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PubMed1997

Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences.

The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rodent species (representing seven families) were analyzed using phenetic, parsimony, and maximum-likelihood methods of phylogenetic inference; the rabbit, Oryctolagus cuniculus (Order Lagomorpha), and cow, Bos taurus (Order Artiodactyla), were used as outgroups. Investigation of 714 base pairs of the protein-coding cytochrome b gene indicate strong base bias at the third codon position with significant rate heterogeneity evident between the three structural domains of this gene. Similar analyses conducted on 816 base pairs of the 12S rRNA gene revealed a transversion bias in the loop sections of all taxa. The cytochrome b gene sequences proved useful in resolving associations between closely related species but failed to produce consistent tree topologies at the family level. In contrast, phylogenetic analysis of the 12S rRNA gene resulted in strong support for the clustering of Pedetidae/Heteromyidae/Geomyidae and Muridae in one clade to the exclusion of the Hystricidae/Thryonomyidae and Sciuridae, a finding which is concordant with studies of rodent fetal membranes as well as reproductive and other anatomical features.

Animals↗
PubMed1997

The mitochondrial control region of Cervidae: evolutionary patterns and phylogenetic content.

The mitochondrial control region (CR) sequence, also known as the D-loop, has been determined for six Cervidae (Artiodactyla, Ruminantia): the red and fallow deers (subfamily Cervinae), the brocket deer and two roe deers (subfamily Odocoileinae), and the Chinese water deer (Hydropotinae). These new sequences have been aligned with available cervid and bovid orthologues. Comparative analyses indicate that the 5'-peripheral domain exhibits a 75-bp length polymorphism near sequences associated with the termination of the H-strand replication. The New World Odocoileinae possess the longest cervid CR due to the presence of an additional 47-bp tandem repeat, located in the 3'-peripheral domain, downstream of the initiation site for H-strand replication (OH) and the first conserved sequence block (CSB-1). This insertion represents a duplication spanning the OH to CSB-1 region and constitutes an exclusive synapomorphy for New World Odocoileinae. Phylogenetic analyses of the complete CR support the paraphyly of antlered deers due to the nesting of the antlerless Hydropotes within Odocoileinae. Capreolus is the closest relative of Hydropotes, and the divergence of this Old World Odocoileinae clade may have occurred between 8.7 and 10.4 MYA. The conserved central domain of CR can be aligned across ungulates and indicates the Pecora monophyly, their close association with cetaceans, and the earlier emergence of suiformes.

Animals↗
PubMed1997

Phylogenetic analysis of cystic fibrosis transmembrane conductance regulator gene in mammalian species argues for the development of a rabbit model for cystic fibrosis.

The species-specific pattern of cystic fibrosis transmembrane conductance regulator (CFTR) expression was investigated in order to identify species closely related to man which can be used as potential cystic fibrosis (CF) animal models. To this purpose, the nucleotide sequences of the CFTR promoter region of eight mammalian species representing four different orders (Primates, Artiodactyla, Lagomorpha and Rodentia) were analyzed. Distance matrices and unrooted trees of the CFTR promoter region sequences yielded two deeply separated groups, one including man (Homo sapiens), nonhuman primates (Hylobates lar, Macaca fascicularis, Saimiri sciureus), cow (Bos taurus), and rabbit (Oryctolagus cuniculus) and the other including the rodents (Rattus norvegicus, Mus musculus). Divergences between rodent and nonrodent groups have been observed in putative cis transcriptional regulatory elements and can be involved in the differences of pattern of expression between these two groups. Comparison of the available CFTR cDNA sequences enabled us to root the tree with a noneutherian outgroup and to perform a phylogenetic analysis. This analysis did not detect any base composition bias and supported polyphyletic Glires. Although a long-branch attraction artifact cannot be completely excluded, these findings converge toward the recent statement (Graur, Duret, and Gouy 1996) that Lagomorpha is more closely related to Primates than to Rodentia. In addition, the phenylalanine residue in exon 10 involved in the most common CF mutation in man is conserved in rabbit. These phylogenetic analyses as well as anatomical and developmental data suggest that, once rabbit embryonic stem cells become available, the rabbit will provide a suitable tool for both gene transfer and pharmacological investigations and could lead to a better CF model than the current murine models.

Animals↗
PubMed1998

The "five-sites" rule and the evolution of red and green color vision in mammals.

Amino acid changes S180A (S-->A at site 180), H197Y, Y277F, T285A, and A308S are known to shift the maximum wavelength of absorption (lambda max) of red and green visual pigments toward blue, essentially in an additive fashion. To test the generality of this "five-sites" rule, we have determined the partial amino acid sequences of red and green pigments from five mammalian orders (Artiodactyla, Carnivora, Lagomorpha, Perissodactyla, and Rodentia). The result suggests that cat (Felis catus), dog (Canis familiaris), and goat (Capra hircus) pigments all with AHYTA at the five critical sites have lambda max values of approximately 530 nm, whereas rat (Rattus norvegicus) pigment with AYYTS has a lambda max value of approximately 510 nm, which is accurately predicted by the five-sites rule. However, the observed lambda max values of the orthologous pigments of European rabbit (Oryctolagus cuniculus), white-tailed deer (Odocoileus virginianus), gray squirrel (Sciurus carolinensis), and guinea pig (Cavia procellus) are consistently more than 10 nm higher than the predicted values, suggesting the existence of additional molecular mechanisms for red and green color vision. The inferred amino acid sequences of ancestral organisms suggest that the extant mammalian red and green pigments appear to have evolved from a single ancestral green-red hybrid pigment by directed amino acid substitutions.

Amino Acid Sequence↗
PubMed2000

The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences.

The complete mitochondrial (mt) genome of the mole Talpa europaea was sequenced and included in phylogenetic analyses together with another lipotyphlan (insectivore) species, the hedgehog Erinaceus europaeus, and 22 other eutherian species plus three outgroup taxa (two marsupials and a monotreme). The phylogenetic analyses reconstructed a sister group relationship between the mole and fruit bat Artibeus jamaicensis (order Chiroptera). The Talpa/Artibeus clade constitutes a sister clade of the cetferungulates, a clade including Cetacea, Artiodactyla, Perissodactyla, and Carnivora. A monophyletic relationship between the hedgehog and the mole was significantly rejected by maximum parsimony and maximum likelihood. Consistent with current systematic schemes, analyses of complete cytochrome b genes including the shrew Sorex araneus (family Soricidae) revealed a close relationship between Talpidae and Soricidae. The analyses of complete mtDNAs, along with the findings of other insectivore studies, challenge the maintenance of the order Lipotyphla as a taxonomic unit and support the elevation of the Soricomorpha (with the families Talpidae and Soricidae and possibly also the Solenodontidae and Tenrecidae) to the level of an order, as previously proposed in some morphological studies.

Animals↗
PubMed2006

Cloning of the genome of Alcelaphine herpesvirus 1 as an infectious and pathogenic bacterial artificial chromosome.

Alcelaphine herpesvirus 1 (AlHV-1), carried asymptomatically by wildebeest, causes malignant catarrhal fever (MCF) following cross-species transmission to a variety of susceptible species of the order Artiodactyla. The study of MCF pathogenesis has been impeded by an inability to produce recombinant virus, mainly due to the fact that AlHV-1 becomes attenuated during passage in culture. In this study, these difficulties were overcome by cloning the entire AlHV-1 genome as a stable, infectious and pathogenic bacterial artificial chromosome (BAC). A modified loxP-flanked BAC cassette was inserted in one of the two large non-coding regions of the AlHV-1 genome. This insertion allowed the production of an AlHV-1 BAC clone stably maintained in bacteria and able to regenerate virions when transfected into permissive cells. The loxP-flanked BAC cassette was excised from the genome of reconstituted virions by growing them in permissive cells stably expressing Cre recombinase. Importantly, BAC-derived AlHV-1 virions replicated comparably to the virulent (low-passage) AlHV-1 parental strain and induced MCF in rabbits that was indistinguishable from that of the virulent parental strain. The availability of the AlHV-1 BAC is an important advance for the study of MCF that will allow the identification of viral genes involved in MCF pathogenesis, as well as the production of attenuated recombinant candidate vaccines.

Animals↗
PubMed1998

Emerging patterns of comparative genome organization in some mammalian species as revealed by Zoo-FISH.

Although gene maps for a variety of evolutionarily diverged mammalian species have expanded rapidly during the past few years, until recently it has been difficult to precisely define chromosomal segments that are homologous between species. A solution to this problem has come from the development of Zoo-FISH, also known as cross-species chromosome painting. The use of Zoo-FISH to identify regions of chromosomal homology has allowed the transfer of information from map-rich species such as human and mouse to a wide variety of other species. From a Zoo-FISH analysis spanning four mammalian orders (Primates, Artiodactyla, Carnivora, and Perissodactyla), and involving eight species (human, pig, cattle, Indian muntjac, cat, American mink, harbor seal, and horse), three distinct classes of synteny conservation have been designated: (1) conservation of whole chromosome synteny, (2) conservation of large chromosomal blocks, and (3) conservation of neighboring segment combinations. This analysis has also made it possible to identify a set of chromosome segments (based on human chromosome equivalents) that probably made up the karyotype of the common ancestor of the four orders. This approach provides a basis for developing a picture of the ancestral mammalian karyotype, but a full understanding will depend on studies encompassing more diverse combinations of mammalian orders.

Animals↗
PubMed1996

Transfer of bovine microsatellites to the cervine (Cervus elaphus).

Bovine microsatellites were used to amplify DNA of red deer (Cervus elaphus). Fourteen of 27 bovine systems (52%) displayed polymorphism, while no (CA)n-repeat was detected in seven systems and six systems gave no amplificates in red deer. The allele number ranged from 2 to 7, the polymorphism information content between 0.24 and 0.76. The results demonstrate that transfer of microsatellite systems between families of the same order (artiodactyla) is possible. Molecular genetic research will help to clarify the differentiation and ecology of wild animals and will contribute to define criteria needed for the preservation of endangered species.

Alleles↗
PubMed1991

Vitamin A (retinol and retinyl esters), alpha-tocopherol and lipid levels in plasma of captive wild mammals and birds.

Vitamin A (retinol and retinyl esters), vitamin E and lipids were determined in a wide variety of wild mammals and birds held in captivity. In mammals plasma levels of vitamin A were generally below 500 ng/ml and those of vitamin E were highly variable (0.1-2 micrograms/ml). In primates, vitamin E levels were 3 to 8 micrograms/ml. Whereas in Marsupialia, Chiroptera, primates, Rodentia, Proboscidea, Sirenia, Perissodactyla and Artiodactyla only retinol was found, retinyl esters (basically retinol palmitate/oleate) represented 10 to 50% of the total plasma vitamin A in some birds of the order Ciconiiformes and Falconiformes. Retinol levels in birds were higher compared to mammals (500-2,000 ng/ml). The same was true for lipids as well as for vitamin E levels (1-26 micrograms/ml) in the plasma of birds.

Animals↗
PubMed1984

Taxonomy and review of the coccidian genus Cryptosporidium (protozoa, apicomplexa).

Reports of Cryptosporidium in various hosts and cross-transmission experiments are reviewed. Cryptosporidium has been found in mammals (Primates, Artiodactyla, Perissodactyla , Carnivora, Lagomorpha, and Rodentia), birds, reptiles, and fish. The only cross-transmission attempts that have been made have been from mammals to other mammals and to a few birds. Names have been given to 19 "species," but it is concluded that only four of these should be considered valid at present. These are: C. muris Tyzzer, 1907 in mammals, C. meleagridis Slavin , 1955 in birds, C. crotali Triffit , 1925 in reptiles, and C. nasorum Hoover , Hoerr , Carlton , Hinsman & Ferguson, 1981 in fish.

Animals↗
PubMed2001

Immunoregulatory activity, biochemistry, and phylogeny of ovine uterine serpin.

PROBLEM: During pregnancy, the endometrium of the ewe secretes a progesterone-induced member of the serpin superfamily of serine proteinase inhibitors called ovine uterine serpin (OvUS) that has immunosuppressive properties. METHOD: Review of the literature. RESULTS AND CONCLUSIONS: OvUS inhibits a wide variety of immune responses, including mixed lymphocyte reaction, mitogen-stimulated lymphocyte proliferation, and T cell-dependent antibody production. Recent data have suggested that OvUS functions by inhibiting protein kinase C and interleukin-2-mediated events. OvUS and similar genes present in cattle and pigs diverged from other serpins prior to the divergence of artiodactyls. Since this time, the serpins have apparently undergone adaptive evolution that has led to a conformational state and biological functions distinct from prototypical serpins. Thus, it is likely that these proteins have an important role in the reproductive biology of Artiodactyla. Several lines of evidence suggest that, in sheep, OvUS functions to mediate the immunosuppressive effects of progesterone and prevent immunological rejection of the fetal allograft.

Animals↗
PubMed1985

Specificity of Fc receptors induced by herpes simplex virus type 1: comparison of immunoglobulin G from different animal species.

Cells infected with herpes simplex virus type 1 (HSV-1) express a cell surface receptor able to bind the Fc portion of immunoglobulin G (IgG). Of the four human IgG subclasses, the HSV-1 Fc receptor, like staphylococcal protein A, binds to all except IgG3. In this paper, we describe the binding of a number of animal IgG and IgG subclass molecules to HSV-1-infected cells and compare this binding to that of protein A. Although only few representatives from each animal order were tested, we found that IgG from Carnivora and Rodentia did not bind or bound only slightly to the HSV-1 receptor, whereas IgG from Primates, Lagomorpha, and Artiodactyla bound well. This pattern was clearly different from the species spectrum of IgG binding of protein A. Differences between the two receptors were also found when animal IgG subclasses were tested. The pronounced differences in affinity for the HSV-1 Fc receptor between immunoglobulins from, for example, mouse and rabbit may influence the interpretation of animal studies with this virus.

Animals↗
PubMed1994

Guidelines for the interpretation of laboratory findings in birds and mammals with unknown reference ranges: plasma biochemistry.

The results of analyses of plasma samples from healthy and sick adult birds and mammals of a wide range of species were used to calculate reference ranges and clinical ranges for 11 biochemical variables (calcium, sodium, chloride, total protein, albumin, globulin, inorganic phosphate, potassium, bicarbonate, urea and creatinine concentrations) in six mammalian Orders (Primata, Carnivora, Pinnipedia, Proboscidea, Perissodactyla and Artiodactyla) and six avian Orders (Ciconiiformes, Gruiformes, Pelecaniformes, Psittaciformes, Falconiformes and Strigiformes). The patterns of variation between Orders for the different biochemical variables were then used to provide guidelines for the interpretation of plasma biochemistry results in the species in these Orders for which there are no reference data. The observed clinical ranges provide an indication of the potential diagnostic value of each variable.

Animal Diseases↗
PubMed2000

Diapause.

Embryonic diapause, or delayed implantation as it is sometimes known, is said to occur when the conceptus enters a state of suspended animation at the blastocyst stage of development. Blastocysts may either cease cell division so that their size and cell numbers remain constant, or undergo a period of very slow growth with minimal cell division and expansion. Diapause has independently evolved on many occasions. There are almost 100 mammals in seven different mammalian orders that undergo diapause. In some groups, such as rodents, kangaroos, and mustelids, it is widespread, whereas others such as the Artiodactyla have only a single representative (the roe deer). In each family the characteristics of diapause differ, and the specific controls vary widely from lactational to seasonal, from estrogen to progesterone, or from photoperiod to nutritional. Prolactin is a key hormone controlling the endocrine milieu of diapause in many species, but paradoxically it may act either to stimulate or inhibit growth and activity of the corpus luteum. Whatever the species-specific mechanisms, the ecological result of diapause is one of synchronization: It effectively lengthens the active gestation period, which allows mating to occur and young to be born at times of the year optimal for that species.

Animals↗
PubMed2000

The species and chromosomal distribution of the centromeric alpha-satellite I sequence from sheep in the tribe Caprini and other Bovidae.

The evolution of chromosomes in species in the family Bovidae includes fusion and fission of chromosome arms (giving different numbers of acrocentric and metacentric chromosomes with a relatively conserved total number of arms) and evolution in both DNA sequence and copy number of the pericentromeric alpha-satellite I repetitive DNA sequence. Here, a probe representing the sheep alpha-satellite I sequence was isolated and hybridized to genomic DNA digests and metaphase chromosomes from various Bovidae species. The probe was highly homologous to the centromeric sequence in all species in the tribe Caprini, including sheep (Ovis aries), goat (Capra hircus) and the aoudad or Barbary sheep (Amnotragus lervia), but showed no detectable hybridization to the alpha-satellite I sequence present in the tribe Bovini and at most very weak to species in the tribes Hippotragini, Alcelaphini or Aepycerotini. The sex chromosomes of sheep, goat and aoudad did not contain detectable alpha-satellite I sequence; in sheep, one of the three metacentric autosomal chromosomes does not carry the sequence, while in aoudad, it is essentially absent in three large autosomal pairs as well as the large metacentric chromosome pair. The satellite probes can be used as robust chromosome and karyotype markers of evolution among tribes and increase the resolution of the evolutionary tree at the base of the Artiodactyla.

Animals↗
PubMed2002

Mitogenomic analyses of eutherian relationships.

Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70-100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place approximately 10 MYBP, a dating consistent with recent findings in primate paleontology.

Animals↗
PubMed2006

Historical biogeography of the strepsirhine primates of Madagascar.

Lying some 400 km off the coast of southeastern Africa, Madagascar is the world's largest oceanic island. It has been in roughly the same position relative to its parent continent for 120 million years, and as a consequence its mammal fauna is unusual in composition, with a low number of major taxa but a high diversity at lower taxonomic levels. Among Madagascar's native terrestrial mammals, only the orders Primates, Rodentia, Carnivora and Insectivora are represented (plus, until recently, the enigmatic and endemic Bibymalagasia, and Artiodactyla in the form of semiaquatic pygmy hippopotamuses). This reflects the fact that terrestrial mammals are notoriously poor over-water dispersers; yet at the same time the ancestors of all of Madagascar's mammals had to have crossed a wide oceanic barrier to get to the island at various points during the Tertiary. Here I examine the palaeogeographic evidence for potential land bridge or 'stepping-stone' connections with adjacent continents from the Mesozoic through the Cenozoic, and review the fossil records and phylogenies of each of Madagascar's mammalian groups in an attempt to estimate the minimum number of crossings necessary to produce the island's current faunal composition. Probable monophyletic origins for each major group, and thus a smaller rather than a larger number of crossings of the Mozambique Channel, imply that this water barrier has acted as a powerful filter; so powerful that it is unclear whether any crossings would have been possible without some form of subaerial connection, however ephemeral, at least from time to time during the Tertiary. Clarification of how Madagascar's terrestrial mammal fauna may have originated is thus as likely to emerge from the geology of the seafloor surrounding the island as it is to come from the fossil record or from the internal and external relationships of its various components.

Animal Migration↗
PubMed1994

Phylogeny through brain traits: more characters for the analysis of mammalian evolution.

We have assembled data on nine brain traits, in addition to the fifteen we have previously described, which provide new evidence for assessing mammalian relationships. States of these characters are tabulated as they occur in each of 152 mammalian species, providing data in numerically ordered form, useful for multiple analyses of phylogenetic relationships in programs which take into account variations in several different characters simultaneously. Derived states of each of the nine traits are characteristic of certain restricted groups of mammals; (1) mirroring of the complete SI body representation in isocortex (anthropoid primates); (2) loss of the accessory olfactory bulbs (sirenians, cetaceans, most bats, catarrhine primates); (3) Rindenkerne, clumps of cell bodies in layer 6 of cerebral cortex (sirenians); (4) posteriorly-pointing digits in the SI body representation (bats, both mega- and micro-); (5) equivalent tectopetal connections to the anterior colliculus of one side from both retinas, rather than predominantly from the contralateral retina (primates and megabats); (6) loss of lamination in dorsal cochlear nuclei (anthropoid primates, bats, seals, sirenians, cetaceans); (7) separation of claustrum from cerebral cortex (diprotodont marsupials, carnivores, artiodactyls, perissodactyls, hyracoids, cetaceans and primates), (8) presence of a complete secondary (SII) somatic sensory region of cerebral cortex (therians-all extant mammals other than monotremes), and (9) presence of a distinct external cuneate nucleus among the nuclei of the dorsal columns (all mammalian groups except monotremes and sirenians). Two examples of phylogenetic trees derived from these data are presented. These sample trees maintain the segregation of the monotremes and the marsupials, and the basic dichotomy of placentals seen in our earlier trees based entirely on brain data. They also show: an orderly sequence of bifurcations (rather than the commonly seen multifurcation near the base of the radiation) in the reconstruction of placental relationships; extremes of derivation for the Cetacea, the Chiroptera, and the Sirenia (in concordance with trees based on other data); a ferungulate association of Carnivora, Perissodactyla, Artiodactyla, Hyracoidea and Sirenia; and an assemblage of related Dermoptera, Primates, Scandentia, and Chiroptera which in this model also includes Insectivora and Macroscelidea. Analyses based on brain characters can reinforce conclusions based on other data, while at the same time introducing new ideas about relationships. Neural traits provide a source of data independent of those commonly used in phylogenetic analysis, and are extremely valuable for testing old hypotheses and for introducing new ones.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗