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Friday, September 12, 2025

African Pygmies

From Wikipedia, the free encyclopedia

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

The African Pygmies (or Congo Pygmies, variously also Central African foragers, African rainforest hunter-gatherers (RHG) or Forest People of Central Africa) are a group of ethnicities native to Central Africa, mostly the Congo Basin, traditionally subsisting on a forager and hunter-gatherer lifestyle. They are divided into three roughly geographic groups:

The western Bambenga, or Mbenga (Cameroon, Gabon, Republic of the Congo, Central African Republic),
the eastern Bambuti, or Mbuti, of the Congo basin (DRC)
the central and southern Batwa, or Twa (Rwanda, Burundi, DRC, Tanzania, Uganda, Zambia, Angola and Namibia). The more widely scattered (and more variable in physiology and lifestyle) Southern Twa are also grouped under the term Pygmoid.

They are notable for, and named for, their short stature (described as "pygmyism" in anthropological literature). They are assumed to be descended from the original Middle Stone Age expansion of anatomically modern humans to Central Africa, albeit substantially affected by later migrations from West Africa, from their first appearance in the historical record in the 19th century limited to a comparatively small area within Central Africa, greatly decimated by the prehistoric Bantu expansion, and to the present time widely affected by enslavement at the hands of neighboring Bantu, Ubangian and Central Sudanic groups.

Most contemporary Pygmy groups partially forage and partially trade with neighboring farmers to acquire cultivated foods and material items; no group lives deep in the forest without access to agricultural products. A total number of about 900,000 Pygmies were estimated to be living in the central African forests in 2016, about 60% of this number in the Democratic Republic of Congo. The number does not include Southern Twa populations, who live outside of the Central Africa forest environment, partly in open swamp or desert environments.

Additionally, West African hunter-gatherers may have dwelled in western Central Africa earlier than 32,000 BP and dwelled in West Africa between 16,000 BP and 12,000 BP until as late as 1000 BP or some period of time after 1500 CE. West African hunter-gatherers, many of whom dwelt in the forest–savanna region, were ultimately acculturated and admixed into larger groups of West African agriculturalists, akin to the migratory Bantu-speaking agriculturalists and their encounters with Central African hunter-gatherers.

Name

The term Pygmy, as used to refer to diminutive people, derives from Greek πυγμαῖος pygmaios (via Latin Pygmaeus, plural Pygmaei), a term for "dwarf" from Greek mythology. The word is derived from πυγμή pygmē, a term for "cubit" (lit. 'fist'), suggesting a diminutive height.

The use of "Pygmy" in reference to the small-framed African hunter-gatherers dates to the early 19th century, in English first by John Barrow, Travels Into the Interior of Southern Africa (1806). However, the term was used diffusely, and treated as unsubstantiated claims of "dwarf tribes" among the Bushmen of the interior of Africa, until the exploration of the Congo basin. In the 1860s, two Western explorers, Paul Du Chaillu and Georg Schweinfurth, claimed to have found the mythical "Pygmies". A commentator wrote in 1892 that, thirty years ago (viz., in the 1860s), "nobody believed in the existence of African dwarf tribes" and that "it needed an authority like Dr. Schweinfurth to prove that pygmies actually exist in Africa" (referencing Georg August Schweinfurth's The Heart of Africa, published 1873). "African Pygmy" is used for disambiguation from "Asiatic Pygmy", a name applied to the Negrito populations of Southeast Asia.

Dembner (1996) reported a universal "disdain for the term 'pygmy'" among the Pygmy peoples of Central Africa: the term is considered a pejorative, and people prefer to be referred to by the name of their respective ethnic or tribal groups, such as Bayaka, Mbuti and Twa. There is no clear replacement for the term "Pygmy" in reference to the umbrella group. A descriptive term that has seen some use since the 2000s is "Central African foragers".

Regional names used collectively of the western group of Pygmies are Bambenga (the plural form of Mbenga), used in the Kongo language, and Bayaka (the plural form of Aka/Yaka), used in the Central African Republic.

Groups

The Congo Pygmy speak languages of the Niger–Congo and Central Sudanic language families. There has been significant intermixing between the Bantu and Pygmies.

There are at least a dozen Pygmy groups, sometimes unrelated to each other. They are grouped in three geographical categories:

the western Bambenga (Mbenga) of Cameroon and Gabon, the Bayaka (Aka and Baka), the Bakola or Bakoya (Gyele and Kola), and the Bongo; these groups are speakers of Bantu and Ubangian languages
the Bambuti (Mbuti) of the Ituri Rainforest, speakers of Bantu and Central Sudanic languages
the widely scattered Batwa:
- the Great Lakes Twa of the Great Lakes, speakers of the Bantu Rundi and Kiga languages
- the "Pygmoid" Southern Twa, not always included in the term "Pygmy", as they tend to be somewhat taller (male average above 155 cm). Subgroups include the Echuya Twa, Mongo Twa, Lukanga Twa and Kafwe Twa.

Origins and history

African Pygmies are often assumed to be the direct descendants of the Middle Stone Age hunter-gatherer peoples of the central African rainforest. Genetic evidence for the deep separation of Congo Pygmies from the lineage of West Africans and East Africans, as well as admixture from archaic humans, was found in the 2010s. The lineage of African Pygmies is strongly associated with mitochondrial (maternal line) haplogroup L1, with a divergence time between 170,000 and 100,000 years ago.

They were partially absorbed or displaced by later immigration of agricultural peoples of the Central Sudanic and Ubangian phyla beginning after about 5,500 years ago, and, beginning about 3,500 years ago, by the Bantu, adopting their languages.

Linguistic substrate

Substantial non-Bantu and non-Ubangian substrates have been identified in Aka and in Baka, respectively, on the order of 30% of the lexicon. Much of this vocabulary is botanical, deals with honey harvesting, or is otherwise specialized for the forest and is shared between the two western Pygmy groups. This substrate has been suggested as representing a remnant of an ancient "western Pygmy" linguistic phylum, dubbed "Mbenga" or "Baaka". However, as substrate vocabulary has been widely borrowed between Pygmies and neighboring peoples, no reconstruction of such a "Baaka" language is possible for times more remote than a few centuries ago.

An ancestral Pygmy language has been postulated for at least some Pygmy groups, based on the observation of linguistic substrates. According to Merritt Ruhlen (1994), "African Pygmies speak languages belonging to either the Nilo-Saharan or the Niger–Kordofanian family. It is assumed that Pygmies once spoke their own language(s), but that, through living in symbiosis with other Africans, in prehistorical times, they adopted languages belonging to these two families."

Roger Blench (1997, 1999) criticized the hypothesis of an ancestral "Pygmy language", arguing that even if there is evidence for a common ancestral language rather than just borrowing, it will not be sufficient to establish a specifically "Pygmy" origin rather than any of the several potential language isolates of (former) hunter-gatherer populations that ring the rainforest. He argued that the Pygmies do not form the residue of a single ancient stock of Central African hunter-gatherers, but that they are rather descended from several neighboring ethno-linguistic groups, independently adapting to forest subsistence strategies. Blench adduced the lack of clear linguistic and archaeological evidence for the antiquity of the African Pygmies, that the genetic evidence, at the time of his writing, was inconclusive, and that there is no evidence of the Pygmies having a hunting technology distinctive from that of their neighbors. He argued that the short stature of Pygmy populations can arise relatively quickly (in less than a few millennia) under strong selection pressures.

West African hunter-gatherers may have spoken a set of presently extinct Sub-Saharan West African languages. In the northeastern region of Nigeria, Jalaa, a language isolate, may have been a descending language from the original set(s) of languages spoken by West African hunter-gatherers.

Genetics

Genetic studies have found evidence that African Pygmies are descended from the Middle Stone Age people of Central Africa, with a separation time from West and East Africans of the order 130,000 years. African Pygmies in the historical period have been significantly displaced by, and assimilated to, several waves of Niger–Congo and Nilo-Saharan speakers, of the Central Sudanic, Ubangian, and Bantu phyla.

Genetically, African pygmies have some key differences between them and Bantu peoples.African pygmies' uniparental markers display the most ancient divergence from other human groups among anatomically modern humans, second only to those displayed among some Khoisan populations. Researchers identified an ancestral and autochthonous lineage of mtDNA shared by Pygmies and Bantus, suggesting that both populations were originally one, and that they started to diverge from common ancestors around 70,000 years ago. After a period of isolation, during which current phenotype differences between Pygmies and Bantu farmers accumulated, Pygmy women started marrying male Bantu farmers (but not the opposite). This trend started around 40,000 years ago, and continued until several thousand years ago. Subsequently, the Pygmy gene pool was not enriched by external gene influxes.

Mitochondrial haplogroup L1c is strongly associated with pygmies, especially with Bambenga groups. L1c prevalence was variously reported as: 100% in Ba-Kola, 97% in Aka (Ba-Benzélé), and 77% in Biaka, 100% of the Bedzan (Tikar), 97% and 100% in the Baka people of Gabon and Cameroon, respectively, 97% in Bakoya (97%), and 82% in Ba-Bongo. Mitochondrial haplogroups L2a and L0a are prevalent among the Bambuti.

Patin, et al. (2009) suggest two unique, late Pleistocene (before 60,000 years ago) divergences from other human populations, and a split between eastern and western pygmy groups about 20,000 years ago.

Ancient DNA

Ancient DNA was able to be obtained from two Shum Laka foragers from the early period of the Stone to Metal Age, in 8000 BP, and two Shum Laka foragers from the late period of the Stone to Metal Age, in 3000 BP.

The mitochondrial DNA and Y-Chromosome haplogroups found in the ancient Shum Laka foragers were Sub-Saharan African haplogroups. Two earlier Shum Laka foragers were of haplogroup L0a2a1 – broadly distributed throughout modern African populations – and two later Shum Laka foragers were of haplogroup L1c2a1b – distributed among both modern West and Central African agriculturalists and hunter-gatherers. One earlier Shum Laka forager was of haplogroup B and one later Shum Laka forager haplogroup B2b, which, together, as macrohaplogroup B, is distributed among modern Central African hunter-gatherers (e.g., Baka, Bakola, Biaka, Bedzan).

The autosomal admixture of the four ancient Shum Laka forager children was ~35% Western Central African hunter-gatherer and ~65% Basal West African – or, an admixture composed of a modern western Central African hunter-gatherer unit, a modern West African unit, existing locally before 8000 BP, and a modern East African/West African unit likely from further north in the regions of the Sahel and Sahara.

The two earlier Shum Laka foragers from 8000 BP and two later Shum Laka foragers from 3000 BP show 5000 years of population continuity in region. Yet, modern peoples of Cameroon are more closely related to modern West Africans than to the ancient Shum Laka foragers. Modern Cameroonian hunter-gatherers, while partly descended, are not largely descended from the Shum Laka foragers, due to the apparent absence of descent from Basal West Africans.

The Bantu expansion is hypothesized to have originated in a homeland of Bantu-speaking peoples located around western Cameroon, a part of which Shum Laka is viewed as being of importance in the early period of this expansion. By 3000 BP, the Bantu expansion is hypothesized to have already begun. Yet, the sampled ancient Shum Laka foragers – two from 8000 BP and two from 3000 BP – show that most modern Niger–Congo speakers are greatly distinct from the ancient Shum Laka foragers, thus, showing that the ancient Shum Laka people were not the ancestral source population of the modern Bantu-speaking peoples.

While Southern African hunter-gatherers are generally recognized as being the earliest divergent modern human group, having diverged from other groups around 250,000 BP – 200,000 BP, as a result of the sampling of the ancient Shum Laka foragers, Central African hunter-gatherers are shown to have likely diverged at a similar time, if not even earlier.

Short stature

Various hypotheses have been proposed to explain the short stature of African pygmies. Becker, et al., suggest African pygmyism may have evolved as an adaptation to the significantly lower average levels of ultraviolet light available beneath the canopy of rainforest environments. In similar hypothetical scenarios, because of reduced access to sunlight, a comparatively smaller amount of anatomically formulated vitamin D is produced, resulting in restricted dietary calcium uptake, and subsequently restricted bone growth and maintenance, resulting in an overall population average skeletal mass near the lowest periphery of the spectrum among anatomically modern humans.

Other proposed explanations include the potentially lesser availability of protein-rich food sources in rainforest environments, the often reduced soil-calcium levels in rainforest environments, the caloric expenditure required to traverse rainforest terrain, insular dwarfism as an adaptation to equatorial and tropical heat and humidity, and pygmyism as an adaptation associated with rapid reproductive maturation under conditions of early mortality.

Additional evidence suggests that, when compared to other Sub-Saharan African populations, African pygmy populations display unusually low levels of expression of the genes encoding for human growth hormone and its receptor associated with low serum levels of insulin-like growth factor 1 and short stature.

A study by Price, et al., provides insight into the role genetics plays in the reduced stature of African pygmies:

[W]e found strong signals for selection in both African Pygmy groups at two genes involved in the iodide-dependent thyroid hormone pathway: TRIP4 in Mbuti Pygmies; and IYD in Biaka Pygmies. [...] These observations suggest that the Efe have adapted genetically to an iodine-deficient diet; we suggest that the signals of recent positive selection that we observe at TRIP4 in Mbuti Pygmies and IYD in Biaka Pygmies may reflect such genetic adaptations to an iodine-deficient diet. Furthermore, alterations in the thyroid hormone pathway can cause short stature. We therefore suggest that short stature in these Pygmy groups may have arisen as a consequence of genetic alterations in the thyroid hormone pathway. [...] [T]his would suggest that short stature [...] arose as an indirect consequence of selection in response to an iodine-deficient diet. Second, since different genes in the thyroid hormone pathway show signals of selection in Mbuti vs. Biaka Pygmies, this would suggest that short stature arose independently in the ancestors of Mbuti and Biaka Pygmies, and not in a common ancestral population. Moreover, most Pygmy-like groups around the world dwell in tropical forests, and hence are likely to have iodine-deficient diets. The possibility that independent adaptations to an iodine-deficient diet might therefore have contributed to the convergent evolution of the short stature phenotype in Pygmy-like groups around the world deserves further investigation.

Music

The African Pygmies are particularly known for their vocal music, usually characterized by dense contrapuntal improvisation. Simha Arom says that the level of polyphonic complexity of Pygmy music was reached in Europe in the 14th century, yet Pygmy culture is unwritten and ancient, some Pygmy groups being the first known cultures in some areas of Africa.

Music permeates daily life, with songs for entertainment, special events, and communal activities. The Pygmie people are known to use an instrument called the n'dehou which is a bamboo flute. The n'dehou only produces a single sound, however, the person using this instrument would wield their breath and inhale making high-pitched sounds; this allows the individual to make polyrhythmic music using a one-note instrument. Along with the different sounds of the breath and the n'dehou, the musician may also stomp their feet or tap on their chest to add even more dimension and complexity to the music. The n'dehou was popularized by Francis Bebey, a Cameroonian musical artist.

Polyphonic music is found among the Aka–Baka and the Mbuti, but not among the Gyele (Kola) or the various groups of Twa.

Contemporary issues in society

Enslavement, cannibalism, and genocide

In the Republic of Congo, where Pygmies are estimated to make up between 1.2% and 10% of the population, many Pygmies live as slaves to Bantu masters. The nation is deeply stratified between these two major ethnic groups. The Pygmy slaves belong from birth to their Bantu masters in a relationship that the Bantus call a time-honored tradition. Even though the Pygmies are responsible for much of the hunting, fishing and manual labor in jungle villages, Pygmies and Bantus alike say Pygmies are often paid at the master's whim: in cigarettes, used clothing, or even nothing at all. In 2022, after decades of facing these conditions and working to get legal protections for the Pygmies, a group of 45 indigenous organizations successfully petitioned the Democratic Republic of the Congo (DRC) government, and the Promotion and Protection of the Rights of the Indigenous Pygmy Peoples, the first legislation in the country that recognizes and safeguards the specific rights of the Indigenous pygmy peoples, was signed into law.

In the Democratic Republic of the Congo, during the Ituri Conflict, Ugandan backed rebel groups were accused by the UN of enslaving Mbutis to prospect for minerals and forage for forest food, with those returning empty handed being killed and eaten.

In 2003, Sinafasi Makelo, a representative of Mbuti pygmies, told the UN's Indigenous People's Forum that during the Congo Civil War, his people were hunted down and eaten as though they were game animals. In neighboring North Kivu province there has been cannibalism by a death squad known as Les Effaceurs ("the erasers") who wanted to clear the land of people to open it up for mineral exploitation. Both sides of the war regarded them as "subhuman", and some say their flesh can confer magical powers.

Makelo asked the UN Security Council to recognize cannibalism as a crime against humanity and an act of genocide. According to Minority Rights Group International there is extensive evidence of mass killings, cannibalism and rape of Pygmies, and they have urged the International Criminal Court to investigate a campaign of extermination against pygmies. Although they have been targeted by virtually all the armed groups, much of the violence against Pygmies is attributed to the rebel group the Movement for the Liberation of Congo, which is part of the transitional government and still controls much of the north, as well as their allies.

Starting in 2013, the Pygmy Batwa people, whom the Luba people often exploit and allegedly enslave, rose up into militias (such as the "Perci" militia) in Northern Katanga Province and attacked Luba villages. A Luba militia known as "Elements" attacked back, notably killing at least 30 people in the "Vumilia 1" displaced people camp in April 2015. Since the start of the conflict, hundreds have been killed, and tens of thousands have been displaced from their homes. The weapons used in the conflict are often arrows and axes, rather than guns.

Ota Benga was a teenage pygmy boy from the Congo. Ota was purchased from slave traders and was brought to the United States to be exhibited for his unique looks. Ota had sharpened teeth as a result of the traditions of his tribe, and he was also short in stature. In 1906, Ota was brought to the Bronx Zoo and exhibited in the monkey house. Ota was given a bow and arrow for protection from the animals. After the exhibit was closed and World War I broke out, Ota was not able to return home to the Congo. He lived out the rest of his life in Virginia, until he became depressed and died by suicide at the age of 33.

Systematic discrimination

Historically, the Pygmy have always been viewed as inferior by both the village dwelling Bantu tribes and colonial authorities. This has translated into systematic discrimination. One early example was the capture of Pygmy children under the auspices of the Belgian colonial authorities, who exported Pygmy children to zoos throughout Europe, including the World's Fair in the United States in 1907.

Pygmies are often evicted from their land and given the lowest paying jobs. At a state level, Pygmies are not considered citizens by most African states, and are refused identity cards, deeds to land, health care and education access.

There are roughly 500,000 Pygmies remaining in the rainforest of Central Africa. This population is rapidly decreasing as poverty, intermarriage with Bantu peoples, Westernization, and deforestation gradually destroy their way of life and culture.

The greatest environmental problem the Pygmies face is the loss of their traditional homeland, the tropical forests of Central Africa. In countries such as Cameroon, Gabon, Central African Republic and the Republic of Congo this is due to deforestation and the desire of several governments in Central Africa to evict the Pygmies from their forest habitat in order to profit from the sale of hardwood and the resettlement of farmers onto the cleared land. In some cases, as in Rwanda and the Democratic Republic of the Congo, this conflict is violent. Certain groups, such as the Hutus of the Interahamwe, wish to eliminate the Pygmy and take the resources of the forest as a military conquest, using the resources of the forest for military as well as economic advancement. Since the Pygmies rely on the forest for their physical as well as cultural survival, as these forests disappear, so do the Pygmy.

Along with Raja Sheshadri, the fPcN-Global.org website conducted research on the Pygmies. The human rights organization states that, as the forest has receded under logging activities, its original inhabitants have been pushed into populated areas to join the formal economy, working as casual laborers or on commercial farms and being exposed to new diseases. This shift has brought them into closer contact with neighboring ethnic communities whose HIV levels are generally higher. This has led to the spread of HIV into the pygmy group.

Since poverty has become very prevalent in Pygmy communities, sexual exploitation of indigenous women has become a common practice. Commercial sex has been bolstered by logging, which often places large groups of male laborers in camps which are set up in close contact with the Pygmy communities.

Human rights groups have also reported widespread sexual abuse of indigenous women in the conflict-ridden eastern Democratic Republic of the Congo. Despite these risks, Pygmy populations generally have poor access to health services and information about HIV. One British medical journal, The Lancet, published a review showing that Pygmy populations often had less access to health care than neighboring communities. According to the report, even where health care facilities exist, many Pygmies do not use them because they cannot pay for consultations and medicines, they do not have the documents and identity cards needed to travel or obtain hospital treatment, and they are subjected to humiliating and discriminatory treatment.

Studies in Cameroon and the DRC in the 1980s and 1990s showed a lower prevalence of HIV in Pygmy populations than among neighboring groups, but recent increases have been recorded. One study found that the HIV prevalence among the Baka Pygmies in eastern Cameroon rose from 0.7 percent in 1993 to 4 percent in 2003.

Deforestation

A consortium of researchers conducted a case study on the Pygmies of Africa and concluded that deforestation has greatly affected their everyday lives. Pygmy culture is threatened today by the forces of political and economic change.

Symbiogenesis

From Wikipedia, the free encyclopedia

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

In the theory of symbiogenesis, a merger of an archaean and an aerobic bacterium created the eukaryotes, with aerobic mitochondria; a second merger added chloroplasts, creating the green plants. The original theory by Lynn Margulis proposed an additional preliminary merger, but this is poorly supported and not now generally believed.

Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes (more closely related to the Bacteria than to the Archaea) taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.

The idea that chloroplasts were originally independent organisms that merged into a symbiotic relationship with other one-celled organisms dates back to the 19th century, when it was espoused by researchers such as Andreas Schimper. The endosymbiotic theory was articulated in 1905 and 1910 by the Russian botanist Konstantin Mereschkowski, and advanced and substantiated with microbiological evidence by Lynn Margulis in 1967.

Among the many lines of evidence supporting symbiogenesis are that mitochondria and plastids contain their own chromosomes and reproduce by splitting in two, parallel but separate from the sexual reproduction of the rest of the cell; that the chromosomes of some mitochondria and plastids are single circular DNA molecules similar to the circular chromosomes of bacteria; that the transport proteins called porins are found in the outer membranes of mitochondria and chloroplasts, and also bacterial cell membranes; and that cardiolipin is found only in the inner mitochondrial membrane and bacterial cell membranes.

History

The Russian botanist Konstantin Mereschkowski first outlined the theory of symbiogenesis (from Greek: σύν syn "together", βίος bios "life", and γένεσις genesis "origin, birth") in his 1905 work, The nature and origins of chromatophores in the plant kingdom, and then elaborated it in his 1910 The Theory of Two Plasms as the Basis of Symbiogenesis, a New Study of the Origins of Organisms. Mereschkowski proposed that complex life-forms had originated by two episodes of symbiogenesis, the incorporation of symbiotic bacteria to form successively nuclei and chloroplasts. Mereschkowski knew of the work of botanist Andreas Schimper. In 1883, Schimper had observed that the division of chloroplasts in green plants closely resembled that of free-living cyanobacteria. Schimper had tentatively proposed (in a footnote) that green plants had arisen from a symbiotic union of two organisms. In 1918 the French scientist Paul Jules Portier published Les Symbiotes, in which he claimed that the mitochondria originated from a symbiosis process. Ivan Wallin advocated the idea of an endosymbiotic origin of mitochondria in the 1920s. The Russian botanist Boris Kozo-Polyansky became the first to explain the theory in terms of Darwinian evolution. In his 1924 book A New Principle of Biology. Essay on the Theory of Symbiogenesis, he wrote, "The theory of symbiogenesis is a theory of selection relying on the phenomenon of symbiosis."

These theories did not gain traction until more detailed electron-microscopic comparisons between cyanobacteria and chloroplasts were made, such as by Hans Ris in 1961 and 1962. These, combined with the discovery that plastids and mitochondria contain their own DNA, led to a resurrection of the idea of symbiogenesis in the 1960s. Lynn Margulis advanced and substantiated the theory with microbiological evidence in a 1967 paper, On the origin of mitosing cells. In her 1981 work Symbiosis in Cell Evolution she argued that eukaryotic cells originated as communities of interacting entities, including endosymbiotic spirochaetes that developed into eukaryotic flagella and cilia. This last idea has not received much acceptance, because flagella lack DNA and do not show ultrastructural similarities to bacteria or to archaea (see also: Evolution of flagella and Prokaryotic cytoskeleton). According to Margulis and Dorion Sagan, "Life did not take over the globe by combat, but by networking" (i.e., by cooperation). Christian de Duve proposed that the peroxisomes may have been the first endosymbionts, allowing cells to withstand growing amounts of free molecular oxygen in the Earth's atmosphere. However, it now appears that peroxisomes may be formed de novo, contradicting the idea that they have a symbiotic origin. The fundamental theory of symbiogenesis as the origin of mitochondria and chloroplasts is now widely accepted.

Symbiogenesis revolutionized the history of evolution by proposing a mechanism for evolutionary development not encompassed in the original Darwininan vision. Symbiogenesis demonstrated that major evolutionary advancements, particularly the origin of eukaryotic cells, may have resulted from symbiotic mergers rather than from gradual mutations and individual competition, i.e., classical natural selection. Accordingly, symbiogenic theory suggests that endosymbiosis may be a powerful force in generating evolutionary novelty, beyond that which can be explained by natural selection alone.

From endosymbionts to organelles

Biologists usually distinguish organelles from endosymbionts – whole organisms living inside other organisms – by their reduced genome sizes. As an endosymbiont evolves into an organelle, most of its genes are transferred to the host cell genome. The host cell and organelle therefore need to develop a transport mechanism that enables the return of the protein products needed by the organelle but now manufactured by the cell.

Free-living ancestors

Alphaproteobacteria were formerly thought to be the free-living organisms most closely related to mitochondria. Later research indicates that mitochondria are most closely related to Pelagibacterales bacteria, in particular, those in the SAR11 clade.

Nitrogen-fixing filamentous cyanobacteria are the free-living organisms most closely related to plastids.

Both cyanobacteria and alphaproteobacteria maintain a large (>6 Mb) genome encoding thousands of proteins. Plastids and mitochondria exhibit a dramatic reduction in genome size when compared with their bacterial relatives. Chloroplast genomes in photosynthetic organisms are normally 120–200 kb encoding 20–200 proteins and mitochondrial genomes in humans are approximately 16 kb and encode 37 genes, 13 of which are proteins. Using the example of the freshwater amoeboid, however, Paulinella chromatophora, which contains chromatophores found to be evolved from cyanobacteria, Keeling and Archibald argue that this is not the only possible criterion; another is that the host cell has assumed control of the regulation of the former endosymbiont's division, thereby synchronizing it with the cell's own division. Nowack and her colleagues gene sequenced the chromatophore (1.02 Mb) and found that only 867 proteins were encoded by these photosynthetic cells. Comparisons with their closest free living cyanobacteria of the genus Synechococcus (having a genome size 3 Mb, with 3300 genes) revealed that chromatophores had undergone a drastic genome shrinkage. Chromatophores contained genes that were accountable for photosynthesis but were deficient in genes that could carry out other biosynthetic functions; this observation suggests that these endosymbiotic cells are highly dependent on their hosts for their survival and growth mechanisms. Thus, these chromatophores were found to be non-functional for organelle-specific purposes when compared with mitochondria and plastids. This distinction could have promoted the early evolution of photosynthetic organelles.

The loss of genetic autonomy, that is, the loss of many genes from endosymbionts, occurred very early in evolutionary time. Taking into account the entire original endosymbiont genome, there are three main possible fates for genes over evolutionary time. The first is the loss of functionally redundant genes, in which genes that are already represented in the nucleus are eventually lost. The second is the transfer of genes to the nucleus, while the third is that genes remain in the organelle that was once an organism. The loss of autonomy and integration of the endosymbiont with its host can be primarily attributed to nuclear gene transfer. As organelle genomes have been greatly reduced over evolutionary time, nuclear genes have expanded and become more complex. As a result, many plastid and mitochondrial processes are driven by nuclear encoded gene products. In addition, many nuclear genes originating from endosymbionts have acquired novel functions unrelated to their organelles.

Gene transfer mechanisms

The mechanisms of gene transfer are not fully known; however, multiple hypotheses exist to explain this phenomenon. The possible mechanisms include the Complementary DNA (cDNA) hypothesis and the bulk flow hypothesis.

The cDNA hypothesis involves the use of messenger RNA (mRNAs) to transport genes from organelles to the nucleus where they are converted to cDNA and incorporated into the genome. The cDNA hypothesis is based on studies of the genomes of flowering plants. Protein coding RNAs in mitochondria are spliced and edited using organelle-specific splice and editing sites. Nuclear copies of some mitochondrial genes, however, do not contain organelle-specific splice sites, suggesting a processed mRNA intermediate. The cDNA hypothesis has since been revised as edited mitochondrial cDNAs are unlikely to recombine with the nuclear genome and are more likely to recombine with their native mitochondrial genome. If the edited mitochondrial sequence recombines with the mitochondrial genome, mitochondrial splice sites would no longer exist in the mitochondrial genome. Any subsequent nuclear gene transfer would therefore also lack mitochondrial splice sites.

The bulk flow hypothesis is the alternative to the cDNA hypothesis, stating that escaped DNA, rather than mRNA, is the mechanism of gene transfer. According to this hypothesis, disturbances to organelles, including autophagy (normal cell destruction), gametogenesis (the formation of gametes), and cell stress release DNA which is imported into the nucleus and incorporated into the nuclear DNA using non-homologous end joining (repair of double stranded breaks). For example, in the initial stages of endosymbiosis, due to a lack of major gene transfer, the host cell had little to no control over the endosymbiont. The endosymbiont underwent cell division independently of the host cell, resulting in many "copies" of the endosymbiont within the host cell. Some of the endosymbionts lysed (burst), and high levels of DNA were incorporated into the nucleus. A similar mechanism is thought to occur in tobacco plants, which show a high rate of gene transfer and whose cells contain multiple chloroplasts. In addition, the bulk flow hypothesis is also supported by the presence of non-random clusters of organelle genes, suggesting the simultaneous movement of multiple genes.

Ford Doolittle proposed that (whatever the mechanism) gene transfer behaves like a ratchet, resulting in unidirectional transfer of genes from the organelle to the nuclear genome. When genetic material from an organelle is incorporated into the nuclear genome, either the organelle or nuclear copy of the gene may be lost from the population. If the organelle copy is lost and this is fixed, or lost through genetic drift, a gene is successfully transferred to the nucleus. If the nuclear copy is lost, horizontal gene transfer can occur again, and the cell can 'try again' to have successful transfer of genes to the nucleus. In this ratchet-like way, genes from an organelle would be expected to accumulate in the nuclear genome over evolutionary time.

Endosymbiosis of protomitochondria

Endosymbiotic theory for the origin of mitochondria suggests that the proto-eukaryote engulfed a protomitochondrion, and this endosymbiont became an organelle, a major step in eukaryogenesis, the creation of the eukaryotes.

Mitochondria

Mitochondria are organelles that synthesize the energy-carrying molecule ATP for the cell by metabolizing carbon-based macromolecules. The presence of DNA in mitochondria and proteins, derived from mtDNA, suggest that this organelle may have been a prokaryote prior to its integration into the proto-eukaryote. Mitochondria are regarded as organelles rather than endosymbionts because mitochondria and the host cells share some parts of their genome, undergo division simultaneously, and provide each other with means to produce energy. The endomembrane system and nuclear membrane were hypothesized to have derived from the protomitochondria.

Nuclear membrane

The presence of a nucleus is one major difference between eukaryotes and prokaryotes. Some conserved nuclear proteins between eukaryotes and prokaryotes suggest that these two types had a common ancestor. Another theory behind nucleation is that early nuclear membrane proteins caused the cell membrane to fold and form a sphere with pores like the nuclear envelope. As a way of forming a nuclear membrane, endosymbiosis could be expected to use less energy than if the cell was to develop a metabolic process to fold the cell membrane for the purpose. Digesting engulfed cells without energy-producing mitochondria would have been challenging for the host cell. On this view, membrane-bound bubbles or vesicles leaving the protomitochondria may have formed the nuclear envelope.

The process of symbiogenesis by which the early eukaryotic cell integrated the proto-mitochondrion likely included protection of the archaeal host genome from the release of reactive oxygen species. These would have been formed during oxidative phosphorylation and ATP production by the proto-mitochondrion. The nuclear membrane may have evolved as an adaptive innovation for protecting against nuclear genome DNA damage caused by reactive oxygen species. Substantial transfer of genes from the ancestral proto-mitochondrial genome to the nuclear genome likely occurred during early eukaryotic evolution. The greater protection of the nuclear genome against reactive oxygen species afforded by the nuclear membrane may explain the adaptive benefit of this gene transfer.

Endomembrane system

Modern eukaryotic cells use the endomembrane system to transport products and wastes in, within, and out of cells. The membrane of nuclear envelope and endomembrane vesicles are composed of similar membrane proteins. These vesicles also share similar membrane proteins with the organelle they originated from or are traveling towards. This suggests that what formed the nuclear membrane also formed the endomembrane system. Prokaryotes do not have a complex internal membrane network like eukaryotes, but they could produce extracellular vesicles from their outer membrane. After the early prokaryote was consumed by a proto-eukaryote, the prokaryote would have continued to produce vesicles that accumulated within the cell. Interaction of internal components of vesicles may have led to the endoplasmic reticulum and the Golgi apparatus, both being parts of the endomembrane system.

Cytoplasm

The syntrophy hypothesis, proposed by López-García and Moreira in 1998, suggested that eukaryotes arose by combining the metabolic capabilities of an archaean, a fermenting deltaproteobacterium, and a methanotrophic alphaproteobacterium which became the mitochondrion. In 2020, the same team updated their syntrophy proposal to cover an promethearchaeon that produced hydrogen with deltaproteobacterium that oxidised sulphur. A third organism, an alphaproteobacterium able to respire both aerobically and anaerobically, and to oxidise sulphur, developed into the mitochondrion; it may possibly also have been able to photosynthesise.

Date

The question of when the transition from prokaryotic to eukaryotic form occurred and when the first crown group eukaryotes appeared on earth is unresolved. The oldest known body fossils that can be positively assigned to the Eukaryota are acanthomorphic acritarchs from the 1.631 Gya Deonar Formation of India. These fossils can still be identified as derived post-nuclear eukaryotes with a sophisticated, morphology-generating cytoskeleton sustained by mitochondria. This fossil evidence indicates that endosymbiotic acquisition of alphaproteobacteria must have occurred before 1.6 Gya. Molecular clocks have also been used to estimate the last eukaryotic common ancestor, however these methods have large inherent uncertainty and give a wide range of dates. Reasonable results include the estimate of c. 1.8 Gya. A 2.3 Gya estimate also seems reasonable, and has the added attraction of coinciding with one of the most pronounced biogeochemical perturbations in Earth history, the early Palaeoproterozoic Great Oxygenation Event. The marked increase in atmospheric oxygen concentrations at that time has been suggested as a contributing cause of eukaryogenesis, inducing the evolution of oxygen-detoxifying mitochondria. Alternatively, the Great Oxidation Event might be a consequence of eukaryogenesis, and its impact on the export and burial of organic carbon.

Organellar genomes

Plastomes and mitogenomes

Some endosymbiont genes remain in the organelles. Plastids and mitochondria retain genes encoding rRNAs, tRNAs, proteins involved in redox reactions, and proteins required for transcription, translation, and replication. There are many hypotheses to explain why organelles retain a small portion of their genome; however no one hypothesis will apply to all organisms, and the topic is still quite controversial. The hydrophobicity hypothesis states that highly hydrophobic (water hating) proteins (such as the membrane bound proteins involved in redox reactions) are not easily transported through the cytosol and therefore these proteins must be encoded in their respective organelles. The code disparity hypothesis states that the limit on transfer is due to differing genetic codes and RNA editing between the organelle and the nucleus. The redox control hypothesis states that genes encoding redox reaction proteins are retained in order to effectively couple the need for repair and the synthesis of these proteins. For example, if one of the photosystems is lost from the plastid, the intermediate electron carriers may lose or gain too many electrons, signalling the need for repair of a photosystem. The time delay involved in signalling the nucleus and transporting a cytosolic protein to the organelle results in the production of damaging reactive oxygen species. The final hypothesis states that the assembly of membrane proteins, particularly those involved in redox reactions, requires coordinated synthesis and assembly of subunits; however, translation and protein transport coordination is more difficult to control in the cytoplasm.

Non-photosynthetic plastid genomes

The majority of the genes in the mitochondria and plastids are related to the expression (transcription, translation and replication) of genes encoding proteins involved in either photosynthesis (in plastids) or cellular respiration (in mitochondria). One might predict that the loss of photosynthesis or cellular respiration would allow for the complete loss of the plastid genome or the mitochondrial genome respectively. While there are numerous examples of mitochondrial descendants (mitosomes and hydrogenosomes) that have lost their entire organellar genome, non-photosynthetic plastids tend to retain a small genome. There are two main hypotheses to explain this occurrence:

The essential tRNA hypothesis notes that there have been no documented functional plastid-to-nucleus gene transfers of genes encoding RNA products (tRNAs and rRNAs). As a result, plastids must make their own functional RNAs or import nuclear counterparts. The genes encoding tRNA-Glu and tRNA-fmet, however, appear to be indispensable. The plastid is responsible for haem biosynthesis, which requires plastid encoded tRNA-Glu (from the gene trnE) as a precursor molecule. Like other genes encoding RNAs, trnE cannot be transferred to the nucleus. In addition, it is unlikely trnE could be replaced by a cytosolic tRNA-Glu as trnE is highly conserved; single base changes in trnE have resulted in the loss of haem synthesis. The gene for tRNA-formylmethionine (tRNA-fmet) is also encoded in the plastid genome and is required for translation initiation in both plastids and mitochondria. A plastid is required to continue expressing the gene for tRNA-fmet so long as the mitochondrion is translating proteins.

The limited window hypothesis offers a more general explanation for the retention of genes in non-photosynthetic plastids. According to this hypothesis, genes are transferred to the nucleus following the disturbance of organelles. Disturbance was common in the early stages of endosymbiosis, however, once the host cell gained control of organelle division, eukaryotes could evolve to have only one plastid per cell. Having only one plastid severely limits gene transfer as the lysis of the single plastid would likely result in cell death. Consistent with this hypothesis, organisms with multiple plastids show an 80-fold increase in plastid-to-nucleus gene transfer compared with organisms with single plastids.

Evidence

There are many lines of evidence that mitochondria and plastids including chloroplasts arose from bacteria.

New mitochondria and plastids are formed only through binary fission, the form of cell division used by bacteria and archaea.
If a cell's mitochondria or chloroplasts are removed, the cell does not have the means to create new ones. In some algae, such as Euglena, the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell: the plastids do not regenerate.
Transport proteins called porins are found in the outer membranes of mitochondria and chloroplasts and are also found in bacterial cell membranes.
A membrane lipid cardiolipin is exclusively found in the inner mitochondrial membrane and bacterial cell membranes.
Some mitochondria and some plastids contain single circular DNA molecules that are similar to the DNA of bacteria both in size and structure.
Genome comparisons suggest a close relationship between mitochondria and Alphaproteobacteria.
Genome comparisons suggest a close relationship between plastids and cyanobacteria.
Many genes in the genomes of mitochondria and chloroplasts have been lost or transferred to the nucleus of the host cell. Consequently, the chromosomes of many eukaryotes contain genes that originated from the genomes of mitochondria and plastids.
Mitochondria and plastids contain their own ribosomes; these are more similar to those of bacteria (70S) than those of eukaryotes.
Proteins created by mitochondria and chloroplasts use N-formylmethionine as the initiating amino acid, as do proteins created by bacteria but not proteins created by eukaryotic nuclear genes or archaea.

Comparison of chloroplasts and cyanobacteria showing their similarities. Both chloroplasts and cyanobacteria have a double membrane, DNA, ribosomes, and chlorophyll-containing thylakoids.

Secondary endosymbiosis

Primary endosymbiosis involves the engulfment of a cell by another free living organism. Secondary endosymbiosis occurs when the product of primary endosymbiosis is itself engulfed and retained by another free living eukaryote. Secondary endosymbiosis has occurred several times and has given rise to extremely diverse groups of algae and other eukaryotes. Some organisms can take opportunistic advantage of a similar process, where they engulf an alga and use the products of its photosynthesis, but once the prey item dies (or is lost) the host returns to a free living state. Obligate secondary endosymbionts become dependent on their organelles and are unable to survive in their absence. A secondary endosymbiosis event involving an ancestral red alga and a heterotrophic eukaryote resulted in the evolution and diversification of several other photosynthetic lineages including Cryptophyta, Haptophyta, Stramenopiles (or Heterokontophyta), and Alveolata.

A possible secondary endosymbiosis has been observed in process in the heterotrophic protist Hatena. This organism behaves like a predator until it ingests a green alga, which loses its flagella and cytoskeleton but continues to live as a symbiont. Hatena meanwhile, now a host, switches to photosynthetic nutrition, gains the ability to move towards light, and loses its feeding apparatus.

Despite the diversity of organisms containing plastids, the morphology, biochemistry, genomic organisation, and molecular phylogeny of plastid RNAs and proteins suggest a single origin of all extant plastids – although this theory was still being debated in 2008.

Nitroplasts

A unicellular marine alga, Braarudosphaera bigelowii (a coccolithophore, which is a eukaryote), has been found with a cyanobacterium as an endosymbiont. The cyanobacterium forms a nitrogen-fixing structure, dubbed the nitroplast. It divides evenly when the host cell undergoes mitosis, and many of its proteins derive from the host alga, implying that the endosymbiont has proceeded far along the path towards becoming an organelle. The cyanobacterium is named Candidatus Atelocyanobacterium thalassa, and is abbreviated UCYN-A. The alga is the first eukaryote known to have the ability to fix nitrogen.