integration of molecular
sequence data and fossils
Per G. P. Ericson1,*, Cajsa L. Anderson2
,
Tom Britton3
, Andrzej Elzanowski4
,
Ulf S. Johansson5
, Mari Ka¨llersjo¨ 1
,
Jan I. Ohlson1,6, Thomas J. Parsons7
,
Dario Zuccon1 and Gerald Mayr8
1
Department of Vertebrate Zoology and Molecular Systematics
Laboratory, Swedish Museum of Natural History, PO Box 50007,
10405 Stockholm, Sweden
2
Department of Systematic Botany, Evolutionary Biology Centre,
University of Uppsala, Norbyva¨gen 18D, 752 36 Uppsala, Sweden 3
Department of Mathematics, and 6
Department of Zoology,
University of Stockholm, 106 91 Stockholm, Sweden
4
Institute of Zoology, University of Wroclaw, 21 Sienkiewicz Street,
50335 Wroclaw, Poland
5
DST/NRF Centre of Excellence at the Percy Fitzpatrick Institute,
Evolutionary Genomics Group, Department of Botany and Zoology,
University of Stellenbosch, Private Bag XI, Maiteland 7602,
South Africa
7
International Commission on Missing Persons, Alipasˇina 45 A,
71000 Sarajevo, Bosnia
8
Forschungsinstitut Senckenberg, Sektion fu¨r Ornithologie,
Senckenberganlage 25, 60325 Frankfurt am Main, Germany
*Author for correspondence ( per.ericson@nrm.se).
Patterns of diversification and timing of
evolution within Neoaves, which includes almost
95% of all bird species, are virtually unknown.
On the other hand, molecular data consistently
indicate a Cretaceous origin of many neoavian
lineages and the fossil record seems to support
an Early Tertiary diversification. Here, we
present the first well-resolved molecular phylogeny for Neoaves, together with divergence time
estimates calibrated with a large number of
stratigraphically and phylogenetically welldocumented fossils. Our study defines several
well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an
initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T
boundary. Our results thus do not contradict
palaeontological data and show that there is no
solid molecular evidence for an extensive preTertiary radiation of Neoaves.
Keywords: Neoaves; phylogeny; nuclear DNA;
fossils; molecular clock; divergence times
1. INTRODUCTION
Birds are used as model organisms in many fields
of biology, and the lack of a thorough understanding
of their systematics has often compromised interpretations of experiments and observations. The
DNA–DNA hybridization studies of Sibley & Ahlquist (1990) have repeatedly been criticized for
methodological reasons (Harshman 1994; Cracraft
et al. 2004), and the few cladistic analyses of Neoaves
with dense taxon sampling show poor resolution of
the deep divergences (Livezey & Zusi 2001; Cracraft
et al. 2004; Fain & Houde 2004). DNA sequence
data have begun to clarify interfamily relationships for
a handful of higher level groups such as some aquatic
birds (van Tuinen et al. 2001), ‘higher land birds’
(Johansson et al. 2001; Mayr et al. 2003), shorebirds
(Ericson et al. 2003; Paton et al. 2003) and passerines
(Barker et al. 2004). Recent analyses of morphological
and molecular data support a sister group relationship
between Galloanseres (land- and waterfowl) and all
other neognathous birds, the Neoaves (Livezey &
Zusi 2001; Mayr & Clarke 2003; Cracraft et al. 2004;
Fain & Houde 2004). However, there are no
hypotheses concerning the most basal neoavian divergences, except for the proposed division of the group
into Metaves and Coronaves based on an analysis of
b-fibrinogen sequence data (Fain & Houde 2004).
Molecular clock analyses have suggested that the
earliest diversification of Neoaves had already
occurred in the Cretaceous (Hedges et al. 1996;
Cooper & Penny 1997; Cracraft 2001; van Tuinen &
Hedges 2001). However, there are few neoavian
fossils from the Cretaceous (Hope 2002; Feduccia
2003) and instead the palaeontological record
suggests that only a few neoavian lineages existed at
the end of the Cretaceous, 65 Myr ago (Feduccia
2003). The considerable diversity of stem group
representatives of modern neoavian taxa, which is
evident in the Early Eocene 50 Myr ago (Mayr 2005),
would thus result from a rapid diversification of taxa,
which filled the many vacant ecological niches after
the K/T boundary (Feduccia 2003). There is an
apparent conflict between earlier molecular datings
and the palaeontological record—but is this conflict
real? The molecular dating methods must be correctly
calibrated to yield reliable data, and this has not
previously been done in studies including Neoaves.
Since all Cretaceous fossils of neornithine birds are
very fragmentary (Hope 2002) and their identification
is often uncertain (Hope 2002), most calibrations
have so far used a calculated age for the split between
galliforms and anseriforms (90 Myr ago) which is in
turn based on the diapsid/synapsid split age at
310 Myr ago (Hedges et al. 1996). However, Graur &
Martin (2004) have argued convincingly that this
estimate is not reliable, and nor are any of the
calibration points that are based on it. Here, we
employ an alternative strategy and use multiple fossils
of more recent neoavian groups as internal calibration
points in order to test the different diversification
models suggested by Penny & Phillips (2004).