Molecular Systematics of the Subfamily Caprinae (Artiodactyla, Bovidae) as Determined from Cytochrome b Sequences

We have sequenced the complete mitochondrial DNA cytochrome b gene from 18 species of the subfamily Caprinae and two outgroup taxa. Additional sequences retrieved from the literature were used to constitute a data set of 32 cytochrome b sequences comprising all genera usually included within the Caprinae. Phylogenetic relationships were assessed by PAUP using three new weighting schemes based on homoplasy analyses. Each type of substitution considered at each of the three codon positions was weighted according to its homoplasy level, as measured by the consistency index (CI), the slope of saturation (S), or their product (CIS). These differentially weighted parsimony analyses indicate that (1) the subfamily Caprinae is monophyletic, but only with the exclusion of Saiga from the group; (2) there is no support for monophyly of the four tribes currently recognized (Caprini, Rupicaprini, Ovibovini, and Saigini), suggesting relationships different from those traditionally accepted; (3) the caprine group consists of three major clades corresponding to (a) Budorcas and Ovis, (b) Capricornis, Ovibos, and Naemorhedus, and (c) Capra, Hemitragus, and Pseudois; and (4) the basal branching pattern is very weakly supported by bootstrap or branch support values except for the sister-group relationship of Pantholops with all other caprines, and the phylogenetic positions of Ammotragus, Oreamnos, and Rupicapra remain unclear.     

G- and C-banded karyotype of the markhor<Emphasis Type="Italic">Capra falconeri heptneri</Emphasis>, and comparison of its banding patterns with the Alpine ibex<Emphasis Type="Italic">Capra ibex</Emphasis> and cattle<Emphasis Type="Italic">Bos taurus</Emphasis>

Here we present the first data on chromosome banding forCapra falconeri heptneri (Zalkin, 1945) (Bovidae: Caprinae), a critically endangered subspecies of the markhor, and compare its G- and C-banding patterns with those of the congeneric Alpine ibexC. ibex Linnaeus, 1758 and the evolutionarily more distant cattleBos taurus Linnaeus, 1758. The two goat species have identical karyotypes whereasB. taurus, which has the same diploid number (2n = 60) and autosomal fundamental number (aFN) differs in the morphology of two pairs of autosomes (9 and 14) and of the X chromosome, as well as in the amount of C heterochromatin. Although the study supports the earlier idea of karyotype homogeneity within the genusCapra, new comparative cytogenetic data for unstudied yet congeneric and other related species are necessary for our understanding of the pattern of chromosome evolution within the subfamily Caprinae and, more broadly, the family Bovidae.     

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.     

CytochromeBSequences Suggest Convergent Evolution of the Asian Takin and Arctic Muskox

Relationships of the takin (Budorcas taxicolor) and muskox (Ovibos moschatus) have been speculated upon for many years. Morphological and behavioral similarities between these species have led to suggestions that they are closely related. To test the hypothesis that characteristics shared by the takin and muskox stem from a recent common ancestor, we compared sequences of their mitochondrial cytochromebgenes with those of three other species of Caprinae. We present data that may support rejection of the hypothesis of recent common ancestry and suggest that similarities in behavior and morphology in these two species might be attributed to convergent evolution rather than shared phylogeny.     

Molecular evolution of coding and non-coding sequences of the growth hormone receptor (GHR) gene in the family Bovidae

The GHR gene exon 1A and exon 4 with fragments of its flanking introns were sequenced in twelve Bovidae species and the obtained sequences were aligned and analysed by the ClustalW method. In coding exon 4 only three interspecies differences were found, one of which had an effect on the amino-acid sequence--leucine 152 proline. The average mutation frequency in non-coding exon 1A was 10.5 per 100 bp, and was 4.6-fold higher than that in coding exon 4 (2.3 per 100 bp). The mutation frequency in intron sequences was similar to that in non-coding exon 1A (8.9 vs 10.5/100 bp). For non-coding exon 1A, the mutation levels were lower within than between the subfamilies Bovinae and Caprinae. Exon 4 was 100% identical within the genera Ovis, Capra, Bison, and Bos and 97.7% identical for Ovis moschatus, Ammotragus lervia and Bovinae species. The identity level of non-coding exon 1A of the GHR gene was 93.8% between species belonging to Bovinae and Caprinae. The average mutation rate was 0.2222/100 bp/MY and 0.0513/100 bp/MY for the Bovidae GHR gene exons 1A and 4, respectively. Thus, the GHR gene is well conserved in the Bovidae family. Also, in this study some novel intraspecies polymorphisms were found for cattle and sheep.     

Cytogenetic aspects of phylogeny in the Bovidae. I. G-banding

An extensive G-banding study of karyotypes of 12 species of Bovidae has been undertaken in an attempt to trace homologies and patterns of evolution of karyotype phenotypes throughout the family. G-banding profiles revealed a considerable degree of chromosome-arm homology throughout the group, which also extended into the related superfamilies, the Giraffoidea and Cervoidea. The conservation of banding patterns in chromosome arms strongly indicates that Robertsonian translocation type rearrangements have provided the major source of interspecies karyotype differences, with inversions and reciprocal and tandem translocations providing relatively minor contributions. Examples of individuals carrying newly arisen Robertsonian translocations are not infrequent, and in one instance there was evidence that two similar rearrangements had arisen independently in two species. Despite the extensive changes in karyotype organization, subfamilies within the Bovidae were characterized by the presence of common rearrangements, and those involving autosomal pairs 11 and 12 of the ox, as well as the X chromosome, separate the Bovinae from the Caprinae and Hippotraginae.     

The diet of Myotragus balearicus Bate 1909 (Artiodactyla: Caprinae), an extinct bovid from the Balearic Islands: evidence from coprolites

Myotragus balearicus Bate 1909 is an artiodactyl Caprinae endemic to the Balearic Islands which became extinct more than 4000 years ago. Coprolites produced by this species have been collected from the excavation of Holocene cave sediments in Cova Estreta (Serra de Tramuntana, Mallorca). The pollen content of several samples of coprolites has been studied in order to determine the diet of Myotragus. Myotragus balearicus from Cova Estreta was a browser, and consumed huge amounts of box, Buxus balearica , a plant known for its high content of steroidal alkaloids. The coprolites are very fine textured, probably due to the result of a very efficient digestive process.     

Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

Efforts have been made to investigate the phylogeny of the family Bovidae; however, the relationships within this group still remain controversial. To further our understanding of the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and Maximum Likelihood methods. The results indicate that the basal divergence within the Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae species. The two Neotragus species (the suni and pygmy antelope) clustered with the impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus, which suggested that the Antilopinae was a paraphyletic subfamily. The present study confirmed a close relationship between the genera Capricornis and Naemorhedus while supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae. Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The very close relationship between Bison and Bos suggested that Bos and Bison should be integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope), unique genera which have sometimes been lumped together, were placed in different groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.     

鬣羚分类与分布的初步研究

鬣羚和斑羚均隶属于偶蹄目、牛科、羊亚科。在对鬣羚的分类上,不同学者持有不同观点。在测量和收集了不同地区的鬣羚和斑羚的头骨数据后,通过SPSS系统软件对数据进行处理,发现鬣羚与斑羚的差异较大,应各单列为一属。通过查阅文献和相关参考资料,对鬣羚种和亚种的分化与分布作了简单的分析和总结。     

Observations on a Wild goat, Capra aegagrus (Artiodactyla: Bovidae) from Oman, E. Arabia

A male Wild goat, Capra aegagrus Erxleben, 1777, is here described, which was obtained in Oman and is now in the gardens of the Zoological Society of London. It is the first known occurrence of the species in peninsular Arabia. The characters of the three species of subfam. Caprinae known to occur in the region are compared.     

Common names of species, the curious case of Capra pyrenaica and the concomitant steps towards the ‘wild-to-domestic’ transformation of a flagship species and its vernacular names

Common names (CN) add to linguistic richness and ultimately derive from how a majority of people refer to a species. CN have a biological and–above all—practical importance given that they are essential for connecting specialists and lay people. To illustrate the diversity of CN between and within species, we made an overview of common name in Caprinae species—flagship species in mountain ecosystems. Then, using Capra pyrenaica as a study case, we highlighted that the choice of CN is inextricably linked to current debates and trends in wildlife management that should never be ignored, given their importance in the fields of ethics, zoology, systematics, conservation and current management. We underline the need to investigate further the probable relationships linking common names, human perception and wildlife management. Researchers, citizens and policy-makers will have to be watchful that clumsy common names, such as ‘wild-to-domestic’ transformed ones, will not hamper the conservation of wild species as a ‘Common Heritage’.     

Cross-Reactivity of Neutralizing Antibodies among Malignant Catarrhal Fever Viruses

Some members of the gamma herpesvirus genus Macavirus are maintained in nature as subclinical infections in well-adapted ungulate hosts. Transmission of these viruses to poorly adapted hosts, such as American bison and cattle, can result in the frequently fatal disease malignant catarrhal fever (MCF). Based on phylogenetic analysis, the MCF viruses (MCFV) cluster into two subgroups corresponding to the reservoir hosts’ subfamilies: Alcelaphinae/Hippotraginae and Caprinae. Antibody cross-reactivity among MCFVs has been demonstrated using techniques such as enzyme linked immunosorbent and immunofluorescence assays. However, minimal information is available as to whether virus neutralizing antibodies generated against one MCFV cross react with other members of the genus. This study tested the neutralizing activity of serum and plasma from select MCFV-infected reservoir hosts against alcelaphine herpesvirus 1 (AlHV-1) and ovine herpesvirus 2 (OvHV-2). Neutralizing antibody activity against AlHV-1 was detected in samples from infected hosts in the Alcelaphinae and Hippotraginae subfamilies, but not from hosts in the Caprinae subfamily. OvHV-2 neutralizing activity was demonstrated in samples from goats (Caprinae) but not from wildebeest (Alcelaphinae). These results show that neutralizing antibody cross reactivity is present to MCFVs within a virus subgroup but not between subgroups. This information is important for diagnosing infection with MCFVs and in the development of vaccines against MCF.     

秦岭羚牛高度重复序列DNA片段的分子克隆和序列分析

羚牛(Budorcas taxicolor)属偶蹄目(Artiodactyla)、牛科(Bovidae),为我国一类大型珍贵保护动物。我们从其基因组中克隆得到若干约800bp的BamHI高度重复序列并对部分克隆进行了序列测定,发现它们显示了很高的同源性。利用其中一个单元为探针,对限制酶消化后的羚牛基因组DNA作杂交分析,发现其杂交谱带不具有个体及亚种间特异性,说明该重复序列在羚牛基因组中具有保守的分布和排列。在牛科动物中,羚牛BamHI片段与绵羊属和山羊属的相关序列具有高度同源性,而与水牛和家牛序列差异较大。这些结果为羚牛与羊亚科物种亲源关系较近的分类学观点提供了分子生物学证据。有证据表明,这些片段可能代表羚牛染色体着丝点的卫星DNA单体。     

Molecular epidemiology of Mycoplasma conjunctivae in Caprinae: transmission across species in natural outbreaks

Mycoplasma conjunctivae is the etiological agent of infectious keratoconjunctivitis, a highly contagious ocular infection that affects both domestic and wild Caprinae species in the European Alps. In order to study the transmission and spread of M. conjunctivae across domestic and wild Caprinae populations, we developed a molecular method for subtyping and identifying strains of M. conjunctivae. This method is based on DNA sequence determination of a variable domain within the gene lppS, a gene that encodes an antigenic lipoprotein of M. conjunctivae. This domain of lppS shows variations among different strains but remains constant upon generations of individual strains on growth medium and thus allows identification of individual strains and estimation of their phylogenetic intercorrelations. The variable domain of lppS is amplified by PCR using primers that match conserved sequences of lppS flanking it. Sequence analysis of the amplified fragment enables fine subtyping of M. conjunctivae strains. The method is applicable both to isolated strains and to clinical samples directly without requiring the cultivation of the strain. Using this method, we show that M. conjunctivae was transmitted between domestic and wild animals that were grazing in proximate pastures. Certain animals also presented infections with two different strains simultaneously.     

Phylogeny for species of Haemonchus (Nematoda: Trichostrongyloidea): considerations of their evolutionary history and global biogeography among Camelidae and Pecora (Artiodactyla)

Phylogenetic analysis of 25 morphological characters among the 12 species of Haemonchus resulted in 1 most parsimonious tree (60 steps; consistency index = 0.67, retention index = 0.80). Monophyly for Haemonchus was diagnosed by 3 unequivocal synapomorphies, including the asymmetric origin of the dorsal ray, relative size of the ventral rays, and the presence of a barb on each spicule tip. Species of Haemonchus have complex histories with respect to host and geographic associations: (1) origins in Africa with basal diversification in antelopes (H. krugeri, H. lawrencei, H. dinniki, H. horaki), (2) independent events of colonization for those species in Caprini and Bovinae (H. contortus, H. placei, H. bedfordi, H. similis), (3) colonization and development of core host associations within Camelidae (H. longistipes) and among Antilopinae, Tragelaphini, and Giraffidae (H. mitchelli, H. okapiae, H. vegliai), and (4) geographically widespread species that are represented only by those that have been translocated with domestic stock. The North American fauna is characterized by 3 introduced and exotic species, H. placei, H. contortus, H. similis, which emphasizes the importance of continued documentation of faunal diversity in the context of predictive foundations derived from phylogenetic studies. Satellite associations for species of Haemonchus, particularly among Cervidae and Camelidae in the Neotropics and Cervidae, Antilocapridae, and possibly wild Caprinae in the Nearctic, have been a consequence of introductions and exchange of parasites at historical interfaces for managed and natural ecosystems. Such distributions are emblematic of the overriding significance of anthropogenic factors as determinants of the global distributions for pathogenic parasites in domestic and wild ruminants.     

秦岭羚牛高度重复序列DNA片段的分子克隆和序列分析

羚牛（Budorcas taxicolor)属偶蹄目（Artiodactyla)、牛科（Bovidae),为我国一类大型珍贵保护动物。我们从其基因组中克隆得到若干约800bp的BamHI高度重复序列并对部分克隆进行了序列测定,发现它们显示了很高的同源性。利用其中一个单元为探针,对限制酶消化后的羚牛基因组DNA作杂交分析,发现其杂交谱带不具有个体及亚种间特异性,说明该重复序列在羚牛基因组中具有保守的分布和排列。在牛科动物中,羚牛BamHI片段与绵羊属和山羊属的相关序列具有高度同源性,而与水牛和家牛序列差异较大。这些结果为羚牛与羊亚科物种亲源关系较近的分类学观点提供了分子生物学证据。有证据表明,这些片段可能代表羚牛染色体着丝点的卫星DNA单体。     

Complete mitochondrial genome of the Himalayan serow (Capricornis thar) and its phylogenetic status within the genus Capricornis

The genus Capricornis (Caprinae, Bovidae) includes six species, i.e., Capriconis sumatraensis, Capricornis swinhoei, Capricornis crispus, Capricornis rubidus, Capricornis milneedwardsii and Capricornis thar. Based on morphological, anatomical and physiological evidence, the Himalayan serow (C. thar), which is distributed in the mountain regions of the Tibetan Plateau and adjacent areas, is generally classified as a species of the genus Capricornis. However, considering the lack of molecular phylogenetic evidence, a heated controversy still exists over the taxonomic position of the Himalayan serow. To determine the phylogenetic status of C. thar, we sequenced the complete mitochondrial genome (mtDNA) of one Himalayan serow using the polymerase chain reaction (PCR) technique. Then, we constructed a molecular phylogenetic tree of the genus Capricornis and its related species in the Caprinae subfamily based on maximum likelihood and Bayesian interference methods. The results reflect that the structural characteristics, nucleotide content and codon usage bias of the mitochondrial genome of the Himalayan serow were similar to those of other serows. A phylogenetic analysis using two rRNA genes and 12 encoded protein-coding genes indicated that C. thar is clustered within the C. milneedwardsii clade, which is a sister group of C. sumatraensis. The present study provides useful information about the evolution of the Himalayan serow, which will be essential for conservation genetic studies.     

Phylogenetic reassessment of gorals with new evidence from northern Myanmar reveals five distinct species

Researchers have recognised one to seven species of goral (Naemorhedus spp., Caprinae, Bovidae). We compared all available whole mitogenomic sequences, including eight new ones from northern Myanmar, and now recognise five distinct species. Naemorhedus caudatus remains a valid species. Naemorhedus griseus is a synonym of Naemorhedus goral. Naemorhedus evansi is a valid species, with a geographic range that extends northwards into southwestern China. Naemorhedus cranbrooki and Naemorhedus baileyi are distinct species, not synonyms. Molecular divergence analyses suggest that goral speciation was closely related to the rapid uplift of the Qinghai-Tibetan Plateau and Hengduan Mountains from the early Pliocene to the Pleistocene.     

Twenty polymorphic microsatellites in two of North Africa's most threatened ungulates: Gazella dorcas and Ammotragus lervia (Bovidae; Artiodactyla)

During the last century, North African ungulate species have suffered from habitat loss and over‐hunting. Gazella dorcas (Antilopidae subfamily) and Ammotragus lervia (Caprinae subfamily) are among the ungulates that have suffered most. To help to protect these species, conservation programs and population genetics studies are being implemented. Here, we tested 30 published microsatellite primer‐pairs from Bovids (cattle, sheep and goat) on eight individuals from each species. From the 30 loci tested, 20 amplified well and showed moderate allelic richness (3.75 and 4.65 mean number of alleles per species, respectively, for G. dorcas and A. lervia), and moderatly high heterozygosity (0.53 and 0.63 per species, respectively). These 20 polymorphic markers will facilitate conservation and genetic studies in these two species, and promise to be widely useful across divergent ungulate taxa.     

Analysis of gut microbiota in three species belonging to different genera (Hemitragus,Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance

This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3–V4 region of the 16S ribosomal RNA gene was analyzed by high‐throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host–microbiome interactions were not significant.