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Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)

Thomas R. Holtz, Jr. <tholtz@umd.edu> wrote:

> Not really. At least, not at conferences. Yes, there was resistence at first, 
> but the discovery of additional basal whales with
> artiodactyl features and the inclusion of many more basal artios and their 
> kin into matrices seems to have convinced the majority of
> paleomammologists I know that this is the correct position in some 
> configuration or other.

I think the qualifier "in some configuration" is telling.  The
Whippomorpha hypothesis originally held that aquatic adaptations were
primitive for hippos and whales, as an integral part of a unique
hippo-whale clade that is derived within Artiodatyla
(Cetartiodactyla).  Recent discoveries - and re-interpretations of old
discoveries - have muddied the waters (so to speak).

For example, Orliac et al. (2010) found support for nesting
hippopotamids inside the anthracothere clade, and linked this expanded
Hippopotamoidea clade with the Eocene _Choeropotamus_.  They favored
(but did not test) a Cetancodonta/Whippomorpha clade.  A previous
morphology-based analysis by Boisserie et al. (2005) also recovered
this expanded Cetancodonta (anthracotheres, hippopotamids, whales).
However, this analysis also recovered a sister group relationship
between Cetancodonta and Suina (pigs and peccaries) as derived
artiodactyls.  This goes against the grain of molecular phylogenies,
which recover a more basal position for Suina, and find
Cetancodonta/Whippomorpha to be closest to Ruminantia.  I know this
proposed anthracothere/hippo/whale link hasn't exactly caught on, but
there's other morphology-based studies that contradict canonical
Whippomorpha.  The morphology-based analysis of Thewissen et al.
(2007) supported a group of semi-aquatic basal artiodactyls called
raoelliids as the sister clade to Cetacea.  Thus in this topology
whales are artiodactyls - although outside the crown Artiodactyla, and
far from hippopotamids.  I know there a taxon sampling taxon issues
with this analysis (as noted by Uhen, 2010), but the basal position of
whales within Cetartiodactyla can't be reconciled with current
molecular-based topologies.

One can accept the Cetartiodactyla hypothesis (= cetaceans are
artiodactyls), as I do, but at the same time be skeptical of the other
claims entailed in the original Whippomorpha hypothesis.  This
includes a derived position for whales + hippos inside
Cetartiodactyla.  I'm keeping an open mind on the Cetancodonta
hypothesis (= a relationship of some sort between hippopotamoids and
cetaceans, to the exclusion of other extant artiodactyls), but the
devil's in the detail.  The molecular and morphological evidence is
certainly converging, and the old cetacean-mesonychian link (without
artiodactyls) looks increasingly precarious.  But I'm not entirely
sold on the current topology of Cetartiodactyla given by
molecular-based analyses, which puts a hippo+whale clade as sister
taxon to Ruminantia as the most derived clade within Cetartiodactyla.

I'm not saying anyone does this, but I don't assume that
molecular-based phylogenies are "correct" simply because they use
genes and proteins rather than bones and teeth.  Even multigene
datasets have problems (e.g., see Rannala & Yang [2008] Annu. Rev.
Genomics Hum. Genet. 9: 217–231).  David's comment regarding alignment
being the elephant in the room is important in this regard.  As
someone who works on the molecular side of life, I long ago came to
the conclusion that molecules are not a panacea for phylogenetics,
even when combined with morphological data ("total evidence").  Mickey
has rightfully pointed out the imperfections of morphology-based
approaches, but I still think it's dangerous to put all your
phylogenetic eggs in the molecular basket.

>  I know some hardliners who still reject
> it, but I'm sure we can all think of some folks who--despite considerable 
> evidence to the contrary--refuse to accept that some taxon
> (I don't know, say... Aves?) does not belong inside some other long 
> established groups (like, say, I don't know... Dinosauria?)

Hey, I'm 100% behind the birds-are-dinosaurs phylogenetic hypothesis.
You won't meet a more ardent fan than me.  But it's worth pointing out
that the well-supported phylogenetic hypothesis that birds (Aves) are
theropod dinosaurs came about as a result of morphology-based
phylogenetic analyses (for obvious reasons).  We have early birds
(_Archaeopteryx_, _Jeholornis_, etc) and proposed close theropod
relatives.  The same situation is true for whales, with the fossil
record doing a fair job of documenting the transition to a fully
aquatic cetacean.  So I think we should give the fossil/morphological
evidence a fair hearing when it comes to inferring the identities of
the closest cetacean relatives (including the sister group).