Om Baraminolgie reg te verstaan, is nie moeilik nie.
Die moderne Christen het een yslike probleem, en dit is dat hy die Bybel letterlik móét verstaan of die hele Christendom is in sy peetjie in. Die enigste oplossing vir die probleem is natuurlik dat die Christen moet aanvaar dat die Bybel Christenmitologie is, net soos daar die Griekse mitologie is. Niemand sal dan kan sê dat pratende slange en bome, of water wat in wyn verander sommer bog is nie.
En dis net hier wat die Christen vasskop soos ’n steeks donkie en wetenskaplik en histories wíl bewys dat die Bybel waar is, buig of bars.
Een van die vele kopsere wat die Bybel veroorsaak is die storie van Noag. Daar bestaan sowat tien tot vyftien miljoen spesies insekte en diere; dit sou arme Noag mal gemaak het as hy elke by- en wurm- en brommer- en vlieg- en sprinkaan- en aap- en bokspesie moes hokslaan in die ark. Dit sou hom duisende jare geneem het net om al die mier- en byspesies te versamel.
Gelukkig vir die Christelike teologie, kom ’n man met die naam Frank Walsh, in 1941 tot hulle redding. Hy ontwerp die Baramin, en hiermee kon die Jongaarde kreasioniste die wetenskap moker totdat dit in ooreenstemming met die Bybel was.
’n Baramin is ’n ander naam vir “soort”, en so is Noag se taak verlig, want hy hoef nou nie meer spesie vir spesie versamel nie, nee, hy versamel baramins; in plek van duisende by-spesies, hoef hy nou net twee bytjies (of is dit nou sewe?) te versamel in sy ark.
Die Kreasionis sien Baraminologie as ’n plaasvervanger van die Linnaeïese taksonomie, en dit is veral die Jongaarde kreasioniste wat dit aangegryp het, en deesdae dit nie eens verbloem dat hulle die wetenskap verkrag om by die Bybelse skeppingsmite in te pas nie.
Groete,
Angus
Kommentaar
Beste Angus
Jy is eintlik die een wat met 'n yslike kopseer sit want daar staan nêrens in die Bybel dat jy dit letterlik
moet verstaan nie. As dit sou was sou Christus nooit deur gelykenisse die Evangelie (goeie Boodskap)
verkondig het nie.
Die begrip aarde en liefde het dus heel ander betekenisse as wat jy en onder ateïste daaraan toeken.
Omdat daar geen bewys van 'n wêreldwye vloed was nie (al sê) wie ook wat is dit dus niks meer as 'n plaaslike vloed nie. (Werk maar self uit wat die volume water moet wees om die hele aarde te bedek en waarheen dit moes wegdreineer of verdamp - die hele natuur en lewe sou onherroeplik verander het).
Dit was dus 'n plaaslike vloed en het die woord 'aarde' die betekenis van die aarde (omgewing) soos die mens van die tyd dit geken het.
Bybelse 'liefde' is inwerklikheid diens en opoffering. As daar dus gepraat word dat mense mekaar moet liehê ,moet hul mekaar in die sin liefhê, ook tussen man en vrou, want dit is die liefde,wat Jesus, wat jy verwerp het, geopenbaar het, toe Hy aarde toe gekom het, om in my plek te sterwe, om die gebroke band tussen mens en mens en mens en sy Skepper te herstel.
Hello Angus,
Baie dankie vir jou skrywe waaroor ek nou sommer baie opgewonde oor voel. Weet jy dalk waar mens Baramins kan versamel of selfs koop? Ek is besonder lief vir die Kat-specie, ook vir Pandas, dolfyne, pappagaaie en uile. Graag sal ek 'n redelike prys betaal vir hulle Baramins om 'n versameling mee te begin.
Laat asb so gou as moontlik van jou hoor.
Beste wense,
Pieter Redelinghuys
Beste Angus, daarby is jy en Richard Dawkins die ekstreme verkondigers dat die hele mensdom uit 'n Tuin van Eden (Afrika) kom, en van 'n Adam en Eva stam ... jy laat my al hoe meer aan 'n pienk een horing met vlerke dink wat om die kreasioniste se ossewatent vlieg ... mitolgiese groete, Cornelius Henn
Beste Pieter,
Beste Cornelius en en F C Boot,
Beste Fc Boot,
... nee, nee Angus, lees weer; is jy nie dalk al heeltemal deurmekaar met die punte en kommentare by die verskillende bydraes nie? ...
Beste Angus,
Dankie vir jou brief. As jy regtig lekker wil lag, sal jy sommer baie materiaal op youtube.com onder "Richard Dawkins" vind, oa. wat hy te sê het oor die bou van Noag se ark. Sy lesing oor die Tien Gebooie is ook baie genotvol om te hoor.
Luister ook na al die haatbriewe wat hy ontvang. Dit is mos nie mooi van "Christene" om hom só te teil nie, of hoe? Waar is hulle liefde vir naaste dan?
Terloops, ek is dood ernstig oor die koop van Bhramins en hulle heilige koeie.
Beste groete,
Pieter Redelinghuys
Hello Angus,
Beste Pieter,
Angus reken heel oortuigend elders dat "fools never differ" ...
Wat moet ek nou van jou entoesiastiese eenstemmigheid hier dink?
Skeptiese groete,
Cornelius Henn
Beste Angus
Ek is 'n Christen en het geen probleem daarmee nie. Ek het wel 'n probleem met mense wat alle Christene oor dieselfde kam skeer en as belaglik en agterlik probeer uitbeeld en dan die wetenskap voorhou as synde die Wet_van_Mede_en_Perse en onfeilbaar te wees.
As alles wat mense glo aanvaar sou word as bewese feite, is die lewe verwerplik.
CM
Beste F C Boot,
Hello FC,
Beste Angus
Kom ons kyk na die skeppingsverhale. Die eerste skeppingsverhaal is geskryf tussen 586-539 vC. Dit is dus geskryf tydens die Babiloniese ballinskap. Daar was baie skeppingsverhale met baie gode. Die Joodse ballinge neem hierteenoor 'n ander stanspunt. 'Nee daar is nie baie gode nie maar wel EEN GOD, nl die Skepper van hemel en aarde en wat die oorsaak (cause) van alle begin was.
Dus in vandag se taal die oorsaak van die die oerknal, waarmee alle kragte in werking gestel is en gelei het tot die ontstaan van die heelal en lewe soos dit ontwikkel het. Daarna volg die periodes van ontwikkeling nie as 24 uur dae nie, want die het eers ontstaan met die omwenteling van die aarde. Wat wat daarna volg is in breë trekke ’n onwikkelingeskiedenis van die lewe hierop aarde.
Die tweede skeppingsverhaal is ’n tuinverhaal en word die skeppingsproses verduidelik aan die hand van voorbeelde uit die landbou. Van al die lewende wesens tree die mens as die dominante wese na vore en word dan die heerser oor allest lewe. Die voortbestaan van alle ander spesies hang dus af van die optrede van die mens.
Dit sê nêrens van hoe geskep is nie, dit is vir die skrywers van sekondêre belang, al wat belangrik is dat GOD die Skepper is deur die inwerkingstelling van die skeppingskragte waarvan evolusie dan ook deel is. Die plasing van die aarde in die heelal veral sy posisie is nie ’n lukrake plasing nie. Al Christene glo ons nie in toeval nie, dus ook nie in die toevallige ontstaan van lewe nie.
Die feit dat ons as mense dieselfde biologiese platform deel as ander primate behoort nie ’n struikelblok te wees nie. Alle primate kommunikeer op een of ander wyse maar die mens is die enigste een wat praat. Die gebruik van verskillende platforms is niks besonders nie, want veral motorvervaardigers maak ruim gebruik daarvan.
So deel Audi en VW modelle dieselfde platform en het die gesogte Porche sy ontstaan te danke aan die VW-kewer. ’n Volkswagen is nie ’n Audi nie, so is die mens ook nie ’n Chimp nie en die verskille is net so duidelik.
In 2004 het die Katolieke kerk al reeds ’n verklaring uitgereik wat reeds as ’n groot oorbruggende stap beskou kan word.(Ek is nie ’n lidmaat van die kerk nie).
Adam, Eve, and Evolution
The controversy surrounding evolution touches on our most central beliefs about ourselves and the world. Evolutionary theories have been used to answer questions about the origins of the universe, life, and man. These may be referred to as cosmological evolution, biological evolution, and human evolution. One’s opinion concerning one of these areas does not dictate what one believes concerning others.
People usually take three basic positions on the origins of the cosmos, life, and man: (1) special or instantaneous creation, (2) developmental creation or theistic evolution, (3) and atheistic evolution. The first holds that a given thing did not develop, but was instantaneously and directly created by God.
The second position holds that a given thing did develop from a previous state or form, but that this process was under God’s guidance.
The third position claims that a thing developed due to random forces alone. Related to the question of how the universe, life, and man arose is the question of when they arose. Those who attribute the origin of all three to special creation often hold that they arose at about the same time, perhaps six thousand to ten thousand years ago.
Those who attribute all three to atheistic evolution have a much longer time scale. They generally hold the universe to be ten billion to twenty billion years old, life on earth to be about four billion years old, and modern man (the subspecies homo sapiens) to be about thirty thousand years old.
Those who believe in varieties of developmental creation hold dates used by either or both of the other two positions. The Catholic Position What is the Catholic position concerning belief or unbelief in evolution?
The question may never be finally settled, but there are definite parameters to what is acceptable Catholic belief. Concerning cosmological evolution, the Church has infallibly defined that the universe was specially created out of nothing. Vatican I solemnly defined that everyone must "confess the world and all things which are contained in it, both spiritual and material, as regards their whole substance, have been produced by God from nothing" (Canons on God the Creator of All Things, canon 5).
The Church does not have an official position on whether the stars, nebulae, and planets we see today were created at that time or whether they developed over time (for example, in the aftermath of the Big Bang that modern cosmologists discuss).
However, the Church would maintain that, if the stars and planets did develop over time, this still ultimately must be attributed to God and his plan, for Scripture records: "By the word of the Lord the heavens were made, and all their host [stars, nebulae, planets] by the breath of his mouth" (Ps. 33:6).
Concerning biological evolution, the Church does not have an official position on whether various life forms developed over the course of time. However, it says that, if they did develop, then they did so under the impetus and guidance of God, and their ultimate creation must be ascribed to him.
Concerning human evolution, the Church has a more definite teaching. It allows for the possibility that man’s body developed from previous biological forms, under God’s guidance, but it insists on the special creation of his soul. Pope Pius XII declared that "the teaching authority of the Church does not forbid that, in conformity with the present state of human sciences and sacred theology, research and discussions . . . take place with regard to the doctrine of evolution, in as far as it inquires into the origin of the human body as coming from pre-existent and living matter—[but] the Catholic faith obliges us to hold that souls are immediately created by God" (Pius XII, Humani Generis 36).
So whether the human body was specially created or developed, we are required to hold as a matter of Catholic faith that the human soul is specially created; it did not evolve, and it is not inherited from our parents, as our bodies are. While the Church permits belief in either special creation or developmental creation on certain questions, it in no circumstances permits belief in atheistic evolution.
The Time Question Much less has been defined as to when the universe, life, and man appeared. The Church has infallibly determined that the universe is of finite age—that it has not existed from all eternity—but it has not infallibly defined whether the world was created only a few thousand years ago or whether it was created several billion years ago.
Catholics should weigh the evidence for the universe’s age by examining biblical and scientific evidence. "Though faith is above reason, there can never be any real discrepancy between faith and reason. Since the same God who reveals mysteries and infuses faith has bestowed the light of reason on the human mind, God cannot deny himself, nor can truth ever contradict truth" (Catechism of the Catholic Church 159).
The contribution made by the physical sciences to examining these questions is stressed by the Catechism, which states, "The question about the origins of the world and of man has been the object of many scientific studies which have splendidly enriched our knowledge of the age and dimensions of the cosmos, the development of life-forms and the appearance of man.
These discoveries invite us to even greater admiration for the greatness of the Creator, prompting us to give him thanks for all his works and for the understanding and wisdom he gives to scholars and researchers" (CCC 283). It is outside the scope of this tract to look at the scientific evidence, but a few words need to be said about the interpretation of Genesis and its six days of creation.
While there are many interpretations of these six days, they can be grouped into two basic methods of reading the account—a chronological reading and a topical reading.
Chronological Reading According to the chronological reading, the six days of creation should be understood to have followed each other in strict chronological order. This view is often coupled with the claim that the six days were standard 24-hour days.
Some have denied that they were standard days on the basis that the Hebrew word used in this passage for day (yom) can sometimes mean a longer-than-24-hour period (as it does in Genesis 2:4). However, it seems clear that Genesis 1 presents the days to us as standard days.
At the end of each one is a formula like, "And there was evening and there was morning, one day" (Gen. 1:5). Evening and morning are, of course, the transition points between day and night (this is the meaning of the Hebrew terms here), but periods of time longer than 24 hours are not composed of a day and a night.
Genesis is presenting these days to us as 24-hour, solar days. If we are not meant to understand them as 24-hour days, it would most likely be because Genesis 1 is not meant to be understood as a literal chronological account.
That is a possibility. Pope Pius XII warned us, "What is the literal sense of a passage is not always as obvious in the speeches and writings of the ancient authors of the East, as it is in the works of our own time. For what they wished to express is not to be determined by the rules of grammar and philology alone, nor solely by the context; the interpreter must, as it were, go back wholly in spirit to those remote centuries of the East and with the aid of history, archaeology, ethnology, and other sciences, accurately determine what modes of writing, so to speak, the authors of that ancient period would be likely to use, and in fact did use.
For the ancient peoples of the East, in order to express their ideas, did not always employ those forms or kinds of speech which we use today; but rather those used by the men of their times and countries. What those exactly were the commentator cannot determine as it were in advance, but only after a careful examination of the ancient literature of the East" (Divino Afflante Spiritu 35–36).
The Topical Reading This leads us to the possiblity that Genesis 1 is to be given a non-chronological, topical reading. Advocates of this view point out that, in ancient literature, it was common to sequence historical material by topic, rather than in strict chronological order. The argument for a topical ordering notes that at the time the world was created, it had two problems—it was "formless and empty" (1:2).
In the first three days of creation, God solves the formlessness problem by structuring different.aspects of the environment. On day one he separates day from night; on day two he separates the waters below (oceans) from the waters above (clouds), with the sky in between; and on day three he separates the waters below from each other, creating dry land. Thus the world has been given form.
But it is still empty, so on the second three days God solves the world’s emptiness problem by giving occupants to each of the three realms he ordered on the previous three days. Thus, having solved the problems of formlessness and emptiness, the task he set for himself, God’s work is complete and he rests on the seventh day.
Real History
The argument is that all of this is real history, it is simply ordered topically rather than chronologically, and the ancient audience of Genesis, it is argued, would have understood it as such. Even if Genesis 1 records God’s work in a topical fashion, it still records God’s work—things God really did.
The Catechism explains that "Scripture presents the work of the Creator symbolically as a succession of six days of divine ‘work,’ concluded by the ‘rest’ of the seventh day" (CCC 337), but "nothing exists that does not owe its existence to God the Creator. The world began when God’s word drew it out of nothingness; all existent beings, all of nature, and all human history is rooted in this primordial event, the very genesis by which the world was constituted and time begun" (CCC 338).
It is impossible to dismiss the events of Genesis 1 as a mere legend. They are accounts of real history, even if they are told in a style of historical writing that Westerners do not typically use.
Adam and Eve:
Real People It is equally impermissible to dismiss the story of Adam and Eve and the fall (Gen. 2–3) as a fiction. A question often raised in this context is whether the human race descended from an original pair of two human beings (a teaching known as monogenism) or a pool of early human couples (a teaching known as polygenism). In this regard, Pope Pius XII stated: "When, however, there is question of another conjectural opinion, namely polygenism, the children of the Church by no means enjoy such liberty.
For the faithful cannot embrace that opinion which maintains either that after Adam there existed on this earth true men who did not take their origin through natural generation from him as from the first parents of all, or that Adam represents a certain number of first parents.
Now, it is in no way apparent how such an opinion can be reconciled that which the sources of revealed truth and the documents of the teaching authority of the Church proposed with regard to original sin which proceeds from a sin actually committed by an individual Adam in which through generation is passed onto all and is in everyone as his own" (Humani Generis 37).
The story of the creation and fall of man is a true one, even if not written entirely according to modern literary techniques. The Catechism states, "The account of the fall in Genesis 3 uses figurative language, but affirms a primeval event, a deed that took place at the beginning of the history of man. Revelation gives us the certainty of faith that the whole of human history is marked by the original fault freely committed by our first parents" (CCC 390).
Science and Religion
The Catholic Church has always taught that "no real disagreement can exist between the theologian and the scientist provided each keeps within his own limits. . . . If nevertheless there is a disagreement . . . it should be remembered that the sacred writers, or more truly ‘the Spirit of God who spoke through them, did not wish to teach men such truths (as the inner structure of visible objects) which do not help anyone to salvation’; and that, for this reason, rather than trying to provide a scientific exposition of nature, they sometimes describe and treat these matters either in a somewhat figurative language or as the common manner of speech those times required, and indeed still requires nowadays in everyday life, even amongst most learned people" (Leo XIII, Providentissimus Deus 18).
As the Catechism puts it, "Methodical research in all branches of knowledge, provided it is carried out in a truly scientific manner and does not override moral laws, can never conflict with the faith, because the things of the world and the things the of the faith derive from the same God. The humble and persevering investigator of the secrets of nature is being led, as it were, by the hand of God in spite of himself, for it is God, the conserver of all things, who made them what they are" (CCC 159). The Catholic Church has no fear of science or scientific discovery.
NIHIL OBSTAT: I have concluded that the materials presented in this work are free of doctrinal or moral errors. Bernadeane Carr, STL, Censor Librorum, August 10, 2004 IMPRIMATUR: In accord with 1983 CIC 827 permission to publish this work is hereby granted. +Robert H. Brom, Bishop of San Diego, August 10, 2004
Beste FC Boot,
Hartlike dank vir hierdie pragtige inset van jou, die beste en intelligentste bydrae oor die ontstaan van die heelal en die mens uit die oogpunt van die Katolieke Kerk. Selfs 'n agnostikus soos myself vind dit heel bekorend.
Met die Bybel het ek egter 'n paar probleme:
Dit is beslis nie die WOORD VAN GOD NIE.
Ek sal nooit kan aanvaar dat die antropomorfiese Joodse stamgod, Jahweh, die "ware God" is nie. Trouens, hy laat my herinner aan 'n tipiese Midde-Ooste, wraaksugtige, despoot. Hy verdien geen lof en prys nie.
Indien God wel bestaan sal sy beeld nie in die Ou Testament gevind word nie. Die herskrywe van lg, bekend as die Nuwe Testament, is reeds 'n verbetering, en miskien beweeg ons begrip en verstaan op 'n skaal soos met biologiese evolusie.
Die bestaan van 'n menslike siel is vir my 'n groot probleem. Dit is 'n kwessie van geloof, en sal nooit deur wetenskap of ander wyse bewys kan word nie.
Nogmaals dankie vir jou skrywe.
Groete,
Pieter Redelinghuys
Beste FC Boot,
Hello FC,
Eintlik is die Bybel die woord van God, want God is die skepping van die menslike verbeelding.
Angus skryf in antwoord op my skrywe onder Baraminologie
“Ek gaan tog, sodra ek die kans kry, antwoord op wat jy van die mens en die chimp sê. Dalk kan jy die bal aan die rol sit en verduidelik waarom jy sê dat die twee van mekaar verskil.”
Kom ons begin by die begin. Natuurlik gaan Kobus by die lees van hierdie skrywe verstik en my vir ewig verdoem en allerhande dinge noem, maar dit pla my bitter min. Terloops Kobus as jy hierdie lees net ‘n klein vragie. Is Christus se versoeningswerk net beperk tot die moderne mens (homo sapiens) en is daar net vir hulle plek in die ‘hemel’ of kan ek verwag om ook ‘n paar ‘Neanderthals’ daar raak te loop of is hulle volgens jou nie ‘mense’ nie.
1.Bron:Encyclopedia britannica
"Human Evolution Is the process by which human beings developed on Earth from now-extinct primates. Viewed zoologically, we humans are Homo sapiens, a culture-bearing, upright-walking species that lives on the ground and first evolved in Africa between 100,000 and 200,000 years ago. We are now the only living members of what many zoologists refer to as the human tribe, Hominini, but there is abundant fossil evidence to indicate that we were preceded for millions of years by other hominins, such as Australopithecus, and that our species also lived for a time contemporaneously with at least one other member of our genus, Homo neanderthalensis (the Neanderthals).
In addition, we and our predecessors have always shared the Earth with other apelike primates, from the modern-day gorilla to the long-extinct Dryopithecus. That we and the extinct hominins are somehow related and that we and the apes, both living and extinct, are also somehow related is accepted by anthropologists and biologists everywhere. Yet the exact nature of our evolutionary relationships has been the subject of debate and investigation since the great British naturalist Charles Darwin published his monumental books On the Origin of Species (1859) and The Descent of Man (1871).
Darwin never claimed, as some of his Victorian contemporaries insisted he had, that “man was descended from the apes,” and modern scientists would view such a statement as a useless simplification—just as they would dismiss any popular notions that a certain extinct species is the “missing link” between man and the apes.
There is theoretically, however, a common ancestor that existed millions of years ago. This ancestral species does not constitute a “missing link” along a lineage but rather a node for divergence into separate lineages. This ancient primate has not been identified and may never be known with certainty, because fossil relationships are unclear even within the human lineage, which is more recent. In fact, the human “family tree” may be better described as a “family bush,” within which it is impossible to connect a full chronological series of species, leading to Homo sapiens, that experts can agree upon.”
2.http://news.sciencemag.org/plants-animals/2012/06/bonobos-join-chimps-closest-human-relatives
Bonobos Join Chimps as Closest Human Relatives 13 June 2012 1:30 pm
Jy gaan nie die prentjies en grafieke sien nie, so ‘google’ die skakel.
Max Planck Society Family ties.
The genome of this bonobo, Ulindi, shows how closely humans, chimps, and bonobos are related. Chimpanzees now have to share the distinction of being our closest living relative in the animal kingdom. An international team of researchers has sequenced the genome of the bonobo for the first time, confirming that it shares the same percentage of its DNA with us as chimps do.
The team also found some small but tantalizing differences in the genomes of the three species—differences that may explain how bonobos and chimpanzees don't look or act like us even though we share about 99% of our DNA. "We're so closely related genetically, yet our behavior is so different," says team member and computational biologist Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "
This will allow us to look for the genetic basis of what makes modern humans different from both bonobos and chimpanzees." Ever since researchers sequenced the chimp genome(see blelow) in 2005, they have known that humans share about 99% of our DNA with chimpanzees, making them our closest living relatives. But there are actually two species of apes that are this closely related to humans: bonobos (Pan paniscus) and the common chimpanzee (Pan troglodytes).
This has prompted researchers to speculate whether the ancestor of humans, chimpanzees, and bonobos looked and acted more like a bonobo, a chimpanzee, or something else—and how all three species have evolved differently since the ancestor of humans split with the common ancestor of bonobos and chimps between 4 million and 7 million years ago in Africa.
The international sequencing effort led from Max Planck chose a bonobo named Ulindi from the Leipzig Zoo as its subject, partly because she was a female (the chimp genome was of a male). The analysis of Ulindi's complete genome, reported online today in Nature, reveals that bonobos and chimpanzees share 99.6% of their DNA.
This confirms that these two species of African apes are still highly similar to each other genetically, even though their populations split apart in Africa about 1 million years ago, perhaps after the Congo River formed and divided an ancestral population into two groups. Today, bonobos are found in only the Democratic Republic of Congo and there is no evidence that they have interbred with chimpanzees in equatorial Africa since they diverged, perhaps because the Congo River acted as a barrier to prevent the groups from mixing.
The researchers also found that bonobos share about 98.7% of their DNA with humans—about the same amount that chimps share with us. When the Max Planck scientists compared the bonobo genome directly with that of chimps and humans, however, they found that a small bit of our DNA, about 1.6%, is shared with only the bonobo, but not chimpanzees.
And we share about the same amount of our DNA with only chimps, but not bonobos. These differences suggest that the ancestral population of apes that gave rise to humans, chimps, and bonobos was quite large and diverse genetically—numbering about 27,000 breeding individuals. Once the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, the common ancestor of bonobos and chimps retained this diversity until their population completely split into two groups 1 million years ago.
The groups that evolved into bonobos, chimps, and humans all retained slightly different subsets of this ancestral population's diverse gene pool—and those differences now offer clues today to the size and range of diversity in that ancestral group. While the function of the small differences in DNA in the three lineages today is not yet known, the Max Planck team sees clues that some may be involved in parts of the genome that regulate immune responses, tumor suppression genes, and perception of social cues.
The common chimpanzee, for example, shows selection for a version of a gene that may be involved in fighting retroviruses, such as HIV—a genetic variant not found in humans or bonobos, which may explain why chimps get a milder strain of HIV (called simian immunodeficiency virus) than humans do. Another difference is that bonobos and humans, but not chimps, have a version of a protein found in urine that may have similar function in apes as it does in mice, which detect differences in scent to pick up social cues.
"This paper is a significant benchmark achievement that lays the groundwork for other types of investigations into Homo-Pan differences," says molecular anthropologist Maryellen Ruvolo of Harvard University, who was not involved in the work. As researchers study the genome in more depth, they hope to find the genetic differences that make bonobos more playful than chimps, for example, or humans more cerebral.
The bonobo genome also should put to rest arguments that humans are more closely related to chimps, says primatologist Frans de Waal of Emory University in Atlanta. "The story that the bonobo can be safely ignored or marginalized from debates about human origins is now off the table," says de Waal.
This item has been updated to reflect that chimps and bonobos are two species of chimpanzees that are close enough to humans to share 99.6% of their DNA. The international sequencing effort was led by Max Planck composed of multiple teams including 454 Life Sciences in Branford, Connecticut.
The researchers also found that the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, not more than 5 million years ago as originally reported.
3:http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11128.html
The bonobo genome compared with the chimpanzee and human genomes Kay Prüfer, Kasper Munch, Ines Hellmann, Keiko Akagi, Jason R. Miller, Brian Walenz, Sergey Koren, Granger Sutton, Chinnappa Kodira, Roger Winer, James R. Knight, James C. Mullikin, Stephen J. Meader, Chris P. Ponting, Gerton Lunter, Saneyuki Higashino, Asger Hobolth, Julien Dutheil, Emre Karakoç, Can Alkan, Saba Sajjadian, Claudia Rita Catacchio, Mario Ventura, Tomas Marques-Bonet, Evan E. Eichler
Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1, 2, 3, 4, and for some of these traits they show more similarity with humans than with each other.
Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.
Whereas chimpanzees are widespread across equatorial Africa, bonobos live only south of the Congo River in the Democratic Republic of Congo (Fig. 1a). As a result of their relatively small and remote habitat, bonobos were the last ape species to be described2 and are the rarest of all apes in captivity. As a consequence, they have, until recently, been little studied2.
It is known that whereas DNA sequences in humans diverged from those in bonobos and chimpanzees five to seven million years ago, DNA sequences in bonobos diverged from those in chimpanzees around two million years ago. Bonobos are thus closely related to chimpanzees.
Moreover, comparison of a small number of autosomal DNA sequences has shown that bonobo DNA sequences often fall within the variation of chimpanzees5. Figure 1: Geographical distribution and test for admixture between chimpanzees and bonobos. a, Geographical distribution of bonobos and chimpanzees. b, D statistics for the admixture test between bonobos and three chimpanzee groups.
Each pairwise comparison between one bonobo and two chimpanzee groups is depicted as one panel. Each point in a panel represents one bonobo individual compared with two chimpanzee individuals from different groups. Admixture between bonobo and chimpanzee is indicated by a Z-score greater than 4.4 or less than −4.4. Bonobos and chimpanzees are highly similar to each other in many respects.
However, the behaviour of the two species differs in important ways1. For example, male chimpanzees use aggression to compete for dominance rank and obtain sex, and they cooperate to defend their home range and attack other groups3. By contrast, bonobo males are commonly subordinate to females and do not compete intensely for dominance rank1.
They do not form alliances with one another and there is no evidence of lethal aggression between groups3. Compared with chimpanzees, bonobos are playful throughout their lives and show intense sexual behaviour3 that serves non-conceptive functions and often involves same-sex partners4. Thus, chimpanzees and bonobos each possess certain characteristics that are more similar to human traits than they are to one another’s.
No parsimonious reconstruction of the social structure and behavioural patterns of the common ancestor of humans, chimpanzees and bonobos is therefore possible. That ancestor may in fact have possessed a mosaic of features, including those now seen in bonobo, chimpanzee and human. To understand the evolutionary relationships of bonobos, chimpanzees and humans better, we sequenced and assembled the genome of a female bonobo individual (Ulindi) and compared it to those of chimpanzees and humans.
Compared with the 6× Sanger-sequenced chimpanzee genome6 (panTro2), the bonobo genome assembly has a similar number of bases in alignment with the human genome, a similar number of lineage-specific substitutions and similar indel error rates (Table 1 and Supplementary Information, sections 2 and 3), suggesting that the two ape genomes are of similar quality. Segmental duplications affect at least 80 Mb of the bonobo genome, according to excess sequence read-depth predictions. Owing to over-collapsing of duplications, only 14.6 Mb are present in the final assembly (Supplementary Information, section 4), a common error seen in assemblies from shorter-read technologies
7. We used the finished chimpanzee sequence of chromosome 21 together with the human genome sequence to estimate an error rate of approximately two errors per 10 kb in the bonobo genome, with comparable qualities for the X chromosome and autosomes.
The bonobo genome can therefore serve as a high-quality sequence for comparative genome analyses. Table 1: Bonobo genome assembly characteristics and genomic features compared with the chimpanzee genome (panTro2) Full table Figures/tables index On average, the two alleles in single-copy, autosomal regions in the Ulindi genome are approximately 99.9% identical to each other, 99.6% identical to corresponding sequences in the chimpanzee genome and 98.7% identical to corresponding sequences in the human genome.
A comprehensive analysis of the bonobo genome is presented in Supplementary Information. Here we summarize the most interesting results. We identified and validated experimentally a total of 704 kb of DNA sequences that occur in bonobo-specific segmental duplications. They contain three partially duplicated genes (CFHR2, DUS2L and CACNA1B) and two completely duplicated genes (CFHR4 and DDX28).
However, bonobos and chimpanzees share the majority of segmental duplications, and they carry approximately similar numbers of bases in lineage-specific duplications (Fig. 2a). Figure 2: Segmental duplications and transposon accumulation. a, Venn diagram showing segmental duplications in the human (H), chimpanzee (C) and bonobo (B) genomes. Each number of megabases refers to the total amount of sequence that occurs in segmental duplications (Supplementary Information, section 4). b, Accumulation of different retrotransposon classes on each lineage.
Full size image (52 KB)Download PowerPoint slide (432K) PreviousFigures/tables indexNext As in other mammals, transposons, that is, mobile genetic elements, make up approximately half of the bonobo genome (Supplementary Information, section 6). In agreement with previous results6, we find that Alu insertions accumulated about twice as fast on the human lineage as on the bonobo and chimpanzee lineages (Fig. 2b). We identified two previously unreported Alu subfamilies in bonobos and chimpanzees, designated AluYp1, which is present in 5 copies in the human genome and in 54 and 114 copies in the bonobo and chimpanzee genomes, respectively, and AluYp2, which is absent from humans and present in 24 and 37 copies, respectively, in the two apes.
We found that, as in mice8, African-ape-specific L1 insertions are enriched near genes involved in neuronal activities or cell adhesion and are depleted near genes encoding transcription factors or involved in nucleic-acid metabolism (Supplementary Information, section 6). In humans, L1 retrotransposition has been shown to occur preferentially in neuronal precursor cells and has been speculated to contribute to functional diversity in the brain9.
The tendency of new L1 integrants to accumulate near neuronal genes on evolutionary timescales may mimic the somatic variation found in the brain. To investigate whether bonobos and chimpanzees exchanged genes subsequent to their separation, we used a test (the D statistic10) to investigate the extent to which the bonobo genomes might be closer to some chimpanzees than to others (Supplementary Information, section 10).
To this end, we generated Illumina shotgun sequences from two western, seven eastern, and seven central chimpanzees (Fig. 1a) and from three bonobos (Supplementary Information, section 5). We then used alignments of sets of four genomes, each consisting of two chimpanzees, the bonobo and the human, and tested for an excess of shared derived alleles between bonobo and one chimpanzee as compared with the other chimpanzee.
We observe no significant difference between the numbers of shared derived alleles (Fig. 1b). There is thus no indication of preferential gene flow between bonobos and any of the chimpanzee groups tested. Such a complete separation contrasts with reports of hybridization between many other primates11. It is, however, consistent with the suggestion that the formation of the Congo River 1.5–2.5 million years ago created a barrier to gene flow that allowed bonobos and chimpanzees to evolve different phenotypes over a relatively short time.
Because the population split between bonobo and chimpanzee occurred relatively close in time to the split between the bonobo–chimpanzee ancestor (Pan ancestor) and humans, not all genomic regions are expected to show the pattern in which DNA sequences from bonobos and chimpanzees are more closely related to each other than to humans.
Previous work using very low-coverage sequencing of ape genomes has suggested that less than 1% of the human genome may be more closely related to one of the two apes than the ape genomes are to one another12. To investigate the extent to which such so-called incomplete lineage sorting (ILS) exists between the three species, we used the bonobo genome and a coalescent hidden Markov model (HMM) approach13 to analyse non-repetitive parts of the bonobo, chimpanzee6, human14 and orang-utan15 genomes.
This showed that 1.6% of the human genome is more closely related to the bonobo genome than to the chimpanzee genome, and that 1.7% of the human genome is more closely related to the chimpanzee than to the bonobo genome (Fig. 3a). Figure 3: Incomplete lineage sorting. a, Schematic description of ILS states and percentage of bases assigned to each state. b, Effective population sizes and split times inferred from ILS and based on a molecular clock with a mutation rate of 10−9 yr−1. Myr, million years.
We note that other estimates of mutation rates will correspondingly affect the estimates of the split times. c, Overlap between predicted ILS transposons and the closest HMM ILS assignments within 100 bp of a transposon insertion. d, Proportion of ILS in exons, introns and across the whole genome, counted within ~1-Mb segments of alignment (Supplementary Information, section 8). e, Proportion of ILS dependent on recombination rates. Errors, 95% confidence interval. To test this result independently, we analysed transposon integrations, which occur so rarely in ape and human genomes that the chance of two independent insertions of the same type of transposon at the same position and in the same orientation in different species is exceedingly low. We identified 991 integrations of transposons absent from the orang-utan genome but present in two of the three species bonobo, chimpanzee and human.
Of these, 27 are shared between the bonobo and human genomes but are absent from the chimpanzee genome, and 30 are shared between the chimpanzee and human genomes but are absent from the bonobo genome, suggesting that approximately 6% (95% confidence interval, 4.1–7.0%) of the genome is affected by ILS among the three species.
The HMM estimation of ILS is further supported by the fact that the HMM tree topology assignments tend to match the ILS status of the neighbouring transposons (P = 7.2 × 10−6 and 0.025 for bonobo–human and chimpanzee–human ILS, respectively; Fig. 3c and Supplementary Information, section 6).
We conclude that more than 3% of the human genome is more closely related to either bonobos or chimpanzees than these are to each other. Such regions of ILS may influence phenotypic similarities that humans share with one of the apes but not the other. In fact, about 25% of all genes contain regions of ILS (Supplementary Information, section 8), and genes encoding membrane proteins and proteins involved in cell adhesion have a higher fraction of bases assigned to ILS than do other genes. Amino-acid substitutions that are fixed in the apes and show ILS may be particularly informative about phenotypic differences.
We identified 18 such amino-acid substitutions shared between humans and bonobos and 18 shared between chimpanzees and humans (Supplementary Information, section 12). These are candidates for further study. An interesting example is the gene encoding the trace amine associated receptor 8 (TAAR8), a member of a family of G-coupled protein receptors that in the mouse detect volatile amines in urine that may provide social cues16.
Although this gene seems to be pseudogenized independently on multiple ape lineages, humans and bonobos share a single amino-acid change in the first extracellular domain and carry the longest open reading frames (of 342 and 256 amino acids, respectively; open reading frames in all other apes, <180 amino acids) (SI 12). Further work is needed to clarify if TAAR8 is functional in humans and apes.
The ILS among bonobos, chimpanzees and humans opens the possibility of gauging the genetic diversity and, hence, the population history of the Pan ancestor. We used the HMM to estimate the effective population size of the Pan ancestor to 27,000 individuals (Fig. 3b), which is almost three times larger than that of present-day bonobos (Supplementary Information, section 9) and humans17 but is similar to that of central chimpanzees5, 18, 19. We also estimated a population split time between bonobos and chimpanzees of one million years, which is in agreement with most previous estimates18, 19. Differences in female and male population history, for example, with respect to reproductive success and migration rates, are of special interest in understanding the evolution of social structure.
To approach this question in the Pan ancestor, we compared the inferred ancestral population sizes of the X chromosome and the autosomes. Because two-thirds of X chromosomes are found in females whereas autosomes are split equally between the two sexes, a ratio between their effective population sizes (X/A ratio) of 0.75 is expected under random mating. The X/A ratio in the Pan ancestor, corrected for the higher mutation rate in males, is 0.83 (0.75–0.91) (Fig. 4 and Supplementary Information, section 8).
Similarly, we estimated an X/A ratio of 0.85 (0.79–0.93) for present-day bonobos using Ulindi single nucleotide polymorphisms in 200-kb windows (Supplementary Information, section 9). Under the assumption of random mating, this would mean that on average two females reproduce for each reproducing male. The difference in the variance of reproductive success between the sexes certainly contributes to this observation, as does the fact that whereas bonobo females often move to new groups upon maturation, males tend to stay within their natal group20.
Because both current and ancestral X/A ratios are similar to each other and also to some human groups (Fig. 4), this suggests that they may also have been typical for the ancestor shared with humans. Figure 4: X/A ratios. The X/A ratios for Ulindi (bonobo), an African human and a European human were inferred from heterozygosity, and that for the Pan ancestor was inferred from ILS. The low X/A ratio for the European has been suggested to be due to demographic effects connected to migrating out of Africa30. Errors, 95% confidence interval (Supplementary Information, sections 8 and 9).
Because factors that reduce the effective population size, in particular positive and negative selection, will decrease the extent of ILS, the distribution of ILS across the genome allows regions affected by selection in the Pan ancestor to be identified. In agreement with this, we find that exons show less ILS than introns (Fig. 3d and Supplementary Information, section 8).
We also find that recombination rates are positively correlated with ILS (Fig. 3e), probably because recombination uncouples regions from neighbouring selective events. Unlike positive and negative selection, balancing selection is expected to increase ILS. In agreement with this, we find that ILS is most frequent in the major histocompatibility complex (MHC), which encodes cell-surface proteins that present antigens to immune cells (Supplementary Information, section 10) and is known to contain genes that evolve under balancing selection21.
To identify regions affected by selective sweeps in the Pan ancestor, we isolated long genomic regions devoid of ILS. The largest such region is 6.1 Mb long and is located on human chromosome 3. This region contains a cluster of tumour suppressor genes22, has an estimated recombination rate of 10% of the human genome average23 and has been found to evolve under strong purifying selection in humans24.
The diversity in the region, corrected for mutation rate, is lower than in neighbouring regions in chimpanzee but not in bonobos (Fig. 5a), and parts of the region show signatures of positive selection in humans10, 25, 26. Apparently this region evolves in unique ways that may involve both strong background selection and several independent events of positive selection among apes and humans. Figure 5: Selection in the bonobo–chimpanzee common ancestor and chimpanzees. a, Diversity in chimpanzee and bonobo around the region on chromosome 3 devoid of ILS. b, Regions where bonobos fall outside the variation of chimpanzee upstream of the MHC. The MHC region is not plotted because the SNP density is sparse there as a result of duplications. Five regions among the 50 longest regions are shown in yellow. Red points show posterior probabilities >0.8.
The fact that the chimpanzee diversity encompasses bonobos for most regions of the genome can be exploited to identify regions that have been positively selected in chimpanzees after their separation from bonobos, because in such regions bonobos will fall outside the chimpanzee variation. We implemented a search for such regions, which is similar to a test previously applied to humans to detect selective sweeps since their split from Neanderthals10 (Homo neanderthalensis), in an HMM that uses coalescent simulations for parameter training, the chimpanzee resequencing data and the megabase-wide average of the human recombination rates (Supplementary Information, section 7).
Because the size of a region affected by a selective sweep will be larger the faster fixation was reached, the intensity of selection will correlate positively with genetic length. We therefore ranked the regions according to genetic length and further corrected for the effect of background selection24. The highest-ranking region contains an miRNA, miR-4465, that has not yet been functionally characterized. Four of the ten highest-ranking regions contain no protein- or RNA-coding genes, and may thus contain structural or regulatory features that have been subject to selection. Notably, four of these ten regions are on chromosome 6, and two of these four are within 2 Mb of the MHC (Fig. 5b).
This suggests that the MHC and surrounding genomic regions have been a major target of positive selection in chimpanzees, presumably as a result of infectious diseases. Indeed, chimpanzees have experienced a selective sweep that targeted MHC class-I genes and reduced allelic diversity across a wide region surrounding the MHC27, perhaps caused by the HIV-1/SIVCPZ retrovirus27, 28.
The bonobo genome shows that more than 3% of the human genome is more closely related to either bonobos or chimpanzees than these are to each other. This can be used to illuminate the population history and selective events that affected the ancestor of bonobos and chimpanzees. In addition, about 25% of human genes contain parts that are more closely related to one of the two apes than the other. Such regions can now be identified and will hopefully contribute to the unravelling of the genetic background of phenotypic similarities among humans, bonobos and chimpanzees. We generated a total of 86 Gb of DNA sequence from Ulindi, a female bonobo who lives in Leipzig Zoo (Supplementary Information, section 1). All sequencing was done on the 454 sequencing platform and included 10 Gb of paired-end reads from clones of insert sizes of 3, 9 and 20 kb.
The genome was assembled using the open-source Celera Assembler software29 (Supplementary Information, section 2). In addition, we sequenced 19 bonobo and chimpanzee individuals on the Illumina GAIIx platform to about one-fold genomic coverage per individual (Supplementary Information, section 5).
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