Talk:Population bottleneck

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From the article:[edit]

All species being survivors in relation to the levels their environment support, there is reasonable thinking that says human beings are due for another bottleneck sometime soon.
Really? Please provide cites that this thinking is mainstream.
World population is rising rapidly. Each year there are far more births than the previous year. That situation is almost certain to continue for decades. Alfred Kinsey (talk) 22:05, 4 June 2009 (UTC)

That is not entirely true. Birth rates are now falling and numbers levelling off, though still projected to be above death rates for the next three decades.(UN and CIA figures)Logical Analyst (talk) 20:03, 26 December 2009 (UTC)

List of species[edit]

It seems like we could benefit from a separate article listing known species which have experienced a genetic bottleneck, eg. CA Condor, Blue Whales.

AIDS[edit]

Also, AIDS, whilst a disastrous pandemic, is not anywhere near the level needed for a bottleneck.

Not globally, but it is approaching (and projected to reach) that level in parts of Africa. (The Black Death was only a regional phenomenon, too.) Mkweise
AIDS is not at, nor projected to be anywhere near, the scale of the Black Death. Sub-Saharan Africans have very high birthrates, preventing a bottleneck. Alfred Kinsey (talk) 22:01, 4 June 2009 (UTC)

YPB[edit]

What is "ybp"? Uncommon abbreviations should either be spelled out in full the first time they are used in an article, or they should be linked to a glossary entry.

"Years before present" should be spelled out in full at the first encounter.--Wetman 12:52, 12 Mar 2005 (UTC)

Drift[edit]

"as the rate of drift is inversely proportional to the population size." No, the rate of drift is a constant. This needs rethinking as well as rephrasing. --Wetman 12:52, 12 Mar 2005 (UTC)

The rate of mutation may be constant; but the rate of genetic drift, ie the changes in the proportions of alleles in a population, does indeed become greater, the smaller the population size. -- Jheald 11:47, 9 February 2006 (UTC).

Put more simply, the changes in general population characteristics will be more rapid in a small population than in a large one. However, inverse proportionality is both unlikely and unprovable. The graph line is more likely to be somewhat hyperbolic.Logical Analyst (talk) 20:02, 26 December 2009 (UTC)

Wisent or Bison?[edit]

Is the table in Example in the animal world section about wisent (European bison) or about American bison? The first row cites "Before 1492", so apparently it refers to the American Bison (arrival of Europeans is always considered a key point in American history); the second one cites 750 living bisons in 1890, and this could refer to both the European and American Bison; the third row clearly reports the number of European Bison (as told in American Bison there are thousand of living bison now). I'm going to assume that the table is about American Bison and fix consequently, if no one answer. GhePeU 21:37, 14 September 2005 (UTC)

I couldn't find a confirmation on the wisent having only 2 different versions of the Y-chromosomes, and I thought if it was so that the paper I read on genetic variation in the Wisent (Luerner et al., 2005) would have mentioned it. However, if you have a source that says there are 2 Y versions, please put it back in! and cite your source. Satyrium 15:37, 9 September 2006 (UTC)

Near-Extinction evolution theory[edit]

Near-Extinction evolution theory was recently created. If there is anything there worth keeping it should be merged here. Zeimusu | Talk page 13:18, 26 December 2005 (UTC)

No. I don't see anything of value in that article, so I'd rather not merge it here. It seems a bit of puffery. As to whether or not it should be deleted, I'll let others decide. Ted 03:26, 21 April 2006 (UTC)
No. I'm in full agreement with TedE. Near-extinction seems very, very hypothetical, and doesn't add anything new and well-supported. Satyrium 15:04, 9 September 2006 (UTC)

Since there was nothing to merge from the article (I concur with the above), and there weren't even any sources to move over, I've redirected that article here. -Harmil 07:45, 6 October 2006 (UTC)

DNA coalescence[edit]

As far as I know, DNA are expected to coalesce, even if there is no population bottleneck. So I changed that part (on Humans). That section would benefit from some outside sources. Krubo 13:32, 29 May 2006 (UTC)

I tried to improved it. How does it look now? Fred Hsu 01:37, 17 March 2007 (UTC)

Toba Catastrophe and coalescence[edit]

Re the discussion post above on human coalescence:

I think the section of the main article labeled "Humans" is now internally contradictory. It begins by saying that coalescence 70K years ago is to be expected and doesn't indicate a bottleneck. Then, the next two paragraphs discuss two theories as to why a bottleneck occurred.

Can somebody explain this apparent contradiction, or is the section actually cohesive, and I'm just not getting it?

If a contradiction does exist, I think the article should be edited to explain that coalescence is a matter of some controversy. --Tannerpittman 16:57, 15 February 2007 (UTC)

Please check the section again to see if the new wordings now clearly state these two contradictory views. Fred Hsu 01:40, 17 March 2007 (UTC)

Calculation of time of bottleneck events[edit]

Can someone add a note or link about how bottleneck times are calculated? I presume that it's done by measurements of genetic variation compared to the background rate of genetic drift (complicated by differences in local sources of mutagenic events and variations in species ability to resist mutations, both mentioned in Deinococcus radiodurans). --Scott McNay 23:18, 16 March 2007 (UTC)

External bottleneck[edit]

User:MichaelCPrice made the following change indicating that genetic evidences do not contradct the Toba catastrophe theory because genetic evidences only disprove the existence of of "external bottleneck". What is an external bottleneck? Can someone provide some references? I am restoring the original version until more references are presented. Fred Hsu 14:33, 4 April 2007 (UTC)

Please see the inline reference to The Ancestor's Tale in the previous paragraph. Based on numerous lineages of different genes, it has been determined that there were no population bottleneck. By bottleneck, researchers mean what is meant by population bottleneck, not a single breeding pair (probably what was meant by "external bottleneck"). Fred Hsu 15:09, 4 April 2007 (UTC)

I wrote extremal , not external :-) And yes, I meant by this a single breeding pair. A population bottleneck the hypothectical size produced by Toba (1,000-10,000?) would contain many lineages; hence convergence of gene lines (Y, mt or nuclear) is not mandatory, and hence does not conflict with the genetic evidence. --Michael C. Price talk 15:34, 4 April 2007 (UTC)
I stand corrected. "Extremal". I'll read more carefully next time. I will go back to re-read these references to make sure. But my understanding is that most researchers do not believe in a human population bottleneck, when all genes are taken into account. Even though we are not talking about a single breeding pair, 1,000-10,000 is still a small population, and this should leave a definite signature on shape of the gene lineages, when the genome is considered as a whole. But no such evidence has been presented. Fred Hsu 15:48, 4 April 2007 (UTC)
Yes, bottleneck sizes can be inferred by the amount of exant variation, but it is certainly not true that more ancient genetic colascence times (such as mt-Eve at ~150kya) disprove the existence of more recent bottlenecks (such as Toba at 75kya).
Perhaps these paragraphs on various articles should be revised to talk about the shape of gene lineages as a whole, instead of just mentioning the discrepancies between mtDNA and Y-chromosome. Looking at just a few genes (e.g. mt, Y or a few nuclear genes) does not prove nor disprove bottleneck. It is the whole picture which is at odds with Toba catastrophe theory. Fred Hsu 16:05, 4 April 2007 (UTC)
Perhaps it is, I don't know, but the statements about mt-Eve etc were incorrect and I have modified/reverted them.--Michael C. Price talk 16:43, 4 April 2007 (UTC)
Notice that the Ancestor's Tale reference is in opposition to the bottleneck. I've rearrange the pargraphs to make that more clear. Fred Hsu 17:10, 4 April 2007 (UTC)
No, Dawkins' The Ancestor's Tale explicitly supports the volcanic bottleneck of c 70,000 ya. See the The Grasshopper's Tale, p416. I shall amend the article accordingly. --Michael C. Price talk 11:49, 21 May 2007 (UTC)

It's a books.google and while a search turned up bottleneck it did not turn up Toba. FYI CarolMooreDC (talk) 16:47, 18 May 2009 (UTC)

Which primate?[edit]

In the third paragraph of the "examples in animal world" section a mention is made of evdience that a certain primate species has suffered such a bottleneck. It seems like the species name should be given(along with a wikilink if there is a corresponding article) and maybe a citation. I know nothing about this myself so does anyone else know what this refers to? -Joshua Davis 01:20, 16 April 2007 (UTC)

Anti-Malthus[edit]

This article does not explain the premises, symptoms, causes and effects of a population bottleneck in a species. Is it a heuristic theory? Is sounds anti-Malthusian anyway. Anwar (talk) 09:47, 27 May 2008 (UTC)

Human bottleneck[edit]

A bottleneck in the Northern European population (not globally) seems pretty well established by now. One reference is here: "Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population" by Claudia Schmegner1, Josef Hoegel1, Walther Vogel1 and Günter Assum1. http://www.springerlink.com/(p3nnrw55on33n5nobeur1533)/app/home/contribution.asp?backto=issue,14,19;journal,10,510;linkingpublicationresults,1:100421,1 but someone should really do some more research on the other articles referenced before modifying the main page.

Moved this thread here, no comment on it's anonymous and undated initial content or the related ones above. However the fact of a population bottleneck that produced the lack of genetic diversity in the surviving human species relative to the other great apes is well established. What is still controversial are the details, less so about when it occurred because this can be established by examination of the genome and more so about where and why. Either the section should be rewritten to show this or a new article created. Lycurgus (talk) 14:52, 22 November 2009 (UTC)

In summarizing reasons for the extinction of Neanderthals, C.B. Stringer says “Explanantions for their extinction have ranged widely from suggestions of disease or warfare through to economic competition from early modern humans.” (“The Neanderthal-H. sapiens interface in Eurasia,” Neanderthals Revisited, 2006, ed. K. Harvati and T. Harrison) That one glancing reference to “disease” is as far as I’ve gotten in advancing my attempt to explain mitochondrial Eve, the bottle neck in human evolution that occurred 100,000 to 200,000 years ago. My argument follows.

Was the "Bottleneck" the Common Cold?

There is an easy way to make the "out-of-Africa" and "multiregional" claims fit together. Suppose that early homo sapiens (the earliest forms of cro magnon, including so-called Neanderthal, dated pre 200,000 BP) developed in Africa and spread fairly broadly across Europe and Asia. Suppose then that a mutation developed in a small family in Africa that made those in that family resistant to a particular virus, which virus had not yet surfaced. They were resistant but not immune. Meanwhile, the rest of the early human population had no viral resistance. The mutated small family could survive the virus but continued to carry it. Then suppose the virus occurred. The resistant members of the population "had colds" and got over them. The non-resistant population died or were so debilitated that they could not bear and raise offspring, which offspring, if they did occur would die from "the cold." This small group, otherwise not distinguishable from the non-resistant group, flourished. As they traveled or migrated they carried a deadly virus with them that wiped out any homo sapiens they met.

With this scenario, we can explain the broad distribution of homo (sapiens or not, Cro Magnon or not) before the dating of mitochondrial "Eve." And we can still trace all humans back to the singular mother.

One-Paragraph Summary: Disease may have been the factor that decimated all homonids but a small disease-resistant population that developed in Africa 100,000 - 200,000 years ago. Archeologists who discuss the fairly sudden and very sweeping replacement of Neanderthals by Cro Magnons throughout Europe (and perhaps rather quickly the whole world) are presently split between those who argue that Homo Sapiens are a melding of two or more races of the same species (including Neanderthals and Cro Magnons, also possibly Java Men) and those who argue that Homo Sapiens came out of Africa as a single species that overwhelmed the rest of the Hominids around the world, having perhaps developed from mitochonrial “Eve” as recently as 200,000 years ago.

“Out of Africa” experts describe the single species replacement in terms of Cro Magnon superiority, concentrating most frequently on intellectual superiority.  They have DNA evidence on their side They tend to emphasize (exaggerate?) anatomical differences between Neanderthals and Cro Magnons in order to argue that Neanderthals were a separate species, an evolutionary dead end. The “melding” experts cite archeological evidence such as the variety of skull shapes and sizes, the early development of stone tools by Neanderthals, evidence of arts and crafts, and Ngandong fossils to bolster their case.  

What I have not seen is discussion of the possible role of disease in the Cro Magnon takeover. My commentary presents an hypothesis that disease was the factor that decimated all homonids but a small disease-resistant population. We are all descendents of this small population.

Commentary

Archeologists who discuss the fairly sudden and very sweeping replacement of Neanderthals by Cro Magnons throughout Europe (and perhaps rather quickly the whole world) are presently split between those who argue that Homo Sapiens are a melding of two or more races of the same species (including Neanderthals and Cro Magnons, also possibly Java Men) and those who argue that Homo Sapiens came out of Africa as a single species that overwhelmed the rest of the Hominids around the world, having perhaps developed from mitochonrial “Eve” as recently as 200,000 years ago. “Out of Africa” experts describe the single species replacement in terms of Cro Magnon superiority, concentrating most frequently on intellectual superiority. One can find conjecture about superior language use, better tool making ability, even greater artistic sense. They have DNA evidence on their side and develop conjectures about language superiority, sense of family and village cooperation, etc., to bolster their arguement. They tend to emphasize (exaggerate?) anatomical differences between Neanderthals and Cro Magnons in order to argue that Neanderthals were a separate species, an evolutionary dead end. The “melding” camp cites archeological evidence such as the variety of skull shapes and sizes, the early development of stone tools by Neanderthals, evidence of arts and crafts, Ngandong fossils to bolster their case. What I have not seen is discussion of the possible role of disease in the Cro Magnon takeover. We all know that smallpox and other communicable diseases wiped out tribes of American Indians as Europeans made first contact with them. Couldn’t disease have played an important or the only role in Cro Magnon success?

   Christopher Stringer, African Exodus, (p. 156 f.) asks “But if there were primitive humans in Africa 100,000 years ago, why did they take so long to reach Europe, Asia, Australia, and the Americas? . . . . Where were our ancestors lurking and what were they doing? Puzzling.  There are few good answers to these questions.”  He continues from there to speculate about “population fluctuations. . . .  These events -- called bottlenecks -- would have occurred when numbers crashed because of drought, volcanic eruptions, or other natural calamities. People perished, slicing their genetic individuality from posterity.
   “Just consider our mitochondrial DNA’s remarkable uniformity, a certain sign of a recent bottleneck.”

Lewin seems to dismiss bottleneck as a factor without giving it much consideration. Apparently, all he means by this is that he knows of no catastrophe like a volcanic eruption or meteor strike that could cause a sudden population decline. However, I believe that Stringer’s analysis is correct as far as it goes; unfortunately, it does not consider disease as the bottleneck event.

I propose the following as hypothetical steps:

   1. A small group of African individuals developed a mutational resistance to viruses 200,000 years ago.  At that time, there were no seriously debilitating viruses plaguing humankind, but the viruses that existed were carried by humans and other primates. In other words, the mutational ability to resist viruses was not made in a vacuum; the response occurred in reaction to existing, weak, but not debilitating, viruses.
[Apparently neutralist theory would suggest that mutations could have arisen without a context. Mutations occur because they occur, not because environmental forces give rise to them. This may have been, but does not have to be, the case.]
   2. This group of resistant individuals grew over the next 100,000 years to a group of 1,000 to 10,000 fairly closely related individuals populating one or more villages and sharing these villages with others who were in all ways similar except for this mutation. 
   3. Then one of the viruses that we associate with the common cold emerged from quiescence.  Except for our 1000 - 10,000 resistant individuals, the rest of the population suffered from colds that did not let up or go away.  Rather quickly they died.  Offspring they bore died even more quickly.
   4. The 1,000 - 10,000 resistant individuals had colds and carried the cold viruses, but had developed resistance. In these individuals, viral infection triggered the immune response by the activation of white cells which acted as killer cells. The resistant individuals recovered from the colds but as a group were never entirely free of the virus.
   5. Any time these resistant individuals came in contact with others, they tended to infect them.  Their contact left non-resistant others forever suffering from cold symptoms.  The others soon died.  If they propagated before they died, their offspring, born with colds, did not survive the first weeks of life.
   6. The resistant individuals found themselves in an empty world. They thrived and propagated because they had little competition.  In following decades, when their villages again filled up, they moved out from their home valley, and everywhere they went, they found populations either already decimated or very soon decimated after contact with the resistant ones (and the virus they carried).
   7.  These people were probably much like their neighbors across central Africa. They were no more nor less strong, fast, smart, verbal.  Their only special trait was their ability to recover from the common cold. But as they grew in number, they found expansion to new areas to be easy. Wherever they went they found vacant villages or villages that soon 

became vacant.

   8. Around 100,000 - 60,000 BP some Africans moved out of Africa and into the Middle East. These were non-resistant and uninfected Africans. In the Middle East  they found themselves living near Neanderthal strangers who had moved south and east to escape the rigors of the penultimate Ice Age. The non-resistant Africans had little contact with these Neanderthals, but when they inevitably did have contact, they interbred somewhat successfully.  They were of the same species, though genetically separated 

for over 200,000 years and different largely because of environmental factors.

   9. The non-resistant Africans moved east, carrying with them some Neanderthal genetic material.  As they drifted east, they came in contact with other early humans, also different because of separation for at least as long, but also of the same species. There may even have been some homo erectus peoples who were not necessarily (in fact probably not) of the same species.
   10.  Even as this eastern migration was taking place, members of the Cold-resistant, infected African population were moving into the south Mediteranean and the Middle East.   As they moved, the resident populations died off, leaving them with little competition.
   11. The resistant race also took over all of Africa.
   12. The resident populations died off regardless of whether they were Neanderthal, African or Asian.
   13. By 30,000 BP this new, thriving cold-resistant population had replaced other populations throughout Africa, Europe and Asia. The last group of Neanderthals had survived to 30,000 BP because they lived an isolated existence in remote French or Spanish locations where for generations they lived without contact with the resistant 

Africans.

   14. Subsequently, the cold-resistant population populated Australia, the Pacific islands, the Americas. They may well have arrived in the Americas after an earlier migration by non-resistant homonids, but when they came in contact with these peoples, the non-resistant died off quickly.
   15.  This population, having arisen (or descended) from a very small number of individuals, carried the unique traits of that group of individuals.  They had anatomical features that were different from Neanderthals. These differences made them perhaps more articulate, perhaps quicker, even more graceful, perhaps, but not necessarily 

smarter. Whatever their qualities, they are us. Whether we trace our origins to Africa, Europe, Asia, Australia, America, it makes no difference. We have the same ancestors and a much tighter genetic bond than individuals of most species have. Genetically, we have hardly changed over this span of time.

Cautions: any of the following might be true without disqualifying my

basic argument:
   a) The disease was not the common cold but some other disease. The common cold is the best candidate because it is one we have a resistance to but not an immunity to.  (We develop temporary immunities to colds that infect us, but there are around 200 cold viruses, more than any of us are likely to confront in our lifetimes.)
   b) Neanderthals were a separate species, genetically incapable of breeding with Africans but still susceptible to a disease the Africans carried but were resistant to.
   c) In spite of their large brains, Neanderthals were not very smart and/or did not have adequate language skills.
   d) The lighter skeletons of Africans were (or were not) genetically connected to the mutations that made them  resistant to colds (or other disease).
   e) The different skull shapes were (or were not) genetically connected to their resistance to colds (or other disease).

I believe this hypothesis unifies the findings of most Archeologists and leads to a consistent theory of human development. I would be interested in suggestions of how to test it or explanations of why it is faulty. — Preceding unsigned comment added by Ezekial Bargrove (talkcontribs) 21:09, 11 December 2012 (UTC)


Also, with the possible exception of some religious actors, nobody thinks there was a single breeding pair. The estimates I've seen range from a little under a thousand to around 20 thousand. The current text of the section distorts the established scientific consensus. Lycurgus (talk) 10:28, 23 November 2009 (UTC)

Selection on non-existing genes?[edit]

The lead contains the following sentence: These new selective pressures may have acted on genetic variation that has already drifted out of the population. I think it says that at a certain past time selection may have acted on gene alleles that weren't there, because they had drifted to extinction. But selection cannot work on non-existing alleles. I think the intention was to say that some alleles that have been in the population but are no longer here because of drift would have been positively selected on by the present environment if it wasn't for the fact that they are gone. --Ettrig (talk) 07:16, 17 February 2011 (UTC)

I have left a message on the student's talk page welcoming them to the world of peer review!--JimmyButler (talk) 15:52, 17 February 2011 (UTC)
Thanks for your input! That is what I meant when I said that; sorry if my wording was a bit confusing. I will change the sentence now. I'll probably use your words, so I hope that is okay.--Rebekah best (talk) 22:51, 17 February 2011 (UTC)
By the way, thanks for letting me fix it myself. I get points for keeping track of my edits.--Rebekah best (talk) 23:01, 17 February 2011 (UTC)

Little adaptation in small populations?[edit]

This article says: Population bottlenecks reduce the genetic variation and thereby also the population's ability to adapt to new selective pressures. This contrasts with punctuated equilibrium that says: Smaller populations on the other hand, which are isolated from the parental stock, are decoupled from the homogenizing effects of gene flow. In addition, pressure from natural selection is especially intense, as peripheral isolated populations exist at the outer edges of ecological tolerance. One says little adaptation in small populations, the other says more adaptation in smaller populations. Is there a real conflict here? Can the differences be clarified? --Ettrig (talk) 06:06, 18 February 2011 (UTC)

Thank you for all of your help! I don't, however, think there is any real conflict. I think that in punctuated equilibrium the main point of those statements was to show the importance of a large population in achieving equilibrium. Natural selection is more accelerated and more likely to occur in small and isolated populations in order to meet new pressures. It is also more necessary in these conditions. I don't believe that my statements were contradicting this. When I put them in there I only wanted to stress the fact that population bottleneck can cause issues for natural selection if it eliminates alleles that could have been useful. Small and isolated populations are the best opportunities for natural selection and speciation, but not if those populations lack a variety of alleles. If you still feel like some things need to be resolved, let me know and we can work it out. Also, feel free to make any changes you see as necessary. Thanks!--Rebekah best (talk) 20:06, 20 February 2011 (UTC)

Critical number[edit]

Can anything be found/included about what happens when a bottleneck occurs such that the remaining population will go extinct? Like is there even such a thing as a critical mass or something? Another question comes up: would that information be better served in a different article (Extinction)? NYMFan69-86 (talk) 21:35, 3 March 2011 (UTC)

term 'unfavoured' needs quantification.[edit]

from the extant article:

"...inbreeding and genetic homogeneity increases and unfavoured alleles can accumulate."

Consanguinious relations over multiple generations yield a decrease in deleterious recessive alleles, not an increase in them. Because inbreeding increases the probability of recessive traits being expressed, when those traits decrease the fitness of the individual, the individual is unlikely to survive long enough to pass the genes on to another generation.

--Vitki1963 (talk) 15:05, 27 August 2013 (UTC)Vitki1963

Cheetah[edit]

According to its article in the Wikipedia the cheetah went through a population bottleneck, too. Should that be mentioned in the article?--Maxl (talk) 15:52, 2 September 2014 (UTC)