Integration of new fossil material of †Indohyus impacts placement of another extinct clade †Mesonychia, pushing it much farther down the tree. The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup.

We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, †Creodonta, Lipotyphla, and the †raoellid artiodactylan †Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to †Indohyus, with †Mesonychia outside of Artiodactyla. The relationships of †Mesonychia and †Indohyus are highly unstable, however - in trees only two steps longer than minimum length, †Mesonychia falls inside Artiodactyla and displaces †Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result.

Funding: Several grants supported this research: NSF DEB-9903964, DEB-0210956, DEB-0629836, EAR-0116517 to M. A. O'Leary, along with a grant from NESCENT, NSF predoctoral fellowship to M. Spaulding, NSF DEB-0614098 to J. Flynn, and NSF DEB-9985847, DEB-0213171, and DEB-0212572 to J. Gatesy. M. A. O'Leary's contribution was also prepared under award NA04OAR4700191 from the National Oceanic and Atmospheric Association, US Department of Commerce. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2009 Spaulding et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

In addition to artiodactylan taxa, we define the completely extinct clade †Mesonychia as a node based taxon that is the common ancestor of †Hapalodectes leptognathus and †Mesonyx obtusidens and all of its descendants. We have not altered the nomenclature of taxa utilized as outgroups to Artiodactyla in the present study. The sampling for these clades is not comprehensive enough to warrant the re-examination of taxonomic terms in the present study. We should note, however, that Carnivora, as a node-based crown clade, has been defined elsewhere [35] , as has the total clade, Carnivoramorpha [13] . Our treatments of Artiodactyla and Cetacea mirror this utilization of a traditional ordinal level name (Carnivora) applied formally to a crown clade. Additional outgroup names used in the discussion below are: crown group Perissodactyla, †Creodonta [13] , [15] , [35] , Ferae [12] , [13] , [18] , and Lipotyphla [12] . For the above terms that have not yet been formally defined cladistically, their current compositions should be unambiguous given the provided references and the taxa in our analysis.

‘Whippomorpha’ was proposed as the name for “Cetacea +Hippopotamidae” [19] . Subsequently, Cetancodonta was offered as a replacement for ‘Whippomorpha’ [34] . We support the formalized use of the term “Cetancodonta” for the crown grouping, based upon arguments made by Arnason when the name was first proposed and the problematic nature of using a term ending in -morpha for a crown clade. We formally define Cetancodonta as a node-based taxon, including all species that are descendants of the most recent common ancestor of Hippopotamus amphibius and Tursiops truncatus. Cetancodontamorpha is applied to the total clade that includes Cetancodonta and all extinct species more closely related to extant cetancodontans than to any other living species ( Table 1 ).

As suggested by de Queiroz [23] , we have applied widely-used artiodactylan names to crown clades. We then added a standard suffix (“-morpha”) to the crown names to identify corresponding total clades. This allows those who are more familiar with extant diversity, presumably the majority of scientists and laypersons, to link extinct diversity broadly to better known extant species. For example, as defined here, Cetacea includes all descendants of the last common ancestor of Tursiops truncatus and Balaena mysticetus ( Table 1 ). Most biologists are familiar with whales and dolphins, and these species have been referred to as ‘cetaceans’ for a very long time. Assigning the traditional name ‘Cetacea’ to this crown clade informs the user that extinct crown cetaceans are close relatives of whales and dolphins and likely have many of the synapomorphies shared by all extant cetaceans (e.g., obligately-aquatic lifestyle, reduced hindlimbs, tail flukes, flipper-shaped forelimbs, pachyostotic ear bones, etc.). In our new taxonomy, Cetaceamorpha is the total clade defined as Cetacea plus all extinct taxa more closely related to extant cetaceans than to any other living species. This replaces the use of ‘Cetacea’ as a stem clade (sensu [32] ). Thus, in addition to the crown clade, Cetaceamorpha includes fossil stem taxa that are successive outgroups to crown Cetacea. Crown and total clade-based taxonomy provides a consistent reference system for both specialists and those less familiar with the systematics of a given clade. As emphasized by [32] , a further significant reason to use crown clades and total clades is their unambiguous representation of data directly available for study. Many types of data (e.g., molecular, soft tissue, behavior) are rarely preserved for direct study outside the crown clade, and thus cannot be optimized below the common ancestor of a crown clade ( [32] , see also Level 1 inference of [33] ). Here we also apply no formal taxonomic rank (i.e., Family, Subfamily, etc.) to the names proposed in this paper.

In the new taxonomy ( Table 1 ), we utilize the name Artiodactyla as a crown clade, the monophyletic group that includes the last common ancestor of cattle, antelope, deer, giraffes, musk deer, chevrotains, hippos, pigs, peccaries, and camels, and all of its descendants. Many analyses have supported the nesting of Cetacea several nodes within Artiodactyla (e.g., [25] , [26] , [27] ). This prompted Montgelard et al. [28] to rename the combined group ‘Cetartiodactyla.’ Despite our prior use of the term ‘Cetartiodactyla’ (e.g., [1] , [29] , [30] ), the topological change of placing Cetacea within Artiodactyla was never grounds to retire the name, Artiodactyla, according to rules of phylogenetic nomenclature. ‘Cetartiodactyla’ has gained some traction in the literature, especially among molecular workers, but here we formally retain the name Artiodactyla following the logic entailed in the Phylocode [24] . All groups that we name as crown clades have been robustly supported by combined phylogenetic analyses of molecules and morphology from living and extinct taxa [1] , [31] and this study). These include Cetacea, Hippopotamidae, Cetancodonta, Ruminantia, Cetruminantia, Suina, Camelidae, and Artiodactyla ( Table 1 ), which are found in all minimum length trees (even if the strict consensus is sometime unresolved due to unstable fossils).

It has become increasingly important to have phylogenetic names for the ingroup in question, Artiodactyla, to discuss character evolution unambiguously. Other groups have greatly benefited from a revision of taxonomic nomenclature to reflect phylogeny. Previous taxonomies for Artiodactyla have not been based on robust phylogenetic results [14] or have ignored extinct diversity [19] . This has led to confusion in discussions of evolutionary relationships in the clade. This disorder can be rectified, in part, by a new taxonomy that utilizes “crown clades” and “total clades” [20] , [21] , [22] , [23] . A crown grouping is based upon a cluster of extant species, and a total clade is the crown group plus the paraphyletic series of fossils at its base. The core of our new system ( Table 1 ) is a set of traditional, commonly-used taxonomic names that in the past have been applied variously as stem, crown, node, or apomorphy based groups. Furthermore, our taxonomy incorporates information from recent combined phylogenetic studies that have shown a highly consistent set of hierarchical relationships among major clades of Artiodactyla (reviewed in [1] ). All higher-level artiodactylan names proposed are being submitted to the Companion Volume to the Phylocode [24] . By formally naming these clades, we hope to assist in providing a unified system of nomenclature for Artiodactyla, consistent with those applied to other mammalian orders.

Although the focus of this paper is to examine the phylogenetic relationships of †Mesonychia and the †raoellid †Indohyus, this study has implications for Ferae (which we recognize as including only Carnivora plus †Creodonta, following [12] , [13] ; we do not follow the more inclusive Ferae of [14] ). The monophyly of both Ferae and †Creodonta has been questioned (e.g., [15] , [16] ). Despite the long-standing grouping of Ferae [12] , this taxon has never been the subject of a rigorous phylogenetic test in a cladistic framework. The modern concept of the †Creodonta, a wholly extinct carnivorous group, includes two sub-clades: †Hyaenodontidae and †Oxyaenidae [15] , but the relationships of these taxa needs further testing [16] . The most recent phylogenetic studies of †Creodonta [15] , [17] have concentrated on subclades within the group, and did not address the relationships of †Creodonta in a broader framework. Other analyses that included †creodonts (e.g., [13] , [18] ) have utilized the taxa as outgroups, and did not specifically test the relationship between the two †creodont families. The expansion in taxon sampling of this study not only benefits our understanding of relationships among Cetacea, other artiodactylans, and †Mesonychia, but also those of Ferae and its component clades.

We reevaluate the position of this significant fossil in the context of the largest total evidence analysis of Artiodactyla and relatives to date. We generate 49 new DNA sequences from five nuclear loci and expand our taxonomic sample to include living and extinct Carnivoramorpha (cats, dogs and fossil relatives) and †Creodonta (archaic extinct carnivorous mammals). Carnivoramorpha and †Creodonta may be critical for determining the position of the wholly extinct clade †Mesonychia, which has played a pivotal role in our understanding of the pattern of character evolution in Cetacea (see discussion in [1] ). In particular, we are interested to know how the carnivorous (or hypothesized to be carnivorous) taxa (Carnivoramorpha, †Creodonta, †Mesonychia) are related to Cetacea, a highly-specialized carnivorous/piscivorous lineage that is nested within a clade composed primarily of herbivores (Artiodactyla). Inclusion of a variety of taxa such as these, that have dental similarities to early whales, could directly influence tree topology and interpretations of dental evolution on the stem lineage of Cetacea. Because the association of diagnostic †raoellid cranial fossils with postcranial remains [3] has not been convincingly established (noted in [11] ), we also examined how exclusion of postcranial information affected the phylogenetic position of †Indohyus. To facilitate discussion of key transitional fossils on the stem lineages of living clades, we revise the higher-level taxonomy of Artiodactyla.

Most cladistic analyses of morphological characters have supported monophyly of extant terrestrial artiodactylans, traditionally called Artiodactyla, as well as the subclades Suiformes and Selenodontia. Note the variable placements of the enigmatic extinct groups †Raoellidae and †Mesonychia in the different topologies. The deeply nested conflict between phylogenetic hypotheses for Artiodactyla is shown very well by these two recent studies: for the major lineages shown, no clades are shared. Lineages that connect extant taxa in the tree are represented by thick gray branches, and wholly extinct lineages are shown as thin black branches. Illustrations are by C. Buell and L. Betti-Nash.

Subsequent to the last large scale total evidence analyses of the position of cetaceans among mammals [1] new specimens of the extinct †raoellid artiodactylan, †Indohyus, were described that potentially offer critical information about the phylogenetic position of Cetacea [3] . Among the new specimens is a skull that preserves quadritubercular dentition (4 major cusps, found in herbivores and omnivores [6] , [7] ) and a pachyostotic auditory bulla (found in mammals derived for underwater hearing [8] ). These features had not previously been recorded in the same individual. Thewissen et al. [3] argued on the basis of these new data that †Indohyus was the sister taxon of living and extinct whales. Many aspects of their published phylogenetic tree were, however, highly incongruent with other recent studies (e.g., [1] ; see Figure 1 ), and their phylogenetic results were subsequently challenged [9] , [10] .

Continued discovery of fossils that capture transitional stages in cetacean evolution (e.g., [3] , [4] , [5] ) provides critical new data on how the stem lineage to Cetacea transformed. By incorporating new fossils into increasingly large total evidence (character congruence) analyses, we are beginning to develop a firm understanding of the evolutionary history of this clade and can start testing explicit hypotheses concerning character transformation. For example, ‘Did whales develop ear bones for underwater hearing while still able to easily move on land?,’ or ‘What came first in the whale lineage - dietary change to aquatic carnivory or committed life in water?’ None of these hypotheses can be assessed without a robust test of the sister taxa to the clade Cetacea.

Establishing the position of Cetacea (whales, dolphins and porpoises) within Mammalia has long been a focus of mammalian systematists. The transition from a primitively quadrupedal terrestrial ancestor to a convergently ‘fish-like’ modern mammal species involved changes in numerous character systems. Almost all anatomical systems of living cetaceans are highly modified for an aquatic lifestyle, with dramatic changes seen in areas such as the ear region, skin, limbs, and cranium relative to terrestrial mammals. The study of phylogenetic data that fossilizes (primarily skeletal and dental morphology) has been particularly important because it is by studying extinct species that we can reconstruct the order of character acquisition that led to the origin of Cetacea (see review of studies in [1] , [2] ).

Results and Discussion

Selected Character Optimizations for Cetancodonta Character reconstructions based on parsimony alone. Since the recognition that whales are highly-derived artiodactylans, it has been of interest to understand how an aquatic, carnivorous clade, Cetacea, evolved within a predominantly terrestrial, herbivorous clade, Artiodactyla. Our primary means of reconstructing characters in hypothetical common ancestors, and of reconstructing soft tissue/behavior characters (that are not directly observable) in fossil taxa, is to use parsimony [59], [60]. We have coded the following behavioral characters in our matrix: aquatic habitat (character 618 [state 1]), herbivorous diet (character 658 [state 2]), and ability to interpret the direction of sounds under water (character 659 [state 1]). These three character states optimize unambiguously to the common ancestor of Cetancodonta. This corroborates predictions about the origin of an aquatic lifestyle as having occurred once in the common ancestor of Hippopotamidae and Cetacea [27]. This common ancestor of Cetancodonta had the derived behavior of spending at least 10% of its time in water (character 618 [state 1]). Parsimony indicates that this state is shared by all extant members of Cetancodonta, and is reconstructed for all taxa nested within Cetancodonta (including basal cetaceamorphans, such as †Indohyus, †Diacodexis and †Helohyus). Gatesy et al. [27] had previously suggested overturning a parsimony-based optimization for some extinct taxa nested in this clade based on absence of osteological correlates for aquatic behavior, but we do not advocate that position here (also see [1], [2]). Using parsimony we reconstruct all fossil hippopotamidamorphans as herbivorous (character 658 [state 2]). The dietary behaviors of taxa along the stem to Cetacea (i.e., noncetacean cetaceamorphs) are, however, equivocal based on optimization of states seen in extant taxa. Somewhere on the stem to Cetacea, diet changed from herbivory to aquatic carnivory (character 658 [state 3]), but using parsimony alone we cannot reconstruct unambiguously where the behavioral change occured Parsimony-based optimization also implies that all living and extinct cetancodontans shared a derived ability to hear underwater sounds at least as well as extant Hippopotamus. This is noteworthy because several cetancodontans (including living members of Hippopotamidae) lack a pachyostotic auditory bulla (involucrum) in the ear. To summarize, in the minimum length trees (e.g., Figure 3A), the †raoellid †Indohyus is reconstructed to have spent at least 10% of its time in water and to have had the derived behavior of directional underwater hearing, but reconstruction of its diet is equivocal. In alternate trees that are two steps longer, parsimony recovers the same character state reconstructions for †Mesonychia, because this taxon is a close relative of Cetacea in slightly longer trees (e.g., Figure 3B).

Extended character reconstructions: inferring behavior from osteology and dentition As discussed by [33], [60] inferences about behavior in fossil taxa, which go beyond parsimony, can be made if there is “compelling morphological evidence” that a certain fossilized trait is strictly correlated with a certain behavior (e.g., distinctive coiling of the cochlea in bats indicating echolocation [61]). These deductions should, however, be clearly delineated from reconstructions based on parsimony. Here we discuss such inferences related to diet and hearing in Artiodactyla. Molars that have a tall, angular protoconid and a compressed talonid are typically associated with carnivorous diets in mammals, and molars with low-crowned, quadritubercular cusps are associated with herbivory/omnivory [6], [7]. Reconstructing behavior from fossilized tooth shape, we would infer that several cetaceamorphans (†Diacodexis, †Helohyus, and †Indohyus) are herbivorous/omnivorous because they have quadritubercular teeth (hypocone on M2, character 419 [1]). It is noteworthy that prior to the description of a relatively complete †Indohyus skull there were no cetaceamorphans that had both the pachyostotic ear region and quadritubercular dentition. Molar shape would suggest that cetaceamorphans from †Ambulocetus through more highly nested taxa were carnivorous due to the presence of narrow talonids on m2 (character 364, state 1) and of tall protoconids on m1 (358, state 1; here technically †Pakicetus and more highly nested taxa due to missing data). According to minimum length trees for the combined data, these character states were independently derived within Cetaceamorpha and in †Mesonychia (Figure 3A). In the slightly longer topology (Figure 3B), however, both of these dental characters are synapomorphies uniting †Mesonychia and Cetacea. Based on the results of the total evidence analysis, we can return to the question posed in the introduction, ‘Did aquatic carnivory precede committed life in the water?’ Inferring carnivory from tooth shape and inferring committed life in the water from detachment of the sacral vertebrae from the pelvis (character 488, state 0), carnivory did precede committed life in the water. Not until the last common ancestor of †Dorudon, †Basilosaurus, and crown Cetacea did cetaceamorphans lose the articulation between the pelvis and the vertebral column, but dentition suggesting carnivory appears at a more basal node (see also [62]). The presence of the pachyostotic bulla and what it implies about hearing has also been of interest because this is a relatively rare anatomical feature among mammals. This structure has been argued to indicate an ear region derived to process underwater sounds [8], a behavior that has evolved in Cetaceamorpha. Luo and Gingerich ([8]:89) stated that acoustic isolation of the left and right ears creates density differences analogous to those created by a pachyostotic bulla, and may confer directional hearing underwater. Interestingly, Hippopotamus lacks a pachyostotic bulla despite the fact that this species has an ability to hear underwater sounds exceeding that of typical terrestrial mammals [63]. Pachyostosis of the ear region, therefore, does not appear to be essential for certain derived types of underwater hearing. Pachyostosis may indicate instead an even more derived level of underwater hearing than previously recognized but confirmation requires further functional studies. Reconstructing auditory function from osteology, we would infer that the presence of a pachyostotic bulla (character 59, state 1) in †Indohyus, and all more highly nested cetaceamorphans (Figure 3A), potentially indicates an even more derived state of underwater hearing than that which developed in the common ancestor of Cetancodonta. If the alternate topology only 2 steps longer (Figure 3B) obtains in future studies, (with †Mesonychia closer to Cetacea and †Indohyus a more distantly related cetaceamorphan), then the pachyostotic bulla developed two times independently in Cetaceamorpha: once in the common ancestor of †Ambulocetus and Cetacea, and once in †Indohyus. Furthermore, optimization by parsimony indicates that underwater hearing is a feature shared by all cetancodontans, thus this character state appeared at a more basal node than detachment of the sacral vertebrae from the pelvis and committed life in the water (character 488, state 0). In summary, these inferences imply that the history of Cetaceamorpha included both carnivorous and herbivorous species. All cetancodontans were at least as aquatic as living hippos and exhibited some ability to hear underwater sounds, even though several cetancodontan species lack a pachyostotic bulla. Appearance of the pachyostotic bulla may indicate a shift to a yet more derived degree of directional underwater hearing, a hypothesis that requires further investigation. In slightly longer trees, in which †Mesonychia groups close to Cetacea, the derived bulla of †Indohyus would be interpreted as convergent with that of cetaceans. Finally the shift to carnivory within Cetaceamorpha preceded the loss of limbs that functioned in terrestrial locomotion in this clade.