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PubMed1998

Kidneys of the killerwhale and significance of reniculism.

BACKGROUND: The kidneys of all Cetacea are composed of many small relatively independent kidneys (renicules) containing considerable interrenicular tissue. Although reniculism is not entirely confined to the Cetacea, it is desirable to consider the possible advantage of reniculism to mammals of gigantic size. The kidneys of the killerwhale, Orcinus orca, are compared from this standpoint to the kidneys of diverse mammals. METHODS: The specific renal parenchymal mass, glomerular counts, glomerular size, and specific glomerular mass of the killerwhale are measured and compared quantitatively (statistically) with similar data from numerous diverse mammals. Simultaneously, a method is described for enumerating the renicules of a cetacean kidney. RESULTS: Specific parenchymal mass of a killerwhale adult's two kidneys (0.33%) is close to the expected value for mammals of its adult body mass (2,087 kg). The diameter of the adult's glomerular capsules (153 microm) is strikingly less than that expected from its body mass (regression equation and graph for mammals in general). However, the number of glomeruli per kidney (approximately 100 x 10[6]) is markedly greater than that for mammals of its body mass (regression equation and graph for mammals in general) and is the first such count for a cetacean. The total glomerular mass relative to parenchymal renal mass of the O. orca infant and adult is, nevertheless, 5.5% and 6.0%, respectively, and is thus close to the general mammalian value of approximately 5%. CONCLUSIONS: Organization of a cetacean kidney into numerous renicules does not increase specific renal parenchymal mass or specific glomerular mass. The apparent advantage of numerous independent renicules is the limit that is afforded for length of tubules in the necessarily large kidneys of gigantic mammals.

Animals↗
PubMed2005

Cloning and characterization of the gene encoding growth hormone in finback whale (Balaenoptera physalus).

In mammals growth hormone (GH) is generally a strongly conserved protein, reflecting a slow rate of molecular evolution. However, during primate and artiodactyl evolution episodes of rapid change occurred, so that the GHs of higher primates and ruminants differ markedly from those of other mammals. To extend knowledge of GH evolution in Cetartiodactyla (Artiodactyla plus Cetacea) we have previously characterized GH genes from several members of this group, including the common dolphin. Surprisingly the sequence deduced for dolphin GH differed at several residues from that described previously for another cetacean, finback whale. To investigate this anomaly we have now cloned and characterized the GH gene from finback whale. The overall organization of this gene is similar to that of dolphin, and the deduced amino acid sequence of finback whale GH differs from that of dolphin GH at only residue 47, and from that of pig GH at only residue 149. Phylogenetic analysis of the data provides further support for inclusion of Cetacea within the order Cetartiodactyla, as sister group of Hippopotamidae. The results support the idea that in Cetartiodactyla a burst of rapid evolution of GH occurred after the separation of the line leading to ruminants from other cetartiodactyls. Overall, the GH gene in cetaceans appears to be evolving more slowly than in most other cetartiodactyls.

Amino Acid Sequence↗
PubMed2005

Cytochrome b and Bayesian inference of whale phylogeny.

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Animals↗
PubMed2003

Classification of Brucella strains isolated from marine mammals by infrequent restriction site-PCR and development of specific PCR identification tests.

Brucella strains have been isolated since the 1990s from a wide variety of marine mammals and represent potential zoonotic pathogens. They have distinctive phenotypic and molecular characteristics from the terrestrial mammal Brucella species, and two new species names have been previously proposed based on DNA polymorphism at the omp2 locus and their preferential host, i.e. Brucella cetaceae for cetacean isolates and Brucella pinnipediae for pinniped isolates. The results presented in this study on characterization of these strains by infrequent restriction site-PCR (IRS-PCR), taking into account the higher number of IS711 elements in their genome compared to terrestrial mammal Brucella species, supports this classification. The nucleotide sequences of specific DNA fragments detected by IRS-PCR were determined and used to develop PCR identification tests for either B. cetaceae or B. pinnipediae.

Animals↗
PubMed2005

The position of Hippopotamidae within Cetartiodactyla.

The origin of late Neogene Hippopotamidae (Artiodactyla) involves one of the most serious conflicts between comparative anatomy and molecular biology: is Artiodactyla paraphyletic? Molecular comparisons indicate that Cetacea should be the modern sister group of hippos. This finding implies the existence of a fossil lineage linking cetaceans (first known in the early Eocene) to hippos (first known in the middle Miocene). The relationships of hippos within Artiodactyla are challenging, and the immediate affinities of Hippopotamidae have been studied by biologists for almost two centuries without resolution. Here, we compare opposing hypotheses implicating several "suiform" families. This morphological analysis of a comprehensive set of taxa and characters offers a robust solution to the origins of Hippopotamidae. This family appears to be deeply nested within the otherwise extinct artiodactyl family Anthracotheriidae, most precisely within the most advanced selenodont forms. The proposed sister group of hippos is the middle to late Miocene African semiaquatic Libycosaurus. Any close relationships of hippos with suoids, particularly with Tayassuidae, are rejected. Furthermore, the clade (Hippopotamidae, Anthracotheriidae) is proposed as the sister group of the Cetacea, offering broad morphological support for a molecular phylogeny, such support being also consistent with the fossil record. Corroboration of this relationship requires an exploration of anthracothere affinities with other Paleogene artiodactyls. Among those, the position of Ruminantia is a central question, still to be solved. Further progress in this debate is likely to come from morphological studies of paleontological data, whether known or still to be discovered.

Animals↗
PubMed1999

Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes.

Aligned protein-coding genes from 19 completely sequenced mammalian mitochondrial genomes were examined by parsimony and maximum likelihood analyses. Particular attention is given to a comparison between gene-based and structure-based data partitions. Because actual structures are not known for most of the mitochondrially encoded proteins, three different surrogate partitioning schemes were examined, each based on the identity of the consensus amino acid at a specific homologous position. One of the amino-acid-based partitioning schemes gave the highest likelihood, but that scheme was based on concordance with a well-corroborated phylogeny from an earlier parsimony analysis. The gene-based partitioning scheme gave a significantly higher likelihood compared to the only structure-based scheme examined that could be generated without prior assumptions about the phylogeny. Two contrasting phylogenetic inferences were supported by the analyses. Both unpartitioned analyses and analyses in which all partitions were constrained to have identical patterns of branch lengths supported ((Artiodactyla, Cetacea) (Perissodactyla, Carnivora)), whereas all analyses with that constraint relaxed supported (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).

Amino Acid Sequence↗
PubMed1998

Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade.

Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.

Animals↗
PubMed1994

Eutherian phylogeny as inferred from mitochondrial DNA sequence data.

The phylogenetic relationships among Primates, Artiodactyla, Cetacea, Carnivora, and Rodentia were estimated from the amino acid sequences of proteins encoded by the mitochondrial genomes, for which entire nucleotide sequence data are available, using Marsupialia, Aves, and Amphibia as outgroups. The overall evidence of the maximum likelihood, as well as maximum parsimony, analyses strongly suggests that Rodentia is an outgroup to the other four eutherian orders, and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon, consistently with the molecular phylogenetic studies of previous authors. However, analyses of individual proteins do not necessarily conform to this conclusion, and some of the proteins reject the putatively correct tree with nearly 5% significance. Furthermore, the 12S mitochondrial ribosomal RNA sequences do not give the putatively correct tree irrespective of the alignments and of the phylogenetic methods, although the tree is not rejected with a statistical significance. The 16S ribosomal RNA sequences give the putatively correct tree with our sequence alignment when the ML method is used, but the result depends on the alignment and on the choice of outgroup species. These results illustrate the limitation of the ribosomal RNA data alone in phylogenetic inference, and suggest that we must analyze as many genes as possible and synthesize the results to draw a reliable conclusion.

Amino Acid Sequence↗
PubMed1994

Mammalian phylogeny inferred from multiple protein data.

On the basis of multiple protein data, the phylogenetic relationships among the major clades of eutherian mammals, Primates, Cetacea, Artiodactyla, Carnivora, Lagomorpha, Myomorpha, and Caviomorpha, were analyzed by the maximum likelihood (ML) method, together with the maximum parsimony (MP) method and the neighbor joining (NJ) method. Using nineteen protein data, we first reexamined the hypothesis of rodent polyphyly proposed by Graur et al. (1991) based on the four taxon system, consisting of human, mouse (or rat), guinea-pig and an outgroup. The ML analysis does not support the rodent polyphyly, but strongly favors the traditional view of rodent monophyly representing the Myomorpha-Caviomorpha association. In the second analysis, the phylogenetic position of Lagomorpha were reexamined using three sets of multiple protein data, 13 mitochondrial DNA-coded proteins from rodents, rabbit, human, seals, bovine, whales and opossum, 25 protein data from human, rabbit and rodents and an outgroup, and 20 protein data from human, rabbit, bovine (or pig) and rodents. Our analysis favors the closer affinity of Lagomorpha to Primates than to Rodentia. The branching sequence of seven mammalian groups revealed by the present analyses is as follows: Myomorpha-Caviomorpha clade (Rodentia), rabbit, Primates, Carnivora, and Artiodactyla-Cetacea clade. Judging from the branch lengths measured by the numbers of synonymous substitutions, a series of divergence of these mammals is likely to be bush-like. The rapid rate of rodent evolution was reexamined in the light of the new phylogeny.

Amino Acid Sequence↗
PubMed2005

Spondylitic changes in long-finned pilot whales (Globicephala melas) stranded on Cape Cod, Massachusetts, USA, between 1982 and 2000.

The primary bone pathology diagnoses recognized in cetacea are osteomyelitis and spondylosis deformans. In this study, we determined the prevalence, type, and severity of vertebral pathology in 52 pilot whales, a mass stranding species that stranded on Cape Cod, Massachusetts, between 1982 and 2000. Eleven whales (21%) had hyperostosis and ossification of tendon insertion points on and between vertebrae, chevron bones, and costovertebral joints, with multiple fused blocks of vertebrae. These lesions are typical of a group of interrelated diseases described in humans as spondyloarthropathies, specifically ankylosing spondylitis, which has not been fully described in cetacea. In severe cases, ankylosing spondylitis in humans can inhibit mobility. If the lesions described here negatively affect the overall health of the whale, these lesions may be a contributing factor in stranding of this highly sociable species.

Animals↗
PubMed2004

Origin and evolution of large brains in toothed whales.

Toothed whales (order Cetacea: suborder Odontoceti) are highly encephalized, possessing brains that are significantly larger than expected for their body sizes. In particular, the odontocete superfamily Delphinoidea (dolphins, porpoises, belugas, and narwhals) comprises numerous species with encephalization levels second only to modern humans and greater than all other mammals. Odontocetes have also demonstrated behavioral faculties previously only ascribed to humans and, to some extent, other great apes. How did the large brains of odontocetes evolve? To begin to investigate this question, we quantified and averaged estimates of brain and body size for 36 fossil cetacean species using computed tomography and analyzed these data along with those for modern odontocetes. We provide the first description and statistical tests of the pattern of change in brain size relative to body size in cetaceans over 47 million years. We show that brain size increased significantly in two critical phases in the evolution of odontocetes. The first increase occurred with the origin of odontocetes from the ancestral group Archaeoceti near the Eocene-Oligocene boundary and was accompanied by a decrease in body size. The second occurred in the origin of Delphinoidea only by 15 million years ago.

Animals↗
PubMed1996

Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships.

By using the maximum likelihood method, we study the reliability of phylogeny based on only four taxa, which have been studied by Philippe and Douzery with the maximum parsimony and neighbor-joining methods. Amino acid sequences of cytochrome b were provided for the analysis to examine the relationships among Ruminantia, Suiformes, and Cetacea with out-group mammals by using one representative species from each group. In accord with Philippe and Douzery's analysis, it was shown that we can find a quartet of species which provides a high bootstrap proportion for each of the three possible trees and that the quartet analyses with only four species can be misleading even with the maximum likelihood. However, if the confidence level of the inferred tree is estimated adequately by the maximum likelihood method and we take a conservative attitude, we can avoid the danger of concluding an erroneous tree by using quartet analysis, although the problem may remain unresolved in many cases. In order to obtain a reliable tree, it is important to carry out analyses based on as many different genes and as many relevant species as possible and to synthesize the results.

Animals↗
PubMed1997

Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata.

Contrary to morphological claims, molecular data indicate that the order Perissodactyla (e.g., horses, rhinoceroses, and tapirs) is neither part of the superordinal taxon Paenungulata (Sirenia, Proboscidea, and Hyracoidea) nor an immediate outgroup of the paenungulates. Rather, Perissodactyla is closer to Carnivora and Cetartiodactyla (Cetacea+Artiodactyla) than it is to the paenungulates. Therefore, two morphologically defined superordinal taxa, Altungulata (Proboscidea, Sirenia, Hyracoidea, and Perissodactyla) and Ungulata (Altungulata and Cetartiodactyla), are invalidated. Perissodactyla, Carnivora, and Cetartiodactyla are shown to constitute a rather tight trichotomy. However, a molecular analysis of 36 protein sequences with a total concatenated length of 7885 aligned amino acids indicates that Perissodactyla is closer to Cetartiodactyla than either taxa is to Carnivora. The relationships among Paenungulata, Primates, and the clade consisting of Perissodactyla, Carnivora, and Cetartiodactylaa could not be resolved on the basis of the available data.

Amino Acid Sequence↗
PubMed1999

Inclusion of cetaceans within the order Artiodactyla based on phylogenetic analysis of pancreatic ribonuclease genes.

Mammalian secretory ribonucleases (RNases 1) form a family of extensively studied homologous proteins that were already used for phylogenetic analyses at the protein sequence level previously. In this paper we report the determination of six ribonuclease gene sequences of Artiodactyla and two of Cetacea. These sequences have been used with ruminant homologues in phylogenetic analyses that supported a group including hippopotamus and toothed whales, a group of ruminant pancreatic and brain-type ribonucleases, and a group of tylopod sequences containing the Arabian camel pancreatic ribonuclease gene and Arabian and Bactrian camel and alpaca RNase 1 genes of unknown function. In all analyses the pig was the first diverging artiodactyl. This DNA-based tree is compatible to published trees derived from a number of other genes. The differences to those trees obtained with ribonuclease protein sequences can be explained by the influence of convergence of pancreatic RNases from hippopotamus, camel, and ruminants and by taking into account the information from third codon positions in the DNA-based analyses. The evolution of sequence features of ribonucleases such as the distribution of positively charged amino acids and of potential glycosylation sites is described with regard to increased double-stranded RNA cleavage that is observed in several cetacean and artiodactyl RNases which may have no role in ruminant or ruminant-like digestion.

Amino Acid Sequence↗
PubMed1979

Complete amino acid sequence of the myoglobin from the Pacific sei whale, Balaenoptera borealis.

The complete amino acid sequence of the major component myoglobin from Pacific sei whale, Balaenoptera borealis, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. The acetimidated apomyoglobin was selectively cleaved at its two methionyl residues with cyanogen bromide and at its three arginyl residues by trypsin. From the sequence analysis of four of these peptides and the apomyoglobin, over 75% of the covalent structure of the protein was obtained. The remainder of the primary structure was determined by the sequence analysis of peptides that resulted from further digestion of the amino-terminal and central cyanogen bromide fragments. The amino-terminal fragment was specifically cleaved at its two tryptophanyl residues with N-chlorosuccinimide and the central cyanogen bromide fragment was cleaved at its glutamyl residues with staphylococcal protease and at its single tyrosyl residue with N-bromosuccinimide. The primary structure of this myoglobin proved identical with that from the gray whale but differs from that of the finback whale at four positions, from that of the minke whale at three positions and from the myoglobin of the humpback whale at one position. The above sequence identities and differences reflect the close taxonomic relationship of these five species of Cetacea.

Amino Acid Sequence↗
PubMed1980

Complete amino acid sequence of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris.

The complete primary structure of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three peptides resulting from the cleavage of the apomyoglobin at its two methionine residues with cyanogen bromide along with the four peptides resulting from the cleavage with trypsin of the citraconylated apomyoglobin at its three arginine residues. Further digestion of the central cyanogen bromide peptide with S. aureus strain V8 protease and the 1,2-cyclohexanedione-treated central cyanogen bromide peptide with trypsin enabled the determination of the remainder of the covalent structure. This myoglobin differs from the cetacean myoglobins determined to date at 12 to 17 positions. These large sequence differences reflect the distant taxonomic relationships between the goose-beaked whale and the other species of Cetacea the myoglobin sequences of which have previously been determined.

Amino Acid Sequence↗
PubMed2001

Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls.

Modern members of the mammalian order Cetacea (whales, dolphins and porpoises) are obligate aquatic swimmers that are highly distinctive in morphology, lacking hair and hind limbs, and having flippers, flukes, and a streamlined body. Eocene fossils document much of cetaceans' land-to-water transition, but, until now, the most primitive representative for which a skeleton was known was clearly amphibious and lived in coastal environments. Here we report on the skeletons of two early Eocene pakicetid cetaceans, the fox-sized Ichthyolestes pinfoldi, and the wolf-sized Pakicetus attocki. Their skeletons also elucidate the relationships of cetaceans to other mammals. Morphological cladistic analyses have shown cetaceans to be most closely related to one or more mesonychians, a group of extinct, archaic ungulates, but molecular analyses have indicated that they are the sister group to hippopotamids. Our cladistic analysis indicates that cetaceans are more closely related to artiodactyls than to any mesonychian. Cetaceans are not the sister group to (any) mesonychians, nor to hippopotamids. Our analysis stops short of identifying any particular artiodactyl family as the cetacean sister group and supports monophyly of artiodactyls.

Animals↗
PubMed2003

The emergence of cetaceans: phylogenetic analysis of male social behaviour supports the Cetartiodactyla clade.

The phylogeny of cetaceans is still unresolved. Two hypotheses prevail for the position of cetaceans among ungulates. The first hypothesis shows that Artiodactyla is monophyletic and is sister taxon to a clade composed of cetaceans and mesonychians. The second one shows that Artiodactyla is paraphyletic and contains Cetacea that is sister taxon of Hippopotamida. These hypotheses are based on fossil records and molecular studies. The behaviour of extant species can provide as much phylogenetic information as other classical parameters. I considered the behaviour observed during male agonistic interactions in placental mammals in order to determine which of these hypotheses was supported by the behaviour of extant species. Headbutting was only observed in ruminants, hippopotamids and cetaceans, supporting the paraphyletic nature of Artiodactyla. Primitive ruminants (tragulids) and two genera of ruminants (Moschus and Oreamnos) were not observed headbutting. These secondary losses were only present in 6.25% of the 48 surveyed ruminant genera. Head-to-head attacks emerged in pigs, which have developed dermal protusions. Yet, these confrontations are not based on mutual blow delivery. The behavioural evidence supports the inclusion of cetaceans in Artiodactyla.

Agonistic Behavior↗