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PubMed1995

Sequence conservation of microsatellites between Bos taurus (cattle), Capra hircus (goat) and related species. Examples of use in parentage testing and phylogeny analysis.

A panel of 70 bovine microsatellites was tested for amplification from goat DNA. Forty-three could be successfully amplified by PCR, 20 of which were tested for polymorphism. Three were applied for parentage testing in goat families and their exclusion probability evaluated. Fourteen were cloned and sequenced from goat DNA, and goat and bovine sequences were compared to evaluate interspecific conservation. Correlation between the structure of the dinucleotide repeat and the number of alleles was studied and indicated that interruption(s) in the repeat could explain the difference in the levels of polymorphism between the two species. This study provides a valuable in vivo clue to the mechanism generating polymorphism in microsatellites. Sequence conservation was also observed for several microsatellites with two wild species of Bovidae, Nilgaï (Boselaphus tragocamelus) and Himalayan Tur (Capra cylindricornis), and with one species of Cervidae, the fallow deer (Cervus dama). This study showed that an estimated 40 per cent of the microsatellites isolated from cattle will prove useful to study the caprine genome and to characterize economically important genetic loci in this species. Moreover, bovine microsatellites were shown to constitute very useful tools for the study of genetic diversity of the Artiodactyla.

Animals↗
PubMed2001

For whales and seals the ocean is not blue: a visual pigment loss in marine mammals.

Most terrestrial mammals have colour vision based on two spectrally different visual pigments located in two types of retinal cone photoreceptors, i.e. they are cone dichromats with long-to-middle-wave-sensitive (commonly green) L-cones and short-wave-sensitive (commonly blue) S-cones. With visual pigment-specific antibodies, we here demonstrate an absence of S-cones in the retinae of all whales and seals studied. The sample includes seven species of toothed whales (Odontoceti) and five species of marine carnivores (eared and earless seals). These marine mammals have only L-cones (cone monochromacy) and hence are essentially colour-blind. For comparison, the study also includes the wolf, ferret and European river otter (Carnivora) as well as the mouflon and pygmy hippopotamus (Artiodactyla), close terrestrial relatives of the seals and whales, respectively. These have a normal complement of S-cones and L-cones. The S-cone loss in marine species from two distant mammalian orders strongly argues for convergent evolution and an adaptive advantage of that trait in the marine visual environment. To us this suggests that the S-cones may have been lost in all whales and seals. However, as the spectral composition of light in clear ocean waters is increasingly blue-shifted with depth, an S-cone loss would seem particularly disadvantageous. We discuss some hypotheses to explain this paradox.

Animals↗
PubMed1995

Interferon, the oxytocin receptor and the maternal recognition of pregnancy in ruminants and non-ruminants: a comparative approach.

Ruminant and non-ruminant members of the Artiodactyla appear to use different mechanisms for the maternal recognition of pregnancy. In ruminants, the trophoblast of the developing blastocyst produces a characteristic Type I interferon of the interferon-tau family; this acts by blocking endometrial synthesis of the oxytocin receptor. A similar mechanism applies to domestic ruminants (sheep, cow, goat) and deer. In roe deer, which have embryonic diapause and are monoestrus, there is no requirement for a pre-implantation blastocyst signal to ensure maternal recognition of pregnancy. This paper compares the mechanisms leading to the maternal recognition of pregnancy in ruminants with that suggested to occur in a non-ruminant (the domestic pig).

Animals↗
PubMed1980

Hormonal and immunological aspects of the phylogeny of sex steroid binding plasma protein.

Sex steoid binding plasma protein (Sbp) in man and in monkeys binds the androgens dihydrotestosterone and testosterone and the estrogen estradiol with high affinity (Kd approximately 0.5, 1, and 2 nM, respectively). Detailed studies of steroid binding specificity give the same results in all primates, except that in humans and chimpanzees estrone does not compete for dihydrotestosterone binding. In other mammals, Sbps of Artiodactyla and Lagomorpha have the same range of affinities for androgens but they do not bind estradiol to any significant extent (Kd > 280 nM). The dog has an unusual Sbp (Kd for dihydrotestosterone, 7.1 nM; for estradiol, 125 nM), and rodents do not have a specific dihydrotestosterone-binding plasma protein. Gel filtration and immunoelectrophoretic experiments have been performed with a monospecific antiserum against human Sbp. The results indicate variable crossreactivities with Sbps of primates (from complete in chimpanzee and gorilla to weak in Prosimii). No crossreaction was observed with specific androgen-binding plasma proteins of other species. These results suggest the evolutionary emergence of bifunctional Sbp.

Animals↗
PubMed1988

Evolutionary and developmental aspects of two hemoglobin beta-chain genes (epsilon M and beta M) of opossum.

A series of gene duplications that began in a stem species of Mammalia and led to five developmentally regulated hemoglobin beta-chain loci (epsilon, gamma, eta, delta, and beta) in a common ancestor of eutherian orders Artiodactyla, Rodentia, Lagomorpha, and Primates had important consequences in mammalian evolution. Findings reported here indicate that two progenitors of the five linked genes existed by the time of the eutherian (placental mammal)-metatherian (marsupial mammal) split and that these two genes were already differentiated with respect to their promoter regions and developmental expression. Southern blot and sequence analyses of the hemoglobin beta-chain genes of the opossum (Didelphis virginiana) revealed only two genes, one with coding and promoter sequences similar to eutherian prenatally expressed epsilon, gamma, and eta genes and the other coding for adult opossum hemoglobin beta-chains and having eutherian adult beta-type promoters. The most parsimonious arrangement of greater than 80 beta-globin exon sequences depicts the opossum embryonic-type gene as orthologously related to eutherian epsilon, gamma, and eta genes and the opossum adult-type gene as orthologously related to delta and beta genes. These data further indicate that after the initial beta duplication in the stem of Mammalia, the locus that became developmentally delayed in its expression evolved at a faster rate than the locus that became embryonically expressed.

Amino Acid Sequence↗
PubMed1993

Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent.

The traditional morphologically grounded placement of South American guinea pig-like rodents (Caviomorpha) within one of the two rodent suborders, Hystricognathi, has been disputed by recent analysis of protein and nucleic acid sequence data. The Caviomorpha and possibly all Hystricognathi would be considered a separate order, distinct from the other rodent suborder, Sciurognathi, and thus of the order Rodentia, and would be placed closer phylogenetically to other mammals [Graur, D., Hide, W. A. & Li, W.-H. (1991) Nature (London) 351, 649-652]. To address the discrepancy between morphological comparisons and sequence analyses, we have applied an alternative form of molecular analysis. We demonstrate that BC1 RNA, a neural-specific small cytoplasmic RNA that is the product of a retropositionally generated gene (a gene derived by reverse transcription of RNA followed by insertion of the DNA copy into the genome), is present in Sciurognathi and guinea pig but not in other mammalian orders including Lagomorpha, Artiodactyla, and Primates. The species-confined, tissue-specific expression of a retroposed sequence therefore supports the morphological evidence for monophyly of Rodentia inclusive of guinea pig and demonstrates the usefulness of such molecular genetic markers. Furthermore, the conservation and tissue-specific expression of the BC1 RNA gene in the two divergent rodent suborders suggests that this macromolecule has been exapted into a functional role (i.e., coopted into a variant or novel function) in the rodent nervous system.

Animals↗
PubMed1998

A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales.

Himalayacetus subathuensis is a new pakicetid archaeocete from the Subathu Formation of northern India. The type dentary has a small mandibular canal indicating a lack of auditory specializations seen in more advanced cetaceans, and it has Pakicetus-like molar teeth suggesting that it fed on fish. Himalayacetus is significant because it is the oldest archaeocete known and because it was found in marine strata associated with a marine fauna. Himalayacetus extends the fossil record of whales about 3.5 million years back in geological time, to the middle part of the early Eocene [ approximately 53.5 million years ago (Ma)]. Oxygen in the tooth-enamel phosphate has an isotopic composition intermediate between values reported for freshwater and marine archaeocetes, indicating that Himalayacetus probably spent some time in both environments. When the temporal range of Archaeoceti is calibrated radiometrically, comparison of likelihoods constrains the time of origin of Archaeoceti and hence Cetacea to about 54-55 Ma (beginning of the Eocene), whereas their divergence from extant Artiodactyla may have been as early as 64-65 Ma (beginning of the Cenozoic).

Animals↗
PubMed2000

Kinetochore reproduction in animal evolution: cell biological explanation of karyotypic fission theory.

Karyotypic fission theory of Todd offers an explanation for the diverse range of diploid numbers of many mammalian taxa. Theoretically, a full complement of acrocentric chromosomes can be introduced into a population by chromosomal fission. Subsequent inheritance of ancestral chromosomes and paired fission derivatives potentially generates a diploid range from the ancestral condition to double its number of chromosomes. Although it is undisputed that both chromosomal fission and fusion ("Robertsonian rearrangements") have significantly contributed to karyological diversity, it is generally assumed that independent events, the fission of single chromosomes or the fusion of two chromosomes, are the sources of such change. The karyotypic fission idea by contrast posits that all mediocentric chromosomes simultaneously fission. Here I propose a specific cell biological mechanism for Todd's karyotypic fission concept, "kinetochore reproduction theory," where a complete set of dicentric chromatids is synthesized during gametogenesis, and kinetochore protein dephosphorylation regulates dicentric chromatid segregation. Three postulates of kinetochore reproduction theory are: (i) breakage of dicentric chromosomes between centromere pairs forms acrocentric derivatives, (ii) de novo capping of newly synthesized acrocentric ends with telomeric DNA stabilizes these derivatives, and (iii) mitotic checkpoints regulate chromosomal disjunction to generate fissioned karyotypes. Subsequent chromosomal rearrangement, especially pericentric inversion, increases the probability of genetic isolation amongst incipient sympatric species polytypic for fission-generated acrocentric autosomes. This mechanism obviates the requirement for numerous independent Robertsonian rearrangements and neatly accounts for mammalian karyotype evolution as exemplified in analyses of Carnivora, Artiodactyla, and Primates.

Animals↗
PubMed1999

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.

Animals↗
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↗
PubMed2000

c-myc gene sequences and the phylogeny of bats and other eutherian mammals.

The complete protein-coding sequences of the c-myc proto-oncogene were determined for five species of four new orders of eutherian (placental) mammals. These newly obtained sequences were aligned to each other and to other available orthologs for the phylogenetic estimation of eutherian interordinal relationships. Several measures of sequence difference and base composition were first calculated to assess the major evolutionary properties of the three codon positions and two protein-coding exons of the gene. On the basis of these calculations, different parsimony, distance, and maximum likelihood approaches were adopted, with the most sophisticated involving the separate, then combined, likelihood analyses of the third codon positions of exon 2 versus all other sites. These phylogenetic approaches provided clear support for the grouping of Chiroptera (bats) with Artiodactyla (ruminants, camels, and pigs) and Carnivora (cats, dogs, and their allies), an interordinal arrangement that receives strong corroboration from other lines of evidence including complete mitochondrial DNA sequences. In contrast, these analyses failed to provide strong to reasonable support for any other interordinal group. This study concludes with specific recommendations about sampling and other strategies for maximizing the phylogenetic contributions of the c-myc gene to the continued resolution of the eutherian ordinal tree.

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↗
PubMed1992

Genes for the trophoblast interferons in sheep, goat, and musk ox and distribution of related genes among mammals.

The trophoblast interferons (IFNs) are a family of Type 1 IFN found in domestic ruminants that are most closely related to the little-studied 172-amino-acid IFN-omega. They are produced in massive amounts by the preimplantation conceptus at a time coincident with maternal recognition of pregnancy, and are implicated in playing an important role in this process. Here we report the characterization of four distinct members of the ovine trophoblast IFN (oTP-1) gene family, and demonstrate that they, along with previously characterized bovine trophoblast (bTP-1) genes, possess distinctive promoter sequences when compared to ovine and bovine IFN-omega genes. Genomic Southern blot analysis of numerous mammalian species (zoo blots) indicate that, whereas the IFN-omega are widely distributed among mammals, genes for the trophoblast IFN appear to be limited to ruminant species within the Artiodactyla order. Further polymerase chain reaction (PCR) analysis of trophoblast IFN genes in these ruminant species has permitted isolation of genes for goat and musk ox trophoblast IFN. These data suggest that the trophoblast IFNs are a distinct family of IFN with a limited distribution among mammals.

Animals↗
PubMed1998

The evolution of the type I interferons.

There are five recognized subtypes within the type I interferons (IFN), IFN-alpha, IFN-beta, IFN-delta, IFN-omega, and IFN-tau, although others may remain to be described, and the IFN-omega may have to be subdivided further because of their evident structural complexity. Together, they constitute an ancient family of intronless genes, possibly present in all vertebrates. THe IFNA/IFNB genes originated by duplication of a progenitor after the divergence of birds, most probably about 250 million years ago (MYA). The avian gene itself proceeded to duplicate to form a series of independent subtypes. The IFND, to date described only in the pig, arose from the IFNA lineage before the emergence of mammals about 180 MYA and might, therefore, be generally distributed in present day species. The IFNB, which occurs as a single gene in primates and rodents, have been duplicated in some other orders. Recent events have produced 10 or more genes in bovid species. The IFNA, which are clustered with the IFNW in humans and cattle, exist as multiple genes in all mammals so far examined as a result of a series of duplication events, some of which occurred recently and, therefore, independently in separate mammalian lineages. The IFNW diverged from the IFNA approximately 130 MYA, just prior to the emergence of mammals, and have continued to duplicate since then. The IFNT, which play a role in reproduction of ruminants, arose from an IFNW within the Artiodactyla suborder about 36 MYA and are found only in the suborder Ruminantia. These genes have also continued to duplicate to form an extensive family. Consequently, their involvement in early pregnancy is a feature of ruminants and not of other mammalian species.

Animals↗
PubMed2001

Divergent evolution in M6P/IGF2R imprinting from the Jurassic to the Quaternary.

M6P/IGF2R imprinting first appeared approximately 150 million years ago following the divergence of prototherian from therian mammals. Although M6P/IGF2R is clearly imprinted in opossums and rodents, its imprint status in humans remains ambiguous. It is also still unknown if M6P/IGF2R imprinting was an ancestral mammalian epigenotype or if it evolved convergently. We report herein that M6P/IGF2R is imprinted in Artiodactyla, as it is in Rodentia and Marsupialia, but that it is not imprinted in Scandentia, Dermoptera and Primates, including ringtail lemurs and humans. These results are most parsimonious with a single ancestral origin of M6P/IGF2R imprinting followed by a lineage-specific disappearance of M6P/IGF2R imprinting in Euarchonta. The absence of M6P/IGF2R imprinting in extant primates, due to its disappearance from the primate lineage over 75 million years ago, demonstrates that imprinting at this locus does not predispose to human disease. Moreover, the divergent evolution of M6P/IGF2R imprinting predicts that the success of in vitro embryo procedures such as cloning may be species dependent.

Animals↗
PubMed1990

Bioenergetic consequences of alopecia induced by Dermacentor albipictus (Acari: Ixodidae) on moose.

Fasting metabolic rates, respiration rates, respiratory minute volumes, and fasted weights were measured on three yearling moose (Alces alces (L.)) (Artiodactyla: Cervidae) infested with 50,000 winter ticks. Dermacentor albipictus (Packard) (Acari: Ixodidae), and on two uninfested controls. Infestations produced no detectable effects on fasting metabolic rates or weight changes. The influence of tick-induced alopecia on lower critical temperatures could not be assessed because of warm temperatures during the winter and spring trials. Destruction of winter hair accompanied a reduction in respiratory minute volumes and respiration rates of heat-stressed moose.

Alopecia↗
PubMed2003

Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins.

The phylogenetic relationships of eukaryotic aspartic proteinases were reconstructed in order to understand the origin of pregnancy-associated glycoproteins (PAGs), which constitute a large gene family expressed in the trophoblast and placenta of mammals in the order Artiodactyla. The phylogeny supported the hypothesis that PAGs originated in mammals, being most closely related to a group of PAG-like molecules (including rodent pepsin F) found in other mammalian orders. These two groups in turn form a sister group to a group of digestive enzymes from birds and mammals, which includes pepsin A. Sequence similarity in the promoter region of artiodactyl PAGs and mouse pepsin F also supported a close relationship between these genes. Ancestral sequence reconstruction revealed that, at the residues corresponding to positions 148-150 of pepsin A, in the ancestor of artiodactyl PAGs the motif QNL was replaced by EPV; and EPV (or occasionally EPI) is conserved at these sites in known PAGs. The conservation of this ancestral change suggests that it may be important to PAG function, particularly the fact that PAGs lack proteinase activity in spite of the conservation of active site residues in most PAGs.

Amino Acid Motifs↗
PubMed1998

Evolution of the trappin multigene family in the Suidae.

Trappins are a group of secretory proteins containing a WAP motif with an anchoring domain. Previous studies showed that their genes, especially those of pig, have undergone rapid evolution, which produced trappins with a broad spectrum of actions. To understand the evolution of such a rapidly evolving multigene family, we isolated trappin genes of the Artiodactyla, including pig, wart hog, collared peccary, hippopotamus, and cow, by means of polymerase chain reaction (PCR). Two genes newly isolated from wart hog are orthologs of trappin-1 (SPAI) and trappin-2 (elafin), the others are novel members of the trappin family and named trappins-6 to 11. The divergence of the sequences is greatest in the region that encodes the reactive site, and intron sequences appear to be more highly conserved than the protein-coding sequences, especially among the pig paralogs. Phylogenetic analysis showed that the trappin multigene family members of pig were generated through gene duplication after the divergence of the Suidae (pig and wart hog) and Tayassuidae (collared peccary). Similarities in the gene structure with seminal vesicle clotting proteins (REST) and WAP motif-containing proteins suggest that trappins are naturally occurring fusion proteins created through exon shuffling between ancestral REST and WAP motif-coding genes.

Amino Acid Sequence↗