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.     

Comparative analysis of the prion protein (PrP) gene in cetacean species

The partial PrP gene sequence and the deduced protein of eight cetacean species, seven of which have never been reported so far, have been determined in order to extend knowledge of sequence variability of the PrP genes in different species and to aid in speculation on cetacean susceptibility to prions. Both the nucleotide and the deduced amino acid sequences have been analysed in comparison with some of the known mammalian PrPs. Cetacean PrPs present typical features of eutherian PrPs. The PrP gene from the species of the family Delphinidae gave identical nucleic acid sequences, while differences in the PrP gene were found in Balaenopteridae and Ziphidae. The phylogenetic tree resulting from analysis of the cetacean PrP gene sequences, together with reported sequences of some ungulates, carnivores and primates, showed that the PrP gene phylogenesis mirrors the species phylogenesis. The PrP gene of cetaceans is very close to species where natural forms of TSEs are known. From an analysis of the sequences and the phylogenesis of the PrP gene, susceptibility to or occurrence of prion diseases in cetaceans can not be excluded.     

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.      

More DNA support for a Cetacea/Hippopotamidae clade: the blood-clotting protein gene gamma-fibrinogen

Recent phylogenetic analyses of DNA sequences suggest that cetaceans (whales) and hippopotamid artiodactyls (hippos) are extant sister taxa. Consequently, the shared aquatic specializations of these taxa may be synapomorphies. This molecular view is contradicted by paleontological data that overwhelmingly support a monophyletic Artiodactyla (even-toed ungulates) and a close relationship between Cetacea and extinct mesonychian ungulates. According to the fossil evidence, molecular, behavioral, and anatomical resemblances between hippos and whales are interpreted as convergences or primitive retentions. In this report, competing interpretations of whale origins are tested through phylogenetic analyses of the blood-clotting protein gene gamma- fibrinogen from cetaceans, artiodactyls, perissodactyls (odd-toed ungulates), and carnivores (cats, dogs, and kin). In combination with published DNA sequences, the gamma-fibrinogen data unambiguously support a hippo/whale clade and are inconsistent with the paleontological perspective. If the phylogeny favored by fossil evidence is accepted, the convergence at the DNA level between Cetacea and Hippopotamidae is remarkable in its distribution across three genetic loci: gamma-fibrinogen, the linked milk casein genes, and mitochondrial cytochrome b.      

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.     

鲸类视觉退化分子机制的研究：基于GNAT2和CNGB3基因的进化分析

鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53~56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525 ~1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。     

Identification of Novel Cetacean Poxviruses in Cetaceans Stranded in South West England

Poxvirus infections in marine mammals have been mainly reported through their clinical lesions and electron microscopy (EM). Poxvirus particles in association with such lesions have been demonstrated by EM and were previously classified as two new viruses, cetacean poxvirus 1 (CePV-1) and cetacean poxvirus 2 (CePV-2). In this study, epidermal pox lesions in cetaceans stranded in South West England (Cornwall) between 2008 and 2012 were investigated by electron microscopy and molecular analysis. PCR and sequencing of a highly conserved region within the viral DNA polymerase gene ruled out both parapox- and orthopoxviruses. Moreover, phylogenetic analysis of the PCR product clustered the sequences with those previously described as cetacean poxviruses. However, taking the close genetic distance of this gene fragment across the family of poxviridae into account, it is reasonable to postulate further, novel cetacean poxvirus species. The nucleotide similarity within each cluster (tentative species) detected ranged from 98.6% to 100%, whilst the similarity between the clusters was no more than 95%. The detection of several species of poxvirus in different cetacean species confirms the likelihood of a heterogeneous cetacean poxvirus genus, comparable to the heterogeneity observed in other poxvirus genera.     

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.     

Attitudes of Scottish City Inhabitants to Cetacean Conservation

In 2003, a survey was conducted in two major Scottish cities in order to investigate current perceptions of the public towards cetaceans and their conservation. Public concern about cetacean conservation was high. Overall the issues considered to be the greatest threats to cetacean populations were related to pollution: oil spills, and chemical and sewage pollution (serious threat: 68, 65, and 63%, respectively). Concern was also high regarding the depletion of cetacean prey from over-fishing, entanglement in fishing gear, marine litter and global warming, (serious threat: 54, 51, 44, and 43%, respectively). Conservation issues that are of specific concern to Scottish waters were also noted: military activities, fish farming and oil exploration. Least concern was expressed about whale-watching (not a threat: 48%). Women and older respondents expressed significantly higher levels of concern about cetacean conservation. Generally, the opinions of the public were similar to those of a test group of marine conservation professionals and advocates, although the public tended to show slightly greater levels of concern for most issues. However, the public expressed significantly higher levels of concern over oil spills, sewage pollution and chemical pollution than did marine conservation professionals/advocates. Most participants (60%) were unsure as to whether there was currently sufficient legal protection for cetaceans in Scotland, but eight out of ten respondents thought that there should be legislation specifically for cetacean conservation. Moreover, 40% stated that the proposal of a law specifically for the protection of cetaceans would make them view a political party or politician more favourably. Eighty percent of those interviewed were in favour of seeing more marine environmental education, including information on cetaceans and their environment, in the Scottish school curriculum.     

Selection of reference genes for quantitative RT-PCR studies in striped dolphin (Stenella coeruleoalba) skin biopsies

Background  

Odontocete cetaceans occupy the top position of the marine food-web and are particularly sensitive to the bioaccumulation of lipophilic contaminants. The effects of environmental pollution on these species are highly debated and various ecotoxicological studies have addressed the impact of xenobiotic compounds on marine mammals, raising conservational concerns. Despite its sensitivity, quantitative real-time PCR (qRT-PCR) has never been used to quantify gene induction caused by exposure of cetaceans to contaminants. A limitation for the application of qRT-PCR is the need for appropriate reference genes which allow the correct quantification of gene expression. A systematic evaluation of potential reference genes in cetacean skin biopsies is presented, in order to validate future qRT-PCR studies aiming at using the expression of selected genes as non-lethal biomarkers.     

Genetic evidence for the ancestral loss of short-wavelength-sensitive cone pigments in mysticete and odontocete cetaceans

All mammals ancestrally possessed two types of cone pigments, an arrangement that persists in nearly all contemporary species. However, the absence of one of these cone types, the short-wavelength-sensitive (SWS) cone, has recently been established in several delphinoid cetacean species, indicating that the loss of this pigment type may be widespread among cetaceans. To evaluate the functional condition of SWS cones in cetaceans, partial SWS cone-opsin gene sequences were obtained from nuclear DNA for 16 species representing 12 out of the 14 extant mysticete (baleen) and odontocete (toothed) families. For all these species one or more mutations were identified that indicate that their SWS cone-opsin genes are pseudogenes and thus do not code for functional visual pigment proteins. Parsimonious interpretation of the distribution of some of these mis-sense mutations indicates that the conversion of cetacean SWS coneopsin genes to pseudogenes probably occurred before the divergences of the mysticete and odontocete suborders. Thus, in the absence of dramatic homoplasy, all modern cetaceans lack functional SWS cone visual pigments and, by extension, the visual capacities that such pigments typically support.     

Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans

The enlargement of cetacean brain size represents an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. One candidate gene associated with brain size evolution is the abnormal spindle-like microcephaly associated (ASPM), as mutations in this gene cause severe reductions in the cortical size of humans. Here, we investigated the ASPM gene in representative cetacean lineages and previously published sequences from other mammals to test whether the expansion of the cetacean brain matched adaptive ASPM evolution patterns. Our analyses yielded significant evidence of positive selection on the ASPM gene during cetacean evolution, especially for the Odontoceti and Delphinoidea lineages. These molecular patterns were associated with two major events of relative brain size enlargement in odontocetes and delphinoids. It is of particular interest to find that positive selection was restricted to cetaceans and primates, two distant lineages both characterized by a massive expansion of brain size. This result is suggestive of convergent molecular evolution, although no site-specific convergence at the amino acid level was found.     

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.      

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.