The subfamilies and tribes of the family Bovidae

In this paper 112 skeletal characters in 27 living species of bovids are used in cladistic and phenetic analyses of the relationships among the tribes in the family. Consideration and modification of the cladistic analysis leads to the conclusion that bovids cluster around four foci in ascending evolutionary sequence: Boselaphini and allies; Antilopini and some Neotragini; the Caprinae; and a group of African antelopes containing Aepyceros , Alcelaphini, Reduncini and Hippotragini. This conclusion is quite closely compatible with the phenetic distance analysis of the same data, provided die latter is read as if primitive or early bovids share more similarities than divergently advanced ones and hence associate more closely. Given the primitiveness of Boselaphini and allies, the crucial finding is that Caprinae link with African antelopes and that Antilopini are more remote. Cladistic and phenetic analyses of 32 characters in 12 extinct bovid species produce similar groupings, but also throw doubt on the classification of Aepyceros , Reduncini and Hippotragini alongside Alcelaphini within a clade of African antelopes. As a result of these two sets of studies, of living and of extinct bovids, minimal alterations are proposed to the arrangement of bovid tribes. In addition, Saiga is placed in the Antilopini, and, with less assurance, Pelea in the Neotragini, Aepyceros in the Alcelaphinae, and Pantholops in the Caprinae. The contribution of the fossil record to understanding bovid evolution is considered.     

Evolution of satellite DNA sequences in two tribes of Bovidae: A cautionary tale

Two clones, Bt1 from Bos taurus and Om1 from Ovis orientalismusimon, were used as probes for hybridization on genomic DNA and onmetaphase chromosomes in members of Bovini and Caprini tribes. Bt1 and Om1 aresequences respectively belonging to the 1.715 and 1.714 DNA satellite I families.Southern blots and fluorescence in situ hybridization experimentsshowed completely coherent results: the Bovini probe Bt1 hybridized only to membersof the Bovini tribe and not to members of Caprini. Likewise, the Caprini probe Om1hybridized only to members of the Caprini tribe and not to members of Bovini.Hybridization signals were detected in the heterochromatic regions of everyacrocentric autosome, except for two pairs of autosomes from Caprahircus that did not show hybridization to probe Om1. No signal wasdetected on X and Y chromosomes or on bi-armed autosomes. Remarkably, probe Om1showed almost 100% homology with a bacterial sequence reported inHelicobacter pylori.     

Phylogenetic relationships and the primitive X chromosome inferred from chromosomal and satellite DNA analysis in Bovidae

The early phylogeny of the 137 species in the Bovidae family is difficult to resolve; knowledge of the evolution and relationships of the tribes would facilitate comparative mapping, understanding chromosomal evolution patterns and perhaps assist breeding and domestication strategies. We found that the study of the presence and organization of two repetitive DNA satellite sequences (the clone pOaKB9 from sheep, a member of the 1.714 satellite I family and the pBtKB5, a 1.715 satellite I clone from cattle) on the X and autosomal chromosomes by in situ hybridization to chromosomes from 15 species of seven tribes, was informative. The results support a consistent phylogeny, suggesting that the primitive form of the X chromosome is acrocentric, and has satellite I sequences at its centromere. Because of the distribution of the ancient satellite I sequence, the X chromosome from the extant Tragelaphini (e.g. oryx), rather than Caprini (sheep), line is most primitive. The Bovini (cow) and Tragelaphini tribes lack the 1.714 satellite present in the other tribes, and this satellite is evolutionarily younger than the 1.715 sequence, with absence of the 1.714 sequence being a marker for the Bovini and Tragelaphini tribes (the Bovinae subfamily). In the other tribes, three (Reduncini, Hippotragini and Aepycerotini) have both 1.714 and 1.715 satellite sequences present on both autosomes and the X chromosome. We suggest a parallel event in two lineages, leading to X chromosomes with the loss of 1.715 satellite from the Bovini, and the loss of both 1.714 and 1.715 satellites in a monophyletic Caprini and Alcelaphini lineage. The presence and X chromosome distribution of these satellite sequences allow the seven tribes to be distributed to four groups, which are consistent with current diversity estimates, and support one model to resolve points of separation of the tribes.     

Characterization and chromosomal organization of satellite DNA sequences in Picea abies

Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37-55 bp in length and had 68.9%-91.9% nucleotide sequence similarity. Two 2F repeats were 305-306 bp in length and had 83% sequence similarity. Two 3C repeats were 193-226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 x 106, 2.9 x 105, and 2.9 x 104, respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.     

Genomic organization and evolution of the soybean SB92 satellite sequence

Repetitive DNA sequences comprise a large percentage of plant genomes, and their characterization provides information about both species and genome evolution. We have isolated a recombinant clone containing a highly repeated DNA element (SB92) that is homologous to ca. 0.9% of the soybean genome or about 10⁵ copies. This repeated sequence is tandemly arranged and is found in four or five major genomic locations. FISH analysis of metaphase chromosomes suggests that two of these locations are centromeric. We have determined the sequence of two cloned repeats and performed genomic sequencing to obtain a consensus sequence. The consensus repeat size was 92 bp and exhibited an average of 10% nucleotide substitution relative to the two cloned repeats. This high level of sequence diversity suggests an ancient origin but is inconsistent with the limited phylogenetic distribution of SB92, which is found an high copy number only in the annual soybeans. It therefore seems likely that this sequence is undergoing very rapid evolution.     

Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective.

The evolutionary history of the family Bovidae remains controversial despite past comprehensive morphological and genetic investigations. In an effort to resolve some of the systematic uncertainties within the group, a combined molecular phylogeny was constructed based on four independent nuclear DNA markers (2,573 characters) and three mitochondrial DNA genes (1,690 characters) for 34 bovid taxa representing all seven of the currently recognized bovid subfamilies. The nuclear DNA fragments were analyzed separately and in combination after partition homogeneity tests were performed. There was no significant rate heterogeneity among lineages, and retention index values indicated the general absence of homoplasy in the nuclear DNA data. The conservative nuclear DNA data were remarkably effective in resolving associations among bovid subfamilies, which had a rapid radiation dating back to approximately 23 MYA. All analyses supported the monophyly of the Bovinae (cow, nilgai, and kudu clade) as a sister lineage to the remaining bovid subfamilies, and the data convincingly suggest that the subfamilies Alcelaphinae (hartebeest, tsessebe, and wildebeest group) and Hippotraginae (roan, sable, and gemsbok clade) share a close evolutionary relationship and together form a sister clade to the more primitive Caprinae (represented by sheep, goat, and muskox). The problematic Reduncinae (waterbuck, reedbuck) seem to be the earliest-diverging group of the Caprinae/Alcelaphinae/Hippotraginae clade, whereas the Antilopinae (gazelle and dwarf antelope clade) were always polyphyletic. The sequence data suggest that the initial diversification of the Bovidae took place in Eurasia and that lineages such as the Cephalophinae and other enigmatic taxa (impala, suni, and klipspringer) most likely originated, more or less contemporaneously, in Africa.     

Examination of hemiplasy, homoplasy and phylogenetic discordance in chromosomal evolution of the Bovidae

Robertsonian chromosomal fusions predominate in shaping the genomes of many species of Bovidae. These and other cytogenetic data (from 52 taxa representing 51 species and 9 tribes of Bovidae) were (i) examined for usefulness in defining phylogenetic relationships and (ii) subsequently mapped to a consensus tree based on mitochondrial and nuclear DNA gene sequences with divergence dates of the corresponding species calculated from cytochrome b sequences. This permitted persistence time estimates for the various rearrangements. The chromosomal data resulted in an unsupported higher-level topology, but with recognition of the monophyly of some genera and tribes within Bovidae. The distribution and temporal spread of character states on the species tree is suggestive of a restricted role for hemiplasy (the retention of an ancestral chromosomal polymorphism through multiple speciation events) and for introgression (resulting from secondary contact among taxa), processes that can potentially lead to phylogenetic discordance. We conclude that the most probable interpretation for these data is that genuine karyotypic homoplasy predominates, but that hemiplasy (and/or introgression) is a realistic hypothesis for the observed patterns of several shared characters in Bovidae.     

Nature and organization of the sequence variations in the long-range periodicity calf satellite DNA I

The nucleotide sequences of a series of cloned repeats of the bovine satellite DNA I have been established and compared to the average sequence already determined by the other workers. Variations, which are essentially single base changes, deletions or additions, are found within clustered copies and, thus, define subfractions and domains of the satellite DNA. These results are confirmed by restriction enzyme analysis of the cloned repeats or of the total purified satellite DNA. These subfractions are essentially overlapping. Certain short regions of the DNA repeat do not appear to be involved in the changes, which are spread in a concerted way through the whole bovine karyotype. The significance of these results is discussed in the light of the recent suggestion made that gene conversion-like events are susceptible to introduce homogeneity of polymorphism within the elements of repeated families of DNA sequences.     

Sequence and evolution of related bovine and caprine satellite DNAs: Identification of a short DNA sequence potentially involved in satellite DNA amplification

The satellite II DNAs of the domestic ox Bos taurus and sheep Ovis aries have been sequenced, and that of the domestic goat Capra hircus partially sequenced. All three are related, and consist of repeat units of about 700 base-pairs. There is no evidence of internal repetition within these repeat units. When matched for maximum homology, the goat and sheep sequences show 83% homology, whereas the ox and sheep sequences share only 70% homology. Factors contributing to the uncertainty of the exact homology between these sequences are discussed, but the results are nevertheless consistent with their progenitor sequence being present in the common ancestor of cattle and sheep. Goat satellite II DNA is shown to contain another, unrelated, tandemly repeated sequence, which is composed of 22 base-pair repeat units. Both this sequence and a region of ox satellite II share good homology with the 11 base-pair progenitor sequence of ox 1.706 g/cm³ satellite DNA. It is suggested that this shared sequence could play a role in bovine satellite DNA amplification.     

Structure, sequence, chromosomal location, and evolution of the human ferredoxin gene family

Ferredoxin is an iron-sulfur protein that serves as an electron transport intermediate for mitochondrial cytochromes P450 involved in steroid, vitamin D, and bile acid metabolism. We cloned and characterized the human ferredoxin gene family, which includes two expressed genes and two pseudogenes. Sequence analysis of this gene family revealed that it encodes only one protein product. The expressed genes were assigned to chromosome 11 and pseudogenes to chromosomes 20 and 21 by identifying single-copy probes from each gene segment and hybridizing them to DNA from rodent-human hybrid cells. The pseudogenes lacked introns and contained numerous mutations, including insertion, deletion, and substitution which rendered them inactive. They were 96% and 85% homologous to the expressed gene, yet they were only 78% homologous with each other. The intronless nature, higher diversity among themselves, and distinct chromosomal location of the pseudogenes suggests that they arose by independent, retroposon-mediated events.     

A new moderately repetitive DNA sequence family of novel organization.

In cloning adenovirus homologous sequences, from a human cosmid library, we identified a moderately repetitive DNA sequence family consisting of tandem arrays of 2.5 kb members. A member was sequenced and several non-adjacent, 15-20 bp G-C rich segments with homology to the left side of adenovirus were discovered. The copy number of 400 members is highly conserved among humans. Southern blots of partial digests of human DNA have verified the tandem array of the sequence family. The chromosomal location was defined by somatic cell genetics and in situ hybridization. Tandem arrays are found only on chromosomes 4 (4q31) and 19 (q13.1-q13.5). Homologous repetitive sequences are found in DNA of other primates but not in cat or mouse. Thus we have identified a new family of moderately repetitive DNA sequences, unique because of its organization in clustered tandem arrays, its length, its chromosomal location, and its lack of homology to other moderately repetitive sequence families.     

Nucleotide sequence, genomic organization and evolution of a major repetitive DNA family in tilapia (Oreochromis mossambicus/hornorum).

A highly repetitive DNA sequence from tilapia (Oreochromis mossambicus/hornorum) has been cloned and sequenced. It is a tandemly arrayed sequence of 237 bp and constitutes 7% of the fish genome. The copy number of the repeat is approximately 3 x 10(5) per haploid genome. DNA sequence analysis of 7 cloned repeats revealed a high degree of conservation of the monomeric unit. Within the monomeric unit, a 9 bp AT rich motif is regularly spaced approximately 30 bp apart and may represent the progenitor of the amplified sequence. One cloned repeat, Ti-14, contained a 30 bp deletion at a position flanked by a 7 bp direct repeat. The Ti-14 sequence appears to have been amplified independently of the major 237 bp tandem array. A higher-order repeat unit, defined by longer-range periodicities revealed by restriction endonuclease digestion, is further imposed on the tandem array.     

Differences in the organization and chromosomal allocation of satellite DNA between the European long tailed house miceMus domesticus andMus musculus

We compared the organization of satellite DNA (stDNA) and its chromosomal allocation inMus domesticus and inMus musculus. The two stDNAs show similar restriction fragment profiles after digestion (probed withM. domesticus stDNA) with some endonucleases of which restriction sequences are present in the 230–240 bp repetitive unit of theM. domesticus stDNA. In contrast, EcoRI digestion reveals thatM. musculus stDNA lacks most of the GAATTC restriction sites, particularly at the level of the half-monomer. The chromosome distribution of stDNA (revealed by anM. domesticus stDNA probe) shows different patterns in theM. domesticus andM. musculus karyotypes, with about 60% ofM. domesticus stDNA retained in theM. musculus genome. It is particularly noteworthy that the pericentromeric regions ofM. musculus chromosomes 1 and X are totally devoid ofM. domesticus stDNA sequences. In both groups, the differences in energy transfer between the stDNA-bound fluorochromes Hoechst 33258 and propidium iodide suggest that AT-rich repeated sequences have a much more clustered array in theM. domesticus stDNA, as if they are organized in tandem repeats longer than those ofM. musculus. Considering the data as a whole, it seems likely that the evolutionary paths of the two stDNAs diverged after the generation of the ancestral 230–240 bp stDNA repetitive unit through the amplification, in theM. domesticus genome, of a family repeat which included the EcoRI GAATTC restriction sequence.     

A micronucleus-limited sequence family in Tetrahymena thermophila: organization and sequence conservation.

During macronuclear development in the ciliated protozoan Tetrahymena thermophila, sequence reorganization including sequence loss occurs. Addressing questions about the organization and nucleotide sequence of micronucleus limited regions can lead to insights about mechanisms of DNA rearrangements during macronuclear development as well as mechanisms for the maintenance of the stability of micronucleus-limited sequence families. We have previously identified a moderately repetitive micronucleus-limited sequence family called X-H (family members hybridize to an approximately 450 bp Xbal-HindIII restriction fragment), completely absent from macronuclear DNA. The first member of this family which we isolated is associated with terminal sequences characteristic of a Tel-1 element, a putative micronuclear transposable element. Two additional family members have been isolated which are not closely associated with Tel-1 terminal sequences. We have nucleotide sequence data for three cloned members of the X-H family. This analysis has demonstrated that the longest cloned members of the X-H family share a region of homology of approximately 2,400 bp and are highly conserved, differing only by small insertions or deletions of 100 bp or less. The sequences from one of the sequenced family members flanking the region of homology are themselves mostly micronucleus-limited.     

The primary sequence of a crustacean satellite DNA containing a family of repeats

The repeating sequence of isopycnic twin Satellite II of the hermit crab, Pagurus pollicaris, has been determined. More than 95% of the primary sequence of the light strand is composed of (CAG)nCTGCACT. The only detectable variation on the repeating sequence is the number of CAGs included in each repeat which varies from 3-12. The sequence of Satellite II differs markedly from that of its twin, whose light strand is greater than 95% CCTA (Skinner et al., 1974). The absence from Satellite II of repeats where (CAG)n less than or equal to 2 further defines the constraints on a recent model for the origin of satellites (Smith, 1976).     

A highly repetitive DNA component common to all Cervidae: its organization and chromosomal distribution during evolution

In recent work we have isolated and characterized a highly repetitive DNA (MMV satellite IA) from Muntiacus muntjak vaginalis, the species with the most reduced karyotype in the Cervidae family. We have now analysed the genomes of nine related species for the presence of MMV satellite IA components, and have determined their organization and chromosomal distribution. Repetitive satellite IA type DNA is present in all species of the Cervidae, and also in the bovine, but not in a species of the Tragulidae suggesting that these sequences were generated after the phylogenetic separation of Bovidae and Tragulidae. Studies on the organization of the satellite IA DNA in the various species revealed three main repeat lengths: 1400, 1000 and 807 bp. The relative proportion of satellite IA sequences present in any one of the three registers is strikingly different within the various species and can be correlated with the phylogeny of the Cervidae. The chromosomal locations of the satellite IA sequences were determined in seven species by in situ hybridization. It turned out that the chromosomal rearrangements leading to the reduction in the number of chromosomes during karyotype evolution have led to the elimination of satellite I DNA at most locations. In all tandem fusions, the satellite IA sequences located at the centromeres of the ancestral acrocentric chromosomes are lost. In contrast, during the centric fusion that generates the M. m. vaginalis X chromosome satellite IA sequences are amplified. Sequence motifs, which are known to be involved in recombinational events are present in the satellite IA and might have contributed to the unique karyotype variation in the Cervidae.