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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
excision.

> 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
paleognaths.

> 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.


*Refs:*

Bock WJ, Bühler P 1990 The evolution and biogeographical history of
the palaeognathous birds. 31-6 _in_ van den Elzen R, Schuchmann K-L,
Schmidt-Koenig K, eds. _Proceedings of the International Centennial
Meeting of the Deutsche Ornithologen-Gesellschaft_. Bonn: Verlag der
Deutschen Ornithologen-Gesellschaft

Cracraft J, Barker FK, Braun M, Harshman J, Dyke GJ, Feinstein J,
Stanley S, Cibois A, Schikler P, Beresford P, García-Moreno J,
Sorenson MD, Yuri T, Mindell DP 2004 Phylogenetic relationships among
modern birds (Neornithes): toward an avian tree of life. 468–89 _in_
Cracraft J, Donoghue M, eds. _Assembling the Tree of Life_. New York:
Oxford Univ Press

Dyke GJ, van Tuinen M 2004 The evolutionary radiation of modern birds
(Neornithes): reconciling molecules, morphology and the fossil record.
Zool J Linn Soc 141(2): 153–77

Elżanowski A 1995 Cretaceous birds and avian phylogeny. Cou
Forsch-Inst Senck 181: 37-53

Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT,
Glenn TC 2012 Ultraconserved elements anchor thousands of genetic
markers for target enrichment spanning multiple evolutionary
timescales. Syst Biol 61(5): 717–26

Haddrath O, Baker AJ 2012 Multiple nuclear genes and retroposons
support vicariance and dispersal of the palaeognaths, and an Early
Cretaceous origin of modern birds. Proc R Soc B 279(1747): 4617–25

Harshman J, Braun EL, Braun MJ, Huddleston CJ, Bowie RCK, Chojnwoski
JL, Hackett SJ, Han K-L, Kimball RT, Marks BD, Miglia KJ, Moore WS,
Reddy S, Sheldon FH, Steadman DW, Steppan SJ, Witt CC, Yuri T 2008
Phylogenomic evidence for multiple losses of flight in ratite birds.
Proc Natl Acad Sci USA 105(36): 13462-7

Johnston P 2011 New morphological evidence supports congruent
phylogenies and Gondwana vicariance for palaeognathous birds. Zool J
Linn Soc 163(3): 959-82

Mitchell KJ, Llamas B, Soubrier J, Rawlence NJ, Worthy TH, Wood J, Lee
MSY, Cooper A 2014 Ancient DNA reveals elephant birds and kiwi are
sister taxa and clarifies ratite bird evolution. Science 344(6186):
898–900

Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante
AA 2011 Evolution of modern birds revealed by mitogenomics: timing the
radiation and origin of major orders. Mol Biol Evol 28(6): 1927–42

Phillips MJ, Gibb GC, Crimp EA, Penny D 2010 Tinamous and moa flock
together: mitochondrial genome sequence analysis reveals independent
losses of flight among ratites. Syst Biol 59(1): 90-107

Pratt RC, Gibb GC, Morgan-Richards M, Phillips MJ, Hendy MD, Penny D
2009 Toward resolving deep Neoaves phylogeny: data, signal
enhancement, and priors. Mol Biol Evol 26(2): 313–26

Smith JV, Braun EL, Kimball RT 2013 Ratite nonmonophyly: independent
evidence from 40 novel loci. Syst Biol 62(1): 35–49

Sorenson MD, Oneal E, García-Moreno J, Mindell DP 2003 More taxa, more
characters: the hoatzin problem is still unresolved. Mol Biol Evol
20(9): 1484–98

Worthy TH, Scofield RP 2012 Twenty-first century advances in knowledge
of the biology of moa (Aves: Dinornithiformes): a new morphological
analysis and moa diagnoses revised. New Zealand J Zool 39(2): 87–153


-- 
David Černý