Nuclear DNA does not reconcile 'rocks' and 'clocks' in Neoaves: a comment on Ericson et al.
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ABSTRACT: The major histocompatibility complex (MHC) plays an important role in immune response. Avian MHCs are not well characterized, only reporting highly compact Galliformes MHCs and extensively fragmented zebra finch MHC. We report the first genomic structure of an endangered Pelecaniformes (crested ibis) MHC containing 54 genes in three regions spanning ~500 kb. In contrast to the loose BG (26 loci within 265 kb) and Class I (11 within 150) genomic structures, the Core Region is condensed (17 within 85). Furthermore, this Region exhibits a COL11A2 gene, followed by four tandem MHC class II αβ dyads retaining two suites of anciently duplicated "αβ" lineages. Thus, the crested ibis MHC structure is entirely different from the known avian MHC architectures but similar to that of mammalian MHCs, suggesting that the fundamental structure of ancestral avian class II MHCs should be "COL11A2-IIαβ1-IIαβ2." The gene structures, residue characteristics, and expression levels of the five class I genes reveal inter-locus functional divergence. However, phylogenetic analysis indicates that these five genes generate a well-supported intra-species clade, showing evidence for recent duplications. Our analyses suggest dramatic structural variation among avian MHC lineages, help elucidate avian MHC evolution, and provide a foundation for future conservation studies.Scientific reports. 01/2015; 5:7963.
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ABSTRACT: Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.PLoS ONE 01/2014; 9(10):e109635. · 3.53 Impact Factor
Biol. Lett. (2007) 3, 257–259
Published online 27 March 2007
Nuclear DNA does not
reconcile ‘rocks’ and
‘clocks’ in Neoaves: a
comment on Ericson et al.
The discrepancy between fossil- and molecular-
based age estimates for the diversification of modern
birds has persisted despite increasingly large datasets
on both sides (Penny & Phillips 2004). For the
purpose of addressing this discrepancy, Ericson et al.
(2006) recently generated a significant neoavian
dataset that is well represented by taxa (87 species
comprising 75 traditional families), characters (five
nuclear genes) and fossil calibrations (nZ23). The
divergence times reported in this study are by far the
youngest yet reported from genetic data. These
authors conclude that there is no reliable molecular
support for extensive diversification of Neoaves in the
Cretaceous. While an increased agreement with the
fossil record is encouraging (and, indeed, sought
after), we find a number of problems with their study
that calls this conclusion into question.
Our first concern with this paper involves the
particular fossils used to calibrate and constrain
estimated divergence times. Fossils are of fundamen-
tal importance in estimating dates with molecular
sequence data, and care should be taken that they are
taxonomically and stratigraphically well identified.
While the fossils used in Ericson et al. (2006) appear
to fit these criteria, we nevertheless take issue with
the particular fossils used. First, Ericson et al. (2006)
use a stem group galliform fossil (53 Myr; Mayr &
Weidig 2004) to date the divergence between Galli-
formes and Anseriformes, despite the fact that an
older (66 Myr), and therefore more appropriate, fossil
anseriform calibration exists (Clarke et al. 2005).
Ericson et al.’s (2006) estimate of the age of the
Galliformes–Anseriformes split is approximately
53 Myr, 13 Myr younger than the minimum age
definitively known from the fossil record (Benton &
Donoghue 2006). Second, for the (required) fixed
calibration, they use a 47.5 Myr stem group represen-
tative of Trochilidae to mark the splitting of hum-
mingbirds from other Apodiformes. No rationale is
given explaining why this fossil was adopted, and we
note that an older (62 Myr), more derived and hence
more appropriate fossil is established from the stem
of Sphenisciformes (Slack et al. 2006). Regardless,
owing to the importance of the single fixed constraint,
alternatives should have been considered. Third, the
authors impose a maximum constraint of 95 Myr on
the age of Neoaves, despite the fact that earlier dates
have been published (e.g. van Tuinen & Hedges
2001; Pereira & Baker 2006). Finally, one of their
fossil calibrations (stem Strigiformes) is uninformative
for dating purposes, as it is superseded by an equally
old (55 Myr) but more derived fossil (Coliidae).
Our second concern involves the reliance on
PATHd8 for estimating lineage ages. Ericson et al.
(2006) also used the program r8s (Sanderson 2003),
but dismissed these results simply because these dates
are older than those generated by PATHd8 (although
the older r8s dates are consistent with previous
molecular-generated dates). The inferred dates from
r8s directly contradict their claim of an absence of
neoavian diversification in the Cretaceous. Agreement
with the fossil record, while satisfying in terms of
congruence, is not a sufficient criterion to arbitrate
between sets of dates generated by different methods.
Rather, arbitration should rely upon the performance of
methods on both empirical and simulated data, and
PATHd8 has yet to be tested in this way. To compare
their PATHd8 results with those from a well-vetted
program, we reanalysed the data of Ericson et al.
(2006) using a Bayesian modelling of rate evolution
(Thorne & Kishino 2002) and the revised calibrations
outlined previously (see electronic supplementary infor-
mation for methods). Contrary to their results, we find
evidence for substantial diversification of Neoaves in
the Cretaceous (figure 1).
Finally, and most importantly, nowhere do Ericson
et al. (2006) mention any error intervals on their dating
estimates. Given the proximity of many nodes to the
K–T boundary, confidence intervals on age estimates
would cross into the Cretaceous and render their
conclusion untenable. Error estimates are easily gener-
ated using either non-parametric bootstrapping or
considering a posterior distribution of trees. As error is
inherent in each step of molecular dating (sequences,
alignment, fossils, trees, etc.), the lack of error calcu-
lation is disturbing and undermines their ultimate
assertion. When incorporating error intervals in our
reanalysis, 24 basal neoavian divergences are restricted
to the Cretaceous (figure 1, green bars). Of these, 15
lead directly to extant families. While the addition of
further family representatives will undoubtedly break
up some of these branches (forming crown clades), a
Tertiary origin for much of Neoaves is clearly rejected.
Given the results of our reanalysis of the data of
Ericson et al. (2006), the noteworthy problems attend-
ant in their study and the plurality of genetic studies
indicating a Cretaceous origin of modern birds, we
respectfully disagree with their conclusion and find
instead that there is no reliable molecular evidence
against an extensive pre-Tertiary radiation of Neoaves.
We thank Ericson et al. for making their data freely
available. J.W.B. thanks I. Pop, R. Asheton, S. Asheton and
D. Alexander for their encouragement during this study.
Joseph W. Brown*, Robert B. Payne,
David P. Mindell
Department of Ecology and Evolutionary Biology,
University of Michigan, Museum of Zoology
(Bird Division), 1109 Geddes Avenue, Ann Arbor,
MI 48109-1079, USA
Electronic supplementary material is available at http://dx.doi.org/
10.1098/rsbl.2006.0611 or via http://www.journals.royalsoc.ac.uk.
The accompanying reply can be viewed at http://dx.doi.org/10.
Received 16 December 2006
Accepted 29 January 2007
This journal is q 2007 The Royal Society
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Threskiornithidae - Theristicus
Diomedidae - Diomedea
Rallidae - Aramides
Rallidae - Laterallus
Mesitornithidae - Mesitornis
Mesitornithidae - Monias
Procellariidae - Fulmarus
Procellariidae - Puffinus
Cathartidae - Cathartes
Cathartidae - Coragyps
Ciconiidae - Mycteria
Diomedidae - Phoebetria
Threskiornithidae - Harpiprion
Accipitridae - Heterospizias
Accipitridae - Leptodon
Cuculidae - Cuculus
Cuculidae - Guira
Falconidae - Falco
Ciconiidae - Jabiru
Falconidae - Polyborus
Accipitridae - Accipiter
Figure 1. Chronogram for Neoaves estimated using a Bayesian modelling of rate evolution. The dashed vertical red line
marks the K–T boundary. Error bars represent posterior probability (0.95) credible intervals (root node 104–154 Myr).
An unambiguous ancient diversification of Neoaves is indicated by 24 credible intervals restricted to the Cretaceous
258J. W.Brown et al.Comment. Rocks and clocks in Neoaves
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J. W.Brown et al.
Biol. Lett. (2007)