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Re: Genes show Neoaves branching before K/Pg extinction



David Marjanović <david.marjanovic@gmx.at> wrote:

> So... only two calibration dates had older limits as well as younger ones: 
> the hummingbird/swift split and the origin of Neornithes.

Is the inclusion of hard upper bounds (maximum age constraints) a
common practice in molecular dating? Many recent papers (e.g. Brown &
van Tuinen 2011; Ronquist et al. 2012) use probability distributions
with a minimum at the age of a fossil and a long low-probability tail
instead of a hard maximum, which seems to make sense, given that
maximum ages cannot be estimated from the fossil record without making
some dubious assumptions.

Tim Williams <tijawi@gmail.com> wrote:

> This topology, with tinamous nested inside traditional ratites, likely
> means that the ratite morphology (especially characters associated
> with flighlessness) arose multiple times in Palaeognathae.  If so,
> instead of Ratitae being the sister group to Tinamidae, the Ratitae is
> now paraphyletic relative to the Tinamidae.  This is probably what the
> authors meant.

Yes, but that's exactly what I meant, too: if the ratite morphology
originated more than once, the group diagnosed by the possession of
that morphology is polyphyletic (it's a union of several monophyletic
groups) rather than paraphyletic (a monophyletic group minus another
monophyletic group). Paraphyly and polyphyly cannot be distinguished
using a tree topology alone. If you don't want to speculate about
ancestral states, all that you can say is that ratites are
non-monophyletic.

> So it can happen in at least one group of insects.  But could it
> happen in birds?  Could something like the modern kagu (which has
> muscles that are too weak for powered flight, but it still glides)
> give rise to powered fliers millions of years in the future?
>
>
> Let's say that the most recent common ancestor of crown palaeognaths
> (ratites + tinamous) was indeed secondarily flightless.  If most of
> the flight equipment was there, but "downgraded" (reduced sternum and
> carina, shorter wings, enlarged scapula-coracoid angle, etc), perhaps
> it could be re-mobilized in order to be fully volant again, if
> circumstances changed.  (Meanwhile, other palaeognath lineages simply
> continued to lose their flight-related characters, until they reached
> the point of no return.)

It could have happened (in fact, Phillips et al. 2010 showed that
almost all ancestral state reconstruction methods, including the
probabilistic ones, favor this scenario) -- it's just extremely
improbable. Only three groups of vertebrates are known to have evolved
flight separately, whereas the loss of flight has happened at least
once in every major group of birds (paleognaths, galloanserines,
"aquatic birds", charadriiforms, and landbirds), with several hundred
independent losses in Rallidae alone (Steadman 1995).

> Of course, multiple losses of flight by ratites does seem more likely
> than tinamous regaining the ability to fly from a flightless ancestor.
> But as unlikely as it seems, we just don't know enough about tinamou
> evolution to automatically discount the possibility that modern
> tinamous are secondarily volant.

I don't call for discounting it automatically, I'm just implying it's
highly unlikely -- not only because the number of independent
transitions to flightlessness is much higher than the number of
separate origins of flight, but also because of what we know about
paleognath biogeography and the fossil record of the group. The oldest
known paleognaths are lithornithids, which were rather strong fliers
(expectable if the last common ancestor of paleognaths could fly,
suspicious if it could not). Also, the phylogenetic relationships
within the group (Madagascan aepyornithids are apparently nested in
the Australasian ratite clade, and the same might be true for the
South American _Diogenornis_) imply several dispersals across oceans,
which again suggests that early paleognaths were able to fly.

evelyn sobielski <koreke77@yahoo.de> wrote:

> Arguably RT might fix this, and the fact that they found 5 RT supporting 
> _Struthio_ as basal among paleognaths is in line with this.

The self-polarizing properties of retroposon insertions are certainly
useful here, but so is morphology. Elżanowski (1995), for example,
provided a nice list of cranial characters in which ostriches either
have the same state as neognaths or are intermediate between neognaths
and all remaining paleognaths.

> It is easy to forget (one would think looking at the literature) that with 
> the usual mutation rates, the null hypothesis is "around the K-Pg boundary, 
> noise exceeds signal for most avian loci; my 100 Ma signal is essentially 
> swamped by noise and any attempts to recover it will yield artefacts, perhaps 
> more artefacts than signal."

If this were the case, adding more data would help -- the phylogenetic
signal is additive, whereas noise is (by definition) random and would
cancel itself out. That's not what happened, though: independent
evidence from mtDNA (Phillips et al. 2010) and 40 novel nuclear loci
(Smith et al. 2012) as well as retroposons (Haddrath & Baker 2012)
still supports essentially the same phylogeny (including the position
of the root between ostriches and the rest of the clade). That doesn't
mean the phylogeny is correct, but any bias capable of producing this
level of agreement would at least have to be non-random -- signal, not
noise. However, it's obvious by now that the basal position of
_Struthio_ cannot be explained by long-branch attraction, base
composition bias, alignment bias, gene tree/species tree discordance,
or heterotachy, which pretty much exhausts the list of biases known to
influence molecular phylogenetics. The fact that the topology
(ostrich, (tinamous, emu)) also resulted from an analysis of
ultraconserved genomic elements (Faircloth et al. 2012) suggests that
the fear of saturation may be misplaced as well.

If there is something problematic about the interrelationships of
paleognaths, it's the position of tinamous, not the placement of the
root -- and incomplete lineage sorting is probably a bigger problem
than both substitution saturation and inadequate taxon sampling. Smith
et al. (2012) argued that the base of non-ostrich paleognaths is not a
hard polytomy because of the total lack of support for one of three
possible topologies in their data set -- the one with tinamous being
sister to a rhea/kiwi/casuariid clade. However, that's the topology
recovered by Haddrath and Baker with both their 10-gene and the
27-gene data sets, so the possibility of non-ostrich paleognaths being
a hard polytomy cannot be ruled out. The extremely short internodes in
the relevant region of the tree would be consistent with it.


*Refs:*

Brown JW, van Tuinen M 2011 Evolving perceptions on the antiquity of
the modern avian tree. 306-24 _in_ Dyke GJ, Kaiser G, eds. _Living
Dinosaurs: The Evolutionary History of Modern Birds._ Chichester:
Wiley & Sons, Ltd.

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
doi:10.1098/rspb.2012.1630

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

Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL,
Rasnitsyn AP 2012 A total-evidence approach to dating with fossils,
applied to the
early radiation of the Hymenoptera. Syst Biol doi:10.1093/sysbio/sys058

Smith JV, Braun EL, Kimball RT 2012 Ratite non-monophyly: Independent
evidence from 40 novel loci. Syst Biol doi:10.1093/sysbio/sys067

Steadman DW 1995 Prehistoric extinctions of pacific island birds:
biodiversity meets zooarchaeology. Science 267(5201): 1123-31


-- 
David Černý