Molecular Support for the Placement of Saiga and Procapra in Antilopinae (Artiodactyla, Bovidae)

The evolutionary history of the bovid subfamily Antilopinae is unclear. Traditionally, this subfamily is subdivided into two tribes: Neotragini (dwarf antelopes) and Antilopini (gazelles and their relatives). Here, we report new sequences for the 12S and 16S rRNA genes in the enigmatic antilopine taxa Procapra gutturosa and Saiga tatarica and analyze the phylogenetic relationships of these taxa relative to other antilopines. Our study demonstrates the close affinity of the saiga antelope to Gazella despite the conventional systematic allocation of Saiga to the Caprinae subfamily. The second member of the Saigini tribe, Pantholops hodgsoni (Tibetan gazelle), falls within Caprinae. In all of our analyses, Procapra gutturosa occupied a basal position in the Antilopinae clade or was a sister-group to the dwarf antelope Madoqua. This suggests early separation of Procapra from other antelopes.     

Molecular characteristics of Tibetan antelope (Pantholops hodgsonii) mitochondrial DNA control region and phylogenetic inferences with related species

Although Tibetan antelope (Pantholops hodgsonii) is a distinctive wild species inhabiting the Tibet-Qinghai Plateau, its taxonomic classification within the Bovidae is still unclear and little molecular information has been reported to date. In this study of Tibetan antelope, the complete control regions of mtDNA were sequenced and compared to those of Tibetan sheep (Ovis aries) and goat (Capra hircus). The length of the control region in Tibetan antelope, sheep and goat is 1067, 1181/1106 and 1121 bp, respectively. A 75-bp repeat sequence was found near the 5′ end of the control region of Tibetan antelope and sheep, the repeat numbers of which were two in Tibetan antelope and three or four in sheep. Three major domain regions, including HVI, HVII and central domain, in Tibetan antelope, sheep and goat were outlined, as well as other less conserved blocks, such as CSB-1, CSB-2, ETAS-1 and ETAS-2. NJ cluster analysis of the three species revealed that Tibetan antelope was more closely related to Tibetan sheep than Tibetan goat. These results were further confirmed by phylogenetic analysis using the partial control region sequences of these and 13 other antelope species. Tibetan antelope is better assigned to the Caprinae rather than the Antilopinae subfamily of the Bovidae.     

从细胞色素b 基因全序列分析岩羊和山羊、绵羊的系统发生关系

本文测定了来自四川和青海岩羊的细胞色素b 基因全序列(1 140 bp) , 结合从GenBank 中检索获得的山羊、北山羊、绵羊和盘羊4 个近缘种细胞色素b 核苷酸同源区序列进行比较, 分析了碱基组成和变异情况以及核苷酸序列差异。分别采用简约法和距离矩阵法构建分子系统树, 得到了基本相同的拓扑结构, 从分子水平初步探讨了岩羊的系统起源问题。岩羊与山羊属的山羊、北山羊有着比绵羊属的绵羊、盘羊更近的亲缘关系。岩羊与山羊、北山羊的分歧时间大约在3～6 百万年, 而与盘羊、绵羊的分歧时间大约在6～8 百万年。     

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.     

The melanocyte-stimulating hormone receptor (MC1-R) gene as a tool in evolutionary studies of artiodactyles

The complete coding region of the melanocyte-stimulating hormone receptor (MC1-R) gene was characterized in species belonging to the two families Bovidae and Cervidae; cattle (Bos taurus), sheep (Ovis aries), goat (Capra hircus), muskox (Ovibos moschatus), roe deer (Capreolus capreolus), reindeer (Rangifer tarandus), moose (Alces alces), red deer (Cervus elaphus) and fallow deer (Dama dama). This well conserved gene is a central regulator of mammalian coat colour. Examination of the interspecies variability revealed a 5.3-6.8% divergence between the Cervidae and Bovidae families, whereas the divergence within the families were 1.0-3.1% and 1.2-4.6%, respectively. Complete identity was found when two subspecies of reindeer, Eurasian tundra reindeer (R.t. tarandus) and Svalbard reindeer (R.t. platvrhynehus), were analyzed. An rooted phylogenetic tree based on Bovidae and Cervidae MC1-R DNA sequences was in complete agreement with current taxonomy, and was supported by bootstrapping analysis. Due to different frequencies of silent vs. replacement mutations, the amino acid based phylogenetic tree contains several dissimilarities when compared to the DNA based phylogenetic tree.     

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.     

Evolution and recombination of bovine DNA repeats

The history of the abundant repeat elements in the bovine genome has been studied by comparative hybridization and PCR. The Bov-A and Bov-B SINE elements both emerged just after the divergence of the Camelidae and the true ruminants. A 31-bp subrepeat motif in satellites of the Bovidae species cattle, sheep, and goat is also present in Cervidae (deer) and apparently predates the Bovidae. However, the other components of the bovine satellites were amplified after the divergence of the cattle and the Caprinae (sheep and goat). A 23-bp motif, which as subrepeat of two major satellites occupies 5% of the cattle genome, emerged only after the split of the water buffalo and other cattle species. During the evolution of the Bovidae the satellite repeat units were shaped by recombination events involving subrepeats, other satellite components, and SINE elements. Differences in restriction sites of homologous satellites indicate a continuing rapid horizontal spread of new sequence variants. Correspondence to: J.A. Lenstra     

The sequence and phylogenesis of the α-globin genes of Barbary sheep (Ammotragus lervia), goat (Capra hircus), European mouflon (Ovis aries musimon) and Cyprus mouflon (Ovis aries ophion)

In order to investigate the polymorphism of α-globin chain of hemoglobin amongst caprines, the linked ^Iα and ^IIα globin genes of Barbary sheep (Ammotragus lervia), goat (Capra hircus), European mouflon (Ovis aries musimon), and Cyprus mouflon (Ovis aries ophion) were completely sequenced, including the 5′ and 3′ untranslated regions. European and Cyprus mouflons, which do not show polymorphic α globin chains, had almost identical α globin genes, whereas Barbary sheep exhibit two different chains encoded by two nonallelic genes. Four different α genes were observed and sequenced in goat, validating previous observations of the existence of allelic and nonallelic polymorphism. As in other vertebrates, interchromosomal gene conversion appears to be responsible for such polymorphism. Evaluation of nucleotide sequences at the level of molecular evolution of the ^Iα-globin gene family in the caprine taxa suggests a closer relationship between the genus Ammotragus and Capra. Molecular clock estimates suggest sheep-mouflon, goat-aoudad, and ancestor-caprine divergences of 2.8, 5.7, and 7.1 MYBP, respectively.     

New aspects of an old discussion - phylogenetic relationships of Ammotragus and Pseudois within the subfamily Caprinae based on comparison of the 12S rDNA sequences

A mitochondrial 12S rDNA fragment was amplified by PCR and directly sequenced from eight members of the Caprinae ( Ammotragus lervia, Capra aegagrus, Ovis ammon, O. musimon, O. nivicola, O. orientalis, O. vignei and Pseudois nayaur ). Multiple alignment of the sequences and genetic distance calculation with the'distance of Taijama and Nei and the algorithms of Saitou and Nei (neighbour-joining - NJ) showed that Pseudois is grouped together with Capra and Ammotragus . All members of the genus Oxis formed a second cluster. Phylogenetic analyses supported these results. NJ-analyses and maximum parsimony (MP) trees did not support the present phylogenetic classification. Bootstrap values of 95% (NJ) and 96% (MP) confirms the grouping of P. nayaur and C. aegagrus . Another clade, O. ammon and O. orientalis supported weakly by bootstrap values of 65% (MP) and 70% (NJ) and the clade O. musimonand O. vignei had bootstrap values of 50% (MP) and 60% (NJ). So the phylogenetic relationship within the genus Oxis is still unsafe. But the parsimony analyses lead to the conclusion that Ammotragus represents an old lineage that diverged from ancestral caprines together with true sheep a long time ago and that both true goats and blue sheep forms represent one evolutionary lineage.     

The species and chromosomal distribution of the centromeric alpha-satellite I sequence from sheep in the tribe Caprini and other Bovidae

The evolution of chromosomes in species in the family Bovidae includes fusion and fission of chromosome arms (giving different numbers of acrocentric and metacentric chromosomes with a relatively conserved total number of arms) and evolution in both DNA sequence and copy number of the pericentromeric alpha-satellite I repetitive DNA sequence. Here, a probe representing the sheep alpha-satellite I sequence was isolated and hybridized to genomic DNA digests and metaphase chromosomes from various Bovidae species. The probe was highly homologous to the centromeric sequence in all species in the tribe Caprini, including sheep (Ovis aries), goat (Capra hircus) and the aoudad or Barbary sheep (Amnotragus lervia), but showed no detectable hybridization to the alpha-satellite I sequence present in the tribe Bovini and at most very weak to species in the tribes Hippotragini, Alcelaphini or Aepycerotini. The sex chromosomes of sheep, goat and aoudad did not contain detectable alpha-satellite I sequence; in sheep, one of the three metacentric autosomal chromosomes does not carry the sequence, while in aoudad, it is essentially absent in three large autosomal pairs as well as the large metacentric chromosome pair. The satellite probes can be used as robust chromosome and karyotype markers of evolution among tribes and increase the resolution of the evolutionary tree at the base of the Artiodactyla.     

从细胞色素b基因全序列差异分析岩羊和矮岩羊的系统进化关系

矮岩羊的分类地位从它被发现后就一直存在着争议。本文测定了分别来自四川和青海的岩羊(Pseudois nayaur)和矮岩羊(Pseudois schaeferi)共7个个体的Cyt b基因全序列(1140bp)，结合山羊(Capra hircus)、北山羊(Capra ibex)、绵羊(Ovis aries)和盘羊(Ovis ammon)同源DNA序列进行比较，分析了碱基组成和变异情况以及核苷酸序列差异。用简约法和距离距阵法构建了分子系统树，得到了相同的拓扑结构。结果显示：岩羊和矮岩羊互为单系群，有着较山羊、北山羊、绵羊和盘羊间更近的亲缘关系，它们之间的序列差异(Cyt b＝3．2％)低于牛科不同种间的序列差异水平(8．3％-12．1％)，明显高于种内个体的序列差异，而处于牛科亚种的序列差异范围内。因此，推测矮岩羊与岩羊之间的差异可能已经达到了亚种的水平。它们的分歧时间为l-3百万年[动物学报49(2)：198—204，2003]。     

Comparative aspects of biochemical polymorphism in the blood of Caprinae species and their hybrids

Biochemical variation at 14 blood loci was reviewed, and specific features compared experimentally in sheep Ovis aries, mouflon Ovis musimon, goat Capra hircus, aoudad Ammotragus lervia and in 2 stillborn aoudad × goat hybrids. Variation at 3 loci was also studied in dall sheep Ovis dalli, bighorn sheep Ovis canadensis and rocky mountain goat Oreamnos americanus. Haemoglobin C production in an anaemic Hb AB mouflon and in mouflon × sheep hybrids was examined. Mouflon differ from domestic sheep in that synthesis of both Hb β^AHb β^Bchains is switched off during Hb C production. The mouflon × sheep hybrids switched off one or both chains depending on whether they had inherited sheep or mouflon Hb β chain genes. In general aoudad showed a closer affinity to goats than to sheep.     

Beta‐globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta‐globin haplotypes. Haplotype A is very similar to the goat beta‐globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta‐C globin, which encodes a globin with high oxygen affinity. We surveyed the beta‐globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2–3 million years old. Approximately 40 kb of the sequence flanking the ~37‐kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta‐globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40‐kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40‐kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non‐Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.     

Conservation of nucleolus organizer regions during evolution in sheep, goat, cattle and aoudad.

There are ten nucleolus organizer regions (NORs) in domestic sheep (Ovis aries L.). cattle (Bos taurus L.), goat (Capra hircus L.) and aoudad (Ammotragus lervia Blyth) and these are located terminally on chromosomes with homologous (G-banding patterns. The similarity in number of nucleolus organizer regions in these species may indicate that their ribosomal DNA regions are infrequently involved in exchange events which could lead to different numbers of active nucleolus organizer regions. Other possible explanations of the conservation of number of nucleolus organizer regions in these species are discussed. The homology of NOR location in these species supports the idea that the Bovidae karyotype tends to be fairly stable apart from changes due to centric fusion events.     

Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences

The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho‐species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.     

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.     

Phylogenetic analysis of the non-pathogenic genusSpiromastix (Onygenaceae) and related onygenalean taxa based on large subunit ribosomal DNA sequences

The phylogenetic positioning of the non-pathogenic genusSpiromastix in the Onygenales was studied based on large subunit rDNA (LSU rDNA) partial sequences (ca. 570 bp.). FourSpiromastix species and 28 representative taxa of the Onygenales were newly sequenced. Phylogenetic trees were constructed by the neighbor-joining (NJ) method and evaluated by the maximum parsimony (MP) method with the data of 13 taxa retrieved from DNA databases.Spiromastix and dimorphic systemic pathogens,Ajellomyces andParacoccidioides, appear to be a monophyletic group with 74% bootstrap probability (BP) in the NJ tree constructed with the representative taxa of the Onygenales. The tree topology was concordant with the NJ tree based on SSU rDNA sequences of our previous work and corresponded to the classification system of the Onygenales by Currah (1985) and its minor modification by Udagawa (1997) with the exception of the classification of the Onygenaceae. The Onygeneceae sensu Udagawa may still be polyphyletic, since three independent lineages were recognized. The taxa forming helicoid peridial appendages were localized to two clades on the tree. The topology of the NJ tree constructed withSpiromastix and its close relatives suggested that the helicoid peridial appendages were apomorphic and acquired independently in the two clades of the Onygenales.     

High-resolution G-banded karyotype and idiogram of the goat: a sheep-goat G-banded comparison

An elongated G-banded karyotype and idiogram of the domestic goat (Capra hircus) is presented. Sheep (Ovis aries)-goat comparison suggests the terminal light band (Xq 2 9) present in the goat is absent in the sheep.     

The Late Neolithic settlement of Latsch, Vinschgau, northern Italy: subsistence of a settlement contemporary with the Alpine Iceman, and located in his valley of origin

Archaeobotanical and archaeozoological analyses conducted on Late Neolithic settlement layers at Latsch provide the first data on the subsistence strategy, diet and environmental conditions in the valley of origin of the Alpine Iceman. The results prove that during the Late Neolithic, the valley was occupied by an agro-pastoral society based on the cultivation of Hordeum vulgare (hulled barley), Triticum monococcum (einkorn), T. dicoccum (emmer) and Pisum sativum (pea), as well as on the rearing of Ovis vel Capra, Ovis orientalis f. aries (sheep), Capra aegagrus f. hircus (goat) and Bos primigenius f. taurus (cattle). The settlement was located on a river terrace of the valley floor close to a river and was surrounded by mixed pine and oak woods beside alluvial woodland.