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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)
`--Macroscelidea
|--Chambius
`--+--Rhynchocyon
`--Myohyrax
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.
Etc.
Enforcing a topology congruent with molecular hypotheses results in trees
only two steps longer-
|--Protungulatum
|--Periptychidae (Mithrandir)
`--+--+--Kolpaniinae (Molinodus)
| `--Hyopsodontidae (Hyopsodus)
`--+--+--Mioclaenidae (Claenodon)
| `--Oxyclaenidae (Chriacus)
`--+--Ferungulata
| |--Artiodactyla (Diacodexis)
| `--+--Mesonychidae (Dissacus)
| `--Perissodactyla (Hyracotherium)
`--Afrotheria
|--Apheliscinae (Apheliscus)
`--+--+--Apheliscinae (Haplomylus)
| `--Macroscelidea
| |--Chambius
| `--+--Rhynchocyon
| `--Myohyrax
`--+--Louisininae (Paschatherium)
`--+--Louisininae (Microhyus)
`--Paenungulata
|--Hyracoidea (Microhyrax)
`--Tethytheria
|--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