Talk:Population genetics

Mutation

I just rewrote the mutation section to improve the balance, add structure, and remove some annoying non sequiturs. I welcome comments. It is maybe 20 to 40 % too long relative to other topics. Even though I wrote this, I feel like there is too much focus on mutation qua deleterious pressure vs. mutation qua source of novelty, but that kinda reflects the field of pop gen. Anyway, the way to make this better, I think, is to shorten it and link out as informatively as possible to mutation-related topics. Dabs (talk) 00:56, 5 April 2023 (UTC)

The Coalescent

Given that all (well, most) modern population genetics revolves around coalesence theory (The Coalescent), there really ought to be a page....There is (for example) already a page on Ewens's sampling formula --DJO 22:24, 19 Apr 2005 (UTC)

Except that the word the should probably not be included in the article title, and if it's included, coalescent should probably have a lower-case initial c. Michael Hardy 22:50, 19 Apr 2005 (UTC)

Point taken - I think that since people usually refer to The Coalescent, it should probably be The coalescent in Wikipedia, or even better Coalescence theory--DJO 08:21, 20 Apr 2005 (UTC)

I prefer coalescence (genetics). - Samsara 00:28, 29 December 2005 (UTC)

Mayr and Dobzhansky

Would it be inappropriate to link Mayr and Dobzhansky as founders of the modern synthesis (maybe Huxley too?), unless you consider them too recent...Slrubenstein

Not at all, but I think that should be on the modern synthesis page, as neither Mayr nor Dobzhansky developed population genetics theory themselves very much (although they obviously did use population genetics). In fact we should probably reword the page, population genetics didn't really "spring" from the modern synthesis, but the other way around, pop gen was an ingredient in the modern synthesis, along with biometrics, paleontology, systematics etc. Douglas Futuyma's Evolutionary Biology (Sinauer 1997) has a very nice breakdown of the contributions of various areas of biology to the modern synthesis. -- Lexor 22:33 22 May 2003 (UTC)

Recruiting for Wikibooks Biology book(s)

Warm greetings from sister project Wikibooks where I am writing a general biology textbook all by my lonesome. My profs donated a sizable bunch of notes that make up the structure of an entire introductory biology book. However these notes are in outline form and need to be fleshed out into full text. Then, some images .. I am confident that this will become the standard college text over time but need some help to get it there. --karlwick

Should this article get merged with quantitative genetics ???

No! Quantitative genetics is a study of the genetic basis of complex (i.e. multi-gene) traits. This may be evolutionary, but more often that not is in terms of artificial breeding/selection. Population genetics is a study of the causes and effects of genetic variation within (and between) populations.--DJO 21:56, 19 Apr 2005 (UTC)

Dysgenics

It'd be nice if the "dysgenics" article could have a better explanation of it's status in current population genetics. I've looked up some stuff at a library, but didn't find anything much :-P I can't tell if it's an avoided subject, something disproved ages ago, or just something nobody cares much about. Flammifer

I've made it a genetics stub. - Samsara 14:08, 9 January 2006 (UTC)

Epistasis - nearly non-stub

Dear All,

I've done a considerable amount of work on the epistasis article today (compared to what was there previously). I am hopeful that we can let it stand as a proper article rather than a stub if one more person who knows anything about it puts in an equivalent amount of work. I'll try and find a few published references for it. Please edit away, and make suggestions on the talk page as to what else might be included. Genetic interactions (where some of the original material contributed to epistasis has found a new home) could perhaps be improved at the same time. Thanks. - Samsara 14:01, 9 January 2006 (UTC)

Math

there's also a considerable amount of math behind population genetics. It would perhaps be useful to include some formuli.

External Links

The basic science of public health genomics is "human genome epidemiology," the set of methods for collecting, analyzing, and synthesizing data on the distribution of gene variants, gene-disease associations, and gene-environment and gene-gene interactions. Population-based epidemiologic studies are the basis for estimating the absolute, relative, and attributable risks that gauge the effects of genomic factors on the health of individuals and populations. Find out more at http://www.cdc.gov/genomics/population.htm

Overpopulation Inbreeding

Overpopulation Inbreeding is a fifth aspect of population genetics which is missing from all the models described so far in the article. It was developed by Wade Gielzecki.

Illustration of the population genetics: Take a population of couples that have a random number of children. There are no restraints on growth to the population. The average number of children per generation the couples have is 2, the maximum is 4 which say is had by one couple only. In the second generation the children in the 4 child family mate with children from 2 child families and these new couples produce 3 children each, whereas the rest of the population again has an average of 2 children. In the third generation, the 12 children in this largest family line are under evolutionary pressure to inbreed, because if they do they will have 3.5 children on average, whereas otherwise they will have only 2.5 children on average. The more generations pass, the more often inbreeding accelerates the growth of the largest family. Natural defenses to inbreeding built up in circumstances of restricted growth are lost to the inbred line. A syndrome develops where the inbred line rejects non-relatives as mates. The largest line overwhelms the rest of the population until the population is far more homozygous (inbred) than it was at the start.

In n generations a subset of the population having c children has offspring on the order of c to the n th power. The subset with the most children outnumbers the rest of the population in not many generations, making the population completely inbred.

This inclusion to population genetics is backed up: 1) Human first cousin marriages indeed produce more children than average. 2) Studies of human genetic variation find no subheterogeniety within races. 3) Aboriginals are relatively outbred. 4) Other primates than man are far more outbred. (eg. Chimpanzees have 10 times the heterozygosity of man.) 5) Dysgenia studies find human dysgenia has consistently been the case for the last century except for the World War II years when the population grew explosively in the last century.

This genetics model predicts declines and long periods of stability whereas natural selection does not. It is an additional factor to existing models postulating genes for the number of offspring humans and other animals have. —Preceding unsigned comment added by 174.137.217.177 (talk) 20:30, 8 March 2011 (UTC)

s or 2s

I believe the probability of a new beneficial allele going to fixation is 2s, and edited the article to say so, with a cite to J.A. Orr; nevertheless, anyone disagree? Evercat (talk) 17:35, 5 July 2012 (UTC)

New review articles on human population genetics based on studies of ancient DNA

Wikipedia has a lot of interesting articles based on the ongoing research in human molecular genetics that helps trace the lineage of people living in various places on the earth. I've been reading university textbooks on human genetics "for fun" since the 1980s, and for even longer I've been visiting my state flagship university's vast BioMedical Library to look up topics on human medicine and health care policy. On the hypothesis that better sources build better articles as all of us here collaborate to build an encyclopedia, I thought I would suggest some sources for improving articles on human genetic history and related articles. The Wikipedia guidelines on reliable sources in medicine provide a helpful framework for evaluating sources.

The guidelines on reliable sources for medicine remind editors that "it is vital that the biomedical information in all types of articles be based on reliable, third-party, published sources and accurately reflect current medical knowledge."

Ideal sources for such content includes literature reviews or systematic reviews published in reputable medical journals, academic and professional books written by experts in the relevant field and from a respected publisher, and medical guidelines or position statements from nationally or internationally recognised expert bodies.

The guidelines, consistent with the general Wikipedia guidelines on reliable sources, remind us that all "Wikipedia articles should be based on reliable, published secondary sources" (emphasis in original). They helpfully define a primary source in medicine as one in which the authors directly participated in the research or documented their personal experiences. By contrast, a secondary source summarizes one or more primary or secondary sources, usually to provide an overview of the current understanding of a medical topic. The general Wikipedia guidelines let us know that "Articles should rely on secondary sources whenever possible. For example, a review article, monograph, or textbook is better than a primary research paper. When relying on primary sources, extreme caution is advised: Wikipedians should never interpret the content of primary sources for themselves."

Two review articles in prominent journals about human population genetics are bringing together analysis of the many recent studies of human DNA, including DNA from ancient individuals.

• Hawks, John (2013). "Significance of Neandertal and Denisovan Genomes in Human Evolution". Annual Review of Anthropology. 42. Annual Reviews: 433–449, 438. doi:10.1146/annurev-anthro-092412-155548. ISBN 978-0-8243-1942-7. ISSN 0084-6570. Retrieved 4 January 2014. The shared evolutionary history of living humans has resulted in a high relatedness among all living people, as indicated for example by the very low fixation index (F_ST) among living human populations. {{cite journal}}: Invalid |ref=harv (help)

• Pickrell, Joseph K.; Reich, David (September 2014). "Toward a new history and geography of human genes informed by ancient DNA". Trends in Genetics. 30 (9): 377–389, 378. doi:10.1016/j.tig.2014.07.007. PMC 4163019. PMID 25168683. Retrieved 16 September 2014. However, the data also often contradict models of population replacement: when two distinct population groups come together during demographic expansions the result is often genetic admixture rather than complete replacement. This suggests that new types of models – with admixture at their center – are necessary for describing key aspects of human history ([14–16] for early examples of admixture models). {{cite journal}}: Invalid |ref=harv (help)

Earlier studies of this issue were based on more limited samples (fewer genes, and fewer human individuals from fewer regions and only recent times). As more samples of more genes from more individuals from more places and times are gathered, the molecular evidence is making it increasingly clear that human beings have been moving back and forth across the Earth's surface and mixing genes over long distances ever since their earliest ancestors moved out of the human homeland in Africa. -- WeijiBaikeBianji (talk, how I edit) 16:03, 18 September 2014 (UTC)

lead

"Population genetics is the study of the distributions and changes of allele frequency in a population, as it is subject to four main evolutionary processes: selection, genetic drift, mutation and genetic recombination."

First, a grammatical issue: "allele frequency" should be 'allele frequencies', because there is generally more than one allele -- each allele has a frequency, multiple alleles have frequencies. Also "distributions and changes of" should possibly be reworded, as change *in* allele frequencies is more common than change *of* allele frequencies. Perhaps 'the study of the distribution and changes in frequency of alleles in a population' would be a suitable replacement.

Second, I have a problem understanding the sentence, mainly the part after the comma, mainly "as it is subject to". Can anyone explain what this means? and what it means in the context of the sentence? I interpret it as 'Population genetics is influenced by four main evolutionary processes and therefore is the study of the distributions and changes of allele frequency in a population'; which, grammatical issues aside, makes little to no sense to me. I'll offer a suggestion for what I think the author may have been meaning to say, and regardless of their intent may make a better lead anyway 'Population genetics is the study of the distribution and change in frequency of alleles within populations, and as such it sits firmly within the field of evolutionary biology'.

Finally, in relation to the 'four evolutionary processes': surely death is an important factor in evolution. As mutation adds variation, death removes variation. I know it's a fundamental component of natural selection, but I'm not sure if natural selection captures all effects of death. Gene flow (distinct from genetic recombination) should also be included as a process, rather than mentioned with the non-evolutionary processes in the following sentence.

A suggestion for the lead paragraph: 'Population genetics is the study of the distribution and change in frequency of alleles within populations, and as such it sits firmly within the field of evolutionary biology. The main processes of evolution (selection, drift, gene flow, mutation, recombination) form an integral part of the theory that underpins population genetics. Studies in this branch of biology examine such phenomena as adaptation, speciation, population subdivision, and population structure.' 129.127.101.245 (talk) 07:22, 22 September 2015 (UTC)

Death is part of both natural selection and genetic drift. It is therefore in there already. There were previously long conversations about where to put gene flow. It does not actually change allele frequencies. You could rework everything I suppose to talk about genotype frequencies instead: this would be a major rewrite. The current text is at least internally consistent. Joannamasel (talk) 20:56, 22 September 2015 (UTC)

Joanna, that isnt what gene flow says, right in the second sentence it says "Migration into or out of a population may be responsible for a marked change in allele frequencies" having described said migration as gene flow in the 1st sentence. Makes sense to me. ♫ RichardWeiss talk contribs 16:43, 23 September 2015 (UTC)

Yes, from the perspective of the local subpopulation from which migration happens into / out of. No, from the perspective of the metapopulation/species. Joannamasel (talk) 00:03, 24 September 2015 (UTC)

this is a population genetics article though, and as such is from the perspective of the population, not the metapopulation/species. Not to mention, hybridisation is a thing -- gene flow across species. Also, it's strange that you say death is part of genetic drift (although I don't disagree with you), because there's no specific mention of death on the genetic drift page (although it's sort of covered in this line "[snip] chance has a role in determining whether a given individual survives and reproduces"). Maybe something should be added there to make it more clear?129.127.101.245 (talk) 05:21, 25 September 2015 (UTC)

I'm not opposed to the change re gene flow, but I would not interpret the term "population genetics" so narrowly. In the scientific literature, the most traditional, classical population genetics studies are those studying differentiation by allele frequency across different subpopulations. Joannamasel (talk) 15:42, 25 September 2015 (UTC)

Okay, I’ll make the change re: gene flow.

Regarding interpretations of population genetics, it seems like you’re arguing semantics – it comes down to what you consider a population or a sub-population. However, by the most logical and objective definition I’ve come across, populations are generally panmictic (Waples and Gaggiottit, 2006). Therefore, allele frequencies shouldn't differ across sub-populations, so studying “differentiation by allele frequency across different subpopulations” would be futile.

It seems there are no other objections to my proposed changes, so I will go ahead and make them.129.127.101.245 (talk) 01:34, 29 September 2015 (UTC)

Remove evolution of mutation rate

Remove this section? The evolutionary forces determining mutation rates are far from settled within the literature, with my favorite being drift. While the section could be re-written to give a more nuanced view of how mutation rates evolve, the whole section seems tangential to the main article on population genetics. LarryBoy79 (talk) 20:13, 14 January 2016 (UTC)

Regarding recent edits to the section: I know the section gives a very poor treatment of the topic, but there is no consensus on what evolutionary mechanisms are the dominant determinants of mutation rates. I don't think we can claim victory for any particular view, and even if we could, this summary here should at least be brought into agreement with the main article on mutation rate evolution. LarryBoy79 (talk) 14:13, 9 March 2016 (UTC)

Forces view

This page currently represents just one view of population genetics, the "forces" view grounded in change in allele frequencies, representing disagreements within this perspective, but not representing disagreements with the perspective itself. There are serious problems with this archaic view of forces: for details and an alternative see http://www.journals.uchicago.edu/doi/abs/10.1086/677571?journalCode=qrb. Over the next few weeks, I hope to put this page through a major overhaul, and make it as pluralistic in its view of population genetics as possible. Joannamasel (talk) 17:30, 3 September 2016 (UTC)

A Commons file used on this page has been nominated for deletion

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Population, evolution, and psychology

Hello @CommonKnowledgeCreator: I'm not sure population genetics and evolutionary psychology are connected enough to justify [1][2][3]. I'm not sure they're not. Can you explain? Invasive Spices (talk) 23 January 2023 (UTC)

@Invasive Spices: There are still some evolutionary psychologists (as well as evolutionary biologists and evolutionary anthropologists) who argue in favor of some version of group selection (particularly in relation to recent human evolution), so I would argue that it's not unrelated (even though evolutionary psychology, unlike behavioural genetics, is supposed to be about human universals rather than individual or group differences). Per the Population article, population geneticists typically define a population as a "set of organisms in which any pair of members can breed together". Following that definition, a set of organisms that only includes members of one sex of an organism that reproduces sexually (e.g. men or women) cannot be a population because its members would be incapable of breeding on their own.

In turn, sexually dimorphic traits, such as those where humans display sex differences, cannot be defined described as displaying group differences, and sex differences in psychology cannot or should not be described as group differences either and why they are part of evolutionary psychology (despite often being described as group differences). The population genetics definition of a population is what clarifies this, and such clarification is necessary because some of the issues related to sex differences (particularly sexual jealousy) are not peripheral topics in evolutionary psychology. For what reasons are you confident that evolutionary psychology and population genetics are not sufficiently related for the inclusion of links to the Population genetics and Population articles in the "Related subjects" section of the Evolutionary psychology navbox? -- CommonKnowledgeCreator (talk) 00:39, 24 January 2023 (UTC)

If I understand correctly you are saying that the question Are particular groups populations is highly relevant to evo psych. If that is correct then I agree. Invasive Spices (talk) 22:00, 2 February 2023 (UTC)

@Invasive Spices: That's exactly what I'm saying, even though evolutionary psychology is supposed to be about cultural universals and the suite of psychological adaptations that constitute behavioral modernity rather than group differences. In keeping with WP:NPOV and WP:FRINGE however, group selection and topics related to it (like how a population is defined in population genetics) should be included in the EP navbox even though it is the heterodox position versus the social selectionist position in debates about altruism and cheater-detection in relations with non-kin. But that's why they are included in the "Related subjects" section rather than the "Processes" or "Areas" sections as opposed to how it was before.

(Personal aside: When I was an undergraduate student at a post-secondary institution in the 2010s and not concentrating in biology, psychology, or anthropology, students that I encountered whose academic concentrations were in biology were not able to explain to me why group selection is not the mainstream viewpoint even though it hasn't been so since the 1960s and I was aware of that. All the more reason why I need to get around to expanding the Group selection article's Criticism section and overhauling the Social selection article.) -- CommonKnowledgeCreator (talk) 18:47, 3 February 2023 (UTC)