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Re: Reduced Consensus (Was: Afrotheria revisited)

Thanks to David Marjanovic for sending me a pdf of Tabuce et al.. I have to revise what I said earlier now that I have the paper. First, they ran a normal analysis of their 52 characters and 23 taxa. That got figure 3a, mostly a huge polytomy. Then they reweighted the characters to get the more resolved figure 3b. Reweighting's an interesting thing that I've just begun to experiment with. Basically it makes characters which reverse or coverge more than others worth less in the analysis. Of course, you have to run the analysis once to figure out what characters reverse or converge less, and that makes me wary. Also, does the fact a character coverges or reverses make it less valuable? And unless you include all relevent taxa (which virtually no analysis does/can), you won't catch all the times a character reverses or converges, so the value PAUP uses to determine its weight will be off.

Anyway, then the authors exclude Arsinoitherium from the analysis. The DO explain their rationale here (pg. 1163)-
"Among the paraphyletic paenungulates, Arsinoitherium occupies a basal position. Since its original description, the systematics and phylogenetic position of Arsinoitherium is disputed: Andrews (1906) related this genus to hyraxes, while, more recently, Court (1992a) and Gheerbrant et al. (2005b) considered Arsinoitherium as the sister group of proboscideans or tethytheres, respectively. Arsinoitherium exhibits an autapomorphic dental morphology. As such, it differs substantially from basal tethytheres in showing an unusual case of hypsodonty and in having a very peculiar bilophodonty of its cheek teeth. Court (1992b) hypothesized that this morphological dental pattern could derive from a hyperspecialized dilambdodonty. It seems to us that the homology of selected dental characters scored in Arsinoitherium with respect to the other ingroup taxa is not attested, thereby we excluded that genus from the phylogenetic analysis."
And doing this, they get a new tree where afrotherians are monophyletic (figure 4a). So yes, they did cheat. Good call, Allen!

To test some things I analyzed their data in PAUP. First I noticed several characters (2, 3, 8, 11, 16, 28, 29, 30, 31, 32, 40, 43, 51) should have been ordered, so I changed that. I also noticed 35 and 36 involved more than one character each (size vs. position of peroneal tubercle; mediolateral vs. dorsoventral concavity of cuboid facet), so I divided each into two characters. This could probably be done with several others as well, but I'm no mammalogist. Then I ran the matrix and got 9 equally parsimonious trees.

|--Periptychidae (Mithrandir)
`--+--+--Kolpaniinae (Molinodus)
  |  `--Hyopsodontidae (Hyopsodus)
  |--+--Mioclaenidae (Claenodon)
  |  `--Oxyclaenidae (Chriacus)
  `--+--+--+--Artiodactylia (Diacodexis)
     |  |  `--Mesonychidae (Dissacus)
     |  `--+--+--Meniscotheriidae (Ectocion)
     |     |  `--Perissodactyla (Hyracotherium)
     |     `--Tethytheria
     |        |--+--Proboscidea (Numidotherium)
     |        |  `--Anthracobunidae (Anthracobune)
     |        `--+--Sirenia (Protosiren)
     |           |--Phenacolophidae (Phenacolophus)
     |           `--Embrithopoda (Arsinoitherium)
     `--+--Apheliscinae (Apheliscus)
        `--+--+--Louisininae (Paschatherium)
           |  `--+--Louisininae (Microhyus)
           |     `--Hyracoidea (Microhyrax)
           `--+--Apheliscinae (Haplomylus)

Pretty good in many respects. I don't know much about 'condylarth' relationships, but as Phenacolophus clades with Arsinoitherium and is stated to be a putative embrithopod, I don't think Arsinoitherium is misplaced. Thus I don't think it should be excluded. And indeed, excluding it and rerunning the analysis generates a tree very much like figure 4a, except Microhyus is resolved as closer to paenungulates than Paschatherium.

Would it be possible to get a DIFFERENT well-resolved tree by excluding one of the other taxa (this is something that time and computer power could check!)?

Yes it would.
Excluding Dissacus results in Molinodus, Chriacus, Claenodon and Diacodexis being successively more closely related to the apheliscine+hyracoid+macroscelidean clade; while Hyopsodus is the sister taxon of 'perissodactylomorphs'+tethytheres.
Excluding Diacodexis results in many poorly resolved trees, with only Haplomylus+Macroscelidea and 'Perissodactylomorpha'+Tethytheria present.
Excluding Hyracotherium results in Arsinoitherium being a basal tethythere, and Protosiren and Phenacolophus being in an unresolved trichotomy with Anthracobune+Numidotherium.

Enforcing a topology congruent with molecular hypotheses results in trees only two steps longer-

|--Periptychidae (Mithrandir)
`--+--+--Kolpaniinae (Molinodus)
  |  `--Hyopsodontidae (Hyopsodus)
  `--+--+--Mioclaenidae (Claenodon)
     |  `--Oxyclaenidae (Chriacus)
        |  |--Artiodactyla (Diacodexis)
        |  `--+--Mesonychidae (Dissacus)
        |     `--Perissodactyla (Hyracotherium)
           |--Apheliscinae (Apheliscus)
           `--+--+--Apheliscinae (Haplomylus)
              |  `--Macroscelidea
              |     |--Chambius
              |     `--+--Rhynchocyon
              |        `--Myohyrax
              `--+--Louisininae (Paschatherium)
                 `--+--Louisininae (Microhyus)
                       |--Hyracoidea (Microhyrax)
                          |--Proboscidea (Numidotherium)
                          `--+--Anthracobunidae (Anthracobune)
                             `--+--Sirenia (Protosiren)
                                |--Phenacolophidae (Phenacolophus)
                                `--+--Embrithopoda (Arsinoitherium)
                                   `--Meniscotheriidae (Ectocion)

So really it's not too unlikely. Especially since tons of relevent taxa weren't included. How about some lipotyphlans, bats, carnivorimorphs, afrosoricans, meridungulates, etc.? Why root it on Protungulatum? Who knows where it goes? Why not Eomaia or an asioryctithere?
Really, the entire tree's poorly supported. Bootstrapping results in 95% support for Rhynchocyon+Myohyrax, and 68% for Macroscelidea. 71% for Haplomylus+Macroscelidea and 66% for the clade of everything except Protungulatum and Mithrandir. Every other node is supported by <50%.

Mickey Mortimer