A new species of orangutan? I doubt it.

Until this week, there were two species of orangutan: the Bornean (Pongo pygmaeus) and the Sumatran (Pongo abelii), living on different islands. These were considered subspecies until 20 years ago, when the measured divergence of their mitochondrial DNA sequences led to them being separated as distinct species.

But now a new paper in Current Biology by Alexander Nater et al. (the “al.s” are numerous: see below for free reference, with the pdf here) adds a third species, P. tapanuliensis, also from Sumatra. Since new great ape species aren’t often described—the last was the Bornean/Sumatran orangs, and before that it was the bonobo, recognized as distinct from the chimp in 1933)—this has gotten a lot of attention, including in the BBC, in Science, and  the Guardian.

But this biologist isn’t going along. Not only do I see this new “species” as merely an isolated and genetically differentiated population (as are many human populations regarded as H. sapiens), but I’d also contend that there is only one species of orangutan overall, with these three groups all being subspecies. Sadly, a lot of systematists don’t see it that way, as they seem to think that any isolated population, if it can be told apart morphologically or genetically from others, warrants being named as a new species. Yet to evolutionists, a “species” is not an arbitrary segment of nature’s continuum, but real entities that maintain their “realness” because they don’t exchange any (or many) genes with other such entities where they cohabit in nature.

On to the paper:

The new species, called the Tapnuli orangutan, as seen in the Guardian’s figure below, occupies only a small patch of forest south of lake Toba, about 1000 km², and numbers only about 800 individuals. They weren’t found until 1997 as the population (endangered due to habitat loss) lies south of the range of P. abelii and was assumed not to harbor orangs. The population is threatened because it’s small and much of the prime habitat is subject to logging.

 

Is this a separate species? While most of the media accept this uncritically, I’m dubious. That’s because the authors base the description on morphological differences and genetic divergence alone (with morphology of the skull based on a single individual, though one that lies outside the ranges of the other species). They give little information on reproductive isolation, and what information they give suggests that the two “species” of Sumatran orang did interbreed. (Data show genetic interchange between the two Sumatran “species” until about 20,000 years ago, when the two groups became completely isolated by the loss of suitable habitat between them.)

What we have, then, is a geographically isolated population of orang that has some morphological difference from the others, some genetic divergence from the others, but has no present opportunity to see if it can interbreed with others when they co-occur in nature: the criterion used in the “biological species concept”. Thus calling P. tapanuliensis a new species is a pure judgment call.  Here are the results of the authors’ analysis:

  • The three orangs are related like this: the Sumatran orang split off from the other two about 3.4 million years ago, so the Tapnuli and Bornean orangs are the most closely related—somewhat surprising as they live on different islands. But the area has been repeatedly sundered by volcanism and sea-level changes over the past several million years, so we don’t know the historical sequence of geographic changes in the ancestor.
  • DNA analysis shows that the  Tapnuli and Bornean orangs diverged about 700,000 years ago: about the same time as the divergence between the modern human and (extinct) Neanderthal lineage. The two populations on Sumatra are, as I said, about 3.4 million years old.
  • The Tapnuli and (northern) Sumatran orangs continued to exchange genes (particularly Y chromosomes, since males are the most mobile sex) up to about 20,000 years ago;  that stopped because the habitat between these two more distantly-related species prevented gene exchange. But clearly these anciently-diverged orangs were capable of hybridizing when they encountered each other, and the hybrids must have been at least partly fertile since Y chromosomes moved between them. It’s likely, then, that the more closely related Tapnuli and Bornean orangs would also be able to successfully hybridize were they to meet. We already know that the Bornean and Sumatran species hybridize well in zoos and produce fertile hybrids (called “cocktail orangutans”).
  • One specimen of Tapnuli orang shot by a local was measured; its cranial dimensions put it outside the range of the other two “species”, so there are likely to be diagnostic differences in the skeletons of this and the other two species, though we need more speciments of P. tapanuliensis.
  • The Tapnuli orangs have a different color and different calls from the other two “species”

So what we have is an isolated population of orangutans that split off about 700,000 years ago from a lineage now inhabiting Borneo. Somewhat isolated from the populations on both Sumatra and Borneo, it accumulated morphological and genetic differences, and possibly difference in vocalization, though these could be cultural?

But is it a new species?

I say no: it’s just an isolated population that’s somewhat different, with individuals being diagnosable. If you use the Biological Species Concept of evolutionists, which deems populations to be different species if they could not produce fertile hybrids when encountering each other in the wild, I’d say that the evidence of interbreeding until physical separation was complete only 20,000 years ago suggests that the Tapnuli and Sumatran orangs are a single species, which also means that the Sumatran and Bornean orangs are a single species as well. My guess would be that the new species would produce fertile hybrids with both of the other “species” in captivity.

If you consider the Tapnuli orang a new species, then you’ll have to consider Neandthals a species different from H. sapiens, for they diverged about 700,000 years ago and also hybridized successfully when they met: that’s why most humans carry some Neanderthal genes—the remnants of that ancient hybridization. Yet Neanderthals are considered by many biologists and anthropologists to be a subspecies of H. sapiens (H. sapiens neanderthalensis vs. H. sapiens sapiens).

If we call every genetically differentiated and diagnosable population a new species, then there’s no end to the mishigass.  We surely don’t call genetically diagnosable populations of humans different species, and yes, if you have enough genes you can diagnose human populations pretty accurately.

Sadly, nearly everyone in the media has uncritically bought into this designation of a new species of great ape—save one scientist quoted in the Guardian:

Dr Andrew Marshall of University of York, said that the study highlighted the importance of conservation, and added that there might even be further species of great ape to be discovered.

But Professor Volker Sommer from University College London was less bowled over, pointing out that there is no clear criteria for what constitutes a new species. “Any bunch of expertised biologists can invent a new species, if they get their arguments together,” he said.

One more point: all the media, as well as the paper itself, emphasize that the new “species” is small in numbers and lives in endangered habitat, and so must in the future be the subject of intensive conservation efforts. Perhaps naming the population as a new species excites people because of the conservation implications, though in the U.S. the Endangered Species Act mandates the conservation of populations, not just species, so if these apes were in America, naming them as a new species would have no implications for conservation.

In the end, we have no strong evidence that this new species—nor the already-named Bornean and Sumatran orangs—would show any reproductive isolation from the other “species” were they to come into contact in nature. All we have is a geographically isolated population that has some genetic and morphological differentiation. To call it a new “species” turns taxonomy into a completely arbitrary exercise, which, as Dr. Sommer notes, becomes purely subjective. Until we have evidence of reproductive isolation or potential isolation between this population and the others, I’d say “forget about calling it a new species.” And on top of that I’d say that “calling the Bornean and Sumatran orangs different species is also a purely subjective decision”. If the latter two produced sterile offspring in zoos, I’d be down with calling those species different. But they don’t: they produce “cocktail orangs.” LUMP ALL THE ORANGS!

It would have been nice had the media asked a few evolutionary biologists whether this population qualifies as a new species. And I’d ask them this: if we really have an astounding new species of great ape here, why wasn’t it published in Nature or Science? My guess is because those journals would bridle at making that call on the basis of the data presented.

h/t: Matthew Cobb

UPDATE: Just as I finished my bit above, I got an email from Greg Mayer, who said he’d contribute his take on the orangs, too. I’m just pasting it in here without reading it so you can get his opinion. (The title of this post is for my bit alone.)

[Note from GCM: The title is Jerry’s, but I concur, so I’m adding it to mine as a second contribution. We spoke briefly by phone this morning, so knew each other’s reaction to the paper was dubious, but wrote separately.]

A new species of orangutan? I doubt it. II.

By Greg Mayer:

The paper’s chief conclusion—that there is a second species of orangutan on Sumatra—is not well-supported by the data presented.

The morphological analysis is risible. They have a single (1!!!) specimen, and compare it to only 33 others. The analysis boils down to “Can we tell this one from the other ones?” They say yes, but that’s not clear from the evidence presented. The most obvious method of doing so—presenting an ordination (e.g. principal components) of the morphological measurements, and showing that the single specimen lies well outside the cloud of points formed by the  other 33—is not used.  They do show several one-dimensional PC plots, and the single specimen is outside the range of variation on a single axis. (Curiously, their first few PC axes account for very little variation, which is highly unusual. This could be explained in the methods, but, as is usual these days, the methods are not in the paper, but in a supplement). They note, as though it supports their claims, that the single specimen is not in the interquartile range of 24 of 39 skull measurements. “Outside of the interquartile range” ?!?—that didn’t qualify as a subspecies in the heyday of oversplitting!

Of course, even if they could recognize this single individual, that wouldn’t mean anything other than individuals are different from one another. If you gave me 34 people, I’d be able to tell them all apart with 39 measurements– that wouldn’t, of course, come close to showing they belonged to different species. (It would be especially easy to tell them apart if 1 of the people was from Sicily, and the other 33 from Germany.) A minimal morphological analysis would require showing that the means and ranges of population multivariate phenotypes are such that individuals in the population are either diagnostically or statistically distinct.

The call differences are presented perfunctorily and incompletely, so no inferences can be drawn. Differences in calls, which are of potential interest as they may entail reproductive isolation (e.g., as in frogs), possibly have large cultural components in orangs (as they do in humans), and thus require careful study to determine their characteristics and effects.

The genetic analysis, taken at face value, indicates gene flow quite recently, until the habitats became geographically separated, directly contradicting their claim of specific status. That the single Y chromosome observed nests neatly within other Sumatran orangs again subverts their claim. I have been unable to determine how many individuals of the “new” species were genotyped in some way– Table S4 in the supplement should have that information, but that table is not in what downloads, and clicking on what seems to be a link to it goes nowhere.

I have additional issues: Does demographic reconstruction software really work? If species are anything I can can distinguish, doesn’t that make everything a different species? Have you tried applying that concept to extant Homo?

The plaintive defense of “operational species” concepts is a bit sad, and deeply confused conceptually. Citing Gorilla and Neaderthals as supporting their case again does the opposite, because there is only one species of Gorilla and Neanderthals are conspecific with sapiens, as the very genetic studies they cite prove. Their own studies prove the conspecificity of their “new ” species.

The above is obviously a quick reaction, not a complete analysis, but fell free to use any or all of it in your post.

I used it all.

___________

Nater, A., M. P. Mattle-Greminger, A. Nurcahyo, M. G. Nowak, M. de Manuel, T. Desai, C. Groves, M. Pybus, T. B. Sonay, C. Roos, A. R. Lameira, S. A. Wich, J. Askew, M. Davila-Ross, G. Fredriksson, G. de Valles, F. Casals, J. Prado-Martinez, B. Goossens, E. J. Verschoor, K. S. Warren, I. Singleton, D. A. Marques, J. Pamungkas, D. Perwitasari-Farajallah, P. Rianti, A. Tuuga, I. G. Gut, M. Gut, P. Orozco-terWengel, C. P. van Schaik, J. Bertranpetit, M. Anisimova, A. Scally, T. Marques-Bonet, E. Meijaard, and M. Krützen. 2017. Morphometric, behavioral, and genomic evidence for a new orangutan species. Current Biology, in press. DOI: http://dx.doi.org/10.1016/j.cub.2017.09.047

77 Comments

  1. Posted November 3, 2017 at 12:10 pm | Permalink

    “Yet to evolutionists, a “species” is not an arbitrary segment of nature’s continuum, but real entities that maintain their “realness” because they don’t exchange any (or many) genes with other such entities.”

    I’ve a question for you Dr PCCE. It has always seemed to me that among all the taxonomic ranks we have devised for the shrubbery of life, it is species alone that is biologically significant. The rest of the taxonomic ranks are categorization; where the rubber meet the road – that is, where evolution actually occurs- is at the species level. So it would seem to me that at the species taxonomic rank it makes sense that all claims about it must be robust and parsimonious as (if I am correct) this is the only rank that has any biological meaning. One skull with some differences in morphology doesn’t seem like very robust evidence for the taxonomic rank that actually has biological meaning.

    Is this a fair understanding of taxonomy as it relates to biology and evolution?

    • GBJames
      Posted November 3, 2017 at 12:16 pm | Permalink

      I don’t see why other levels of taxonomic organization aren’t equally “real”. They represent the most recent common ancestors of whatever more sub-units you might be considering. MCRAs were real beings.

      • Posted November 3, 2017 at 12:27 pm | Permalink

        Not true, because there are multiple levels of ancestry, so you could make a genus out of a pair of sister species, or out of that pair and the most recently related species to them, and so on. A phylogeny may be real, but not a particular genus, since deciding how to group species into genera is a more or less arbitrary decision. Remember that there is only a small and fixed number of groupings.

        You are confusing the reality of ancestry with the existence of human reifications like genera.

        • GBJames
          Posted November 3, 2017 at 12:39 pm | Permalink

          Got it. Of course.

        • nicky
          Posted November 3, 2017 at 6:35 pm | Permalink

          “You are confusing the reality of ancestry with the existence of human reifications like genera.” That really is the crux of much confusion. Don’t confuse the reality of ancestry with human reifications… beautiful!
          It should be the title page in any book on taxonomy, like the “Don’t Panic” in the ‘Hitchhiker’s Guide’

        • Posted November 7, 2017 at 11:57 am | Permalink

          What I often ask is: do you reify (say) halogens? There’s no evolutionary relationship, which makes it somewhat disanalogous, but it makes for an interesting way into exploring the alternatives.

      • Guilherme Garbino
        Posted November 6, 2017 at 5:08 am | Permalink

        A big difference between species and all other “higher” categories is that the cohesion of species is kept by ongoing processes, while all other categories (families, genera), orignated by the same processes that happened in the past. So for this reason I think that delimiting these other categories is more arbitrary than delemiting species (which does not mean that species delimitation is not arbitrary at all)

    • Posted November 3, 2017 at 12:16 pm | Permalink

      Yep. Species are real units in nature, by and large, and understanding why nature is discontinuous, why you can tell that a bird outside your window is a robin or a pigeon or a cardinal with no problems, is THE problem of speciation. “Higher level groups,” like genera and so on, are more or less arbitrary distinctions, and have no objective reality like species do. See chapter 1 of my book Speciation written with Allen Orr.

      • Posted November 3, 2017 at 12:19 pm | Permalink

        I have the book and will review it. I thought I’d read that.

      • Posted November 3, 2017 at 1:47 pm | Permalink

        Thank you!

    • Posted November 3, 2017 at 5:29 pm | Permalink

      The confusion here is, I believe, between ranking and grouping criteria. As a systematists you have to first group individuals into a taxon, and then you have to assign a rank to that taxon.

      Grouping should be done objectively, by relatedness. Ranking however – is this group of plants a tribus or a subtribus? – is arbitrary above and below the species level, merely a human convention, and strongly informed by tradition.

      There are colleagues who also believe that the species level is arbitrary, but I believe that is wrong, although that discussion would take book length on its own.

      • nicky
        Posted November 5, 2017 at 4:02 am | Permalink

        The species concept is definitely reflecting reality, but it has some fuzzy fringes. That is to be expected of course, since evolution is true 🙂

    • Seth cohen
      Posted November 5, 2017 at 5:55 pm | Permalink

      Evolution occurs at the gene level, not the species level. However, the species is still distinct from the other taxonomic levels, which have practical but still externally imposed boundaries. Species have a functional definition: a pool of interacting genes via the mechanism of interbreeding individuals. This is the most useful and clear definition this taxonomic level that I have seen. In this case since the gene pool of this orang population does not interbreed with that of Sumatran orangutans and if it is shown that there is a functionally and statistically significant difference in the gene frequencies of functional genes within those gene pools, then I would have to consider it a separate species.

  2. GBJames
    Posted November 3, 2017 at 12:12 pm | Permalink

    sub

  3. Posted November 3, 2017 at 12:15 pm | Permalink

    A new species or orangutan?

    Must resist obvious Trump joke… Sorry, can’t.

    • nicky
      Posted November 5, 2017 at 4:03 am | Permalink

      Typo: ‘of’ not ‘or’, but still 🙂 🙂 🙂

  4. garman
    Posted November 3, 2017 at 12:16 pm | Permalink

    “I say no: it’s just an isolated population that’s somewhat different, with individuals being diagnosable. If you use the Biological Species Concept of evolutionists, which deems populations different species if they could produce fertile hybrids when encountering each other in the wild”

    I think there’s a typo here. Shouldn’t it be “deems populations different species if they could NOT produce fertile hybrids”. Right?

  5. Posted November 3, 2017 at 12:24 pm | Permalink

    There was some interesting stuff on orangutans on the week’s QI. They are amazing escape artists. Ken Allen, the ‘Hairy Houdini’, apparently planned his escapes by observing the keeper’s behaviour much like a human would.

    • nicky
      Posted November 3, 2017 at 6:42 pm | Permalink

      Orangutans are not unique there, we have ratels (aka honey-badgers) too.
      And the no 1 champ escapist -I’m not 100% sure if there is unanimity there- is the octopus. Yes, it does use observation.

  6. Posted November 3, 2017 at 12:29 pm | Permalink

    A very good and detailed post. I had just heard about this on Science News.
    I expect that the interpretation that this could be a new species of great ape is in large part because its a bigger deal to discover a new species of this group rather than a new race of this group. The authors are being careerist.

    I do think though that the sympathy for preserving a new species will be broader than for preserving a new race. So the media will be reluctant to spin things in the other direction.

    • nicky
      Posted November 3, 2017 at 6:45 pm | Permalink

      You are undoubtedly right about a new species being more sexy in conservation terms. Jerry did mention it, but truth should prevail…

  7. busterggi
    Posted November 3, 2017 at 12:31 pm | Permalink

    I wish we would come up with a new ape species, I have vague hope that the orang pendak may yet turn out to be a new siamang or gibbon. But no, if isolated populations are going to be pronounced new species than what does that say about small town USA?

    • nicky
      Posted November 3, 2017 at 6:47 pm | Permalink

      In terms of cosmogeny and ideas they might as well be a different species 🙂

  8. Jenny Haniver
    Posted November 3, 2017 at 12:32 pm | Permalink

    I know only from a few high school Mendelian peas and am thoroughly confused –PCC(E) writes “If you use the Biological Species Concept of evolutionists, which deems populations different species if they could produce fertile hybrids when encountering each other in the wild.” I don’t understand why it wouldn’t be that populations would be considered different species if they could NOT produce fertile hybrids. I’ve got my head up my fundament and need a fundamental explanation from someone to clear up my confusion.

    • Jenny Haniver
      Posted November 3, 2017 at 12:33 pm | Permalink

      I see that my question was answered as I was framing it. At least I’m not quite as dumb as I thought!

  9. Paul S
    Posted November 3, 2017 at 1:19 pm | Permalink

    I don’t understand why they wouldn’t be considered a subspecies. E.g. all tigers are subspecies of Panthera tigris. Isn’t this the same?

    • Posted November 3, 2017 at 2:43 pm | Permalink

      Given the probable relationships (as in this is probably not a new species but is instead a regionally distinct variety), it seems ok to me for the rest of us to consider this a subspecies.

  10. Curt Nelson
    Posted November 3, 2017 at 1:29 pm | Permalink

    I would think one problem with identifying the orangutans as separated species, when one could reasonably argue they are not, is that when it comes to saving them from extinction it would be beneficial to cross breed the different groups to increase their genetic diversity. Respecting the groups as separate species could therefor be bad for them all.

    • Posted November 3, 2017 at 1:40 pm | Permalink

      That, in fact, is exactly what zoos are doing making “cocktail orangs” by breeding Sumatran and Bornean orangs. They’re trying to keep the genetic diversity of both populations in captivity.

      • Tom
        Posted November 6, 2017 at 5:20 am | Permalink

        As far as I know, the SSP for orangutans does explicitly mention that hybrids do not breed in captivity. Orangutans are bred as two different species: Sumatran and Bornean.

        • Posted November 6, 2017 at 5:38 am | Permalink

          From the NYT:

          http://www.nytimes.com/1995/02/28/science/orangutan-hybrid-bred-to-save-species-now-seen-as-pollutant.html?pagewanted=all

          IGNORE the absurd nickname Junior: this scowling, hulking he-ape, his fur like flame and his belly like Buddha’s, his face ostentatiously swollen with the fatty cheek flaps and throat sac of a fully mature male, is not the sort to elicit clucks and kootchie-koos from the human primates who watch him through the Plexiglas of his zoo enclosure. As the oldest male orangutan at the National Zoo (29 years old in April), and the father of five other orangutans here, Junior looks the perfectly feral ambassador for his species, the Great Red Ape, a piece of the jungle caged but never conquered.

          In fact, Junior, or Atjeh as he is more formally named, is an entirely zoo-made creation, a version of orangutan that almost certainly would never be found in the forests of Indonesia, the ape’s native home. He and about 80 other orangutans in captivity around the country are zoo-bred crosses between two subspecies of orangutans, those originating in Borneo and those from the neighboring island of Sumatra. They are called hybrids, or “cocktail orangutans,” or simply mutts, and they are history.

          Many scientists lately have decided that Sumatran and Bornean orangutans are so genetically distinct they may even qualify as separate species. They are more genetically different from one another than lions are from tigers, or chimpanzees are from the more gracile bonobos, said Dr. Stephen J. O’Brien, a molecular geneticist at the National Cancer Institute who has studied orangutan DNA.

          As a result of the recent molecular work, the Indonesian Government and the organization that oversees zoo programs in the United States has called a halt to interbreeding Sumatran and Bornean orangutans and to allowing the current crop of hybrids to reproduce. Despite the endangered status of orangutans in the wild, the cocktails will not be considered a genetic reservoir for possibly replenishing wild populations. Atjeh and others like him have been vasectomized, tubally ligated or implanted with heavy-duty birth control treatments. The hybrids will serve out their time in zoos (which can be a long time, for orangutans live up to 60), but as sexual beings they are pongo non grata.

          • Tom
            Posted November 6, 2017 at 5:45 am | Permalink

            The website mentions that the hybrids are a non-breeding population

            “A third, non-breeding population is made up of hybrid orangutans, which are crosses between the two species.”

            http://www.orangutanssp.org/the-ssp.html

        • Posted November 6, 2017 at 5:42 am | Permalink

          Could you give a link, because the SSP page implies that they do, and so they sterilize the hybrids, which I think means they are fertile:

          http://www.orangutanssp.org/taxonomy.html

          Because the species (at the time, subspecies) distinction was not clearly understood until the late 1980s, there was a sizeable population of “hybrid” orangutans in captivity worldwide. In 1985, the Orangutan SSP adopted a policy placing a moratorium on the production of hybrid orangutans. The other regional captive management programs (Europe and United Kingdom, Australia and New Zealand, Southeast Asia, Japan) adopted similar policies during the same time period. In 1994, the Orangutan SSP Steering Committee extended the policy to recommend that permanent surgical sterilization be accomplished for all hybrid orangutans held in situations in which there was any possibility of potential reproduction (whether by accident or by design), if the health of the animal permitted such surgery. This recommendation was based on the fact that despite the 1985 breeding moratorium, a low rate of production of hybrid orangutans persisted through accident; constraints on captive holding space made it difficult to find future suitable homes for orangutans thus produced unintentionally; and despite the potential value of hybrid orangutans as social companions and in assisted reproductive technology or other research, the Steering Committee did not believe that value would ever outweigh the potential risk inherent in maintaining their intact reproductive status. The preferred methods of sterilization are tubal ligation for females and vasectomy for males.

          • Tom
            Posted November 6, 2017 at 5:46 am | Permalink

            BTW: I don’t doubt that Bornean and Sumatran orangutans can interbreed. Just the part about cocktail orangutans seems weird, as the hybrids are non-breeding.

    • HBB
      Posted November 3, 2017 at 3:24 pm | Permalink

      I think this is an interesting practical point. IIRC, if this situation were occurring in the US, the “cocktail orangs” could not be federally protected in the wild under the US Endangered Species Act because the ESA prohibits hybrids (i.e., crosses between different species)from being protected. This was part of the original ruckus with listing the red wolf under the ESA. Florida panthers and Illinois prairie chickens benefited genetically from crosses with individuals from different subspecies from Texas and Kansas, respectively.

      • Posted November 3, 2017 at 7:03 pm | Permalink

        Subspecies, and geographical population segments, can be protected under the ESA, so cocktail orangs would be protected if they were members of the same species.

        GCM

  11. Posted November 3, 2017 at 1:32 pm | Permalink

    Is it just a coincidence that the ‘four species of giraffe’ paper and the ‘new’ orang were published in Current Biology?

    • Posted November 3, 2017 at 1:38 pm | Permalink

      I dunno; maybe the journal uses reviewers that like the “separate lineage” species concept.

    • nicky
      Posted November 3, 2017 at 6:50 pm | Permalink

      splitters and lumpers 🙂

  12. Mark Perew
    Posted November 3, 2017 at 1:42 pm | Permalink

    Clade Time for Pongo

    • HBB
      Posted November 3, 2017 at 3:12 pm | Permalink

      Wow – Nice one! Ronald Reagan must be spinning in his grave. Thanks!

    • Posted November 3, 2017 at 4:31 pm | Permalink

      🙂

    • Diane G.
      Posted November 5, 2017 at 3:51 am | Permalink

      Lol!

  13. Posted November 3, 2017 at 1:52 pm | Permalink

    Excellent post, thanks to both of you.

    When I heard this on the BBC (website plus via NPR yesterday or the day before) my initial reaction was: Too much hype! Can’t be true (or should I say, not very likely).

    viz:

    Prof Wich told BBC News that the decades of collaborative genetic, anatomical and acoustic studies had achieved an “amazing breakthrough”.

    “There are only seven great ape species – not including us,” he said. “So adding one to that very small list is spectacular.

    “It’s something I think many biologists dream of.”

    Yes, I’m sure they do — hence the hype.

    I’m am not surprised that you and Greg (with much, much better analysis and knowledge) feel the same way.

    The media really gloss over the paucity of data that supports the authors’ conclusions.

  14. Alex
    Posted November 3, 2017 at 2:00 pm | Permalink

    Hello, I doubt the new species based only on one exemplar, but I strongly encourage you to read De Queiroz, 2007 about species concept, maybe could help change some ideas.

    • Posted November 3, 2017 at 2:06 pm | Permalink

      I’ve read that and several other papers by De Queiroz, and it hasn’t changed my mind. I discuss some of his ideas in my book Speciation with Allen Orr. That paper simply reiterates the idea that a species is a “metapopulation lineage” that evolves separately from other lineages. See the Appendix of our book where I discuss and criticize the “lineage” concept of species, of which this is a specimen. It’s not by any means a “unifying” species concept, but I’ll refer you to the Appendix to see my reasons.

  15. Liz
    Posted November 3, 2017 at 2:08 pm | Permalink

    “…the Biological Species Concept of evolutionists, which deems populations to be different species if they could not produce fertile hybrids when encountering each other in the wild…”

    That is the way I learned it.
    So I just have a question, though. Wouldn’t horses and donkeys be the same species still because the female mules are able to reproduce with the male parent animal to make foals? That would be fertile offspring even though the male mules are sterile. I tried to figure out if the foals that the female mules give birth to are able to reproduce. This is what I found from this article: http://www.denverpost.com/2007/07/25/mules-foal-fools-genetics-with-impossible-birth/

    “Ryder said that tests in the Nebraska case showed there was no evidence the mother passed along any genetic markers from her father – a donkey that was also the father of the foals. The phenomenon is called “hemiclonal transmission,” which in simple terms means that the mare’s genes canceled out the male’s genes as if they didn’t even exist. That phenomenon has been observed in amphibians but not in mammals. ‘No recombinations took place. There was no reassortment. We looked at markers on every chromosome,’ Ryder said. “This was an extremely unexpected finding.’”

    What does that mean? I looked it up but don’t really know. Can the foal (jule and jack/stallion) offspring potentially reproduce with each other, a jule, or even a mare, jenny, jack, or stallion?

    “Until we have evidence of reproductive isolation or potential isolation between this population and the others, I’d say ‘forget about calling it a new species.’” Would horses and donkeys being different species be because of the potential isolation? Mules aren’t completely sterile and I have no idea about the mule foals that the jules give birth to. It’s so interesting.

    • Posted November 3, 2017 at 2:54 pm | Permalink

      I hope I have this right. Jerry will use the term ‘good species’ to describe species with unambiguous reproductive isolation from related species. Then there are cases where a species is divided into two or more distinct regional varieties, but the varieties could hybridize successfully. These can be regarded as a single species. Then there are a wide variety of cases where there is some sort of ambiquity about species separation. These defy clear designation as a single species but they also do not clearly fit criteria for being ‘good’ (meaning in separate) species for one reason or another. My bet is that horses and donkeys fall into that category.

    • Posted November 3, 2017 at 3:08 pm | Permalink

      The results of a cross between a horse and a donkey are almost invariably sterile. Thus, though they will accept one another as sexual partners, alleles cannot pass from donkeys into horses, and vice versa. Thus, they are different species due to what’s called postzygotic barriers.

      GCM

      • Liz
        Posted November 3, 2017 at 3:28 pm | Permalink

        Thank you very much. Maybe that’s also the reason for the hemiclonal transmission in the jule offspring.

  16. Liz
    Posted November 3, 2017 at 3:21 pm | Permalink

    Thank you very much. I am wondering if the foals that the female mules give birth to are able to reproduce and if so, if horses, donkeys, mules, the foals, and foal offspring would all be one species like the second group you described above. I don’t know but am guessing the foals don’t reproduce and so that’s why it’s in the third group you described. I wonder also if it’s ethical to breed the fertile mules to make these foals to then breed the foals to research them to find out. Thanks so much again.

    • Liz
      Posted November 3, 2017 at 3:29 pm | Permalink

      This was meant to be @ Mark. Thank you.

  17. Posted November 3, 2017 at 4:08 pm | Permalink

    Great post. Thanks Jerry and Matthew for the thorough write-ups!

    I spend most of my time studying gulls, a family that is of course well-known for its frequent cross-breeding between species. The longer that I study them though, the more I think that the family has been broken down into far too many species. (Disclaimer: I’m a statistician, not a trained biologist.)

    Concerning North American gulls alone, the longest chain of hybridization is probably: Yellow-footed Gull, Western Gull, Glaucous-winged Gull, Slaty-backed Gull, Glaucous Gull, American Herring Gull. Those last four are more of a net than a chain.

    Now, there are definite morphological differences between these species, and even some significant ecological differences (e.g. AHEGulls are continental, while the others above are strictly coastal), but they all hybridize routinely with each other where their ranges overlap.

    Also, there is a lot of clinal variation within each species and this suggests that a subpopulation at one end of the clinal extreme could interbreed with another species, but a different subpopulation at the other extreme could not; e.g. the southern subspecies of Western Gull is ecologically and genetically different in notable ways from the northern subspecies that hybridizes with the GWGull. We don’t know for sure though if the southern subspecies is incapable of producing viable hybrid offspring with the GWGull since the two populations never meet. I suppose this could be tested in a laboratory, but I am unaware of anyone ever doing this.

    All this to say that I think it is unfortunate how gulls have been categorized into species, as the designation does not carry much meaning for this family. Rather than the current 55 or so species, it might be more meaningful to regroup them according to the presence or absence of stable chains of hybridization. This would mean we would only be looking at 20 or so species of gull worldwide. I think this reclassification would be a more biologically meaningful one.

    • Posted November 3, 2017 at 4:17 pm | Permalink

      Oops, sorry Greg! I meant to thank you above for the write-up.

    • Diane G.
      Posted November 5, 2017 at 4:03 am | Permalink

      You must have been pleased that the AOS finally decided to lump Thayer’s with Iceland Gull. 🙂

  18. Torbjörn Larsson
    Posted November 3, 2017 at 4:09 pm | Permalink

    I briefly noted this paper the other day but backed out when I saw the overlapping morphological analysis and the discussion about the impossibility of using biological species. And I hoped Jerry would consider analyzing it before I returned to, so I am happy now! Evidently I backed out so quickly that I did not note the claim of later split with the Borneo than the remaining Sumatran population!

    Yet Neanderthals are considered by many biologists and anthropologists to be a subspecies of H. sapiens (H. sapiens neanderthalensis vs. H. sapiens sapiens).

    Before my teacher in Population Genetics Analysis Mattias Jacobsson split off to go to Africa and sample genomes and study population structure in some way or other, he said something that I interpreted like that. Roughly that that both groups should be considered humans, if I remember correctly.

    Does demographic reconstruction software really work? If species are anything I can can distinguish, doesn’t that make everything a different species? Have you tried applying that concept to extant Homo?

    I am not sure how you mean here. Those that are used do well in tests against data and in comparisons against each other; note that the paper use several methods to try to tease out what happened. PCA of course but also ADMIXTURE is often used [ http://dalexander.bol.ucla.edu/preprints/admixture-preprint.pdf ] and the PGA course above taught ABC methods (based on Joe Felsenstein’s work). With PCA and ADMIXTURE you cannot see races but both agree that the small population differences there are correlate to geography [ https://deepblue.lib.umich.edu/bitstream/handle/2027.42/62552/nature06742.pdf?sequence=1 ; https://www.nature.com/articles/nature07331 ].

    Figure from the last reference:

    So, given that I have not used these methods myself yet, I would say that after reading I cannot see that the PCA or ADMIXTURE analysis support that the south of Lake Toba population should be clustered with anything else than the remaining Sumatran population (though the split looks deep). The phylogenetic analysis tells me nothing at a glance, since it is using the optimistic bayesian analysis instead of preferably maximum likelihood with bayesian as support. And the same goes for the ABC analysis, since it does not compare with two (or more than three) populations that according to at least ADMIXTURE and PCA is feasible.

    If I am misunderstanding something, please tell me in the comments.

    • Torbjörn Larsson
      Posted November 3, 2017 at 4:12 pm | Permalink

      Let me try that image again:

  19. Posted November 3, 2017 at 5:33 pm | Permalink

    I once heard a conference talk discussing the problem of using minimal diagnosable units as species. The speaker showed that a population of wild chickens that has been geographically isolated for less than two hundred years came up as a ‘separately evolving lineage’ in coalescent-based species delimitation analysis.

    He also made the point that treating such populations as species may doom both them and their closest relatives, when both could be saved from long term lethal inbreeding depression by mixing them up.

  20. ThyroidPlanet
    Posted November 3, 2017 at 7:10 pm | Permalink

    Saw this headline flick by in the news and knew I could count on a good WEIT post – and here it is.

  21. kelskye
    Posted November 3, 2017 at 8:06 pm | Permalink

    Part of me wonders if the announcement is a form of activism – t there’s a new species and it’s almost extinct! Not that we shouldn’t be doing everything in our power to protect them anyway…

  22. kelskye
    Posted November 3, 2017 at 8:10 pm | Permalink

    The only species concept that really makes sense to me (not being a biologist this isn’t a surprise) is the biological species concept. But then that has trouble when grisly bears and polar bears can still breed despite significant morphological and behavioral divergence.

    So my immediate reaction to the announcement of the new species of orangutan was to wonder if they had infertile offspring when mated with the known species of orangutan.

    • Posted November 4, 2017 at 6:08 am | Permalink

      The grizzly versus polar bear thing is a case in which two biological species, isolated by genetically based habitat preference, were prevented from meeting each other by those preferences (that IS a form of reproductive isolation). Then the climate changed, grizzlies moved north, and they hybridized (I’m not sure whether hybrids are fertile, but I suspect they are. If they’re not, then they’re good biological species.)

      Nobody ever claimed that biological species were permanent in the face of environmental change. Whether they are two species or one now is dubious, and if it keeps getting warmer, they will eventually merge.

  23. andreschuiteman
    Posted November 4, 2017 at 6:32 am | Permalink

    When you are in Indonesia or Malaysian Borneo and would like to see orangutans, it is not advisable to ask “Where can I see orangs?”

    ‘Orang’ is just the Malay/Indonesian word for ‘person’, so, unless they understand from the context that you are probably a tourist wanting to see orangutans, people will think you are asking a rather strange question.

    • nicky
      Posted November 5, 2017 at 4:13 am | Permalink

      Utan being the forest? Forest persons?

      • andreschuiteman
        Posted November 6, 2017 at 1:20 am | Permalink

        Yes, except that the word for ‘forest’ is spelled ‘hutan’. For some reason the ‘h’ is dropped in orang utan (both in Malay and Indonesian).

        • busterggi
          Posted November 6, 2017 at 12:16 pm | Permalink

          Droppin’ h’s are they? Bloody Asian cockneys they is.

  24. andreschuiteman
    Posted November 4, 2017 at 7:08 am | Permalink

    In my view, this could have been a better paper if the data had been used to argue that the Sumatran and Bornean orangutan do not belong to different species. Sadly, the authors went for the sensationalist route.

  25. mlerdau
    Posted November 5, 2017 at 12:23 am | Permalink

    The ‘new’ orang is another example of what I named (in 1990) Feldman’s rule, “The closer a study organism is to humans, the lower the bar for publication. Marc Feldman stated this during a grad seminar in which we were reading the 1990 Minnesota twin study published in Science. Marc was happy with my formulation, but he was less happy when I named it after him. Three exceptions to the rule are the works John Mitani, Charles Janson, and Erin Vogel, but they prove the rule.

  26. Hari Peayogo
    Posted November 5, 2017 at 3:51 am | Permalink

    Good, I’m agree that only one species of orangutan both sumatera and borneo

  27. Christopher Gordon
    Posted November 5, 2017 at 6:32 pm | Permalink

    I disagree with the notion that hybrids between species must be sterile if those species are to be considered truly separated. There are many, many examples of fertile hybrids between species of the same genus — as well as across genera, in some cases.

    The addendum I always remembered is that offspring would resemble both parents or, in the case of species with sexual dimorphism, one parent or the other, without a blending of the two. So while Scarlet Macaws (Ara macao) and Blue & Gold Macaws (A. ararauna) are distinct species within the same genus, they do produce fertile offspring — which do not resemble one or the other parent, but rather a blend of the two.

    In the plant kingdom, even chromosome count isn’t a barrier to creating (at least partially-) fertile hybrids. The entire genus Rosa seems capable of creating fertile hybrids with other members of the genus — in fact, most modern garden roses contain the genes of at least eight different species. Look up Rosa gallica, R. fedtschenkoana, R. foetida, R. moschata, R. gigantea, R. chinensis, R. wichurana, and R. multiflora. The first three are tetraploid, the rest are diploid. These species’ genes are found in the typical modern Hybrid Tea rose. Now, because of their fertile hybrid offspring but despite their vast differences, should all seven of these species be lumped together?

    🙂

    • Posted November 5, 2017 at 6:35 pm | Permalink

      I didn’t say what you claim I said. What I said (or so I thought) was that if populations are allopatric, bringing them together in captivity will show they’re separate species IF the hybrids are sterile, for they’d be sterile in nature. If captive hybrids are fertile, you can’t tell.

      This is all in my book with Allen Orr, Speciataion.

  28. William L Jungers
    Posted November 6, 2017 at 1:28 am | Permalink

    Colin Groves is a devoted disciple of the Phylogenetic Species Concept. If it can be “diagnosed”, then it’s a species for him and many others. He’s largely responsible for the ongoing inflation of primate species(and genera!) and other mammalian groups. Diagnosability is a pretty low bar for erecting new species. BTW, 2 species of gorilla are now recognized by many researchers.

  29. Posted November 6, 2017 at 9:15 am | Permalink

    The third paragraph actually illustrates the fact that you disagree with the authors of the description for a reason that’s really something of a distant past.
    Correct me if I’m wrong, but you seem to think there is a (single, natural) thing called species, and that all ‘species concepts’ are merely competing definitions for this ‘species’. They are not. Systematists use whatever they can based on the material they work with (mostly dead organisms in low numbers), leading to the use of what’s known as the morphological species concept, at times more or less integrated with bits and pieces of the biological species concept of Mayr. Evolutionary biologists learn from breeding, for instance, hundreds of generations of insects, enabling them to theorize ‘species as lineages’.

    Mayer, luckily, ignores semantics and shares with us a few remarks that the authors of the description should think about very hard, including above all the fact that the only examined specimen is the holotype.

    • Posted November 6, 2017 at 9:19 am | Permalink

      I suggest you read the first chapter of Speciation (the book I wrote with Allen Orr), where I do say that there are objectively discernible species (robins vs bluejays vs. starlings), but that different people use species concepts for different purposes, and the definitions are more or less useful for their purposes. The BSC, as I argue, is the most useful for understanding “why nature is divided up into discrete clusters, visible in sympatry, rather than being a continuum.”

      It’s as if you know little about my take on this issue, but of course you might not have read my book; so I do suggest reading Chapter 1, which supplies the corrective you’ve asked for.

      • Posted November 6, 2017 at 10:02 am | Permalink

        I’m pretty aware of your stance, and indeed I understand how to interpret your opinion regarding the Orangutan article. What I’m trying to get across is that the biological species concept is a concept of its own, quite apart from all others. It is not ‘better’ or ‘more inclusive’ than any other, just because the Concepts are just that, not definitions of a single concept.
        You again indicate that you feel that ‘species’ are somehow a natural entity, which begs the question how they can be recognized not only in theory, but in practice as well.
        For a more modern take on the issue, see for instance:
        http://www.sciencedirect.com/science/article/pii/S1369848604000949
        http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2009.00266.x/full

        • andreschuiteman
          Posted November 7, 2017 at 5:13 pm | Permalink

          You appear to think that “more modern” equals better. That’s a fallacy. Also, the ‘species problem’ is a biological problem, not a philosophical one. It has to do with modes of reproduction and exchange of genetic material. It has nothing to do with metaphysics.


3 Trackbacks/Pingbacks

  1. […] The big zoology news this week is probably the discovery of a third species of orang-utan, Pongo tapanuliensis, on Sumatra. The paper, published in Current Biology by Nater et al. sets out a range of behavioural, morphometric and genomic data to support the hypothesis that an isolated population of orang-utans are in fact a distinct species. But not everyone is convinced: @EvolutionIsTrue (evolutionary biologist Jerry Coyne at the University of Chicago) has responded with a blog post outlining why he thinks that this new species is just an isolated population. […]

  2. […] The report also generated discussion about what we mean by the word ‘species’. Jerry Coyne, professor emeritus at the University of Chicago and author of the excellent Why Evolution is True, wrote in his blog: […]

  3. […] Flores waktu silam, dan yang belakangan agak populer di kalangan kawan-kawan ekologi-evolusi adalah apakah kita sungguh punya spesies orang utan baru. (Baca kegalauan salah seorang penelitinya di sini dan respon lanjut media di sini jika kalian […]

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