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The place of the New Guinea Singing Dog on the canid branch of the tree of life

Please comment on this paper.

http://www.publish.csiro.au/paper/AM07005 http://newguinea-singing-dog-conservation.org/Tidbits/AusMamPap.pdf

We're trying to give this article, NGSD, the right kind of infobox and otherwise find the proper place for it in our system.

Thanks for the link to the full pdf. I find that paper very unsettling. First, there's not a single taxonomist or systematist author. Second, all of the evidence they cite and discuss (more like a review than primary data) is largely anecdotal; there is very little data to go on. There are no statistical tests of the significance of the data. And clearly the authors have a POV to push since the lead author is associated with the NGSD conservation group (based in Oregon?). I tend to err on the side of caution as well and I would advocate, like they do, that this is an evolutionary significant unit for conservation purposes. But what that unit is called - a variety, subspecies, or species - is extremely unclear. Their argument for species status is not compelling. I may just be in my first year of a PhD program in taxonomy and systematics, but it's already clear to me that this paper would have required more data (molecular systematics, morphometrics) to be convincing. I'm surprised it was published. Regardless, I would be very careful when discussing it in the text or using it for citations. Avoid using it as the sole citation for an assertion, while still avoiding weasel words. Discuss it in the context of the uncertainty of the taxon.

As for the kind of infobox, at this point I see no reason to keep the taxobox on the article. The dogbox would be fine. Rkitko 14:24, 12 November 2011 (UTC)

Is that your opinion of the paper itself, or the references upon which the paper is based — or perhaps both? Specifically, the discussion at the NGSD article currently seems to revolve around the statement in THE NEW GUINEA SINGING DOG: ITS STATUS AND SCIENTIFIC IMPORTANCE at the end of page 47 and continuing on page 48: "It is, at minimum, an evolutionarily significant unit, and, at maximum, could be its own distinct species (Simonsen 1976; Gollan 1982; S Bulmer 2001; Bininda-Emonds 2002; Koler-Matznick et al. 2002; Clark et al. 2004; Savolainen et al. 2004). Therefore, for conservation purposes, the wild singing dog should be considered a unique taxon until the contrary is clearly demonstrated", which I used as justification for the "Unresolved" paramater in the taxobox. But it appears the issue is more complex than just relating to that parameter in the taxobox... Did you (or anyone else who understands this stuff) examine SIMONSEN V, 1976. Electrophoretic studies on the blood proteins of domestic dogs and other Canidae. Hereditas 82: 7–28 or SAVOLAINEN P, LEITNER T, WILTON A, MATISOO-SMITH E, LUNDEBERG J, 2004. A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA. Proceedings of the National Academy of Science USA 101: 12387-12390. or CLARK LA, FAMULA TR and MURPHY KE, 2004. Evaluation of a rapid single multiplex microsatellite-based assay for use in forensic genetic investigations in dogs. American Journal of Veterinary Research 65:1446 – 1450. (which seems to cost money to view) or any other of those eight references for that statement in the paper? If not, could you possibly take a look and give some feedback? I don't know if that information changes anything, but this stuff is beyond my layman's understanding of genetics. Mojoworker (talk) 22:15, 23 November 2011 (UTC)

Ok, I think that I can contribute to this. I read the first paper you referenced and it already listed the NGSD (Hallstromdog) as a seperate species and when you go by the differences in blood enzymes the jackal would be closer to the domestic dog. However this is at odds with the genetic data published in the second referenced article which clearly shows a connection with other dogs as well as the dingo. Another published article (http://www.nature.com/nature/journal/v464/n7290/full/nature08837.html) clearly showed that they are descended from wolves and among domestic dogs belong to the "Asian Group" together with dingoes, Chows, Akuitas and Shar-Peis. I also read a newly published scientifc article on the origin of the dingo, NGSD and Polynesian dogs (which can be found here: http://rspb.royalsocietypublishing.org/content/early/2011/09/06/rspb.2011.1395.full.pdf) and it states: The study of mtDNA among Australian dingoes and Polynesian dogs showed that archaeological samples of pre-European dog from across Polynesia (the Cook Islands, Hawaii and New Zealand) carried only two haplotypes: Arc1 and Arc2 . It also showed that Australian dingoes carried only haplotype A29 or haplotypes differing from A29 by a single mutation, indicating that the dingo population was founded from a small number of dogs carrying a single mtDNA haplotype (A29). Importantly, all three haplotypes are typical for East Asian dogs: Arc2 and A29 are absent and Arc1 rarely found west of the Himalayas . Furthermore, two New Guinea singing dogs (NGSDs; a feral dog from the New Guinean highlands, close in morphology and behaviour to Australian dingoes but clearly distinguishable ) were shown to carry haplotypes A29 and A79 (which differs by one substitution from A29). Since A29 is also found among East Asian dogs, an origin from domestic dogs seems clear for these two wild populations.

...

This study shows a distinct pattern in the geographical distribution of the two Polynesian dog mtDNA haplotypes Arc1 and Arc2, and the dingo and NGSD founder mtDNA haplotype A29, with a total frequency of 12 per cent in Southern China, 17 per cent in southeast Asia and 50 per cent in Indonesia, but complete absence in samples from Taiwan and the Philippines. This gives a clear indication that Polynesian dogs as well as dingoes and NGSDs trace their ancestry back to South China through Mainland Southeast Asia and Indonesia. Thus, there is no indication that these dogs were introduced via Taiwan and the Philippines together with the expansion of the Neolithic culture and Austronesian languages, as suggested in some theories about Polynesian origins.

So it clearly indicates an origin in Southern China and a route via Southeast Asia and Indonesia. Also that they are not a seperate species. So for several years now genetic analyses do not support a classification as a seperate species albeit the term Canis hallstromi is still in use. Morphological data also doesn't support it, to a huge degree due to the high morphological range of the domestic dog and as even Matznick states the physical capabilities of the NGSD are not as unique as often stated, since the Lundehund is very similar in that regard. Furthermore I know of no source that ever stated that NGSD males have an actual breeding cycle and an annual breeding cycle for females is not unknown among the domestic dog (and NGSD females can have three heats per year), it is simply not the most common. Furthermore reduced relative brain size, hypertrophied tail form (curled tail), reduction of facial expression with a stronger emphasis on phonetic expression and a less sophisticated social system when compared to examined grey wolves are all characteristics of the domestic dog and they are shared by the NGSD. So neither genetic nor morphological data support a classification as a separate species from the dog. In addition a big part of the few founding dogs of the captive population already came from humans so simply classifying them as wild is also on shaky grounds, but this last argument we should not use.

Now the biological definition of species also doesn't fit, especially not when all of the wild population, or at least the major part, has mixed with other dogs. Two seperate species don't mix so readily and so extensively. I know that at least some authors state that all members of the genus Canis can produce fertile offspring. I don't know of the basis of that statement only that it was proven for lupus, aureus, simensis, rufus, latrans and possibly lycaon (if that is a seperate wolf-species), and the gray wolf and domestic dog are considered one species due to proven voluntary mating when sufficent number of partners where there (so neither a shortage of dogs or wolves), this was under captive conditions. And an average unrestricted fertility of the hybrids and no sudden increase in genetic disorders even when only bred among each other since the first generation of hybrids was only proven when you mix gray wolves with domestic dogs.

Now, as far as is known to me the taxonomic classification of the NGSD is according to Mammal Species of the World the NGSD is under Canis lupus dingo http://www.bucknell.edu/msw3/browse.asp?id=14000751 and the term hallstromi is listed among the synonyms which also contains many old names of the dingo. Also the entry for c.l. dingo also stated as a comment "domestic dog" which is also in the entry for c.l. familiaris http://www.bucknell.edu/msw3/browse.asp?id=14000752 . Under the entry for Canis lupus http://www.bucknell.edu/msw3/browse.asp?id=14000738 it is stated Includes the domestic dog as a subspecies, with the dingo provisionally separate--artificial variants created by domestication and selective breeding (Vilá et al., 1999; Wayne and Ostrander, 1999; Savolainen et al., 2002). Although this may stretch the subspecies concept, it retains the correct allocation of synonyms. Corbet and Hill (1992) suggested treating the domestic dog as a separate species in SE Asia. However the seperate species argument doesn't held up for the reasons I have mentioned.

So I am sure that the current classification of the NGSD is c.l. dingo and since the NGSD has the mtDNA type A29 like the Australian dingo that is as far as I know regarded as the current justification for its subspecies classifcation. However, it is clearly seperate from the Australian and Thai version of the dingo due to morphology and also phonetic and social characteristics (all based on the captive population of course), therefore it needs a seperate article in my eyes just like most breeds of dog have, also the topic has the necessary amount of material and holds enough interest for a seperate article.

Due to all this: A classification as a subspecies is basically just as arbitrary as that for race or breed and when we cannot get rid of the c.l. dingo in the taxobox it has to stay. But the article needs to state the other terms that were once and are often still in use along with the published material on genetic and morphological analysis. I hope I could help. --Inugami-bargho (talk) 19:47, 7 December 2011 (UTC)

Taxonomy of Canis in general

Well, the taxonomy of Canis is a nightmare, with species, semi-species and subspecies blending neatly into each other, and likely several paraphyletic groups at the species level. Just to top it off, the species barriers seem to be social (pre-zygotic) rather than genetic, and with domestication humans are having a hand in it as well. I think it would be useful to accnowledge that in Canis there are possibly no good species, they are as much human constructs as a biological reality. Petter Bøckman (talk) 15:45, 12 November 2011 (UTC)

I don't know exactly what you mean, but I've noticed a few things that cause problems for Misplaced Pages. First of all, even though the dog is a domesticated wolf, now Canis lupus isn't doesn't jive with the English (just to mention one language) "wolf" because dogs aren't wolves and dogs are Canis lupus too, so unless we merge the articles wolf and dog we have no article for Canis lupus in general anymore. Next, the dog is now two taxa even though one is the other gone feral or wild, Canis lupus familiaris and C.l.dingo, which causes a mess for wikipedia in terms of what to put where and how much each article should cover. Next, the Golden Jackal on the one hand and the other two jackals on the other turn out now to belong to two differnet branches, so the article Jackal has headaches. All existing red wolves, and maybe all Canis lupus rufus or Canis rufus turn out to be Coydogs, but the editors of that article can't handle the truth so it's a mess. The "Canis latrans" around here NYS are maybe 80% latrans, tops, it turns out, the rest is lupus, mostly wolf but partly dog. I could go on, but wikipedia is steadily sorting through it all, it's kinda fun to watch/be a part of, sort of a puzzle. But this NGSD article has been a headache from day one. Chrisrus (talk) 05:00, 13 November 2011 (UTC)

Oh, it is a puzzle indeed! There are at least three distinct problems mixed in together:

• The Species problem, just how do one define a species? Below the species level, what really defines a taxon?
• Paraphyly, how do you treat paraphyletic, but obviously useful groups (like "wolf")? Even worse, what do you do with polyphyletic (hybrid) species?
• Language vs phylogeny, what do you do when the two don't match?

The point I was trying to make (and which I think apply to the NGSDs) is thet there is quite possibly no one correct solution here. Petter Bøckman (talk) 08:43, 13 November 2011 (UTC)

This is, of course, not specific to Canis, but is a general problem in groups where geographically and morpologically distinct populations are quite capable of inter-breeding and do so regularly. The number of species of Ophrys (bee orchids) recognized in reliable sources varies from about 10 to 375! There are two different issues in Misplaced Pages: which entities should have their own articles, which should surely be determined by interest and the amount of information available, and what (if anything) should be put in taxoboxes. I'm a little concerned that some editors (not those who have commented here) seem to want the latter to determine the former. Peter coxhead (talk) 10:01, 13 November 2011 (UTC)

A huge part of the problem is also the classification of the domestic dog and especially in the english speaking world it seems hard to accept for many that domestic dog and gray wolf are the same species. Partly this comes from the inconsistency on what is regard a typical characteristic of the domnestic dog (e.g. many see lack of regurgitating of food as normal while others as a sign of degeneration since other dogs still show it perfectly ) as well as idological reasons (e.g. the arbitrary seperation of nature and culture). So yeah, we probably should have a different article for canis lupus than the current one, but I don't know whether such an article would ever make it. Does anybody here know whether such an article would find support?--Inugami-bargho (talk) 19:47, 7 December 2011 (UTC)

For some time, a search for Canis lupus linked to the article Wolf. Then, when it was pointed out that the article wasn't talking about the whole of Canis lupus per se when it said things such thing such as their being less adaptable to civilized times than coyotes and many other such statements, a hatnote was added to indicate that the article was about wolves, not dogs, which are also canis lupus. Then, for awhile, the hatnote was removed and Canis lupus searchers were sent directly to Subspecies of Canis lupus, I suppose because it was the closest thing to an article about Canis lupus in general and if such an article as you describe would be created, it might incorporate that one. Then, perhaps reasoning that "Canis lupus" searchers were probably looking for the Wolf article, Canis lupus searchers were direct back to the "wolf" article again, but hatnote was re-added and changed so that the if anyones clicks on the hatnote Canis lupus link at the top of the wolf article, s/he is sent to the subspecies article. That's how it stands today.

The dog article and every doginfobox was at first assigned C.l.familiaris and there was only one article, Dingo, which was also Canis lupus dingo. Then it was noticed that halstromi Australian Dingo" and Canis lupus dingo was created to embark all dogs so classified. Meanwhile, the article "Dog" was changed so that it would cover both c.l.familiaris and c.l.dingo, and these two were tied together using the brackets around the term "", in imitation of the way it's done in MSW3, but no one seems to understand" because editors regularly change it because they don't understand why the domestic dog and the dingo are both the "" in the chart. So some other way to make MSW3's point in the chart seems needed. Chrisrus (talk) 01:17, 8 December 2011 (UTC)

What a mess! The problem here is that we seek to make articles to cover specific phenomena, and these phenomena aren't clear-cut phylogenetic units. As a zoologist I very much like to see articles follow scientific naming, but in this case case I'm tempted to say "screw phylogeny" and stick to the vernacular expressions. There really should be an article on wolf, on dog, on dingo, on domestic dog etc. The relevant phylogenetic information clearly should be given in each, but should not dictate what articles to write. (This is why I prefer to stick to wild animals, things get difficult when humans start meddling) Petter Bøckman (talk) 08:21, 8 December 2011 (UTC)

Oh, great. This is one of the reasons I don't get why the english wikipedia doesn't have a peer review system that prevents that every edit of a site can be seen immedidiately. Ok, lets see.

I think the main problem was the original wolf article because it wasn't in accordance with the facts. I just checked it and its worse than I imagined since it isn't even in accordance with the sources it states (e.g. it references MSW3 for the classifcation of subspecies but excludes familiaris and dingo nonetheless). It is the old problem of generalization of things that are not the same. So basically that one would need to be changed first but I doubt we can do it if there is such massive resistance to it. I think a new article should be done and reviewed before published. The chart implies that dingoes don't have the traits typical for domestic dogs. The main problem we would face, based on what you wrote, would be the opposition against stating that the domestic dog is a gray wolf. In addition the article on the domestic dog needs to be seriously reviewed. But that is such a huge project that we would need several dozen authors.--Inugami-bargho (talk) 08:25, 8 December 2011 (UTC)

As an outsider in "dog matters", it seems to me that Petter Bøckman is right. What readers want is articles on topics they expect to be different, i.e. wolf, dingo, domestic dog, etc. These terms have clear meanings regardless of the taxon referred to. By the way, I think it's wrong to say that "the domestic dog is a gray wolf". The domestic dog and the gray wolf may belong to the same species, but this doesn't make their ordinary language meanings the same. (A similar issue of language arises regularly at Ape and Primate, where people try to impose the usage "apes" = "hominoids including humans", instead of reporting this as one of the usages attested to in reliable sources.)

I think that we also sometimes run into trouble with plant articles by not separating out cultivated and wild forms. Popular ornamental plants which have many cultivars and have probably been been massively crossed, for example, don't fit well into taxonomic hierarchies. Peter coxhead (talk) 11:16, 8 December 2011 (UTC)

No offense but "ordinary language meanings" doesn't count. Misplaced Pages is basically a lexicon and not a forum where people get their expectations confirmed. Furthermore you are wrong in thinking that the canine terms you mentioned have clear meanings. I know of a t least three definitions for dingo as well as three different usages regarding what dogs are dingoes and what not. The same with the Australian term of "wild dog". It is the same with the term domestic dog, for some this includes all canids with a history of domestication so including the dingo, for others the term only means pet varietes and either including or excluding working dogs, for others again feral dogs are domestic dogs but for others not, others call feral dogs stray dogs or wild dogs, it is the same with horses. To go deeper, if we would take such "ordinary language meanings" into account we would have to classify British Bulldogs as perfectly healthy because owners and breeders might be offended, despite the fact that from an objective point of view they are cripples. So we cannot afford to take "ordinary language meaning" into account when we want to have good and reliable articles.--Inugami-bargho (talk) 07:11, 10 December 2011 (UTC)

The idea of having one article about Canis lupus the taxon is maybe a good one. It be Subspecies of Canis lupus and about the history of the term, how it used to be just wolves and then started to cover dogs when it was determined that they are domesticated from wolves, and so on. The idea that we should merge the articles Wolf and dog just because taxonomy has done so just not reasonable, neither in English nor German nor any of the other languages. Chrisrus (talk) 13:53, 10 December 2011 (UTC)

I think your may have misunderstood my stance, Inugami-bargho. Of course we need an article on Canis lupus in it′s full meaning. It just does not need to be the article "Wolf". Misplaced Pages has plenty of room, there′s room for both, and with links and room to explain the changing meaning of terms, no reader needs to feel confused over where to find what on Misplaced Pages. Petter Bøckman (talk) 19:22, 10 December 2011 (UTC)

And I think you misunderstand me. When you say wolf in science you mean Canis lupus unless you first stated what subspecies you are talking about. For the respective subspecies you need to name the non-taxonomic name. That in english speaking countries they often exclude dogs from that is because there is such a problem for most people in recognizing that both are the same species, as far as I know that is due to the phenomenon that most dog researchers have no idea about wolves and most wolf-researchers do not even own a dog. So yes the article "wolf" would have to be about the whole of Canis lupus especially since the current article implies that all these wild populations are the same, but there are differences among them as well (e.g. North American wolves were often eradicated after only 20 years of European colonization while in Europe it was only successfull in the 19th century and even then only slowly). Therefore we need this one article stating the basic facts and including the current accepted list of subspecies and from there links to articles on each subspecies, including articles (if possible) on domestication, mythology and the like. This article can actually be very short since more detailed information on the various wolf-populations can be covered in the various subspecies entries. I don't see how that could be confusing. --Inugami-bargho (talk) 08:39, 13 December 2011 (UTC)

Your suggestion would have been the sensible one if phylogeny was the main criterium for organizing articles. However, phylogeny is but one of several criteria, and the size of any article depends on what people want to put in it. A lot of people are interested in wolfs, no matter how short the article could have been after your suggestion, it would soon bloat out and become the de facto main article. Your suggestion that wolfs really are not a single species is interesting, but would violate WP:OR and WP:WEIGHT until the species is formally split, and I don't see that happening anytime soon. If we do not insist on fighting a never ending uphill battle, the sensible thing to do is to have an article on Wolf (Canis lupus) with all that normally goes into a species article, and treat the subspecies and the cultivar (dog) is small sections (a couple of paragraphs) with links to their respective main articles. Petter Bøckman (talk) 10:42, 13 December 2011 (UTC)

It doesn't matter whether people would bloat the article or not. You can't just give in to pressure because of what people want, when you go by that criteria the wolf article would contain info about the thylacine or the maned wolf as well. And I didn't say that wolves are not a single species. There is only one species named gray wolf and it consists of several variations that differ from each other, e.g. polar wolves are on average much bigger and heavier than Italian wolves but they are still the same species. " If we do not insist on fighting a never ending uphill battle, the sensible thing to do is to have an article on Wolf (Canis lupus) with all that normally goes into a species article, and treat the subspecies and the cultivar (dog) is small sections (a couple of paragraphs) with links to their respective main articles." That was what I was saying the whole time. However we would need to have the actual full range meaning in the size it would be from e.g. the weight of a toy dog to that of a mastino and there we could have a problem. We would need a fool proof argument for the inclusion of the domestic dog since many will probably oppose that no matter what behavioral and genetic examinations tell us. Anyway the best approach would be to first create an appropriate article on the user page of an author, when that one is sufficient it can be published and we should request for a protection of the article. Maybe even have it locked.--Inugami-bargho (talk) 14:36, 16 December 2011 (UTC)

Are you talking at cross purposes? There should be one article for Dog, one for Wolf, and one for Dingo, so the criticism about "giving in to what people want" does not apply unless you are arguing that all of these be merged into one Canis lupus article, which alternately seem to be advocating and then not advocating. But if you really want to merge these into one Canis lupus article, please try that on German Misplaced Pages first and see what happens there. I can't believe that's what you are really suggesting, but that's what the Peters and I were arguing against, and what you seemed to be arguing for when you object to "ordinary language meanings" and "giving people what they want". If on the other hand you'd like to have an additional article about Canis lupus the taxon, please go ahead and create it out of the existing article Subspecies of Canis lupus, as that's the existing article about that referent and could be expanded, for example it presently lacks a history of the taxon, starting with Linnaeus, and other things. Then you could move that article to Canis lupus and let the wolf and dog articles continue to just talk about wolves and dogs as that's quite enough for each of them. Chrisrus (talk) 18:35, 16 December 2011 (UTC)

The Case of the Red Wolf

Please everyone please read the article Red Wolf and its discussion page TALK:Red wolf and comment here and/or there. There are some similar issues and some different ones and room for improvement and lessons to be learned for the wider project. Chrisrus (talk) 18:05, 11 December 2011 (UTC)

First, there are some debates, not all of which are closed, on the talk page that may need resolution.

But to my mind, the problem is this: about half-way through the Taxonomy section the reader is told that all existant red wolves are coywolves, based on DNA evidence. The lead says nothing about this, calling it simply a "canid", which isn't particularly enlightening. I can't evaluate the genetic evidence, but it seems that for at least a decade the evidence has been conclusive that two branches on the tree of life in this case have merged into one, and it seems to me that if that's true and the last word has been said about that, it should be in the lead because it goes to the heart of what this animal fundementally is, which is a rare and to my mind significant thing, because even though Canis hybrids and others aren't so rare, they rarely form "true-breeding" sustained populations, and in no other case has mammology ever recognized one as a taxon. So it seems to me one of the most important things about it, what is fundementally is, is not in the lead, and that the way the Taxonomy section is done undue weight seems to lie on the theory that it's not a coywolf if that's no longer a tenable theory. But as I'm not qualified to evaluate the various points of view on the subject I wanted to ask before changing the lead based on only the second half of the Taxonomy section. Chrisrus (talk) 00:36, 12 December 2011 (UTC)

(Copy of my post at TALK:Red wolf) OK, my two øre:

First off, there's no one good solution to the species problem of the red wolf. No form of scientific classification really handle ambiguity well. We will have to accept that we are left with a "best of a bad situation" as the optimum solution. As long as everyone realize that whatever solution is found, it will have flaws, then we should be able to find consensus.

From a phylogenetic POW, the problem with the red wolf is not really that it appears to be a good species ecologically, but that wolf appears to be one too. Phylogenetic nomenclature is based on species neatly splitting in two and the ancestor species then going extinct. This assumption if of course just a model, not real life, and every now and then we run into situations where this assumption very clearly do not hold. There are quite a few instances of paraphyletic species out there, and hybridization of recently diverged species may be more common in mammals than assumed, our own speciation from the chimpanzee being a point in question. We just need to find how to best handle this situation in the taxobox, and make sure the whole mess is explained clearly in the text.

As far as I can see, the red wolf as a hybrid species seems fairly conclusive. Then again, hybrid species are species too, or can at least give rise to species if allowed to evolve. At what point do a species cease to be "just a hybrid" and start becoming a species of it's own? Petter Bøckman (talk) 18:32, 12 December 2011 (UTC)

Thanks for all you've done with regard to this. Please, don't stop there. As I said before (scroll up), the problem is the "lede" sentence(s). We need to state in reader-friendly language what it is. How about "a hybrid "species"" or a descriptive phrase to that effect? "Canid" just isn't very enlightening. Don't worry so much about taxonomy. Chrisrus (talk) 23:31, 6 February 2012 (UTC)

The terminology would be "suspected/presumed/hypothesized/whatever hybridogenic species" (or hybridogenic species if you prefer it blue). Dysmorodrepanis (talk) 23:33, 15 June 2012 (UTC)

Ok, then, please do go there and make that change because not just the body but also the lead should say in as upfront and clear a way as appropriate that this is a hybrid species or a hybridogenic species. Because it still takes to much digging for the reader to understand this. Chrisrus (talk) 00:00, 16 June 2012 (UTC)

Please if you would do have a look at Talk:Coywolf re: Redwolf, and comment as you would. I will add an opposite message there. Chrisrus (talk) 17:22, 6 September 2012 (UTC)

Blackbacked and Side-striped Jackals:

Dear WikiProject Tree of Life page watcher;

I found this uncited section here Canid_hybrid#Genetic_considerations. We could, I suppose, delete it on the grounds that i's uncited, but the context kinda needs it and it sounds like it was written by someone who knows what they are talking about and seems logical. So instead, I'm trying to cite it. But I'm not really able without some help from an expert. It needs checking and citing or correcting if the numbers something's wrong. Could this here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC53565/pdf/pnas01030-0152.pdf be used to cite the part about the Black-backed Jackal and the Side-striped Jackal?

Thank you for your kind attention! Chrisrus (talk) 06:10, 21 December 2011 (UTC)

I've found some sources for the chromosome numbers, but not yet for hybridization. Petter Bøckman (talk) 08:46, 21 December 2011 (UTC)

African Wild Dog

On a related matter, please see this thread/problem: Talk:Canid_hybrid#African_wild_dog. Chrisrus (talk) 15:38, 21 December 2011 (UTC)

Dingoes: feral domestic dogs gone wild?

Please, expert needed to explain MSW3's statements on the taxon Canis lupus dingo page has only two words in the comments section, placed in brackets, here: http://www.bucknell.edu/MSW3/browse.asp?id=14000751. This is also true of their Canis lupus familiaris page. What does this mean? Please, any/every expert, what does this mean?

Of course, before you answer, you should read the exlanation that there seems to be on their Canis lupus page, here: http://www.bucknell.edu/MSW3/browse.asp?id=14000738. It says many things about the taxonomic questions about this species, but it says this about this matter:

(Canis lupus) includes the domestic dog as a subspecies, with the dingo provisionally separate--artificial variants created by domestication and selective breeding (Vilá et al., 1999; Wayne and Ostrander, 1999; Savolainen et al., 2002). Although this may stretch the subspecies concept, it retains the correct allocation of synonyms. Corbet and Hill (1992) suggested treating the domestic dog as a separate species in SE Asia. Synonyms allocated according to Ellerman and Morrison-Scott (1951), Mech (1974), and Hall (1981).

Maybe you should also have a look at the article Canis lupus dingo, which is not the same as the Australian Dingo article, and not overequate the Australian native dog with all the dogs covered by the taxon Canis lupus dingo.

Thank you for your kind attention to this matter. Chrisrus (talk) 04:43, 16 February 2012 (UTC)

Darwin was Nearly Right

We all know that taxonomy is a 'bag of worms' and that a species may be (and often is) classified with virtually equal accuracy from a dozen different perspectives. Ever stopped to wonder why?

I thought you might be interested in a recent paper by Eugene McCarthy http://www.macroevolution.net/support-files/forms_of_life.pdf

Darwin was spot on with natural selection, and so very close on many occasions to the real source of genetic variation. This approach by McCarthy unlocks the last riddle - Saltation - which plagued Darwin's theory.

Unfortunately, it demonstrates that the other half of the 'Tree of Life' is missing - there is now a huge amount of work to be done to identify 'the other half' and start to put in place all the crossing links.

Your thoughts would be appreciated.

Thanks - Derek

DerekSmith (talk) 12:47, 15 June 2012 (UTC)

There's a "brief" synopsis here for those of us who are TLDR-challenged. AFAICT, he is basically restating the well-known genetics behind punctuated equilibrium, although I'm not sure he realizes that. He's not the first to challenge the gradualism of Darwin's views, and if investigators continue to ignore the older literature, he won't be the last.--Curtis Clark (talk) 16:16, 15 June 2012 (UTC)

It seems to start off OK (e.g. what on a cursory skim looks like a decent review of hybridisation), but gets worse (e.g. armadillos are descended from ankylosaurs, and whales from mososaurs). Lavateraguy (talk) 16:20, 15 June 2012 (UTC)

Yes, I'm afraid it gets solidly into very shaky ground there. When you put their plates flat on their backs, stegosaurs look kind of like pangolins, so pangolins must be surviving stegosaurs—never mind the fact that stegosaur plates are bony, while pangolin ones are epidermal (quite apart from the numerous other features that identify one group as mammalian, the other as archosaurian). And I wonder what made him think that multituberculate and rodent dentitions are similar. Ucucha (talk) 17:51, 15 June 2012 (UTC)

@Ucucha - you are thinking in classical Neo-Darwinian linear evolutionary terms with this response - with hybridisation characteristics of each parent are shared / mixed up making it entirely possible for bone plates to become epidermal in the hybrid. We don't understand the rules of hybridisation yet - when do hybrids come out half and half, when do they come out blends, but the old way of thinking stands in the way of 'seeing' what seems to be in front of our noses. DerekSmith (talk) 20:16, 15 June 2012 (UTC)

If we don't understand the rules of hybridization after all this time, we must not understand much of anything. Don't get me wrong; I even go looking for hybrids. But there's no revolutionary new science here.--Curtis Clark (talk) 01:53, 16 June 2012 (UTC)

Well, Multituberculata does say "multituberculates had a cranial and dental anatomy similar to rodents" ...

I'd guess that he doesn't know anatomy and palaeontology, so there's nothing to stop him running with impressionistic similarities. The lack of DNA from fossil organisms shields his conjectures from DNA testing to a degree, but I expect that sequence data doesn't match the expectations of his conjectures. Lavateraguy (talk) 18:09, 15 June 2012 (UTC)

Snakes are descended from annelids! —innotata 19:59, 15 June 2012 (UTC)

Some of the suggestions may well to turn out to be wrong, but what of the principle that every 'species' did not slowly evolved through gradual mutation, but sprang into (geologically) instant existance through hybridisation of two compatable parents. It happens frequently in ducks and fish, sometimes the parents are driven out because of the hybrid vigor and environmental suitability of the hybrids and a new species is born. Does this not explain the extreme problems often encountered in taxonomy - each 'species' does not have one parent, but two, and there are no 'missing intermediary fossils' because there were none. DerekSmith (talk) 18:52, 15 June 2012 (UTC)

The simple answer is "no". Some species arose by hybridisation (it's quite common in plants), but DNA sequence data generally supports a dichotomising tree of descent. If wide hybridisation was a common occurrence it would show up as more horizontal tranfer in genomes than is seen. (BTW, can you give even one example in ducks - ducks, geese and swans hybridise readily, but I'm not aware that this has resulted in a new hybridogenetic species. Outside ducks, there is an example in Passer.) Lavateraguy (talk) 19:12, 15 June 2012 (UTC)

Interspecific hybrids are fairly common, intergeneric hybrids are generally rare, but common in a few groups (e.g. orchids, cacti, pome fruits, water fowl, wild fowl) and not all that rare in general in birds and plants, and interfamilial hybrids very scarce (all that I recall are among wild fowl); I get the impression that he is talking about rather wider hybridisation. Lavateraguy (talk) 19:12, 15 June 2012 (UTC)

There's rather shaky grounds to say even the Italian Sparrow or Mariana Mallard are hybridogenetic. Genera and families are of course arbitrary, but I doubt there's any interfamilial hybridisation under modern taxonomies (there are only two families of wildfowl, Magpie Geese and everything else). —innotata 19:59, 15 June 2012 (UTC)

(By wild fowl I meant Galliformes.) IIRC, there are hybrids between Cracidae and Phasianidae. There are also hybrids between Numididae and Phasianidae Lavateraguy (talk) 20:10, 15 June 2012 (UTC)

Yes, I'm remembering the galliforms now, though don't know how they fall in newer classifications. (Wildfowl is the British term for waterfowl, galliforms are called landfowl or gamefowl.) —innotata 20:18, 15 June 2012 (UTC)

When I still did research, I studied hybrid speciation in plants. One of the consequences of genetics is that hybrid species ordinarily share apomorphies of both parents. In plant groups with a fair amount of hybrid speciation, divergent speciation (as measured by patterns of apomorphies) greatly outweighs hybrid speciation (in the genus I studied, Encelia, only two of over a dozen species had well-substantiated hybrid origins. (These were diploid species, not alloploids.)

I'm responding quickly here, but I can look up studies that state that the vast majority of angiosperms (and therefore the vast majority of plants) are of hybrid origin. So a genus having just two members of hybrid origin does not strike me as a plant group "with a fair amount of hybrid speciation." But, of course, the mere fact that the other members of Encelia were not shown to be of hybrid origin does not mean they aren't. Nor does it mean that they are of gradual, nonhybrid origin. The tendency, all too often, I find, is to ASSUME gradual origins until hybrid origins are firmly demonstrated. In the present context, that's a real bias. Koolokamba (talk) 17:25, 16 June 2012 (UTC)

On the other hand, any character state distribution can be explained by hybridization events; i.e., hybridization cannot be falsified through phylogenetic analysis. In the final edition of Plant Speciation, Verne Grant made the statement that hybridization in flowering plants was so pervasive that we would never figure out their phylogeny. It didn't turn out that way.--Curtis Clark (talk) 19:30, 15 June 2012 (UTC)

Was that before DNA sequencing became technically and economically feasible? Lavateraguy (talk) 20:10, 15 June 2012 (UTC)

In my specific case, we found chimeric ITS sequences and shared RAPD markers. But the Angiosperm Phylogeny Group demonstrates that congruent molecular and morphological trees are reasonably common.--Curtis Clark (talk) 01:50, 16 June 2012 (UTC)

The intended target of my question was the statement made by Verne Grant. Lavateraguy (talk) 13:49, 16 June 2012 (UTC)

Any character state can be explained, that is, a phylogeny can be constructed, also under the assumption that no hybridization has occurred. But that doesn't make the explanation true. So, yes, "hybridization cannot be falsified through phylogenetic analysis," if by phylogenetic analysis you mean "construction of a phylogeny." But if you look at the situation historically, you do see a pervasive phenomenon across a broad range of taxa: inconsistent phylogenies have been produced by different research groups when different sets of traits/genes were used as a basis of comparison. In this respect, phylogenetic analysis speaks clearly for a pervasive role of hybridization in evolution. And, I think it's fair to say that it also suggests that the current, most popular angiosperm phylogeny is but the latest most popular angiosperm phylogeny. There have been many others, in many ways inconsistent with the current one, and if we keep thinking the same way, imagining a true tree must exists when everything is actually reticulate, this historical trend will, no doubt, continue. Before long we'll have another most popular angiosperm phylogeny. But isn't that just a bit sisyphean? Looking at things historically, people engaged in the production of phylogenies have always claimed that their own phylogenies are valid and satisfactory (how could they not?), and yet in each case subsequent workers using new data sets come up with new, supposedly more accurate phylogenies. But the mere continuation of debate here suggests that different data sets are generating different phylogenies (the expectation under the hypothesis that hybridization is rampant). I think this is what McCarthy is arguing. — Preceding unsigned comment added by Koolokamba (talk • contribs) 17:39, 16 June 2012 (UTC)

McCarthy's first book extensively covers avian hybrids http://www.oup.com/us/catalog/general/subject/LifeSciences/VertebrateZoology/Ornithology/?view=usa&ci=9780195183238 I have not read it, so I cannot offer any examples to answer your question, but the summary claims thousands of hybrid species. DerekSmith (talk) 20:05, 15 June 2012 (UTC)

Didn't know he was the same person. I've read it (and cited it on Misplaced Pages), and don't remember any suggestion of large-scale hybrid descent in its discussion or from its contents. —innotata 20:18, 15 June 2012 (UTC)

You've misinterpreted it. It claims (and I believe it) hybrids with 4,000 different species parentages. A hybrid (nothospecies) is not the same as the species. For example ligers and tigons, reciprocal crosses between Panthera leo and Panthera tigris are not (yet, and probably will never be) a hybridogenetic species.

If you were to read the book you'd find that something like 90% of those pairings represent intrageneric hybrids (between a natural tendency to broader hybridisation, taxonomic biases, and human intervention birds have a relatively high rate of intergeneric hybridisation).

For an accessible database of avian hybrids see here Lavateraguy (talk) 20:20, 15 June 2012 (UTC)

Thanks, my mistake, as I said, I had not read the book and misread the summary, indeed, it says thousands of hybrids, not species. Would it be reasonable to think though, that, in the fullness of time, some of those hybrids might establish themselves as species? Wouldn't this be a demonstration of the McCarthy proposal? DerekSmith (talk) 21:02, 15 June 2012 (UTC)

Thanks for posting it, hadn't seen it before. Before anybody says it supports McCarthy's claims, note that the site doesn't distinguish between copulation and actual (much less fertile) hybrids—it's a database of sources to look at. —innotata 20:28, 15 June 2012 (UTC)

There are two parts to the proposal, first that hybridisation creates the instant genetic difversity, then, second, Stabilisation Theory under natural selection fixes the genetic makeup and increases fertility. Massively reduced fertility is initially compensated for by improved fitness. DerekSmith (talk) 21:07, 15 June 2012 (UTC)

Just to be fair to McCarthy, guys, can any one cite even one instance where a species is KNOWN to be of gradual, not hybrid origin? Granted that a very small percentage of species are KNOWN to be of hybrid origin. But these are documented. Koolokamba (talk) 21:25, 15 June 2012 (UTC)

Any autopolyploid species. But, if you want to bend over backwards, novel autopolyploid populations may also display genomic shock. Lavateraguy (talk) 22:19, 15 June 2012 (UTC)

As a point of order, McCarthy self-published this "book" on his website, so it's a WP:SPS. I haven't evaluated his resume to see if he's an expert in his field, but one does wonder why he didn't get it published by one of the many academic press operations out there. Rkitko 21:31, 15 June 2012 (UTC)

"Eugene M. McCarthy earned his Ph.D. in genetics from the University of Georgia, where he has conducted research into genomics and hybridization for more than a decade." He has a few papers on LTRs, and on old paper on recombinational speciation. Lavateraguy (talk) 22:17, 15 June 2012 (UTC)

Thanks. Of his own admission, the book was self-published because he couldn't get it published elsewhere. He claims reviewers were just cruel and clearly blind, which lead to constant rejection. I can sympathize with repeated rejection, but there is almost always a good reason. I'm leaning toward an assessment of the work as fringe, at the moment. Rkitko 23:05, 16 June 2012 (UTC)

I'm at a library, guys, and I see that in the introduction to his Avian Hybrids book McCarthy lists (pp. 29-30) a lot of birds of hybrid origin that have been treated as species. I also see, in flipping through the book, that most of the crosses seem to be interspecific, not intergeneric as somebody claimed above. 72.152.228.149 (talk) 21:44, 15 June 2012 (UTC)

"intrageneric" rather than "intergeneric" - interspecific includes intergeneric and interfamilial, intrageneric excludes them. Lavateraguy (talk) 21:51, 15 June 2012 (UTC)

Seems to me that a hypothesis of pervasive hybridization COULD be falsified: If it were true for the typical set of related organisms, then if distinct gene trees were concordant, it would be consistent with the idea that hybridization was rare. If, on the other hand, different genes regularly generated distinct species phylogenies, then the pervasive hybridization would be supported. I won't name any names, but a GREAT figure in population genetics once told me that the only way to get clean results with phylogenies is to limit the number of markers. In simple terms, his advice was don't look at too many genes or you'll get conflicting results and you won't be able to publish. 72.152.228.149 (talk) 22:01, 15 June 2012 (UTC)

In repsonse to Genomic Shock's comment above: An autopolyploid is the product of a spontaneous chromosome doubling that generally occurs in ONE generation--not a very good example of gradual origin if you ask me. Actually, I see autopolyploidy is one of the stabilization processes that McCarthy mentions on his site. Koolokamba (talk) 22:13, 15 June 2012 (UTC)

I did a site search of McCarthy's site for the term "autopolyploid" and on one page he writes this: "Many supposed autopolyploid are actually derived from hybridization, but are not recognized as such due to the official taxonomic treatment of the hybridizing forms. That is, they are products of hybridization between forms that are distinct, but treated as conspecific. Suomalainen et al. (1987: 100) state that polyploid vertebrates of known origin have generally 'proven either to be species hybrids or hybrids between different cytological races of a single species.' " Koolokamba (talk) 22:21, 15 June 2012 (UTC)

What you meant by gradual was unclear, especially as you opposed it to hybrid. Lavateraguy (talk) 13:45, 16 June 2012 (UTC)

Stebbins called these "segmental allopolyploids" in plants. Many botanists dont' regard strict autopolyploidy as a means of speciation, since there is continued gene flow into the polyploids through non-reduced gametes.--Curtis Clark (talk) 01:45, 16 June 2012 (UTC)

Taking the comment above "GREAT figure in population genetics once told me that the only way to get clean results with phylogenies is to limit the number of markers. In simple terms, his advice was don't look at too many genes or you'll get conflicting results and you won't be able to publish. 72.152.228.149 (talk)" -- isn't this true across the board? and if so, does this not directly imply that hybridisation is behind the vast majority of species origins? And if this is true, then is there not a huge amount of taxanomic work to be done to identify the other hybridisation parent for each of these hybridisation generated species? The 'simple' linear 'Tree of Life' then takes on the form of a genealogical structure with most of the crosses being quite close, but some conceivably quite distant if the Hybridisation Zone was stable and the hybridisation compatability high enough. DerekSmith (talk) 12:25, 16 June 2012 (UTC)

Common descent with dichotomising speciation results in nested hierarchies inferred from different data sets being correlated - not identical. It's generally better to improve taxon sampling that to throw base pairs at a taxonomy - more loci means more opportunities to find a long branch artefact. On a smaller scale, differential fixation of ancestral polymorphisms results in differences between the trees inferred from different loci.

Even if you got more greatly divergent trees this wouldn't imply that hybridisation was behind the vast majority of species origins - if one species in 10 resulted from hybridisation between divergent parents that would be enough to mess up the trees. Lavateraguy (talk) 13:42, 16 June 2012 (UTC)

This reasoning begs the question. If descent truly were strictly dichotomous, then it would be fine to talk about correlated data sets. However, given the two hypotheses we are considering (A: descent is dichotomous and hybridization so rare it can be ignored; and B: descent is reticulate and hybridization is pervasive) any contradictory data that reduces the correlation is actually evidence for hybridization and cannot be merely discounted (as it usually, and reasonably, is under the assumption that hybridization is rare). The comment about differential fixation reflects the same bias: it assumes that the differences are due to differential fixation when they might just as well be evidence of hybridization.DerekSmith (talk) 16:33, 16 June 2012 (UTC)

So, this is a nice discussion, but is there any point to it? Are you suggesting improvements to an existing article or trying to gain support for a policy or guideline, or alert other editors to an existing issue in an article? Those are the typical functions of a Misplaced Pages talk page. All I see here is so far is a decent discussion of the article you posted, its merits, and the ideas within that article. I see no connection to how it is to be used on Misplaced Pages. There are better venues to continue that discussion as Misplaced Pages is not a forum. Have any specific proposals on what you want to see done? Or was this just a general "for your interest" post? If the latter, I suggest wrapping up the conversation. What is clear from this discussion is that many of our articles on phylogenetic topics could use improvement. For example, at present incomplete lineage sorting currently redirects to coalescent theory. Rkitko 17:26, 16 June 2012 (UTC)

Seems to me there's a VERY BIG POINT. This discussion has a direct bearing on how the "tree of life" should be treated in this article: Is it (i.e., the tree of life) a valid notion or not? If it probably isn't, SURELY that should be at least mentioned in the article. Likewise, if there is disagreement concerning its validity, that should be mentioned, too. — Preceding unsigned comment added by Koolokamba (talk • contribs) 18:47, 16 June 2012 (UTC)

Good point Rkitko, I was starting to worry that this discussion was getting quite large. Is there any point to it? Again good question. From the discussions so far posted, it seems that there is a significant probability that the two processes proposed by McCarthy are substantiated, and that they answer the Saltation problem as yet unanswered by Neo-Darwinism. Consequently the subject of this page - WikiProject Tree of Life will be found to be sadly lacking in describing the lineage of species. Had McCarthy's book been trashed by the expert editors here present, that would have been the end of it, but it wasn't, in fact some posters brought forward supportive examples. So rather than asking is there a point to the discussion, it would perhaps be more pertinent to ask - how are the editors going to correct the present rendition of this page to adapt to new science? DerekSmith (talk) 18:57, 16 June 2012 (UTC)

Derek: Beyond the scope of whether we think there's that much new science presented, its merits, and whether we think it's revolutionary (I don't, and frankly I'm beginning to think much the same that Peter coxhead said below), Misplaced Pages does not respond to immediate changes like this. McCarthy has proposed ideas. Have others opined on the weight of his evidence? Have others supported it? Has it been incorporated into phylogenetics textbooks? Misplaced Pages is descriptive, not prescriptive. We will incorporate McCarthy's ideas once the relevant fields have done so. That is the nature of an encyclopedia. Rkitko 23:05, 16 June 2012 (UTC)

The claim that in a high proportion of cases speciation in eukaryotes proceeds via hybridization is an extraordinary one and would require extraordinarily good evidence. It's at odds with the vast body of molecular phylogenetic data accumulated since the mid-1990s and seems to be sourceable to a single self-published book. Classic fringe science as far as I can see. So there is at present no need to make any changes. Peter coxhead (talk) 19:19, 16 June 2012 (UTC)

Cite your sources, please, not your opinions. "Vast body" says nothing. And please keep in mind it's not a "claim." It's a hypothesis with a great deal of empirical support. Angiosperms, for example, are eukaryotes, and, as almost any biologist must have heard by now, most angiosperms are of hybrid origin. Koolokamba (talk) 19:40, 16 June 2012 (UTC)

Cite your sources that "most angiosperms are of hybrid origin".--Curtis Clark (talk) 23:12, 16 June 2012 (UTC)

Yes, please. Let's avoid ad hominem arguments! Sylvia 1024 (talk) 21:03, 16 June 2012 (UTC)

Peter, your point about there being a 'vast body of molecular phylogenetic data' is aptly at the very heart of this discussion, because as pointed out above by 72.152.228.149, (s)he was advised by a 'GREAT' name that this means of grouping is so confused that the researcher has to be utterly blinkered in order to make any connection at all - vis - "the only way to get a clean result with phylogenies is to limit the number of markers". Indeed, McCarthy makes exactly the same comment himself, and goes on to explain the reason for this being due to the fact that the hybrids contain mixed markers from both (all) parents of the cross. A vast quantity of 'manipulated' data is still manipulated data. Perhaps it is time that the editors of this page should look to amending the phylogenies of at least the 'species' now known to be hybrids, and then develop the page from there. Could we perhaps start by developing a consensus of known hybrids? DerekSmith (talk) 23:15, 16 June 2012 (UTC)

The book in question is still self-published, and the anatomy and palaeontology is still shaky, to be generous. —innotata 23:11, 16 June 2012 (UTC)

A comment by an unnamed person reported by an anonymous person isn't evidence for anything. Molecular phylogenetic work published in the late 1990s and early 2000s did use a relatively small portion of the genome. More recent work uses "multigene supermatrices" and/or compares trees produced from different subsets of sites within genomes and the criticism simply doesn't apply. (A couple of examples I've read recently are: Qiu, Yin-Long (2006), "The deepest divergences in land plants inferred from phylogenomic evidence", Proceedings of the National Academy of Sciences, 103 (42): 15511–15516, doi:10.1073/pnas.0603335103 {{citation}}: Unknown parameter |coauthors= ignored (|author= suggested) (help) and Zhong, Bojian (2011), "Systematic error in seed plant phylogenomics", Genome Biology and Evolution, doi:10.1093/gbe/evr105 {{citation}}: Unknown parameter |coauthors= ignored (|author= suggested) (help).) Similarly, early work used rather simplistic and atheoretical methods of analysis, such as parsimony. More recent work uses models for genomic changes which can be tested statistically. I'm not saying that there aren't still some papers published based on carefully selected sites, but there are now many that are scientifically much stronger.

These molecular phylogenetic approaches have clearly shown when the splitting/branching model fails, e.g. because lateral gene transfer has taken place (e.g. between some angiosperm parasite species and their hosts). Equally they have clearly shown that the branching model is correct in most cases. (At least as regards the rarity of hybridization across widely separated branches. In groups where significant gene flow is still occurring between populations morphologically recognized as "species" (e.g. Ophrys, Dactylorhiza), it doesn't make a lot of sense genetically to talk about "hybrids between species".) Peter coxhead (talk) 07:26, 18 June 2012 (UTC)

One thing to note. If species A splits into species B and C, and species B and C hybridise to produce species D, then tens of million years later, if the only descendants of A are also descendants of D, then the fact of species hybridogensis in the lineage doesn't change the tree of living species.

Reticulation in various forms is widespread, and is one of many processes that can interfere with producing a clean tree from DNA sequence data (see also parology, base substitution biases, variations in base substitution rate, homoplasy, ...). Much of what McCarthy writes is not novel, and is not ignored by phylogeneticists (and doesn't require modification to the tree of life in Misplaced Pages). Lavateraguy (talk) 08:28, 18 June 2012 (UTC)

Arbitrary break to make editing easier

1. Derek, I assume you mean a "consensus of species known to be of hybrid origin". A list of known hybrids would be more noise than signal here, except to someone who already had their mind made up about mechanism.
2. Incongruent phylogenetic data can be explained as homoplasy or as lateral transfer (through hybridization or other means). Any homoplasy can be explained as lateral transfer, and any lateral transfer can be explained as homoplasy. So appeals to incongruence are not useful in convincing people, since it can mean anything.
3. If I'm understanding the mechanisms he postulates, at least some of them are well-known and documented (recombinational speciation, for example). He's saying nothing new, at least there, about mechanism; it seems to me that his new argument is about scope, and the burden of proof is on him. There are ways to positively identify species of hybrid origin, but afaik they still require examining each candidate species individually.--Curtis Clark (talk) 00:40, 17 June 2012 (UTC)

On his website, McCarthy quotes John Avise (someone, I trust, all the phylogeneticists among you will have heard of) as follows about his, McCarthy's, theory:

"In his recent book, In the Light of Evolution (2008), renowned evolutionary biologist John Avise says that if the views presented on this website are correct, our ideas of biology and the evolutionary process will have to be revised at a fundamental level. There, he states that: 'First, phylogeneticists would have to admit that their dream of reconstructing a branched tree of life had been merely a pipedream, and they would have to accept the new and probably far more difficult challenge of working out the precise history of reticulation events for each organismal group and how such reticulate genealogical histories have idiosyncratically distributed particular bits and pieces of DNA from disparate sources to extant taxa. Traditional concepts of species, phylogeny, ancestry, and classification, as well as the significance of reproductive isolation, would all have to be reevaluated. Biologists would have to embrace the notion that biological processes falling somewhat outside the standard neo-Darwinian paradigm for speciation (such as interspecific hybridization and the reproductive stabilization of genetic-recombinant derivatives) could play major and previously underappreciated roles in evolution. They would have to reevaluate the origins of genetic variation on which natural selection acts and how novel phenotypic adaptations and different forms of life mechanistically come into being. In short, major shifts in evolutionary thought would be required, and this would open wonderful opportunities for the eventual emergence of a grandly updated evolutionary synthesis, 21st-century style.' — From In the Light of Evolution, Volume II: Biodiversity and Extinction, 2008, pp. 288–289." McCarthy took the quotation from Avise's online discussion of the theory (Avise calls it the "Network Theory"), which is available on line . Here's the link: http://books.nap.edu/openbook.php?record_id=12501&page=288 Koolokamba (talk) 22:21, 17 June 2012 (UTC)

For those of you who don't know, you can find more about John Avise here: http://www.faculty.uci.edu/profile.cfm?faculty_id=5292 — Preceding unsigned comment added by Koolokamba (talk • contribs) 22:47, 17 June 2012 (UTC)

So... one favorable mention in 2008 from someone McCarthy once worked with at the University of Georgia (probably the only reason he was aware of the work) and then crickets since then? I'm sorry if this sounds a bit harsh, but I don't think this discussion is productive any longer. McCarthy didn't even address one of the sources of homoplasy, incomplete lineage sorting, in his work. One would think that such important ideas would at least warrant a mention, especially if he's suggesting it is not as important as hybridization. The point? It does not seem like the important paradigm-shifting work that McCarthy, as a self-promoter, and his supporters here want it to be. There is nothing of relevance to Misplaced Pages that can come from continuing, unless we collaborate to work on some of the articles that are in desperate need of attention that I pointed out above. And continued promotion of McCarthy's ideas should not be tolerated until they gain wider acceptance - see WP:NOTSOAPBOX and again WP:NOTFORUM. Rkitko 23:00, 17 June 2012 (UTC)

Collaboration entails entertaining alternative viewpoints. I don't know about anyone else who's looking at this conversation, but I can't see much of that here. So I, for one, will leave you to your phony, pointless tree of life and move on to other articles, NOT suggested by you, narrow-minded Rkitco, Mr. Keeper of the Truth. And I'm really NOT sorry if that sounds a bit harsh. Koolokamba (talk) 23:23, 17 June 2012 (UTC)

Actually, when I went away, I was copyediting the article on the Moghul Empire, and there I noticed alternative viewpoints are in fact allowed, for example, alternative views on the reasons for the empire's decline during the 18th century. So it really isn't true that unestablished alternative views aren't allowed on Misplaced Pages. It's that you, Mr. Rkitco, are setting yourself up a little fiefdom here where you can suppress opinions that differ from your own. You don't even have your Ph.D. yet. So how can you possibly in good conscience set yourself up as such an expert? Even someone with a degree shouldn't do that. Anyway, bye. This time for good. Koolokamba (talk) 23:53, 17 June 2012 (UTC)

(edit conflict)Collaboration in building the encyclopedia certainly does include entertaining alternative views, but we as editors do not decide which views have merit. We simply describe the current consensus of whatever field or topic we're writing about and do so with a neutral point of view. Yes, this also includes providing information on major competing hypotheses, but not WP:FRINGE ones and certainly not ones that have not been fully evaluated by other scientists and authors. What I see here is anything but and is extremely thin on details on what the proponents want us to do with McCarthy's self-published book. I don't see, given how little attention has been paid to his ideas, how we could incorporate anything from that manuscript into Misplaced Pages. Also, what you observe as narrow-mindedness is not; I am simply reminding you (or introducing you) to what Misplaced Pages is not. Please avoid personal attacks of that nature. My qualifications are not of concern, here, and I provide them for those that are curious. I did not claim to be an expert on the subject, but I did evaluate the manuscript in terms of its merits as a reliable source for use on Misplaced Pages. That's what matters here. Please stick to that discussion and do not get distracted by my personal details. Cheers, Rkitko 00:05, 18 June 2012 (UTC)

LOL. GOODBYE, MR. PRONOUNCER OF THE CONSENSUS. Koolokamba (talk) 00:16, 18 June 2012 (UTC)

Oh, and folks, unless there was any mistake, it is possible that Koolokamba (talk · contribs) is indeed Eugene M. McCarthy himself, here to promote his own work. On a website that linked to his own, someone with the same username, koolokamba, commented and signed it "Gene McCarthy Ph.D. Genetics" after thanking the original poster for linking to his website. So there is an added conflict of interest and I wouldn't be surprised if the WP:SPA Sylvia 1024 (talk · contribs) who jumped into this discussion and edited twice turned out to be a sockpuppet or meatpuppet. Rkitko 00:20, 18 June 2012 (UTC)

That's just sad, that someone with actual academic credentials should fall so low that they would feel compelled to defend their ideas on Misplaced Pages. --Curtis Clark (talk) 03:20, 18 June 2012 (UTC)

I just have to respond to the allegation that all scientists self-promote: real scientists concentrate on research; don't justify your self-aggrandizement by tarring others. Promoting our own publications in wikipedia is infra dig. Promoting a theory as "new" that is (1) a straw man fallacy and (2) a collection of other people's work, is similarly unworthy of a scientist. DS please also desist from spamming other editors' talk pages. Sminthopsis84 (talk) 20:57, 18 July 2012 (UTC)

List of animal cartoon characters sorted by biological taxonomy

I am interested in seeing an article "List of animal cartoon characters sorted by biological taxonomy".
—Wavelength (talk) 19:00, 29 June 2012 (UTC)

Two articles with the same taxobox

A taxobox was added to the article pet skunk. The use of this animal in this way is a subset of the taxon Mephitis mephitis, and as such shouldn't get the same taxon, don't you think? Chrisrus (talk) 05:16, 5 July 2012 (UTC)

I've removed it. From sources, it's not restricted to M. mephitis at all, although the latter is the most commonly domesticated.-- OBSIDIAN†SOUL 08:24, 5 July 2012 (UTC)

Discussion at Misplaced Pages:Categories_for_discussion/Log/2012_July_5

You are invited to join the discussion at Misplaced Pages:Categories_for_discussion/Log/2012_July_5. Several bird categories have been nominated for renaming because their latin names are ambiguous. Inputs welcome. KarlB (talk) 18:59, 9 July 2012 (UTC)Template:Z48

Heads up......

Any big/broad biology articles that are in poor shape are fair game for Misplaced Pages:Core_contest over the month of August? WWII might be a tad tricky but surely there are some other big'uns.....Casliber (talk · contribs) 00:20, 18 July 2012 (UTC)

Categories (section)

Added reference to Biota (ecology) in addition to the internal link Biota (taxonomy). The closed reference was placed at the end of the section as it was the first reference used in this article; being a lengthy article, uncertainty of MOS in this case the reference was placed in proximity to the reader's concern for ambiguity.  O = M _C   22:45, 19 July 2012 (UTC)

How to make a cladogram?

Are there any guides how to write a cladogram for a Misplaced Pages article? FunkMonk (talk) 16:29, 20 July 2012 (UTC)

Well, there's the {{clade}} template. ErikHaugen (talk | contribs) 17:21, 20 July 2012 (UTC)

Thanks, I'll take a look. FunkMonk (talk) 17:32, 20 July 2012 (UTC)

I made an attempt at one here, but is there a way I can get the branch with Didunculus moved below the rest, instead of above? That's how it is in the paper. FunkMonk (talk) 20:42, 20 July 2012 (UTC)

How is this? ErikHaugen (talk | contribs) 06:09, 21 July 2012 (UTC)

Thanks, that's what I was thinking of, I tried something similar, but seems the placement of Didunculus should correspond exactly with the placement of its sister branch down in those. Thanks! FunkMonk (talk) 09:09, 21 July 2012 (UTC)

I've attempted to make a cladogram for moa, but the result is rather mangled: Would anyone be able to fix it so it looks more like this? The original figure is here, I have removed lineages within species from the other version. Thanks. FunkMonk (talk) 17:17, 14 August 2012 (UTC)

Have attempted a cladogram. Please check and modify as needed. The key is to add some dummy nodes. Shyamal (talk) 15:04, 15 August 2012 (UTC)

Thanks, looks correct. Is there a way to left align it? FunkMonk (talk) 15:12, 15 August 2012 (UTC)

Box moved to left. Hope that was what you meant. Shyamal (talk) 15:52, 15 August 2012 (UTC)

Exactly, and thanks again, I'll add "clear" so it won't interfere with the following sections. FunkMonk (talk) 16:00, 15 August 2012 (UTC)

WT:WikiProject_Biology#A-class

Just a pointer to a discussion about creating an A-class review process for Tree of Life and related projects. - Dank (push to talk) 19:14, 23 July 2012 (UTC)

Brock's Yellow-eared Bat

I know that Brock's Yellow-eared Bat was discovered by Stan Brock (philanthropist) while he worked on the Dadanawa Ranch in British Guyana, but I don't know just how to show that the Binomial name Vampyressa brocki was derived from Stanley Brock. Check talk:Stan Brock (philanthropist) for a source.--DThomsen8 (talk) 01:04, 3 September 2012 (UTC)

brocki is a normal Latin masculine genitive form, derived from "Brock". The genus name, Vampyressa, has a completely different etymology. Ucucha (talk) 02:14, 3 September 2012 (UTC)

This dictionary, the Eponym Dictionary of Mammals, is excellent for mammal names like this. It states explicitly that V. brocki is named after Stanley E. Brock. --Stemonitis (talk) 18:40, 6 September 2012 (UTC)

Genus navbox templates

Hi, all. I've opened a discussion on a whole bunch of relatively new genus navbox templates here: Misplaced Pages:Templates for discussion/Log/2012 September 9#Genus navboxes (2). Your comments would be welcomed on the merits of these as a navigation tool for our genus and species articles. Cheers, Rkitko 16:59, 9 September 2012 (UTC)

Fourth domain of life?

According to a recent study giant viruses may represent a fourth grouping of life, along side archaea, bacteria, and eukarya. Would this go only in domain (biology) or would it also be in scope of kingdom (biology) ? -- 76.65.131.248 (talk) 13:29, 17 September 2012 (UTC)

PMID 22920653 -- 76.65.131.248 (talk) 13:55, 17 September 2012 (UTC)

One million new species of sea life

The discovery of one million new species of sea life has been reported.

• Tara Research Vessel Discovers One Million New Species Of Microscopic Sea Life (PICTURES)

—Wavelength (talk) 19:33, 28 September 2012 (UTC)

• Project-Class taxonomic pages
• NA-importance taxonomic pages
• WikiProject Tree of Life articles