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A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)

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Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains controversial. Using the supertree approach of matrix representation with parsimony, we present the first phylogeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However, due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus, Muntiacus, Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses across entirely aquatic and terrestrial species within a single mammalian order.
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A complete phylogeny of the whales,
dolphins and even-toed hoofed
mammals (Cetartiodactyla)
Samantha A. Price
1
*, Olaf R. P. Bininda-Emonds
2
and John L. Gittleman
1
1
Department of Biology,Gilmer Hall,University of Virginia,Charlottesville,VA 22904-4328, USA
2
Lehrstuhl fur Tierzucht,Technical University of Munich,Alte Akademie 12, 85354 Freising-Weihenstephan,Germany
(Received 7June 2004; revised 13 January 2005 ; accepted 17 January 2005 )
ABSTRACT
Despite the biological and economic importance of the Cetartiodactyla, the phylogeny of this clade remains
controversial. Using the supertree approach of matrix representation with parsimony, we present the first phy-
logeny to include all 290 extant species of the Cetacea (whales and dolphins) and Artiodactyla (even-toed
hoofed mammals). At the family-level, the supertree is fully resolved. For example, the relationships among
the Ruminantia appear as (((Cervidae, Moschidae) Bovidae) (Giraffidae, Antilocapridae) Tragulidae). However,
due to either lack of phylogenetic study or contradictory information, polytomies occur within the clades Sus,
Muntiacus,Cervus, Delphinidae, Ziphiidae and Bovidae. Complete species-level phylogenies are necessary for both
illustrating and analysing biological, geographical and ecological patterns in an evolutionary framework. The
present species-level tree of the Cetartiodactyla provides the first opportunity to examine comparative hypotheses
across entirely aquatic and terrestrial species within a single mammalian order.
Key words: Cetacea, Artiodactyla, Cetartiodactyla, supertree, matrix representation with parsimony (MRP),
comparative methods.
CONTENTS
I. Introduction ................................................................................................................................................. 446
II. Methodology ................................................................................................................................................ 447
(1) Data collection ....................................................................................................................................... 447
(2) Tree building ......................................................................................................................................... 447
(3) Assessing support ................................................................................................................................... 448
(4) Tree comparison ................................................................................................................................... 450
III. Results and discussion ................................................................................................................................. 451
(1) Resolution, robustness and support .................................................................................................... 451
(2) Higher-level relationships .................................................................................................................... 452
(a) Placement of Cetacea ..................................................................................................................... 452
(b) Basal clades ...................................................................................................................................... 452
(c) Family-level relationships within Artiodactyla ............................................................................ 452
(d) Family-level relationships within Cetacea .................................................................................... 454
(3) Tree comparison: supertree versus supermatrix .............................................................................. 454
IV. Conclusions .................................................................................................................................................. 454
V. Acknowledgements ...................................................................................................................................... 456
VI. References .................................................................................................................................................... 456
VII. Appendix ...................................................................................................................................................... 462
* Author for correspondence : E-mail: SPrice@virginia.edu
Biol. Rev. (2005), 80, pp. 445–473. fCambridge Philosophical Society 445
doi:10.1017/S1464793105006743 Printed in the United Kingdom
I. INTRODUCTION
Taxonomically complete phylogenies are needed to conduct
rigorous comparative analyses of evolutionary patterns
and processes. Comparative methods are now inherently
statistical in nature (Harvey & Pagel, 1991) and require
sufficient statistical power to be done properly. This power
is ultimately derived from the number of sister-group re-
lationships that are resolved in a given phylogeny. Larger
phylogenies enhance the potential number of sister pairings
and therefore allow for more statistical power and a greater
confidence in the results. An immediate approach for
constructing a complete phylogeny is the supertree method,
which quickly provides rigorous and comprehensive phy-
logenies (Bininda-Emonds & Bryant, 1998 ; Bininda-Emonds
et al., 2002). To provide an independent assessment of
the phylogenetic relationships resolved in the supertree, the
topology is compared to the most comprehensive character-
based tree available for the Cetartiodactyla, that of Gatesy
et al. (2002).
Here, we present the first synthesis of cetacean and
artiodactyl phylogeny into an inclusive species-level phylo-
genetic hypothesis using supertree methodology. Aside from
its systematic value, the phylogeny of the Cetartiodactyla
is also of general interest because the phylogeography of
domesticated artiodactyls might illuminate certain aspects
of human evolution.
Throughout human history, cetaceans and artiodactyls
have been of both cultural and economic importance.
For example, recent discovery of rock carvings in South
Korea provides evidence that whaling existed in prehistoric
times (somewhere between 6000 and 1000 B.C.) (Lee &
Robineau, 2004) and in the 18th and 19th century whaling
briefly became a commercial industry to provide oil for
lamps and heating. Since the moratorium on commercial
whaling in 1986 the most immediately obvious value of
cetaceans stems from their aesthetic appeal to all cultures
as illustrated by the popularity of whale-watching trips and
by the rich mythology associated with these animals. One
of the earliest records is from the 5th century B.C., where
Herodotus chronicles the myth of the musician Arion who
is saved from the sea and carried to shore by a dolphin.
The importance of the artiodactyls stems from their
utility; the earliest known art, circa 28000 B.C., is cave
paintings (Chauvet Cave, Vallon-Pont-d’Arc, France)
depicting large hoofed mammals some of which have been
wounded by arrows. Between 8000 and 2500 B.C. artio-
dactyls were domesticated, providing a variety of products
and services such as meat, transportation, draft power, fer-
tiliser, wool, leather and dairy. It is this utility that has led
to the assertion that animal domestication was crucial to
the development of human civilisation (Diamond, 1996).
Worldwide, the Artiodactyla is the most valuable source of
domesticated species, including pigs (Sus scrofa), sheep (Ovis
aries), goats (Capra hircus), cows (Bos taurus), bactrian camels
(Camelus bactrianus), dromedary camels (Camelus dromedarius),
water buffalo (Bubalus bubalis), llamas (Lama glama) and
alpacas (Lama pacos). Domesticated artiodactyls are of global
economic value far beyond the native range of their ances-
tors. For example, the revenue from meat of B. taurus, which
is thought to have originated in the Middle East, totalled
$36 322 million dollars in the USA in 1997 (USDA, 1997).
In Australia, 7 % of gross agricultural production and A$3.8
billion in export income is obtained from the wool industry
alone (Shafron et al. 2002).
Despite the interest shown in cetaceans and artiodactyls,
their precise phylogenetic relationships remain contro-
versial. As early as 1891, Flower observed a close affinity
between the superficially very different Artiodactyla and
Cetacea. Flower emphasised the resemblances of the larynx,
stomach, liver, reproductive organs, and foetal membrane
between pigs and whales (as summarised in Gregory, 1910).
Until recently, it was generally believed that although
artiodactyls and cetaceans both shared a condylarthran
ancestry, the whales were the sister-taxon of the extinct
mesonychids (e.g. Van Valen, 1966), whereas artiodactyls
descended from arctocyonid condylarths ( Van Valen, 1971 ;
Rose, 1996). This view was supported by modern morpho-
logical evidence (O’Leary, 1999 ; Gatesy & O’Leary, 2001).
By contrast the majority of post-1994 molecular studies
resolved a paraphyletic Artiodactyla with Cetacea nested
within the artiodactyls as sister to hippopotamids (Irwin &
Arnason, 1994 ; Gatesy et al., 1996 ; Shimamura et al., 1997),
forming a clade known as the Cetartiodactyla. The recent
description of two archaic whales that revealed clear
morphological homology between cetaceans and artio-
dactyls to the exclusion of mesonychids (Gingerich et al.,
2001; Thewissen et al., 2001) has more or less reconciled
the morphological and molecular view of cetacean and
artiodactyl phylogeny. However, little morphological evi-
dence exists to support the sister-taxon relationship between
Hippopotamidae and Cetacea.
Relationships within, as opposed to between, the ceta-
ceans and artiodactyls have been no less controversial. The
higher-level phylogeny of the artiodactyls remains highly
unstable. The only consensus is that six families cluster
to form the Ruminantia (Tragulidae, Moschidae, Antilo-
capridae, Cervidae, Bovidae and Giraffidae) with the
tragulids at the base (e.g. Randi et al., 1996 ; Montgelard
et al., 1997; Matthee et al., 2001). Relationships both with-
in the Pecora (Ruminantia minus Tragulidae) (e.g. Gatesy
et al., 1996; Hassanin & Douzery, 1999 b;Suet al., 1999;
Hassanin & Douzery, 2003) and among non-ruminants
(e.g. Cronin et al., 1996 ; Geisler, 2001 ; Madsen et al., 2001)
remain controversial.
There have been several proposals that cetaceans are
polyphyletic in origin (e.g. Yablokov, 1964), with toothed
and baleen whales having evolved independently from dif-
ferent ancestors. Although upholding cetacean monophyly,
Milinkovitch et al. (1993) questioned the monophyly of each
of these two groups, suggesting that Physeteridae are more
closely related to Mysticeti (baleen whales) than they are to
the other Odonotoceti (toothed-whales). Both suggestions
were debated, with the current consensus favouring the
traditional view of a monophyletic Cetacea (e.g. Van Valen,
1968) composed of the two traditional monophyletic sub-
orders (e.g. Arnason & Gullberg, 1994 ; Cerchio & Tucker,
1998; Messenger & McGuire, 1998).
Here, we address these phylogenetic controversies within
the Cetartiodactyla using supertree construction to produce
446 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
the first complete species-level phylogeny of this clade based
on a robust methodology. Supertrees combine previously
published phylogenetic estimates, as compared to the more
conventional method of combining raw character data
(DNA sequences, morphological characters). Supertree ap-
proaches currently represent the best possibility for building
a complete cetartiodactyl phylogeny. At present, building a
complete tree from a single molecular or morphological
dataset is not possible because not all the species have been
sampled for the same character(s). Even the combination of
these single raw datasets in a total-evidence framework
(sensu Kluge, 1989) is hindered by the lack of compatible
overlapping datasets. Currently, the largest published
cetartiodactyl total-evidence tree based on a broad selection
of data sources contains only 51 out of the 290 extant
species (Gatesy et al., 2002), although a virtually complete
tree could be constructed from the mitochondrial genes
cytochrome band 12S rDNA (John Gatesy, personal com-
munication). By contrast, supertrees can combine all available
phylogenetic hypotheses to yield a complete cetartiodactyl
tree that may serve as a foundation for phylogenetic com-
parative analyses and will highlight poorly known or con-
troversial areas that are especially in need of additional data
collection.
II. METHODOLOGY
(1 ) Data collection
Sources of phylogenetic information were collected from
the literature by searching Web of Science and Bio-
Abstracts using the keywords Artiodactyl* and Cetace* and
extracting articles that were likely to contain phylogenetic
information. Additional information was found by searching
BIOSIS using the terms Artiodactyl* or Cetace* with any
of phylogen*, fossil*, systematic*, cladistic*, cladogram*,
phenogram* and taxonom*. Finally, bibliographies of all
collected papers were searched to find any additional
papers.
All methods of phylogenetic estimation (including infor-
mal techniques with no algorithm) were accepted from
sources dating from 1960 onwards. However, the only
taxonomies to be included were those from Grubb (1993)
and Mead & Brownell (1993), which include all 212
extant artiodactyl species and all 78 extant cetacean species.
Together, these two taxonomies act as a ‘ seed tree
(Bininda-Emonds & Sanderson, 2001) that overlaps with all
source trees to produce a backbone for the analysis. The
seed tree will provide minimal phylogenetic information
for taxa that are little studied but can be easily overruled
by more robust source trees where more phylogenetic in-
formation is available. No other taxonomy was included
because there is no way of accounting for duplication of
information among taxonomies. The source trees were
stored by drawing the tree exactly as presented in the orig-
inal paper into the tree view window of MacClade
(Maddison & Maddison, 2003) and saving them in a single
nexus-formatted treefile (Maddison, 1997).
(2 ) Tree building
There are an increasing number of methods of supertree
construction (Bininda-Emonds, 2004). We employ the most
commonly used approach, matrix representation with par-
simony (MRP) (Baum, 1992 ; Ragan, 1992). MRP converts
all source-tree topologies into a matrix based on simple
graph theoretic principles. For every source tree, the in-
formative nodes are represented as a series of partial binary
pseudocharacters ’. Taxa descended from a given node are
coded as ‘1 ’, taxa that are not descended from that node
are coded as ‘0 ’, and taxa that do not appear on a given
source tree are represented by a ‘ ?’. Both rooted and
unrooted source trees were used. For rooted source trees, an
all-zero hypothetical ancestor is added to the matrix to
preserve this rooting information. For unrooted source
trees, this hypothetical ancestor is coded entirely using ‘ ?
(Bininda-Emonds, Beck & Purvis, in press). The final matrix
is then analysed using conventional parsimony analysis to
generate the supertree topology. Like all methods of phy-
logenetic inference, critical selection of the source data in a
supertree analysis is key. Without quality control, duplicated
datasets and phylogenies derived using less robust inference
methods can bias the resultant supertree ( Springer & de
Jong, 2001; Gatesy et al., 2002). To reduce the occurrence of
dataset duplication, the protocol of Bininda-Emonds et al.
(2004) was followed. It establishes a set of rules that lead to
the rejection of all source trees that duplicate character data
in other studies without adding a substantial amount of new
data/species. The addition of new data/species can lead to
very different phylogenetic results and hence were such
studies considered ‘ independent ’ phylogenetic estimates.
Another issue with particular importance for the cetartio-
dactyl clade is the inherent historical dimension of supertree
analyses (see Bininda-Emonds et al., 1999). For example, the
hippo-whale clade was first proposed by Irwin and Arnason
(1994) and is supported by the vast majority of molecular
data. However, this relationship is likely to be swamped in
the matrix by traditional hypotheses that have a longer his-
tory in the literature. In this study, neither the Artiodactyla
nor the Cetacea were assumed to be monophyletic because
such assumptions are inadvisable (Springer & de Jong,
2001; Gatesy et al., 2002), particularly when there is con-
flicting evidence, as seen in the Cetartiodactyla.
To account for differences in species definitions and
taxonomy, species names were standardised using the syn-
onymy list in Grubb (1993) and Mead & Brownell (1993)
implemented in the Perl script synonoTree.pl (Bininda-
Emonds et al., 2004). All species discovered post-1993 (e.g.
Pseudoryx nghetinhensis) were necessarily excluded because
they could not be placed with respect to the reference tax-
onomy (Grubb, 1993 ; Mead & Brownell, 1993). Genus-level
tips in the source trees were assigned the type species for that
taxon (following Jones et al., 2002 ; Bininda-Emonds et al.,
2004). Any taxon that could not be unambiguously assigned
to a species was pruned from the source tree. All mam-
malian species in the source trees that were not members
of the cetartiodactyl clade were reduced to a single ter-
minal taxon (outgroup) that was used to root the supertree :
source studies consisting of cetartiodactyl species only were
Phylogeny of the whales, dolphins and even-toed hoofed mammals 447
purposely unrooted and encoded as such (following Bininda-
Emonds et al., in press). All other taxa in the source trees that
were not extant mammals were deleted from the source tree.
After standardization of species names, the source trees were
converted to MRP additive binary coding (Ragan, 1992 ;
Baum & Ragan, 1993) using the Perl script SuperMRP.pl.
(Matrix available at www.treebase.org/treebase study ac-
cession number S1188, matrix accession number M2055).
The full MRP matrix was analysed without topological
constraints (i.e. without assumptions on sub-ordinal mono-
phyly). A parsimony ratchet was used to analyse the matrix
as it searches a greater proportion of tree space more effec-
tively than other heuristic searches (Nixon, 1999 ; Quicke
et al., 2001). Briefly, the ratchet operates through a series of
fast searches coupled with differential character weighting.
From an initial starting tree, a random proportion of the
characters are upweighted and further searches on the tree
are continued. The characters are then returned to their
original weights and the search is continued. The single tree
resulting from this iteration is then saved and a new iteration
of re-weighting is initiated. Specifically, the form of the
ratchet was 100 batches of 1000 reweighting iterations each
(i.e. a ‘100.1000 ’ ratchet). The initial tree was found using a
single random addition sequence followed by Tree Bisection
Reconnection (TBR) branch swapping. For each iteration,
a randomly chosen 25 % of the pseudocharacters were
upweighted by a factor of two; TBR branch swapping was
used in all cases to return a single tree at each step. All saved
trees were then taken as the starting points for a final brute-
force TBR search with all pseudocharacters given equal
weight. For quicker processing, the ratchet search was
split into 10 batches each running 10 000 replicates (i.e. 10
10.1000 ratchets) and submitted to the University of
Virginia Aspen Linux cluster running the Linux version
of PAUP* v4b10 (Swofford, 2003). The outputs from the
10 batches were combined and the final brute-force search
was run on a single node of the cluster saving 100 000
equally most parsimonious trees. These were combined as a
strict consensus tree to give the full species-level supertrees
presented in Figs 1–4. The instructions for the ratchet were
written using the Perl script perlRat.pl and implemented in
PAUP*.
(3 ) Assessing support
We employed two different techniques to assess the support
for our inferred supertree topology in relation to the set of
source trees. First, we examined the impact of poorer quality
source trees on the supertree. The inclusion of such source
trees in a supertree analysis remains a point of contention.
Despite strong empirical evidence that poor-quality source
trees generally do not impact the supertree analysis nega-
tively (Purvis, 1995 ; Bininda-Emonds et al., 1999 ; Jones
et al., 2002; Stoner, Bininda-Emonds & Caro, 2003), the
inclusion of such data remains sharply criticized (Gatesy
et al., 2002, 2003 ; Gatesy et al., 2004 ; Gatesy & Springer,
2004). The conventional method to assess the effect of
source tree quality has been to downweight poorer quality
source trees by a factor of 4:1. However, we employed the
more stringent criterion advocated by Gatesy et al. (2004) of
excluding all source trees derived from informal or less
rigorous phylogenetic techniques (e.g. chromosome band-
ing, parsimony by eye, best phylogenetic guesses, UPGMA)
altogether. This resulted in the removal of 396 (of 2068
total) pseudocharacters from the full matrix as well as 38
species, the positions of which were known only from the
Outgroup
Antilocapra americana
Giraffa camelopardalis
Okapia johnstoni
MOSCHIDAE
CERVIDAE
BOVIDAE
Hyemoschus aquaticus
Moschiola meminna
Tragulus javanicus
Tragulus napu
CETACEA
HIPPOPOTAMIDAE
Babyrousa babyrussa
Phacochoerus africanus
Phacochoerus aethiopicus
Hylochoerus meinertzhagen
i
Potamochoerus porcus
Potamochoerus larvatus
Sus barbatus
Sus bucculentus
Sus cebifrons
Sus celebensis
Sus heureni
Sus philippensis
Sus salvanius
Sus scrofa
Sus timoriensis
Sus verrucosus
Pecari tajacu
Tayassu pecari
Catagonus wagneri
Camelus bactrianus
Camelus dromedarius
Lama glama
Lama guanicoe
Lama pacos
Vicugna vicugna
Fig. 1. Complete higher-level cetartiodactyl supertree. The
Bovidae, Cervidae and Cetacea have been collapsed down to
the family level; the species-level phylogenies of these families
are presented in Figs 2–4.
448 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
two taxonomic sources. The reduced matrix was analysed in
the same manner as for the full matrix to yield a second,
reduced supertree.
Second, we assessed the amount of support for indi-
vidual nodes of the supertree among the set of source trees
Addax nasomaculatus
Oryx dammah
Oryx gazella
Oryx leucoryx
Hippotragus equinus
Hippotragus niger
Alcelaphus buselaphus
Sigmoceros lichtensteinii
Connochaetes gnou
Connochaetes taurinus
Damaliscus hunteri
Damaliscus lunatus
Damaliscus pygargus
Ammotragus lervia
Budorcas taxicolor
Ovis ammon
Ovis aries
Ovis vignei
Ovis canadensis
Ovis dalli
Ovis nivicola
Capra caucasica
Capra cylindricornis
Capra falconeri
Capra hircus
Capra ibex
Capra nubiana
Capra pyrenaica
Capra sibirica
Capra walie
Hemitragus hylocrius
Hemitragus jayakari
Hemitragus jemlahicus
Pseudois nayaur
Pseudois schaeferi
Rupicapra pyrenaica
Rupicapra rupicapra
Ovibos moschatus
Naemorhedus swinhoei
Naemorhedus baileyi
Naemorhedus caudatus
Naemorhedus crispus
Naemorhedus goral
Naemorhedus sumatraensis
Oreamnos americanus
Pantholops hodgsonii
Aepyceros melampus
Ammodorcas clarkei
Antidorcas marsupialis
Antilope cervicapra
Gazella bennettii
Gazella saudiya
Gazella cuvieri
Gazella leptoceros
Gazella subgutturosa
Gazella dorcas
Gazella gazella
Gazella spekei
Gazella dama
Gazella soemmerringii
Gazella granti
Gazella rufifrons
Gazella thomsonii
Litocranius walleri
Saiga tatarica
Cephalophus adersi
Cephalophus callipygus
Cephalophus ogilbyi
Cephalophus weynsi
Cephalophus dorsalis
Cephalophus silvicultor
Cephalophus spadix
Cephalophus jentinki
Cephalophus harveyi
Cephalophus natalensis
Cephalophus nigrifrons
Cephalophus rufilatus
Cephalophus leucogaster
Cephalophus niger
Cephalophus rubidus
Cephalophus zebra
Sylvicapra grimmia
Cephalophus maxwellii
Cephalophus monticola
Raphicerus campestris
Raphicerus sharpei
Raphicerus melanotis
Dorcatragus megalotis
Kobus ellipsiprymnus
Kobus leche
Kobus megaceros
Kobus kob
Kobus vardonii
Redunca arundinum
Redunca redunca
Redunca fulvorufula
Pelea capreolus
Madoqua guentheri
Madoqua kirkii
Madoqua piacentinii
Madoqua saltiana
Neotragus moschatus
Neotragus batesi
Neotragus pygmaeus
Oreotragus oreotragus
Ourebia ourebi
Procapra gutturosa
Procapra picticaudata
Procapra przewalskii
Bison bison
Bison bonasus
Bos grunniens
Bos sauveli
Bos taurus
Bos frontalis
Bos javanicus
Bubalus bubalis
Bubalus depressicornis
Bubalus mindorensis
Bubalus quarlesi
Syncerus caffer
Boselaphus tragocamelus
Tetracerus quadricornis
Taurotragus derbianus
Taurotragus oryx
Tragelaphus strepsiceros
Tragelaphus angasii
Tragelaphus buxtoni
Tragelaphus eurycerus
Tragelaphus spekii
Tragelaphus scriptus
Tragelaphus imberbis
Fig. 2. Complete species-level phylogeny of the Bovidae.
Alces alces
Capreolus capreolus
Capreolus pygargus
Hydropotes inermis
Blastocerus dichotomus
Ozotoceros bezoarticus
Hippocamelus bisulcus
Hippocamelus antisensis
Mazama americana
Mazama bricenii
Mazama chunyi
Mazama gouazoupira
Mazama nana
Mazama rufina
Odocoileus hemionus
Odocoileus virginianus
Pudu mephistophiles
Pudu puda
Rangifer tarandus
Axis axis
Axis calamianensis
Axis kuhlii
Axis porcinus
Cervus albirostris
Cervus alfredi
Cervus duvaucelii
Cervus elaphus
Cervus eldii
Cervus mariannus
Cervus nippon
Cervus timorensis
Cervus unicolor
Elaphurus davidianus
Dama dama
Dama mesopotamica
Elaphodus cephalophus
Muntiacus atherodes
Muntiacus crinifrons
Muntiacus feae
Muntiacus gongshanensis
Muntiacus muntjak
Muntiacus reevesi
Fig. 3. Complete species-level phylogeny of the Cervidae.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 449
using the qualitative support (QS) index (Bininda-Emonds,
2003). Unlike traditional character-based phylogenetic
support measures (e.g. Bremer support or the boot-
strap), the QS index was specifically designed for (MRP)
supertree analyses and accounts for the inherent non-
independence among MRP-encoded ‘ pseudocharacters ’.
Briefly, the QS index quantifies the relative degree of
support among the set of source trees for each node in
the supertree. Specifically, it determines whether a given
source tree supports, conflicts, or is equivocal with respect
to a given node. The results are then summed across the
set of source trees and normalized to fall between +1 and
x1, with the two values indicating that all source trees
directly support (+1) or conflict (x1) with the supertree
clade in question. Intermediate values indicate the rela-
tive amount of support versus conflict among the set of
source trees. Note that the QS index is purely descriptive,
such that factors that increase the likelihood that the
supertree clade will be contradicted (e.g. a clade of large
size and/or a high number of source trees) will result
in increasingly negative values (for more information, see
Bininda-Emonds, 2003).
We used two variants of the QS index. In the first (the full
QS index, QS), the supertree as given was compared to
the source trees. In this case, some taxa present on the super-
tree might be missing from the source tree, such that it
must be determined whether the source tree can potentially
support or conflict with a given supertree clade, leading to
hard and soft concepts of support and conflict. In the second
variant (the reduced QS index, rQS), the supertree was
pruned to the same taxon set as the source tree it is being
compared to and support versus conflict can be determined
absolutely.
(4 ) Tree comparison
Calculations of congruence between tree topologies were
performed in PAUP* (Swofford, 2003) using two different
tests: the symmetric difference metric (d
S
, Robinson &
Foulds, 1979, 1981) and the consensus fork index (sensu
Colless, 1981). The symmetric difference distance calculates
the number of groups that appear on one tree or the other
but not on both. The consensus fork index (CFI) quantifies
the amount of resolution in the consensus tree (of the trees
being compared) by dividing the number of non-trivial
clusters (two or more taxa) by the maximum possible
(number of terminal taxa minus 2) number of non-trivial
clusters. If one or more of the trees being compared contains
polytomies, the CFI will be lower as polytomies are treated
as incorrect. Three comparisons were made : full supertree
versus reduced supertree, full supertree versus most compre-
hensive total-evidence tree (Gatesy et al., 2002) and reduced
supertree versus most comprehensive total-evidence tree
(Gatesy et al., 2002). Because the trees contained different
taxon sets, the more inclusive supertrees were pruned in
MacClade (Maddison & Maddison, 2003) until the taxon
sets were matching. In cases where higher taxon names were
used, the supertree species names were converted to the
appropriate genus/tribe and collapsed to a single terminal
branch.
Australophocaena dioptrica
Neophocaena phocaenoides
Phocoena phocoena
Phocoena sinus
Phocoena spinipinnis
Phocoenoides dalli
Cephalorhynchus commersoni
i
Cephalorhynchus eutropia
Cephalorhynchus hectori
Cephalorhynchus heavisidii
Lagenorhynchus australis
Lagenorhynchus cruciger
Lagenorhynchus obliquidens
Lagenorhynchus obscurus
Lissodelphis borealis
Lissodelphis peronii
Delphinus delphis
Stenella attenuata
Stenella clymene
Stenella coeruleoalba
Stenella frontalis
Tursiops truncatus
Feresa attenuata
Pseudorca crassidens
Globicephala macrorhynchus
Globicephala melas
Peponocephala electra
Grampus griseus
Lagenodelphis hosei
Lagenorhynchus acutus
Lagenorhynchus albirostris
Orcaella brevirostris
Orcinus orca
Sotalia fluviatilis
Sousa chinensis
Sousa teuszii
Stenella longirostris
Steno bredanensis
Delphinapterus leucas
Monodon monoceros
Inia geoffrensis
Pontoporia blainvillei
Lipotes vexillifer
Berardius arnuxii
Berardius bairdii
Hyperoodon ampullatus
Hyperoodon planifrons
Indopacetus pacificus
Mesoplodon bidens
Mesoplodon bowdoini
Mesoplodon carlhubbsi
Mesoplodon densirostris
Mesoplodon europaeus
Mesoplodon ginkgodens
Mesoplodon grayi
Mesoplodon hectori
Mesoplodon layardii
Mesoplodon mirus
Mesoplodon peruvianus
Mesoplodon stejnegeri
Tasmacetus shepherdi
Ziphius cavirostris
Platanista gangetica
Platanista minor
Kogia breviceps
Kogia simus
Physeter catodon
Balaena mysticetus
Eubalaena australis
Eubalaena glacialis
Caperea marginata
Balaenoptera acutorostrata
Balaenoptera borealis
Balaenoptera edeni
Balaenoptera musculus
Balaenoptera physalus
Megaptera novaeangliae
Eschrichtius robustus
Fig. 4. Complete species-level phylogeny of the Cetacea.
450 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
III. RESULTS AND DISCUSSION
The full supertree (see Fig. 1 for higher-level supertree and
Figs 2–4 for the expansion of Bovidae, Cervidae and
Cetacea to the species level) was obtained from 201 source
trees derived from 141 published articles (denoted by a * in
the References), representing 0.69 source trees per species.
This latter value is comparable to that in previous large-
scale supertrees of well-studied mammalian orders ; 0.6
in primates (Purvis, 1995) and 0.7 in carnivores (Bininda-
Emonds et al., 1999). Thirty-nine source trees were derived
from purely morphological data, with the number of mor-
phological studies being relatively constant over time see
Fig. 5. By contrast, 65 % of the 147 purely molecular source
trees were from 1997 onwards.
(1 ) Resolution, robustness and support
The resolution of the full tree was 59.9 %, which is lower
than in the primate (79.2 % : Purvis, 1995), carnivore
(78.1% : Bininda-Emonds et al., 1999), insectivore (69.9%:
Grenyer & Purvis, 2003) and marsupial supertrees (73.7 %:
Cardillo et al., 2004). The low resolution stems largely from
a lack of information. In particular, many species are poorly
known such that they can cluster equally parsimoniously
with several other species, thereby reducing resolution
locally. Although it is possible to identify such ‘ floating
species using safe taxonomic reduction (Wilkinson, 1995),
the application of this approach in order to unambiguously
re-include the removed species produced negligible gains in
resolution (data not shown). The least resolved areas of the
tree are within the families Ziphiidae, Cervidae, Suidae and
Bovidae. The genera Sus,Muntiacus and Cervus, and the
family Ziphiidae are each completely unresolved owing to
a lack of phylogenetic information. For example, excluding
the seed trees, only five source trees included two or more
of the 10 species in Sus. The largest Sus source tree included
six species (Groves, 1997), the next largest three species
(Randi et al., 2002), and rest included only two species apiece.
In sharp contrast, the polytomy at the base of the Bovidae
is caused by conflicting phylogenetic information among
the 35 source trees providing information for this node.
The full and reduced supertrees are highly congruent
(CFI=0.56, which means 56 % clades are shared ; d
S
=
0.114, which means 11.4 % clades were not shared), the
differences between the indices are due to the CFI index
being adversely affected by the lower resolution in the full
supertree. The only difference at the family level between
the two trees is the collapsing of the ((Phocoenidae+
Delphinidae) Monodontidae) clade in the full supertree to
a polytomy in the reduced tree. This suggests that the
majority of the higher-level relationships are robust to the
effects of poorly known species and ‘ poor ’ quality methods
of phylogenetic reconstruction. However, the reduced ver-
sion has noticeably higher resolution within the Bovidae,
probably due to the removal of many floating species. As
a result, the resolution of the entire reduced tree (68.5 %)
is noticeably higher than for the full supertree (59.9 %).
The full and reduced QS index (QS and rQS, respect-
ively) for the clades in the full and the reduced tree are
presented in Appendices 2 and 3 (available at www.
faculty.virginia.edu/gittleman/CetartiodactylSupertree-
Appendix.zip). Most of the nodes have negative QS
index values indicating that there are more mismatches
0
5
10
15
20
25
30
35
40
1968
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003_partial
Year
Number of source trees
Fig. 5. Number of studies per year since 1960 to halfway through 2003 (2003_partial) contributing source trees to the unweighted
cetartiodactyl supertree. Cross-hatched bars represent molecular data and black bars represent purely non-molecular data e.g.
morphological, behavioural. Trees that combined datasets from different publishing years were not included.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 451
than matches between the source trees and the supertree
clade. By contrast the rQS index shows support for the
majority of clades, with only nine negative nodes and eight
equivocal nodes. It is therefore not surprising that the rQS
index for the supertree as a whole (rQS
Tree
) shows weak
support for the supertree topology (0.034) and that the
QS
Tree
shows little or no support for the supertree topology
(x0.087). The sharp differences between the QS and
the rQS index are due to the way taxa missing from the
source tree but within the supertree clade are treated. The
QS index is highly conservative ; it takes into account every
missing species that can potentially contradict the supertree
clade, creating many soft mismatches. By contrast the rQS
index prunes the supertree to contain only the taxa in the
source tree so there can be no soft matches or mismatches,
which allows for many more matches between source tree
and supertree. 60.7 % of nodes are contradicted by at least
one tree and in the QS index 98.3% of all nodes have at
least one hard or soft mismatch. However, a negative QS
index does not necessarily indicate poor support for the
clade as it is known to become more negative when
the tree is built using a large number of poorly overlapp-
ing sources (Bininda-Emonds, 2003). The QS
Tree
value of
x0.087 compares well to that of the marsupial supertree
x0.09 (Cardillo et al., 2004) and the lagomorph super-
tree x0.109 (Bininda-Emonds, 2003). Most family-level
relationships have a highly negative QS index, with less
negative values occurring towards the tips of the tree where
the clade sizes are smaller. This trend is consistent with
the results of simulation tests and is again due to the greater
possibility of conflict in large versus small clades (Bininda-
Emonds, 2003).
(2 ) Higher-level relationships
(a)Placement of Cetacea
The supertree (see Fig. 1) supports the hypothesis that ceta-
ceans are the sister taxon to hippopotamids as upheld by
the majority of molecular source trees (e.g. Arnason &
Gullberg, 1994 ; Gatesy et al., 1999). Support for the
Cetacea-Hippopotamidae clade is strong, with 31 source
trees supporting it and 13 directly contradicting it (rQS=
0.09). The traditional morphological view that cetaceans
and mesonychids are sister taxa (e.g. O’Leary, 1999) could
not be examined directly as only extant taxa were added to
the matrix. However, it is indirectly refuted by our data
because of the nesting of Cetacea within Artiodactyla.
(b)Basal clades
The placement of hippopotamids as sister taxon to ceta-
ceans contradicts the traditional view that hippopotamids
cluster with the suids (pigs) and tayassuids (peccaries)
(Langer, 2001) to form the Suiformes. The supertree sup-
ports the hypothesis that suids and tayassuids are sister taxa
and together they form the sister group to all remaining
cetartiodactyls excluding camelids. The uncertainty regard-
ing basal relationships in the Cetartiodactyla is illustrated
by the rQS index value of x0.005, with 23 hard matches
to 24 hard mismatches and by the sample of 15 source trees
and the recent artiodactyl supertree (Mahon, 2004) pre-
sented in Fig. 6. Four trees in Fig. 6 support the topology
found here of the camelids being the most basal clade fol-
lowed by the suid-tayassuid clade. Nine contradict this set
of relationships, whereas the remaining topologies are
equivocal. The nine contradictory trees instead propose
many different clades as being basal within Cetartiodactyla:
a hippopotamid-cetacean clade (Arnason & Gullberg,
1994 minisupertree ; Beintema et al., 2003), a suid-tayassuid
clade (Gatesy et al., 1996 ; Mahon, 2004) or the traditional
Suiformes (Perez-Barberia & Gordon, 1999 ; Geisler, 2001).
(c)Family-level relationships within Artiodactyla
The six families of the suborder Ruminantia (Tragulidae,
Moschidae, Giraffidae, Cervidae, Bovidae and Antilo-
capridae) form a monophyletic clade. Support for ruminant
monophyly is strong ; only seven source trees present con-
tradictory topologies (e.g. Cronin et al., 1996 ; Gatesy et al.,
1999) whereas 47 are in agreement. Relationships among
the ruminant families were fully resolved in the supertree
to give (((Bovidae (Cervidae, Moschidae)) (Antilocapridae,
Giraffidae)) Tragulidae). Support for the tragulids as the
basal ruminant family is strong (rQS=0.199) and derives
from all data types and tree construction methods (e.g.
Chikuni et al., 1995; Gatesy & Arctander, 2000 a). Support
for the supertree topology among the five remaining rumi-
nant families (the Pecora) is mixed, particularly as only three
source trees include all six families (Perez-Barberia &
Gordon, 1999 ; Su et al., 1999 ; Hassanin & Douzery, 2003).
The sister-taxon relationship between Cervidae and
Moschidae is also well supported (rQS=0.109) but the
sample size is very small ; only three source trees support
the relationship and one source contradicts it. The sister-
taxon relationship between the cervid and moschid clade
and Bovidae has weaker support ; 36 source trees are in
agreement with the placement and 25 contradict it (rQS=
0.055). The sister-taxon relationship between Giraffidae and
Antilocapridae is equivocal (rQS=x0.005) with 11 source
trees contradicting the relationship and 10 supporting it. Of
the three source trees that include all five pecoran families
and the partial artiodactyl supertree of Mahon (2004), only
Su et al. (1999) resolve the same relationships as the super-
tree. The Mahon (2004) and the Hassanin & Douzery (2003)
trees differ by placing the moschids as sister taxa to the
bovids. The tree of Hassanin and Douzery (2003) is also
equivocal in its support for the sister-taxon relationship
between giraffids and antilocaprids. The Perez-Barberia &
Gordon (1999) tree disagrees entirely with the supertree
topology for the Pecora.
Moschidae (musk deer) and the monotypic Antilo-
capridae (pronghorn) account for most of the instability
within Pecora. Historically, these two clades have always
been difficult to place. It was not until fairly recently that
moschids were even recognised as a separate family distinct
from Cervidae (Corbert & Hill, 1980 ; Leinders & Heintz,
1980); they are now typically held to cluster with the cervids
(e.g. Fig. 5 in Cap et al., 2002) and/or the bovids (Hassanin
& Douzery, 2003). Antilocapridae has floated around the
tree, with proposed sister-taxon relationships with Cervidae
452 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Beintema et al. (2003)
Figure 4
Camelidae
Cervidae
Moschidae
Bovidae
Giraffidae
Suidae
Cap et al. (2002)
Figure 5
Hippopotamidae
CETACEA
Camelidae
Tayassuidae
Suidae
Tragulidae
Bovidae
Cervidae
Antilocapridae
CervidaeB
Giraffidae
Arnason & Gullberg
(1994) dataset
Camelidae
Tayassuidae
Suidae
Hippopotamidae
CETACEA
Tragulidae
Bovidae
Giraffidae
CHRS SINES
dataset
CETACEA
Suidae
Hippopotamidae
Camelidae
Cervidae
Bovidae
Antilocapridae
Giraffidae
Fitch & Beintema (1990)
Figure 1
Gatesy (1997)
Figure 3A
Camelidae
Suidae
Tayassuidae
Hippopotamidae
CETACEA
Tragulidae
Antilocapridae
Giraffidae
Cervidae
Bovidae
Bovidae
Giraffidae
Antilocapridae
Cervidae
Tragulidae
CETACEA
Hippopotamidae
Tayassuidae
Suidae
Camelidae
Gatesy et al. (1999)
Figure 11
Tayassuidae
Suidae
CETACEA
Hippopotamidae
Tragulidae
Antilocapridae
Giraffidae
Bovidae
Cervidae
Camelidae
Tayassuidae
Suidae
Hippopotamidae
Camelidae
Tragulidae
BovidaeB
Cervidae
Bovidae
Geisler (2001)
Figure 8
Tragulidae
Antilocapridae
Giraffidae
Cervidae
Bovidae
Camelidae
Suidae
Suidae
Tayassuidae
Hippopotamidae
Camelidae
Tragulidae
Giraffidae
Cervidae
Bovidae
Tayassuidae
Suidae
Camelidae
Hippopotamidae
Cervidae
Moschidae
Bovidae
Antilocapridae
Giraffidae
Tragulidae
Mahon Supertree
(2004)
Tayassuidae
Suidae
Hippopotamidae
Bovidae
Moschidae
Antilocapridae
Cervidae
Giraffidae
Tragulidae
Camelidae
PERISSODACTYLA
CETACEA
Hippopotamidae
Tayassuidae
Suidae
Bovidae
CervidaeB
Giraffidae
Antilocapridae
Cervidae
Camelidae
Camelidae
Tayassuidae
Suidae
CETACEA
Hippopotamidae
Tragulidae
Giraffidae
Antilocapridae
Bovidae
Cervidae
Moschidae
Supertree from
this study
Gatesy & Arctander
(2000b) Figure 9.2
Kuznetsova et al. (2002)
Figure 1
Langer (2001)
Figure 8a
Gatesy et al. (1996)
Figure 2c
Randi et al. (1996)
Figure 2
Perez-Barberia & Gordon
(1999) Figure 1
Camelidae
Cervidae
Bovidae
Antilocapridae
Giraffidae
Suidae
Camelidae
Tayassuidae
Suidae
Hippopotamidae
CETACEA
Tragulidae
Cervidae
Bovidae
Giraffidae
Fig. 6. A sample of previous phylogenetic hypotheses concerning the higher-level cetartiodactyl phylogeny. The Cetacea are
reduced to a single terminal taxon. CHRS SINES dataset is the mini-supertree that combines all source trees built using CHRS
SINES (denoted by
y
in the References).
Phylogeny of the whales, dolphins and even-toed hoofed mammals 453
(e.g. Arnason & Gullberg, 1994 minisupertree), Giraffidae
(e.g. Douzery & Catzeflis, 1995) and the clade comprising
Bovidae, Cervidae and Giraffidae (e.g. Gatesy & Arctander,
2000b). It is therefore not surprising that the QS index for
the inter-family nodes in the Pecora are more negative than
for any other family-level cluster within the supertree.
(d)Family-level relationships within Cetacea
The traditional odontocete and mysticete suborders are
both monophyletic in the supertree. However, support for a
monophyletic Odontoceti is weak ; 17 source trees support
monophyly and 16 oppose it (rQS=0.005). The poor sup-
port is due to a proliferation of studies supporting the claims
of Milinkovitch et al. (1993) that the odontocete family
Physeteridae (sperm whales) clusters with the Mysticeti (e.g.
Milinkovitch et al., 1996 ; Montgelard et al., 1997 ; Yang &
Zhou, 1999). This hypothesis has since been rejected by the
majority of researchers due to the lack of morphological
support and the sensitivity of the result on outgroup choice
and sequence alignment (Messenger & McGuire, 1998). It is
therefore not surprising that the support for the placement
of the Physteridae at the base of the odontocetes is also
weak; 15 studies support its placement and 10 contradict
it (rQS=0.025). The basal position of the Physeteridae is
the preferred placement of the majority of studies that
reconstruct the traditional Odontoceti (e.g. Messenger &
McGuire, 1998; Nikaido et al., 2001). The Platanistidae
(river dolphins) are paraphyletic in agreement with current
molecular phylogenies (e.g. Hamilton et al., 2001 ; Nikaido
et al., 2001). The positions of the Platanistidae genera within
the supertree receive no support : Platanista is placed as
next basal clade to the Physeteridae (rQS=0), whereas
the remaining three genera cluster together further up the
tree in the clade (Lipotes (Inia+Pontoporia)) (rQS=x0.01).
The remaining relationships in the supertree among
odontocete families largely agree with the current literature.
The close relationship between Phocoenidae, Delphinidae
and Monodontidae is well supported ; 25 source trees sup-
port it whereas only two contradict it (rQS=0.114). The
full supertree also supports a Delphinidae+Phocoenidae
pairing, which is the most frequently resolved sister-taxon
relationship among these three families ; 16 sources uphold
this pairing while only four provide topologies that go
against it (rQS=0.045). It is difficult to assess support for
the position of the Ziphiidae because its position in the
source trees is highly dependent on whether a paraphyletic
Odontoceti and/or Platanistidae are reconstructed ; how-
ever, the rQS index shows weak support for its placement
within the supertree (rQS=0.085).
Mysticete relationships within the supertree contradict
most traditional taxonomic groupings ; however, this is not
surprising given that most of the source trees also challenge
the traditional views. The nesting of Eschrichtiidae within
the Balaenopteridae is supported by 11 source trees and also
the total evidence tree of Gatesy et al. (2003). Support for
a monophyletic clade comprising the Eschrichtiidae and
Balaenopteridae is even higher, with 18 source trees sup-
porting this relationship and only one contradicting it; the
majority of the support is due to source trees reconstructing
a Balaenopteridae-Eschrichtiidae polytomy (e.g. Hasegawa
et al., 1997). The sister-taxon relationship between Neo-
balaenidae and Balaenidae is equivocal (rQS=0) with four
source trees supporting the relationship (e.g. Randi et al.,
1996; Gatesy & Arctander, 2000 b), and four contradicting
it (e.g. Adegoke et al., 1993 ; Arnason et al., 1993).
(3 ) Tree comparison : supertree
versus supermatrix
The full and reduced supertree topologies were highly
congruent with the most comprehensive published tree
of the Cetartiodactyla, namely the supermatrix of Gatesy
et al. (2002) see Fig. 7. There was between 72 % and 79 %
congruence between the supertrees and the supermatrix
(full CFI=0.729, d
S
=0.213; reduced CFI=0.75, d
S
=
0.213). At higher taxonomic levels, the differences between
the supertree and the supermatrix topologies are minimal.
In the supermatrix tree, the sister-taxon relationship
between Giraffidae and Antilocapridae is not resolved
but they appear in the same position within the Pecora
(((Bovidae, Cervidae) Giraffidae) Antilocapridae) as apposed
to ((Bovidae, Cervidae) (Giraffidae, Antilocapridae)). The
supermatrix also resolves a sister-taxon relationship between
Monodontidae and Phocoenidae rather than the supertree
grouping of Delphinidae and Phocoenidae. This is not sur-
prising because there is contradictory evidence concerning
the sister-taxon relationship among these three families as
illustrated by the polytomy in the reduced supertree. The
last difference is the appearance of the novel, but unstable
clade ((Suidae, Tayassuidae) Camelidae) in the supermatrix
analysis at the base of the cetartiodactyl tree, whereas the
supertree decomposes this clade into the more traditional
(Suidae, Tayassuidae) followed by Camelidae at the very
base of the tree. This degree of congruence between the
supertrees and the supermatrix tree suggests indepen-
dent support for the phylogenetic hypothesis proposed by
the supertree. Altogether, this result implies that with care-
ful source tree selection, supertree methods can give valid
topologies that agree with other methods of tree construc-
tion (contra Gatesy et al., 2002).
IV. CONCLUSIONS
(1) We present the first phylogeny to include all 290
extant species of artiodactyls and cetaceans recognised
in Wilson and Reeder (1993). The supertree topology is
fully resolved at the family level and is highly congruent
(72–79%) with the largest total-evidence cetartiodactyl tree.
It supports the current consensus that Cetacea are nested
within Artiodactyla as sister taxa to Hippopotamidae rather
than to Artiodactyla as a whole and that the sub-order
Ruminantia is a valid monophyletic clade. The other re-
lationships within the tree are more controversial because
no consensus exists within the literature and support is often
inconclusive due to inadequate taxon sampling.
(2) The complete tree is provided as a guide for further
phylogenetic research while simultaneously facilitating
454 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
large-scale comparative analyses. In particular, a complete
species-level tree of the Cetartiodactyla provides the first
opportunity to study functional and behavioural ecology
hypotheses across obligate aquatic and terrestrial species
in the same clade. Representative questions include : (i)
whether changes in the rate of morphological or life history
evolution exist that are associated with the terrestrial–
aquatic boundary ; (ii) whether the social evolution hypoth-
eses in the terrestrial hoofed mammals linking group size
and structure to body size, predation and life-history (Estes,
1974; Geist, 1974 ; Jarman, 1974) can be extrapolated to
the aquatic species; and (iii) to what degree the factors
that correlate with extinction risk (sensu Purvis et al., 2000)
are ecologically determined in that the same traits do not
predict extinction risk in the ecologically diverse Artio-
dactyla and Cetacea. The supertree topology can be used
to control for phylogenetic relationships with a degree of
confidence due to the independent support for many of
the relationships given by the supermatrix of Gatesy et al.
(2002).
(3) The supertree highlights areas in need of further
phylogenetic research and data collection. Work needs to
be focussed especially on Suidae, Ziphiidae, Cervidae and
Delphinidae, where very little phylogenetic information is
Sus scrofa
Babyrousa babyrussa
Tayassu tajacu
Camelus dromedarius
Camelus bactrianus
Lama spp.
Balaenoptera physalus
Megaptera novaeangliae
Balaenoptera acutorostrata
Eschrichtius robustus
Balaenoptera musculus
Balaena mysticetus
Tursiops truncatus
Lagenorhynchus spp.
Globicephala spp.
Orcinus orca
Delphinapterus leucas
Monodon monoceros
Phocoenidae
Inia geoffrensis
Ziphius cavirostris
Mesoplodon spp.
Kogia spp.
Physeter catadon
Hippopotamus amphibius
Hexaprotodon liberiensis
Tragulus spp.
Antilocapra americana
Giraffa camelopardalis
Okapia johnstoni
Odocoileus spp.
Cervus spp.
Muntiacus spp.
Alces alces
Bubalis bubalis
Bubalis depressicornis
Syncerus caffer
Bos spp.
Boselaphus tragocamelus
Tragelaphini
Naemorhaedus crispus
Ovibos moschatus
Naemorhaedus spp.
Capra hircus
Ovis spp.
Oryx spp.
Damaliscus spp.
Gazella spp.
Kobus spp.
Aepyceros melampus
Cephalophus spp.
Camelus dromedarius
Camelus bactrianus
Lama spp.
Sus scrofa
Babyrousa babyrussa
Tayassu tajacu
Balaenoptera physalus
Megaptera novaeangliae
Balaenoptera musculus
Eschrichtius robustus
Balaenoptera acutorostrata
Balaena mysticetus
Tursiops truncatus
Lagenorhynchus spp.
Globicephala spp.
Orcinus orca
Phocoenidae
Delphinapterus leucas
Monodon monoceros
Inia geoffrensis
Ziphius cavirostris
Mesoplodon spp.
Kogia spp.
Physeter catadon
Hippopotamus amphibius
Hexaprotodon liberiensis
Tragulus spp.
Giraffa camelopardalis
Okapia johnstoni
Antilocapra americana
Odocoileus spp.
Alces alces
Cervus spp.
Muntiacus spp.
Bubalis bubalis
Bubalis depressicornis
Syncerus caffer
Bos spp.
Boselaphus tragocamelus
Tragelaphini
Naemorhaedus crispus
Naemorhaedus spp.
Ovibos moschatus
Capra hircus
Ovis spp.
Oryx spp.
Damaliscus spp.
Gazella spp.
Kobus spp.
Aepyceros melampus
Cephalophus spp.
Supertree from this study Gatesy et al. (2002)
Fig. 7. The full supertree from this study reduced to the cetartiodactyl taxon set of Gatesy et al. (2002) and the Gatesy et al. (2002)
supermatrix tree pruned to contain only cetartiodactyl species.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 455
currently available. However, since the completion of the
major search for source trees in 2001, several much-needed,
nearly complete, molecular trees of the Ziphiidae have been
published (Dalebout et al., 2002, 2003).
(4) In Cetacea, the lack of phylogenetic information
also mirrors the deficiency of data in other aspects of their
biology. This is illustrated by the fact that 56 % of delphinids
and 75% of ziphiids are categorised as data deficient in
the IUCN Red List of threatened species (www.redlist.org).
In the genera Sus and Cervus, the polytomies have more
immediate and serious conservation implications as ap-
proximately 40 % of species in these genera are categorised
as threatened by the Red List.
(5) The polytomy at the tribal level within Bovidae also
highlights this as an area in need of further research. In
contrast to the Suidae, Ziphiidae, Cervidae and Delphinidae,
the loss of resolution stems from a lack of consensus among
studies. However, consensus might be difficult to achieve
if, as the fossil record suggests, there was rapid radiation
around 15 million years ago when all the tribes first ap-
peared. As such, the short branch lengths in this region of
the tree may represent a genuinely difficult phylogenetic
problem that might not be solvable simply by sequencing
additional genes. Instead, a more profitable strategy may
be to identify rare genomic changes (see Rokas & Holland,
2000) that resolve the relationships in question because such
changes are less prone to convergent evolution.
V. ACKNOWLEDGEMENTS
We thank Marcel Cardillo, Rich Grenyer, Andy Purvis, Robin
Beck, Kate Jones and Mike Habib for discussion on methods, and
the University of Virginia’s Information Technology Research
Computing division and Ed Hall in particular for help with run-
ning the phylogenetic analyses. All Perl scripts mentioned in this
paper are freely available at http://www.tierzucht.tum.de:8080/
WWW/Homepages/Bininda-Emonds. Financial support was re-
ceived by NSF (DEB/0129009) to J. L. G. and the BMBF-funded
project ‘Bioinformatics for the Functional Analysis of Mammalian
Genomes’ to O.R. P. B.-E.
VI. REFERENCES
* Publications from which the source trees have been taken.
y
Source trees combined in a mini-supertree to represent the
CHRS SINES dataset.
w
Source trees combined in a mini-supertree to represent the
Milinkovitch et al. (1994) dataset.
l
Source trees combined in a mini-supertree to represent the
Arnason and Gullberg (1994) dataset.
*ADEGOKE, J. A., ARNASON,U.&WIDEGREN, B. (1993). Sequence
organization and evolution, in all extant whalebone whales, of
a DNA satellite with terminal chromosome localization.
Chromosoma 102, 382–388.
*ALI, S., ANSARI, S., EHTESHAM, N. Z., AZFER, M. A., HOMKAR, U.,
GOPAL,R.&HASNAIN, S. E. (1998). Analysis of the evolutionarily
conserved repeat motifs in the genome of the highly endangered
central Indian swamp deer Cervus duvauceli branderi.Gene 223,
361–367.
*ALLARD, M. W., MIYAMOTO, M. M., JARECKI, L., KRAUS,F.&
TENNAT, M. R. (1992). DNA Systematics and evolution of the
Artiodactyl Family Bovidae. Proceedings of the National Academy of
Sciences of the United States of America 89, 3972–3976.
*AMATO, G., EGAN,M.G.&RABINOWITZ, A. (1999 a). A new
species of muntjac, Muntiacus putaoensis (Artiodactyla : Cervidae)
from northern Myanmar. Animal Conservation 2, 1–7.
*AMATO, G., EGAN, M. G., SCHALLER, G. B., BAKER, R. H.,
ROSENBAUM, H. C., ROBICHAUD,W.G.&DESALLE, R. (1999 b).
Rediscovery of Roosevelt’s barking deer (Muntiacus rooseveltorum).
Journal of Mammalogy 80, 639–643.
*ARAI, K., MUNECHIKA, I., ITO, I., KIKKAWA,A.&NAKAMURA, K.,
KANAZAWA,T.&KOSUGIYAMA, M. (1997). Phylogenetic relation-
ship of Caprini estimated by cytochrome b gene sequence
analysis. Animal Science and Technology 68, 148–155.
*
l
ARNASON,U.&GULLBERG, A. (1994). Relationship of baleen
whales established by cytochrome b gene sequence comparison.
Nature 367, 726–728.
*ARNASON, U., GULLBERG,A.&WIDEGREN, B. (1993). Cetacean
mitochondrial DNA control region : sequences of all extant
baleen whales and two sperm whale species. Molecular Biology and
Evolution 10, 960–970.
*
l
ARNASON,U.&GULLBERG, A. (1996). Cytochrome b nucleotide
sequences and the identification of five primary lineages of
extant cetaceans. Molecular Biology and Evolution 13, 407–417.
*ARNASON,U.&JANKE, A. (2002). Mitogenomic analyses of
eutherian relationships. Cytogenetic and Genome research 96, 20–32.
*ARNASON,U.&LEDJE, C. (1993). The use of highly repititive DNA
for resolving Cetaean and Pinniped phylogenies. In Mammal
Phylogeny (eds. F. S. Szalay, M. J. Novacek and M. C. McKenna),
pp. 74–80. Springer Verlag, New York.
*ARNOLD,P.W.&HEINSOHN GEORGE, E. (1996). Phylogenetic
status of the Irrawaddy Dolphin Orcaella brevirostris (Owen in
Gray) : a cladistic analysis. Memoirs of the Queensland Museum 39,
141–204.
*BARNES, L. G. (1985). Evolution, taxonomy and antitropical dis-
tributions of the porpoises. Marine Mammal Science 1, 149–165.
*BARRIEL, V., DARLU,P.&TASSY, P. (1993). Mammalian phylogeny
and conflicts between morphological and molecular data. Annales
des Sciences Naturelles Zoologie et Biologie Animale 14, 157–171.
BAUM, B. R. (1992). Combining trees as a way of combining data
sets for phylogenetic inference, and the desirability of combining
gene trees. Taxon 41, 3–10.
BAUM,B.R.&RAGAN, M. A. (1993). Reply to A. G. Rodrigo’s ‘‘ A
comment on Baum’s method for combining phylogenetic trees ’’.
Taxon 42, 637–640.
*BEINTEMA, J. J. (1980). Primary structures of pancreatic rib-
onucleases from Bovidae; impala, Thomson’s gazelle, niglai and
water buffalo. Biochimica et Biophysica Acta 621, 89–103.
*BEINTEMA, J. J., BREUKELMAN, H. J., DUBOIS,J.Y.F.&WARMELS,
H. W. (2003). Phylogeny of ruminants secretory ribonuclease
gene sequences of pronghorn (Antilocapra americana). Molecular
Phylogenetics and Evolution 26, 18–25.
BININDA-EMONDS, O. R. P. (2003). Novel versus unsupported clades:
assessing the qualitative support for clades in MRP supertrees.
Systematic Biology 52, 839–848.
BININDA-EMONDS, O. R. P. (2004). The evolution of supertrees.
Trends in Ecology & Evolution 19, 315–322.
BININDA-EMONDS, O. R. P., BECK,R.M.D.&PURVIS, A. (in press).
Getting to the roots of matrix representation. Systematic Biology.
456 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
BININDA-EMONDS,O.R.P.&BRYANT, H. N. (1998). Properties of
matrix representation with parsimony analysis. Systematic Biology
47, 497–508.
BININDA-EMONDS, O. R. P., GITTLEMAN,J.L.&PURVIS, A. (1999).
Building large trees by combining phylogenetic information : a
complete phylogeny of the extant Carnivora (Mammalia). Biological
Reviews 74, 143–175.
BININDA-EMONDS, O. R. P., JONES, K. E., PRICE, S. A., CARDILLO,
M., GRENYER,R.&PURVIS, A. (2004). Garbage in, garbage out :
data issues in supertree construction. In Phylogenetic Supertrees :
Combining Information to Reveal the Tree of Life (ed. O. R. P. Bininda-
Emonds), pp. 267–280. Kluwer Academic, Dordrecht.
BININDA-EMONDS,O.R.P.&SANDERSON, M. J. (2001). Assessment
of the accuracy of matrix representation with parsimony analysis
supertree construction. Systematic Biology 50, 565–579.
BININDA-EMONDS, O. R. P., STEEL,M.&GITTLEMAN, J. L. (2002).
The (super)tree of life : procedures, problems and prospects.
Annual Review of Ecology and Systematics 33, 265–289.
*BIRUNGI,J.&ARCTANDER, P. (2001). Molecular systematics
and phylogeny of the Reduncini (Artiodactyla : Bovidae) inferred
from the analysis of mitochondrial cytochrome b gene
sequences. Journal of Mammalian Evolution 8, 125–147.
*BOUVRAIN, G., GERAADS,D.&JEHENNE, Y. (1989). New data
relating to the classification of the Cervidae (Artiodactyla,
Mammalia). Zoologische Anzeiger 223, 82–90.
*BUBENIK, A. B. (1990). Evolution of horns, pronghorns and
antlers. In Horns, Pronghorns, and Antlers (eds. G. A. Bubenik
and A. B. Bubenik), pp. 3–133. Springer-Verlag, New York.
*BUNCH,T.D.&NADLER, C. F. (1980). Giemsa-band patterns of
the tahr and chromosomal evoluton of the tribe Caprini. Journal
of Heredity 71, 110–116.
*BUNTJER, J. B., OTSEN, M., NIJMAN, I. J., KUIPER,M.T.R.&
LENSTRA, J. A. (2002). Phylogeny of bovine species based on
AFLP fingerprinting. Heredity 88, 46–51.
*BURZYNSKA, B., OLECH,W.&TOPCZEWSKI, J. (1999). Phylogeny
and genetic variation of the European bison Bison bonasus based
on mitochondrial DNA D-loop sequences. Acta Theriologica 44,
252–262.
*CAP, H., AULAGNIER,S.&DELEPORTE, P. (2002). The phylogeny
and behaviour of Cervidae (Ruminantia Pecora). Ethology Ecology
& Evolution 14, 199–216.
CARDILLO, M., BININDA-EMONDS, O. R. P., BOAKES,E.&PURVIS,A.
(2004). A species-level phylogenetic supertree of marsupials.
Journal of Zoology 264, 11–31.
*
w
CERCHIO,S.&TUCKER, P. (1998). Influence of alignment
of the mtDNA phylogeny of Cetacea : questionable support
for a mysticeti/physeteroidea clade. Systematic Biology 47,
336–344.
*CHIKUNI, K., MORI, Y., TABATA, T., SAITO, M., MONMA,M.&
KOSUGIYAMA, M. (1995). Molecular phylogeny based on the
kappa-casein and cytochrome b sequences in the mammalian
suborder ruminantia. Journal of Molecular Evolution 41, 859–866.
COLLESS, D. H. (1981). Predictivity and stability in classifi-
cations: some comments on recent studies. Systematic Biology 30,
325–331.
*COMINCINI, S., SIRONI, M., BANDI, C., GIUNTA, C., RUBINI,M.&
FONTANA, F. (1996). RAPD analysis of systematic relationships
among the Cervidae. Heredity 76, 215–221.
CORBERT,G.B.&HILL, J. E. (1980). A World List of Mammalian
Species. Cornell University Press, Ithaca.
*CRONIN, M. A. (1991). Mitochondrial-DNA phylogeny of deer
(Cervidae). Journal of Mammalogy 72, 533–566.
*CRONIN, M. A., STUART, R., PIERSON,B.J.&PATTON, J. C. (1996).
K-casein gene phylogeny of higher ruminants (Pecora,
Artiodactyla). Molecular Phylogenetics and Evolution 6, 295–311.
DALEBOUT, M. L., MEAD, J. G., BAKER, C. S., BAKER,A.N.&VAN-
HELDEN, A. (2002). A new species of beaked whale Mesoplodon
perrini sp. n. (Cetacea : Ziphiidae) discovered through phylogen-
etic analyses of mitochondrial DNA sequences. Marine Mammal
Science 18, 577–608.
DALEBOUT, M. L., ROSS, G. J. B., BAKER, S. C., ANDERSON, R. C.,
BEST, P. B., COCKCROFT, V. G., HINZ, H. L., PEDDEMORS,V.
&P
ITMAN, R. L. (2003). Appearance, distribution, and genetic
distinctiveness of Longman’s beaked whale, Indopacetus pacificus.
Marine Mammal Science 19, 421–461.
DIAMOND, J. (1996). Guns, Germs and Steel. The Fates of Human Societies.
W.W. Norton & Company, New York and London.
*DEMUIZON, C. (1988). Le polyphyletisme des Acrodelphidae,
Odontocetes longirostres du Miocene europeen. Bulletin du
Musaeum national d’histoire naturelle. Section C, Sciences de la terre,
palaeontologie, gaeologi, minaeralogie 10, 31–88.
*DEMUIZON, C. (1990). A new Ziphiidae Cetacea from the early
Miocene of Washington State USA and phylogenetic analysis of
the major groups of Odontocetes. Bulletin du Museum National
d’Histoire Naturelle Section C Sciences de la Terre Paleontologie Geologie
Mineralogie 12, 279–326.
*DOUZERY, E. (1993). Evolutionary relationships among Cetacea
based on the sequence of the mitochondrial 12s rRNA gene :
possible paraphyly of toothed-whales (odontocetes) and long
separate evolution of sperm whales (Physeteridae). Comptes Rendus
De L’Academie des Sciences Serie III. Sciences de la vie (Life Sciences)316,
1511–1518.
*DOUZERY,E.&CATZEFLIS, F. M. (1995). Molecular evolution of
the mitochondrial 12S rRNA in Ungulata (mammalia). Journal
of Molecular Evolution 41, 622–636.
*DOUZERY,E.&RANDI, E. (1997). The mitochondrial control
region of cervidae : evolutionary patterns and phylogenetic
content. Molecular Biology and Evolution 14, 1154–1166.
*DUNG, V., GIAO, P. M., CHINH, N. N., TUOC, D., ARCTANDER,P.
&M
ACKINNON, J. (1993). A new species of living bovid from
Vietnam. Nature 363, 443–445.
*EFFRON, M., BOGART, M. H., KUMAMOTO,A.T.&BENIRSCHKE,
K. (1976). Chromosome studies in the mammalian subfamily
Antilopinae. GENETICA (The Hague)46, 419–444.
*EMERSON,B.C.&TATE, M. L. (1993). Genetic analysis of evol-
utionary relationships among deer (subfamily Cervinae). Journal
of Heredity 84, 266–273.
*ESSOP, M. F., HARLEY,E.H.&BAUMGARTEN, I. (1997). A
molecular phylogeny of some bovidae based on restriction-site
mapping of mitochondrial DNA. Journal of Mammalogy 78,
377–387.
ESTES, R. D. (1974). Social organisation of the African Bovidae.
In The Behaviour of Ungulates and its Relation to Management., Vol. 1
(ed. F. Walther), pp. 166–205. IUCN, University of Calgary,
Alberta, Canada.
*FITCH,W.M.&BEINTEMA, J. J. (1990). Correcting Parsimonious
trees for unseen nucleotide substitutions: the effect of dense
branching as explemified by ribonuclease. Molecular Biology and
Evolution 7, 438–443.
*FONTANA,F.&RUBINI, M. (1990). Chromosomal evolution in
Cevidae. Biosystems 24, 157–174.
*GATESY, J. (1997). More DNA support for a Cetacea/
Hippopotamidae clade : the blood-clotting protein gene gamma-
fibrinogen. Molecular Biology and Evolution 14, 537–543.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 457
GATESY, J., AMATO, G., VRBA, E., SCHALLER,G.&ROB,D.
(1997). A cladistic analysis of mitochondrial ribosomal
DNA from the Bovidae. Molecular Phylogenetics and Evolution 7,
303–319.
GATESY, J., AMATO, G., NORELL, M. A., DESALLE,R.&HAYASHI,C.
(2003). Combined support for wholesale taxic atavism in gavia-
line crocodylians. Systematic Biology 52, 403–422.
GATESY,J.&ARCTANDER, P. (2000 a). Hidden morphological
support for the phylogenetic placement of Pseudoryx nghetinhensis
with bovine bovids : a combined analysis of gross anatomical
evidence and DNA sequences from five genes. Systematic Biology
49, 515–538.
*GATESY,J.&ARCTANDER, P. (2000 b). Molecular evidence for
phylogenetic affinities. In Antelopes, Deer and Relatives (ed. G.
Schaller). Yale university Press, New Haven and London.
GATESY, J., BAKER,R.H.&HAYASHI, C. (2004). Inconsistencies in
arguments for the supertree approach : supermatrices versus
supertrees of Crocodylia. Systematic Biology 53, 324–355.
*GATESY, J., HAYASHI, C., CRONIN,M.A.&ARCTANDER, P. (1996).
Evidence from milk casein genes that cetaceans are close relatives
of hippopotamid artiodactyls. Molecular Biology and Evolution 13,
954–963.
GATESY, J., MATTHEE, C. A., DESALLE,R.&HAYASHI, C. (2002).
Resolution of a supertree/supermatrix paradox. Systematic Biology
51, 652–664.
*GATESY, J., O’GRADY,P.&BAKER, R. H. (1999). Corroboration
among data sets in simultaneous analysis : hidden support for
phylogenetic relationships among higher level artiodactyl taxa.
Cladistics 15, 271–313.
GATESY, J. & O’LEARY, M. A. (2001). Deciphering whale origins
with molecules and fossils. Trends in Ecology and Evolution 16,
562–570.
*GATESY,J.&SPRINGER, M. S. (2004). A critique of matrix rep-
resentation with parsimony supertrees. In Phylogenetic Supertrees :
Combining Information to Reveal the Tree of Life (ed. O. R. P. Bininda-
Emonds), pp. 369–388. Kluwer Academic Publishers,
Dordrecht.
*GEISLER, J. H. (2001). New morphological evidence for the
phylogeny of the Artiodactyla, Cetacea and Mesonychidae.
American Museum Novitates 3344, 1–53.
*GEIST, V. (1974). On the relationship of ecology and behaviour in
the evolution of Ungulates : theoretical considerations. In The
Behaviour of Ungulates and its Relation to Management., Vol. 1 (ed. F.
Walther), pp. 235–246. IUCN, University of Calgary, Alberta,
Canada.
*GENTRY, A. W. (1978). Bovidae. In Evolution of African Mammals
(eds. V. J. Maglioi and H. B. S. Cooke), pp. 540–572. Harvard
University Press, Cambridge, MA.
*GENTRY, A. W. (1992). The subfamilies and tribes of the family
Bovidae. Mammal Review 22, 1–32.
*GEORGIADIS, N. J., KAT,P.W.&OKETCH, H. (1990). Allozyme
divergence within the Bovidae. Evolution 44, 2135–2149.
*GERAADS, D. (1992). Phylogenetic analysis of the tribe Bovini
mammalia Artiodactyla. Zoological Journal of the Linnean Society
104, 193–207.
*GIAO, P. M., TUOC, D., DUNG, V. V., WIKRAMANAYAKE, E. D.,
AMATO, G., ARCTANDER,P.&MACKINNON, J. R. (1998).
Description of Muntiacus truongsonensis, a new species of muntjac
(Artiodactyla : Muntiacidae) from central Vietnam, and impli-
cations for conservation. Animal Conservation 1, 61–68.
GINGERICH, P. D., UL HAQ, M., ZALMOUT, I. S., KHAN,I.H.
&M
ALKANI, M. S. (2001). Origin of whales from early
Artiodactyls; hands and feet of Eocene Protocetidae from
Pakistan. Science 293, 2239–2242.
*GOODMAN, M., CZELUSNIAK,J.&BEEBER, J. E. (1985). Phylogeny
of primates and other Eutherian orders a cladistic analysis using
amino-Acid and nucleotide sequence data. Cladistics 1, 171–185.
GREGORY, W. K. (1910). The orders of mammals. Bulletin of the
American Museum of Natural History 27, 1–524.
GRENYER,R.&PURVIS, A. (2003). A composite species-level
phylogeny of the ‘Insectivora ’ (Mammalia : Order Lipotyphla
Haekel, 1866). Journal of Zoology 260, 245–257.
*GRETARSDOTTIR,S.&ARNASON, U. (1992). Evolution of the
common Cetacean highly repetitive DNA component and the
systematic position of Orcaella-Brevirostris.Journal of Molecular
Evolution 34, 201–208.
*GRETARSDOTTIR,S.&ARNASON, U. (1993). Molecular studies on
two variant repeat types of the common cetacean DNA satellite
of the sperm whale, and the relationship between Physeteridae.
Molecular Biology and Evolution 10, 306–318.
*GROVES, C. P. (1981). Systematic relationships in the Bovini
(Artiodactyla, Bovidae). Zeitschrift fuer Zoologische Systematik
Evolutionforschung 19, 265–278.
GROVES, C. P. (1997). Taxonomy of wild pigs (Sus) of
the Philippines. Zoological Journal of the Linnean Society 120,
163–191.
*GROVES,P.&SHIELDS, G. F. (1996). Phylogenetics of the
Caprinae based on cytochrome b sequence. Molecular Phylogenetics
and Evolution 5, 467–476.
*GROVES,P.&SHIELDS, G. F. (1997). Cytochrome B sequences
suggest convergent evolution of the Asian Takin and Arctic
Muskox. Molecular Phylogenetics and Evolution 8, 363–374.
*GROVES, C. (2000). Phylogenetic relationships within recent
Antilopini (Bovidae). In Antelopes, Deer and Relatives (eds. E. Vrba
and G. B. Schaller), pp. 223–233. Yale University Press,
New Haven.
*GRUBB, P. (1993). Artiodactyla. In Mammal Species of the World (ed.
D. M. Reader), pp. 377–414. Smithsonian Institution Press,
Washington, D.C.
*GUSTAFSON, E. P. (1985). Antlers of Bretzia and Odocoileus
(Mammalia, Cervidae) and the evolution of New World deer.
Transactions of the Nebraska Academy of Sciences 13, 83–92.
*HAMILTON, H., CABALLERO, S., COLLINS,A.G.&BROWNELL,
R. L. J. (2001). Evolution of river dolphins. Proceedings of the Royal
Society of London B 268, 549–558.
*HAMMOND, R. L., MACASERO, W., FLORES, B., MOHAMMED, O. B.,
WACHER,T.&BRUFORD, M. W. (2001). Phylogenetic reanalysis
of the Saudi gazelle and its implications for conservation.
Conservation Biology 15, 1123–1133.
*HARTL, G. B., BURGER, H., WILLING,R.&SUCHENTRUNK,
F. (1990a). On the biochemical systematics of the Caprini
and the Rupicaprini. Biochemical Systematics and Ecology 18,
175–182.
*HARTL, G. B., WILLING,R.&SUCHENTRUNK, F. (1990b). On the
biochemical systematics of selected mammalian taxa empirical
comparison of qualitative and quantitative approaches in the
evaluation of protein electrophoretic data. Zeitschrift fuer
Zoologische Systematik und Evolutionsforschung 28, 191–216.
HARVEY,P.H.&PAGEL, M. D. (1991). The Comparative Method in
Evolutionary Biology. Oxford University Press, Oxford.
*HASEGAWA,M.&ADACHI, J. (1996). Phylogenetic position of
Cetaceans relative to Artiodactyls : reanalysis of mitochondrial
and nuclear sequences. Molecular Biology and Evolution 13,
710–717.
458 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
*
l
HASEGAWA, M., ADACHI,J.&MILINKOVITCH, M. C. (1997). Novel
phylogeny of whales supported by total molecular evidence.
Journal of Molecular Evolution 44, s117–s120.
*HASSANIN,A.&DOUZERY, E. (1999 a). Evolutionary affinities of
the enigmatic saola (Pseudoryx nghetinhensis) in the context of
the molecular phylogeny of Bovidae. Proceedings of the Royal Society
of London B 266, 893–900.
*HASSANIN,A.&DOUZERY, E. (1999b). The tribal radiation of
the family Bovidae (Artiodactyla) and the evolution of the
mitochondrial cytochrome b gene. Molecular Phylogenetics and
Evolution 13, 227–243.
*HASSANIN,A.&DOUZERY, E. (2003). Molecular and Morpho-
logical phylogenics of Ruminantia and the alternative position
of the Moscuidae Systematic Biology 52(2), 206–228.
*HASSANIN, A., PASQUET,E.&VIGNE, J. D. (1998). Molecular
systematics of the subfamily caprinae (Artiodactyla, Bovidae) as
determined from cytochrome b sequences. Journal of Mammalian
Evolution 5, 217–236.
*HASSANIN, A., SEVEAU, A., THOMAS, H., BOCHERENS, H., BILLIOU,
D. & NGUYEN, B. X. (2001). Evidence from DNA that the mys-
terious ‘‘Linh Duong’’ (Pseudonovibos spiralis) is not a new bovid.
Comptes Rendus de l’Academie des Sciences de la vie 324, 71–80.
Position of the Moschidae. Systematic Biology 52, 206–228.
IRWIN,D.M.&ARNASON, U. (1994). Cytochrome b gene of
marine mammals: phylogeny and evolution. Journal of
Mammalian Evolution 2, 37–55.
*JANECEK, L. L., HONEYCUTT, R. L., ADKINS,R.M.&DAVIS,S.K.
(1996). Mitochondrial gene sequences and the molecular
systematics of the artiodactyl subfamily bovinae. Molecular
Phylogenetics and Evolution 6, 107–119.
*JANIS,C.M.&SCOTT, K. M. (1987). The interrelationships of
higher ruminant families with special emphasis on the members
of the Cervoidea. American Museum Novitates 2893, 1–86.
JARMAN, P. J. (1974). The social organisation of antelope in relation
to their ecology. Behaviour 48, 215–267.
JONES, K. E., PURVIS, A., MACLARNON, A., BININDA-EMONDS,
O. R. P. & SIMMONS, N. B. (2002). A phylogenetic supertree
of the bats (Mammalia : Chiroptera). Biological Reviews 77,
223–259.
*KINGDON, J. (1989). East African Mammals : An Atlas of Evolution in
Africa. Chicago University Press, Chicago.
*KLEINEIDAM, R. G., PESOLE, G., BREUKELMAN, H. J., BEINTEMA,
J. J. & KASTELEIN, R. A. (1999). Inclusion of Cetaceans within
the order Artiodactyla based on phylogenetic analysis of
pancreatic ribonucleases genes. Journal of Molecular Evolution 48,
360–368.
KLUGE, A. G. (1989). A concern for evidence and a phylogenetic
hypothesis of relationships among Epicrates (Boidae, Serpentes).
Systematic Zoology 38, 7–25.
*KRAUS,F.&MIYAMOTO, M. M. (1991). Rapid Cladogenesis
among the Pecoran ruminants evidence from mitochondrial
DNA sequences. Systematic Zoology 40, 117–130.
*KUWAYAMA,R.&OZAWA, T. (2000). Phylogenetic relationships
among European red deer, wapiti, and sika deer inferred
from mitochondrial DNA sequences. Molecular Phylogenetics and
Evolution 15, 115–123.
*KUZNETSOV, G. V., KULIKOV, E. E., PETROV, N. B., IVANOVA,
N. V., LOMOV, A. A., KHOLODOVA,M.V.&POLTARAUS,A.B.
(2002). Mitochondrial 12S rDNA sequence relationships suggest
that the enigmatic bovid ‘‘Linh Duong ’’ Pseudonovibos spiralis is
closely related to buffalo. Molecular Phylogenetics and Evolution 23,
91–94.
*KUZNETSOVA, M. V., KHOLODOVA,M.V.&LUSCHEKINA,A.A.
(2002). Phylogenetic analysis of sequences of the 12S and 16S
rRNA mitochondrial genes in the family Bovidae : new evidence.
Russian Journal of Genetics 38, 942–950.
LALUEZA-FOX, C., SHAPIRO, B., BOVER, P., ALCOVER,J.A.&
BERTRANPETIT, J. (2002). Molecular phylogeny and evolution of
the extinct bovid Myotragus balearicus.Molecular Phylogenetics and
Evolution 25, 501–510.
*LAN, H., WANG,W.&SHI, L. (1995). Phylogeny of Muntiacus
(Cervidae) based on mitochondrial DNA restriction maps.
Biochemical Genetics 33, 377–388.
*LANGER, P. (2001). Evidence from the digestive tract on phylo-
genetic relationships in ungulates and whales. Journal of Zoology,
Systematics, Evolution and Research 39, 77–90.
LEE, S.-M. & ROBINEAU, D. (2004). The cetaceans of the Neolithic
rock carvings of Bangu-dae (South Korea) and the beginning of
whaling in the North-West Pacific. L’Anthropologie 108, 137–151.
LEINDERS, J.J.M. & HEINTZ, E. (1980). The configuration of the
lacrimal orifices in pecorans and tragulids (Artiodactyla,
Mammalia) and its significance for the distinction between
Bovidae and Cervidae. Beaufortia 30, 155–162.
*LEDUC, R. G., PERRIN,W.F.&DIZON, A. E. (1999). Phylogenetic
relationships among the delphinid cetaceans based on full
cytochrome b sequences. Marine Mammal Science 15, 619–648.
*LI, M., SHENG, H., TAMATE, H., MASUNDA, R., NAGATA,J.&
OHTAISHI, N. (1998). MtDNA difference and molecular phylo-
geny among musk deer, chinese water deer and muntjak deer.
Acta theriologica Sinica 18, 184–191.
*LOWENSTEIN, J. M. (1986). Molecular phylogenetics. Annual Reviews
of Earth and Planetary Science 14, 71–83.
*LUDWIG,A.&FISCHER, S. (1998). New aspects of an old dis-
cussion-phylogenetic relationships of Ammotragus and Pseudois
within the subfamily Caprinae based on comparison of the 12S
rDNA sequences. Journal of Zoological Systematics and Evolutionary
Research 36, 173–178.
*MA,S.&WANG, Y.-X. (1986). Taxonomic and phylogenetic
studies on the genus Muntiacus.Acta theriologica Sinica 6, 191–209.
MADDISON,D.R.&MADDISON, W. P. (2003). MacClade. Sinauer
Associates, Sunderland, Massachusetts.
MADDISON, W. P. (1997). Gene trees in species trees. Systematic
Biology 46, 523–536.
*MADSEN, O., SCALLY, M., DOUADY, C., KAO, D. J., DEBRY, R. W.,
ADKINS, R. M., AMRINE, H. M., STANHOPE, M. J., DE JONG,
W. W. & SPRINGER, M. S. (2001). Parallel adaptive radi-
ations in two major clades of placental mammals. Nature 409,
610–614.
*MADSEN, O., WILLEMSEN, D., URSING, B. M., ARNASON,U.&DE
JONG, W. W. (2002). Molecular evolution of the mammalian
alpha 2B adrenergic receptor. Molecular Biology and Evolution 19,
2150–2160.
MAHON, A. (2004). A molecular supertree of the Artiodactyla.
In Phylogenetic Supertrees : Combining Information to Reveal the Tree of
Life. (ed. O. R. P. Bininda-Emonds), pp. 411–437. Chapter 19.
Kluwer Academic Publishers, Dordrecht.
*MANCEAU, V., DESPRES, L., BOUVET,J.&TABERLET, P. (1999).
Systematics of the genus Capra inferred from mitochondrial
DNA sequence data. Molecular Phylogenetics and Evolution 13,
504–510.
*MATTAPALLIL,M.J.&ALI, S. (1999). Analysis of conserved
microsatellite sequences suggests closer relationship between
water buffalo Bubalus bubalis and sheep Ovis aries. DNA and
Cell Biology 18, 513–519.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 459
MATTHEE, C. A., BURZLAFF, J. D., TAYLOR,J.F.&DAVIS,S.K.
(2001). Mining the mammalian genome for artiodactyl sys-
tematics. Systematic biology 50, 367–390.
*MEAD,J.G.&BROWNELL, R. L. (1993). Cetacea. In Mammal
Species of the World (ed. D. M. Reader), pp. 349–364. Smithsonian
Institution Press, Washington, D.C.
*MESSENGER,S.L.&MCGUIRE, J. A. (1998). Morphology, mol-
ecules, and the phylogenetic of cetaceans. Systematic Biology 47,
90–124.
*
l
MILINKOVITCH, M. C., LEDUC, R. G., ADACHI, J., FARNIR, F.,
GEORGES,M.&HASEGAWA, M. (1996). Effects of character
weighting and species sampling on phylogeny reconstruction : a
case study based on DNA sequence data in cetaceans. Genetics
144, 1817–1833.
*
w
MILINKOVITCH, M. C., MEYER,A.&POWELL, J. R. (1994).
Phylogeny of all major groups of cetaceans based on DNA
sequences from three mitochondrial genes. Molecular Biology and
Evolution 11, 939–948.
*MILINKOVITCH, M. C., ORTI,G.&MEYER, A. (1993). Revised
phylogeny of whales suggested by mitochondrial ribosomal
DNA sequences. Nature 361, 346–348.
*MING,L.&MING, W. X. (1999). Mitochondrial DNA divergence
and phylogeny of four species of deer of the genus Cervus. Acta
Zoologica Sinica 45, 99–105.
*MIYAMOTO, M. M., TANHAUSER,S.M.&LAIPIS, P. J. (1989).
Systematic relationships in the artiodactyla tribe Bovini (family
Bovidae), as determined from mitochondrial DNA sequences.
Systematic Zoology 38, 342–349.
*MONTGELARD, C., CATZEFLIS,F.M.&DOUZERY, E. (1997).
Phylogenic relationships of artiodactyls and cetaceans as
deduced from the comparison of cytochrome b and 12S rRNA
mitochondrial sequences. Molecular Biology and Evolution 14,
550–559.
*MOORE, J. C. (1968). The relationships among the living gener-
ation of beaked whales with classifications, diagnoses and keys.
Fieldiana, Zoology 53, 209–298.
*NIKAIDO, M., MATSUNO, F., HAMILTON, H., BROWNELL,R.L.JR.,
CAO, Y., DING, W., ZUOYAN, Z., SHEDLOCK, A. M., FORDYCE,
R. E., HASEGAWA,M.&OKADA, N. (2001). Retroposon analysis
of major cetacean lineages: the monophyly of toothed
whales and the paraphyly of river dolphins. Proceedings of the
National Academy of Sciences of the United States of America 98,
7384–7389.
*
y
NIKAIDO, M., ROONEY,A.P.&OKADA, N. (1999). Phylogenetic
relationships among cetartiodactyls based on insertions of short
and long interspersed elements : Hippopotamuses are the closest
extant relatives of whales. Proceedings of the National Academy of
Sciences, USA 96, 10261–10266.
NIXON, K. C. (1999). The parsimony ratchet, a new method for
rapid parsimonu analysis. Cladistics 15, 407–414.
*OHLAND, D. P., HARLEY,E.H.&BEST, P. B. (1995). Systematics
of cetaceans using restriction site mapping of mitochondrial
DNA. Molecular Phylogenetics and Evolution 4, 10–19.
*O’LEARY, M. A. (1999). Parsimony analysis of total evidence from
extinction and extant taxa and the cetacean-artiodactyl question
(Mammalia, Ungulata). Cladistics 15, 315–330.
*O’LEARY, M. A. (2001). The phylogenetic position of cetaceans :
further combined data analyses, comparisons with the strati-
graphic record and a discussion of character optimization.
American Zoologist 41, 487–506.
*PASITSCHNIAK-ARTS, M., FLOODS, P. F., SCHMUTZ,M.&SEIDEL,B.
(1994). A comparison of G-band patterns of the muskox and
takin and their evolutionary relationship to sheep. Journal of
Heredity 85, 143–147.
*PEREZ-BARBERIA,J.F.&GORDON, I. J. (1999). The functional re-
lationship between feeding type and jaw and cranial morphology
in ungulates. Oecologia 118, 157–165.
*PICHLER, F. B., ROBINEAU, D., GOODALL, R. N. P., MEYER, M. A.,
OLIVARRIA,C.&BAKKER, C. S. (2001). Origin and radiation of
southern hemisphere coastal dolphins (genus Cephalorhynchus).
Molecular Ecology 10, 2215–2223.
*PITRA, C., FURBASS,R.&SEYFERT, H. M. (1997). Molecular
phylogeny of the tribe Bovini (Mammalia : Artiodactyla) :
alternative placement of the Anoa. Journal of Evolutionary Biology
10(4), 598–600.
*PITRA, C., KOCK, R. A., HOFMANN,R.R.&LIECKFELDT,D.
(1998). Molecular phylogeny of the critically endangered
Hunter’s antelope (Beatragus hunteri Sclater 1889). Journal of
Zoological Systematics and Evolutionary Research 36, 179–184.
*POLZIEHN,R.O.&STROBECK, C. (2002). A phylogenetic com-
parison of red deer and wapiti using mitochondrial DNA.
Molecular Phylogenetics and Evolution 22, 342–356.
PURVIS, A. (1995). A composite estimate of primate phylogeny.
Proceedings of the Royal Society of London B 248, 405–421.
PURVIS, A., GITTLEMAN, J. L., COWLISHAW,G.&MACE,G.M.
(2000). Predicting extinction risk in declining species. Proceedings
of the Royal Society of London B 267, 1947–1952.
*QUERALT, R., ADROER, R., OLIVA, R., WINKFEIN, R. J., RETIEF,
J. D. & DIXON, G. H. (1995). Evolution of protamine P1 genes in
mammals. Journal of Molecular Evolution 40, 601–607.
QUICKE, D. L., TAYLOR,J.&PURVIS, A. (2001). Changing the
landscape : a new strategy for estimating large phylogenies.
Systematic Biology 50, 60–66.
RAGAN, M. A. (1992). Phylogenetic inference based on matrix
representation of trees. Molecular Phylogenetics and Evolution 1,
53–58.
*RANDI, E., D’HUART, J. P., LUCCHINI,V.&AMAN, R. (2002).
Evidence of two genetically deeply divergent species of warthog,
Phacochoerus africanus and P-aethiopicus (Artiodactyla :
Suiformes) in East Africa. Mammalian Biology 67, 91–96.
*RANDI, E., FUSCO, G., LORENZINI, R., TOSO,S.&TOSI, G. (1991).
Allozyme divergence and phylogenetic relationships among
Capra Ovis and Rupicapra Artiodactyla Bovidae. Heredity 67,
281–286.
*RANDI, E., LUCCHINI,V.&DIONG, C. H. (1996). Evolutionary
genetics of the Suiformes as reconstructed using mtDNA
sequencing. Journal of Mammalian Evolution 3, 163–195.
*RANDI, E., MUCCI, N., PIERPAOLI,M.&DOUZERY, E. (1998). New
phylogenetic perspectives on the Cervidae (Artiodactyla) are pro-
vided by the mitochondrial cytochrome b gene. Proceedings of the
Royal Society of London B 265, 793–801.
*RAUTIAN, G. S., AGADJANIAN,A.K.&MIRONENKO, I. V. (2000).
Morphological and genetic differentiation within bulls and buf-
faloes. Paleonotologicheskii Zhurnal 5, 95–104.
*REBHOLZ,W.&HARLEY, E. (1999). Phylogenetic relationships
in the Bovid subfamily Antilopinae based on mitochon-
drial DNA sequences. Molecular Phylogenetics and Evolution 12,
87–94.
*RITZ, L. R., GLOWATZKI-MULLIS, M. L., MACHUGH,D.E.&
GAILLARD, C. (2000). Phylogenetic analysis of the tribe Bovini
using microsatellites. Animal Genetics 31, 178–185.
ROBINSON,D.F.&FOULDS, L. R. (1979). Comparison of
weighted labelled trees. In Lecture Notes in Mathematics, Vol. 748,
pp. 119–126. Springer-Verlag, Berlin.
460 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
ROBINSON,D.F.&FOULDS, L. R. (1981). Comparison of phylo-
genetic trees. Mathematical Biosciences 53, 131–147.
ROKAS,A.&HOLLAND, P. W. H. (2000). Rare genomic changes as a
tool for phylogenetics. Trends in Ecology & Evolution 15, 454–459.
*ROSEL, P. E., HAYGOOD,M.G.&PERRIN, W. F. (1995).
Phylogenetic relationships among the true porpoises (Cetacea :
Phocoenidae). Molecular Phylogenetics and Evolution 4, 463–474.
ROSE, K. R. (1996). On the origin of the order Artiodactyla.
Proceedings of the National Academy of Science 93, 1705–1709.
*SCHREIBER, A., ERKER,D.&BAUER, K. (1990). Artiodactylan
phylogeny an immunogenetic study based on comparative
determinant analysis. Experimental and Clinical Immunogenetics 7,
234–243.
*SCHREIBER, A., SEIBOLD, I., NOETZOLD,G.&WINK, M. (1999).
Cytochrome b gene haplotypes characterized chromosomal
lineages of anoa, the Sulawesi dwarf buffalo (Bovidae : Bubalus
sp.). Journal of Heredity 90, 165–176.
*SCOTT,K.M.&JANIS, C. M. (1993). Relationships of the
Ruminantia (Artiodactyla) and an analysis of the characters used
in Ruminant taxonomy. In Mammal Phylogeny (eds. F. S. Szalay,
M. J. Novacek and M. C. McKenna), pp. 282–302. Springer
Verlag, New York.
SHAFRON, W., MARTIN,P.&ASHTON, D. (2002). Profile of
Australian wool producers 1997–1998 to 2000–2001. Report on
the Australian Agriculture and Grazing Industries Survey of
Wool Producers. In 46th Annual Conference of Australian Agriculture
and Resource Economic Society. Australian Bureau of Agricultural
and Resource Economics, Canberra.
*SHIMURA,E.&NUMACHI, K. I. (1987). Genetic variability and
differentiation in the toothed whales. Scientific Reports of the Whales
Research Institute Tokyo 38, 141–163.
*
y
SHIMAMURA, M., YASUE, H., OHSHIMA, K., ABE, H., KATO, H.,
KISHIRO, T., GOTO, M., MUNECHIKA,I.&OKADA, N. (1997).
Molecular evidence from retroposons that whales form a clade
within even-toed ungulates. Nature 388, 666–670.
*SMITH, M. H., BRANAN, W. V., MARCHINTON, R. L., JOHNS,E.&
WOOTON, M. C. (1986). Genetic and morphologic comparisons
of red brocket, brown brocket, and white-tailed deer. Journal of
Mammalogy 97, 103–111.
*SPOTORNO, A. E., BRUM,N.&DITOMASO, M. (1987). Compara-
tive cytogenetics of South American deer. Fieldiana 39, 473–484.
*SPRINGER, M. S., BURK, A., KAVANAGH, J. R., WADDELL,V.J.&
STANHOPE, M. J. (1997). The interphotoreceptor retinoid bind-
ing protein gene in therian mammals : implications for higher
level relationships and evidence for loss of function in the
marsupial mole. Proceedings of the National Academy of Science USA
94, 13754–13759.
SPRINGER,M.S.&DE JONG, W. W. (2001). Which mammalian
supertree to bark up ? Science 291, 1709–1711.
*STANLEY, H. F., KADWELL,M.&WHEELER, J. C. (1994). Molecular
evolution of the family Camelidae : a mitochondrial DNA study.
Proceedings of the Royal Society of London B 256, 1–6.
STONER, C. J., BININDA-EMONDS,O.R.P.&CARO, T. (2003). The
adaptive significance of coloration in lagomorphs. Biological
Journal of Linnean Society 79, 309–328.
*SU, B., WANG, Y.-X., HONG, L., WANG,W.&YAPING, Z. (1999).
Phylogenetic study of complete cytochrome b genes in musk deer
(genus Moschus) using museum samples. Molecular Phylogenetics and
Evolution 12, 241–249.
SWOFFORD, D. L. (2003). PAUP*. Phylogenetic Analysis Using Parsi-
mony (*and Other Methods). Sinauer Associates, Sunderland,
Massachusetts.
*TANAKA, K., SOLIS, C. D., MASANGKAY, J. S., MAEDA, K. I.,
KAWAMOTO,Y.&NAMIKAWA, T. (1996). Phylogenetic relation-
ship among all living species of the genus Bubalus based on DNA
sequences of the cytochrome b gene. Biochemical Genetics 34,
443–452.
*THEIMER,T.C.&KEIM, P. (1998). Phylogenetic relationships
of peccaries based on mitochondrial cytochrome b DNA
sequences. Journal of Mammalogy 79, 566–572.
*THEWISSEN, J. G. M., WILLIAMS, E. M., ROE,L.J.&HUSSAIN,
S. T. (2001). Skeletons of terrestrial cetaceans and the relation-
ship of whales to artiodactyls. Nature 413, 277–281.
USDA (1997). Meat animals production, disposition, and income.
Final estimates 1993–1997. In USDA. Statistical Bulletin Number
959a., pp. 1–73. National Agricultural Statistics Service. United
States Department of Agriculture.
*VAN DEN BUSSCHE, R. A., HOOFER,S.R.&HANSEN, E. W. (2002).
Characterization and phylogenetic utility of the mammalian
protamine PI gene. Molecular Phylogenetics and Evolution 22,
333–341.
VAN VALEN, L. (1966). The Deltatheridia, a new order of
mammals. Bulletin of the American Museum of Natural History 132,
1–126.
VAN VALEN, L. (1968). Monophyly or diphyly in the origin of
whales. Evolution 22, 37–41.
VAN VALEN, L. (1971). Toward the origin of Artiodactyls. Evolution
25, 523–529.
*VAN VUUREN,B.J.&ROBINSON, T. J. (2001). Retrieval of four
adaptive lineages in duiker antelope : evidence from mitochon-
drial DNA sequences and fluorescence in situ hybridization.
Molecular Phylogenetics and Evolution 20, 409–425.
*VRBA, E. (1979). Phylogenetic analysis and classification of fossil
and recent Alcelaphini (Family Bovidae, Mammalia). Biological
Journal of Linnean Society 11, 207–228.
*WADDELL, V., MILINKOVITCH, M. C., BERUBE,M.&STANHOPE,
M. J. (2000). Molecular phylogenetic examination of the
Delphinoidea trichotomy : congruent evidence from three nu-
clear loci indicates that porpoises (Phocoenidae) share a more
recent common ancestry with white whales (Monodontidae)
than they do with true dolphins (Delphinidae). Molecular
Phylogenetics and Evolution 15, 314–318.
*WALL, D. A., DAVIS,S.K.&READ, B. M. (1992). Phylo-
genetic relationships in the subfamily Bovinae Mammalia
Artiodactyla based on ribosomal DNA. Journal of Mammalogy 73,
262–275.
*WANG,W.&LAN, H. (2000). Rapid and parallel chromosomal
number reductions in Muntjac deer inferred from mitochon-
drial DNA phylogeny. Molecular Biology and Evolution 17,
1326–1333.
*WEBB,S.D.&TAYLOR, B. E. (1980). The phylogeny of horn-
less ruminants and a description of the Cranium of Archaeo-
meryx. Bulletin of the American Museum of Natural History 167,
117–158.
WILKINSON, M. (1995). Coping with abundant missing entries in
phylogenetic inference using parsimony. Systematic Biology 44,
501–514.
WILSON,D.E.&REEDER, D. M. (1993). Mammal Species of the World :
A Taxonomic and Geographic Reference. Smithsonian Institution
Press, Washington, D.C.
YABLOKOV, A. V. (1964). Convergence or parallelism in the evol-
ution of cetaceans. Paleonotologicheskii Zhurnal 1, 97–106.
*YANG,G.&ZHOU, K. (1999). A study on the molecular phylogeny
of river dolphins. Acta Theriologica Sinica 19, 1–9.
Phylogeny of the whales, dolphins and even-toed hoofed mammals 461
VII. APPENDIX
Full QS index (QS) and reduced QS (rQS) index for full cetartiodactyl supertree. Nodes are numbered from the base of the
tree along the left-hand backbone of the tree until the first tip is reached then each clade is coded in the same way always
starting at the most basal clade and going to the left first.
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
1 284 softConflict x0.527 0 24 7 3 167
2 265 softConflict x0.527 0 26 13 1 161
3 185 softConflict x0.413 0 7 42 0 152
4 181 softConflict x0.413 0 7 42 0 152
5 178 softConflict x0.458 0 25 42 0 134
6 132 softConflict x0.368 0 15 68 0 118
7 109 softConflict x0.289 0 17 102 0 82
8 46 softConflict x0.249 0 14 115 0 72
9 13 softConflict x0.112 0 6 162 0 33
10 6 softConflict x0.07 0 1 174 0 26
11 4 equivocal x0.04 0 0 185 0 16
12 3 softSupport x0.032 0 0 184 2 15
13 2 softConflict x0.015 0 1 180 8 12
14 7 equivocal x0.09 0 0 165 0 36
15 2 softConflict x0.035 0 3 182 4 12
16 2 softSupport x0.027 0 0 180 5 16
17 3 softConflict x0.087 0 4 168 1 28
18 2 softSupport x0.06 0 0 167 5 29
19 33 softConflict x0.201 0 7 127 0 67
20 32 softConflict x0.204 0 9 128 0 64
21 24 softConflict x0.229 0 19 128 0 54
22 21 softConflict x0.224 0 18 129 0 54
23 7 softConflict x0.167 0 2 136 0 63
24 6 softConflict x0.157 0 1 137 1 62
25 3 softConflict x0.137 0 1 143 2 55
26 2 softConflict x0.127 0 1 143 4 53
27 3 softSupport x0.03 0 0 187 1 13
28 2 softSupport x0.022 0 0 188 2 11
29 14 softConflict x0.124 0 3 154 0 44
30 12 softConflict x0.127 0 3 153 0 45
31 3 softSupport x0.015 0 0 193 1 7
32 2 softSupport x0.012 0 0 192 2 7
33 2 softSupport x0.015 0 0 189 3 9
34 8 softConflict x0.082 0 5 173 0 23
35 7 softConflict x0.07 0 2 175 0 24
36 18 softConflict x0.122 0 4 156 0 41
37 17 softConflict x0.117 0 4 158 0 39
38 14 softConflict x0.109 0 4 161 0 36
39 13 softConflict x0.102 0 4 162 1 34
40 8 softConflict x0.037 0 1 185 1 14
41 5 softConflict x0.022 0 2 192 1 6
42 2 softConflict 0 0 1 194 4 2
43 3 softSupport x0.01 0 0 193 2 6
44 2 softSupport 0.005 0 0 195 4 2
45 3 softSupport x0.015 0 0 187 4 10
46 2 softSupport 0.002 0 0 188 7 6
47 3 softSupport x0.05 0 0 177 2 22
48 2 softSupport x0.007 0 0 188 5 8
49 2 softSupport x0.02 0 0 183 5 13
50 19 equivocal x0.067 0 0 174 0 27
51 17 softConflict x0.062 0 2 178 0 21
52 15 softConflict x0.04 0 1 184 1 15
53 3 softConflict x0.002 0 1 197 2 1
54 4 softSupport x0.025 0 0 189 1 11
462 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Appendix (cont.)
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
55 3 softSupport x0.02 0 0 189 2 10
56 2 softSupport 0.007 0 0 194 5 2
57 4 softSupport x0.01 0 0 195 1 5
58 2 softSupport x0.002 0 0 192 4 5
59 2 softSupport 0.01 0 0 197 4 0
60 2 softSupport x0.025 0 0 181 5 15
61 4 equivocal x0.03 0 0 189 0 12
62 3 softSupport x0.012 0 0 192 2 7
63 2 softConflict x0.01 0 2 189 5 5
64 9 softConflict x0.067 0 1 175 0 25
65 8 softConflict x0.065 0 2 177 0 22
66 5 softConflict x0.045 0 2 183 1 15
67 3 softConflict x0.047 0 3 183 1 14
68 2 softSupport x0.012 0 0 188 4 9
69 2 softSupport 0.002 0 0 194 4 3
70 3 softConflict x0.04 0 2 185 1 13
71 2 softConflict x0.007 0 1 189 5 6
72 3 softSupport x0.012 0 0 194 1 6
73 23 softConflict x0.256 0 7 105 0 89
74 12 softConflict x0.244 0 7 110 0 84
75 7 softConflict x0.221 0 3 115 0 83
76 5 softConflict x0.244 0 12 115 0 74
77 3 softConflict x0.097 0 8 170 0 23
78 2 softConflict x0.052 0 3 169 7 22
79 2 softSupport x0.197 0 0 114 4 83
80 2 softConflict x0.032 0 4 178 7 12
81 5 softConflict x0.114 0 3 158 0 40
82 4 softConflict x0.095 0 2 165 0 34
83 11 softConflict x0.124 0 11 162 0 28
84 2 softConflict x0.027 0 1 169 11 20
85 9 equivocal x0.082 0 0 168 0 33
86 3 softConflict x0.075 0 5 176 0 20
87 2 softSupport x0.052 0 0 176 2 23
88 3 softConflict x0.02 0 2 187 4 8
89 2 softConflict 0.005 0 1 190 7 3
90 46 softConflict x0.236 0 9 115 0 77
91 42 softConflict x0.234 0 9 116 0 76
92 19 softConflict x0.192 0 12 136 0 53
93 4 softConflict x0.137 0 9 155 0 37
94 3 softConflict x0.075 0 5 176 0 20
95 2 softConflict x0.025 0 1 182 5 13
96 15 softConflict x0.124 0 7 158 0 36
97 14 softConflict x0.109 0 3 160 0 38
98 3 softConflict x0.02 0 2 195 0 4
99 2 softSupport x0.01 0 0 195 1 5
100 6 softConflict x0.032 0 1 187 1 12
101 2 softConflict x0.07 0 1 160 7 33
102 2 softSupport x0.005 0 0 197 1 3
103 23 softConflict x0.189 0 7 132 0 62
104 16 softConflict x0.164 0 5 140 0 56
105 4 softSupport x0.017 0 0 192 1 8
106 12 softConflict x0.157 0 6 144 0 51
107 10 softConflict x0.147 0 3 145 0 53
108 2 softSupport x0.03 0 0 185 2 14
109 7 softConflict x0.06 0 1 178 0 22
110 6 softSupport x0.052 0 0 178 1 22
111 4 softSupport x0.015 0 0 193 1 7
112 3 softSupport 0.002 0 0 200 1 0
113 2 softSupport 0.005 0 0 199 2 0
114 3 softConflict x0.144 0 11 154 0 36
Phylogeny of the whales, dolphins and even-toed hoofed mammals 463
Appendix (cont.)
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
115 2 softSupport x0.085 0 0 159 4 38
116 4 equivocal x0.085 0 0 167 0 34
117 2 softSupport x0.025 0 0 165 13 23
118 80 softConflict x0.209 0 13 128 1 59
119 78 softConflict x0.179 0 2 131 0 68
120 67 softConflict x0.204 0 16 135 0 50
121 64 softConflict x0.182 0 10 138 0 53
122 62 softConflict x0.189 0 13 138 0 50
123 43 softConflict x0.164 0 4 139 0 58
124 40 softConflict x0.159 0 2 139 0 60
125 38 softConflict x0.152 0 7 147 0 47
126 6 softConflict x0.07 0 1 174 0 26
127 2 softSupport x0.002 0 0 192 4 5
128 32 softConflict x0.124 0 2 153 0 46
129 10 softConflict x0.057 0 3 181 0 17
130 8 softConflict x0.05 0 2 183 0 16
131 4 softConflict x0.022 0 1 191 1 8
132 3 softConflict x0.015 0 1 194 1 5
133 2 softSupport x0.007 0 0 194 2 5
134 4 softSupport x0.032 0 0 186 1 14
135 2 softSupport x0.027 0 0 184 3 14
136 2 softSupport x0.007 0 0 192 3 6
137 6 softConflict x0.087 0 2 168 0 31
138 2 softSupport x0.01 0 0 193 2 6
139 5 softConflict x0.06 0 2 179 0 20
140 4 softConflict x0.057 0 1 179 0 21
141 2 softConflict x0.007 0 1 193 3 4
142 2 softSupport x0.04 0 0 179 3 19
143 2 softSupport x0.017 0 0 192 1 8
144 2 softConflict x0.015 0 1 172 12 16
145 3 softConflict x0.047 0 7 187 1 6
146 2 softConflict x0.007 0 5 185 9 2
147 19 equivocal x0.067 0 0 174 0 27
148 2 softSupport x0.01 0 0 191 3 7
149 3 softConflict x0.075 0 1 172 0 28
150 2 softSupport x0.007 0 0 186 6 9
151 11 softConflict x0.134 0 2 149 0 50
152 4 softConflict x0.045 0 4 187 0 10
153 3 equivocal x0.022 0 0 192 0 9
154 2 softSupport x0.015 0 0 193 1 7
155 7 softConflict x0.112 0 1 157 0 43
156 6 softConflict x0.102 0 5 165 0 31
157 2 softSupport 0.02 0 0 191 9 1
158 3 softConflict x0.097 0 4 164 1 32
159 2 softSupport x0.042 0 0 164 10 27
160 19 softConflict x0.119 0 1 154 0 46
161 16 softConflict x0.119 0 1 154 0 46
162 15 equivocal x0.117 0 0 154 0 47
163 13 equivocal x0.117 0 0 154 0 47
164 2 softSupport x0.002 0 0 198 1 2
165 10 softSupport x0.114 0 0 153 1 47
166 2 softSupport x0.007 0 0 192 3 6
167 3 softConflict x0.017 0 1 193 1 6
168 2 softSupport 0.005 0 0 195 4 2
169 6 equivocal x0.09 0 0 165 0 36
170 2 softSupport x0.05 0 0 167 7 27
171 4 equivocal x0.04 0 0 185 0 16
172 2 softConflict x0.025 0 1 182 5 13
173 2 softConflict x0.01 0 2 191 4 4
464 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Node
Clade
size
Mean rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
1 284 x0.005 23 24 154
2 265 0.045 35 26 140
3 185 0.199 47 7 147
4 181 0.229 53 7 141
5 178 0.055 36 25 140
6 132 0.09 33 15 153
7 109 0.055 28 17 156
8 46 0.085 31 14 156
9 13 0.065 19 6 176
10 6 0.055 12 1 188
11 4 0.035 7 0 194
12 3 0.04 8 0 193
13 2 0.04 9 1 191
14 7 0.075 15 0 186
15 2 0 3 3 195
16 2 0.025 5 0 196
17 3 0.01 6 4 191
18 2 0.02 4 0 197
19 33 0.129 33 7 161
20 32 0.109 31 9 161
21 24 0.01 21 19 161
22 21 0.01 20 18 163
23 7 0.06 14 2 185
24 6 0.045 10 1 190
25 3 0.01 3 1 197
26 2 0.005 2 1 198
27 3 0.02 4 0 197
28 2 0.005 1 0 200
29 14 0.045 12 3 186
30 12 0.045 12 3 186
31 3 0.005 1 0 200
32 2 0.01 2 0 199
33 2 0.015 3 0 198
34 8 0.01 7 5 189
35 7 0.03 8 2 191
36 18 0.06 16 4 181
37 17 0.035 11 4 186
38 14 0.005 5 4 192
39 13 0.01 6 4 191
40 8 0.02 5 1 195
41 5 0.005 3 2 196
42 2 0.01 3 1 197
43 3 0.015 3 0 198
44 2 0.01 2 0 199
45 3 0.01 2 0 199
46 2 0.01 2 0 199
47 3 0.025 5 0 196
48 2 0.015 3 0 198
49 2 0.02 4 0 197
50 19 0.075 15 0 186
51 17 0.01 4 2 195
52 15 0.01 3 1 197
53 3 0.005 2 1 198
54 4 0.02 4 0 197
55 3 0.02 4 0 197
56 2 0.015 3 0 198
57 4 0.015 3 0 198
58 2 0.01 2 0 199
59 2 0.015 3 0 198
60 2 0.02 4 0 197
61 4 0.045 9 0 192
Phylogeny of the whales, dolphins and even-toed hoofed mammals 465
Appendix (cont.)
Node
Clade
size
Mean rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
62 3 0.045 9 0 192
63 2 0.005 3 2 196
64 9 0.065 14 1 186
65 8 0.05 12 2 187
66 5 0.04 10 2 189
67 3 0.025 8 3 190
68 2 0.015 3 0 198
69 2 0.015 3 0 198
70 3 0.04 10 2 189
71 2 0.015 4 1 196
72 3 0.01 2 0 199
73 23 0.159 39 7 155
74 12 0.119 31 7 163
75 7 0.144 32 3 166
76 5 0.03 18 12 171
77 3 0.015 11 8 182
78 2 0.015 6 3 192
79 2 0.005 1 0 200
80 2 0 4 4 193
81 5 0.1 23 3 175
82 4 0.075 17 2 182
83 11 0.005 12 11 178
84 2 0.045 10 1 190
85 9 0.1 20 0 181
86 3 0 5 5 191
87 2 0.01 2 0 199
88 3 0.01 4 2 195
89 2 0.01 3 1 197
90 46 0.109 31 9 161
91 42 0.114 32 9 160
92 19 x0.01 10 12 179
93 4 x0.03 3 9 189
94 3 x0.01 3 5 193
95 2 0.02 5 1 195
96 15 0.01 9 7 185
97 14 0.035 10 3 188
98 3 x0.005 1 2 198
99 2 0.005 1 0 200
100 6 0.005 2 1 198
101 2 0.03 7 1 193
102 2 0.005 1 0 200
103 23 0.055 18 7 176
104 16 0.055 16 5 180
105 4 0.005 1 0 200
106 12 0.035 13 6 182
107 10 0.055 14 3 184
108 2 0.01 2 0 199
109 7 0.02 5 1 195
110 6 0.04 8 0 193
111 4 0.01 2 0 199
112 3 0.005 1 0 200
113 2 0.005 1 0 200
114 3 x0.005 10 11 180
115 2 0.02 4 0 197
116 4 0.055 11 0 190
117 2 0.05 10 0 191
118 80 0.09 31 13 157
119 78 0.184 39 2 160
120 67 0.005 17 16 168
121 64 0.025 15 10 176
466 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Appendix (cont.)
Node
Clade
size
Mean rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
122 62 0 13 13 175
123 43 0.085 21 4 176
124 40 0.114 25 2 174
125 38 0.045 16 7 178
126 6 0.07 15 1 185
127 2 0.005 1 0 200
128 32 0.1 22 2 177
129 10 x0.005 2 3 196
130 8 0 2 2 197
131 4 0.005 2 1 198
132 3 0 1 1 199
133 2 0.005 1 0 200
134 4 0.005 1 0 200
135 2 0.01 2 0 199
136 2 0.015 3 0 198
137 6 0.045 11 2 188
138 2 0.005 1 0 200
139 5 x0.005 1 2 198
140 4 0.005 2 1 198
141 2 0 1 1 199
142 2 0.015 3 0 198
143 2 0.005 1 0 200
144 2 0.055 12 1 188
145 3 x0.01 5 7 189
146 2 0.015 8 5 188
147 19 0.075 15 0 186
148 2 0.01 2 0 199
149 3 0.055 12 1 188
150 2 0.03 6 0 195
151 11 0.065 15 2 184
152 4 0 4 4 193
153 3 0.04 8 0 193
154 2 0.005 1 0 200
155 7 0.085 18 1 182
156 6 0.03 11 5 185
157 2 0.025 5 0 196
158 3 0.025 9 4 188
159 2 0.05 10 0 191
160 19 0.045 10 1 190
161 16 0.045 10 1 190
162 15 0.035 7 0 194
163 13 0.035 7 0 194
164 2 0.005 1 0 200
165 10 0.035 7 0 194
166 2 0.015 3 0 198
167 3 0.015 4 1 196
168 2 0.015 3 0 198
169 6 0.065 13 0 188
170 2 0.035 7 0 194
171 4 0.025 5 0 196
172 2 0.02 5 1 195
173 2 0.01 4 2 195
Phylogeny of the whales, dolphins and even-toed hoofed mammals 467
Full QS (QS) index and reduced QS (rQS) index for reduced cetartiodactyl supertree. Nodes are numbered from the base of
the tree along the left-hand backbone of the tree until the first tip is reached then each clade is coded in the same way always
starting at the most basal clade and going to the left first.
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
1 246 softConflict x0.536 0 23 6 3 120
2 236 softConflict x0.53 0 23 12 1 116
3 162 softConflict x0.424 0 5 28 0 119
4 158 softConflict x0.424 0 5 28 0 119
5 155 softConflict x0.477 0 21 28 0 103
6 121 softConflict x0.398 0 14 45 0 93
7 100 softConflict x0.303 0 13 73 0 66
8 42 softConflict x0.263 0 8 80 0 64
9 13 softConflict x0.115 0 4 121 0 27
10 6 softConflict x0.076 0 1 130 0 21
11 4 equivocal x0.046 0 0 138 0 14
12 3 softSupport x0.036 0 0 137 2 13
13 2 softConflict x0.026 0 1 133 6 12
14 7 equivocal x0.099 0 0 122 0 30
15 4 softConflict x0.062 0 5 138 0 9
16 2 softSupport x0.016 0 0 139 4 9
17 2 softSupport x0.03 0 0 137 3 12
18 3 softConflict x0.099 0 3 123 1 25
19 2 softSupport x0.079 0 0 122 3 27
20 29 softConflict x0.227 0 5 88 0 59
21 28 softConflict x0.23 0 7 89 0 56
22 7 softConflict x0.197 0 1 93 0 58
23 6 softConflict x0.194 0 1 92 1 58
24 3 softSupport x0.161 0 0 99 2 51
25 2 softSupport x0.151 0 0 98 4 50
26 11 softConflict x0.128 0 1 114 0 37
27 9 softConflict x0.132 0 1 113 0 38
28 7 softConflict x0.138 0 4 112 1 35
29 6 softConflict x0.138 0 4 112 1 35
30 4 softConflict x0.128 0 4 113 2 33
31 2 softSupport 0 0 0 148 2 2
32 2 softSupport x0.01 0 0 145 2 5
33 6 softConflict x0.079 0 2 130 0 20
34 2 softSupport x0.023 0 0 141 2 9
35 4 softConflict x0.086 0 3 129 0 20
36 3 softSupport x0.023 0 0 143 1 8
37 2 softSupport 0.01 0 0 149 3 0
38 2 softSupport x0.003 0 0 145 3 4
39 2 softConflict x0.039 0 5 125 10 12
40 56 softConflict x0.188 0 14 109 0 29
41 47 softConflict x0.188 0 14 109 0 29
42 27 softConflict x0.128 0 1 114 0 37
43 13 softConflict x0.112 0 2 118 1 31
44 8 softConflict x0.036 0 1 140 1 10
45 5 softConflict x0.023 0 2 145 1 4
46 2 softConflict 0 0 1 145 4 2
47 3 softSupport x0.007 0 0 146 2 4
48 2 softSupport 0.013 0 0 148 4 0
49 5 softSupport x0.079 0 0 126 1 25
50 3 softSupport x0.056 0 0 133 1 18
51 2 softSupport x0.003 0 0 143 4 5
52 2 softSupport x0.016 0 0 139 4 9
53 3 softSupport x0.013 0 0 144 2 6
54 2 softConflict x0.016 0 2 141 4 5
55 20 softConflict x0.118 0 7 123 0 22
56 19 equivocal x0.076 0 0 129 0 23
57 17 softConflict x0.066 0 1 133 0 18
58 15 softSupport x0.036 0 0 139 1 12
468 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Appendix (cont.)
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
59 3 softConflict 0 0 1 149 2 0
60 4 softSupport x0.023 0 0 143 1 8
61 3 softSupport x0.023 0 0 143 1 8
62 2 softSupport 0.013 0 0 148 4 0
63 4 softSupport x0.007 0 0 148 1 3
64 2 softSupport 0.003 0 0 145 4 3
65 2 softSupport 0.013 0 0 148 4 0
66 2 softSupport x0.033 0 0 134 4 14
67 9 softConflict x0.069 0 1 132 0 19
68 8 softConflict x0.066 0 2 134 0 16
69 5 softConflict x0.046 0 2 138 1 11
70 2 softSupport 0.007 0 0 148 3 1
71 2 softSupport x0.01 0 0 143 3 6
72 3 softConflict x0.049 0 2 137 1 12
73 2 softSupport x0.007 0 0 144 3 5
74 21 softConflict x0.296 0 6 68 0 78
75 12 softConflict x0.293 0 7 70 0 75
76 7 softConflict x0.263 0 2 74 0 76
77 3 softConflict x0.105 0 7 127 0 18
78 2 softConflict x0.066 0 3 125 5 19
79 2 softConflict x0.033 0 3 133 6 10
80 2 softSupport x0.234 0 0 73 4 75
81 5 softConflict x0.128 0 3 116 0 33
82 4 softConflict x0.105 0 2 122 0 28
83 9 softConflict x0.112 0 8 126 0 18
84 2 softConflict x0.03 0 1 124 10 17
85 7 equivocal x0.069 0 0 131 0 21
86 6 softConflict x0.066 0 3 135 0 14
87 5 softConflict x0.053 0 2 138 0 12
88 3 softSupport 0 0 0 144 4 4
89 2 softSupport 0.016 0 0 143 7 2
90 34 softConflict x0.263 0 6 78 0 68
91 30 softConflict x0.266 0 8 79 0 65
92 13 softConflict x0.217 0 9 95 0 48
93 4 softConflict x0.151 0 6 112 0 34
94 3 softConflict x0.072 0 3 133 0 16
95 2 softSupport x0.016 0 0 137 5 10
96 9 softConflict x0.132 0 4 116 0 32
97 8 softConflict x0.132 0 4 116 0 32
98 7 softConflict x0.118 0 2 118 0 32
99 4 softConflict x0.112 0 1 119 0 32
100 3 softConflict x0.036 0 1 142 0 9
101 2 softSupport x0.03 0 0 141 1 10
102 17 softConflict x0.224 0 6 90 0 56
103 11 softConflict x0.201 0 5 96 0 51
104 2 softSupport x0.016 0 0 145 1 6
105 6 softConflict x0.062 0 1 134 0 17
106 5 softSupport x0.049 0 0 135 1 16
107 4 softConflict x0.026 0 1 143 1 7
108 3 softSupport x0.007 0 0 148 1 3
109 2 softSupport 0.007 0 0 146 4 2
110 4 softSupport x0.013 0 0 146 1 5
111 3 softSupport 0.003 0 0 151 1 0
112 2 softSupport 0.007 0 0 150 2 0
113 3 softConflict x0.181 0 10 107 0 35
114 2 softSupport x0.115 0 0 111 3 38
115 4 equivocal x0.109 0 0 119 0 33
116 2 softSupport x0.036 0 0 117 12 23
117 74 softConflict x0.23 0 13 93 1 45
118 72 softConflict x0.194 0 2 95 0 55
Phylogeny of the whales, dolphins and even-toed hoofed mammals 469
Appendix (cont.)
Node
Clade
size Status
Mean
QS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
Number of
sources with
soft matches
Number of
sources with
soft mismatches
119 62 softConflict x0.23 0 16 98 0 38
120 59 softConflict x0.201 0 10 101 0 41
121 57 softConflict x0.207 0 12 101 0 39
122 42 softConflict x0.178 0 2 100 0 50
123 39 equivocal x0.171 0 0 100 0 52
124 6 softConflict x0.066 0 1 133 0 18
125 3 softConflict x0.02 0 1 145 1 5
126 2 softSupport x0.007 0 0 144 3 5
127 31 softConflict x0.138 0 2 112 0 38
128 10 softConflict x0.066 0 2 134 0 16
129 8 softConflict x0.062 0 2 135 0 15
130 4 softConflict x0.03 0 1 142 1 8
131 3 softConflict x0.02 0 1 145 1 5
132 2 softSupport x0.01 0 0 145 2 5
133 4 softSupport x0.039 0 0 138 1 13
134 2 softSupport x0.033 0 0 136 3 13
135 2 softSupport x0.007 0 0 144 3 5
136 5 softConflict x0.089 0 1 126 0 25
137 2 softSupport x0.01 0 0 145 2 5
138 5 equivocal x0.043 0 0 139 0 13
139 4 equivocal x0.039 0 0 140 0 12
140 3 equivocal x0.039 0 0 140 0 12
141 2 softSupport x0.03 0 0 137 3 12
142 2 softConflict x0.026 0 1 127 9 15
143 3 softConflict x0.03 0 2 143 1 6
144 2 softSupport 0.02 0 0 142 8 2
145 15 equivocal x0.076 0 0 129 0 23
146 14 softConflict x0.076 0 2 131 0 19
147 12 softConflict x0.053 0 1 137 0 14
148 2 softSupport x0.007 0 0 144 3 5
149 3 softConflict x0.095 0 1 124 0 27
150 2 softSupport x0.003 0 0 139 6 7
151 10 softConflict x0.161 0 2 105 0 45
152 3 softConflict x0.043 0 3 142 0 7
153 2 softSupport 0.013 0 0 142 7 3
154 7 softConflict x0.148 0 1 108 0 43
155 6 softConflict x0.125 0 4 118 0 30
156 2 softSupport 0.023 0 0 143 8 1
157 3 softConflict x0.118 0 3 117 1 31
158 2 softSupport x0.053 0 0 116 10 26
159 10 softConflict x0.148 0 1 108 0 43
160 7 softConflict x0.148 0 1 108 0 43
161 6 equivocal x0.145 0 0 108 0 44
162 2 softSupport x0.007 0 0 144 3 5
163 4 equivocal x0.145 0 0 108 0 44
164 3 softSupport x0.135 0 0 109 1 42
165 2 softSupport 0 0 0 146 3 3
166 3 softConflict x0.02 0 1 145 1 5
167 2 softSupport 0.01 0 0 147 4 1
168 6 equivocal x0.115 0 0 117 0 35
169 2 softSupport x0.062 0 0 119 7 26
170 4 equivocal x0.049 0 0 137 0 15
171 2 softConflict x0.03 0 1 134 5 12
172 2 softConflict x0.013 0 2 142 4 4
470 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Node
Clade
size
Mean
rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
1 246 x0.026 19 23 110
2 236 0.046 30 23 99
3 162 0.243 42 5 105
4 158 0.283 48 5 99
5 155 0.072 32 21 99
6 121 0.099 29 14 109
7 100 0.072 24 13 115
8 42 0.138 29 8 115
9 13 0.092 18 4 130
10 6 0.053 9 1 142
11 4 0.039 6 0 146
12 3 0.053 8 0 144
13 2 0.033 6 1 145
14 7 0.079 12 0 140
15 4 0 5 5 142
16 2 0.02 3 0 149
17 2 0.02 3 0 149
18 3 0.013 5 3 144
19 2 0.013 2 0 150
20 29 0.158 29 5 118
21 28 0.132 27 7 118
22 7 0.072 12 1 139
23 6 0.046 8 1 143
24 3 0.02 3 0 149
25 2 0.013 2 0 150
26 11 0.059 10 1 141
27 9 0.053 9 1 142
28 7 x0.007 3 4 145
29 6 x0.013 2 4 146
30 4 x0.013 2 4 146
31 2 0.007 1 0 151
32 2 0.013 2 0 150
33 6 0.033 7 2 143
34 2 0.007 1 0 151
35 4 0.013 5 3 144
36 3 0.013 2 0 150
37 2 0.013 2 0 150
38 2 0.02 3 0 149
39 2 0 5 5 142
40 56 x0.066 4 14 134
41 47 x0.053 6 14 132
42 27 0.079 13 1 138
43 13 0.013 4 2 146
44 8 0.02 4 1 147
45 5 0.007 3 2 147
46 2 0.013 3 1 148
47 3 0.02 3 0 149
48 2 0.013 2 0 150
49 5 0.026 4 0 148
50 3 0.02 3 0 149
51 2 0.02 3 0 149
52 2 0.02 3 0 149
53 3 0.053 8 0 144
54 2 0 2 2 148
55 20 x0.02 4 7 141
56 19 0.079 12 0 140
57 17 0.013 3 1 148
58 15 0.013 2 0 150
59 3 0.007 2 1 149
60 4 0.02 3 0 149
61 3 0.02 3 0 149
Phylogeny of the whales, dolphins and even-toed hoofed mammals 471
Appendix (cont.)
Node
Clade
size
Mean
rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
62 2 0.02 3 0 149
63 4 0.02 3 0 149
64 2 0.013 2 0 150
65 2 0.02 3 0 149
66 2 0.02 3 0 149
67 9 0.066 11 1 140
68 8 0.046 9 2 141
69 5 0.026 6 2 144
70 2 0.013 2 0 150
71 2 0.013 2 0 150
72 3 0.026 6 2 144
73 2 0.013 2 0 150
74 21 0.178 33 6 113
75 12 0.112 24 7 121
76 7 0.164 27 2 123
77 3 0.013 9 7 136
78 2 0.007 4 3 145
79 2 0 3 3 146
80 2 0.007 1 0 151
81 5 0.099 18 3 131
82 4 0.092 16 2 134
83 9 0.013 10 8 134
84 2 0.053 9 1 142
85 7 0.105 16 0 136
86 6 0.033 8 3 141
87 5 0.033 7 2 143
88 3 0.026 4 0 148
89 2 0.02 3 0 149
90 34 0.145 28 6 118
91 30 0.132 28 8 116
92 13 x0.007 8 9 135
93 4 x0.02 3 6 143
94 3 0 3 3 146
95 2 0.033 5 0 147
96 9 0.02 7 4 141
97 8 0.02 7 4 141
98 7 0.026 6 2 144
99 4 0.02 4 1 147
100 3 0 1 1 150
101 2 0.007 1 0 151
102 17 0.072 17 6 129
103 11 0.059 14 5 133
104 2 0.007 1 0 151
105 6 0.02 4 1 147
106 5 0.039 6 0 146
107 4 0.007 2 1 149
108 3 0.026 4 0 148
109 2 0.02 3 0 149
110 4 0.013 2 0 150
111 3 0.007 1 0 151
112 2 0.007 1 0 151
113 3 0 10 10 132
114 2 0.02 3 0 149
115 4 0.066 10 0 142
116 2 0.059 9 0 143
117 74 0.112 30 13 109
118 72 0.237 38 2 112
119 62 x0.007 15 16 121
120 59 0.013 12 10 130
472 Samantha A. Price, Olaf R. P. Bininda-Emonds and John L. Gittleman
Appendix (cont.)
Node
Clade
size
Mean
rQS
index
Number of
sources with
hard matches
Number of
sources with
hard mismatches
Number of
sources with
equivocal trees
121 57 x0.013 10 12 130
122 42 0.112 19 2 131
123 39 0.132 20 0 132
124 6 0.053 9 1 142
125 3 0 1 1 150
126 2 0.007 1 0 151
127 31 0.099 17 2 133
128 10 0 2 2 148
129 8 0 2 2 148
130 4 0.007 2 1 149
131 3 0 1 1 150
132 2 0.007 1 0 151
133 4 0.007 1 0 151
134 2 0.013 2 0 150
135 2 0.02 3 0 149
136 5 0.026 5 1 146
137 2 0.007 1 0 151
138 5 0.013 2 0 150
139 4 0.007 1 0 151
140 3 0.007 1 0 151
141 2 0.02 3 0 149
142 2 0.053 9 1 142
143 3 0.02 5 2 145
144 2 0.046 7 0 145
145 15 0.086 13 0 139
146 14 0.039 8 2 142
147 12 0.039 7 1 144
148 2 0.013 2 0 150
149 3 0.059 10 1 141
150 2 0.039 6 0 146
151 10 0.079 14 2 136
152 3 0.007 4 3 145
153 2 0.053 8 0 144
154 7 0.099 16 1 135
155 6 0.046 11 4 137
156 2 0.033 5 0 147
157 3 0.039 9 3 140
158 2 0.066 10 0 142
159 10 0.053 9 1 142
160 7 0.053 9 1 142
161 6 0.046 7 0 145
162 2 0.02 3 0 149
163 4 0.046 7 0 145
164 3 0.046 7 0 145
165 2 0.013 2 0 150
166 3 0.02 4 1 147
167 2 0.02 3 0 149
168 6 0.079 12 0 140
169 2 0.046 7 0 145
170 4 0.033 5 0 147
171 2 0.026 5 1 146
172 2 0.013 4 2 146
Phylogeny of the whales, dolphins and even-toed hoofed mammals 473
... A longstanding concern regarding MRP supertrees is a tendency to recover clades that are not present in any of the source studies [40,41]. To evaluate clade support, we computed a modified version of the reduced qualitative support (rQS) metric [42,43] that is appropriate for metatrees (see the electronic supplementary material). This metric ranges from −1, indicating that a bipartition in the metatree is contradicted by all characters in all source trees, and +1 indicating that the bipartition is consistent with all characters in all source trees. ...
Article
A clade’s evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant ( n = 419) and extinct ( n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.
... Prior to annotation, the genome was masked with RepeatMasker (Smit et al. 2013) using Cetartiodactyla and ancestral repeat sequences in the RepBase Update repeat database (Bao et al. 2015). Cetartiodatyla includes cetaceans and even-toed ungulates (Price et al. 2005). Soft-masking of repeat sequences using RepeatMasker was used to increase annotation speed and accuracy (Hoff et al. 2019). ...
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Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20,651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes. Subject Area: Genome Resources
... The giraffoid clade now consists only of Giraffes, Okapis and Pronghorns [5] but they were much more widespread in the Miocene era [6]. They are now restricted to a few species in marked comparison with the enormous expansion of the other ruminant clades, in particular the Bovidae. ...
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Introduction: Mature granulated trophoblast binucleate cells (BNC) have been found in all ruminant placentas examined histologically so far. BNC are normally fairly evenly distributed throughout the fetal villus and all their granules contain a similar variety of hormones and pregnancy associated glycoproteins (PAGs). Only the Giraffe is reported to show a different BNC protein expression, this paper is designed to investigate that. Results: Gold labelled Lectin histochemistry and protein immunocytochemistry were used on deplasticised 1 μm sections of a wide variety of ruminant placentomes with a wide range of antibodies and lectins. Results: In the Giraffe placentomes, even though the lectin histochemistry shows an even distribution of BNC throughout the trophoblast of the placental villi, the protein expression in the BNC granules is limited to the BNC either in the apex or the base of the villi. Placental lactogens and Prolactin (PRL) are present only in basally situated BNC: PAGs only in the apical BNC. PRL is only found in the Giraffe BNC which react with many fewer of the wide range of antibodies used here to investigate the uniformity of protein expression in ruminant BNC. Discussion: The possible relevance of these differences to ruminant function and evolution is considered to provide a further example of the versatility of the BNC system.
... We took benefit of our extensive genomic data set to produce a phylogeny of the Cetartiodactyla clade. Analysed with RaxML, the reduced and complete data set supported topologies that were identical (figure 1) and in very good agreement with previously published phylogenies (Agnarsson and May-Collado, 2008;Hassanin et al., 2012;Price et al., 2005). Of note, Tylopoda branch out as the sister group to all other Cetartiodactyla in this tree, contradicting the speciesrich mitochondrial-based analysis of Hassanin et al. (2012), in which Suina was the earliest diverging group. ...
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Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontolo