The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

Abstract

We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the 'Mouse Goat' and the 'Irish Elk'. Previous primary analyses have included only a small portion of the species diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid phylogenetic estimates for a large number of species. However, single-gene phylogenies often differ dramatically from studies involving multiple datasets suggesting that they often are unreliable. However, based on recovery of benchmark clades-clades supported in prior studies based on multiple independent datasets-and recovery of undisputed traditional taxonomic groups, Cytb performs extraordinarily well in resolving cetartiodactyl phylogeny when taxon sampling is dense. Missing data, however, (taxa with partial sequences) can compromise phylogenetic accuracy, suggesting a tradeoff between the benefits of adding taxa and introducing question marks. In the full data, a few species with a short sequences appear misplaced, however, sequence length alone seems a poor predictor of this phenomenon as other taxa with equally short sequences were not conspicuously misplaced. Although we recommend awaiting a better supported phylogeny based on more character data to reconsider classification and taxonomy within Cetartiodactyla, the new phylogenetic hypotheses provided here represent the currently best available tool for comparative species-level studies within this group. Cytb has been sequenced for a large percentage of mammals and appears to be a reliable phylogenetic marker as long as taxon sampling is dense. Therefore, an opportunity exists now to reconstruct detailed phylogenies of most of the major mammalian clades to rapidly provide much needed tools for species-level comparative studies.

Full text

The phylogeny of Cetartiodactyla: The importance of dense taxon sampling,
missing data, and the remarkable promise of cytochrome b to provide reliable
species-level phylogenies
Ingi Agnarsson
a,b,*,1
, Laura J. May-Collado
c,1
a
Department of Biology, University of Akron, Akron, OH 44325-3908, USA
b
Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi trg 2, P.O. Box 306, SI-1001 Ljubljana, Slovenia
c
Department of Environmental Science & Policy, George Mason University, MSN 5F2, 4400 University Drive, Fairfax VA 22030, USA
article info
Article history:
Received 27 November 2007
Revised 8 May 2008
Accepted 21 May 2008
Available online 12 June 2008
Keywords:
Adding taxa
Antilocapridae
Bovidae
Cervidae
Cetacea
Cetancodonta
Giraffidae
Irish Elk
Mammalia
Missing data
Mitochondrial DNA
Moschidae
Mouse goat
Mysticeti
Odontoceti
Pecora
Perissodactyla
Phylogeny of mammals
Ruminantia
Suina
Taxon sampling
Tragulidae
abstract
We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant
cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the ‘Mouse
Goat’ and the ‘Irish Elk’. Previous primary analyses have included only a small portion of the species
diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths
limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid
phylogenetic estimates for a large number of species. However, single-gene phylogenies often differ dra-
matically from studies involving multiple datasets suggesting that they often are unreliable. However,
based on recovery of benchmark clades—clades supported in prior studies based on multiple independent
datasets—and recovery of undisputed traditional taxonomic groups, Cytb performs extraordinarily well in
resolving cetartiodactyl phylogeny when taxon sampling is dense. Missing data, however, (taxa with par-
tial sequences) can compromise phylogenetic accuracy, suggesting a tradeoff between the benefits of
adding taxa and introducing question marks. In the full data, a few species with a short sequences appear
misplaced, however, sequence length alone seems a poor predictor of this phenomenon as other taxa
with equally short sequences were not conspicuously misplaced. Although we recommend awaiting a
better supported phylogeny based on more character data to reconsider classification and taxonomy
within Cetartiodactyla, the new phylogenetic hypotheses provided here represent the currently best
available tool for comparative species-level studies within this group. Cytb has been sequenced for a large
percentage of mammals and appears to be a reliable phylogenetic marker as long as taxon sampling is
dense. Therefore, an opportunity exists now to reconstruct detailed phylogenies of most of the major
mammalian clades to rapidly provide much needed tools for species-level comparative studies.
Ó2008 Elsevier Inc. All rights reserved.
1. Introduction
The mammalian superorder Cetartiodactyla (whales and even-
toed ungulates) contains nearly 300 species including many of
immense commercial importance (cow, pig, and sheep) and of con-
servation interest and aesthetic value (antelopes, deer, giraffe, dol-
phins, and whales) (MacDonald, 2006). Certain members of this
superorder count among the best studied organisms on earth,
whether speaking morphologically, behaviorally, physiologically
or genetically. Understanding the interrelationships among cetar-
tiodactyl species, therefore, is of obvious importance.
Much of the recent phylogenetic work has focused either on high-
er level questions such as the placement of Cetacea with respect to
Artiodactyla, and the monophyly and relationships among Cetartio-
dactylan suborders and families (e.g., Gatesy et al., 1999; Nikaido
et al., 1999; Lum et al., 2000; Matthee et al., 2001; Murphy et al.,
2001; Naylor and Adams, 2001; Thewissen et al., 2001; Hassanin
and Douzery, 2003; Arnason et al., 2004; Reyes et al., 2004;
1055-7903/$ - see front matter Ó2008 Elsevier Inc. All rights reserved.
doi:10.1016/j.ympev.2008.05.046
* Corresponding author.
E-mail address: iagnarsson@gmail.com (I. Agnarsson).
URL: http://theridiidae.com (I. Agnarsson).
1
Present address: Department of Biology, University of Puerto Rico,P.O. Box 23360,
San Juan PR 00931-3360, USA.
Molecular Phylogenetics and Evolution 48 (2008) 964–985
Contents lists available at ScienceDirect
Molecular Phylogenetics and Evolution
journal homepage: www.elsevier.com/locate/ympev

Gu et al., 2007; Wada et al., 2007; O’Leary and Gatesy, 2008), or on
lower level questions of some smaller clades within the superorder
(e.g., Pitra et al., 2004; Ropiquet and Hassanin, 2004, 2005; Hassanin
and Ropiquet, 2004; Willows-Munro et al., 2005; Gilbert et al., 2006;
Guha et al., 2007). Hence, while a consensus seems to be emerging
from a range of datasets (morphology, mitochondrial and nuclear
DNA, SINEs) on many of the higher level relationships (for reviews
see Price et al., 2005; Hernandez and Vrba, 2005; May-Collado and
Agnarsson, 2006; O’Leary and Gatesy, 2008), understanding of
species-level phylogenetics across the superorder is patchy.
Detailed species-level phylogenies are of paramount impor-
tance for comparative studies (Harvey and Pagel, 1991). In general,
statistical power of comparative methods increases as taxon sam-
pling approaches completion and as resolution increases (both
adding to the number of possible sister-taxon comparisons). In
addition, many methods in the toolkit of comparative biology per-
form best when branch length estimates are available (e.g., Felsen-
stein, 2004; Bollback, 2006).
To date, however, the most comprehensive primary-data-based
phylogenetic study on cetartiodactylans included only 51 extant
species (Gatesy et al., 2002; note that May-Collado and Agnarsson,
2006 and May-Collado et al., 2007 included 90 and 92 species,
respectively, but focused on Cetacea and O’Leary and Gatesy,
2008 include 64 species but focus on extinct taxa). By combining
multiple types of data for a strategically chosen set of taxa Gatesy
et al. (2002) and O’Leary and Gatesy (2008) offered strong hypoth-
eses of higher level relationships within Cetartiodactyla. However,
lack of a more detailed phylogeny limits the types of questions that
can be address using the comparative method. To remedy this Price
et al. (2005), (see also Hernandez and Vrba, 2005) combined multi-
ple phylogenetic studies, and non-quantitative taxonomies, to pro-
duce a complete phylogeny of Cetartiodactyla using a supertree
approach (Bininda-Emonds and Bryant, 1998; Bininda-Emonds et
al., 2002). While representing a significant advancement, the
supertree has some shortcomings (for a general critique of super-
tree techniques see e.g. Gatesy et al., 2002). For example, large por-
tions of the tree are simply reflecting taxonomy, rather than
quantitatively addressing species interrelationships. Equally
important for its use for comparative studies, the resolution of
the supertree is relatively low (59.9%) and it does not provide esti-
mates of branch lengths. A better resolved phylogeny with branch
lengths, even though taxon-incomplete, may represent a more
powerful tool for many comparative questions and methods.
Here, we present a near species-complete phylogeny of Cetar-
tiodactyla based on cytochrome b sequence data. We evaluate
the ‘‘reliability” of the phylogeny based on the recovery of numer-
ous higher level benchmark clades and undisputed taxonomic
groups. We argue that, at least for cytb within this group of mam-
mals, dense taxon sampling may simultaneously overcome some of
the commonly cited shortcomings of single-gene phylogenies and
increase the value of the resulting phylogenies. We conclude that
a profitable short-term research program will be the use of cytb
data to rapidly provide species-level phylogenies for large clades
across mammals providing valuable tools for comparative biology.
Such phylogenies are not competing with character rich studies of
relatively few taxa, nor with supertrees, but offer alternative tools,
and ultimately will increase the power of supertree approaches to
reconstruct even larger and better resolved ‘‘megatrees”.
2. Materials and methods
2.1. Data and phylogenetic analyses
Cytochrome data was compiled from GenBank for 276 taxa rep-
resenting 266 cetartiodactylans (including two recently extinct
taxa, Myotragus balearicus, the ‘Mouse Goat’, and Megaloceros
giganteus, the ‘Irish Elk’ or ‘Giant Deer’), and 10 outgroups (see Ta-
ble 1 for Accession Nos.). We chose outgroup taxa representing two
groups from Pegasoferae a recently proposed group hypothesized
to be sister to Cetartiodactyla (Nishihara et al., 2006). Given that
missing data can cause problems in phylogenetic reconstruction,
we created three data matrices; one in which all taxa with avail-
able cytb sequences at least 15% of the full length (1140pb) were
included (full dataset = 276 species), another set where taxa with
less than 30% full sequence length were excluded (pruned dataset
1 = 249 spp) and a third one where taxa with less than 50% of the
full cytb sequence length were excluded (pruned dataset 2 = 203
spp). Sequences were managed and results examined in Mesquite
(Maddison and Maddison, 2007) and graphic tree files were ex-
ported from Mesquite and manipulated in Adobe Illustrator where
illustrations were rendered. The sequences were aligned—a trivial
task as Cytb is a protein coding gene resulting in unambiguous
alignment without any gaps—using the Needleman–Wunsch algo-
rithm in MacClade 4.07 (Maddison and Maddison, 2003). The
appropriate model for the Bayesian analyses was selected with
Modeltest (Posada and Crandall, 1998, 2001), using the AIC crite-
rion (Posada and Buckley, 2004) with a parsimony tree chosen as
the basis for Modeltest. The best model was GTR+
c
+I (Rodríguez
et al., 1990; Yang, 1994). Bayesian analysis was performed using
MrBayes V3.1.2 (Huelsenbeck and Ronchist, 2001) with settings
as in May-Collado and Agnarsson (2006) with separate model esti-
mation for first, second and third codon positions.
The Markov chain Monte Carlo search for each matrix was run
with four chains for 10,000,000 generations (repeated two times),
sampling the Markov chain every 1000 generations, and the
sample points of the first 5,000,000 generations (pruned datasets
1–2) or 8,000,000 generations (full dataset) were discarded as
‘‘burnin”. Previously (May-Collado and Agnarsson, 2006), we
showed that parsimony performed relatively poorly (in terms of
recovery of benchmark clades) compared to Bayesian analyses of
Cytb sequences within Cetartiodactyla. For simplicity, therefore,
we here restrict our analysis to Bayesian methods.
2.2. Benchmarck clades
As argued by May-Collado and Agnarsson (2006) one intuitively
satisfying way to judge the reliability of phylogenetic results is the
recovery of benchmark clades—clades that can be treated a priori
as ‘known’ due to independent support from multiple lines of evi-
dence. This can be particularly valuable when character data are
relatively few, such as in single-gene analyses of many taxa, as
many of the existing measures of support in one way or another
scale with absolute number of characters. As Cytb is, due to high
substitution rates, thought to be most reliable at lower taxonomic
levels, recovering ‘known’ deeper clades gives credibility to the
phylogeny as a whole.
We consider a benchmark clade ‘recovered’ in a given analysis
simplyifit is present in the majority rule tree from the Bayesian anal-
ysis, regardless of the posterior probability value for that clade. We
are here interested in the ability of Cytb to recover clades that are
undisputed. That these may in some cases be very weakly supported
is unsurprising as few data are being used to resolve relationships
among many taxa. Also, in the full matrix, we expect missing data
to have an effect on branch support and thus note that for the few
benchmark clades that are supported by valuesclose to or lower than
50% in the full analyses, they are always more strongly supported in
the pruned dataset 2, where missing data is much less of a problem.
The following clades are here treated as ‘benchmark clades’
(clade names followed by studies and types of data that have recov-
ered them, this list of studies is meant to be representative, not
exhaustive). Note that we do not wish to imply that no historical
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 965

Table 1
Species included in each analysis, and their GenBank Accession Nos
Species Accession No. Full 276 spp. Pruned 1 240 spp. Pruned 2 203 spp.
Carnivora
Canis familiares AY729880 X X X
Panthera leo AF053052 X X X
Euungulata
Order Perissodactyla
Fam. Rhinocerotidae
Dicerorhinus sumatrensis AJ245723 X X X
D. bicornis X56283 X X X
Fam. Equidae
Equus caballus AY515162 X X X
Equus grevyi X56282 X X X
Fam. Tapiridae
Tapirus indicus AF145734 X X X
Tapirus terrestris AF056030 X X X
Cetartiodactyla
Sub order Tylopoda
Fam. Camelidae
Camelus dromedarius X56281 X X X
Camelus bactrianus EF076246 X X X
Lama glama U06429 X X X
Lama guanicoe Y08812 X
Lama pacos AY839860 X
Vicugna vicugna U06430 X X X
Sub order Suina
Fam. Suidae
Sus barbatus Z50107 X X X
Sus cebifrons AY920906 X X X
Sus celebensis AY534298 X X X
Sus philippensis AY920905 X X X
Sus scrofa DQ315604 X
Sus verrucosus AJ314553 X X X
Babyrousa babyrussa Z50106 X X X
Potamochoerus larvatus AY534300 X
Potamochoerus porcus DQ315602 X X X
Phacochoerus aethiopicus AJ314551 X X X
Phacochoerus africanus DQ470799 X X
Fam. Tayassuidae
Pecari tajacu X56296 X X X
Tayassu pecari AY534303 X X X
Catagonus wagneri U66291 X X X
Sub order Ruminantia
Fam. Tragulidae
Moschiola meminna DQ676954 X
Tragulus napu X56288 X X X
Tragulus javanicus AB122110 X X X
Fam. Moschidae
Moschus berezovskii AB019640 X
Moschus chrysogaster AY684631 X
Moschus fuscus DQ417658 X X
Moschus leucogaster AF026889 X X X
Moschus moschiferus AY121995 X X X
Fam. Cervidae
Sub Fam. Muntiacinae
Megaloceros giganteus*AM182645 X X X
Elaphodus cephalophus DQ379305 X X X
Muntiacus crinifrons DQ445735 X X X
Muntiacus feae AF042721 X X X
Muntiacus muntjak DQ832255 X X
Muntiacus reevesi AF042719 X X X
Megamuntiacus (Muntiacus) vuquangensis AF042720 X X X
Sub Fam. Cervinae
Axis axis AY540851 X
Axis porcinus EF491197 X
Dama mesopotamica DQ379304 X X X
Cervus albirostris AY044863 X X X
Cervus dama AY397663 X X
Cervus duvaucelii AY456908 X
Cervus eldi AY540849 X
Cervus elaphus AY397658 X X
Cervus nippon DQ191158 X X
Cervus schomburgki AY607036 X X
966 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

Table 1 (continued)
Species Accession No. Full 276 spp. Pruned 1 240 spp. Pruned 2 203 spp.
Cervus unicolor AY456907 X
Elaphurus davidianus AY158081 X X
Sub. Fam. Hydropotinae
Hydropotes inermis AJ000028 X X X
Sub. Fam. Capreolinae
Odocoileus hemionus X56291 X X X
Odocoileus virginianus DQ673136 X X X
Capreolus capreolus Y14951 X X X
Capreolus pygargus AY820968 X X
Alces alces M98484 X X X
Rangifer tarandus DQ673135 X X
Blastoceros dichotomus AY326234 X X
Ozotoceros bezoarticus L48404 X X
Hippocamelus antisensis DQ379307 X X X
Mazama gouazoupira DQ379308 X X X
Pudu puda DQ379309 X X X
Fam. Giraffidae
Giraffa camelopardalis X56287 X X X
Okapia johnstoni AY121993 X X X
Fam. Antilocapridae
Antilocapra americana AF091629 X X X
Fam. Bovidae
Sub. Fam. Bovinae X
Myotragus balearicus
*
AY380560 X X X
Tetracerus quadricornis DQ984134 X
Boselaphus tragocamelus AY286441 X
Bubalus depressicornis D88642 X X X
Bubalus bubalis EF529451 X X X
Bubalus quarlesi D82891 X X X
Bubalus mindorensis D82895 X X X
Bos sauveli EF382665 X
Bos frontalis AY689187 X X X
Bos gaurus DQ459331 X X X
Bos grunniens DQ856609 X X
Bos indicus DQ459332 X X X
Bos javanicus AY689188 X X X
Bos taurus AB090987 X X X
Pseudoryx nghetinhensis AF091635 X X
Syncerus caffer AY534338 X X
Bison bison AY840096 X
Bison bonasus Y15005 X X X
Pseudonovibos spiralis AF281084 X
Tragelaphus angasii AF091633 X X
Tragelaphus buxtoni AF030263 X
Tragelaphus derbianus AF022062 X X
Tragelaphus euryceros AF036276 X X X
Tragelaphus imberbis DQ470778 X X
Tragelaphus oryx AF036278 X X
Tragelaphus scriptus AF036277 X X
Tragelaphus spekii AJ222680 X X X
Tragelaphus strepsiceros AF036280 X X X
Sub. Fam. Cephalophinae
Cephalophus adersi AF153883 X X X
Cephalophus callipygus AF153885 X X X
Cephalophus dorsalis AF153884 X X X
Cephalophus nigrifrons AF153896 X X
Cephalophus harveyi AF153887 X X X
Cephalophus jentinki AF153888 X X X
Cephalophus leucogaster AF153889 X X X
Cephalophus maxwellii AF153894 X
Cephalophus monticola AF153893 X X X
Cephalophus natalensis AF153890 X X X
Cephalophus niger AF153895 X X X
Cephalophus ogilbyi AF153897 X X X
Cephalophus rubidus AF153900 X X X
Cephalophus rufilatus AF153901 X X X
Cephalophus silvicultor AF153898 X X X
Cephalophus spadix AF153899 X X X
Cephalophus weynsi AF153902 X X X
Cephalophus zebra AF153903 X X X
Sub. Fam. Hippotraginae
Redunca arundinum AF096628 X X X
Redunca fulvorufula AF022060 X X X
(continued on next page)
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Table 1 (continued)
Species Accession No. Full 276 spp. Pruned 1 240 spp. Pruned 2 203 spp.
Redunca redunca AF096626 X X X
Pelea capreolus AF030591 X
Kobus ellipsiprymnus DQ470800 X X
Kobus kob AF052940 X X X
Kobus megaceros AJ222686 X X X
Kobus vardoni AF096630 X X
Beatragus hunteri AF034968 X X
Alcelaphus buselaphus AF300932 X X
Alcelaphus (Sigmoceros) lichtensteinii AF016636/AF034967 X X
Connochaetes gnou AF016637 X X
Aepyceros melampus AF301739 X
Hippotragus equinus AF022060 X X X
Hippotragus niger AF364809 X
Hippotragus leucophaeus U18274 X
Oryx beisa DQ138210 X
Oryx dammah AJ222685 X X X
Oryx gazella AF249973 X X X
Oryx leucoryx AF036286 X X X
Sub. Fam. Antilopinae
Gazella bennettii DQ919166 X
Gazella cuvieri AF030609 X
Gazella dama AF025954 X X X
Gazella dorcas AF187709 X X
Gazella gazella AF187697 X X
Gazella granti AY534343 X X
Gazella leptoceros AF187699 X X
Gazella rufifrons AF030606 X
Gazella saudilla AF187722 X X
Gazella soemmerringii AF030605 X
Gazella spekei AF030608 X
Gazella subgutturosa AF187718 X X
Gazella thomsoni DQ470795 X X
Antilope cervicapra AF022058 X X X
Procapra gutturosa DQ001162 X X
Procapra picticaudata EF554685 X
Antidorcas marsupialis AF036281 X X X
Litocranius walleri AF249974 X X X
Neotragus moschatus AF022069 X X
Madoqua kirkii AF022070 X X X
Madoqua guentheri AY534340 X X
Raphicerus campestris AF030595 X
Raphicerus melanotis AF030596 X
Raphicerus sharpie AF022050 X X X
Ourebia ourebi AF320574 X X X
Saiga tatarica AF064487 X X X
Oreotragus oreotragus AF036288 X X X
Sub. Fam. Caprinae
Capricornis crispus AB097260 X X X
Capricornis sumatraensis EF202142 X X
Naemorhedus caudatus AY356357 X X X
Naemorhedus goral AY286436 X
Rupicapra rupicapra AF034725 X X
Rupicapra pyrenaica AF034726 X X
Oreamnos americanus D32198 X X
Budorcas taxicolor AY669320 X X X
Ovibos moschatus AY839564 X X X
Hemitragus hylocrius AY846792 X X X
Hemitragus jayakari AY846791 X X X
Hemitragus jemlahicus AF034733 X X
Ammotragus lervia AF034731 X X
Pseudois nayaur AY382880 X X
Pseudois schaeferi AF473605 X X
Capra aegagrus DQ246788 X X
Capra caucasica DQ246801 X X X
Capra cylindricornis DQ246798 X X X
Capra falconeri DQ246797 X X
Capra hircus DQ519412 X
Capra ibex AF034735 X X X
Capra nubiana AF034740 X X X
Capra pyrenaica AJ010056 X X X
Capra sibirica DQ246800 X X X
Ovis aries AB006800 X X X
Ovis ammon ammon AF242349 X X
Ovis canadensis canadensis AF1121139 X X X
Ovis dalli U17860 X X X
Ovis nivicola AJ867264 X X X
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Table 1 (continued)
Species Accession No. Full 276 spp. Pruned 1 240 spp. Pruned 2 203 spp.
Ovis vignei AF034729 X X X
Sub. Fam. Panthalopinae
Pantholops hodgsoni AF034724 X X
Cetancodonta
Fam. Hippopotamidae
Hippopotamus amphibius Y08813 X X X
Hexaprotodon liberiensis Y08814 X X X
Cetacea (Rice, 1993)
Sub order Mysticeti
Fam. Balaenidae
Balaena glacialis X75587 X X X
Balaena mysticetus U13125 X X X
Eubalaena australis AP006473 X X X
Eubalaena japonica AP006474 X X X
Fam. Balaenopteridae
Sub. Fam. Balaenopterinae
Balaenoptera bonaerensis X75581 X X X
Balaenoptera acutorostrata AY770548 X X
Balaenoptera borealis X75582 X X X
Balaenoptera edeni X75583 X X
Balaenoptera musculus AY235202 X X
Balaenoptera physalus U13126 X X
Balaenoptera brydei AB201259 X X X
Balaenoptera omurai AB201257 X X X
Sub. Fam. Megapterinae
Megaptera novaeangliae X75584 X X X
Fam. Neobalaenidae
Capera marginata X75586 X X X
Fam. Eschirichtiidae
Eschrichtius eschrichtius X75585 X X X
Sub order Odontoceti
Super Fam. Physeteroidea
Fam. Physeteridae
Physeter macrocephalus (catodon) X75589 X X X
Fam. Kogidae
Kogia breviceps U72040 X X X
Kogia simus AF304072 X X X
Super Fam. Ziphoidea
Fam. Ziphiidae
Sub. Fam. Ziphiinae
Ziphius cavirostris AF304075 X X X
Berardius bairdii X92541 X X X
Tasmacetus shepherdi AF334484 X X X
Sub. Fam. Hyperoodontinae
Hyperoodon planifrons AY579560 X X
Hyperoodon ampullatus AY579558 X X
Indopacetus pacificus AY162441 X
Mesoplodon densirostris X92536 X X X
Mesoplodon bidens X92538 X X X
Mesoplodon layardii AY579550 X X
Mesoplodon mirus AY579552 X X
Mesoplodon grayi AY579546 X X
Mesoplodon stejnegeri AY579554 X X
Mesoplodon ginkgodens AY579544 X X
Mesoplodon hectori AY228109 X X
Mesoplodon peruvianus AF492414 X X
Mesoplodon europaeus AY579543 X X
Mesoplodon carlhubbsi AY579539 X X
Mesoplodon traversii AY579555 X
Super Fam. Platanistoidea
Fam. Platanistidae
Platanista gangetica AF304070 X X X
Platanista minor X92543 X X X
Super Fam. Inoidea
Fam. Pontoporidae
Pontoporia blainvelli AF334488 X X X
Fam. Iniidae
Inia geoffrensis boliviensis AF334487 X X X
Inia geoffrensis geoffrensis AF334485 X X X
Inia geoffrensis humboldtiana AF521110 X X X
(continued on next page)
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data have contradicted these clades, but rather that recent major
studies seem to be converging on an answer, that therefore seems
believable.
Cetartiodactyla—whales plus even-toed ungulates: Thewissen
et al. (2001) and Boisserie et al. (2005) (morphology including
fossil taxa); Arnason et al. (2002, 2004) (mitogenomic data); Mat-
thee et al. (2001); and Murphy et al. (2001) (nuclear and mitochon-
drial data); Shimamura et al. (1997, 1999) (retroposon SINE data);
Lum et al. 2000 (SINE data); O’Leary et al. (2004) (combined mor-
phology, nuclear DNA, mitochondrial DNA, and amino acids,
including fossils); May-Collado and Agnarsson (2006) (cytb data);
Amrine-Madsen et al. (2003) (apolipoprotein B); Corneli (2003)
(complete mitochondrial genome); Gatesy et al. (1999) (nuclear
and mitochondrial data); O’Leary and Gatesy (2008) (combined
morphology, nuclear DNA, mitochondrial DNA, including fossils).
Tylopoda—camels, llamas, and relatives: Montgelard et al.
(1997) (mitochondrial DNA); Gatesy et al. (1999) (nuclear and
mitochondrial data); O’Leary et al. (2004) (combined morphology,
nuclear DNA, mitochondrial DNA, and amino acids, including fos-
sils); Shimamura et al.1999 (SINE data); Lum et al. 2000 (SINE
data); Price et al. (2005) and Hernandez and Vrba (2005) (from
super trees based on morphological, behavioral, and molecular
phylogenies; O’Leary and Gatesy (2008) (combined morphology,
nuclear DNA, mitochondrial DNA, including fossils).
Table 1 (continued)
Species Accession No. Full 276 spp. Pruned 1 240 spp. Pruned 2 203 spp.
Super Fam. Lipotoidea
Fam. Lipotidae
Lipotes vexillifer AF304071 X X X
Super Fam. Delphinoidea
Fam. Monodontidae
Delphinapterus leucas U72037 X X X
Monodon monocerus U72038 X X X
Fam. Phocoenidae
Neophocaena phocaenoides AF334489 X X X
Phocoena phocoena U72039 X X X
Phocoena dioptrica U09681 X X X
Phocoena sinus AF084051 X X X
Phocoena spinipinnis U09676 X X X
Phocoenoides dalli U09679 X X X
Fam. Delphinidae (Leduc et al., 1999)
Sub. Fam. Lissodelphininae
Cephalorhynchus commersonii AF084073 X X X
Cephalorhynchus eutropia AF084072 X X X
Cephalorhynchus hectori AF084071 X X X
Cephalorhynchus heavisidii AF084070 X X X
Lagenorhynchus australis AF084069 X X X
Lagenorhynchus cruciger AF084068 X X X
Lagenorhynchus obliquidens AF084067 X X X
Lagenorhynchus obscurus AY257161 X X X
Lissodelphis borealis AF084099 X X X
Lissodelphis peronii AF084064 X X X
Sub. Fam. Delphininae
Delphinus delphis AF084085 X X X
Delphinus capensis AF084087 X X X
Delphinus tropicalis AF084088 X X X
Lagenodelphis hosei AF084099 X X X
Tursiops truncatus AF084095 X X X
Tursiops aduncus AF084091 X X X
Stenella clymene AF084083 X X X
Stenella coeruleoalba AF084082 X X X
Stenella frontalis AF084090 X X X
Stenella longirostris AF084103 X X X
Stenella attenuata AF084096 X X X
Sousa chinensis AF084080 X X X
Sub. Fam. Globicephalinae
Feresa attenuata AF084052 X X X
Globicephala macrorhynchus AF084055 X X X
Globicephala melas AF084056 X X X
Grampus griseus AF084059 X X X
Pseudorca crassidens AF084057 X X X
Sub. Fam. Orcininae
Orcinus orca AF084061 X X X
Orcaella brevirostris AF084063 X X X
Sub. Fam. Stenoninae
Sotalia fluviatilis AF304067 X X X
Sotalia guianensis DQ086827 X X X
Steno bredanensis AF084077 X X X
Incertae sedis
Lagenorhynchus acutus AF084075 X X X
Species included in each of the analyses with respective GenBank accession numbers of cytochrome b sequences, extinct taxa are flagged with an asterix. Classification used
in the table is based on MacDonald 2006 and Rice, 1998. Note however, in some cases ‘traditional’ taxon membership of some families/subfamilies in MacDonald (2006) is
inconsistent with recent phylogenies and in recovery of benchmark clades and in labeling clades on Figures we follow the latter when available, see text for discussion.
970 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

Ruminantia—subgroup of cetartiodactylans that digest food in
two steps by regurgitating semi-digested food from the rumen:
Montgelard et al. (1997) (mitochondrial DNA); Gatesy et al.
(1999) (nuclear and mitochondrial data); O’Leary et al. (2004)
(combined morphology, nuclear DNA, mitochondrial DNA, and
amino acids, including fossils); Price et al. (2005) and Hernandez
and Vrba (2005) (from super trees based on morphological, behav-
ioral, and molecular phylogenies); Shimamura et al. 1999 and Lum
et al. 2000 (SINE data); O’Leary and Gatesy (2008) (combined mor-
phology, nuclear DNA, mitochondrial DNA, including fossils).
Pecora—horned ruminants, all ruminants except tragulids: Janis
and Scott (1987, 1988), Janis (2000), Gentry (2002), Leinders and
Heintz (1980), Vislobokoda (1990) (morphological data); Montge-
lard et al. (1997) (mitochondrial DNA); Gatesy et al. (1999) (nuclear
and mitochondrial data); Hassanin and Douzery (2003) (morphol-
ogy, mitochondrial, and nuclear DNA); O’Leary et al. (2004) (com-
bined morphology, nuclear DNA, mitochondrial DNA, and amino
acids, including fossils); Price et al. (2005) and Hernandez and Vrba
(2005) (from super trees based on morphological, behavioral, and
molecular phylogenies); Shimamura et al. 1999 and Lum et al.
2000 (SINE data). O’Leary and Gatesy (2008) (combined morphol-
ogy, nuclear DNA, mitochondrial DNA, including fossils).
Bovidae—bovids, cloven-hoofed cetartiodactylans with un-
branched horns (incl. cow, sheep, goat, and antelopes): Janis and
Scott (1987, 1988), Janis (2000), Gentry (2002), Leinders and Hei-
ntz (1980), Vislobokoda (1990), Hassanin and Douzery (2003)
(morphology, mitochondrial and nuclear DNA); Cronin et al.
(1996) (K-casein gene); Cap et al. (2002) (behavioral and citogenet-
ic data); Price et al. (2005) and Hernandez and Vrba (2005) (from
super trees based on morphological, behavioral, and molecular
phylogenies); Gatesy et al. (1999) (nuclear and mitochondrial
data). O’Leary and Gatesy (2008) (combined morphology, nuclear
DNA, mitochondrial DNA, including fossils).
Moschidae—musk deer: Groves et al. (1995), Janis and Scott
(1987, 1988), Janis (2000),Gentry (2002),Leinders and Heintz
(1980),Vislobokoda (1990) (morphological data); Hassanin and
Douzery (2003) (morphology, mitochondrial and nuclear DNA);
Guha et al. (2007) (16S rRNA and cytb); Cap et al. (2002) (behav-
ioral and cytogenetic data); Price et al. (2005) and Hernandez
and Vrba (2005) (from super trees based on morphological, behav-
ioral, and molecular phylogenies).
Cervidae—deer and muntjacs: Groves et al. (1995), Janis and Scott
(1987, 1988), Janis (2000), Gentry (2002), Leinders and Heintz
(1980), Vislobokoda (1990) (morphological data); Hassanin and
Douzery (2003) (morphology, mitochondrial, and nuclear DNA); Pi-
tra et al. 2004 (cytb); Randi et al. (1998) (mtDNA control region); Gil-
bert et al.2006 (nuclear DNA); Guha et al. (2007) (16S rRNA and
cytb), Cronin et al.(1996) (K-casein gene); Cap et al. (2002) (behav-
ioral and cytogenetic data); Price (2005); and Hernandez and Vrba
(2005) (from super trees based on morphological, behavioral, and
molecular phylogenies). O’Leary and Gatesy (2008) (combined mor-
phology, nuclear DNA, mitochondrial DNA, including fossils).
Giraffidae—giraffe, okapi: Janis and Scott (1987, 1988), Janis
(2000),Gentry (2002),Leinders and Heintz (1980),Vislobokoda
(1990) (morphological data), Hassanin and Douzery (2003) mor-
phology, mitochondrial, and nuclear DNA), Guha et al. (2007)
(16S rRNA and cytb), Cronin et al. (1996) (K-casein gene); Cap
et al. (2002) (behavioral and cytogenetic data); Price (2005); and
Hernandez and Vrba (2005) (from super trees based on morpho-
logical, behavioral, and molecular phylogenies).
Antilocapridae—pronghorn (refers to evidence for placing this
monotypic family outside any other family): Janis and Scott
(1987, 1988), Janis (2000),Gentry (2002),Leinders and Heintz
(1980),Vislobokoda (1990), Hassanin and Douzery (2003)
(morphology, mitochondrial, and nuclear DNA), Cronin
et al.(1996) (K-casein gene), Price et al. (2005) and Hernandez
and Vrba (2005) (from super trees based on morphological, behav-
ioral, and molecular phylogenies).
Suina, Suidae, and Tayassuidae—pigs, warthog, peccari, javelina:
Montgelard et al. (1997) (mitochondrial DNA); Gatesy 1997; Gate-
sy et al. 1996; Gatesy et al. (1999) (nuclear and mitochondrial
data); O’Leary et al. (2004) (combined morphology, nuclear DNA,
mitochondrial DNA, and amino acids, including fossils); Montge-
lard et al. (1998) (combined cranioskeletal and mitochondrial
DNA); Randi et al. (1996) (molecular data); Gongora and Moran
(2005), Gongora et al. (2006) (mitochondrial DNA), Cronin et al.
(1996) (K-casein gene), Shimamura et al. (1999), and Lum et al.
(2000) (SINE data). O’Leary and Gatesy (2008) (combined morphol-
ogy, nuclear DNA, mitochondrial DNA, including fossils).
Cetancodonta (Cetacea +Hippopotamidae)—toothed/baleen
whales plus hippos: Geisler and Sanders (2003) and Boisserie
et al. (2005) (morphology including fossils); Gatesy, 1997 and
Gatesy et al. (1999) (nuclear data); Lum et al. (2000) (SINE
data); Arnason et al. (2000, 2002, 2004) (mitogenomic data);
O’Leary et al. (2004) (combined morphology, nuclear DNA,
mitochondrial DNA, and amino acids, including fossils);
May-Collado and Agnarsson (2006) (cytb); Amrine-Madsen
et al. (2003) (apolipoprotein B); Corneli (2003) (complete
mitochondrial genome); O’Leary and Gatesy (2008) (com-
bined morphology, nuclear DNA, mitochondrial DNA, includ-
ing fossils).
Cetacea—toothed and baleen whales: Montgelard et al. (1997)
(mitochondrial DNA); Lum et al. (2000), (retroposon SINE data); Shi-
mamura et al. (1999) (SINEs); Arnason et al. (2000, 2002, 2004)
(mitogenomic data); O’Leary et al. (2004) (combined morphology,
nuclear DNA, mitochondrial DNA, and amino acids); Messenger and
McGuire(1998)(morphology);O’LearyandGatesy (2008)(combined
morphology, nuclear DNA, mitochondrial DNA, including fossils).
Mysticeti—baleen whales: Arnason and Gullberg (1993) (cytb);
Cassens et al. (2000) (mitochondrial DNA and proteins); Gatesy
et al. (1999) and Rychel et al. (2004) (nuclear and mitochondrial
data); Lum et al. (2000) (SINE data); Arnason et al. (2000, 2002,
2004) (mitogenomic data); Hamilton et al. (2001), May-Collado
and Agnarsson (2006), and Yang et al. (2005) (cytb); Messenger
and McGuire (1998) (morphology); Geisler and Sanders (2003)
(morphology including fossils); O’Leary et al. (2004) (combined
morphology, nuclear DNA, mitochondrial DNA, and amino acids);
Steeman (2007) (morphological data, including fossils).
Odontoceti—toothed whales: Arnason and Gullberg (1993)
(cytb); Cassens et al. (2000) (mitochondrial DNA and proteins);
Lum et al. (2000), Nikaido et al. (2001, 2007) (SINE data); Arnason
et al. (2000, 2002, 2004) (mitogenomic data); Hamilton et al.
(2001), May-Collado and Agnarsson (2006), and Yang et al.
(2005) (cytb); Messenger and McGuire (1998) (morphology); Geis-
ler and Sanders (2003) (morphology including fossils); O’Leary et
al. (2004) (combined morphology, nuclear DNA, mitochondrial
DNA, and amino acids); O’Leary and Gatesy (2008) (combined mor-
phology, nuclear DNA, mitochondrial DNA, including fossils).
Delphina (Delphinoidea plus river dolphins (minus Platanisti-
dae))—porpoises, monodontids, and dolphins plus river dolphins
other than Platanista.Cassens et al. (2000) (mitochondrial DNA
and proteins); May-Collado and Agnarsson (2006),Yang et al.
(2005), and Hamilton et al. (2001) (cytb); Arnason et al. (2004)
(mitogenomic data); Messenger and McGuire (1998) and De Mui-
zon (1988) (morphological data); O’Leary et al. (2004) (combined
morphology, nuclear DNA, mitochondrial DNA, and amino acids,
including fossils). O’Leary and Gatesy (2008) (combined morphol-
ogy, nuclear DNA, mitochondrial DNA, including fossils).
Delphinoidea (Phocoenidae + Monodontidae + Delphinidae)—por-
poises, monodontids, and dolphins: Gatesy et al. (1999) (nuclear
and mitochondrial data); Cassens et al. (2000) (mitochondrial
DNA and proteins); May-Collado and Agnarsson (2006) and
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 971

Hamilton et al. (2001) (cytb); Heyning (1989) (morphology);
Waddell et al. (2000) (nuclear DNA); Arnason et al. (2004) (mitog-
enomic data); Messenger and McGuire (1998) and De Muizon,
1988 (morphology); O’Leary et al. (2004) (combined morphology,
nuclear DNA, mitochondrial DNA, and amino acids, including fos-
sils); O’Leary and Gatesy (2008) (combined morphology, nuclear
DNA, mitochondrial DNA, including fossils).
Physeteroidea (Kogiidae + Physeteridae)—sperm whales: Gatesy
et al. (1999) (nuclear and mitochondrial data); Cassens et al.
(2000) (mitochondrial DNA and proteins); Hamilton et al. (2001),
Verma et al. (2004), and May-Collado and Agnarsson (2006) (cytb);
Arnason et al. (2004) (mitogenomic data); O’Leary et al. (2004)
(combined morphology, nuclear DNA, mitochondrial DNA, and
amino acids, including fossils).
Ziphiidae—beaked whales: Gatesy et al. (1999) (nuclear and
mitochondrial data); Cassens et al. (2000) (mitochondrial DNA
and proteins); Hamilton et al. (2001), Verma et al. (2004), and
May-Collado and Agnarsson (2006) (cytb); O’Leary et al. (2004)
(combined morphology, nuclear DNA, mitochondrial DNA, and
amino acids, including fossils); Lambert (2005) (morphological
data, including fossils).
Monodontidae—monodontids, narwhal, and beluga: Cassens
et al. (2000) (mitochondrial DNA and proteins); Hamilton et al.
(2001), Verma et al. (2004) and May-Collado and Agnarsson
(2006) (cytb); Waddell et al. (2000) (nuclear DNA); O’Leary et al.
(2004) (combined morphology, nuclear DNA, mitochondrial DNA,
and amino acids, including fossils).
Phocoenidae—porpoises: Cassens et al. (2000) (mitochondrial
DNA and proteins); Hamilton et al. (2001), Verma et al. (2004), Ro-
sel et al. (1995), and May-Collado and Agnarsson (2006) (cytb);
Fajardo-Mellor et al. (2006) (morphological data, including fossils);
O’Leary et al. (2004) (combined morphology, nuclear DNA, mito-
chondrial DNA, and amino acids, including fossils).
Delphinidae—dolphins: Cassens et al. (2000) (mitochondrial DNA
and proteins); Caballero et al. (2008) (nuclear and mitochondrial
DNA); Hamilton et al. (2001),LeDuc et al. (1999) and May-Collado
and Agnarsson (2006) (cytb); O’Leary et al. (2004) (combined mor-
phology, nuclear DNA, mitochondrial DNA, and amino acids, includ-
ing fossils); O’Leary and Gatesy (2008) (combined morphology,
nuclear DNA, and mitochondrial DNA, including fossils).
3. Results
3.1. Benchmark clades
In the full dataset, all of the benchmark clades were recovered
(Figs. 1 and 2 and Table 2), except that one species Moschiola mem-
inna, a member of Tragulidae grouped with Bovidae (Fig. 3), there-
by rendering both families paraphyletic (according with current
taxonomic classification). Moschiola has available sequence shorter
than 30% (but slightly longer than 15%) of the full cytb sequence
length is thus only included in the full matrix. In a subsequent
analysis of the full matrix with this species removed the mono-
phyly of all benchmark clades were supported (not shown). All
benchmark clades were recovered in the pruned two data subset
(see Table 2) and in general support was higher for many clades
than in the full analysis. In the pruned 1 data subset, all benchmark
clades were supported, except Odontoceti due to the placement of
Physeteroidea whose exact placement (like in the full analysis) is
particularly weakly supported.
In all the analyses, most of the currently recognized subfami-
lies/tribes within Cetartiodactyla were recovered as monophyletic,
except subfamilies that have consistently been rejected by recent
phylogenetic analyses (see Section 4). It should be noted that it
can be difficult to accurately estimate agreement with taxonomy
as different authors have presented different taxonomic classifica-
tions. Our results, in general, closely resemble the most recent and
most detailed phylogenetic analyses of the group, but resemble
slightly less well the rather more ‘traditional’ classification pre-
sented in (MacDonald, 2006 see Table 1). The latter does not take
into account some recent suggested changes in taxonomy based
on both morphological and especially molecular data. Hence,
where our results disagree with the classification presented in
MacDonald (2006) the disagreement typically involves taxa whose
placement has been questioned by previous phylogenetic work
(e.g. Neotragus,Oreotragus, see Fig. 4) and/or monotypic subfami-
lies (e.g. Megapterinae, Hydropotinae, Panthalopinae).
For clade support and detailed species-level relationships, see
Fig. 5.
3.2. Higher level relationships
Our results support the following relationship among the four
major cetartiodactylan lineages (((Tylopoda ((Cetancodonta
(Ruminantia + Suina))), with variable support (Figs 1, 2, and 5a
and Table 2). This arrangement has not been suggested previously,
to our knowledge (see review in O’Leary and Gatesy, 2008 and
discussion).
Relationships among clades within Cetancodonta are identical
to those found by May-Collado and Agnarsson (2006) (Figs. 2 and
5d).
Within Ruminantia all our analyzes suggest the following rela-
tionships among families: (((((Tragulidae((((Antilocapridae(((Gir-
affidae((Cervidae(Moschidae + Bovidae))))) with relatively high
support (Figs. 1, 2, and 5a–c and Table 2), supporting the subdivi-
sion of Ruminantia into Tragulina and Pecora.
3.3. Family and subfamilies relationships
We recovered the monophyly of all families within Suina and
Ruminantia in all analyses (Figs. 2 and 5a–c), with the exception
noted above in the full data matrix where Moschiloa (Tragulidae)
seems misplaced within Bovidae ( Figs. 2 and 5c, all Ruminantia
families were monophyletic in the full matrix when this species
was removed prior to analysis and the monophyly of Bovinae re-
ceived much higher support, see Table 2).
Within Bovidae all analyses support Bovinae and Cephalophi-
nae as defined by (MacDonald, 2006)(Figs. 2 and 5a–c). All analyses
also support slightly modified Caprinae and Antelopinae, (see Table
2and Section 4). All analyses support the groups Reduncini, Hippo-
tragini, and Alcelaphini, variously treated as tribes (e.g. by Mac-
Donald, 2006) or subfamilies ( Figs. 2 and 5a–c). However, our
results conclusively reject Hippotraginae sensu MacDonald
(2006) that groups these three. Our results are also consistent with
the monotypic subfamilies Aepycerotinae (Impala, Aepyceros mel-
ampus) and Peleinae (Grey Rhebok, Pelea capreolus) as these do
not nest within other subfamilies, but not with the monotypic Pan-
tholopinae (Tibetan antelope, Pantholops hodgsonii) which nests
within Caprinae (Figs. 2 and 5a–b). Within Bovidae the following
relationship between subfamilies is supported by the three analy-
ses ((((((Bovinae (((((Aepycerotinae (((((Reduncinae + Peleinae)
(((Cephalopinae + Antilopinae) (Caprinae (Hippotraginae + Alcela-
phinae)))))))))) (Fig. 3). Our results support prior findings (e.g. Mat-
thee and Davis, 2001) that Neotragus moschatus (Suni Antelope)
does not belong to Antilopinae. In the full dataset analyses Neotra-
gus groups with Aepycerotinae (Impala) but with weak support
(Figs. 2 and 5b). Our results also reject the inclusion of Oreotragus
(Klipspringer) in Antelopinae (Figs. 2 and 5b), which rather may be-
long to Cephalophinae where it groups with strong support in all
analyses and with which it shares striking morphological similari-
ties (Fig. 4).
972 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

In the pruned datasets 1 and 2, our results support the mono-
phyly of the five major groups (treated variously as subfamilies
or tribes) within Cervidae (Figs. 3 and 5b): Cervinae (including
the extinct Megaloceros ‘Giant deer”), Odocoileinae, Muntiacinae,
Capreolinae, and Alceinae (see Gilbert et al., 2006 where these
are treated as tribes). However, our results differ from those of
Gilbert et al. (2006) in the interrelationships of these groups.
We find that Capreolinae and Alceinae are sister and together
Cat, dog, bear
Horse, rhino
Camel, llama
Pig, warthog
Peccari, javelina
Mouse deer
Pronghorn
Giraffe, okapi
Deer, muntjac
Musk deer
Cow, sheep, antelop e
Hippo
Baleen whales
Toothed whales
PERISSODACTYLA
Odd toed ungulates
TYLOPODA - Camelidae
SUINA
Tragulidae
Antilocapridae
Giraffidae
Cervidae
Bovidae
Moschidae
Hippopotamidae
Odontoceti
Mysticeti
RUMINANTIA
CETANCODONTA
Tayassudidae
Suidae
CARNIVORA
C
E
T
A
R
T
I
O
D
A
C
T
Y
L
A
Fig. 1. Summary cladogram of the full analyses showing higher level relationships among major clades within Cetartiodactyla. Photos by I. Agnarsson and L. May-Collado,
except: warthog and mouse deer provided by M. Kuntner, peccary by M. Saborío, and musk deer (copyright K. Kutunidisz) and pronghorn (copyright J.O. Wolff) obtained with
permission from the ASM Mammal Image Library.
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 973

Panthera leo
Panthera tigris
Canis fam iliaris
Dicerorhinus sum atrensis
Dice ro s bico rnis
Tapirus indicus
Tap irus terre s tris
Eq u u s c ab allu s
Equus grevyi
Lama g lama
Vicugna vicugna
Camelus dromedarius
Camelus bactrianus
Sus barba tus
Sus verrucosus
Sus philippensis
Sus cebifrons
Su s ce le be n sis
Potamocho erus larvatu s
Phacochoerus aethiopicus
Potamocho erus porcus
Phacochoerus africanus
Bab yro u sa bab yru ssa
Pecari tajacu
Tayassu pe c ar i
Catagonus wagneri
Tragulus napu
Tragulus javanicus
Antilocapra americana
Giraffa cam elopardalis
Okapia johnstoni
Alces alces
Hydropotes inerm is
Ca p reo lus ca p re o lu s
Capreolus pygargus
Cervus sc hom burgki
Cervus duvaucelii
Axis porcinus
Dama mesopotam ica
Cervus dama
Cervus nippon
Ce rv u s a lbirostris
Cervus elaphus
Elaphurus davidianus
Megaloceros giganteus
Muntiacus feae
M u n tiac u s c r in ifron s
Muntiacus muntjak
Megamuntiacus vuquangensis
Muntiacus reevesi
Elaphodus ce ph a lophus
Odocoileus hemionus
Od oc o ileu s vir g inia n us
Ozotoceros bezoarticus
Hippocam e lus antisensis
Blastoce ros dichotomus
Mazama gouazoupira
Pudu pud a
Rangifer tarandus
Cervus unicolor
Cervus eldi
Axis axis
Moschus leucogaster
Moschus fuscus
Mo sc hu s chryso g aster
Moschus berezovskii
Moschus m oschiferu s
Bos taurus
Bos grunniens
Pse u d on ov ib os s p ira lis
Bos indicus
Bos gaurus
Bison bonasus
Bos sauveli
Bos frontalis
Bos javanicus
Bison bison
Pseudoryx nghetinhensis
Tra g e lap h u s im be rb is
Tragelaphus euryceros
Tragelap h us sp e kii
Tragelaphus buxtoni
Tragelap h us scr iptus
Tragelap h us stre ps iceros
Tragelaphus oryx
Tragelaphus derbianus
Tragelap h us a ng asii
Bu b alu s q u arle si
Bubalus mindorensis
Bu b alu s b u ba lis
Bub alu s d epressi co rn is
Syncerus caffer
Tetracerus quad ricornis
Boselaphus tragocamelus
Moschiola meminna
Cephalophus zeb ra
Ce p h a lo p h u s c al lip yg u s
Cep ha loph u s we yn si
Cephalophus ogilbyi
Cep ha loph u s rub idus
Cephalophus niger
Cephalophus spadix
Ce p h a lo p h u s s ilvic u lto r
Ce ph a lop hu s do rsa lis
Cephalophus jentinki
Cephalophus nigrifrons
Cep ha loph u s rufilatus
Cephalophus natalensis
Cephalophus harveyi
Cephalophus leucogaster
Cephalophus adersi
Cephalophus monticola
Oreotragus oreotragus
An t ilo pe c erv ic a pra
Ga z ella sa u d illa
Gazella dorcas
Gazella leptoceros
Gazella cuvieri
Gazella subgutturosa
Gazella spekei
Gazella gazella
Antidorcas marsupialis
Gazella granti
Gazella dama
Ga z ella so e m m er ring ii
Gazella bennettii
Litocranius walleri
Ga z e lla rufifro n s
Ga z ella tho m s on ii
Saiga tatarica
Ourebia ourebi
Procapra picticaudata
Procapra gutturosa
Madoqua kirkii
Madoqua guentheri
Raphicerus sharpei
Ra p hic e ru s c am p e s t ris
Raphicerus melanotis
Oryx gazella
Oryx dammah
Oryx leucoryx
Hippotragus niger
Hippotragus equ inus
Connochaetes gnou
Alce lap h u s licht e n ste ini
Alcelaphus buselaphus
Beatragus hunteri
Ovis aries
Ovis canadensis can ade nsis
Ovis dalli
Ovis nivicola
Ovis ammon ammon
Capra cylindricornis
Ovis vignei
He m it ra g u s h ylo criu s
Hemitragus jemlahicus
Capra sibirica
Capra nub iana
Capra caucasica
Capra pyrenaica
Capra ibex
Capra falconeri
Capra aeg agrus
Pseudois schaeferi
Pseudois nayaur
Budorcas taxicolor
Naemorhedus goral
Capricornis crispus
Capricornis sum atraen sis
Ovibos moschatus
Naemorhedus caudatus
Oream nos americanus
Pantholops hodgsoni
Rupicapra rupicapra
Rupicapra pyrenaica
Hemitragus jayakari
Ammotragus lervia
M y o trag us ba le aric u
Kobus vardoni
Kobus ellipsiprym nus
Kobus megaceros
Kobus kob
Redunca redunca
Redunca arundinum
Redunca fulvorufula
Pelea capreolus
Neotragus moschatus
Aepyceros me lampus
Hippopotamus am ph ibius
Hexaprotodon liberiensis
Balaena glacialis
Eu b a lae na a u s tra lis
Eubalaena japonica
Balaena mysticetus
Cap erea m a rginat a
Balaenoptera acuto rostrata
Balaenoptera bonaerensis
Balaenoptera brydei
Balaenoptera eden i
Ba la e n o p ter a bo rea lis
Balaenoptera omurai
Balaenoptera physalus
M e g ap t era no vae an glia e
Balaenoptera musculus
Eschrichtius rob us tus
Kogia breviceps
Kogia sim us
Physeter catodon
Hyperoodon ampullatus
Hyperoodon planifrons
Ind o p a ce t u s p ac ificu s
Ziphius cavirostris
Be r a r d ius b air d ii
Mesoplodon bidens
Mesoplodon traversii
Mesoplodon mirus
Mesoplodon densirostris
Mesoplodon grayi
Mesoplodon stejnegeri
Mesoplodon peruvianus
Mesoplodon ginkgodens
Mesoplodon europaeus
Mesoplodon hectori
Mesoplodon layardii
Mesoplodon carlhubbsi
Tasmac etus sh eph erdi
Platanista gang etica
Platanista m inor
Po n to p oria b lain villei
Inia g eo ffre n sis
Inia geoffren sis h um b o ld tiana
Inia geoffren sis b oliviensis
Lipotes vexillifer
Delphinapterus leucas
Monodon monoceros
Australophocaen a d ioptrica
Ph o c o e n a s p in ip in nis
Phocoena sinus
Phocoena phocoena
Phocoenoides dalli
Neoph ocae na ph ocae noides
Or c a e lla b r e v iro str is
Orcinus orca
Glo b ic ep h ala m a c r or h yn c h u s
Glo b ic ep h ala m e la s
Peponoceph ala electra
Feresa attenuata
Grampus griseus
Pseudorca crassidens
Cephalorhynchus com m ersonii
Cephalorhynchus eutropia
Cephalorhynchus hectori
Cephalorhynchus heavisidii
Lag e n o rhy n c h u s au stralis
Lageno rhynch u s c ruciger
Lageno rhynch u s o bliquidens
Lageno rhynch u s o bscurus
Lissodelphis borealis
Lissodelphis peronii
Delphinus capensis
Delphinus delphis
Delphinus tropicalis
Stenella clym en e
Stenella coeruleoalba
Ste ne lla fr o n ta lis
Tursiops aduncus
Tursio p s tru nca tu s
Sousa chinensis
Stenella atte nua ta
Lagenodelphis hosei
Ste ne lla lo n giro str is
So t a lia fluv ia tilis
So t a lia gu ian e ns is
Steno bredan ens is
Lageno rhynch u s a cu tus
Lag e n o rhy n c h u s alb iro st ris
Balaenopteridae
incl. Eschrichtidae
Neobalaenidae
Balaenidae
Stenoninae
CARNIVORA
PERISSODACTYLA
Tylopoda
R
u
m
i
n
a
n
t
i
a
Suina
C
e
t
a
n
c
o
d
o
n
t
a
Cetartiodactyl
a
Lissodelphinae
Delphininae
Globicephalinae
Orcinae
Caprinae
Cephalophinae
incl. Oreotragus
Alcelaphinae
Hippotraginae
Antelopinae
Reduncinae
Bovinae
Muntiacinae
Cervinae
Cervinae
Capreolinae
Odocoileinae
P
e
c
o
r
a
CAMELIDAE
SUIDAE
TRAGULIDAE
ANTILOCAPRIDAE
TAYASSUIDAE
BOVIDAE
DELPHINIDAE
PHOCENIDAE
MONODONTIDAE
GIRAFFIDAE
CERVIDAE
MOSCHIDAE
HIPPOPOTAMIDAE
PHYSETEROIDEA
ZIPHIDAE
PLATANISTIDAE
INIIDAE, PONTOPORIDAE, LIPOTIDAE
Alceinae
Aepycerotinae*
Kogidae
Physeteridae
MYSTICETI
C
e
t
a
c
e
a
ODONTOCETI
DELPHINA
DELPHINOIDEA
Fig. 2. Majority rule consensus of the Bayesian analyses of the full dataset. Cladogram is colored according with families, labels include all benchmark clades and major
groups at the level of subfamily and above. Subfamilies whose monophyly has been consistently rejected by prior phylogenetic analyses (e.g. ziphiid subfamilies) are omitted.
Arrows indicate species that appear misplaced given current knowledge. At the family level this includes only the tragulid Moschiola meminna that groups within Bovidae. At
the subfamily level, this includes a clade of three Southeast Asian Cervinae species placed sister to the remaining Cervidae and apart from other cervines.
974 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

more closely related to Muntiacinae + Cervinae than to
Odocoileinae.
There is additional conflict in the full dataset, where three sup-
posedly Cervinae species, the Southeast Asian Cervus unicolor,Cer-
vus eldi, and Axis axis, group sister to the remaining Cervidae
rendering Cervinae (and Plesiometacarpalia) paraphyletic (Fig. 2).
This arrangement appears well supported in our analyses, but con-
tradicts prior phylogenies and may be due to the fact that the three
all have short sequences and are thus only present in the full
dataset.
Table 2
Recovery and support of benchmark clades and subfamilies within Cetartiodactyla. Numbers are posterior probability values
Benchmark clades Full matrix Pruned matrix 1 Pruned matrix 2
Cetartiodactyla 50 100 99
Tylopoda 98 100 100
Ruminantia 60 100 100
Pecora 60 100 100
Bovidae NO/41
j
65 80
Moschidae 100 100 100
Cervidae 100 100 100
Giraffidae 64 60 64
Antilocapridae
a
60 83 98
Suina 100 100 100
Suidae 100 100 100
Tayassuidae 100 100 100
Cetancodonta 99 100 100
Cetacea 100 100 100
Mysticeti 100 100 100
Odontoceti 27 NO 84
Delphina 100 100 100
Delphinoidea 86 41 70
Physeteroidea 99 90 88
Ziphiidae 100 100 100
Monodontidae 100 100 100
Phocoenidae 100 100 100
Delphinidae 100 100 100
Subfamilies
Odocoileinae
b
100 100 100
Capreolinae 100 100 100
Hydropodinae
c
100 100 100
Cervinae NO 88 100
Muntiacinae 99 100 100
Bovinae 49 100 100
Reduncinae/Reduncinae incl. Peleaeninae 72/95 86 100
Antelopinae/sans Neotragus and Oreotragus
d
NO/100 NO/100 NO/100
Hippotraginae sensu MacDonald/Hippotraginae
e
NO/99 NO/100 NO/100
Alcelaphinae (Alcelaphini) 56 100 100
Cephalophinae 100 100 100
Caprinae
f
100 100 100
Balaenopterinae/sensu lato
g
NO/100 NO/100 NO/100
*
Megapterinae
h
NO NO NO
*
Ziphiinae NO NO NO
*
Hyperodontinae NO NO NO
Lissodelphininae
i
100 100 100
Delphininae 100 92 100
Globicephalinae 100 100 100
Orcininae 95 91 92
Stenoninae 69 70 87
Recovery of Benchmark clades and subfamilies in the three matrices. Full matrix (including all species with at least 15% of full length cytb sequence available), pruned matrix
1 (species with 30% or more of full sequence length), and pruned matrix 2 (species with 50% or more of full sequence length). Classification follows MacDonald (2006) and/or
recent phylogenetic studies as discussed in text. Subfamilies marked with an asterix are ones that have been consistently rejected by prior phylogenetic work and whose
rejection here thus indicates signal congruent with other data.
a
Represented by a single species, number refers to support for its placement outside any other family.
b
Odocoileini sensu Gilbert et al. (2006).
c
This monotypic subfamily in all analyses nests sister to the remaining Capreolinae with strong support, consistent with either its inclusion in Capreolinae or its reduntant
placement in its own family, see also Gilbert et al. (2006).
d
Previous studies have questioned the placement of Neotragus and Oreotragus in Antelopinae (e.g. Matthee and Davis, 2001 based on nuclear and mitochondrial DNA), see
text for discussion.
e
Hippotraginae sensu (MacDonald, 2006) includes the tribes Reduncini, Alcelaphini, and Hippotragini, whereas some other authors treat these three groups as separate
subfamilies, in all our analyses the three are tribes are monophyletic, but Reduncini never clusters with the other two. This finding supports the latter view of treating the
three as subfamilies.
f
Caprinae is here treated as including Pantholops hodgsoni, traditionally in Antilopinae or its own subfamly Pantholopinae (see MacDonald, 2006), however, multiple
studies based on both morphology and molecular data have shown that this species, the ‘‘Tibetan antelope”, is in fact, a goat (Gentry 2002). Caprinae also includes the extinct
Balearic Island Cave Coat (Myotragus balearicus).
g
The monophyly of Balaneopteridae has been refuted numerous times based on molecular data, the monotypic family Eschirichtiidae always nests within it. Based on
these results both Eschrichtius eschrichtius, and Megaptera novaeangliae should be placed in the genus Balaneoptera, hence within Balaneopterinae (also rejecting the
subfamily Megapterinae).
h
See footnote g, this monotypic subfamiliy in most studies nests within the genus Balaneoptera.
i
Sensu May-Collado and Agnarsson (2006) and excluding Lagenorynchus acutus and L. albirostris, treated by MacDonald (2006) as incertae sedis.
j
Moschiola meminna (Tragulidae) here nests within Bovidae rendering both families paraphyletic, see text. Support value after ‘‘/” refers to Bovidae including Moschiola.
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 975

Within cetaceans, with the exception of Balaenopteridae and
Eschrichtidae (which have consistently been rejected, see e.g.
May-Collado and Agnarsson, 2006 and Discussion), all families
within Cetacea were recovered (Figs. 2 and 5d). At the level of sub-
families the picture is more complex. As we and others have found
previously (e.g. May-Collado and Agnarsson, 2006), molecular data
continues to reject the monophyly of the subfamilies within Ziph-
iidae (Ziphiinae = Ziphius, Tasmacetus, and Berardius, Hyper-
Capreolinae+Alcinae
New World Deer,
Water Deer + Moose
Cervinae -True Deer
Aepycerotinae
Impala,*Suni antelope
Caprinae - Goats
Alcelaphinae
Hartebeast,
Wilderbeast
Hippotraginae
Grazing Antelopes
Antelopinae
Antelopes,
gazelles
Cephalophinae
Duikers,*Klipspringer
Reduncinae + Peleinae
Waterbucks, Reedbucks
+ Rhebok
Bovinae, Cattle, Bison
large ‘Antelopes’
Moschinae
Musk Deer
Odocoileinae
New World Deer
Muntiacinae, muntjacs
CERVIDAE
MOSCHIDAE
BOVIDAE
Plesiometacarpalia
Fig. 3. Summary cladogram of Bovidae, Cervidae and Moschidae. Photos by I. Agnarsson and L. May-Collado, except: Capreolus capreolus copyright Ralf Schmode; and
Sylvicapra grimmia copyright G.C. Hickman, and Moschus moschiferus copyright K. Kutunidisz, the latter two obtained with permission from the ASM Mammal Image Library.
976 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

oodontidae = Hyperoodon, Mesoplodon, and Indopacetus) and within
Phocoenidea (Phocoeninae and Phocoenoidinae). Within Delphini-
dae we recover all subfamilies except Delphinidae (Figs. 2 and 5d)
due to the placement of Lagenorhynchus (as found previously by
LeDuc et al., 1999, and May-Collado and Agnarsson, 2006). Our full
analysis suggests the following subfamilies relationships:
((((Orciniae (((Globicephalinae ((Lissodelphininae (Stenoni-
nae + Delphininae)))). However, this arrangement had very weak
support (Fig. 2) and the phylogenetic relationships between sub-
families were not consistent between analyses (Fig. 5d). Our re-
sults continue to reject current taxonomic classification with
regards to Lagenorhynchus (May-Collado and Agnarsson, 2006).
3.4. Extinct species
The extinct ‘mouse goat’ ( M. balearicus) did not group with
goats, but rather as sister to remaining Caprinae, the clade contain-
ing goats, sheep, and relatives. Lalueza-Fox et al. (2005) similarly
refuted the placement of Myotragus among goats, but in their anal-
ysis it grouped sister to sheep. The extinct ‘Irish Elk’ (M. giganteus)
is here within Cervinae sister to Père David’s Deer (Elaphurus
davidianus) and together these group with fallow deer (Dama).
4. Discussion
4.1. Recovery of benchmark clades: the reliability of cytochrome b and
importance of dense taxon sampling
Nearly all benchmark clades were recovered in all analyses
(Figs. 1–3 and 5 and Table 2). At the level of families the only
real inconsistency surrounds a single species with a very short
sequences available (Moschiola,Fig. 2). Otherwise, our results dif-
fer only from some traditional classifications in the placement of
species whose phylogenetic position has been questioned by
many previous studies (i.e. taxa that recent evidence suggests
are misplaced in traditional classifications). Furthermore, our re-
sults, as far as comparable, are identical to the most character-
complete analysis of extant Cetartiodactyla to date, scoring 28
taxa for a massive dataset of over 600 morphological and
40.000 molecular characters (O’Leary and Gatesy, 2008, their
Fig. 7, but note that the inclusion of fossils impacted their results
and their total evidence tree differs slightly in the placement of
Suina and Moschidae). This is a remarkable result for several rea-
sons. First, single-gene analyses rarely give results that agree
with global optima. Second, the ratio of character data to num-
ber of taxa is relatively low so that cytb seems to contain
remarkable level of information at various phylogenetic levels.
In fact, cytb has been used successfully for phylogenetic analyses
of populations within species (Ludt et al., 2004), yet it resolves
divergences as old as 60 million years (see e.g. O’Leary and Gate-
sy, 2008) or more. Third, previous studies involving two to many
genes often fail to recover ‘known’ clades within Cetartiodactyla,
including previous analyses using cytb. The latter implies that
sparse taxon sampling in previous studies is, at least partially,
to blame.
We provide two examples to show evidence that dense taxon
sampling increases phylogenetic accuracy with the cytb gene.
Guha et al. (2007) analyzed relationships within the infraorder
Pecora using many fewer taxa than included here, but using
an additional loci, 16S. They found that ‘‘Consistent with the
findings of most previous molecular investigations, we could
not unambiguously resolve the monophyly of Bovidae... This
apparent paraphyly of Bovidae may be attributed to the distant
position of the Tragulidae outgroup and the subsequent satura-
tion of substitutions in the Pecora/Tragulina comparisons. In an
evolutionary context, the rapid cladogenesis of Bovidae offered
little time for mutations to accumulate along common stems,
thereby complicating the molecular analysis. Future work with
additional data and more taxa will be required to unambigu-
ously resolve the monophyly of Bovidae” (Guha et al. 2007, p.
593). Similarly Wada et al. (2007) analyzed a small set of taxa
and emphasized that cytb failed to recover the monophyly of
Bovidae, while analysis of 13 mitochondrial genes did recover
it. In contrast, our study with much denser taxon sampling,
even though based on a single gene, recovers the monophyly
of Bovidae (apart from the wayward Moschiola in the full anal-
ysis, see below) and every subfamily within it (Figs. 2 and 5a–
c). For another example O’Leary and Gatesy (2008) discuss how
their finding differs from several previous studies in the place-
ment of Camelidae as sister to the remaining Cetartiodactyla.
They suggest that the more distal placement of Camelidae in
previous studies ‘‘...apparently was driven by the extensive
mitochondrial genome data...in these combined matrices...,
but the larger sampling of nuclear loci in the present study
overturned the mitochondrial genome data and supported a ba-
sal positioning of Camelidae within Cetartiodactyla”. However,
our study, even though based only on a single mitochondrial
gene, also supports Camelidae + remaining Cetartiodactyla
(Fig. 1); hence it may not be that the mitochondrial data were
misleading in previous studies, but rather that dense taxon sam-
pling just like adding character data increases phylogenetic
accuracy (e.g., Graybeal, 1998; Hillis, 1996, 1998; Hillis et al.,
2003; Pollock et al., 2002; Zwickl and Hillis, 2002; contra e.g.
Rokas and Carroll 2005).
In the rare cases where our results are inconsistent with
benchmark clades, ad hoc explanations seem reasonable. The
placement of M. meminna (Tragulidae) within Bovidae is likely
an artifact of missing data, although remarkably it is the only
conspicuous misplacement of a species across the whole phylog-
eny at the family level (while three species appear to be mis-
placed at the subfamily level within Cervidae in the full
analysis, see Fig. 5a). This is supported by the fact that the place-
ment of Moschiola receives low support, and the removal of
Moschiola prior to analysis increases dramatically the support
for clades close to where it nested (not shown, analysis available
from authors), suggesting it had a tendency to ‘jump around’. Two
other possibilities cannot be ruled out, however. One, that possi-
bly the available sequence in Genbank may be mislabeled. And
second, it should be kept in mind that the validity of Tragulidae
has never been tested with molecular data including more than
two species (see e.g. Price et al., 2005). Hence, it seems too early
to rule out the possibility that it is not monophyletic. That the
Fig. 4. The Klipspringer (Oreotragus) (left) traditionally is placed within Antilopi-
nae, but shares striking similarities with the Duikers (Cephalophinae) (right) where
it groups with strong support in all our analysis. Photo of Klipspringer provided by
S. Barrett, that of the duiker obtained from the Karee Safari website: http://
www.kareesafaris.co.za.
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 977

sequence of Moschiola is conspicuously different from the two
other tragulids here included (personal observation) is consistent
with either of these two possibilities.
The non-monophyly of Odontoceti in the pruned dataset 1 is
unsurprising. There is a long history of failure to recover Odonto-
ceti with mitochondrial data, presumably because an explosive
Panthera leo
Panthera tigris
Canis familiaris
Dicerorhinus sumatrensis
Diceros bicornis
100
100
Tapirus indicus
Tapirus terrestris
62
Equus caballus
Equus grevyi
100
100
Lama glama
Vicugna vicugna
100
100
100
100
Camelus dromedarius
Camelus bactrianus
99
98
Sus barbatus
Sus verrucosus
97
96
Sus philippensis
Sus cebifrons
77
100
100
Sus celebensis
99
Potamochoerus larvatus
100
100
Phacochoerus aethiopicus
Potamochoerus porcus
98
87
Phacochoerus africanus
N/A
55
87
95
Babyrousa babyrussa
100
100
Pecari tajacu
Tayassu pecari
100
100
100
100100
Catagonus wagneri
100
100
Tragulus napu
Tragulus javanicus
100
93
Antilocapra americana
Giraffa camelopardalis
Okapia johnstoni
64
64
Alces alces
Hydropotes inermis
Capreolus capreolus
Capreolus pygargus
N/A
100
94
100
100
94
Cervus schomburgki
Cervus duvaucelii
N/A
N/A
N/A
N/A
N/A
64
100
Axis porcinus
Dama mesopotamica
Dama dama
59
Cervus nippon
Cervus albirostris
Cervus elaphus
43
90
36
58
0.54
54
Elaphurus davidianus
Megaloceros giganteus
N/A
31
100
99
Muntiacus feae
Muntiacus crinifrons
100
N/A
100
100
100
73
Muntiacus muntjak
69
Megamuntiacus vuquangensis
67
Muntiacus reevesi
100
Elaphodus cephalophus
99
100
99
85
Odocoileus hemionus
Odocoileus virginianus
100
100
Ozotoceros bezoarticus
Hippocamelus antisensis
N/A
84
Blastoceros dichotomus
Mazama gouazoupira
N/A
100
67
92
90
Pudu puda
100
99
100
98
Rangifer tarandus
100
100
N/A
91
Cervus unicolor
Cervus eldi
100
Axis axis
100
100
Moschus leucogaster
Moschus fuscus
32
Moschus chrysogaster
57
Moschus berezovskii
74
Moschus moschiferus
100
100
84
44
88
50
100
60
100
60
97
49
99
60
99
50
100
100
100
100
100
99
BOVIDAE
CETANCODONTA
see p. xx
Suina
Tylopoda
Perissodactyla
Cetartiodactyla
Ruminantia
Pecora
Cervidae
Tragulina/Tragulidae
Antilocapridae
Giraffidae
Moschidae
86
N/A
N/A
N/A
N/A
N/A
Suidae
Tayassuidae
Alcinae
Capreolinae
Cervinae
Muntiacinae
Odocoileinae
remaining Cervinae
Fig. 5. Majority rule consensus of the Bayesian analyses of the full dataset with major clades labeled. Values above branches show posterior probabilities in the full analysis,
below branches posterior probabilities of the analysis of the pruned dataset 2. Clades that are not tested in the pruned dataset 2 (due to absence of species in the analysis) are
labeled ‘‘N/A”, clades recovered in the full analysis but rejected in the pruned dataset 2 analysis are marked with a star. (a) Outgroups, Tylopoda, Suina, and Ruminantia minus
Bovidae. (b) Bovidae, minus Bovinae. (c) Bovinae plus Moschiola (Tragulidae). Note that when Moschiola is removed prior to analysis (see Section 4) the support for Bovinae in
the full dataset increases dramatically to 97. (d) Cetancodonta.
978 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

radiation took place early in the evolutionary history of whales,
with little time to accumulate synapomorphies for major lineages
such as Odontoceti (Arnason et al. 2004). However, with large en-
ough character data sets (entire mitochondrial genome, Arnason
et al. 2004), or dense taxon sampling (May-Collado and Agnarsson
2006) Odontoceti has been supported by mitochondrial data. Here,
we find that Odontoceti is recovered when missing data is mini-
mized (pruned dataset 2) and when taxon sampling is most dense
(full dataset, although there is essentially equal support for the
placement of Physeteroidae within, or outside, Odontoceti). This
suggests a complicated relationship between the benefits of adding
taxa versus the problems with missing data (i.e. adding taxa with
Cephalophus zebra
Cephalophus callipygus
Cephalophus weynsi
Cephalophus ogilbyi
Cephalophus rubidus
Cephalophus niger
Cephalophus spadix
Cephalophus silvicultor
Cephalophus dorsalis
Cephalophus jentinki
Cephalophus nigrifrons
Cephalophus rufilatus
Cephalophus natalensis
Cephalophus harveyi
Cephalophus leucogaster
Cephalophus adersi
Cephalophus monticola
Oreotragus oreotragus
Antilope cervicapra
Gazella saudilla
Gazella dorcas
Gazella leptoceros
Gazella cuvieri
Gazella subgutturosa
Gazella spekei
Gazella gazella
Antidorcas marsupialis
Gazella granti
Gazella dama
Gazella soemmerringii
Gazella bennettii
Litocranius walleri
Gazella rufifrons
Gazella thomsonii
Saiga tatarica
Ourebia ourebi
Procapra picticaudata
Procapra gutturosa
Madoqua kirkii
Madoqua guentheri
Raphicerus sharpei
Raphicerus campestris
Raphicerus melanotis
Oryx gazella
Oryx dammah
Oryx leucoryx
Hippotragus niger
Hippotragus equinus
Connochaetes gnou
Alcelaphus lichtensteini
Alcelaphus buselaphus
Beatragus hunteri
Ovis aries
Ovis canadensis canadensis
Ovis dalli
Ovis nivicola
Ovis ammon ammon
Capra cylindricornis
Ovis vignei
Hemitragus hylocrius
Hemitragus jemlahicus
Capra sibirica
Capra nubiana
Capra caucasica
Capra pyrenaica
Capra ibex
Capra falconeri
Capra aegagrus
Pseudois schaeferi
Pseudois nayaur
Budorcas taxicolor
Naemorhedus goral
Capricornis crispus
Capricornis sumatraensis
Ovibos moschatus
Naemorhedus caudatus
Oreamnos americanus
Pantholops hodgsoni
Rupicapra rupicapra
Rupicapra pyrenaica
Hemitragus jayakari
Ammotragus lervia
Myotragus balearicu
Kobus vardoni
Kobus ellipsiprymnus
Kobus megaceros
Kobus kob
Redunca redunca
Redunca arundinum
Redunca fulvorufula
Pelea capreolus
Neotragus moschatus
Aepyceros melampus
99
100
96
100
100
100
94
95
76
90
BOVINAE
52
90 100
100
100
100
100
100 95
95
79
64
91
96 100
100
100
100
100
100
100
97
36
95
33
48
51
55
71
47
82
30
81
58
68
37 40
99
68
35
97
75
100
77 97
58
99 100
100
97
78
39
61
36
100
66 N/A
100
47
56
99
100
100 98 100
99
99 100
100
100
100 100
100
100
100
100
100
100
100
18
100
87
97
57
55
N/A
35
17
11
21
70
13
46
50
88
51
34
100
100
100
100
100
100
100
100
95
72 N/A
100
93
98
86
98
50
57
100
49
100
100
100
35
99
50
46
25
41
88
22 99
85
86
87
75
100
100
80
100
N/A
N/A
N/A
N/A
N/A
N/1
N/A
N/A
N/A
N/A
N/A N/A
N/A N/A
N/A
N/A N/A N/A N/A
N/A
N/A
N/A
N/A
N/A
Aepycerotinae*
Reduncinae
Caprinae
Hippotraginae
Alcelaphinae
Cephalophinae*
Antilopinae
Peleinae
Fig. 5 (continued)
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 979

partial sequences). The generally higher support values for clades
in the pruned datasets 1 and 2 than in the full dataset similarly
suggest a complex relationship. Broadly it seems that clades sup-
ported by values of 25 or above in the full analysis tend to be
recovered with higher support (often much higher) in the pruned
analyses, while clades supported by values of 20 of less in the full
analyses are typically contradicted by the pruned analyses (Fig, 5).
In general, we find that adding taxa with incomplete sequences ap-
pears rarely misleading in our analysis (as few clades are contra-
dictory between the full and the pruned datasets), but often
results in lowered support values.
Our findings suggest that cytb contains a remarkable amount
of phylogenetic information at various taxonomic levels. They
also serve to remind us that just like adding characters adding
taxa adds data (e.g. Miller and Hormiga, 2004; Geuten et al.
2007). While character rich (but typically relatively taxon poor)
studies such as the one of O’Leary and Gatesy (2008) may be
better suited to address high-level relationships than an analysis
such as ours (e.g. Rokas and Carroll 2005), poor taxon sampling
can also be problematic (e.g., Naylor and Brown, 1998; Soltis
et al., 2004; Philippe et al., 2005; Hedtke et al., 2006) and thus
densely sampling taxa may be just as important for phylogenetic
accuracy (e.g., Graybeal, 1998; Hillis, 1996, 1998; Hillis et al.,
2003; Pollock et al., 2002; Zwickl and Hillis, 2002). And, as a
beneficial side effect, dense taxon sampling also results in phy-
logenies with a broader general utility than taxon-sparse
analyses.
4.2. Higher level relationships
In terms of higher level relationships, our findings in many
cases agree with recent studies based on more character data but
sparser taxon sample (Figs. 1, 2, and 5). This is particularly true
for relationships that have been relatively stable in previous anal-
yses and for comparisons with studies using SINE’s, multiple genes,
and/or genes plus morphology. However, for relationships among
groups that have been much disputed, our findings are most sim-
ilar to the most character-complete study of Cetartiodactyla to
date, that of O’Leary and Gatesy (2008). Previous studies disagree
on the relationships among the four major cetartiodactylan lin-
eages, often finding low support for any given arrangement (e.g.
Ursing et al., 2000). Perhaps the most frequently suggested
arrangement is (((Tylopoda ((Suina (Cetancodonta + Ruminantia)))
(e.g. Boisserie et al., 2005; Price et al., 2005; O’Leary and Gatesy,
2008), while Arnason et al. (2002) and O’Leary et al. (2004) sug-
gested ((Suina + Tylopoda) (Cetancodonta + Ruminantia)), and
Ursing et al. (2000) proposed (((Suina ((Tylopoda (Cet-
ancodonta + Ruminantia))) among others. Our results suggest
(((Tylopoda ((Cetancodonta (Ruminantia + Suina))) (see Figs. 1
and 2) which differs from O’Leary and Gatesy (2008) only in the
placement of Suina with Ruminantia, instead of sister to Ruminan-
tia plus Cetancodonta. However, in their study, the placement of
Suina was unresolved in the strict consensus suggesting we must
still conclude that the relationship among these groups, or mini-
mally the placement of Suina, is still an open question.
Relationships among clades within Cetancodonta are better
agreed upon in general and, unsurprisingly, our results are near
identical to those found by our previous analyses of that clade
(see May-Collado and Agnarsson, 2006 for discussion).
Within Ruminantia all our results support its subdivision into
Tragulina and Pecora and suggest the following relationships
among families: (((((Tragulidae((((Antilocapridae(((Giraffidae
((Cervidae(Moschidae + Bovidae))))) (see Figs. 1, 2. and 5). The rela-
tionship of these large groups has been unstable in previous stud-
ies (for reviews see Hassanin and Douzery, 2003 and Price et al.,
2005; see also Beintema et al., 2003; Mahon, 2004; Guha et al.,
2007; O’Leary and Gatesy, 2008). For example, Hassanin and Douz-
ery (2003) analyzed seven loci including both mitochondrial and
nuclear data their parsimony analysis supported the same relation-
ships as we present here. However, they did not find conclusive
support for the relative position of Antilocapridae and Giraffidae
and hence they left these unresolved in their preferred hypothesis
as sister to ((Cervidae (Moschidae +Bovidae)). In all our analyses,
however, the placement of Antilocapridae as sister to the remain-
ing Pecora is well supported (Fig. 5a, the same arrangement was
found by Kuznetsova et al., 2002, although their analysis did not
include Moschidae). Similarly, O’Leary and Gatesy (2008) did not
conclusively resolve the relationships among these groups. Inter-
estingly, our results are identical to their analysis of extant taxa
based on extensive molecular and morphological character data
(their Fig. 7). However, their combined extant and extinct data
placed Moschidae as sister to the remaining Pecora representing
‘‘a rare case where inclusion of fossils overturned relationships
supported by an extensive sample of molecular and morphological
data for extant species”. Given that his arrangement was supported
by a minimal Bremer support of 1 (O’Leary and Gatesy, 2008, Fig.
4), further work is needed to examine why the inclusion of fossil
taxa has this effect on the placement of Moschidae.
Bos taurus
Bos grunniens
Pseudonovibos spiralis
Bos indicus
Bos gaurus
Bison bonasus
Bos sauveli
Bos frontalis
Bos javanicus
Bison bison
Pseudoryx nghetinhensi
Tragelaphus imberbis
Tragelaphus euryceros
Tragelaphus spekii
Tragelaphus buxtoni
Tragelaphus scriptus
Tragelaphus strepsicer
o
Tragelaphus oryx
Tragelaphus derbianus
Tragelaphus angasii
Bubalus quarlesi
Bubalus mindorensis
Bubalus bubalis
Bubalus depressicornis
Syncerus caffer
Tetracerus quadricornis
Boselaphus tragocamel
u
Moschiola meminna
100
100 57
N/A
55
98
85
56
100
100
100 37
56
69
25
90
N/A
69
42
100
99
97
83
62
54
99
100
82
71
14
34
29
100
49
N/A
50
92 100
99
N/A
N/A
N/A
61
29
40
100
100 100
Bovinae
N/A
98 N/A
N/A
40
Fig. 5 (continued)
980 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

4.3. Family and subfamily relationships
It is more complicated to estimate the agreement of our results
with existing taxonomy at the levels of subfamilies and tribes both
because different authors propose conflicting taxonomic hypothe-
ses that often coexist in literature, and sufficiently detailed spe-
cies-level phylogenies have often previously been lacking to
choose among these hypotheses. The extensive use of detailed
ranks also confuses (e.g. Kuntner and Agnarsson, 2006), and the
same clades are treated as different ranks by different authors.
However, our findings generally agree well with the best available
recent low-level phylogenies.
Orcaella brevirostris
Orcinus orca
Globicephala macrorhynchus
Globicephala melas
Peponocephala electra
Feresa attenuata
Grampus griseus
Pseudorca crassidens
Cephalorhynchus commersonii
Cephalorhynchus eutropia
Cephalorhynchus hectori
Cephalorhynchus heavisidii
Lagenorhynchus australis
Lagenorhynchus cruciger
Lagenorhynchus obliquidens
Lagenorhynchus obscurus
Lissodelphis borealis
Lissodelphis peronii
Delphinus capensis
Delphinus delphis
Delphinus tropicalis
Stenella clymene
Stenella coeruleoalba
Stenella frontalis
Tursiops aduncus
Tursiops truncatus
Sousa chinensis
Stenella attenuata
Lagenodelphis hosei
Stenella longirostris
Sotalia fluviatilis
Sotalia guianensis
Steno bredanensis
Lagenorhynchus acutus
Lagenorhynchus albirostris
Delphinapterus leucas
Monodon monoceros
Australophocaena dioptrica
Phocoena spinipinnis
Phocoena sinus
Phocoena phocoena
Phocoenoides dalli
Neophocaena phocaenoides
Pontoporia blainvillei
Inia geoffrensis
Inia geoffrensis humboldtiana
Inia geoffrensis boliviensis
Lipotes vexillifer
Platanista gangetica
Platanista minor
Hyperoodon ampullatus
Hyperoodon planifrons
Indopacetus pacificus
Ziphius cavirostris
Berardius bairdii
Mesoplodon bidens
Mesoplodon traversii
Mesoplodon mirus
Mesoplodon densirostris
Mesoplodon grayi
Mesoplodon stejnegeri
Mesoplodon peruvianus
Mesoplodon ginkgodens
Mesoplodon europaeus
Mesoplodon hectori
Mesoplodon layardii
Mesoplodon carlhubbsi
Tasmacetus shepherdi
Kogia breviceps
Kogia simus
Physeter catodon
Balaena glacialis
Eubalaena australis
Eubalaena japonica
Balaena mysticetus
Caperea marginata
Balaenoptera acutorostrata
Balaenoptera bonaerensis
Balaenoptera brydei
Balaenoptera edeni
Balaenoptera borealis
Balaenoptera omurai
Balaenoptera physalus
Megaptera novaeangliae
Balaenoptera musculus
Eschrichtius robustus
Hippopotamus amphibius
Hexaprotodon liberiensis
N/A
64
100
100
100
100
86
96
100
100
100
100
100
100 100
100
100
100
100
N/A
N/A
75
99
68
49
37
94
54
94
100
99
100
99
100
100
87
71
14
12
92
43
44 37
60
85
76
63
98
41
50
71
67
20
34
46
44
72
100
66
92
65
100
84 100 100
100
81 100 100
100
100
100
100
100
100
100
67
100
100
100
100
99
100
100 98
100
87
87
40
49
62
55 88
43
99 89
93 77
99
77
99
99
68
96
100
95
64 78
99
62
100
73
99
77
69
100
58
55 57 100
51
92
94
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
37
27
70
36
73
43
84
27
100
100
100
99
N/A N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
100
100
N/A
Orcinae
Globicephalinae
Lissodelphinae
Delphininae
Stenoninae
Lagenorhynchus sensu stricto
Monodontidae
Phocoenidae
Delphinidae
Lipotoidea
Inoidea
Platanistoidea
Delphina
Pandelphina
Delphinoidea
Physeteroidea
Ziphidae
Odontoceti
Cetacea
Mysticeti
Hippopotamidae
Balaenidae
Neobalaenidae
Balaenopteridae
(incl. Eschrictidae)
Fig. 5 (continued)
I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985 981

Within Bovidae all analyses support Bovinae and Cephalophi-
nae as defined by (MacDonald, 2006)(Figs. 3 and 5b–c). All analy-
ses also support slightly modified Caprinae and Antelopinae (Fig.
5b), following strong evidence from previous studies that was
not incorporated by MacDonald (2006, see e.g. Matthee and Davis,
2001; Hassanin and Douzery, 2003). All analyses support the
groups Reduncini, Hippotragini and Alcelaphini, variously treated
as tribes (e.g. by MacDonald, 2006) or subfamilies. However, our
results conclusively reject Hippotraginae sensu MacDonald
(2006) that groups these three (Figs 2, 5b), as have other studies
(e.g. Matthee and Davis, 2001; Hassanin and Douzery, 2003). With-
in Bovidae the following relationship between subfamilies is sup-
ported by the three analyses (((((Bovinae ((((Reduncinae
(((Cephalopinae + Antilopinae) (Caprinae (Hippotraginae + Alcela-
phinae))))))))) (Fig. 3). This arrangement is consistent with the
phylogeny of Hassanin and Douzery (2003) but better resolved.
Our results support prior findings that Neotragus does not belong
to Antilopinae (e.g. Matthee and Davis, 2001), and according with
our results it could possibly belong to Aepycerotinae (with the Im-
pala) (see Figs. 2 and 3), however, support is weak for its placement
and further analyses are necessary to clarify its phylogenetic place-
ment. Our results also reject the inclusion of Oreotragus (Klipsprin-
ger) in Antelopinae, but rather may belong to Cephalophinae
(Duikers). In light of this result, it is worth noting the striking sim-
ilarities between the Klipspringer and the Duikers (Fig. 4).
Within Cervidae there is, similarly, little stability in the taxo-
nomic categories (both ranks and membership of taxa) used by dif-
ferent authors. MacDonald (2006) includes the subfamilies
Muntiacinae, Cervinae, Capreolinae, and the monotypic Hydropot-
inae, while Gilbert et al. (2006), in a recent detailed phylogeny
using multiple genes, divided the familiy into two subfamilies
(Cervinae containing two tribes Cervini and Muntiacini, a group
also termed ‘‘Plesiometacarpalia”) and Capreolinae containing
three tribes Odocoileini, Capreolini and Alceini (a group also
termed ‘‘Telemetacarpalia”). Our results are more consistent with
Gilbert et al. (2006) and we will compare our results to their taxo-
nomic groups, although for consistency we will discuss their five
tribes as subfamilies. In the pruned datasets 1 and 2 our results
support the monophyly of all six subfamilies: Cervinae, Odocoilei-
nae, Muntiacinae, Hydropotinae, Capreolinae, and Alceinae). How-
ever, the relationships among these groups differ in our study from
those found by Gilbert et al. (2006) in that Capreolinae and Alcei-
nae are sister and together more closely related to muntiaci-
nae + Cervinae than to Odocoileinae. Hence, our results are
inconsistent with Telemetacarpalia, but still support Plesiometa-
carpalia. It should be noted that these two groups were originally
proposed based on a single character (defining one group by the
plesiomorphic and the other by the derived character state), an ap-
proach that has historically, and unsurprisingly, often resulted in
paraphyletic taxonomic groups. Despite its name, the Plesiometa-
carpalia condition, the presence of only the proximal part of the
lateral metacarpals, is the derived one (see e.g. Gilbert et al.,
2006) and our results from the pruned analyses support this con-
dition as a synapomorphy.
In the full dataset, however, our results differed further from
Gilbert et al. (2006) in the placement of three supposedly Cervinae
species (C. unicolor,C. eldi, and A. axis) as sister to the remaining
Cervidae. This renders both Cervinae and Plesiometacarpalia para-
phyletic in our full analyses and represents probably the greatest
disagreement between our study and recent well supported phy-
logenies (Gilbert et al. 2006). All three species have short se-
quences, but in general clades within Cervidae are well
supported in the full dataset. Here, we have a conflict between a
study with more character data but fewer taxa (Gilbert et al.
2006) and one with a dense taxon sample but a single-gene. While
it is not obvious what to conclude about this conflict, other than
Cervidae phylogenetics need further attention, our study by dense
taxon sampling provides a particularly useful tool for comparative
studies while we recommend adopting the Cervidae classification
of Gilbert et al. (2006), until more detailed studies become
available.
Within cetaceans, with the exception of Balaenopteridae and
Eschrichtidae (see May-Collado and Agnarsson, 2006), all families
within Cetacea were recovered ( Figs. 2 and 5d). The grey whale
(Eschrichtius) the only member Eschrichtidae consistently nested
within Balaenopteridae as has been found in many other studies
(e.g. Rychel et al., 2004; May-Collado and Agnarsson, 2006). Only
fossil evidence still supports Balaenopteridae exclusive of Eschric-
tius (Steeman, 2007), however, a more detailed combined analysis
remains to be done.
The phylogenetic position of Platanistidae is perhaps the most
disputed in Cetacean phylogenetics. In this study, it consistently
placed sister to Delphina (recovering the clade Pandelphina as pro-
posed by May-Collado et al., 2007). However, it is important to
notice that the support, although consistent, is low (Fig. 5d and
Table 2).
All analyses support the following relationship between the
Delphinoidea families ((Delphinidae (Monodontidae + Phocoeni-
dae) (Figs. 2 and 5d), previously found by both morphological
and molecular analyses (e.g., Heyning, 1989; Waddell et al., 2000).
In general, subfamilies within Cetacea were also recovered (see
May-Collado and Agnarsson, 2006 for discussion), while our results
continue to reject the monophyly of the traditional subfamilies
within Ziphiidae or Phocenidae ( Figs. 2 and 5d). The monophyly
of and relationships among taxonomic groups within Ziphiidae thus
remains unclear, as has been found in other recent studies (e.g.
Dalebout et al., 2004). As for species relationships within Phocoeni-
dae, our results are identical to a recent morphological phylogeny
by Fajardo-Mellor et al. (2006). Within Delphinidae, our study sup-
ports the monophyly of subfamilies as proposed by LeDuc et al.
(1999) with the following relationships suggested by the pruned
datasets 1 and 2: ((((Orciniae ((Globicephalinae (Stenoninae (Del-
phininae + Lissodelphininae)))) ( Figs. 2 and 5d). However, as
pointed before by several authors (e.g. LeDuc et al., 1999; Price et
al., 2005), the genera Lagenorhynchus,Stenella, and Tursiops appear
not to be monophyletic. Our results, agreeing with LeDuc et al.
(1999) suggest that Lagenorhynchus acutus andLagenorhynchus albi-
rostris (the type of the genus) are the only ‘true’ Lagenorhynchus spe-
cies and may best be placed in their own subfamily (for example,
Lagenorhynchinae). The remaining members of this genus should
be transferred to Cephalorhynchus and included within Lissodelphi-
niae. The phylogenetic relationships between subfamilies varied
somewhat across analyses, particularly the placement of Orcininae
(Orcinus and Orcaella), Lissodelphininae (Lissodelphis,Cephalorhyn-
chus, and some species of Lagenorhychus) was not consistent be-
tween analyses. Previous studies have not conclusively resolved
relationships among dolphins and relatives either highlighting the
need for further effort to better resolve delphinid phylogeny.
4.4. Extinct species
Our results agree with recent molecular studies that the re-
cently extinct ‘mouse goat’ (M. balearicus) is not a goat (Lalueza-
Fox et al., 2005). Our results, however, differ in the exact placement
of Myotragus, placing it sister to the remaining Caprinae (Fig. 5b),
instead of sister to sheep as found by Lalueza-Fox et al. (2005). La-
lueza-Fox et al. (2005) included more character data, while we
here include many more Caprinae species. Again, as it is well
known that both adding characters and taxa can improve phyloge-
netic accuracy (see above) it is unclear which placement is more
probable given the available evidence and we conclude that the ex-
act placement of Myotragus remains an open question. The ‘Irish
982 I. Agnarsson, L.J. May-Collado / Molecular Phylogenetics and Evolution 48 (2008) 964–985

Elk’ or Giant Deer (Lister et al., 2005)(M. giganteus) in our study is
sister to Père David’s Deer (E. davidianus) together forming the sis-
ter clade to the remaining Cervinae (Fig. 5a). This contradicts the
proposed sister relationship of Megaloceros and Dama found in pre-
vious studies (Lister et al., 2005; Hughes et al., 2006). Given that
Lister et al. used both morphology and molecules their result
may be more credible. However, Hughes et al. (2006) had a more
complete taxon sampling (as we do as well) and were not able to
conclusively place Megalocerus. In fact they found that a reasonable
alternative placement of Megalocerus was sister to the remaining
Cervinae, similar to what we find. Hence while clearly belonging
to Cervinae, we may again conclude that the exact position of Meg-
aloceros remains to be conclusively determined.
5. Conclusions
By analyzing a large number of cetartiodactylan species using a
single mitochondrial gene our primary goal here is to provide a tool
for species-level comparative studies. This approach offers rapid
phylogenetic estimates for large clades, but may suffer by providing
less reliable (less accurate) results than studies that include propor-
tionally greater amount of character data. However, our results are,
by and large, consistent with all major clades that can be treated as
‘known’ due to strong support from multiple lines of evidence in
prior studies. This suggests that cytb performs extraordinarily well
in resolving Cetartiodactyl phylogeny when taxon sampling is dense
and reiterates arguments that adding taxa is as important a consid-
eration as adding characters when the aim is to improve phyloge-
netic accuracy. Given that the phylogeny recapitulates current
knowledge on higher level Cetartiodactyla phylogeny, it seems rea-
sonable to expect the phylogeny as a whole to be a good working
hypothesis and hence a useful tool. If cytb is similarly informative
within related clades, an opportunity exists now to rapidly recon-
struct detailed phylogenies of major mammalian clades to provide
much needed tools for species-level comparative studies.
Acknowledgments
Funding for this project came from a Slovenian Research Agency
research fellowship (ARRS Z1-9799-0618-07) to Ingi Agnarsson,
and Judith Parker Travel Grant, Lerner-Gray Fund for Marine Re-
search of the American Museum of Natural History, Cetacean Inter-
national Society, Latin American Student Field Research Award of
the American Society of Mammalogists, Whale and Dolphin Con-
servation Society, the Russell E. Train Education Program-WWF,
and FIU Dissertation Year Fellowship all to Laura May-Collado. This
research was in part supported by NSF Grant DEB-0516038.
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