The phylogenetic position of the ‘giant deer’ Megaloceros giganteus

Abstract

The giant deer, or 'Irish elk', has featured extensively in debates on adaptation, sexual selection, and extinction. Its huge antlers--the largest of any deer species, living or extinct--formed a focus of much past work. Yet the phylogenetic position of the giant deer has remained an enigma. On the basis of its flattened antlers, the species was previously regarded as closely related to the living fallow deer. Recent morphological studies, however, have challenged that view and placed the giant deer closer to the living red deer or wapiti. Here we present a new phylogenetic analysis encompassing morphological and DNA sequence evidence, and find that both sets of data independently support a sister-group relationship of giant and fallow deer. Our results include the successful extraction and sequencing of DNA from this extinct species, and highlight the value of a joint molecular and morphological approach.

Full text

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The phylogenetic position of the ‘giant deer’
Megaloceros giganteus
A. M. Lister
1
, C. J. Edwards
2
, D. A. W. Nock
1
†, M. Bunce
3
†, I. A. van Pijlen
1,4
, D. G. Bradley
2
, M. G. Thomas
1
& I. Barnes
1
The giant deer, or ‘Irish elk’, has featured extensively in debates on
adaptation, sexual selection, and extinction. Its huge antlers
—
the
largest of any deer species, living or extinct
—
formed a focus of
much past work
1–4
. Yet the phylogenetic position of the giant deer
has remained an enigma. On the basis of its flattened antlers, the
species was previously regarded as closely related to the living
fallow deer
5–7
. Recent morphological studies
8
, however, have
challenged that view and placed the giant deer closer to the living
red deer or wapiti. Here we present a new phylogenetic analysis
encompassing morphological and DNA sequence evidence, and
find that both sets of data independently support a sister-group
relationship of giant and fallow deer. Our results include the
successful extraction and sequencing of DNA from this extinct
species, and highlight the value of a joint molecular and morpho-
logical approach.
With a fossil record extending from 400 kyr ago to its extinction
about 8 kyr ago
1–4
, the giant deer (Megaloceros giganteus) ranged
from Ireland to central Siberia. Reaching a shoulder height of about
2 m and with antlers spanning up to 3.5 m, it was the largest known
member of the ‘Old World deer’ (subfamily Cervinae)
7
.
The core taxa included in the study were the giant deer and its two
putative alternative living sister-groups within the Cervinae, the
fallow deer (European fallow, Dama dama, and Mesopotamian
fallow, D. mesopotamica) and red deer (Cervus elaphus). To these
were added the southeast Asian axis deer (Axis axis) and hog deer
(Axis porcinus), in view of suggestions that Axis is a close living
relative of fallow deer
3
. To broaden taxonomic sampling, wapiti
(C. canadensis), sika (C. nippon) and Eld’s deer (C. eldi) were
added. The small muntjac deer of eastern Asia (Muntiacus spp.),
which have been shown on morphological and molecular grounds
to be basal living members of the Cervinae
9–11
, were used as an
outgroup. In this way, every major clade of the Cervinae, identified in
recent molecular studies
11
, was represented.
A total of 988 base pairs (bp) of M. giganteus mitochondrial DNA
(mtDNA) was obtained (see Methods) from two specimens of
M. giganteus of widely divergent geographical origin. The first,
from Ballynamintra Cave, Waterford, Ireland, has an uncalibrated
AMS radiocarbon date of 11,567 ^ 42 yr
BP (KIA25446); the other,
from Kamyshlov Mire in western Siberia, has an uncalibrated date of
7,065 ^ 38 yr
BP (ref. 4). The sequences of the two specimens are
99.9% similar (one substitution) and so only the Siberian sequence
was used in subsequent phylogenetic analyses. Homologous
sequences were obtained for all the species in the study (Table 1).
Analysis of the mtDNA data under parsimony, likelihood, distance
and bayesian criteria gave the same tree topology (Fig. 1a), and
indicates a sister-group relationship between M. giganteus and Dama.
To determine whether the molecular data could discriminate
between the two previous morphologically derived hypotheses
regarding the position of Megaloceros, a Kishino–Hasegawa (KH)
test
12
was used to determine the significance of differences in like-
lihood values between on the one hand a topology in which
Megaloceros forms a monophyletic group with species of Dama,
and on the other a topology in which Megaloceros forms a mono-
phyletic group with all or any species of the genus Cervus. Using the
parameters derived above, a two-tailed KH test identifies the second
of these as significantly less likely than the first, at P , 0.01.
A thorough examination of antlers, skulls, teeth and postcranial
bones among the selected species led to a preliminary list of 250
variable characters. After discarding those with a high degree of
intraspecific variability or difficulty of scoring (see Methods and
Supplementary Information), the remaining set comprised 74
characters (Supplementary Table S1), of which 69 were phylogeneti-
LETTERS
Table 1 | Deer species and GenBank accession numbers of mtDNA sequences in this study
Taxon Common name ATP8 Control region Cytochrome b
Dama dama Fallow deer AM072730 AF291895 AJ000022
Dama mesopotamica Mesopotamian fallow deer AM072731 AM072738 AM072742
Axis axis Axis deer AM072732 AM072739 AM072743
Axis porcinus Hog deer AM072733 AF291897 AY035874
Cervus canadensis Wapiti AM072737 AF058369 AF423199
Cervus elaphus Red deer AF104683 AF291886 AF423195
Cervus nippon yesoensis Hokkaido Sika deer AB108507 D50129 AB021095
Cervus eldi Eld’s deer AM072734 AY137117 AY157735
Muntiacus muntjak Indian muntjak AY225986 AY225986 AY225986
Muntiacus crinifrons Black muntjak AY239042 AY239042 AY239042
Megaloceros giganteus Giant deer (Russia) AM072736 AM072740 AM072744
Megaloceros giganteus Giant deer (Eire) AM072736 AM072740 AM072745
1
Department of Biology, University College London, London WC1E 6BT, UK.
2
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
3
Ancient Biomolecules Centre,
Department of Zoology, Oxford University, Oxford OX1 3PS, UK.
4
Department of Zoology, University of Leicester, Leicester LE1 7RH, UK. †Present addresses: MRC Clinical Trials
Unit, 222 Euston Road, London NW1 2DA, UK (D.A.W.N.); Department of Anthropology, McMaster University, Ontario L8S 4L9, Canada (M.B.).
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cally informative. A single most-parsimonious tree was recovered,
with strong statistical support for a monophyletic M. giganteus–
Dama clade (Fig. 1b). Bayesian analysis produced a compatible but
slightly less resolved tree, again with strong support for the Mega-
loceros–Dama grouping. The monophyletic clade of red deer, wapiti
and sika was also recovered in both analyses, supporting the tra-
ditional view that red deer and wapiti are sister-species, in contrast to
the wapiti-sika clade found in mtDNA (Fig. 1a; ref. 11). Axis, hog
deer and Eld’s deer were generally more basal on the tree but their
topology was unstable. Neither our molecular analyses nor our
morphological analyses provide evidence of a close relationship
between Axis and the Megaloceros–Dama clade.
Combined analyses of the molecular and morphological data were
undertaken with both bayesian and maximum-parsimony methods.
The analyses consistently supported the Megaloceros–Dama and
Cervus elaphus–canadensis–nip pon clades. The bayesian topology
was identical to the DNA-only tree (Fig. 1a), whereas using parsi-
mony, detailed features such as the internal relationships of Cervus,
depended on the relative weighting of morphological and molecular
characters (Supplementary Information).
Eight derived morphological characters are unique to the M.
giganteus–Dama clade in our data set (Supplementary Table S2);
six of them occur in M. giganteus and both Dama species, and two in
M. giganteus and D. dama only. They comprise two antler, one skull,
two dental, one vertebral and two limb-bone characters (Fig. 2).
Three further derived dental and one derived postcranial character
are shared, apparently convergently, by the Megaloceros–Dama clade
and one other species in the study. A final possible shared character,
not included in the analysis, is the characteristic ‘swollen larynx’
(‘Adam’s apple’) of Dama, seen in Palaeolithic representations of M.
giganteus
13
(Fig. 2a).
The sister-group relationship of M. giganteus and living Dama,
shown by both our morphological and molecular data, corroborates
the hypothesis of their relationship but must be viewed in the context
of other Plio-Pleistocene fossil deer. M. giganteus is part of an array of
well-documented species of ‘giant deer’ restricted to Eurasia, which
have been grouped as Tribe Megacerini Viret 1961 (refs 14–17). These
share characters such as thickened mandible bones and, in most
species, palmated antlers, although many authors
15,18
have argued
that they fall into two groups that might even have a biphyletic origin,
one (Praemegaceros) derived from the Eurasian Plio-Pleistocene
genus Eucladoceros, the other (including M. giganteus) of uncertain
origin. However, a cladistic analysis
19
found strong support for
megacerine monophyly.
Our preliminary study of the other megacerine taxa indicates that
the characters here identified as synapomorphies of M. giganteus and
living Dama are common among them, but much less so among
Eucladoceros, suggesting that Dama and all of the megacerine deer
form a natural group. In this respect, we might invert the nineteenth-
century appellation of M. giganteus as a ‘giant fallow buck’
5
and
consider the living fallow deer rather as the last representatives of a
formerly speciose giant deer tribe. Although earlier forms have been
claimed
18
, the first appearance of unquestionable megacerines is in
the middle part of the Early Pleistocene epoch (about 1.4 Myr ago
(ref. 16)), that of the Dama dama/D. mesopotamica lineage in the
early Middle Pleistocene (about 700 kyr ago) and that of M. gigan-
teus, plus related oriental forms, in the late Middle Pleistocene (about
400 kyr ago). This indicates the possibly rapid radiation of the clade
in this relatively recent interval.
However, a series of European Pliocene to Early Pleistocene
medium-sized cervids (spanning the approximate interval 3.0–
1.0 Myr ago) have been regarded as forming a stem-group to modern
Dama and have been placed in that genus by some authors
8,20
.A
recent cladistic analysis
8,19
found derived characters linking these
species and later Dama, although our preliminary observations on
these taxa indicate that they lack most of the synapomorphies of
modern Dama and M. gigant eus identified here. This indicates
homoplasy in the data. Either the entire clade of megacerines and
modern Dama is of recent origin and postdates the split with the
earlier ‘Dama-like’ forms, or else the latter are the sister-group of
modern Dama and the split with megacerines is older. The latter
would conform more closely to the deep divergence in mtDNA
Figure 1 | Phylogenetic relationships among deer species based on
molecular and morphological analyses.
a, Maximum-likelihood
phylogram constructed from 986–989 bp of mtDNA. Numbers above
branches indicate, respectively, the percentage of trees that upheld that
branch in an analysis of 1,000 bootstrap replicates, in a bayesian analysis of
the molecular data set, and in a bayesian analysis of the combined
morphological and molecular data set. b, The single most parsimonious
morphological cladogram. Tree length 123 steps, consistency index ¼ 0.61,
retention index ¼ 0.58. Numbers above branches indicate, respectively, the
percentage of trees (over 50%) in which a clade occurred in a maximum-
parsimony analysis of 20,000 bootstrap replicates of the data, posterior
probabilities from a bayesian analysis, and Bremer support indices.
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sequence, with the Dama–Megaloceros split placed at 4–5 Myr ago
(assuming a molecular clock and a divergence of the muntiacine and
cervine deer at about 7 Myr ago
11
). Resolving the relationships
between these taxa, Eucladoceros spp., and other fossils sometimes
implicated in megacerine ancestry
17,18
, would enable us to explore
palaeobiological questions such as the direction of size change, antler
evolution, and associated adaptive issues. Some features of modern
Dama, such as the robust axis vertebra (Fig. 2c) and relict parietal
foramen
21
, suggest former adaptation to very large antler size and
could correspond to ancestry from a large megacerine, but a
comprehensive cladistic analysis of all these taxa is needed to address
these issues further.
Last, the deep (7.85%) mtDNA divergence between European
fallow deer and the endangered
22
Mesopotamian fallow deer Dama
mesopotamica highlights the distinctive nature of the latter taxon
(corroborated by data in a recent study
11
), in spite of its current
demotion to a subspecies on the basis of similarities in gross
morphology and in behaviour, and ease of cross-breeding in captiv-
ity
9,23
. The morphological closeness of red deer and wapiti, to the
exclusion of sika, is also notable, recalling earlier hypotheses of their
relationship
24
, but is in conflict with mtDNA data, inviting further
investigation.
METHODS
Morphological analysis. Because of extensive intra-specific variability, all 250
original characters were scored on a series of individuals for each species.
Variation was quantified as described previously
25
, and characters were regarded
as fixed only if they reached a high level of consistent expression (Supplementary
Information). Intraspecific polymorphism was recoded as an ordered series with
scaled weighting, and the data were analysed under parsimony by exhaustive
search with PAUP 4.0b10 (ref. 26), as well as by bayesian analysis (Supplementary
Information).
Extraction and identification of ancient DNA. Sequence data were generated
from about 0.1 g of cortical bone or tooth samples (Supplementary Information)
with the use of established protocols for ancient DNA (University College
London and the Ancient Biomolecules Centre, as in ref. 27; Trinity College
Dublin, as in ref. 28).
In ancient mtDNA analysis, sequences can be recovered that are not authentic
but derive from some external contaminant or the nuclear genome. We regard
our Megaloceros sequences as genuine for the following reasons. First, entirely
independently and without any exchange of materials, the two lead laboratories
(University College London and Trinity College Dublin) generated near-iden-
tical (99.9%) sequences from different specimens obtained, directly in each case,
from distant collections (in Eire and western Siberia respectively), by different
workers (I.B. and C.J.E.) using different extraction methods and primer pairs.
Second, by using separate samples of bone, a subset of sequences from the
Kamyshlov specimen (from primers amplifying ATP8, Cerv_cytb160F/288R,
Cerv_cytb269F/403R and Cerv_cytb467F/604R) were independently replicated
by M.B. at the Ancient Biomolecules Centre; and from the Ballynamintra
specimen (using primers amplifying ATP8 and Cerv_cytb63F/176R,
Cerv_cytb643F/760R and Cerv_cytb675F/786R) by I.B. at University College
London. Third, the mtDNA sequences of the two M. giganteus specimens are
clearly of cervid origin but are unique, sharing eight base substitutions not found
in the other cervid taxa studied. Fourth, each sequence in the cytb contigs had a
perfect match to overlapping fragments. Last, sequences of PCR product clones
for several cytb fragments revealed a damage pattern characteristic for ancient
DNA but not indicative of the presence of another contaminating sequence
(Supplementary Information).
Molecular phylogenetic analyses. Between 986 and 989 characters (118 bp of
ATPase 8, 113–116 bp of the control region, 755 bp of cytochrome b) were
obtained for all taxa in the study (Table 1), of which 267 (27%) were variable and
158 (16%) were phylogenetically informative. We used PAUP 4.0b10 (ref. 26) for
the initial analyses. Likelihood ratio tests supported the use of a GTR model (six
Figure 2 | Examples of morphological characters. a, M. giganteus (left) and
D. dama (right), showing antler palmation, back tine, and expanded larynx.
(Modified from Valerius Geist, Deer of the World, Stackpole Books, ref. 3.)
b, Metacarpal of C. canadensis (left) and M. giganteus (right), showing
separation of facets in Cervus. c, Posterior view of axis vertebra in C. elaphus
(left) and M. giganteus (right), showing single medial ridge in C. elaphus, two
ridges bounding groove in M. giganteus. d, Posterior view of M
3
in C. elaphus
(left) and D. dama (right), showing convex root in C. elaphus, concavity and
labial ridge in D. dama. e, Labial view of upper molar of C. elaphus (left) and
M. giganteus (right), showing horizontal basal ridges in M. giganteus. Scale
bars, 2 cm (b), 5 cm (c) and 1 cm (d, e). See Supplementary Information for
details of specimens.
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substitution types), incorporating site-specific rates for each of the four site
categories (first, second, third and non-coding). For maximum-likelihood
analyses, heuristic searches were conducted with starting trees generated by
ten randomly derived stepwise addition sequences, with branch swapping by tree
bisection-reconnection (TBR) and re-estimation of parameters. The maximum-
likelihood topology (Fig. 1a) was also recovered by using both maximum
parsimony and neighbour-joining with the HKY85 substitution model. Boot-
strap support values were obtained by an analysis of 1,000 replicate data sets,
with the use of maximum-likelihood analysis under a GTR þ SS model with re-
estimation of parameters at each step. Replicate data sets that maintained
proportionality of each site type were generated with PAML v3.14 (ref. 29).
Bayesian analyses of the morphological, molecular and combined data sets were
conducted with MrBayes v3.1. Topology searches were initiated from random
starting trees, with molecular data assigned a GTR þ SS model, and morpho-
logical data analysed with distributed rates and likelihoods corrected for scoring
bias caused by the presence of only variable characters in the data set. Both
combined and molecular analyses were run for 5,000,000 generations, and the
morphology-only analysis was run for 2,500,000 generations. Trees were
sampled every 100 generations, with the first 25% discarded as burn-in
30
.
Received 22 April; accepted 16 August 2005.
Published online 4 September 2005.
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Acknowledgements We thank A. Currant, A. Friday, D. Hills, P. Jenkins,
P. Kosintsev, L. Martin, N. Monaghan, T. Stuart, A. Vorobiev and E. Westwig for
sampling and access to material; P. Grubb, D. MacHugh, C. O’hUigin and
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´
nchez-Villagra for advice on cladistics;
A. Murray and R. Rabinovich for technical assistance; and V. Geist and
Stackpole Books for permission to reproduce the drawings in Fig. 2a. C.J.E. was
supported by the Irish Research Council for Science, Engineering and
Technology Basic Research Grant Scheme. I.A.vP was funded by BBSRC.
Author Information Sequences are deposited in GenBank under accession
numbers AM072730–AM072749. Reprints and permissions information is
available at npg.nature.com/reprintsandpermissions. The authors declare no
competing financial interests. Correspondence and requests for materials should
be addressed to I.B. (I.Barnes@ucl.ac.uk).
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