A phylogeny of the extant Phocidae inferred from complete mitochondrial DNA coding regions

Despite extensive interest in the systematics of Pinnipedia, questions remain concerning phylogenetic relationships within the Phocidae or "true" seals. Relationships within the phocids and their placement relative to the remaining pinnipeds and major lineages of arctoid carnivores were examined using a large molecular data set consisting of 12 mitochondrial protein coding genes. Phylogenetic analysis including 15 extant species of the Phocidae, and representatives of the Otariidae, Odobenidae, Ursidae, Mustelidae, Canidae, and Felidae confirmed the monophyletic origins of the Pinnipedia within the Arctoidea. Slightly more support was found for an ursid affinity of the pinnipeds, however, this relationship remains contentious. The Phocidae were placed as the sister group to a common odobenid-otariid clade. Within the family Phocidae, strong support for the traditionally accepted subfamilies Phocinae (northern seals), and Monachinae (southern seals plus monk seals) was found. In contrast to recent suggestions, a monophyletic Monachus was strongly supported and was placed in a deep branching position within the Monachinae. Evidence from sequence divergence under a maximum likelihood model illustrated that the rarely used tribal distinction within the Monachinae are comparable, in terms of evolutionary distance, to accepted tribal distinctions within the Phocinae. In addition, results suggest that Pagophilus should be accepted as a genus within the Phocini. Sequence divergence between Phoca, Pusa, and Halichoerus is minimal, supporting a taxonomic reclassification of the three genera into an emended genus Phoca, without subgeneric distinctions.     

Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes

Phylogenetic relationships among 37 living species of order Carnivora spanning a relatively broad range of divergence times and taxonomic levels were examined using nuclear sequence data from exon 1 of the IRBP gene (approximately 1.3 kb) and first intron of the TTR gene (approximately 1 kb). These data were used to analyze carnivoran phylogeny at the family and generic level as well as the interspecific relationships within recently derived Felidae. Phylogenetic results using a combined IRBP+TTR dataset strongly supported within the superfamily Califormia, the red panda as the closest lineage to procyonid-mustelid (i.e., Musteloidea) clade followed by pinnipeds (Otariidae and Phocidae), Ursidae (including the giant panda), and Canidae. Four feliform families, namely the monophyletic Herpestidae, Hyaenidae, and Felidae, as well as the paraphyletic Viverridae were consistently recovered convincingly. The utilities of these two gene segments for the phylogenetic analyses were extensively explored and both were found to be fairly informative for higher-group associations within the order Carnivora, but not for those of low level divergence at the species level. Therefore, there is a need to find additional genetic markers with more rapid mutation rates that would be diagnostic at deciphering relatively recent relationships within the Carnivora.     

Whence the red panda?

The evolutionary history of the red panda (Ailurus fulgens) plays a pivotal role in the higher-level phylogeny of the "bear-like" arctoid carnivoran mammals. Characters from morphology and molecules have provided inconsistent evidence for placement of the red panda. Whereas it certainly is an arctoid, there has been major controversy about whether it should be placed with the bears (ursids), ursids plus pinnipeds (seals, sea lions, walrus), raccoons (procyonids), musteloids (raccoons plus weasels, skunks, otters, and badgers [mustelids]), or as a monotypic lineage of uncertain phylogenetic affinities. Nucleotide sequence data from three mitochondrial genes and one nuclear intron were analyzed, with more complete taxonomic sampling of relevant taxa (arctoids) than previously available in analyses of primary molecular data, to clarify the phylogenetic relationships of the red panda to other arctoid carnivorans. This study provides detailed phylogenetic analyses (both parsimony and maximum-likelihood) of primary character data for arctoid carnivorans, including bootstrap and decay indices for all arctoid nodes, and three statistical tests of alternative phylogenetic hypotheses for the placement of the red panda. Combined phylogenetic analyses reject the hypotheses that the red panda is most closely related to the bears (ursids) or to the raccoons (procyonids). Rather, evidence from nucleotide sequences strongly support placement of the red panda within a broad Musteloidea (sensu lato) clade, including three major lineages (the red panda, the skunks [mephitids], and a clearly monophyletic clade of procyonids plus mustelids [sensu stricto, excluding skunks]). Within the Musteloidea, interrelationships of the three major lineages are unclear and probably are best considered an unresolved trichotomy. These data provide compelling evidence for the relationships of the red panda and demonstrate that small taxonomic sample sizes can result in misleading or possibly erroneous (based on prior modeling, as well as conflict between the results of our analyses of less and more complete data sets) conclusions about phylogenetic relationships and taxonomy.     

Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets

Phylogenetic relationships of 79 caniform carnivores were addressed based on four nuclear sequence-tagged sites (STS) and one nuclear exon, IRBP, using both supertree and supermatrix analyses. We recovered the three major arctoid lineages, Ursidae, Pinnipedia, and Musteloidea, as monophyletic, with Ursidae (bears) strongly supported as the basal arctoid lineage. Within Pinnipedia, Phocidae (true seals) were sister to the Otaroidea [Otariidae (fur seals and sea lions) and Odobenidae (walrus)]. Phocid subfamily and tribal designations were supported, but the otariid subfamily split between fur seals and sea lions was not. All family designations within Musteloidea were strongly supported: Mephitidae (skunks), Ailuridae (monotypic red panda), Mustelidae (weasels, badgers, otters), and Procyonidae (raccoons). A novel hypothesis for the position of the red panda was recovered, placing it as branching after Mephitidae and before Mustelidae+Procyonidae. Within Mustelidae, subfamily taxonomic changes are considered. This study represents the most comprehensive sampling to date of the Caniformia in a molecular study and contains the most complete molecular phylogeny for the Procyonidae. Our data set was also used in an empirical examination of the effect of missing data on both supertree and supermatrix analyses. Sequence for all genes in all taxa could not be obtained, so two variants of the data set with differing amounts of missing data were examined. The amount of missing data did not have a strong effect; instead, phylogenetic resolution was more dependent on the presence of sufficient informative characters. Supertree and supermatrix methods performed equivalently with incomplete data and were highly congruent; conflicts arose only in weakly supported areas, indicating that more informative characters are required to confidently resolve close species relationships.     

A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes

Evolutionary relationships of the order Carnivora have been extensively studied. However, phylogenetic studies based on different types of data, species samples, and methods of analysis provide contradictory results. Consequently, phylogenetic relationships of Carnivora remain contentious. Here, the sequence of 12 mitochondrial genes (10,842 nucleotides) from a total of 38 carnivore species was used to investigate the phylogeny of the caniform (dog-like) carnivores. An analysis using maximum parsimony, maximum likelihood, and Bayesian approaches provided a unique and well-supported solution to most contentious relationships within Caniformia. The clade Arctoidea was shown to consist of three major monophyletic groups: Pinnipedia, Ursidae, and Musteloidea. Within Pinnipedia, the families Otariidae and Odobenidae formed a clade, sister to Phocidae. Within Musteloidea, there was a sister relationship between true mustelids (i.e., excluding the skunks) and procyonids, and between ailurids and mephitids (skunks). Despite a high level of confidence obtained at most nodes, uncertainty remained about the relative position of the three major arctoid clades.     

Amino acid sequences of hemoglobin β chains of five species of pinnipeds:Neophoca cinerea,Otaria byronia,Eumetopias jubatus,Pusa hispida,andPagophilus groenlandica

Pinnipeds (Otariidae, Odobenidae, and Phocidae) in the order Carnivora have one or two types (Hb I and Hb II) of hemoglobin components. These hemoglobins consist of identicalβ chains and differentα chains. We determined the complete amino acid sequences of the hemoglobinβ chain of three species of Otariidae (Australian sea lion, South American sea lion, and northern sea lion) and two species of Phocidae (ringed seal and harp seal) from intactβ chain and chemical cleavage fragments. The sequences are similar toβ chains of the already known sequences of pinnipeds. These sequences were compared with those of other carnivores (Mustelidae, Ursidae, Canidae, and Felidae) and adult human hemoglobinβ chain. Using Artiodactyla (pig) as an outgroup, we find that the tree constructed by means of phylogenetic analysis shows that Odobenidae is closest to Otariidae, and that Otariidae and Odobenidae are closer to Mustelidae than to Phocidae.     

Phylogeny of the caniform carnivora: evidence from multiple genes

The monophyletic group Caniformia in the order Carnivora currently comprises seven families whose relationships remain contentious. The phylogenetic positions of the two panda species within the Caniformia have also been evolutionary puzzles over the past decades, especially for Ailurus fulgens (the red panda). Here, new nuclear sequences from two introns of the β-fibrinogen gene (β-fibrinogen introns 4 and 7) and a complete mitochondrial (mt) gene (ND2) from 17 caniform representatives were explored for their utilities in resolving higher-level relationships in the Caniformia. In addition, two previously available nuclear (IRBP exon 1 and TTR intron 1) data sets were also combined and analyzed simultaneously with the newly obtained sequence data in this study. Combined analyses of four nuclear and one mt genes (4417 bp) recover a branching order in which almost all nodes were strongly supported. The present analyses provide evidence in favor of Ailurus fulgens as the closest taxon to the procyonid-mustelid (i.e., Musteloidea sensu stricto) clade, followed by pinnipeds (i.e., Otariidae and Phocidae), Ursidae (including Ailuropoda melanoleuca), and Canidae, the most basal lineage in the Caniformia. The potential utilities of different genes in the context of caniform phylogeny were also evaluated, with special attention to the previously unexplored β-fibrinogen intron 4 and 7 genes.     

Use of spectral analysis to test hypotheses on the origin of pinnipeds

The evolutionary origin of the pinnipeds (seals, sea lions, and walruses) is still uncertain. Most authors support a hypothesis of a monophyletic origin of the pinnipeds from a caniform carnivore. A minority view suggests a diphyletic origin with true seals being related to the mustelids (otters and ferrets). The phylogenetic relationships of the walrus to other pinniped and carnivore families are also still particularly problematic. Here we examined the relative support for mono- and diphyletic hypotheses using DNA sequence data from the mitochondrial small subunit (12S) rRNA and cytochrome b genes. We first analyzed a small group of taxa representing the three pinniped families (Phocidae, Otariidae, and Odobenidae) and caniform carnivore families thought to be related to them. We inferred phylogenetic reconstructions from DNA sequence data using standard parsimony and neighbor-joining algorithms for phylogenetic inference as well as a new method called spectral analysis (Hendy and Penny) in which phylogenetic information is displayed independently of any selected tree. We identified and compensated for potential sources of error known to lead to selection of incorrect phylogenetic trees. These include sampling error, unequal evolutionary rates on lineages, unequal nucleotide composition among lineages, unequal rates of change at different sites, and inappropriate tree selection criteria. To correct for these errors, we performed additional transformations of the observed substitution patterns in the sequence data, applied more stringent structural constraints to the analyses, and included several additional taxa to help resolve long, unbranched lineages in the tree. We find that there is strong support for a monophyletic origin of the pinnipeds from within the caniform carnivores, close to the bear/raccoon/panda radiation. Evidence for a diphyletic origin was very weak and can be partially attributed to unequal nucleotide compositions among the taxa analyzed. Subsequently, there is slightly more evidence for grouping the walrus with the eared seals versus the true seals. A more conservative interpretation, however, is that the walrus is an early, but not the first, independent divergence from the common pinniped ancestor.      

A MORPHOLOGICAL CONSIDERATION OF THE RELATIONSHIPS OF PINNIPEDS TO OTHER CARNIVORANS BASED ON THE BONY TENTORIUM AND BONY FALX

The close relationships of pinnipeds to other carnivorans were studied based on morphological characteristics of the bony tentorium (BT) and bony falx (BF) of carnivorans. It appears to be an important characteristic of the Carnivora that the clear BT is present in almost all species including pinnipeds. The BF is present in all species of pinnipeds, and only in the genus Ursus among fissipeds observed.
The parietal bone of all otariids and odobenids observed shows an extremely characteristic form as compared with other carnivorans. The sagittal and squa-mous borders of the parietal bone of these groups are bridged by a thin bony plate which forms large portions of the BT and BF. In phocids, the aspects of the BT and BF vary among species, but are apparently distinct from those of otariids and odobenids.
The BT of carnivorans can be divided into four types which appear to be useful for classification of the Carnivora. On the basis of the BT and BF form, the Otariidae and Odobenidae appear to have a specific sister relationship to the Ursidae, while the Phocidae appears to have dose affinities to the Mustelidae. Morphological differences of the BT and BF among pinnipeds strongly support the diphyletic origin of pinnipeds.     

Phylogenetic reconstruction of carnivore social organizations

It is generally assumed that carnivore social organizations evolved directionally from a solitary ancestor into progressively more advanced forms of group living. Although alternative explanations exist, this evolutionary hypothesis has never been tested. Here, I used literature data and maximum likelihood reconstruction on a complete carnivore phylogeny to test this hypothesis against two others: one assuming directional evolution from a non-solitary ancestor, and one assuming parallel evolutions from a socially flexible ancestor, that is, an ancestor with abilities to live in a variety of social organizations. The phylogenetic reconstructions did not support any of the three hypotheses of social evolution at the root of Carnivora. At the family level, however, there was support for a non-solitary and socially flexible ancestor to Canidae, a socially flexible or solitary ancestor to Mustelidae, a solitary or socially flexible ancestor to Mephitidae, a solitary or group living ancestor to Phocidae, a group living ancestor to Otariidae and a solitary ancestor to Ursidae, Felidae, Herpestidae and Viverridae. There was equivocal support for the ancestral state of Procyonidae and Hyaenidae. It is unclear whether the common occurrence of a solitary ancestry at the family level was caused by a solitary ancestor at the root of Carnivora or by multiple transitions into a solitary state. The failure to support a solitary ancestor to Carnivora calls for caution when using this hypothesis in an evolutionary framework, and I suggest continued investigations of the pathways of the evolution of carnivore social organizations.     

Swimming Mode Inferred from Skeletal Proportions in the Fossil Pinnipeds Enaliarctos and Allodesmus (Mammalia, Carnivora)

Swimming modes are crucial for understanding evolutionary transitions from land to sea, because locomotion affects many aspects of an animal’s life. The modern pinniped families Otariidae (fur seals and sea lions), Phocidae (true seals), and Odobenidae (walruses) are thought to share a common origin, but each differs in its primary mode of aquatic locomotion. Previous studies of locomotor evolution in pinnipeds suggested: (1) forelimb swimming was ancestral; (2) hind limb swimming evolved once at the base of the clade including Phocidae, Odobenidae, and the extinct Desmatophocidae; and (3) reversal to forelimb swimming occurred in the odobenid subfamily Dusignathinae. The oldest and most basal pinnipedimorph Enaliarctos mealsi has been portrayed as a forelimb swimmer, and the desmatophocid Allodesmus kelloggi has been portrayed as a hind limb swimmer. These interpretations have been questioned by others and are tested here. Principal components analysis of trunk and limb measurements from 58 modern semiaquatic mammals demonstrates that Enaliarctos is most similar in skeletal proportions to hind limb-dominated swimmers, whereas Allodesmus is most similar to forelimb-dominated swimmers. Principal components and discriminant function analyses of trunk and limb measurements from 24 modern pinniped species demonstrate that Enaliarctos is most similar to hind limb-swimming phocids, while Allodesmus is most similar to forelimb-swimming otariids. These interpretations complicate previous portrayals of swimming evolution in pinnipeds and can paint a very different picture of how this behavior evolved when viewed in the context of alternative phylogenetic hypotheses.     

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds,the Walrus,the Steller Sea Lion and the Baikal Seal (Pinnipedia,Carnivora)

Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.     

Pinniped phylogeny and a new hypothesis for their origin and dispersal

The relationships and the zoogeography of the three extant pinniped families, Otariidae (sea lions and fur seals), Odobenidae (one extant species, the walrus), and Phocidae (true seals), have been contentious. Here, we address these topics in a molecular study that includes all extant species of true seals and sea lions, four fur seals and the walrus. Contrary to prevailing morphological views the analyses conclusively showed monophyletic Pinnipedia with a basal split between Otarioidea (Otariidae+Odobenidae) and Phocidae. The northern fur seal was the sister to all remaining otariids and neither sea lions nor arctocephaline fur seals were recognized as monophyletic entities. The basal Phocidae split between Monachinae (monk seals and southern true seals) and Phocinae (northern true seals) was strongly supported. The phylogeny of the Phocinae suggests that the ancestors of Cystophora (hooded seal) and the Phocini (e.g. harp seal, ringed seal) adapted to Arctic conditions and ice-breeding before 12 MYA (million years ago) as supported by the white natal coat of these lineages. The origin of the endemic Caspian and Baikal seals was dated well before the onset of major Pleistocene glaciations. The current findings, together with recent advances in pinniped paleontology, allow the proposal of a new hypothesis for pinniped origin and early dispersal. The hypothesis posits that pinnipeds originated on the North American continent with early otarioid and otariid divergences taking place in the northeast Pacific and those of the phocids in coastal areas of southeast N America for later dispersal to colder environments in the N Atlantic and the Arctic Basin, and in Antarctic waters.     

Hydrodynamic perception in true seals (Phocidae) and eared seals (Otariidae)

Pinnipeds, that is true seals (Phocidae), eared seals (Otariidae), and walruses (Odobenidae), possess highly developed vibrissal systems for mechanoreception. They can use their vibrissae to detect and discriminate objects by direct touch. At least in Phocidae and Otariidae, the vibrissae can also be used to detect and analyse water movements. Here, we review what is known about this ability, known as hydrodynamic perception, in pinnipeds. Hydrodynamic perception in pinnipeds developed convergently to the hydrodynamic perception with the lateral line system in fish and the sensory hairs in crustaceans. So far two species of pinnipeds, the harbour seal (Phoca vitulina) representing the Phocidae and the California sea lion (Zalophus californianus) representing the Otariidae, have been studied for their ability to detect local water movements (dipole stimuli) and to follow hydrodynamic trails, that is the water movements left behind by objects that have passed by at an earlier point in time. Both species are highly sensitive to dipole stimuli and can follow hydrodynamic trails accurately. In the individuals tested, California sea lions were clearly more sensitive to dipole stimuli than harbour seals, and harbour seals showed a superior trail following ability as compared to California sea lions. Harbour seals have also been shown to derive additional information from hydrodynamic trails, such as motion direction, size and shape of the object that caused the trail (California sea lions have not yet been tested). The peculiar undulated shape of the harbour seals’ vibrissae appears to play a crucial role in trail following, as it suppresses self-generated noise while the animal is swimming.     

Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, and cestodes.

Congruence in biogeographic patterns among diverse assemblages of taxa indicates uniformity in the historical determinants of biotic distributions. Comparisons of host and parasite phylogenies and the elucidation of distributional area relationships are requisite components of analyses in historical biogeography. Host-parasite associations with broad geographic ranges are often archaic and have been structured largely by coevolutionary processes. In contrast, the origins and radiation of the primary cestode faunas of some seabirds (Alcataenia spp./Alcidae) and pinnipeds (Anophryocephalus spp./Phocidae and Otariidae) are associated with colonization. These young colonizing faunas, in the Holarctic Region, were influenced by a common history during the late Pliocene and Pleistocene epochs. Periodic range contraction, with isolation in refugial centers, and subsequent expansion into postglacial habitats for hosts and parasites coincided with the cyclic pattern of stadials and interstadials. During the past 2-3 million years following colonization, these dramatic climatic fluctuations strongly influenced the continuity of ecological associations in marine habitats and appear to have been the determinants of congruent and synchronic patterns of speciation among these disparate taxa of marine homeotherms and eucestodes.     

Cope's rule and the evolution of body size in Pinnipedimorpha (Mammalia: Carnivora)

Cope's rule describes the evolutionary trend for animal lineages to increase in body size over time. In this study, we tested the validity of Cope's rule for a marine mammal clade, the Pinnipedimorpha, which includes the extinct Desmatophocidae, and extant Phocidae (earless seals), Otariidae (fur seals and sea lions), and Odobenidae (walruses). We tested for the presence of Cope's rule by compiling a large dataset of body size data for extant and fossil pinnipeds and then examined how body size evolved through time. We found that there was a positive relationship between geologic age and body size. However, this trend is the result of differences between early assemblages of small-bodied pinnipeds (Oligocene to early Miocene) and later assemblages (middle Miocene to Pliocene) for which species exhibited greater size diversity. No significant differences were found between the number of increases or decreases in body size within Pinnipedimorpha or within specific pinniped clades. This suggests that the pinniped body size increase was driven by passive diversification into vacant niche space, with the common ancestor of Pinnipedimorpha occurring near the minimum adult body size possible for a marine mammal. Based upon the above results, the evolutionary history of pinnipeds does not follow Cope's rule.     

Comparative analysis of vestibular system development in various groups of mammals living under different environmental conditions

We have conducted for the first time a comparative study of the prenatal development of the vestibular system in representatives of pinnipeds (Phocidae, Otariidae, Odobenidae) and cetaceans (Odontoceti, Mysticeti) in comparison with terrestrial mammals. This allowed us to perform a detailed study of the structural organization of the inner ear in species with different ecological specialization, to find out adaptive aspects and stages of the formation of cochlear and vestibular structures in each of the studied species, and to correlate it with the properties of the environment. Studies on early embryogenesis of the labyrinth in cetaceans and pinnipeds, which represent a special direction in the evolution of placentates, give a significant contribution to the solution of problem about the evolutionary origin of the labyrinth in mammals studied. Sensory systems clearly demonstrate the scope of evolutionary and adaptive transformations, which appear in mammals during the transition from the terrestrial to the aquatic mode of life. At the same time, these results may provide help in understanding the general trends of the development of structure and function of the inner ear in mammals as a whole.     

Comparative Analysis of Vestibular System Development in Various Groups of Mammals Living under Different Environmental Conditions

We have conducted for the first time a comparative study of the prenatal development of the vestibular system in representatives of pinnipeds (Phocidae, Otariidae, Odobenidae) and cetaceans (Odontoceti, Mysticeti) in comparison with terrestrial mammals. This allowed us to perform a detailed study of the structural organization of the inner ear in species with different ecological specialization, to find out adaptive aspects and stages of the formation of cochlear and vestibular structures in each of the studied species, and to correlate it with the properties of the environment. Studies on early embryogenesis of the labyrinth in cetaceans and pinnipeds, which represent a special direction in the evolution of placentates, give a significant contribution to the solution of the problem of the evolutionary origin of the labyrinth in the mammals studied. Sensory systems clearly demonstrate the scope of evolutionary and adaptive transformations, which appear in mammals during the transition from the terrestrial to the aquatic mode of life. At the same time, these results may provide help in understanding the general trends of the development of structure and function of the inner ear in mammals as a whole.     

Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA.

The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species.