Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.     

Sequence variation in the Tbx4 gene in marine mammals

The amino-acid sequences of the T-domain region of the Tbx4 gene, which is required for hindlimb development, are 100% identical in humans and mice. Cetaceans have lost most of their hindlimb structure, although hindlimb buds are present in very early cetacean embryos. To examine whether the Tbx4 gene has the same function in cetaceans as in other mammals, we analyzed Tbx4 sequences from cetaceans, dugong, artiodactyls and marine carnivores. A total of 39 primers were designed using human and dog Tbx4 nucleotide sequences. Exons 3, 4, 5, 6, 7, and 8 of the Tbx4 genes from cetaceans, artiodactyls, and marine carnivores were sequenced. Non-synonymous substitution sites were detected in the T-domain regions from some cetacean species, but were not detected in those from artiodactyls, the dugong, or the carnivores. The C-terminal regions contained a number of non-synonymous substitutions. Although some indels were present, they were in groups of three nucleotides and therefore did not cause frame shifts. The dN/dS values for the T-domain and C-terminal regions of the cetacean and artiodactylous Tbx4 genes were much lower than 1, indicating that the Tbx4 gene maintains it function in cetaceans, although full expression leading to hindlimb development is suppressed.     

Cytochromeb gene of marine mammals: Phylogeny and evolution

The DNA sequences of the mitochondrial cytochromeb gene of marine mammals (Cetacea, Pinnipedia, Sirenia) were compared with cytochromeb genes of terrestrial mammals including the semiaquatic hippopotamus. The comparison included 28 sequences, representing 22 families and 10 orders. The dugong (order Sirenia) sequence associated with that of the elephant, supporting the Tethytheria clade. The fin whale and dolphin (order Cetacea) sequences are more closely related to those of the artiodactyls, and the comparison suggests that the hippopotamus may be the extant artiodactyl species that is most closely related to the cetaceans. The seal sequence may be more closely related to those of artiodactyls, cetaceans, and perissodactyls than to tethytheres, rodents, lagomorphs, or primates. The cytochromeb proteins of mammals do not evolve at a uniform rate. Human and elephant cytochromeb amino acid sequences were found to evolve the most rapidly, while those of myomorph rodents evolved slowest. The cytochromeb of marine mammals evolves at an intermediate rate. The pattern of amino acid substitutions in marine mammals is similar to that of terrestrial mammals.     

Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence

A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved morphological traits of the astragalus and deciduous dentition provide strong corroboration of artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and uniquely derived morphological features of the skull and auditory regions provide robust corroboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleotide similarities do exist between physeteroids and mysticetes; however, most are either silent third-position transversions or occur also in two or more odontocete families. We suggest that increased taxon sampling, combined with functional considerations of amino acids and their secondary structure in protein-coding genes, are essential requirements for the phylogenetic interpretations of molecules at higher taxonomic levels, especially when they conflict with well-supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morphological traits from extant and fossil taxa.     

Ankle morphology of the earliest Cetaceans and its implications for the phylogenetic relations among ungulates

Recent molecular studies are inconsistent with ungulate phylogenetic trees that are based on morphological traits. These inconsistencies especially relate to the position of cetaceans and perissodactyls. Evaluation of the close phylogenetic ties between artiodactyls and cetaceans has been hampered by the absence of tarsal bones of primitive cetaceans, as artiodactyls are often diagnosed on the basis of their tarsus. We here describe newly discovered tarsal bones that are the oldest cetacean tarsals known. We present a character analysis for primitive ungulate tarsals and evaluate their impact on the ungulate phylogenetic tree. Tarsal data are consistent with some molecular studies in suggesting that the extant sister group of Cetacea is Artiodactyla or that Cetacea should be included within the latter order. Tarsal data do not support Cete (Mesonychia plus Cetacea) and are consistent with the exclusion of perissodactyls from paenungulates as suggested by some molecular studies.     

DNA-DNA hybridizations support ungulate ancestry of Cetacea

Recent morphological data on Pakicetus spp. and Basilosaurus spp. fossils suggest that cetaceans (whales, dolphins and porpoises) originate from carnivorous Mesonychid land mammals (Condylarthra) and made a gradual transition from land to sea in early Eocene (Gingerich et al. 1983; 1990). On the other hand, there is convincing evidence that Artiodactyla and Perissodactyla have evolved from Condylarthra (Van Valen 1978, Carrol 1988). Therefore, the Pakicetus and Basilosaurus data suggest a close genetic relationship between cetaceans and ungulates. An approach based on molecular genetics was used in this study to test the morphological hypothesis. Liver samples of two Delphinoidea species were obtained from animals caught in a Peruvian gillnet fishery. ³²P- or ³⁵S-labeled single copy nuclear genomes (scn-DNA) of the two cetacean species were hybridized each with unlabeled total DNA of various cetaceans, ungulates and other mammals including primates, rodents, lagomorphs and carnivores. The T_median (T_m) and T_mode of all melting curves, used as a measure of the DNA-DNA hybrids stability, clearly show a greater sequence similarity — and thus a lower genetic distance — between cetaceans and ungulates than between cetaceans and other mammals.     

Astragali of Pakicetidae and other early-to-middle Eocene archaeocetes (Mammalia,Cetacea) of Pakistan: locomotion and habitat in the initial stages of whale evolution

Richard Dehm and colleagues of the Bayerische Staatssammlung für Paläontologie und Geologie in Munich made an important collection of early-to-middle Eocene mammals at Ganda Kas in Pakistan during the winter of 1955/56. The genera and species Ichthyolestes pinfoldi and Gandakasia potens were named from this collection. Both are now recognized as early and primitive archaeocete cetaceans. In addition, Dehm’s group collected 16 complete or partial astragali of archaeocetes that were misidentified as artiodactyls. These bring the total number of archaeocete astragali known from Ganda Kas to 28. They separate clearly into four species distinguished by size: from smallest to largest Ichthyolestes pinfoldi Dehm and Oettingen-Spielberg, Pakicetus attocki (West), Gandakasia potens Dehm and Oettingen-Spielberg, and Ambulocetus natans Thewissen et al. Ganda Kas artiodactyls are smaller and rare in comparison. Ichthyolestes and Pakicetus are pakicetid archaeocetes, Gandakasia is presently indeterminate to family, and Ambulocetus is an ambulocetid. Tooth size and astragalus size are highly correlated, corroborating reference of astragali to the first three archaeocete taxa based on teeth. Multivariate morphometric comparison (Auto3Dgm) shows that pakicetid astragali overlap almost completely in shape with those of early artiodactyls. Middle Eocene protocetid astragali are divergent from both. Retention of an astragalus indistinguishable from that of artiodactyls shows that pakicetids are closely related to artiodactyls phylogenetically, but does not make Ichthyolestes and Pakicetus terrestrial or cursorial. Other skeletal elements and bone microstructure indicate that pakicetids were semiaquatic like later protocetids. Tropical riverine and marginal marine facies of the Kuldana Formation are likely habitats for initial stages of the transition from terrestrial artiodactyls to semiaquatic and fully aquatic archaeocetes.     

Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenarthra (Edentata) and Ferungulates

Phylogenetic analysis of 12 protein-coding genes from complete mitochondrial DNA (mtDNA) molecules of various mammals including a xenarthran representative, the armadillo (Dasypus novemcinctus), showed that the order Xenarthra (Edentata) is a sister group to the ferungulates (carnivores, perissodactyls, artiodactyls, cetaceans). Morphological and previous molecular analyses have placed the Xenarthra basal to other extant eutherians. The present findings are in striking contrast with that understanding. The results suggest that Xenarthra and ferungulates separated about 86 MYA.      

The complete nucleotide sequence of the mitochondrial DNA of the fin whale,Balaenoptera physalus

Summary The composition of the mitochondrial DNA (mtDNA) of the fin whale,Balaenoptera physalus, was determined. The length of the molecule is 16,398 bp, and its organization conforms with that of other mammals. The general similarity between the mtDNA of the fin whale and the cow is greater than the similarity between the fin whale and other species (human, mouse, rat) in which the composition of the entire molecule has been described. The D-loop region of the mtDNA of the fin whale is 81% identical to the D-loop of dolphin DNA, and the central portion of the D-loop is similar to the bovine D-loop. The accumulation of transversions and gaps in the 12S and 16S rRNA genes was assessed by comparing the fin whale, cow, and human. The sequence difference between human and the whale and human and the cow was at the same level, indicating that the rate of evolution of the mtDNA rRNA genes is about the same in artiodactyls and cetaceans. In the 12S rRNA gene an accumulation rate of 0.05% per million years places the separation of cetaceans and artiodactyls at about 55 million years ago. The corresponding figure for human and either the whale or the cow is about 80 million years. In the 16S rRNA gene a 0.08% accumulation rate of transversions and gaps per million years yields concurring figures. A comparison between the cytochromeb gene of the fin whale and cytochromeb sequences in the literature, including dolphin (Stenella) sequences, identified the cetaceans as monophyletic and the artiodactyls as their closest relatives. The comparison between the cytochromeb sequences of the fin whale andStenella showed that differences in codon positions one or two were frequently associated with a change in another codon position.     

Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes

Ursing, B. M., Slack, K. E. & Arnason, U. (2000) Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes. — Zoologica Scripta , 29 , 83–88.
Extant artiodactyls (even-toed hoofed mammals) are traditionally divided into three main lineages: Suiformes (pigs, peccaries and hippopotamuses), Tylopoda (camels and llamas) and Ruminantia (bovids, deer, tragulids and giraffes). Recent molecular studies have not supported a close relationship between pigs and hippopotamuses, however, instead grouping hippopotamuses with Cetacea (whales, dolphins and porpoises). In this study we have sequenced the complete mitochondrial genome of a tylopod — the alpaca (Lama pacos), the only artiodactyl suborder not previously represented by a complete mitochondrial sequence. This sequence was included in phylogenetic analyses together with the complete mitochondrial protein-coding sequences of other artiodactyls plus two cetaceans. Despite the length of the data set, the relationship between Suina (Suiformes sine Hippopotamidae), Tylopoda and Ruminantia/Hippopotamidae/Cetacea could not be fully resolved, however, a basal position of the alpaca (Tylopoda) relative to the other artiodactyls/cetaceans was unsupported.     

Avian sebokeratocytes and marine mammal lipokeratinocytes: structural, lipid biochemical, and functional considerations

In terrestrial mammals, stratum corneum lipids derive from two sources: deposition of lamellar body lipids in stratum corneum interstices and excretion of sebaceous lipids onto the skin surface, resulting in a two-compartment ("bricks and mortar") system of lipid-depleted cells surrounded by lipid-enriched intercellular spaces. In contrast, intracellular lipid droplets, normally not present in the epidermis of terrestrial mammals, are prominent in avian and marine mammal epidermis (cetaceans, manatees). We compared the transepidermal water loss, ultrastructure, and lipid biochemistry of the viable epidermis and stratum corneum of pigeon apterium, fledgling (featherless) zebra finches, painted storks, cetaceans, and manatees to those of humans and mice. Marine mammals possess an even more extensive lamellar-body secretory system than do terrestrial mammals; and lamellar-body contents, as in terrestrials, are secreted into the stratum corneum interstices. In cetaceans, however, glycolipids, but not ceramides, persist into the stratum corneum; whereas in manatees, glycolipids are replaced by ceramides, as in terrestrial mammals. Acylglucosylceramides, thought to be critical for lamellar-body deposition and barrier function in terrestrial mammals, are present in manatees but virtually absent in cetaceans, a finding that indicates that they are not obligate constituents of lamellar-body-derived membrane structures. Moreover, cetaceans do not elaborate the very long-chain, saturated N-acyl fatty acids that abound in terrestrial mammalian acylglucosylceramides. Furthermore, cold-water marine mammals generate large, intracellular neutral lipid droplets not found in terrestrial and warm-water marine mammals; these lipid droplets persist into the stratum corneum, suggesting thermogenesis, flotation, and/or cryoprotectant functions. Avians generate distinctive multigranular bodies that may be secreted into the intercellular spaces under xerotic conditions, as in zebra fledglings; ordinarily, however, the internal lamellae and limiting membranes deteriorate, generating intracellular neutral lipid droplets. The sphingolipid composition of avian stratum corneum is intermediate between terrestrials and cetaceans (approximately equal to 50% glycolipids), with triglycerides present in abundance. In the midstratum corneum of avians, neutral lipid droplets are released into the interstices, forming a large extracellular, lipid-enriched compartment, surrounding wafer-thin corneocytes, with a paucity of both lipid and keratin ("plates-and-mortar" rather than the "bricks-and-mortar" of mammals).(ABSTRACT TRUNCATED AT 400 WORDS)     

Artiodactyl interspersed DNA repeats in cetacean genomes

Interspersed repeats that emerged at different evolutionary times are informative in mammalian phylogeny. Here we show that the ancient short interspersed elements (SINEs) ARE1 and ARE2 are abundantly present in the genomes of artiodactyls and cetaceans but not in other mammalian genomes. This supports the classification of the cetaceans with the artiodactyls by a shared character that is unlikely to be the result of convergence. Received: 16 October 1996 / Accepted: 13 December 1996     

Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans

Relationships among and within baleen and toothed whales were examined using the complete sequence of the mitochondrial cytochrome b gene. Based on parsimony analyses of conservative nucleotide substitutions, five primary evolutionary lineages of extant cetaceans were identified, one represented by baleen whales (Mysticeti) and four represented by odontocetes (toothed whales). Based on the most comprehensive representation of taxa, both cetaceans and artiodactyls, the most parsimonious relationship among the five lineages is (Mysticeti, Odontoceti (Platanistoidea (Physeteroidea (Ziphioidea (Delphinida))))). This relationship, however, is labile and sensitive to ingroup representation and the choice of outgroup. The short nodes among the five cetacean lineages suggest that the divergence among these lineages occurred over a narrow time period, a finding consistent with the limited fossil evidence that indicates a major cetacean radiation 30-34 Mya. The level of divergence among the five cetacean lineages, and that seen between cetaceans and artiodactyls, suggests that cetaceans and artiodactyls had a common ancestor approximately 60 Mya.      

A molecular perspective on the phylogeny of placental mammals based on mitochondrial 12S rDNA sequences,with special reference to the problem of the Paenungulata

Part of the 12S rDNA gene was amplified and sequenced for 11 placental mammals, 3 marsupials, and 2 monotremes. Multiple alignments for these sequences and nine additional placental sequences taken from GenBank were obtained using CLUSTAL. Phylogenetic analyses were performed using standard parsimony, transversion parsimony, and Lake's method of invariants. All of our analyses uniteLoxodontia withDugong. Procavia, in turn, is a sister group to these taxa, thus supporting the monophyly of the Paenungulata. Perissodactyls are a sister group to paenungulates when transitions and transversions are both included but not when transitions are omitted. Likewise, cetaceans are a sister group to artiodactyls on minimum length trees under standard parsimony but not under transversion parsimony. Rodent monophyly and bat monophyly also receive mixed support, as does a putative alliance between primates and lagomorphs. Interestingly, the percentage divergence between the echidna and the platypus is less than for the rat and mouse.     

From limb to fin: an Eocene protocetid forelimb from Senegal sheds new light on the early locomotor evolution of cetaceans

Cetaceans constitute a textbook example of the secondary adaptation of tetrapods to aquatic life. This major event in the evolutionary history of mammals is often linked in the literature to the limb-to-fin transition. Paradoxically, limb bones are scarce in the fossil record of early cetaceans, and the transition from a limb-adapted morphology for an amphibious life in shallow water to a fin-adapted morphology for a pelagic lifestyle remains poorly documented. Here, we describe new protocetid remains from the upper Lutetian of Senegal, including a nearly complete articulated forelimb. A cladistic analysis including 24 taxa and 137 morphological characters recovers the new African specimen close to Carolinacetus. It also confirms that cetacean dispersal to the New World was not the result of a single colonization event. A 3D model of the forelimb was reconstructed. Anatomical comparisons suggest that it is unlikely that the Senegalese forelimb was used as a rigid pectoral flipper for steering as in basilosaurids and modern cetaceans. Instead, we suggest that the hand was actively used during swimming. This challenges previous reconstructions of protocetids as mainly foot-powered swimmers, and suggests that swimming specializations of early cetaceans were probably more diverse than previously considered.     

Feline Ventricular Ganglion Cells

IN mammals, with the exception of artiodactyls and cetaceans, it is generally accepted that intrinsic cardiac ganglion cells are confined distally by the atrioventricular groove¹. This is interpreted as indicating that vagal influence is limited to the atrial and specialized tissues and this concept is supported by much physiological evidence. It has been suggested that, in dogs, the vagi exert a direct negative inotropic effect on the ventricles², although Furnival et al.³ found that this effect was relatively insignificant. Morphologists have, however, reported ventricular ganglion cells in primates^4–6. We offer here morphological evidence for the existence of ventricular ganglion cells in the cat.     

Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs.

Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA(Glu) in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated successively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA(Arg) into the 5' region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA(Glu)-derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA(Glu)-related families of SINEs that are now found in the genomes of artiodactyls and cetaceans.     

WHO ARE THE WHALES?

ABSTRACT

Whales, dolphins and porpoises, 80 species of entirely aquatic mammals, constitute the order Cetacea. In the early Eocene, about 55 to 60 million years ago according to paleontologists, distant ancestors of modern cetaceans left land for aquatic life. Cetaceans are diverse; average adult size of cetacean species varies by 1000 to 2000 times. Small and large species occupy all oceans from the equator to the polar seas, some forms inhabit rivers and four species live only in fresh water.

Cetaceans are born in water and spend their entire lives in the aquatic medium. There is a great gap in knowledge about hearing in most cetacean species and especially about how noise and high-intensity sound may affect all cetaceans and other mammals underwater. Studies of temporary threshold shift (TTS) and occupational noise exposure in human divers suggest a cautious approach to cetacean noise exposure until data on cetacean TTS can give us some idea of the dynamic range of cetacean ears.     

Plasma and urine levels of electrolytes, urea and steroid hormones involved in osmoregulation of cetaceans

Cetaceans are well adapted to their hyperosmotic environment by properly developed osmoregulatory ability. A question here is how they regulate water and mineral balances in marine habitats. In the present study, we determined blood and urine levels of various chemicals involved in osmoregulation, compared them with those in artiodactyls, and characterized the values in the whales. Blood and urine samples obtained from baleen whales of common minke (Balaenoptera acutorostrata), sei (B. borealis), and Bryde's whales (B. brydei), and toothed whales of sperm whales (Physeter macrocephalus) were analyzed for osmolality, major electrolytes, urea, steroid hormones and glucose. The urine osmolality and Na(+) concentrations in the cetaceans were much higher than those in the cattle. Furthermore, the cetaceans had 5 to 11-fold urea in plasma than the cattle, and 2 to 4-fold urea in urine. There were no significant difference in the plasma concentrations of corticosteroids between the cetaceans and the cattle. The present results indicate that the osmoregulatory parameters seem to be not affected by the reproductive stage and sex steroid hormones. The concentrations of urea in plasma and urine of the baleen whales were higher than those of the sperm whales, indicating a possibility that their osmoregulatory mechanisms may be correlated to their feeding habits. The present results suggest that cetaceans have unique osmoregulatory mechanisms by which they excrete strongly hypertonic urine to maintain fluid homeostasis in marine habitats.