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"Ratite" polyphyly and paleognathous dromornithids

A new molecular study provides additional evidence for "ratite"
polyphyly, which has already been supported by the Early Bird
phylogenomic data set (Chojnowski et al. 2008; Hackett et al. 2008;
Harshman et al. 2008), mtDNA (Phillips et al. 2010), and various
papers on morphology (Bock & Bühler 1990; Elżanowski 1995; Johnston
2011) or eggshell characters (Grellet-Tinner 2006). Four years and 40
loci later, the non-ostrich paleognath clade is well-supported, but
the placement of tinamous remains tricky -- both rheas and the clade
of "Australasian ratites" (Apterygidae + Casuariidae) are still
plausible as their sister taxa. The authors find the tinamou position
to be highly alignment-sensitive: sequences aligned according to a
guide tree with a rhea-tinamou clade always resulted in a rhea-tinamou
clade on the final tree. An emu-tinamou clade exclusive of rheas is
less dependent on the guide tree topology and somewhat better
supported, but the difference is not large and support measures are
weak for both clades.

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

Large-scale multi-locus studies have become common in molecular
phylogenetics, but the best way to interpret these studies when their
results strongly conflict with prior information about phylogeny
remains unclear. An example of such a conflict is provided by the
ratites (the large flightless birds of southern land masses, including
ostriches, emus, and rheas). Ratite monophyly is strongly supported by
both morphological data and many earlier molecular studies and is used
as a textbook example of vicariance biogeography. However, recent
studies have indicated that ratites are not monophyletic; instead, the
volant tinamous nest inside the ratites rather than forming their
sister group within the avian superorder Palaeognathae. Large-scale
studies can exhibit biases that reflect a number of factors, including
limitations in the fit of the evolutionary models used for analyses
and problems with sequence alignment, so the unexpected conclusion
that ratites are not monophyletic needs to be rigorously evaluated. A
rigorous approach to testing novel hypotheses generated by large-scale
studies is to collect independent evidence (i.e., excluding the loci
and/or traits used to generate the hypotheses). We used 40 nuclear
loci not used in previous studies that investigated the relationship
among ratites and tinamous. Our results strongly support the recent
molecular studies, revealing that the deepest branch within
Palaeognathae separates the ostrich from other members of the clade,
rather than the traditional hypothesis that separates the tinamous
from the ratites. To ensure these results reflected evolutionary
history, we examined potential biases in types of loci used,
heterotachy, alignment biases, and discordance between gene trees and
the species tree. All analyses consistently supported non-monophyly of
the ratites and no confounding biases were identified. This
confirmation that ratites are not monophyletic using independent
evidence will hopefully stimulate further comparative research on
paleognath development and genetics that might reveal the basis of the
morphological convergence in these large, flightless birds.

However, "ratite" monophyly is still supported by morphological data:

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

The iconic moa (Aves: Dinornithiformes) from New Zealand continue to
attract much scientific scrutiny, as they have done since their
discovery in the 1840s. Here, we review moa research since 2001 that
advances our knowledge of the biology of these families; in
particular, their breeding, diet and phylogenetic relationships. Then
we perform a phylogenetic analysis based on morphological characters
using a broader range of taxa and many more characters than hitherto
used in moa analyses. Finally, we provide revised diagnoses of all moa
taxa to reflect current knowledge.
In this last decade, molecular analyses have been at the forefront of
much of this research. Indeed, moa have become model subjects for
advances in ancient DNA technology on account of their preservation
and young geological age, and the fact that several of the foremost
proponents of ancient DNA research are New Zealanders. Much of this
research has been about extending the capacity of ancient DNA
technology as much as about answering biological questions, but the
resultant insights with regard to the latter have been profound for
moa. Complete mitochondrial genomes for three species of moa have been
published and extensive datasets of a number of mitochondrial genes
are now available for all species over their entire geographic range.
Analyses of nuclear DNA is limited to a sex specific gene and some
preliminary microsatellite identifications, but it seems likely that
improved technology will allow greater use of this resource in the
near future. Phylogenetic analyses of mitochondrial molecular data
have precipitated several changes to moa taxonomy and nine species are
now recognised. The significance of deep phylogenetic structure among
populations in some taxa continues to attract debate and likely will
require nuclear data and a more profound understanding of natural
variation in extant species to resolve. Significantly, molecular data
have enabled new insights into diet, with direct identification of
species responsible for coprolites, and by its new-found propensity to
identify eggshell, foreshadows further advances in understanding their
breeding biology and distribution.
Our phylogenetic analysis, based on 179 characters scored for 23
ingroup palaeognath taxa and three galloanseres as outgroups, resulted
in several strongly supported relationships. Firstly, the Eocene
palaeognath _Lithornis_ was either sister to remaining palaeognaths or
had a weak affinity towards tinamous. All ratites formed a
monophyletic clade exclusive of tinamous. Moa were monophyletic and
sister to aepyornithids in the unconstrained analysis. Attempts to
constrain moa as sister to tinamous to reflect molecular-based
conclusions resulted in moa as sister to all ratites in a clade that
was unresolved with respect to tinamous and _Lithornis_. This
relatively basal position of moa was not a significantly worse
reflection of the data compared to their more crownward location in
the initial analyses. The casuariids were sister to _Struthio_ and the
rheas. In our revised diagnoses for Dinornithiformes and all its
constituent taxa, we give updated information on the type specimens
based on recent research by the authors. We accept three families, six
genera and nine species, and make the new combinations of _Euryapteryx
curtus curtus_ (Owen) and _E. curtus gravis_ (Owen). Complete or near
complete exemplars of the skull of all moa taxa, most not illustrated
before, are shown in dorsal, lateral and ventral views.

Finally, a new paper on Australian fossil anhimids suggests that
dromornithids are in fact paleognaths and Richard Owen was right after
all. This contradicts many recent phylogenies that place dromornithids
either in the stem group of Anseriformes (Murray & Vickers-Rich 2004)
or the stem lineage of Galloanserae (Mayr 2011).

Elżanowski A, Boles WE 2012 Australia's oldest Anseriform fossil: a
quadrate from the Early Eocene Tingamarra Fauna. Palaeontol 55(4):

A partial quadrate (essentially the otic part) from the nonmarine,
earliest Eocene (54.6 Ma) Tingamarra Local Fauna in Queensland,
Australia, has been identified as the oldest Australian anseriform
fossil. The Tingamarra quadrate shows a combination of plesiomorphic
anseriform characters with a unique synapomorphic character complex of
the Anhimidae (screamers), which today are endemic to South America.
In concert with the basal position of the Anhimidae among the
crown-group anseriforms, this set of characters suggests a stem group
of the Anhimidae, raising a possibility of the Transantarctic
migration of stem anhimids to South America. The quadrate morphology
supports palaeognathous rather than recently claimed anhimid
relationships of the Dromornithidae and identifies _Sylviornis_ as an
anseriform rather than a galliform.


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

Chojnowski JL, Kimball RT, Braun EL 2008 Introns outperform exons in
analyses of basal avian phylogeny using clathrin heavy chain genes.
Gene 410: 89-96

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

Grellet-Tinner G 2006 Phylogenetic interpretation of eggs and
eggshells: implications for the phylogeny of Palaeognathae. Alcheringa
30: 141-82

Hackett SJ, Kimball RT, Reddy S, Bowie RC, Braun EL, Braun MJ,
Chojnowski JL, Cox WA, Han K, Harshman J, Huddleston CJ, Marks BD,
Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T 2008 A
phylogenomic study of birds reveals their evolutionary history.
Science 320(5884): 1763-8

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

Mayr G 2011 Cenozoic mystery birds - on the phylogenetic affinities of
bony-toothed birds (Pelagornithidae). Zool Scr 40(5): 448-67

Murray PF, Vickers-Rich P 2004 _Magnificent Mihirungs. The Colossal
Flightless Birds of the Australian Dreamtime_. Bloomington: Indiana
Univ Press

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

David Černý