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Re: Moa-Tinamou Clade Found Within Ratites

evelyn sobielski <koreke77@yahoo.de> wrote:

> Did anyone count how often paleognath phylogeny was "resolved" yet?

It's been resolved pretty well since 2008. Among living and subfossil
taxa, the only remaining uncertainty is limited to the basal
divergence within Notopalaeognathae (= non-ostrich paleognaths), and
even there, it's not that different analyses support different
topologies -- rather, they all fail to provide decisive support for
any of the three possible topologies.

> And do Baker et al (2014) address the concerns [...] regarding the need to 
> test any "new phylogenomic sequences from 1,448 nuclear DNA loci totalling 
> almost one million base pairs" (and RGCs just as well) on whether they 
> actually retain phylogenetic signal?

They do. They use an entropy-based index to estimate how much
saturation there is in different partitions of their dataset, and the
level is subcritical for all of them. They also account for both
across-site and across-lineage composition heterogeneity using mixture
models, and infer species trees for both of their main partitions
(ultraconserved elements and protein-coding genes) using maximum
pseudo-likelihood. The species trees are identical to the
concatenation trees, which suggests that the topology of the latter
isn't an artefact of gene tree/species tree discordance. The idea of
testing retroposon insertions for retention of phylogenetic signal
seems a bit weird -- once it's established they are of the same
(sub)type and share the same insertion site, orientation, and
truncation point, they are basically guaranteed to carry a signal
(even though, when there is incomplete lineage sorting, it might not
be the signal we are interested in).

Interestingly, there is one retroposon in the Baker et al. dataset
which is absent in tinamous but present in all "ratites" (including
the ostrich). However, it is contradicted by eight insertions that
link tinamous to moa, and the authors suggest that it was secondarily
lost in the last common ancestor of tinamous through a near-perfect

> An additional question: considering we have no problems getting the 
> artificial (Paleognaths,(Passerines,other neognaths)) or 
> (Paleognaths,(Galloanseres,(Passerines,other Neoaves))) quite robustly 
> supported - how can we be sure (Ostrich,other paleognaths) is not artificial?

The basal position of ostriches is robustly supported by several
independent lines of data, including morphology (Bock & Bühler 1990;
Elżanowski 1995; Johnston 2011), mitochondrial sequences (Phillips et
al. 2010), multiple non-overlapping or partially overlapping nuclear
sequence datasets (Harshman et al. 2008; Faircloth et al. 2012;
Haddrath & Baker 2012; Smith et al. 2013), and rare genomic changes
(Haddrath & Baker 2012). The authors of these papers were also
generally pretty careful to test for possible biases in their results
(e.g. the impressive tests of sensitivity to different alignment guide
tree topologies in Smith et al. 2013), and the fact they didn't find
any suggests we can indeed be quite confident that the hypothesis is
correct. The same can't be said for the only viable alternative
hypothesis (monophyletic "ratites" as a sister group to tinamous),
which actually seems to have been a curious (and disturbing) case of
several lines of data converging on the same wrong answer for
unrelated reasons (multiple losses of flight and subsequent
convergence in postcranial morphology, base composition bias in
mt-genome, long branch attraction of fast-evolving tinamous to the
root in nuclear gene analyses).

On the other hand, the basal divergence of passerines within Neoaves
or Neornithes* has (AFAIK) only been recovered using mitochondrial
DNA. It is strongly contradicted by other sources of data, including
morphology, large phylogenomic datasets, and RGCs. It's also worth
mentioning that many mtDNA analyses didn't find support for it either
(Sorenson et al. 2003; Pratt et al. 2009; Pacheco et al. 2011), while
the support for Notopalaeognathae is universal among phylogenomic
datasets and the same topology has occasionally surfaced even in
single gene analyses (Cracraft et al. 2004: Figure 27.4). Finally,
there is a robust alternative hypothesis (Psittacopasserae) for the
phylogenetic position of passerines, whereas the monophyly of ratites
-- seemingly a well-supported alternative to the monophyly of
Notopalaeognathae -- has been thoroughly discredited. The two cases
don't appear to be analogous after all.

*I'm not aware of any published analysis that would recover
(Palaeognathae,(Passeriformes,other Neognathae)), but I'd be grateful
for a reference.

Tim Williams <tijawi@gmail.com> wrote:

> The alternative hypothesis - that the palaeognath clade is primitively
> flightless, and tinamous regained flight from a flightless ancestor - isn't
> given much truck.  This "secondary volant" hypothesis is considered
> unlikely because secondary loss of flight is very common across Aves,
> but there are no known examples of bird lineages that have lost and
> regained flight

Another reason is that the biogeographic distribution of paleognaths
in combination with the relatively young age of the clade (supported
by several molecular dating analyses) requires extensive transoceanic
dispersal that flightless birds wouldn't be capable of. Johnston
(2011) claimed that the Notopalaeognathae topology is compatible with
a strictly vicariant scenario (although he still favored multiple
losses of flight over a single re-acquisition of flight in tinamous),
but his hypothesis relied on incorrect positions of moa and
elephantbirds and an unrealistically old estimate for the age of

> Palaeognaths may have begun as rather small, volant birds with
> excellent flight abilities (unlike the tinamous).  Key to this is
> _Proapteryx_, the fossil kiwi (apterygid) from the early Miocene of New
> from the early Miocene of New Zealand, which was smaller than extant
> kiwis and possibly volant (Worthy, 2013).

It may be even more important to find out where lithornithids -- some
of which were highly volant -- belong within the (pan-)paleognath
tree. Dyke & van Tuinen (2004) and Worthy & Scofield (2012) recovered
_Lithornis_ as a stem-ratite and a stem-paleognath, respectively, but
since they also found monophyletic "ratites", their results probably
can't be trusted. Johnston (2011) and most recently Mitchell et al.
(2014) supported a sister-group relationship between _Lithornis_ and
tinamous, but I wonder if that's not just a result of the high degree
of overall similarity between the two taxa.


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David Černý