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The average inbreeding coefficient for gaur (Bos gaurus H. Smith) born in captivity has ranged from 0.139 to 0.234 per year since 1969. Juvenile mortality is significantly higher among inbred young, and a significantly higher proportion of males occur in inbred than in noninbred offspring.
Silver nitrate (Ag-AS) staining was applied to chromosome preparations from the llama (Lama glama). The NORs were detected on the secondary constrictions of the short arms or the stalks of five small acrocentric chromosome pairs.
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Concentrations of potassium (K) and sodium (Na) were determined in the erythrocytes of 28 members of an interbreeding herd of Speke's gazelle. The distribution of K concentrations and Na/K concentration ratios suggested the presence of the high-K/low-K (HK/LK) polymorphism known in erythrocytes of domestic bovids. The pedigree of the herd of gazelles is known completely, permitting examination of the inheritance of HK/LK polymorphism by overlaying the distribution of phenotypes on the pedigree. Statistical analyses clearly indicate a strong genetic component in the phenotypic variability that is entirely consistent with a single autosomal locus, two-allele mode of inheritance, with the LK allele being dominant. This is the first demonstration of HK/LK polymorphism in a wild bovid species. The evidence indicates that HK/LK polymorphism is of considerable evolutionary age, is of monophyletic origin, and is maintained by selection.
Extensive monobrachial QFH-band homologies were found among cattle (Bovidae), pronghorn (Antilocapridae), Masai giraffe (Giraffidae), and mule and whitetail deer (Cervidae). The deer species had identical karyotypes (2n = 70, NAA = 70). Interfamily comparisons demonstrated that cattle (2n = 60, NAA = 58) and pronghorn (2n = 58, NAA = 60) were karyotypically the most similar. The giraffe possessed a 2n = 30, NAA = 54, and differed from the other artiodactyls by having a preponderance of biarmed autosomes. The primarily acrocentric deer karyotypes showed several chromosome arm disruptions relative to the other species. Comparative cytogenetic data among the advanced pecorans strongly suggest that the 2n = 60, NAA = 58 karyotype found in several species of the tribe Bovini is probably near the primitive condition for the Bovidae. However, the ancestral conditions of the sex chromosomes within the Bovidae and among the advanced pecorans remain in question.
alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical to recognition of and binding to target proteinases, is highly divergent within and among species. This appears to be a consequence of accelerated rates of evolution that may have been driven by positive Darwinian selection. In order to examine this and other features of alpha 1-PI evolution in more detail, we have isolated and sequenced cDNAs representing alpha 1-PI mRNAs of the mouse species Mus saxicola and Mus minutoides and have compared these with a number of other mammalian alpha 1-PI mRNAs. Relative to other mammalian mRNAs, the extent of nonsynonymous substitution is generally high throughout the alpha 1-PI mRNA molecule, indicating greater overall rates of amino acid substitution. Within and among mouse species, the 5'-half of the mRNA, but not the 3'-half, has been homogenized by concerted evolution. Finally, the reactive center is under diversifying or positive Darwinian selection in murid rodents (rats, mice) and guinea pigs yet is under purifying selection in primates and artiodactyls. The significance of these findings to alpha 1-PI function and the possible selective forces driving evolution of serpins in general are discussed.
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.
By a maximum likelihood analysis of mitochondrial DNA sequences, we examine Graur and Higgins' hypothesis of the Ruminantia/Cetacea clade with Suiformes as an outgroup. Graur and Higgins analyzed these sequences by the neighbor-joining and parsimony methods, as well as by the maximum likelihood method under the assumption that the substitution rate is the same for all sites. The Ruminantia/Suiformes clade assumed by the traditional taxonomy was rejected strongly by this analysis and the Ruminantia/Cetacea clade was supported. Adoption of a more realistic model distinguishing among rates at different codon positions in the maximum likelihood analysis of the same data, however, grossly reduces the significance level on the Graur-Higgins hypothesis. Thus, although the Ruminantia/Suiformes grouping is indeed least likely from Graur and Higgins' data set of mitochondrial DNA, this traditional tree cannot be rejected with statistical significance under the new analysis, and more data are needed to settle the issue. In the same way, we examine Irwin and Arnason's suggestion of the Hippopotamus/Cetacea clade by using cytochrome b and hemoglobins alpha and beta, and it turn out that their suggestion is also fragile. This analysis demonstrates the importance of selecting an appropriate model among the alternatives in the maximum likelihood analysis and of using many different genes from many relevant species in order to make reliable phylogenetic inferences.
The inferred transition from terrestrial hoofed mammal to fully aquatic cetacean has been intensively studied with fossil evidence. However, large sections of this remarkable evolutionary sequence are missing. Phylogenetic analysis of extant taxa may help to fill in some of these gaps. In this report, kappa-casein (exon 4) and beta-casein (exon 7) milk protein genes from cetaceans and other placental mammals were PCR-amplified, sequenced, and aligned to previously published sequences. Phylogenetic analyses of the casein data suggest that hippopotamid artiodactyls are more closely related to cetaceans than to other artiodactyls (even-toed hoofed mammals). An analysis of the nuclear casein sequences combined with published mitochondrial cytochrome b DNA sequences also supports the Cetacea/Hippopotamidae sister group. This affinity implies that some of the aquatic traits of cetaceans were derived in the common ancestor of Cetacea and Hippopotamidae. An extant "missing link" to Cetacea may have been overlooked by science since the description of the semiaquatic Hippopotamus in 1758. Paleontological information is grossly inconsistent with this hypothesis. If the casein phylogeny is accurate, large gaps in the fossil record as well as extensive morphological reversals and convergences must be acknowledged.
In addition to the universally expressed and highly polymorphic class Ia genes, the major histocompatibility complex (MHC) of placental mammals includes class Ib genes that are characterized by restricted expression and low levels of sequence polymorphism. The functional importance of class Ib genes as well as their actual function has long been controversial. Phylogenetic analyses have suggested that there are no orthologous relationships among class Ib loci of mammals belonging to different orders, suggesting that these loci have evolved independently since the placental mammals diverged. Here, we present evidence of convergent evolution at the molecular sequence level in the putative peptide-binding regions (PBRs) of human and mouse class Ib genes. So far, there are few if any convincing examples of convergent evolution at the amino acid sequence level, and such evolution is believed to be likely to occur only as a result of strong positive selection. Because the present case involves the functionally important PBR and because the primate and rodent molecules are known to bind similar peptides, this study represents both a convincing case of molecular-level convergence and evidence that MHC class Ib molecules, although not orthologous, may evolve similar functions convergently.
The phylogeography of three species of African bovids, the hartebeest (Alcelaphus buselaphus), the topi (Damaliscus lunatus), and the wildebeest (Connochaetes taurinus), is inferred from sequence variation of 345 sequences at the control region (d-loop) of the mtDNA. The three species are closely related (tribe Alcelaphini) and share similar habitat requirements. Moreover, their former distribution extended over Africa, as a probable result of the expansion of open grassland on the continent during the last 2.5 Myr. A combination of population genetics (diversity and structure) and intraspecific phylogeny (tree topology and relative branch length) methods is used to substantiate scenarios of the species history. Population dynamics are inferred from the distribution of sequence pairwise differences within populations. In the three species, there is a significant structuring of the populations, as shown by analysis of molecular variance (AMOVA) pairwise and hierarchical differentiation estimations. In the wildebeest, a pattern of colonization from southern Africa toward east Africa is consistent with the asymmetric topology of the gene tree, showing a paraphyletic position of southern lineages, as well as their relatively longer branch lengths, and is supported by a progressive decline in population nucleotide diversity toward east Africa. The phylogenetic pattern found in the topi and the hartebeest differs from that of the wildebeest: lineages split into monophyletic clades, and no geographical trend is detected in population diversity. We suggest a scenario where these antelopes, previously with wide pan-African distributions, became extinct except in a few refugia. The hartebeest, and probably also the topi, survived in refugia north of the equator, in the east and the west, respectively, as well as one in the south. The southern refugium furthermore seems to have been the only place where the wildebeest has survived.
Occurrence of an AATA interrupt in the IGF-I microsatellite was investigated in a number of Artiodactyl species, namely pigs, camels, deer, cattle, goats, and sheep. Comparison of DNA sequences in the 5' flank of the microsatellite in these species revealed that the interrupt within the microsatellite is conserved in deer, cattle, sheep, and goats but is absent from camels and pigs. The interrupt was introduced into the Artiodactyl phylogeny after the divergence of the Camelidae but before the divergence of the Cervidae, and thus its time of origin can be estimated to be 19-35 MYA. In contrast to the repeat units which are hypermutable, the interrupt has been conserved for a very long time and may even have suppressed microsatellite variation by inhibiting replication slippage. A 12-bp deletion in the 5' flank of the microsatellite in camels corresponds to a consensus reversed repeat in deer, cattle, sheep, and goats with unknown functional significance. Apart from this deletion, the 5' flank of the microsatellite is highly conserved in Artiodactyl species.
Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.
Exon 2 sequences of an expressed MHC-DRB locus from sheep were examined for polymorphisms in both the antigen-binding regions and the adjacent intronic mixed simple tandem repeat. Twenty-one novel exon 2 Ovar-DRB alleles were identified. Short nucleotide motifs are extensively shared between certain exon 2 regions of Ovar-DRB alleles. The simple repeat variations, the number of different amino acids at usually polymorphic sites, and the number of silent substitutions were reduced in the intraspecies analyses of sheep DRB sequences, compared with those of cattle and goats. It was paradoxical that the abundance of different sheep alleles was similar to that of cattle and goats. This paradox may be explained by postulating a relatively small number of "ancient" alleles, with the present-day Ovar-DRB alleles being generated by reciprocal exchange of nucleotide motifs. At the antigen-binding sites, new combinations of amino acids were maintained in Ovar-DRB alleles by strong positive selection. In sheep--and less pronounced in goats and cattle--the DRB alleles can be divided into two groups. In one group, silent substitutions are increased when compared with the other. This suggests separate evolutionary pathways for certain groups of DRB alleles within a species. The simple repetitive sequences are also discussed with respect to the evolution of DRB alleles.
Variation in mutation rate, attributed to differences in both generation time and in metabolic rate, has been invoked under the neutral theory of molecular evolution to account for differences in substitution rate among mammalian lineages. We show that substitution rates at fourfold-degenerate sites and at sites in noncoding regions do not vary between the primate and rodent lineages, implying mutation-rate uniformity. In contrast, the substitution rates at nondegenerate sites vary both within and between lineages. This difference in substitution-rate pattern between the two types of site is incompatible with neutral theory but may result from substitutions occurring by fixation of slightly deleterious mutations. Variation in the rate of protein evolution among mammalian lineages appears to be due more to differences in population fixation rates than to biochemical or physiological differences affecting mutation rates.
Mitochondrial DNA (mtDNA) sequence variation was examined in eight taxa of the African rodent family Bathyergidae, as well as in two taxa representative of the Old-World hystricognathid rodent families Petromyidae and Thryonomyidae. A total of 812 bp, constituting domains I-III of the 12S ribosomal rRNA gene, were compared for each taxon. The high levels of intrafamilial mtDNA sequence divergence observed (average 16.8, range 3.5-23.2) support an ancient origin for the five genera, 20-38 Mya. These data do not support the current subfamilial groupings of the Bathyergidae. The eastern African naked mole-rat, Heterocephalus glaber, is the most basal representative of the family, with the silvery mole-rat, Heliophobius, being the next most basal. South African forms [dune, common, and cape mole-rats (Bathyergus, Cryptomys, and Georychus, respectively)] group together. The independent origin of the common mole-rat, relative to the naked mole-rat, suggests that complex social systems evolved in parallel along different bathyergid lineages. The 12S rRNA gene is not evolving at a higher rate within the rodent lineages, relative to that seen for artiodactyls and primates. Bathyergid rodents appear to fall at an extreme end of the spectrum of mammalian variation, with respect to both transition/transversion ratios and divergence, showing much lower transition/transversion ratios than those previously reported for intrafamilial comparisons.
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