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PubMed1999

Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition.

We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid-binding protein (IRBP), von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora, Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set, we recognized nine mitochondrial partitions (both stems and loops, for each of 12S rRNA, tRNA valine, and 16S rRNA; and first, second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony, minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99-100% bootstrap support for Afrotheria and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also high bootstrap support (89-100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic analyses. Mitochondrial-gene trees associate cow with horse, whereas nuclear-gene trees associate cow with hedgehog and these two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.

Animals↗
PubMed1998

Cloning and sequencing of the cDNA coding for pig pre-uteroglobin/Clara cell 10 kDa protein.

Using reverse transcription-polymerase chain reaction (RT-PCR) on pig lung mRNAs, we have cloned and sequenced an almost full-length complementary DNA (cDNA) coding for pig pre-uteroglobin/Clara cell 10 kDa protein (UG/CC10), a major secretory protein of lung Clara cells. The deduced amino acid sequence indicated a preprotein of 91 residues, 21 of which corresponded to the signal peptide. Comparison of the sequence with those of known pre-UG/CC10 from other species indicated that the pig protein resembles the structure shared by human and Lagomorpha pre-UG/CC10 but differ from the proteins from Rodentia that are composed of 96 aminoacids and contain signal peptides of 19 residues. Some amino acids, that form part of a hydrophobic pocket inside the mature protein, are well conserved in all UG/CC10 suggesting an important function of this cavity. Northern analysis indicated that pig UG/CC10 mRNA is abundant in lung but is not detectable in liver, uterus or epididymis. The results are discussed in relation to a possible physiological function of UG/CC10.

Animals↗
PubMed1997

Synthetic DNA-based genetic markers reveal intra- and inter-species DNA sequence variability in the Bubalus bubalis and related genomes.

A series of synthetic oligonucleotide probes were developed as markers for genetic analysis and molecular systematics of Bubalus bubalis and other eutherian mammals. A very high level of heterozygosity (approximately 95%) was observed in the bubaline genome, with an overall band-sharing probability of 2.08 x 10(-11) using (TGG)6 and Hinf I probe-enzyme combination. Breed affiliation studies on different buffalo breeds, viz. Toda, Surti, Mehsana, and Murrah, revealed that the semiwild Toda breed belonged to a distinct group. The desired genotypes in each successive generation in an actual breeding program were also identified by employing a DNA fingerprinting approach using these markers. Estimation of genetic distances by calculating the mean allelic frequencies at (CA)n, (TGG)n, and (GGAT)n repeat loci between buffalo and other related animals such as horse (order Perisodactyla), rabbits (order Lagomorpha, (pigs, cattle, goat, and sheep (order Artiodactyla) revealed that with respect to the genetic distance coefficient (GDC), goat (caprine) was closer to buffalo (GDC = 0.0005) than sheep (ovine) (GDC = 0.0007). The genetic distance between horse and buffalo was calculated to be 0.4085, indicating that compared to other animals, horse was distantly related to buffalo. The understanding of overall allelic variations and breed affiliation of the bubaline genome will contribute to the propagation and conservation of the desired germ plasm and better management of this species.

Alleles↗
PubMed2006

Housekeeping genes for phylogenetic analysis of eutherian relationships.

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.

Animals↗
PubMed1998

Complete mitochondrial DNA sequence of the fat dormouse, Glis glis: further evidence of rodent paraphyly.

The complete mitochondrial genome of the fat dormouse, Glis glis, has been sequenced (16,602 bp). A total of 23 complete mitochondrial mammalian genomes have been taken into account for phylogenetic reconstruction. Phylogenetic analyses were performed with parsimony, distance (stationary Markov model), and maximum-likelihood methods. In all cases, data strongly support the paraphyly of rodents, with dormouse and guinea pig in a different clade from rat and mouse, reaching bootstrap values of 95%. Rodent monophyly and the existence of Glires (Rodentia and Lagomorpha) are weakly supported, with maximum bootstrap values of 11% and 8.6%, respectively. This result agrees with the analyses of isochore patterns in the nuclear genome and the B2 and B2-like retroposons, which show a close relationship between dormice and guinea pigs rather than between dormice and rats and mice.

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↗
PubMed1999

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.

Amino Acid Sequence↗
PubMed2000

The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders.

The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the general organization of the mammalian mitochondrial genome. Thus, features such as start codon usage, incomplete stop codons, and overlapping coding regions, as well as the presence of tandem repeats in the control region, are within the range of mammalian mitochondrial (mt) DNA variation. To address the question of a possible close phylogenetic relationship between primates and Tupaia, the evolutionary affinities among primates, Tupaia and bats as representatives of the Archonta superorder, ferungulates, guinea pigs, armadillos, rats, mice, and hedgehogs were examined on the basis of the complete mitochondrial DNA sequences. The opossum sequence was used as an outgroup. The trees, estimated from 12 concatenated genes encoded on the mitochondrial H-strand, add further molecular evidence against an Archonta monophyly. With the new data described in this paper, most of both the mitochondrial and the nuclear data point away from Scandentia as the closest extant relatives to primates. Instead, the complete mitochondrial data support a clustering of Scandentia with Lagomorpha connecting to the branch leading to ferungulates. This closer phylogenetic relationship of Tupaia to rabbits than to primates first received support from several analyses of nuclear and partial mitochondrial DNA data sets. Given that short sequences are of limited use in determining deep mammalian relationships, the partial mitochondrial data available to date support this hypothesis only tentatively. Our complete mitochondrial genome data therefore add considerably more evidence in support of this hypothesis.

Animals↗
PubMed1987

Amino acid sequence versus morphological data and the interordinal relationships of mammals.

To a large extent, the mutual affinities of the mammalian orders continue to puzzle systematists, even though comparative anatomy and amino acid sequencing offer a massive data base from which these relationships could potentially be adduced. In the present paper the consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular-sequence data. Consistency indices were calculated for previously published alpha crystallin A chain and myoglobin amino acid-sequence cladograms and for four original amino acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta hemoglobin); these were found to be comparable to the consistency indices of morphologically based cladograms. Qualitative comparisons between the morphologically based and molecularly based trees were also made; only moderate congruence between the two was observed. Moreover, there was a general lack of congruence between the cladograms specified by each of the four proteins. Amino acid-sequence and morphological data agreed on the placement of edentates as an early eutherian offshoot and on the grouping of hyracoids, proboscideans, and sirenians. Otherwise there was only limited congruence: morphology strongly supported the grouping of lagomorphs and rodents and the alliance of pholidotes and edentates, but sequence analyses did not. The placement of tubulidentates differed widely among proteins. Morphology indicated the close association of sirenians with proboscideans; proteins suggested a pairing of sirenians with hyracoids. Sequence data did not identify many (morphologically well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1997

Molecular cloning and hormone-dependent expression of rabbit Muc1 in the cervix and uterus.

The microenvironment of the endocervix is regulated by secretory (> 10-15 x 10(6) Da) and cell-surface (< or = 1 x 10(6) Da) mucins. A survey with antisense and sense (control) oligonucleotides for eight epithelial mucin genes revealed that only MUC1, an anti-adhesive protein believed to modulate immune function and the only transmembrane mucin for which molecular probes exist, is expressed in the rabbit cervix. pMUC7, a 500-base pair cDNA probe to the tandem repeat domain of human MUC1, was used to clone the cDNA for the rabbit homologue. Although the GC-rich tandem repeat of rabbit Muc1 had only 40% sequence identity with its human counterpart, its transmembrane domain and cytoplasmic tail maintained 93% sequence identity with the same regions of human MUC1. Detection of restriction length polymorphisms confirmed the Lagomorpha Muc1 gene, like the human, is polymorphic. Temporal expression of Muc1 transcripts (2.4 kilobases) correlated closely with epithelial differentiation in the cervix. However, compared with the adult cervix, uterine endometrium expressed the highest levels of Muc1. In the endometrium, Muc1 was increased (p < 0.0004) by progesterone and returned to estrous levels by treatment with estrogen. Muc1 levels in the cervix were unaffected by ovarian steroids, confirming tissue-specific regulation of Muc1 in the lower reproductive tract.

Amino Acid Sequence↗
PubMed2001

The evolution of body armor in mammals: plantigrade constraints of large body size.

Predictions associated with opposing selection generating minimum variance in basal metabolic rate (BMR) in mammals at a constrained body mass (CBM; 358 g) were tested. The CBM is presumed to be associated with energetic constraints linked to predation and variable resources at intermediate sizes on a logarithmic mass scale. Opposing selection is thought to occur in response to energetic constraints associated with predation and unpredictable resources. As body size approaches and exceeds the CBM, mammals face increasing risks of predation and daily energy requirements. Fast running speeds may require high BMRs, but unpredictable and low resources may select for low BMRs, which also reduce foraging time and distances and thus predation risks. If these two selection forces oppose each other persistently, minimum BMR variance may result. However, extreme BMR outliers at and close to the CBM should be indicative of unbalanced selection and predator avoidance alternatives (escapers vs. defenders), and may therefore provide indirect support for opposing selection. It was confirmed that body armor in defenders evolves at and above the CBM, and armored mammals had significantly lower BMRs than their nonarmored counterparts. However, analyses comparing the BMR of escapers--the fastest nonarmored runners (Lagomorpha)--with similar-sized counterparts were inconclusive and were confounded by limb morphology associated with speed optimization. These analyses suggest that the risks and costs of predation and the speed limitations of the plantigrade foot may constrain the evolution of large body sizes in plantigrade mammals.

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↗
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↗
PubMed2002

Novel endogenous retrovirus in rabbits previously reported as human retrovirus 5.

Human retrovirus 5 (HRV-5) represented a fragment of a novel retrovirus sequence identified in human RNA and DNA preparations. In this study, the genome of HRV-5 was cloned and sequenced and integration sites were analyzed. Using PCR and Southern hybridization, we showed that HRV-5 is not integrated into human DNA. A survey of other species revealed that HRV-5 is present in the genomic DNA of the European rabbit (Oryctolagus cuniculus) and belongs to an endogenous retrovirus family found in rabbits. The presence of rabbit sequences flanking HRV-5 proviruses in human DNA extracts suggested that rabbit DNA was present in our human extracts, and this was confirmed by PCR analysis that revealed the presence of rabbit mitochondrial DNA sequences in four of five human DNA preparations tested. The origin of the rabbit DNA and HRV-5 in human DNA preparations remains unclear, but laboratory contamination cannot explain the preferential detection of HRV-5 in inflammatory diseases and lymphomas reported previously. This is the first description of a retrovirus genome in rabbits, and sequence analysis shows that it is related to but distinct from A-type retroelements of mice and other rodents. The species distribution of HRV-5 is restricted to rabbits; other species, including other members of the order Lagomorpha, do not contain this sequence. Analysis of HRV-5 expression by Northern hybridization and reverse transcriptase PCR indicates that the virus is transcribed at a low level in many rabbit tissues. In light of these findings we propose that the sequence previously designated HRV-5 should now be denoted RERV-H (for rabbit endogenous retrovirus H).

Amino Acid Sequence↗
PubMed1999

Comparative anatomy of the claustrum in selected species: A morphometric analysis.

The morphology of the claustrum was studied by stereological methods in representatives of five mammalian orders (Insectivora, Rodentia, Lagomorpha, Carnivora and Primates). In each species under study, a dorsal and a ventral part of the nucleus can be distinguished. Based on differences in shape and separation from surrounding structures, five morphological types of the claustrum occur. The claustrum of Insectivora and some rodents represents the least complicated morphological type. The nucleus is very poorly separated from the surrounding structures. The human claustrum is morphologically the most complicated, although the two above-mentioned principal divisions are apparent. The ventrally situated paraamygdalar part of the human claustrum may correspond to the endopiriform nucleus or ventral part of the claustrum of other mammals, because of its morphological characteristics and connections with the limbic system. In guinea pigs, traditionally classified as members of the Rodentia, a characteristic morphological type of the claustrum is present. This observation may support arguments questioning the current position of this species in mammalian classification. Based on stereological studies, the increase of the claustral volume that occurs with increase of the hemispheric volume is significantly smaller than the increase of the isocortical volume and larger than the increase of the allocortical volume. The increase of the volume of the dorsal and ventral parts of the claustrum does not differ significantly in the species under study. Neurons of the claustrum represent differentiated morphology. The numerical density of neurons in the dorsal part of the claustrum is significantly higher than in the ventral one. Differences in the morphology and cellular structure of the two parts of the claustrum may suggest differences in function of the two parts of the nucleus, most probably concerned with transfer of information among various cortical regions. Changes in the claustrum, a cortico-related structure, that occur with increased brain volume, may suggest that its development is less dynamic than that of the isocortex.

Animals↗
PubMed2001

Chromosome homologies between man and mountain zebra (Equus zebra hartmannae) and description of a new ancestral synteny involving sequences homologous to human chromosomes 4 and 8.

Using human chromosome painting probes, we looked for homologies between human and mountain zebra (Equus zebra hartmannae, Equidae, Perissodactyla) karyotypes. Except for two very short segments, all euchromatic regions were found to have a human homologous chromosome segment. Conserved syntenies previously described in various mammalian orders were detected. Each synteny corresponded to a chromosomal region homologous to two parts of human chromosomes: HSA3 and HSA21, HSA7 and HSA16, HSA12 and HSA22, and HSA16 and HSA19. Chromosomal segments homologous to a part of HSA11 and HSA19p are found syntenic in zebra, horse and donkey, suggesting that this group of synteny has been inherited from an Equidae or Perissodactyla common ancestor. A synteny of segments homologous to parts of HSA4 and HSA8 was observed in zebra and horse. It also exists in the rabbit (Lagomorpha) and several Carnivora species. A second group of taxa which does not have this region of synteny is composed of primates, Chiroptera and Insectivora, and possibly also Cetacea and Scandantia. Thus, the presence or absence of this region of synteny may separate two groups of eutherian mammals.

Animals↗
PubMed1980

Phylogeny through brain traits. Relation of lateral olfactory tract fibers to the accessory olfactory formation as a palimpsest of mammalian descent.

In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells. The use of this trait as a phylogenetic indicator in 181 specimens representing 131 species of 16 orders yielded evidence for common ancestry of Insectivora, Chiroptera, Dermoptera, Rodentia, and Primates (including Tupaia), since all share the derived trait, their dorsal lateral olfactory tract fibers passing through the accessory olfactory formation. Carnivora (including Pinnipedia), Hyracoidea, Perissodactyla, and most Artiodactyla share the primitive condition (fibers passing under) with the one order of monotremes and three marsupial orders. The Edentata and Lagomorpha may be separate from the two major placental groups and from each other, or they may represent successive stages in the evolution of the derived state through progressive alterations in the relative chronology of development of olfactory system components, or one or both orders may occupy an ancestral position with respect to the dichotomy within placental mammals.

Animals↗
PubMed2003

Correlation between DNA synthesis in the second, third and fourth generations of spermatogonia and the occurrence of apoptosis in both spermatogonia and spermatocytes.

In the seminiferous epithelium, both DNA synthesis and apoptosis occur at equivalent stages in various species, with apoptosis taking place mainly at the same stages as DNA replication in the second, third and fourth spermatogonial generations. As preservation of the cellular associations found at these stages may have some functional significance, it is important to determine whether there is a correlation between these cellular events. In this study, pairs of immunoperoxidase-stained adjacent testis sections from rats, mice, rabbits and cats in which either bromodeoxyuridine incorporated into the newly synthesized DNA strand (BrdU labelling) or DNA 3' end labelling of the apoptotic DNA fragments (TUNEL assay) were detected were compared. In addition, both events were analysed in double-labelled sections. These two methods revealed a clear correlation between the occurrence of DNA replication in the second to fourth generations of spermatogonia and most physiological apoptosis taking place in both spermatogonia and spermatocytes in the three different mammalian orders (Rodentia, Lagomorpha and Carnivora). This correlation may result from the synchronization of mitotic spermatogonial and meiotic spermatocyte cell cycle checkpoints operating at these stages.

Animals↗