Max Planck Institute for Evolutionary Anthropology and head of its Neanderthal genome project.

In February 2009, the Max Planck Institute's team led by Svante Pääbo announced that they had completed the first draft of the Neanderthal genome. An early analysis of the data suggested in "the genome of Neanderthals, a human species driven to extinction" "no significant trace of Neanderthal genes in modern humans". New results suggested that some adult Neanderthals were lactose intolerant. On the question of potentially cloning a Neanderthal, Pääbo commented, "Starting from the DNA extracted from a fossil, it is and will remain impossible."

In May 2010, the project released a draft of their report on the sequenced Neanderthal genome. Contradicting the results discovered while examining mitochondrial DNA (mtDNA), they demonstrated a range of genetic contribution to non-African modern humans ranging from 1% to 4%. From their Homo sapiens samples in Eurasia (French, Han Chinese and Papuan) the authors stated that it is likely that interbreeding occurred in the Levant before Homo sapiens migrated into Europe. This finding is disputed because of the paucity of archeological evidence supporting their statement. The fossil evidence does not conclusively place Neanderthals and modern humans in close proximity at this time and place. According to preliminary sequences from 2010, 99.7% of the nucleotide sequences of the modern human and Neanderthal genomes are identical, compared to humans sharing around 98.8% of sequences with the chimpanzee. (For some time, studies concerning the commonality between chimps and humans modified the commonality of 99% to a commonality of only 94%, showing that the genetic gap between humans and chimpanzees was far larger than originally thought, but more recent knowledge states the difference between humans, chimpanzees, and bonobos at just about 1.0–1.2% again.)

Additionally, in 2010, the discovery and analysis of mtDNA from the Denisova hominin in Siberia revealed that it differed from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. Analysis of the specimen's nuclear DNA was then still under way and expected to clarify whether the find is a distinct species. Even though the Denisova hominin's mtDNA lineage predates the divergence of modern humans and Neanderthals, coalescent theory does not preclude a more recent divergence date for her nuclear DNA.

A rib fragment from the partial skeleton of a Neanderthal infant found in the Mezmaiskaya cave in the northwestern foothills of the Caucasus Mountains was radiocarbon-dated in 1999 to 29,195±965 B.P., and therefore belonging to the latest lived Neanderthals. Ancient DNA recovered for a mtDNA sequence showed 3.48% divergence from that of the Feldhofer Neanderthal, some 2,500 km to the west in Germany and in 2011 Phylogenetic analysis placed the two in a clade distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool.

In 2015, Israel Hershkovitz of Tel Aviv University reported that a skull found in a cave in northern Israel, is "probably a woman, who lived and died in the region about 55,000 years ago, placing modern humans there and then for the first time ever", pointing to a potential time and location when modern humans first interbred with Neanderthals.

In 2016, the project found that Neanderthals bred with modern humans multiple times, and that Neanderthals interbred with Denisovans only once, as evidenced in the genome of modern-day Melanesians.

In 2006, two research teams working on the same Neanderthal sample published their results, Richard Green and his team in Nature, and James Noonan's team in Science. The results were received with some scepticism, mainly surrounding the issue of a possible admixture of Neanderthals into the modern human genome.

In 2006, Richard Green's team had used a then new sequencing technique developed by 454 Life Sciences that amplifies single molecules for characterization and obtained over a quarter of a million unique short sequences ("reads"). The technique delivers randomly located reads, so that sequences of interest – genes that differ between modern humans and Neanderthals – show up at random as well. However, this form of direct sequencing destroys the original sample so to obtain new reads more samples must be destructively sequenced.

Noonan's team, led by Edward Rubin, used a different technique, one in which the Neanderthal DNA is inserted into bacteria, which make multiple copies of a single fragment. They demonstrated that Neanderthal genomic sequences can be recovered using a metagenomic library-based approach. All of the DNA in the sample is "immortalized" into metagenomic libraries. A DNA fragment is selected, then propagated in microbes. The resulting Neanderthal DNA sequences can then be sequenced or specific sequences can be studied.

Overall, their results were remarkably similar. One group suggested there was a hint of mixing between human and Neanderthal genomes, while the other found none, but both teams recognized that the data set was not large enough to give a definitive answer.

The publication by Noonan, and his team revealed Neanderthal DNA sequences matching chimpanzee DNA, but not modern human DNA, at multiple locations, thus enabling the first accurate calculation of the date of the most recent common ancestor of H. sapiens and H. neanderthalensis. The research team estimates the most recent common ancestor of their H. neanderthalensis samples and their H. sapiens reference sequence lived 706,000 years ago (divergence time), estimating the separation of the human and Neanderthal ancestral populations to 370,000 years ago (split time).

"Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor ~706,000 years ago, and that the human and Neanderthal ancestral populations split ~370,000 years ago, before the emergence of anatomically modern humans."

— Noonan et al. (2006)

Based on the analysis of mitochondrial DNA, the split of the Neanderthal and H. sapiens lineages is estimated to date to between 760,000 and 550,000 years ago (95% CI).

Mutations of the speech-related gene FOXP2 identical to those in modern humans were discovered in Neanderthal DNA from the El Sidrón 1253 and 1351c specimens, suggesting Neanderthals might have shared some basic language capabilities with modern humans.

Hybrid (biology)

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Hybrid_(biology) 

A mule is a sterile hybrid of a male donkey and a female horse. Mules are smaller than horses but stronger than donkeys, making them useful as pack animals.

In biology, a hybrid is the offspring resulting from combining the qualities of two organisms of different breeds, varieties, species or genera through sexual reproduction. Hybrids are not always intermediates between their parents (such as in blending inheritance), but can show hybrid vigor, sometimes growing larger or taller than either parent. The concept of a hybrid is interpreted differently in animal and plant breeding, where there is interest in the individual parentage. In genetics, attention is focused on the numbers of chromosomes. In taxonomy, a key question is how closely related the parent species are.

Species are reproductively isolated by strong barriers to hybridisation, which include genetic and morphological differences, differing times of fertility, mating behaviors and cues, and physiological rejection of sperm cells or the developing embryo. Some act before fertilization and others after it. Similar barriers exist in plants, with differences in flowering times, pollen vectors, inhibition of pollen tube growth, somatoplastic sterility, cytoplasmic-genic male sterility and the structure of the chromosomes. A few animal species and many plant species, however, are the result of hybrid speciation, including important crop plants such as wheat, where the number of chromosomes has been doubled.

Human impact on the environment has resulted in an increase in the interbreeding between regional species, and the proliferation of introduced species worldwide has also resulted in an increase in hybridisation. This genetic mixing may threaten many species with extinction, while genetic erosion from monoculture in crop plants may be damaging the gene pools of many species for future breeding. A form of often intentional human-mediated hybridisation is the crossing of wild and domesticated species. This is common in both traditional horticulture and modern agriculture; many commercially useful fruits, flowers, garden herbs, and trees have been produced by hybridisation. One such flower, Oenothera lamarckiana, was central to early genetics research into mutationism and polyploidy. It is also more occasionally done in the livestock and pet trades; some well-known wild × domestic hybrids are beefalo and wolfdogs. Human selective breeding of domesticated animals and plants has resulted in the development of distinct breeds (usually called cultivars in reference to plants); crossbreeds between them (without any wild stock) are sometimes also imprecisely referred to as "hybrids".

Hybrid humans existed in prehistory. For example, Neanderthals and anatomically modern humans are thought to have interbred as recently as 40,000 years ago.

Mythological hybrids appear in human culture in forms as diverse as the Minotaur, blends of animals, humans and mythical beasts such as centaurs and sphinxes, and the Nephilim of the Biblical apocrypha described as the wicked sons of fallen angels and attractive women.

Etymology

Liger, a lion/tiger hybrid bred in captivity

The term hybrid is derived from Latin hybrida, used for crosses such as of a tame sow and a wild boar. The term came into popular use in English in the 19th century, though examples of its use have been found from the early 17th century. Conspicuous hybrids are popularly named with portmanteau words, starting in the 1920s with the breeding of tiger–lion hybrids (liger and tigon).

As seen by different disciplines

Animal and plant breeding

From the point of view of animal and plant breeders, there are several kinds of hybrid formed from crosses within a species, such as between different breeds. Single cross hybrids result from the cross between two true-breeding organisms which produces an F1 hybrid (first filial generation). The cross between two different homozygous lines produces an F1 hybrid that is heterozygous; having two alleles, one contributed by each parent and typically one is dominant and the other recessive. Typically, the F1 generation is also phenotypically homogeneous, producing offspring that are all similar to each other. Double cross hybrids result from the cross between two different F1 hybrids (i.e., there are four unrelated grandparents). Three-way cross hybrids result from the cross between an F1 hybrid and an inbred line. Triple cross hybrids result from the crossing of two different three-way cross hybrids. Top cross (or "topcross") hybrids result from the crossing of a top quality or pure-bred male and a lower quality female, intended to improve the quality of the offspring, on average.

Population hybrids result from the crossing of plants or animals in one population with those of another population. These include interspecific hybrids or crosses between different breeds.

In horticulture, the term stable hybrid is used to describe an annual plant that, if grown and bred in a small monoculture free of external pollen (e.g., an air-filtered greenhouse) produces offspring that are "true to type" with respect to phenotype; i.e., a true-breeding organism.

Biogeography

Further information: Hybrid zone

Hybridisation can occur in the hybrid zones where the geographical ranges of species, subspecies, or distinct genetic lineages overlap. For example, the butterfly Limenitis arthemis has two major subspecies in North America, L. a. arthemis (the white admiral) and L. a. astyanax (the red-spotted purple). The white admiral has a bright, white band on its wings, while the red-spotted purple has cooler blue-green shades. Hybridisation occurs between a narrow area across New England, southern Ontario, and the Great Lakes, the "suture region". It is at these regions that the subspecies were formed. Other hybrid zones have formed between described species of plants and animals.

Genetics

Oenothera lamarckiana is a permanent natural hybrid, studied intensively by the geneticist Hugo de Vries. Illustration by De Vries, 1913

From the point of view of genetics, several different kinds of hybrid can be distinguished. A genetic hybrid carries two different alleles of the same gene, where for instance one allele may code for a lighter coat colour than the other. A structural hybrid results from the fusion of gametes that have differing structure in at least one chromosome, as a result of structural abnormalities. A numerical hybrid results from the fusion of gametes having different haploid numbers of chromosomes. A permanent hybrid results when only the heterozygous genotype occurs, as in Oenothera lamarckiana, because all homozygous combinations are lethal. In the early history of genetics, Hugo de Vries supposed these were caused by mutation.

Taxonomy

From the point of view of taxonomy, hybrids differ according to their parentage. Hybrids between different subspecies (such as between the Dog and Eurasian wolf) are called intra-specific hybrids. Interspecific hybrids are the offspring from interspecies mating; these sometimes result in hybrid speciation. Intergeneric hybrids result from matings between different genera, such as between sheep and goats. Interfamilial hybrids, such as between chickens and guineafowl or pheasants, are reliably described but extremely rare. Interordinal hybrids (between different orders) are few, but have been made with the sea urchin Strongylocentrotus purpuratus (female) and the sand dollar Dendraster excentricus (male).

Biology

Expression of parental traits

Hybrid between Lady Amherst's pheasant (Chrysolophus amherstiae) and another species, probably golden pheasant (Chrysolophus pictus)

When two distinct types of organisms breed with each other, the resulting hybrids typically have intermediate traits (e.g., one plant parent has red flowers, the other has white, and the hybrid, pink flowers). Commonly, hybrids also combine traits seen only separately in one parent or the other (e.g., a bird hybrid might combine the yellow head of one parent with the orange belly of the other).

Mechanisms of reproductive isolation

Main article: Reproductive isolation

Interspecific hybrids are bred by mating individuals from two species, normally from within the same genus. The offspring display traits and characteristics of both parents, but are often sterile, preventing gene flow between the species. Sterility is often attributed to the different number of chromosomes between the two species. For example, donkeys have 62 chromosomes, horses have 64 chromosomes, and mules or hinnies have 63 chromosomes. Mules, hinnies, and other normally sterile interspecific hybrids cannot produce viable gametes, because differences in chromosome structure prevent appropriate pairing and segregation during meiosis, meiosis is disrupted, and viable sperm and eggs are not formed. However, fertility in female mules has been reported with a donkey as the father.

A variety of mechanisms limit the success of hybridisation, including the large genetic difference between most species. Barriers include morphological differences, differing times of fertility, mating behaviors and cues, and physiological rejection of sperm cells or the developing embryo. Some act before fertilization; others after it.

In plants, some barriers to hybridisation include blooming period differences, different pollinator vectors, inhibition of pollen tube growth, somatoplastic sterility, cytoplasmic-genic male sterility and structural differences of the chromosomes.

Speciation

Durum wheat is tetraploid, derived from wild emmer wheat, which is a hybrid of two diploid wild grasses, Triticum urartu and a wild goatgrass such as Aegilops searsii or Ae. speltoides.

 

Main articles: Hybrid speciation and Hybrid zone

A few animal species are the result of hybridization. The Lonicera fly is a natural hybrid. The American red wolf appears to be a hybrid of the gray wolf and the coyote, although its taxonomic status has been a subject of controversy. The European edible frog is a semi-permanent hybrid between pool frogs and marsh frogs; its population requires the continued presence of at least one of the parent species. Cave paintings indicate that the European bison is a natural hybrid of the aurochs and the steppe bison.

Plant hybridization is more commonplace compared to animal hybridization. Many crop species are hybrids, including notably the polyploid wheats: some have four sets of chromosomes (tetraploid) or six (hexaploid), while other wheat species have (like most eukaryotic organisms) two sets (diploid), so hybridization events likely involved the doubling of chromosome sets, causing immediate genetic isolation.

Hybridization may be important in speciation in some plant groups. However, homoploid hybrid speciation (not increasing the number of sets of chromosomes) may be rare: by 1997, only 8 natural examples had been fully described. Experimental studies suggest that hybridization offers a rapid route to speciation, a prediction confirmed by the fact that early generation hybrids and ancient hybrid species have matching genomes, meaning that once hybridization has occurred, the new hybrid genome can remain stable.

Many hybrid zones are known where the ranges of two species meet, and hybrids are continually produced in great numbers. These hybrid zones are useful as biological model systems for studying the mechanisms of speciation. Recently DNA analysis of a bear shot by a hunter in the North West Territories confirmed the existence of naturally-occurring and fertile grizzly–polar bear hybrids.

Hybrid vigour

Hybrid vigour: Salvia jurisicii x nutans hybrids (top centre, with flowers) are taller than their parents Salvia jurisicii (centre tray) or Salvia nutans (top left).

Main article: Heterosis

Hybridization between reproductively isolated species often results in hybrid offspring with lower fitness than either parental. However, hybrids are not, as might be expected, always intermediate between their parents (as if there were blending inheritance), but are sometimes stronger or perform better than either parental lineage or variety, a phenomenon called heterosis, hybrid vigour, or heterozygote advantage. This is most common with plant hybrids. A transgressive phenotype is a phenotype that displays more extreme characteristics than either of the parent lines. Plant breeders use several techniques to produce hybrids, including line breeding and the formation of complex hybrids. An economically important example is hybrid maize (corn), which provides a considerable seed yield advantage over open pollinated varieties. Hybrid seed dominates the commercial maize seed market in the United States, Canada and many other major maize-producing countries.

In a hybrid, any trait that falls outside the range of parental variation (and is thus not simply intermediate between its parents) is considered heterotic. Positive heterosis produces more robust hybrids, they might be stronger or bigger; while the term negative heterosis refers to weaker or smaller hybrids. Heterosis is common in both animal and plant hybrids. For example, hybrids between a lion and a tigress ("ligers") are much larger than either of the two progenitors, while "tigons" (lioness × tiger) are smaller. Similarly, the hybrids between the common pheasant (Phasianus colchicus) and domestic fowl (Gallus gallus) are larger than either of their parents, as are those produced between the common pheasant and hen golden pheasant (Chrysolophus pictus). Spurs are absent in hybrids of the former type, although present in both parents.

Human influence

Anthropogenic hybridization

Hybridization is greatly influenced by human impact on the environment, through effects such as habitat fragmentation and species introductions. Such impacts make it difficult to conserve the genetics of populations undergoing introgressive hybridization. Humans have introduced species worldwide to environments for a long time, both intentionally for purposes such as biological control, and unintentionally, as with accidental escapes of individuals. Introductions can drastically affect populations, including through hybridization.

Management

Examples of hybrid flowers from hybrid swarms of Aquilegia pubescens and Aquilegia formosa

There is a kind of continuum with three semi-distinct categories dealing with anthropogenic hybridization: hybridization without introgression, hybridization with widespread introgression (backcrossing with one of the parent species), and hybrid swarms (highly variable populations with much interbreeding as well as backcrossing with the parent species). Depending on where a population falls along this continuum, the management plans for that population will change. Hybridization is currently an area of great discussion within wildlife management and habitat management. Global climate change is creating other changes such as difference in population distributions which are indirect causes for an increase in anthropogenic hybridization.

Conservationists disagree on when is the proper time to give up on a population that is becoming a hybrid swarm, or to try and save the still existing pure individuals. Once a population becomes a complete mixture, the goal becomes to conserve those hybrids to avoid their loss. Conservationists treat each case on its merits, depending on detecting hybrids within the population. It is nearly impossible to formulate a uniform hybridization policy, because hybridization can occur beneficially when it occurs "naturally", and when hybrid swarms are the only remaining evidence of prior species, they need to be conserved as well.

Genetic mixing and extinction

Main article: Genetic pollution

Further information: Genetic mixing and Introgression

Regionally developed ecotypes can be threatened with extinction when new alleles or genes are introduced that alter that ecotype. This is sometimes called genetic mixing. Hybridization and introgression, which can happen in natural and hybrid populations, of new genetic material can lead to the replacement of local genotypes if the hybrids are more fit and have breeding advantages over the indigenous ecotype or species. These hybridization events can result from the introduction of non-native genotypes by humans or through habitat modification, bringing previously isolated species into contact. Genetic mixing can be especially detrimental for rare species in isolated habitats, ultimately affecting the population to such a degree that none of the originally genetically distinct population remains.

Effect on biodiversity and food security

The Green Revolution of the 20th century relied on hybridization to create high-yielding varieties, along with increased reliance on inputs of fertilizers, pesticides, and irrigation.

Main articles: Biodiversity and Food security

In agriculture and animal husbandry, the Green Revolution's use of conventional hybridization increased yields by breeding "high-yielding varieties". The replacement of locally indigenous breeds, compounded with unintentional cross-pollination and crossbreeding (genetic mixing), has reduced the gene pools of various wild and indigenous breeds resulting in the loss of genetic diversity. Since the indigenous breeds are often well-adapted to local extremes in climate and have immunity to local pathogens, this can be a significant genetic erosion of the gene pool for future breeding. Therefore, commercial plant geneticists strive to breed "widely adapted" cultivars to counteract this tendency.

In different taxa

In animals

Further information: List of genetic hybrids

Mammals

Familiar examples of equid hybrids are the mule, a cross between a female horse and a male donkey, and the hinny, a cross between a female donkey and a male horse. Pairs of complementary types like the mule and hinny are called reciprocal hybrids. Polar bears and brown bears are another case of a hybridizing species pairs, and introgression among non-sister species of bears appears to have shaped the Ursidae family tree. Among many other mammal crosses are hybrid camels, crosses between a bactrian camel and a dromedary. There are many examples of felid hybrids, including the liger.

The first known instance of hybrid speciation in marine mammals was discovered in 2014. The clymene dolphin (Stenella clymene) is a hybrid of two Atlantic species, the spinner and striped dolphins. In 2019, scientists confirmed that a skull found 30 years earlier was a hybrid between the beluga whale and narwhal; dubbed the narluga.

Birds

See also: Bird hybrid

Cagebird breeders sometimes breed bird hybrids known as mules between species of finch, such as goldfinch × canary.

Amphibians

Among amphibians, Japanese giant salamanders and Chinese giant salamanders have created hybrids that threaten the survival of Japanese giant salamanders because of competition for similar resources in Japan.

Fish

Among fish, a group of about fifty natural hybrids between Australian blacktip shark and the larger common blacktip shark was found by Australia's eastern coast in 2012.

Russian sturgeon and American paddlefish were hybridized in captivity when sperm from the paddlefish and eggs from the sturgeon were combined, unexpectedly resulting in viable offspring. This hybrid is called a sturddlefish.

Invertebrates

Among insects, so-called killer bees were accidentally created during an attempt to breed a strain of bees that would both produce more honey and be better adapted to tropical conditions. It was done by crossing a European honey bee and an African bee.

The Colias eurytheme and C. philodice butterflies have retained enough genetic compatibility to produce viable hybrid offspring. Hybrid speciation may have produced the diverse Heliconius butterflies, but that is disputed.

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  A "zonkey", a zebra/donkey hybrid

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  A "jaglion", a jaguar/lion hybrid

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  A domestic canary/goldfinch hybrid

In plants

The London plane, Platanus × acerifolia is a natural hybrid, popular for street planting.

 

Further information: List of plant hybrids

Plant species hybridize more readily than animal species, and the resulting hybrids are fertile more often. Many plant species are the result of hybridization, combined with polyploidy, which duplicates the chromosomes. Chromosome duplication allows orderly meiosis and so viable seed can be produced.

Plant hybrids are generally given names that include an "×" (not in italics), such as Platanus × acerifolia for the London plane, a natural hybrid of P. orientalis (oriental plane) and P. occidentalis (American sycamore). The parent's names may be kept in their entirety, as seen in Prunus persica × Prunus americana, with the female parent's name given first, or if not known, the parent's names given alphabetically.

Plant species that are genetically compatible may not hybridize in nature for various reasons, including geographical isolation, differences in flowering period, or differences in pollinators. Species that are brought together by humans in gardens may hybridize naturally, or hybridization can be facilitated by human efforts, such as altered flowering period or artificial pollination. Hybrids are sometimes created by humans to produce improved plants that have some of the characteristics of each of the parent species. Much work is now being done with hybrids between crops and their wild relatives to improve disease-resistance or climate resilience for both agricultural and horticultural crops.

Some crop plants are hybrids from different genera (intergeneric hybrids), such as Triticale, × Triticosecale, a wheat–rye hybrid. Most modern and ancient wheat breeds are themselves hybrids; bread wheat, Triticum aestivum, is a hexaploid hybrid of three wild grasses. Several commercial fruits including loganberry (Rubus × loganobaccus) and grapefruit (Citrus × paradisi) are hybrids, as are garden herbs such as peppermint (Mentha × piperita), and trees such as the London plane (Platanus × acerifolia). Among many natural plant hybrids is Iris albicans, a sterile hybrid that spreads by rhizome division, and Oenothera lamarckiana, a flower that was the subject of important experiments by Hugo de Vries that produced an understanding of polyploidy.

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  A sterile hybrid between Trillium cernuum and T. grandiflorum

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  An ornamental lily hybrid known as Lilium 'Citronella'

Sterility in a non-polyploid hybrid is often a result of chromosome number; if parents are of differing chromosome pair number, the offspring will have an odd number of chromosomes, which leaves them unable to produce chromosomally-balanced gametes. While that is undesirable in a crop such as wheat, for which growing a crop that produces no seeds would be pointless, it is an attractive attribute in some fruits. Triploid bananas and watermelons are intentionally bred because they produce no seeds and are also parthenocarpic.

In humans

Main article: Interbreeding between archaic and modern humans

 

Oase 2 skull may be a human-Neanderthal hybrid.

There is evidence of hybridisation between modern humans and other species of the genus Homo. In 2010, the Neanderthal genome project showed that 1–4% of DNA from all people living today, apart from most Sub-Saharan Africans, is of Neanderthal heritage. Analyzing the genomes of 600 Europeans and East Asians found that combining them covered 20% of the Neanderthal genome that is in the modern human population. Ancient human populations lived and interbred with Neanderthals, Denisovans, and at least one other extinct Homo species. Thus, Neanderthal and Denisovan DNA has been incorporated into human DNA by introgression.

In 1998, a complete prehistorical skeleton found in Portugal, the Lapedo child, had features of both anatomically modern humans and Neanderthals. Some ancient human skulls with especially large nasal cavities and unusually shaped braincases represent human-Neanderthal hybrids. A 37,000- to 42,000-year-old human jawbone found in Romania's Oase cave contains traces of Neanderthal ancestry from only four to six generations earlier. All genes from Neanderthals in the current human population are descended from Neanderthal fathers and human mothers. A Neanderthal skull unearthed in Italy in 1957 reveals Neanderthal mitochondrial DNA, which is passed on through only the maternal lineage, but the skull has a chin shape similar to modern humans. It is proposed that it was the offspring of a Neanderthal mother and a human father.

In mythology

Main article: Mythological hybrid

 

The Minotaur of ancient Greek mythology was (in one version of the myth) supposedly the offspring of Pasiphaë and a white bull.

Folk tales and myths sometimes contain mythological hybrids; the Minotaur was the offspring of a human, Pasiphaë, and a white bull. More often, they are composites of the physical attributes of two or more kinds of animals, mythical beasts, and humans, with no suggestion that they are the result of interbreeding, as in the centaur (man/horse), chimera (goat/lion/snake), hippocamp (fish/horse), and sphinx (woman/lion). The Old Testament mentions a first generation of half-human hybrid giants, the Nephilim, while the apocryphal Book of Enoch describes the Nephilim as the wicked sons of fallen angels and attractive women.

 

Heterosis

From Wikipedia, the free encyclopedia

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

Time course imaging of two maize inbreds and their F1 hybrid (middle) exhibiting heterosis.

Heterosis, hybrid vigor, or outbreeding enhancement is the improved or increased function of any biological quality in a hybrid offspring. An offspring is heterotic if its traits are enhanced as a result of mixing the genetic contributions of its parents. These effects can be due to Mendelian or non-Mendelian inheritance.

Definitions

In proposing the term heterosis to replace the older term heterozygosis, G.H. Shull aimed to avoid limiting the term to the effects that can be explained by heterozygosity in Mendelian inheritance.

The physiological vigor of an organism as manifested in its rapidity of growth, its height and general robustness, is positively correlated with the degree of dissimilarity in the gametes by whose union the organism was formed … The more numerous the differences between the uniting gametes — at least within certain limits — the greater on the whole is the amount of stimulation … These differences need not be Mendelian in their inheritance … To avoid the implication that all the genotypic differences which stimulate cell-division, growth and other physiological activities of an organism are Mendelian in their inheritance and also to gain brevity of expression I suggest … that the word 'heterosis' be adopted.

Heterosis is often discussed as the opposite of inbreeding depression, although differences in these two concepts can be seen in evolutionary considerations such as the role of genetic variation or the effects of genetic drift in small populations on these concepts. Inbreeding depression occurs when related parents have children with traits that negatively influence their fitness largely due to homozygosity. In such instances, outcrossing should result in heterosis.

Not all outcrosses result in heterosis. For example, when a hybrid inherits traits from its parents that are not fully compatible, fitness can be reduced. This is a form of outbreeding depression.

Dominance versus overdominance

Dominance versus overdominance is a scientific controversy in the field of genetics that has persisted for more than a century. These two alternative hypotheses were first stated in 1908.

Genetic basis

When a population is small or inbred, it tends to lose genetic diversity. Inbreeding depression is the loss of fitness due to loss of genetic diversity. Inbred strains tend to be homozygous for recessive alleles that are mildly harmful (or produce a trait that is undesirable from the standpoint of the breeder). Heterosis or hybrid vigor, on the other hand, is the tendency of outbred strains to exceed both inbred parents in fitness.

Selective breeding of plants and animals, including hybridization, began long before there was an understanding of underlying scientific principles. In the early 20th century, after Mendel's laws came to be understood and accepted, geneticists undertook to explain the superior vigor of many plant hybrids. Two competing hypotheses, which are not mutually exclusive, were developed:

Genetic basis of heterosis. Dominance hypothesis. Scenario A. Fewer genes are under-expressed in the homozygous individual. Gene expression in the offspring is equal to the expression of the fittest parent. Overdominance hypothesis. Scenario B. Over-expression of certain genes in the heterozygous offspring. (The size of the circle depicts the expression level of gene A)

• Dominance hypothesis. The dominance hypothesis attributes the superiority of hybrids to the suppression of undesirable recessive alleles from one parent by dominant alleles from the other. It attributes the poor performance of inbred strains to loss of genetic diversity, with the strains becoming purely homozygous at many loci. The dominance hypothesis was first expressed in 1908 by the geneticist Charles Davenport. Under the dominance hypothesis, deleterious alleles are expected to be maintained in a random-mating population at a selection–mutation balance that would depend on the rate of mutation, the effect of the alleles and the degree to which alleles are expressed in heterozygotes.
• Overdominance hypothesis. Certain combinations of alleles that can be obtained by crossing two inbred strains are advantageous in the heterozygote. The overdominance hypothesis attributes the heterozygote advantage to the survival of many alleles that are recessive and harmful in homozygotes. It attributes the poor performance of inbred strains to a high percentage of these harmful recessives. The overdominance hypothesis was developed independently by Edward M. East (1908) and George Shull (1908). Genetic variation at an overdominant locus is expected to be maintained by balancing selection. The high fitness of heterozygous genotypes favours the persistence of an allelic polymorphism in the population.

Dominance and overdominance have different consequences for the gene expression profile of the individuals. If overdominance is the main cause for the fitness advantages of heterosis, then there should be an over-expression of certain genes in the heterozygous offspring compared to the homozygous parents. On the other hand, if dominance is the cause, fewer genes should be under-expressed in the heterozygous offspring compared to the parents. Furthermore, for any given gene, the expression should be comparable to the one observed in the fitter of the two parents.

Historical retrospective

Population geneticist James Crow (1916–2012) believed, in his younger days, that overdominance was a major contributor to hybrid vigor. In 1998 he published a retrospective review of the developing science. According to Crow, the demonstration of several cases of heterozygote advantage in Drosophila and other organisms first caused great enthusiasm for the overdominance theory among scientists studying plant hybridization. But overdominance implies that yields on an inbred strain should decrease as inbred strains are selected for the performance of their hybrid crosses, as the proportion of harmful recessives in the inbred population rises. Over the years, experimentation in plant genetics has proven that the reverse occurs, that yields increase in both the inbred strains and the hybrids, suggesting that dominance alone may be adequate to explain the superior yield of hybrids. Only a few conclusive cases of overdominance have been reported in all of genetics. Since the 1980s, as experimental evidence has mounted, the dominance theory has made a comeback.

Crow wrote:

The current view ... is that the dominance hypothesis is the major explanation of inbreeding decline and [of] the high yield of hybrids. There is little statistical evidence for contributions from overdominance and epistasis. But whether the best hybrids are getting an extra boost from overdominance or favorable epistatic contributions remains an open question.

Controversy

The term heterosis often causes confusion and even controversy, particularly in selective breeding of domestic animals, because it is sometimes (incorrectly) claimed that all crossbred plants and animals are "genetically superior" to their parents, due to heterosis. but two problems exist with this claim:

• First, according to an article published in the journal Genome Biology, "genetic superiority" is an ill-defined term and not generally accepted terminology within the scientific field of genetics. A related term fitness is well defined, but it can rarely be directly measured. Instead, scientists use objective, measurable quantities, such as the number of seeds a plant produces, the germination rate of a seed, or the percentage of organisms that survive to reproductive age. From this perspective, crossbred plants and animals exhibiting heterosis may have "superior" traits, but this does not necessarily equate to any evidence of outright "genetic superiority". Use of the term "superiority" is commonplace for example in crop breeding, where it is well understood to mean a better-yielding, more robust plant for agriculture. Such a plant may yield better on a farm, but would likely struggle to survive in the wild, making this use open to misinterpretation. In human genetics any question of "genetic superiority" is even more problematic due to the historical and political implications of any such claim. Some may even go as far as to describe it as a questionable value judgement in the realm of politics, not science.
• Second, not all hybrids exhibit heterosis (see outbreeding depression).

An example of the ambiguous value judgements imposed on hybrids and hybrid vigor is the mule. While mules are almost always infertile, they are valued for a combination of hardiness and temperament that is different from either of their horse or donkey parents. While these qualities may make them "superior" for particular uses by humans, the infertility issue implies that these animals would most likely become extinct without the intervention of humans through animal husbandry, making them "inferior" in terms of natural selection.

Genetic and epigenetic bases

Main articles: Heterozygote advantage, Histone H3, and microRNA

Since the early 1900s, two competing genetic hypotheses, not necessarily mutually exclusive, have been developed to explain hybrid vigor. More recently, an epigenetic component of hybrid vigor has also been established.

The genetic dominance hypothesis attributes the superiority of hybrids to the masking of expression of undesirable (deleterious) recessive alleles from one parent by dominant (usually wild-type) alleles from the other (see Complementation (genetics)). It attributes the poor performance of inbred strains to the expression of homozygous deleterious recessive alleles. The genetic overdominance hypothesis states that some combinations of alleles (which can be obtained by crossing two inbred strains) are especially advantageous when paired in a heterozygous individual. This hypothesis is commonly invoked to explain the persistence of some alleles (most famously the Sickle cell trait allele) that are harmful in homozygotes. In normal circumstances, such harmful alleles would be removed from a population through the process of natural selection. Like the dominance hypothesis, it attributes the poor performance of inbred strains to expression of such harmful recessive alleles. In any case, outcross matings provide the benefit of masking deleterious recessive alleles in progeny. This benefit has been proposed to be a major factor in the maintenance of sexual reproduction among eukaryotes, as summarized in the article Evolution of sexual reproduction.

An epigenetic contribution to heterosis has been established in plants, and it has also been reported in animals. MicroRNAs (miRNAs), discovered in 1993, are a class of non-coding small RNAs which repress the translation of messenger RNAs (mRNAs) or cause degradation of mRNAs. In hybrid plants, most miRNAs have non-additive expression (it might be higher or lower than the levels in the parents). This suggests that the small RNAs are involved in the growth, vigor and adaptation of hybrids.

'Heterosis without hybridity' effects on plant size have been demonstrated in genetically isogenic F1 triploid (autopolyploid) plants, where paternal genome excess F1 triploids display positive heterosis, whereas maternal genome excess F1s display negative heterosis effects. Such findings demonstrate that heterosis effects, with a genome dosage-dependent epigenetic basis, can be generated in F1 offspring that are genetically isogenic (i.e. harbour no heterozygosity). It has been shown that hybrid vigor in an allopolyploid hybrid of two Arabidopsis species was due to epigenetic control in the upstream regions of two genes, which caused major downstream alteration in chlorophyll and starch accumulation. The mechanism involves acetylation and/or methylation of specific amino acids in histone H3, a protein closely associated with DNA, which can either activate or repress associated genes.

Major histocompatibility complex in animals

One example of where particular genes may be important in vertebrate animals for heterosis is the major histocompatibility complex (MHC). Vertebrates inherit several copies of both MHC class I and MHC class II from each parent, which are used in antigen presentation as part of the adaptive immune system. Each different copy of the genes is able to bind and present a different set of potential peptides to T-lymphocytes. These genes are highly polymorphic throughout populations, but are more similar in smaller, more closely related populations. Breeding between more genetically distant individuals decreases the chance of inheriting two alleles that are the same or similar, allowing a more diverse range of peptides to be presented. This, therefore, gives a decreased chance that any particular pathogen will not be recognised, and means that more antigenic proteins on any pathogen are likely to be recognised, giving a greater range of T-cell activation, so a greater response. This also means that the immunity acquired to the pathogen is against a greater range of antigens, meaning that the pathogen must mutate more before immunity is lost. Thus, hybrids are less likely to succumb to pathogenic disease and are more capable of fighting off infection. This may be the cause, though, of autoimmune diseases.

Plants

Crosses between inbreds from different heterotic groups result in vigorous F1 hybrids with significantly more heterosis than F1 hybrids from inbreds within the same heterotic group or pattern. Heterotic groups are created by plant breeders to classify inbred lines, and can be progressively improved by reciprocal recurrent selection.

Heterosis is used to increase yields, uniformity, and vigor. Hybrid breeding methods are used in maize, sorghum, rice, sugar beet, onion, spinach, sunflowers, broccoli and to create a more psychoactive cannabis.

Corn (maize)

Nearly all field corn (maize) grown in most developed nations exhibits heterosis. Modern corn hybrids substantially outyield conventional cultivars and respond better to fertilizer.

Corn heterosis was famously demonstrated in the early 20th century by George H. Shull and Edward M. East after hybrid corn was invented by Dr. William James Beal of Michigan State University based on work begun in 1879 at the urging of Charles Darwin. Dr. Beal's work led to the first published account of a field experiment demonstrating hybrid vigor in corn, by Eugene Davenport and Perry Holden, 1881. These various pioneers of botany and related fields showed that crosses of inbred lines made from a Southern dent and a Northern flint, respectively, showed substantial heterosis and outyielded conventional cultivars of that era. However, at that time such hybrids could not be economically made on a large scale for use by farmers. Donald F. Jones at the Connecticut Agricultural Experiment Station, New Haven invented the first practical method of producing a high-yielding hybrid maize in 1914–1917. Jones' method produced a double-cross hybrid, which requires two crossing steps working from four distinct original inbred lines. Later work by corn breeders produced inbred lines with sufficient vigor for practical production of a commercial hybrid in a single step, the single-cross hybrids. Single-cross hybrids are made from just two original parent inbreds. They are generally more vigorous and also more uniform than the earlier double-cross hybrids. The process of creating these hybrids often involves detasseling.

Temperate maize hybrids are derived from two main heterotic groups: 'Iowa Stiff Stalk Synthetic', and nonstiff stalk.

Rice (Oryza sativa)

Rice production has seen enormous rise in China due to heavy uses of hybrid rice. In China, efforts have generated a super hybrid rice strain ('LYP9') with a production capability around 15 tons per hectare. In India also, several varieties have shown high vigor, including 'RH-10' and 'Suruchi 5401'.

Hybrid livestock

The concept of heterosis is also applied in the production of commercial livestock. In cattle, crosses between Black Angus and Hereford produce a cross known as a "Black Baldy". In swine, "blue butts" are produced by the cross of Hampshire and Yorkshire. Other, more exotic hybrids (two different species, so genetically more dissimilar), such as "beefalo", are also used for specialty markets.

Poultry

Within poultry, sex-linked genes have been used to create hybrids in which males and females can be sorted at one day old by color. Specific genes used for this are genes for barring and wing feather growth. Crosses of this sort create what are sold as Black Sex-links, Red Sex-links, and various other crosses that are known by trade names.

Commercial broilers are produced by crossing different strains of White Rocks and White Cornish, the Cornish providing a large frame and the Rocks providing the fast rate of gain. The hybrid vigor produced allows the production of uniform birds at a marketable carcass weight at 6–9 weeks of age.

Likewise, hybrids between different strains of White Leghorn are used to produce laying flocks that provide the majority of white eggs for sale in the United States.

Dogs

In 2013, a study found that mixed breeds live on average 1.2 years longer than pure breeds.

John Scott and John L. Fuller performed a detailed study of purebred Cocker Spaniels, purebred Basenjis, and hybrids between them. They found that hybrids ran faster than either parent, perhaps due to heterosis. Other characteristics, such as basal heart rate, did not show any heterosis—the dog's basal heart rate was close to the average of its parents—perhaps due to the additive effects of multiple genes.

Sometimes people working on a dog-breeding program find no useful heterosis.

All this said, studies do not provide definitive proof of hybrid vigor in dogs. This is largely due to the unknown heritage of most mixed breeds mutts used. Results vary wildly, with some studies showing benefit and others finding the mixed breed dogs to be more prone to genetic conditions.

Birds

In 2014, a study undertaken by the Centre for Integrative Ecology at Deakin University in Geelong, Victoria, concluded that intraspecific hybrids between the subspecies Platycercus elegans flaveolus and P. e. elegans of the crimson rosella (P. elegans) were more likely to fight off diseases than their pure counterparts.

Humans

See also: Exogamy

Human beings are all extremely genetically similar to one another. Michael Mingroni has proposed heterosis, in the form of hybrid vigor associated with historical reductions of the levels of inbreeding, as an explanation of the Flynn effect, the steady rise in IQ test scores around the world during the 20th century.