Sunday, October 11, 2015


There are many problems with the analyses of the dino to bird theory. Here is one of them:
Also, the use of bipedal coelurosaurian
outgroups, as in the analysis by Clark et
al. (2002), may be contributing to a potentially
misleading topology. Outgroup choice determines
the polarity of character states, including
ancestral reconstructions for entire clades (Nixon
and Carpenter 1993). In this case, using bipedal
cursors as outgroups may obscure phylogenetic
signal by wrongly treating characters indicating
flight loss as plesiomorphy.
The "maniraptors" such as oviraptors and alvarezsaurids were flightless. They lived on the ground. The question is whether their ancestor was a ground-living creature (such as a dinosaur) or whether their ancestor was a flying, primitive bird.
When a cladistic analysis uses a ground-based dinosaur (eg. allosaurus) as the outgroup it takes the flightlessness of the "maniraptors" as being inherited from a dinosaur lineage, when in fact they actually descended (in both senses) from a flying primitive bird ancestor.


    Ji and Yuan (2002) and Czerkas and Ji (2002) regarded
    the fibrous integumentary structures of
    pterosaurs as potentially homologous with avian
    feathers, implying that feathers are basal to the
    clade stemming from the last common ancestor
    of pterosaurs and birds, but no evidence from the
    fossil record indicates such a distribution.

  2. For reference:
    They also plan to not polarize their characters (e.g. not assume
    that "0" is primitive and "1" is advanced...which is a perfectly
    reasonable and interesting bit of data to publish)

    Huh? PAUP* doesn't care about such silly assumptions. PAUP* makes _unrooted_ trees -- you see, at every change between 0 and 1, 0 is an autapomorphy in one direction and 1 is an autapomorphy in the other direction --, then arranges them in such a way that the outgroup lies on the outside, and then calls that a rooted tree. The outgroup polarizes the characters, not any people. That's what the outgroup is there for.

    If the outgroup is all-1 instead of all-0, then 1 will be the plesiomorphic state for each character. If the outgroup has states with different numbers of different characters (the normal case), then which state is plesiomorphic will differ between the characters. Which states you give which numbers is arbitrary, it's just for your own purposes as a mnemonic or whatever you like.


  3. James and Pourtless critics: