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The paper is about species, not subspecies. The paper says: > Thus, population genetic, phylogenetic, and network analyses of nuclear sequences demonstrate tha

by dalke 10y ago

The paper is about species, not subspecies. The paper says: > Thus, population genetic, phylogenetic, and network analyses of nuclear sequences demonstrate that the giraffe is genetically well structured into four distinct species. This is consistent with divergence times of 1.25 to 2 million years ago (mya) among the four clusters (Figure 3C). That genetic isolation is 100x longer than the human migration to the Americas. It's also 10x longer than the time to "Mitochondrial Eve" and about 8x longer than to "Y-chromosomal Adam". Humans do not meet the phylogenetic criteria which justifies the use of "subspecies". See http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html and many others. Quoting that reference: > Modern human genetic variation does not structure into phylogenetic subspecies (geographical 'races'), nor do the taxa from the most common racial classifications of classical anthropology qualify as 'races' (Box 1). The social or ethnoancestral groups of the US and Latin America are not 'races', and it has not been demonstrated that any human breeding population is sufficiently divergent to be taxonomically recognized by the standards of modern molecular systematics. These observations are not to be taken as statements against doing research on demographic groups or populations. They only support a brief for linguistic precision and careful descriptions of groups under study. Terms and labels have qualitative implications.

MustardTiger 10y ago
>The paper is about species, not subspecies. And my reply is about subspecies, and our refusal to apply the same standards we apply to other animals to ourselves. I do not understand your confusion. >Humans do not meet the phylogenetic criteria which justifies the use of "subspecies" We have greater genetic difference between races than ANY example of subspecies in existence. I am very aware that a large group of people have a political agenda in denying this fact. But no amount of "we can get rid of racism by pretending races don't exist" will change basic facts. DNA does not lie.
- dalke 10y ago
  Yes, my complaint is that you are highjacking an article on species differentiation in giraffes to talk about purported human subspecies. No, we emphatically do not have that high of a genetic difference. Quite the opposite. The diversity in human genetics is relatively small compared to other species. For example, quoting http://www.nature.com/ng/journal/v27/n2/full/ng0201_155.html http://www.nature.com/ng/journal/v27/n2/full/ng0201_155.html : > The extent of DNA sequence variation of chimpanzees is several-fold greater than that of humans[1]. It is unclear, however, if humans or chimpanzees are exceptional among primates in having low and high amounts of DNA sequence diversity, respectively. To address this, we have determined approximately 10,000 bp of noncoding DNA sequences at Xq13.3 (which has been extensively studied in both humans and chimpanzees[1, 2]) from 10 western lowland gorillas (Gorilla gorilla gorilla) and 1 mountain gorilla (Gorilla gorilla beringei; that is, from 2 of the 3 currently recognized gorilla subspecies[3]), as well as 8 Bornean (Pongo pygmaeus pygmaeus) and 6 Sumatran (Pongo pygmaeus abelii) orang-utans, representing both currently recognized orang-utan subspecies[4]. We show that humans differ from the great apes in having a low level of genetic variation and a signal of population expansion. I'll repeat that last line for emphasis: "humans differ from the great apes in having a low level of genetic variation" The paper I linked to previously specifically compares the differences in DNA between chimpanzee subspecies to any putative human subspecies. > We know that there is human geographical variation, but does this infraspecific diversity reach a threshold that merits the designation 'subspecies', as is true with chimpanzees[14]? ... > The within- to between-group variation is very high for genetic polymorphisms (approx85%; refs. 16,17). This means that individuals from one 'race' may be overall more similar to individuals in one of the other 'races' than to other individuals in the same 'race'. This observation is perhaps insufficient[18], although it still is convincing because it illustrates the lack of a boundary. Coalescence times[19, 20] calculated from various genes suggest that the differentiation of modern humans began in Africa in populations whose morphological traits are unknown; it cannot be assumed from an evolutionary perspective that the traits used to define 'races' emerged simultaneously with this divergence[15]. There was no demonstrable 'racial' divergence. ... > Race' is a legitimate taxonomic concept that works for chimpanzees but does not apply to humans (at this time). The nonexistence of 'races' or subspecies in modern humans does not preclude substantial genetic variation that may be localized to regions or populations. DNA doesn't lie. Humans lie, or are mistaken. Please demonstrate that you are not mistaken, and tell us the source of your statement that "We have greater genetic difference between races than ANY example of subspecies in existence". What are the two most distinct human subspecies, and what is their level of DNA similarity? How does that compare to the difference in chimp subspecies?
  - DougWebb 10y ago
    If human races (which clearly exist) are not genetically distinct enough to be considered subspecies, how about the inverse? Can you point out examples of animal species/subspecies that have races? Are different dog breeds the equivalent of human races, for example?
    - danieltillett 10y ago
      Many animal species have races (or sub-species). Dogs breeds are not generally considered as different species despite it being impossible for many to interbreed (think chihuahuas and Great Danes). Isn't biology wonderful :)
    - dalke 10y ago
      In the post you replied to I pointed out gorilla (with three subspecies, two of which are Gorilla gorilla gorilla and Gorilla gorilla beringei) and orang-utans (with Pongo pygmaeus pygmaeus and Pongo pygmaeus abelii) as two species with recognized subspecies. I also earlier mentioned chimpanzees as a species with multiple subspecies. https://en.wikipedia.org/wiki/Common_chimpanzee#Taxonomy https://en.wikipedia.org/wiki/Common_chimpanzee#Taxonomy says there are four. This uses the taxonomic definition of race, which http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html says "Although 'race' and subspecies are usually treated as equivalent, some zoological taxonomists reserve the word 'race' for local breeding populations, with subspecies being geographical collections of populations that are similar or the same in the defining traits." That same article is careful to point out that the taxonomical definition is different from the sociopolitical, "socially constructed" definitions used by humans when talking about themselves. Concerning dogs, https://en.wikipedia.org/wiki/Dog#Taxonomy https://en.wikipedia.org/wiki/Dog#Taxonomy points out that it's unresolved if domesticated animals should be list as a subspecies, so that dogs are "Canis lupus familiaris", or if they are their own species, as in "Canis familiaris". In either case, dog breeds are "artificial variants created by ... selective breeding", from http://vertebrates.si.edu/msw/mswCFApp/msw/taxon_browser.cfm?msw_id=11374&CFID=12634444&CFTOKEN=cc1f55b96a5e34a-FC9CD852-C674-9147-2845FC003C9BEC28&jsessionid=28306b88028b8491c0804d7c347a623b6e31 http://vertebrates.si.edu/msw/mswCFApp/msw/taxon_browser.cfm... . The term "variety" has no formal definition in mammalian taxonomy. See https://en.wikipedia.org/wiki/Variety_(botany)#Other_nomenclature_uses https://en.wikipedia.org/wiki/Variety_(botany)#Other_nomencl... .
- saynsedit 10y ago
  Physical difference is not the same thing as genetic difference. Humans may subjectively look very different but genetically humans aren't very different. This is empiracle fact. Stop living in the 19th century.
  - MustardTiger 10y ago
    Physical difference has nothing to do with the discussion. That is a complete red herring you just pulled out from no where. The empirical fact is that humans are genetically quite different. The genetic distance between human races is greater than many species, and virtually all subspecies distinctions made in the animal kingdom. Stop denying science because of a false belief that lying will somehow get rid of racism.
    - Dylan16807 10y ago
      Humans have accumulated an enormous amount of genetic variation between groups in only a few thousand years? Citation needed.
      - MustardTiger 10y ago
        http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html You can barely even discuss the facts much less publish them because of histrionic accusations of racism and eugenics. Also, it hasn't been a few thousands years, it has been tens of thousands of years at the low end.
        Dylan16807 10y ago
        >The average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1,000 and 1 in 1,500 (refs. 9,10). This proportion is low compared with those of many other species, from fruit flies to chimpanzees11, 12, reflecting the recent origin of our species from a small founding population13. >In other words, approx90% of total genetic variation would be found in a collection of individuals from a single continent, and only approx10% more variation would be found if the collection consisted of Europeans, Asians and Africans. >The pi value for Homo sapiens can be put into perspective by considering that humans differ from chimpanzees at only 1 in 100 nucleotides, on average14, 15. > Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. I'm not sure how this supports your point. What species are separated by a pi value of 1 in 10000 or less?
- Myrmornis 10y ago
  MustardTiger I sympathize with the points you are trying to get across (and the undeserved downvotes and careless replies you are getting). Just one thing though > We have greater genetic difference between races than ANY example of subspecies in existence. You went too far with that comment. I think I know what you're trying to say: that if intrahuman genetic divergence and superficial morphology differences were observed in any other organism it would be classified as subspecies, but as a matter of fact there remain many examples of strongly genetically divergent populations in nature that have not been elevated from subspecies to species, and some which are unlikely to be due to known introgression etc. EDIT: yes I know that introgression doesn't contradict species status for many species definitions, but taxonomy literature is determined by practices local to the community studying the taxon in question and for many taxa introgression is still certainly an argument against classifying as species.
  - MustardTiger 10y ago
    Yes, upon further research I see that you are correct. Thanks for the info.

by dalke 10y ago

MustardTiger 10y ago

>The paper is about species, not subspecies. And my reply is about subspecies, and our refusal to apply the same standards we apply to other animals to ourselves. I do not understand your confusion. >Humans do not meet the phylogenetic criteria which justifies the use of "subspecies" We have greater genetic difference between races than ANY example of subspecies in existence. I am very aware that a large group of people have a political agenda in denying this fact. But no amount of "we can get rid of racism by pretending races don't exist" will change basic facts. DNA does not lie.

dalke 10y ago
Yes, my complaint is that you are highjacking an article on species differentiation in giraffes to talk about purported human subspecies. No, we emphatically do not have that high of a genetic difference. Quite the opposite. The diversity in human genetics is relatively small compared to other species. For example, quoting http://www.nature.com/ng/journal/v27/n2/full/ng0201_155.html http://www.nature.com/ng/journal/v27/n2/full/ng0201_155.html : > The extent of DNA sequence variation of chimpanzees is several-fold greater than that of humans[1]. It is unclear, however, if humans or chimpanzees are exceptional among primates in having low and high amounts of DNA sequence diversity, respectively. To address this, we have determined approximately 10,000 bp of noncoding DNA sequences at Xq13.3 (which has been extensively studied in both humans and chimpanzees[1, 2]) from 10 western lowland gorillas (Gorilla gorilla gorilla) and 1 mountain gorilla (Gorilla gorilla beringei; that is, from 2 of the 3 currently recognized gorilla subspecies[3]), as well as 8 Bornean (Pongo pygmaeus pygmaeus) and 6 Sumatran (Pongo pygmaeus abelii) orang-utans, representing both currently recognized orang-utan subspecies[4]. We show that humans differ from the great apes in having a low level of genetic variation and a signal of population expansion. I'll repeat that last line for emphasis: "humans differ from the great apes in having a low level of genetic variation" The paper I linked to previously specifically compares the differences in DNA between chimpanzee subspecies to any putative human subspecies. > We know that there is human geographical variation, but does this infraspecific diversity reach a threshold that merits the designation 'subspecies', as is true with chimpanzees[14]? ... > The within- to between-group variation is very high for genetic polymorphisms (approx85%; refs. 16,17). This means that individuals from one 'race' may be overall more similar to individuals in one of the other 'races' than to other individuals in the same 'race'. This observation is perhaps insufficient[18], although it still is convincing because it illustrates the lack of a boundary. Coalescence times[19, 20] calculated from various genes suggest that the differentiation of modern humans began in Africa in populations whose morphological traits are unknown; it cannot be assumed from an evolutionary perspective that the traits used to define 'races' emerged simultaneously with this divergence[15]. There was no demonstrable 'racial' divergence. ... > Race' is a legitimate taxonomic concept that works for chimpanzees but does not apply to humans (at this time). The nonexistence of 'races' or subspecies in modern humans does not preclude substantial genetic variation that may be localized to regions or populations. DNA doesn't lie. Humans lie, or are mistaken. Please demonstrate that you are not mistaken, and tell us the source of your statement that "We have greater genetic difference between races than ANY example of subspecies in existence". What are the two most distinct human subspecies, and what is their level of DNA similarity? How does that compare to the difference in chimp subspecies?
- DougWebb 10y ago
  If human races (which clearly exist) are not genetically distinct enough to be considered subspecies, how about the inverse? Can you point out examples of animal species/subspecies that have races? Are different dog breeds the equivalent of human races, for example?
  - danieltillett 10y ago
    Many animal species have races (or sub-species). Dogs breeds are not generally considered as different species despite it being impossible for many to interbreed (think chihuahuas and Great Danes). Isn't biology wonderful :)
  - dalke 10y ago
    In the post you replied to I pointed out gorilla (with three subspecies, two of which are Gorilla gorilla gorilla and Gorilla gorilla beringei) and orang-utans (with Pongo pygmaeus pygmaeus and Pongo pygmaeus abelii) as two species with recognized subspecies. I also earlier mentioned chimpanzees as a species with multiple subspecies. https://en.wikipedia.org/wiki/Common_chimpanzee#Taxonomy https://en.wikipedia.org/wiki/Common_chimpanzee#Taxonomy says there are four. This uses the taxonomic definition of race, which http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html http://www.nature.com/ng/journal/v36/n11s/full/ng1455.html says "Although 'race' and subspecies are usually treated as equivalent, some zoological taxonomists reserve the word 'race' for local breeding populations, with subspecies being geographical collections of populations that are similar or the same in the defining traits." That same article is careful to point out that the taxonomical definition is different from the sociopolitical, "socially constructed" definitions used by humans when talking about themselves. Concerning dogs, https://en.wikipedia.org/wiki/Dog#Taxonomy https://en.wikipedia.org/wiki/Dog#Taxonomy points out that it's unresolved if domesticated animals should be list as a subspecies, so that dogs are "Canis lupus familiaris", or if they are their own species, as in "Canis familiaris". In either case, dog breeds are "artificial variants created by ... selective breeding", from http://vertebrates.si.edu/msw/mswCFApp/msw/taxon_browser.cfm?msw_id=11374&CFID=12634444&CFTOKEN=cc1f55b96a5e34a-FC9CD852-C674-9147-2845FC003C9BEC28&jsessionid=28306b88028b8491c0804d7c347a623b6e31 http://vertebrates.si.edu/msw/mswCFApp/msw/taxon_browser.cfm... . The term "variety" has no formal definition in mammalian taxonomy. See https://en.wikipedia.org/wiki/Variety_(botany)#Other_nomenclature_uses https://en.wikipedia.org/wiki/Variety_(botany)#Other_nomencl... .
saynsedit 10y ago
Physical difference is not the same thing as genetic difference. Humans may subjectively look very different but genetically humans aren't very different. This is empiracle fact. Stop living in the 19th century.
- MustardTiger 10y ago
  Physical difference has nothing to do with the discussion. That is a complete red herring you just pulled out from no where. The empirical fact is that humans are genetically quite different. The genetic distance between human races is greater than many species, and virtually all subspecies distinctions made in the animal kingdom. Stop denying science because of a false belief that lying will somehow get rid of racism.
  - Dylan16807 10y ago
    Humans have accumulated an enormous amount of genetic variation between groups in only a few thousand years? Citation needed.
    - MustardTiger 10y ago
      http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html http://www.nature.com/ng/journal/v36/n11s/full/ng1435.html You can barely even discuss the facts much less publish them because of histrionic accusations of racism and eugenics. Also, it hasn't been a few thousands years, it has been tens of thousands of years at the low end.
      - Dylan16807 10y ago
        >The average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1,000 and 1 in 1,500 (refs. 9,10). This proportion is low compared with those of many other species, from fruit flies to chimpanzees11, 12, reflecting the recent origin of our species from a small founding population13. >In other words, approx90% of total genetic variation would be found in a collection of individuals from a single continent, and only approx10% more variation would be found if the collection consisted of Europeans, Asians and Africans. >The pi value for Homo sapiens can be put into perspective by considering that humans differ from chimpanzees at only 1 in 100 nucleotides, on average14, 15. > Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. I'm not sure how this supports your point. What species are separated by a pi value of 1 in 10000 or less?
Myrmornis 10y ago
MustardTiger I sympathize with the points you are trying to get across (and the undeserved downvotes and careless replies you are getting). Just one thing though > We have greater genetic difference between races than ANY example of subspecies in existence. You went too far with that comment. I think I know what you're trying to say: that if intrahuman genetic divergence and superficial morphology differences were observed in any other organism it would be classified as subspecies, but as a matter of fact there remain many examples of strongly genetically divergent populations in nature that have not been elevated from subspecies to species, and some which are unlikely to be due to known introgression etc. EDIT: yes I know that introgression doesn't contradict species status for many species definitions, but taxonomy literature is determined by practices local to the community studying the taxon in question and for many taxa introgression is still certainly an argument against classifying as species.
- MustardTiger 10y ago
  Yes, upon further research I see that you are correct. Thanks for the info.