Accelerated Evolutionary Rate of the Myoglobin Gene in Long-Diving Whales

Cetaceans, early in their evolutionary history, had developed many physiological adaptations to secondarily return to the sea. Among these adaptations, changes in molecules that transport oxygen and that ultimately support large periods of acute tissue hypoxia probably represent one big step toward the conquest of aquatic environments. Myoglobin contributes to intracellular oxygen storage and transcellular diffusion of oxygen in muscle, and plays an important role in supplying oxygen in hypoxic or ischemic conditions. Here we looked for evidence of adaptive molecular evolution of myoglobin in the cetacean lineage, relative to their terrestrial counterparts. We performed a comparative analysis to examine the variation of the parameter ω (d _N/d _S) and infer past period of adaptive evolution during the cetacean transition from the terrestrial to the aquatic environment. We also analyzed the changes in amino acid properties. At the nucleotide level, the results showed significant differences in selective pressure between cetacean and non-cetacean myoglobin (ω value three times higher in cetaceans when compared to terrestrial mammals), and also among cetacean lineages according to their diving capacities. Interestingly, both families with long duration diving cetaceans present two parallel substitutions (on sites 4 and 12). Regarding the amino acid properties, our analysis identified four significant physicochemical amino acid changes among residues in myoglobin protein under positive destabilizing selection.     

From Land to Water: the Origin of Whales, Dolphins, and Porpoises

Cetaceans (whales, dolphins, and porpoises) are an order of mammals that originated about 50 million years ago in the Eocene epoch. Even though all modern cetaceans are obligate aquatic mammals, early cetaceans were amphibious, and their ancestors were terrestrial artiodactyls, similar to small deer. The transition from land to water is documented by a series of intermediate fossils, many of which are known from India and Pakistan. We review raoellid artiodactyls, as well as the earliest families of cetaceans: pakicetids, ambulocetids, remingtonocetids, protocetids, and basilosaurids. We focus on the evolution of cetacean organ systems, as these document the transition from land to water in detail.     

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.     

鲸类低氧耐受的分子机制初探:基于HIF1α和TSC1基因的生物信息学分析

鲸类(Cetacea)具有超强潜水能力,长时间潜水造成的体内低氧是其适应完全水生生活面临的挑战之一.为了克服体内低氧环境,鲸类产生了一系列低氧耐受相关的解剖和生理等方面的适应特征,然而这一适应的分子机制仍不清楚.本研究选择在细胞感知和适应内环境氧分压变化的过程中发挥重要作用的低氧诱导因子(Hy-poxia-induci...     

Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins

Cetaceans have most likely experienced metabolic shifts since evolutionarily diverging from their terrestrial ancestors, shifts that may be reflected in the proteins such as cytochrome b that are responsible for metabolic efficiency. However, accepted statistical methods for detecting molecular adaptation are largely biased against even moderately conservative proteins because the primary criterion involves a comparison of nonsynonymous and synonymous substitution rates (dN/dS); they do not allow for the possibility that adaptation may come in the form of very few amino acid changes. We apply the MM01 model to the possible molecular adaptation of cytochrome b among cetaceans because it does not rely on a dN/dS ratio, instead evaluating positive selection in terms of the amino acid properties that comprise protein phenotypes that selection at the molecular level may act upon. We also apply the codon-degeneracy model (CDM), which focuses on evaluating overall patterns of nucleotide substitution in terms of base exchange, codon position, and synonymy to estimate the overall effect of selection. Using these relatively new models, we characterize the molecular adaptation that has occurred in the cetacean cytochrome b protein by comparing revealed amino acid replacement patterns to those found among artiodactyls, the modern terrestrial mammals found to be most closely related to cetaceans. Our findings suggest that several regions of the cetacean cytochrome b protein have experienced molecular adaptation. Also, these adaptations are spatially associated with domain structure, protein function, and the structure and function of the cytochrome bc(1) complex and its constituents. We also have found a general correlation between the results of the analytical software programs TreeSAAP (which implements the MM01 model) and CDM (which implements the codon-degeneracy model).     

Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown

Cetaceans (dolphins and whales) have undergone a radical transformation from the original mammalian bodyplan. In addition, some cetaceans have evolved large brains and complex cognitive capacities. We compared approximately 10 000 protein-coding genes culled from the bottlenose dolphin genome with nine other genomes to reveal molecular correlates of the remarkable phenotypic features of these aquatic mammals. Evolutionary analyses demonstrated that the overall synonymous substitution rate in dolphins has slowed compared with other studied mammals, and is within the range of primates and elephants. We also discovered 228 genes potentially under positive selection (dN/dS > 1) in the dolphin lineage. Twenty-seven of these genes are associated with the nervous system, including those related to human intellectual disabilities, synaptic plasticity and sleep. In addition, genes expressed in the mitochondrion have a significantly higher mean dN/dS ratio in the dolphin lineage than others examined, indicating evolution in energy metabolism. We encountered selection in other genes potentially related to cetacean adaptations such as glucose and lipid metabolism, dermal and lung development, and the cardiovascular system. This study underlines the parallel molecular trajectory of cetaceans with other mammalian groups possessing large brains.     

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.     

A killer appetite: metabolic consequences of carnivory in marine mammals

Among terrestrial mammals, the morphology of the gastrointestinal tract reflects the metabolic demands of the animal and individual requirements for processing, distributing, and absorbing nutrients. To determine if gastrointestinal tract morphology is similarly correlated with metabolic requirements in marine mammals, we examined the relationship between basal metabolic rate (BMR) and small intestinal length in pinnipeds and cetaceans. Oxygen consumption was measured for resting bottlenose dolphins and Weddell seals, and the results combined with data for four additional species of carnivorous marine mammal. Data for small intestinal length were obtained from previously published reports. Similar analyses were conducted for five species of carnivorous terrestrial mammal, for which BMR and intestinal length were known. The results indicate that the BMRs of Weddell seals and dolphins resting on the water surface are 1.6 and 2.3 times the predicted levels for similarly sized domestic terrestrial mammals, respectively. Small intestinal lengths for carnivorous marine mammals depend on body size and are comparatively longer than those of terrestrial carnivores. The relationship between basal metabolic rate (kcal day(-1)) and small intestinal length (m) for both marine and terrestrial carnivores was, BMR=142.5 intestinal length(1.20) (r(2)=0.83). We suggest that elevated metabolic rates among marine mammal carnivores are associated with comparatively large alimentary tracts that are presumably required for supporting the energetic demands of an aquatic lifestyle and for feeding on vertebrate and invertebrate prey.     

Decay of TRPV3 as the genomic trace of epidermal structure changes in the land‐to‐sea transition of mammals

The epidermis plays an indispensable barrier function in animals. Some species have evolved unique epidermal structures to adapt to different environments. Aquatic and semi‐aquatic mammals (cetaceans, manatees, and hippopotamus) are good models to study the evolution of epidermal structures because of their exceptionally thickened stratum spinosum, the lack of stratum granulosum, and the parakeratotic stratum corneum. This study aimed to analyze an upstream regulatory gene transient receptor potential cation channel, subfamily V, member 3 (TRPV3) of epidermal differentiation so as to explore the association between TRPV3 evolution and epidermal changes in mammals. Inactivating mutations were detected in almost all the aquatic cetaceans and several terrestrial mammals. Relaxed selective pressure was examined in the cetacean lineages with inactivated TRPV3, which might contribute to its exceptionally thickened stratum spinosum as the significant thickening of stratum spinosum in TRPV3 knock‐out mouse. However, functional TRPV3 may exist in several terrestrial mammals due to their strong purifying selection, although they have “inactivating mutations.” Further, for intact sequences, relaxed selective constraints on the TRPV3 gene were also detected in aquatic cetaceans, manatees, and semi‐aquatic hippopotamus. However, they had intact TRPV3, suggesting that the accumulation of inactivating mutations might have lagged behind the relaxed selective pressure. The results of this study revealed the decay of TRPV3 being the genomic trace of epidermal development in aquatic and semi‐aquatic mammals. They provided insights into convergently evolutionary changes of epidermal structures during the transition from the terrestrial to the aquatic environment.     

Head morphology in perinatal dolphins: a window into phylogeny and ontogeny

In this paper on the ontogenesis and evolutionary biology of odontocete cetaceans (toothed whales), we investigate the head morphology of three perinatal pantropical spotted dolphins (Stenella attenuata) with the following methods: computer-assisted tomography, magnetic resonance imaging, conventional X-ray imaging, cryo-sectioning as well as gross dissection. Comparison of these anatomical methods reveals that for a complete structural analysis, a combination of modern imaging techniques and conventional morphological methods is needed. In addition to the perinatal dolphins, we include series of microslides of fetal odontocetes (S. attenuata, common dolphin Delphinus delphis, narwhal Monodon monoceros). In contrast to other mammals, newborn cetaceans represent an extremely precocial state of development correlated to the fact that they have to swim and surface immediately after birth. Accordingly, the morphology of the perinatal dolphin head is very similar to that of the adult. Comparison with early fetal stages of dolphins shows that the ontogenetic change from the general mammalian bauplan to cetacean organization was characterized by profound morphological transformations of the relevant organ systems and roughly seems to parallel the phylogenetic transition from terrestrial ancestors to modern odontocetes.     

Lipokeratinocytes of the epidermis of a cetacean (Phocena phocena)

Summary Biochemical and ultrastructural analysis of epidermis from the porpoise, Phocena phocena, revealed certain similarities and differences between cetaceans and terrestrial mammals. The predominant cell of cetacean epidermis, not found in normal terrestrial mammals, is a lipoker-atinocyte, which elaborates not only keratin filaments, but also two types of lipid organelles: first, lamellar bodies, morphologically identical to those of terrestrial mammals, are elaborated in great abundance in all suprabasal epidermal layers, forming intercellular lipid bilayers in the stratum corneum interstices: and second, non-membrane-bounded droplets appear and persist in all epidermal layers. Although the porpoise lipokeratinocyte morpologically resembles the sebokeratocyte of avians in certain respects, nonmembrane-bounded lipid droplets are not released into the intercorneocyte space as they are in avian stratum corneum. Whereas phospholipid/neutral lipid gradients are similar in porpoise and terrestrial mammals, PAS-positive glycoconjugates, specifically glycosphingolipids, are retained in porpoise stratum corneum, but lost from these layers in terrestrials. The novel, non-polar acylglucosyl-ceramides, which also are lost during cornification in terrestrial mammals, are retained in porpoise stratum corneum. The lipid components of porpoise lipokeratinocytes appear to subserve not only barrier function in a hypertonic milieu, but also underlie the unique buoyancy, streamlining, insulatory, and caloric properties exhibited as adaptations to the cetacean habitat.     

BUFFERING CAPACITY OF THE LOCOMOTOR MUSCLE IN CETACEANS: CORRELATES WITH POSTPARTUM DEVELOPMENT, DIVE DURATION, AND SWIM PERFORMANCE

Skeletal muscles of marine mammals must support the metabolic demands of exercise during periods of reduced blood flow associated with the dive response. Enhanced muscle buffering could support anaerobic metabolic processes during apnea, yet this has not been fully investigated in cetaceans. To assess the importance of this adaptation in the diving and swimming performance of cetaceans, muscle buffering capacity due to non-bicarbonate buffers was measured in the longissimus dorsi of ten species of odontocete and one mysticete. Immature specimens from a subset of these species were studied to assess developmental trends. Fetal and neonatal cetaceans have low buffering capacities (range: 34.8–53.9 slykes) that are within the range measured for terrestrial mammals. A lengthy developmental period, independent of muscle myoglobin postnatal development, is required before adult levels are attained. Adult cetacean buffering capacities (range: 63.7–94.5 slykes) are among the highest values recorded for mammals. Cetacean species that demonstrate extremely long dive durations or high burst speed swimming tend to have greater buffering capacities. However, the wide range of body size across cetaceans may complicate these trends. Enhanced muscle buffering capacity may enable small-bodied species to extend breath-hold beyond short aerobic dive limits for foraging or predator evasion when necessary.     

Adaptive Evolution of the Hox Gene Family for Development in Bats and Dolphins

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.     

Molecular cloning and histological localization of LH-like substances in a bottlenose dolphin (Tursiops truncatus) placenta

All mammals exhibit pituitary-specific expression of LH and FSH, whereas placental expression of gonadotropins has been reported only in primates and equids. Some cetaceans, such as dolphins, have a long gestational period and a sexual cycle of about 27 days almost comparable with that of humans. Histologically, dolphins have an epitheliochorial placentae that resembles placentas of Perissodactyla including horses. In the present study, we cloned cDNAs encoding gonadotropins and observed their immunohistochemical localization in the placenta of bottlenose dolphin. The cDNAs obtained encoded 120 amino acids for the alpha-subunit (including 96 amino acids of mature proteins), and 141 amino acids for the beta-subunit (including 121 amino acids of mature proteins). The sequence of the alpha-subunit was similar to that in the pig (Artiodactyla) pituitary glycoprotein hormone [96.7% homology at amino acids (aa) level], and the sequence of the beta-subunit was similar to that of luteinizing hormone (LH) in the pig [94.3% homology at aa level] and white rhinoceros (Perissodactyla) [93.3% homology at aa level]. Of interest, dolphin LHbeta lacks carboxyl-terminal-peptides (CTP). This fact suggests that CTP are not essential for placental expression of gonadotropin in dolphins. Immunohistochemical observations employing anti-ovine LHbeta antibody revealed positive staining in the villositycal tissue. Our observations suggest placental expression of gonadotropin homologues in cetaceans and possible evolutionary conservation of placentae-derived hormonal control of ovarian functions during pregnancy.     

鲸类二次水生生境适应Epac1和Epac2基因的分子进化

心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白（Epac1 和Epac2）基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸（Physeter macrocephalus）组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰（θ=0.5296 ± 0.1300;P<0.001）。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸（Balaena mysticetus）中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1和Epac2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。     

Amino acid sequence variations of signaling lymphocyte activation molecule and mortality caused by morbillivirus infection in cetaceans

Morbillivirus infection is a severe threat to marine mammals. Mass die‐offs caused by this infection have repeatedly occurred in bottlenose dolphins (Turiops truncatus) and striped dolphins (Stenella coeruleoalba), both of which belong to the family Delphinidae, but not in other cetaceans. However, it is unknown whether sensitivity to the virus varies among cetacean species. The signaling lymphocyte activation molecule (SLAM) is a receptor on host cells that allows morbillivirus invasion and propagation. Its immunoguloblin variable domain‐like (V) region provides an interface for the virus hemagglutinin (H) protein. In this study, variations in the amino acid residues of the V region of 26 cetacean species, covering almost all cetacean genera, were examined. Three‐dimensional (3D) models of them were generated in a homology model using the crystal structure of the marmoset SLAM and measles virus H protein complex as a template. The 3D models showed 32 amino acid residues on the interface that possibly bind the morbillivirus. Among the cetacean species studied, variations were found at six of the residues. Bottlenose and striped dolphins have substitutions at five positions (E68G, I74V, R90H, V126I, and Q130H) compared with those of baleen whales. Three residues (at positions 68, 90 and 130) were found to alternate electric charges, possibly causing changes in affinity for the virus. This study shows a new approach based on receptor structure for assessing potential vulnerability to viral infection. This method may be useful for assessing the risk of morbillivirus infection in wildlife.     

L’origine et l’histoire évolutive des Cétacés

Cetaceans are the most highly modified mammals. They originate among terrestrial ariodactyles during the Early Eocene. The oldest known cetacean is Pakicetus, a terrestrial and cursorial taxon of the Early Eocene (50 Ma), which entered the water in search for food or, possibly, to protect its skin from the sun. A few million years later, Ambulocetus is an amphibious cetacean capable of moving on land but also an agile swimmer using its hind limbs for propulsion. Ambulocetus was a formidable predator with powerful teeth. The nares of Pakicetus and Ambulocetus were anteriorly placed, at the apex of the snout. During the Late Eocene, there appeared the first strictly aquatic cetaceans, the Basilosauridae. Their hind limbs are totally atrophied and are not functional. The nares are on the dorsal face of the rostrum on the anterior third of the skull. From that time, the way toward modern cetaceans was opened; the oldest mysticetes are from the Latest Eocene and the oldest odontocetes from the Early Oligocene.