11 ms·

DNA analysis reveals there are four distinct giraffe species, not one

109 points by Jerry2 10y ago

thaumasiotes 10y ago
> The findings suggest that genetic exchange among the four species is rare, maybe even nonexistent. This genetic isolation defines them as distinct species, as opposed to subspecies. A bold, up-front assertion that Native Americans were in fact a distinct species from Europeans.
- D4N_ 10y ago
  The quoted statement should be interpreted in the context of the study. Specifically, in the context that "species’ current ranges are not always delineated by geography". The genetic isolation of Native Americans was clearly a result of a geography.
  - MustardTiger 10y ago
    The context does not contradict that statement. Every single measure used on every other animal would at minimum place humans in several subspecies. But we do not apply the same standards to ourselves for political reasons.
    - Retric 10y ago
      Humans have not really had enough time as independent populations to diverge much. The north american land bridge disappeared ~14,500 years ago so only ~14,000 years as separate populations. African > Eurasia had regular exchanges as they where within relatively short walking distances.
      - MustardTiger 10y ago
        >Humans have not really had enough time as independent populations to diverge much There is no scientific basis for that claim. Many other animals have diverged less, in less time and are still separate subspecies. >African > Eurasia had regular exchanges as they where within relatively short walking distances. Interbreeding does not mean subspecies don't exist. Coyotes and wolves are totally separate species and they interbreed. This does not make them the same species, much less the same subspecies. Or the very example given in the article: polar bears and brown bears. Separate species, overlapping geographical regions, crossbreeding occurs in the overlap. Or again from the article example: giraffes. Also note they talk about the genetic distance, but the genetic distance between a west african and an australian aboriginal is greater than the difference between wolves and dogs, which are subspecies. Again, by all measures we use for wild animals, humans consist of several subspecies at least.
        louhike 10y ago
        The thing is we're talking about species here, not subspecies.
        MustardTiger 10y ago
        If you pay attention, we're talking about both. My replies have all very clearly been about subspecies, read my first post.
        Retric 10y ago
        Genetically Brown and polar bears are subspecies not separate species. They have also had 3+X as many generations since the last ice age vs people.
        MustardTiger 10y ago
        People have been separated far longer than just since the ice age. And no, some people think brown bears and polar bears should be reclassified, others do not. As it stands, they are separate species. Take the 2 seconds to google basic information before posting incorrect things that are so easy to verify. Even if you reclassify them, it still supports my point: humans consist of several subspecies.
        Retric 10y ago
        People also talk about Europe and Asia as separate despite being a contiguous landmass on the same plate. Genetically brown and polar bears can and in reality often do interbreed producing viable offspring and exchanging genetic information between populations.
        MustardTiger 10y ago
        >People also talk about Europe and Asia as separate despite being a contiguous landmass on the same plate That analogy is not useful at all. Continents are not biological organisms. >Genetically brown and polar bears can and in reality often do interbreed producing viable offspring and exchanging genetic information between populations And yet they are separate species. Just like the 4 separate species of giraffe the article is about, which can and do all interbreed. The concept of species is in no way reliant on an inability to produce fertile offspring.
      - dogma1138 10y ago
        That's not true we've seen speciation happening in front of our eyes with some species. While time is a factor 14,000 is more than enough for humans to speciate, the reason why this hasn't happened to humans is something that is actually a subject of research today.
        Retric 10y ago
        Humans have a long reproductive cycle, so that's under 1,000 generations. For comparison bacteria can reach 1,000 generations in ideal conditions in less than 1 year.
        dogma1138 10y ago
        We've had documented cases of speciation of various types of animals within only a few generations, birds for example tend to do that rather quickly as well as rapidly form ring species. And this isn't because birds are special but because they tend to migrate, in other cases natural or manmade barriers that split a species into distinct groups have also causes speciation after only a handful of generations. Besides birds where it's common due to migration patterns "man caused" rapid speciation has also been observed in rodents (squirrels/mice) and various types of fish. http://evolution.berkeley.edu/evolibrary/news/100201_speciation http://evolution.berkeley.edu/evolibrary/news/100201_speciat... You do not need a 1000 generations to speciate.
        dalke 10y ago
        The first description in what you pointed to says "could signify the beginning of a speciation event". It doesn't say the result is a new species. The second description concerns a pairing between two hybrids which started a new lineage. It uses the term "lineage" instead of saying there is a new species. > These two examples make it clear that the division between species is not a black-and-white issue. Rather, speciation occurs as many different sorts of traits (physical, behavioral, and genetic) diverge from one another along a continuum. Because of this, biologists sometimes disagree about where to draw the line between incipient species — about when a division has become deep enough to warrant a new species name. Whatever we choose to call them, these two cases clearly illustrate how a lineage can split and begin to make its way down two separate evolutionary paths. Regarding ring species, https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species says "Currently, there are four known forms of life that appear to match the definition of a ring species". Frankly, I thought there were more. It would suggest that birds don't tend to rapidly form ring species. > You do not need a 1000 generations to speciate. Are either of those two cases described in the literature as a new species, or are they given as a subspecies, or variant, or fertile hybrid, or some other term?
      - adekok 10y ago
        > ~14,000 years as separate populations. Perhaps even less. http://www.andrewcollins.com/page/articles/romanbust.htm http://www.andrewcollins.com/page/articles/romanbust.htm There was at least some contact between North America and Europe, close to 2K years ago.
        Retric 10y ago
        The baring strait is also only 51 miles so there was likely quite a bit of accidental crossings if nothing else. For comparison Australia was populated around 65,000 to 75,000 years ago and that takes more than 200 miles by sea.
        danieltillett 10y ago
        I don't think there is any good evidence for Australia being populated before 45,000 years ago. Modern humans hadn't even left Africa 75,000 years ago.
        Retric 10y ago
        Your dates for leaving Africa seem to be off base. Homo sapiens ventured out of Africa around 100,000 years ago https://en.wikipedia.org/wiki/Early_human_migrations https://en.wikipedia.org/wiki/Early_human_migrations There where early tool across Afro-Eurasia as far back as 1.7 to 2.6 million years. Early human ancestors may have maintained separate populations spreading genetic mutations between them with occasional waves of migration displacing existing populations. Supporting the first idea is the wide range of habitat giving advantages to prior populations who are better able to cope with existing conditions. http://www.nature.com/news/teeth-from-china-reveal-early-human-trek-out-of-africa-1.18566 http://www.nature.com/news/teeth-from-china-reveal-early-hum... There really does not seem to be much evidence to tell one way or another.
        danieltillett 10y ago
        The data regarding the early venturing out of Africa is not good, but even the wiki article says humans reached Australia 46,000 years ago.
    - 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?
- bcraven 10y ago
  https://en.wikipedia.org/wiki/Species_problem https://en.wikipedia.org/wiki/Species_problem The word "Species" is mixed up in all manner of biological and sociological turmoil. I was even of the impression that becuase of DNA sequencing the term is falling out of favour amongst researchers.
  - kristofferR 10y ago
    Would DNA sequencing just make it easier to distinguish different species (like in this case) from each other instead of making the term more problematic?
    - Scarblac 10y ago
      It's all a gray area, the distinction between two individuals being the same or different species is pretty arbitrary. DNA sequencing just replaces it with more accurate things (say the amount of DNA two individuals have in common, estimates of how long ago the last common ancestor lived, etc).
    - Myrmornis 10y ago
      The problem is more the definition of the term, rather than availability of adequate data. A lot of biologists (and humans!) grew up thinking that "species" had a clear and obvious definition. One result is that their views are very entrenched and people don't realize that there's even a serious definitional problem at hand affecting a critical area of biology.
    - dogma1138 10y ago
      Well it depends on how you define a "species" this isn't a technical problem this is a philosophical one. The most commonly used definition of a species today is a group that is capable and commonly practices interbreeding between its members. There are different species that are capable of interbreeding and even producing fertile offsprings but they do not breed for various reasons this can be as simple as a geographical barrier or as nuanced as a small visual difference like a red patch of feathers vs a black one that restricts them from breeding outside of their group. A more wider definition of a species is the largest gene pool of individuals technically capable of breeding but this one is not often used. Overall there would be more loose and more strict definition of species that would be used based on the subject matter at any given moment.
dforrestwilson1 10y ago
So is Pluto a planet or not then?
kristofferR 10y ago
Since this wasn't known before, am I right to assume that a lot of giraffes in zoos are hybrids of the different species?
- sandworm101 10y ago
  They were believed to be sub-species and so I doubt zoos mixed and matched. The real outcome seems to be that the species is now 1/4 its previous size. Where there was once one endangered species, now stand four very endangered species. Similar and more dramatic story with mantas: http://news.nationalgeographic.com/news/2008/07/080731-new-ray.html http://news.nationalgeographic.com/news/2008/07/080731-new-r...
  - kristofferR 10y ago
    There's a philosophical question in the fact that something just became more treasured because of DNA testing results, but I'm not even going to attempt answering that.
    - jacobrobbins 10y ago
      the philosophical questions raised by multiple, visually similar species being considered as one have come up before. Zebras were discovered to be 3 separate species. See "What, if anything, is a Zebra?" from 1983 http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf
    - dredmorbius 10y ago
      Value isn't absolute, but a relation between the valuer and that being valued. W.F. Lloyd, 1833, "A Lecture on the Notion of Value as Distinguished Not Only from Utility, but also from Value in Exchange". http://socserv2.socsci.mcmaster.ca/~econ/ugcm/3ll3/lloyd/value http://socserv2.socsci.mcmaster.ca/~econ/ugcm/3ll3/lloyd/val...
    - rcthompson 10y ago
      There's no need to invoke philosophy here. It's pretty well accepted that an ecosystem with less biodiversity is more fragile, and from that perspective the extinction of a species is a concerning event, particularly if the extinction was accelerated by human actions. If new information indicates that a species or group of species is in much greater danger of going extinct than was previously thought, then it makes sense to prioritize conservation efforts for those species more highly.
guessmyname 10y ago
Off topic — How do I click the links at the bottom of this website? EDIT: To clarify, as some people thought this was a stupid question... Every time I scroll down to click one of the links the website scrolls my browser back up and loads a new article below the one I was reading. I don't want to read more articles, I want to click the links at the bottom of the website!!! I was not asking if the links work, they probably do, I am asking how do I "click them" if the website keeps moving the webview back up when I scroll to the bottom?
- wodenokoto 10y ago
  they work for me
  - guessmyname 10y ago
    How? Every time I scroll down to click one of the links the website scrolls my browser back up and loads a new article below the one I was reading. I don't want to read more articles, I want to click the links at the bottom of the website!!! I was not asking if the links work, they probably do, I am asking how do I "click them" if the website keeps moving the webview back up when I scroll to the bottom?
    - nitrogen 10y ago
      Are you talking about the linked site? HN cerainly doesn't do that. As for infinite scrolling, I am definitely not a fan myself, and this is an example of why.
      - Dylan16807 10y ago
        Infinite scrolling is fine as long as you don't try to also have a footer. And as long as it's not the only option.
    - wodenokoto 10y ago
      safari OS X fully updated with adblock, no infinite scrolling on linked site.
dschiptsov 10y ago
The classic operational definition of different species, as far as I remember, is that cross-breading between species is not possible.
- achr2 10y ago
  It's a very blurred line.
  - micahbright 10y ago
    It's really just a social construct.
- seanc 10y ago
  My understanding was that they might be able to crossbreed, but offspring are not fertile, e.g. hybrids such as mules and ligers.
- alexbock 10y ago
  Two individuals may be capable of breeding and reliably producing fertile offspring but still be considered different species if they would never mate "naturally". This may be due to geography, different mating seasons, different songs or appearances, etc.
  - dschiptsov 10y ago
    So, are there different species of people?)
    - frozenport 10y ago
      Not if you consider alcohol.
- openasocket 10y ago
  If only it was! But then we discovered "ring species" (https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species) which threw a monkey wrench into what was once a simple definition. Basically, there are populations of animals A, B and C, where A and B can inter-breed, B and C can inter-breed, but A and C can't. So our definition of species no longer satisfies the transitive property, and it all falls apart. As far as I know, this issue hasn't yet been satisfactorily answered in the case of ring species.
bfuller 10y ago
Giraffes? Giraffes!
Myrmornis 10y ago
A few comments on the academic field that this paper lies in. The aim is to use DNA sequences to make inferences about the history of the populations. It's a really vexed area. The core objective is to make statistical inferences about whether giraffes are one "species" or multiple based on observed DNA sequences. The core problem is that we can't easily know or approximate the relevant probability distributions. Compare species-level giraffe taxonomy with a classification problem in which a large training data set is available, like determining whether a speech recording is male or female. For speech we can collect an arbitrarily large training data set. But for giraffes, the equivalent would be to find a large sample of biological lineages which are in all other respects like giraffes but differ in that some of them are one "species" and some multiple, and collect DNA sequences from each of these. It's fantasy -- it doesn't exist. To go into a bit more detail: to do the inference task we would need at least three things: 1. A definition of "species" 2. The probability distribution of DNA sequences under the null hypothesis 3. (For Bayesian approaches) The probability distribution of DNA sequences under the alternate hypotheses (1) Is a huge problem because many biologists don't think it's necessary to worry about the definition. Putting that aside temporarily: (2). If Giraffes are a single species, what is the probability distribution from which our observed DNA sequences were sampled? The answer is that it depends critically on all sorts of other things: social and reproductive biology of giraffes, giraffe demographics, giraffe post-natal dispersal patterns. Maybe the most important is that it depends on the geographic distribution of savanna vegetation types over the past few million years in sub-saharan Africa. We do not know the effects of any of these on the relevant probability distributions. The field of population genetics does allow us to define probability distributions over sampled DNA sequences, but you have to specify the model. And all the above-listed unknowns and more are relevant to the model. From a formal statistical point of view you could place priors on these unknown things and simulate from the marginal distribution of interest, but in practice that is of course fantasy: there's no convincing way to choose priors for such things, and there's no way to test it because giraffe evolution happened once only. (3). See (2). The upshot of all this is that while making evolutionary inferences from DNA sequences is a fascinating discipline, it has some serious challenges and limitations: we need to recognize that it is not in as happy a place as other sorts of statistical inferences for which arguments can be made about the relevant probability distributions needed to make the inference. There is a huge disconnect between the statistical and theoretical machinery used in the field, and the ability of practitioners to understand that material. This is absolutely fair enough: people publishing papers on a particular species are likely to be ecologists and conservation biologists; but to understand coalescent theory and the statistical inference techniques used requires graduate-level understanding of stochastic processes, statistical inference theory, computational statistics and other stuff from discrete math etc. But that's not to imply that it would all be fine if people publishing the papers were professional computational statisticians. The real problem is that while we wish that we had the ability to make, and more importantly test, these inferences, the truth is that it's a wildly ambitious inference problem. Throwing fancy math and computational statistics algorithms at it will get some people tenure, and will make graduate students in organismal biology feel intimidated, but it doesn't change that problem.
sndean 10y ago
I'm pretty happy with a (the?) species definition in microbiology: <97% 16S rRNA gene sequence identity? You're a different species [0]. It's a little more complicated than that, and some important people (especially in the older generation) don't like it, but it's a good / quick standard. [0] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/
- benkuykendall 10y ago
  Presumably a "species" should be an equivalence class, right? So the relation "A and B are of the same species" should be transitive, symmetric, and reflexive. Symmetry is easy (an organism shares 100% of its genome with itself) as is reflexivity (A shares n% with B iff B shares n% with A). However, transitivity does not follow obviously: for example, A and B could share 98%, B and C could share 98%, but A and C could share 96%. Which species(es) do the three belong to?
  - rcthompson 10y ago
    Unfortunately, speciation is mostly a continuous process, so there's no way to define species by some kind of "degree of similarity/dissimilarity" metric and have it be a transitive relationship. Any species definition that is completely transitive will necessarily have edge cases where two extremely similar organisms fall on different sides of an arbitrary threshold and are declared to belong to two different species. The classic example of non-transitive species relationships from sexually reproducing organisms is a "ring species": https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species
    - sn9 10y ago
      A continuous process and also a human construct that we created to help us reason about how that continuous process works. Every biology major learns about the different species concepts/definitions [0] and why different subfields of biology might prioritize one over another. [0] https://en.wikipedia.org/wiki/Species https://en.wikipedia.org/wiki/Species
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109 points by Jerry2 10y ago

> The findings suggest that genetic exchange among the four species is rare, maybe even nonexistent. This genetic isolation defines them as distinct species, as opposed to subspecies. A bold, up-front assertion that Native Americans were in fact a distinct species from Europeans.

D4N_ 10y ago
The quoted statement should be interpreted in the context of the study. Specifically, in the context that "species’ current ranges are not always delineated by geography". The genetic isolation of Native Americans was clearly a result of a geography.
- MustardTiger 10y ago
  The context does not contradict that statement. Every single measure used on every other animal would at minimum place humans in several subspecies. But we do not apply the same standards to ourselves for political reasons.
  - Retric 10y ago
    Humans have not really had enough time as independent populations to diverge much. The north american land bridge disappeared ~14,500 years ago so only ~14,000 years as separate populations. African > Eurasia had regular exchanges as they where within relatively short walking distances.
    - MustardTiger 10y ago
      >Humans have not really had enough time as independent populations to diverge much There is no scientific basis for that claim. Many other animals have diverged less, in less time and are still separate subspecies. >African > Eurasia had regular exchanges as they where within relatively short walking distances. Interbreeding does not mean subspecies don't exist. Coyotes and wolves are totally separate species and they interbreed. This does not make them the same species, much less the same subspecies. Or the very example given in the article: polar bears and brown bears. Separate species, overlapping geographical regions, crossbreeding occurs in the overlap. Or again from the article example: giraffes. Also note they talk about the genetic distance, but the genetic distance between a west african and an australian aboriginal is greater than the difference between wolves and dogs, which are subspecies. Again, by all measures we use for wild animals, humans consist of several subspecies at least.
      - louhike 10y ago
        The thing is we're talking about species here, not subspecies.
        MustardTiger 10y ago
        If you pay attention, we're talking about both. My replies have all very clearly been about subspecies, read my first post.
      - Retric 10y ago
        Genetically Brown and polar bears are subspecies not separate species. They have also had 3+X as many generations since the last ice age vs people.
        MustardTiger 10y ago
        People have been separated far longer than just since the ice age. And no, some people think brown bears and polar bears should be reclassified, others do not. As it stands, they are separate species. Take the 2 seconds to google basic information before posting incorrect things that are so easy to verify. Even if you reclassify them, it still supports my point: humans consist of several subspecies.
        Retric 10y ago
        People also talk about Europe and Asia as separate despite being a contiguous landmass on the same plate. Genetically brown and polar bears can and in reality often do interbreed producing viable offspring and exchanging genetic information between populations.
        MustardTiger 10y ago
        >People also talk about Europe and Asia as separate despite being a contiguous landmass on the same plate That analogy is not useful at all. Continents are not biological organisms. >Genetically brown and polar bears can and in reality often do interbreed producing viable offspring and exchanging genetic information between populations And yet they are separate species. Just like the 4 separate species of giraffe the article is about, which can and do all interbreed. The concept of species is in no way reliant on an inability to produce fertile offspring.
    - dogma1138 10y ago
      That's not true we've seen speciation happening in front of our eyes with some species. While time is a factor 14,000 is more than enough for humans to speciate, the reason why this hasn't happened to humans is something that is actually a subject of research today.
      - Retric 10y ago
        Humans have a long reproductive cycle, so that's under 1,000 generations. For comparison bacteria can reach 1,000 generations in ideal conditions in less than 1 year.
        dogma1138 10y ago
        We've had documented cases of speciation of various types of animals within only a few generations, birds for example tend to do that rather quickly as well as rapidly form ring species. And this isn't because birds are special but because they tend to migrate, in other cases natural or manmade barriers that split a species into distinct groups have also causes speciation after only a handful of generations. Besides birds where it's common due to migration patterns "man caused" rapid speciation has also been observed in rodents (squirrels/mice) and various types of fish. http://evolution.berkeley.edu/evolibrary/news/100201_speciation http://evolution.berkeley.edu/evolibrary/news/100201_speciat... You do not need a 1000 generations to speciate.
        dalke 10y ago
        The first description in what you pointed to says "could signify the beginning of a speciation event". It doesn't say the result is a new species. The second description concerns a pairing between two hybrids which started a new lineage. It uses the term "lineage" instead of saying there is a new species. > These two examples make it clear that the division between species is not a black-and-white issue. Rather, speciation occurs as many different sorts of traits (physical, behavioral, and genetic) diverge from one another along a continuum. Because of this, biologists sometimes disagree about where to draw the line between incipient species — about when a division has become deep enough to warrant a new species name. Whatever we choose to call them, these two cases clearly illustrate how a lineage can split and begin to make its way down two separate evolutionary paths. Regarding ring species, https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species says "Currently, there are four known forms of life that appear to match the definition of a ring species". Frankly, I thought there were more. It would suggest that birds don't tend to rapidly form ring species. > You do not need a 1000 generations to speciate. Are either of those two cases described in the literature as a new species, or are they given as a subspecies, or variant, or fertile hybrid, or some other term?
    - adekok 10y ago
      > ~14,000 years as separate populations. Perhaps even less. http://www.andrewcollins.com/page/articles/romanbust.htm http://www.andrewcollins.com/page/articles/romanbust.htm There was at least some contact between North America and Europe, close to 2K years ago.
      - Retric 10y ago
        The baring strait is also only 51 miles so there was likely quite a bit of accidental crossings if nothing else. For comparison Australia was populated around 65,000 to 75,000 years ago and that takes more than 200 miles by sea.
        danieltillett 10y ago
        I don't think there is any good evidence for Australia being populated before 45,000 years ago. Modern humans hadn't even left Africa 75,000 years ago.
        Retric 10y ago
        Your dates for leaving Africa seem to be off base. Homo sapiens ventured out of Africa around 100,000 years ago https://en.wikipedia.org/wiki/Early_human_migrations https://en.wikipedia.org/wiki/Early_human_migrations There where early tool across Afro-Eurasia as far back as 1.7 to 2.6 million years. Early human ancestors may have maintained separate populations spreading genetic mutations between them with occasional waves of migration displacing existing populations. Supporting the first idea is the wide range of habitat giving advantages to prior populations who are better able to cope with existing conditions. http://www.nature.com/news/teeth-from-china-reveal-early-human-trek-out-of-africa-1.18566 http://www.nature.com/news/teeth-from-china-reveal-early-hum... There really does not seem to be much evidence to tell one way or another.
        danieltillett 10y ago
        The data regarding the early venturing out of Africa is not good, but even the wiki article says humans reached Australia 46,000 years ago.
  - 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?
bcraven 10y ago
https://en.wikipedia.org/wiki/Species_problem https://en.wikipedia.org/wiki/Species_problem The word "Species" is mixed up in all manner of biological and sociological turmoil. I was even of the impression that becuase of DNA sequencing the term is falling out of favour amongst researchers.
- kristofferR 10y ago
  Would DNA sequencing just make it easier to distinguish different species (like in this case) from each other instead of making the term more problematic?
  - Scarblac 10y ago
    It's all a gray area, the distinction between two individuals being the same or different species is pretty arbitrary. DNA sequencing just replaces it with more accurate things (say the amount of DNA two individuals have in common, estimates of how long ago the last common ancestor lived, etc).
  - Myrmornis 10y ago
    The problem is more the definition of the term, rather than availability of adequate data. A lot of biologists (and humans!) grew up thinking that "species" had a clear and obvious definition. One result is that their views are very entrenched and people don't realize that there's even a serious definitional problem at hand affecting a critical area of biology.
  - dogma1138 10y ago
    Well it depends on how you define a "species" this isn't a technical problem this is a philosophical one. The most commonly used definition of a species today is a group that is capable and commonly practices interbreeding between its members. There are different species that are capable of interbreeding and even producing fertile offsprings but they do not breed for various reasons this can be as simple as a geographical barrier or as nuanced as a small visual difference like a red patch of feathers vs a black one that restricts them from breeding outside of their group. A more wider definition of a species is the largest gene pool of individuals technically capable of breeding but this one is not often used. Overall there would be more loose and more strict definition of species that would be used based on the subject matter at any given moment.

dforrestwilson1 10y ago

So is Pluto a planet or not then?

kristofferR 10y ago

Since this wasn't known before, am I right to assume that a lot of giraffes in zoos are hybrids of the different species?

sandworm101 10y ago
They were believed to be sub-species and so I doubt zoos mixed and matched. The real outcome seems to be that the species is now 1/4 its previous size. Where there was once one endangered species, now stand four very endangered species. Similar and more dramatic story with mantas: http://news.nationalgeographic.com/news/2008/07/080731-new-ray.html http://news.nationalgeographic.com/news/2008/07/080731-new-r...
- kristofferR 10y ago
  There's a philosophical question in the fact that something just became more treasured because of DNA testing results, but I'm not even going to attempt answering that.
  - jacobrobbins 10y ago
    the philosophical questions raised by multiple, visually similar species being considered as one have come up before. Zebras were discovered to be 3 separate species. See "What, if anything, is a Zebra?" from 1983 http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf
  - dredmorbius 10y ago
    Value isn't absolute, but a relation between the valuer and that being valued. W.F. Lloyd, 1833, "A Lecture on the Notion of Value as Distinguished Not Only from Utility, but also from Value in Exchange". http://socserv2.socsci.mcmaster.ca/~econ/ugcm/3ll3/lloyd/value http://socserv2.socsci.mcmaster.ca/~econ/ugcm/3ll3/lloyd/val...
  - rcthompson 10y ago
    There's no need to invoke philosophy here. It's pretty well accepted that an ecosystem with less biodiversity is more fragile, and from that perspective the extinction of a species is a concerning event, particularly if the extinction was accelerated by human actions. If new information indicates that a species or group of species is in much greater danger of going extinct than was previously thought, then it makes sense to prioritize conservation efforts for those species more highly.

guessmyname 10y ago

Off topic — How do I click the links at the bottom of this website? EDIT: To clarify, as some people thought this was a stupid question... Every time I scroll down to click one of the links the website scrolls my browser back up and loads a new article below the one I was reading. I don't want to read more articles, I want to click the links at the bottom of the website!!! I was not asking if the links work, they probably do, I am asking how do I "click them" if the website keeps moving the webview back up when I scroll to the bottom?

wodenokoto 10y ago
they work for me
- guessmyname 10y ago
  How? Every time I scroll down to click one of the links the website scrolls my browser back up and loads a new article below the one I was reading. I don't want to read more articles, I want to click the links at the bottom of the website!!! I was not asking if the links work, they probably do, I am asking how do I "click them" if the website keeps moving the webview back up when I scroll to the bottom?
  - nitrogen 10y ago
    Are you talking about the linked site? HN cerainly doesn't do that. As for infinite scrolling, I am definitely not a fan myself, and this is an example of why.
    - Dylan16807 10y ago
      Infinite scrolling is fine as long as you don't try to also have a footer. And as long as it's not the only option.
  - wodenokoto 10y ago
    safari OS X fully updated with adblock, no infinite scrolling on linked site.

dschiptsov 10y ago

The classic operational definition of different species, as far as I remember, is that cross-breading between species is not possible.

achr2 10y ago
It's a very blurred line.
- micahbright 10y ago
  It's really just a social construct.
seanc 10y ago
My understanding was that they might be able to crossbreed, but offspring are not fertile, e.g. hybrids such as mules and ligers.
alexbock 10y ago
Two individuals may be capable of breeding and reliably producing fertile offspring but still be considered different species if they would never mate "naturally". This may be due to geography, different mating seasons, different songs or appearances, etc.
- dschiptsov 10y ago
  So, are there different species of people?)
  - frozenport 10y ago
    Not if you consider alcohol.
openasocket 10y ago
If only it was! But then we discovered "ring species" (https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species) which threw a monkey wrench into what was once a simple definition. Basically, there are populations of animals A, B and C, where A and B can inter-breed, B and C can inter-breed, but A and C can't. So our definition of species no longer satisfies the transitive property, and it all falls apart. As far as I know, this issue hasn't yet been satisfactorily answered in the case of ring species.

bfuller 10y ago

Giraffes? Giraffes!

Myrmornis 10y ago

A few comments on the academic field that this paper lies in. The aim is to use DNA sequences to make inferences about the history of the populations. It's a really vexed area. The core objective is to make statistical inferences about whether giraffes are one "species" or multiple based on observed DNA sequences. The core problem is that we can't easily know or approximate the relevant probability distributions. Compare species-level giraffe taxonomy with a classification problem in which a large training data set is available, like determining whether a speech recording is male or female. For speech we can collect an arbitrarily large training data set. But for giraffes, the equivalent would be to find a large sample of biological lineages which are in all other respects like giraffes but differ in that some of them are one "species" and some multiple, and collect DNA sequences from each of these. It's fantasy -- it doesn't exist. To go into a bit more detail: to do the inference task we would need at least three things: 1. A definition of "species" 2. The probability distribution of DNA sequences under the null hypothesis 3. (For Bayesian approaches) The probability distribution of DNA sequences under the alternate hypotheses (1) Is a huge problem because many biologists don't think it's necessary to worry about the definition. Putting that aside temporarily: (2). If Giraffes are a single species, what is the probability distribution from which our observed DNA sequences were sampled? The answer is that it depends critically on all sorts of other things: social and reproductive biology of giraffes, giraffe demographics, giraffe post-natal dispersal patterns. Maybe the most important is that it depends on the geographic distribution of savanna vegetation types over the past few million years in sub-saharan Africa. We do not know the effects of any of these on the relevant probability distributions. The field of population genetics does allow us to define probability distributions over sampled DNA sequences, but you have to specify the model. And all the above-listed unknowns and more are relevant to the model. From a formal statistical point of view you could place priors on these unknown things and simulate from the marginal distribution of interest, but in practice that is of course fantasy: there's no convincing way to choose priors for such things, and there's no way to test it because giraffe evolution happened once only. (3). See (2). The upshot of all this is that while making evolutionary inferences from DNA sequences is a fascinating discipline, it has some serious challenges and limitations: we need to recognize that it is not in as happy a place as other sorts of statistical inferences for which arguments can be made about the relevant probability distributions needed to make the inference. There is a huge disconnect between the statistical and theoretical machinery used in the field, and the ability of practitioners to understand that material. This is absolutely fair enough: people publishing papers on a particular species are likely to be ecologists and conservation biologists; but to understand coalescent theory and the statistical inference techniques used requires graduate-level understanding of stochastic processes, statistical inference theory, computational statistics and other stuff from discrete math etc. But that's not to imply that it would all be fine if people publishing the papers were professional computational statisticians. The real problem is that while we wish that we had the ability to make, and more importantly test, these inferences, the truth is that it's a wildly ambitious inference problem. Throwing fancy math and computational statistics algorithms at it will get some people tenure, and will make graduate students in organismal biology feel intimidated, but it doesn't change that problem.

sndean 10y ago

I'm pretty happy with a (the?) species definition in microbiology: <97% 16S rRNA gene sequence identity? You're a different species [0]. It's a little more complicated than that, and some important people (especially in the older generation) don't like it, but it's a good / quick standard. [0] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/

benkuykendall 10y ago
Presumably a "species" should be an equivalence class, right? So the relation "A and B are of the same species" should be transitive, symmetric, and reflexive. Symmetry is easy (an organism shares 100% of its genome with itself) as is reflexivity (A shares n% with B iff B shares n% with A). However, transitivity does not follow obviously: for example, A and B could share 98%, B and C could share 98%, but A and C could share 96%. Which species(es) do the three belong to?
- rcthompson 10y ago
  Unfortunately, speciation is mostly a continuous process, so there's no way to define species by some kind of "degree of similarity/dissimilarity" metric and have it be a transitive relationship. Any species definition that is completely transitive will necessarily have edge cases where two extremely similar organisms fall on different sides of an arbitrary threshold and are declared to belong to two different species. The classic example of non-transitive species relationships from sexually reproducing organisms is a "ring species": https://en.wikipedia.org/wiki/Ring_species https://en.wikipedia.org/wiki/Ring_species
  - sn9 10y ago
    A continuous process and also a human construct that we created to help us reason about how that continuous process works. Every biology major learns about the different species concepts/definitions [0] and why different subfields of biology might prioritize one over another. [0] https://en.wikipedia.org/wiki/Species https://en.wikipedia.org/wiki/Species

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