Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus

Myotragus balearicus was a dwarf artiodactyl endemic to the Eastern Balearic Islands, where it evolved in isolation for more than 5 million years before becoming extinct between 3640 and 2135 cal BC (calibrated years BC). Numerous unusual apomorphies obscure the relationship between Myotragus and the extant Caprinae. Therefore, genetic data for this species would significantly contribute to the clarification of its taxonomic position. In this study, we amplify, sequence, and clone a 338-base pair (bp) segment of the mitochondrial cytochrome b (cyt b) gene from a >9Kyr Myotragus subfossil from la Cova des Gorgs (Mallorca). Our results confirm the phylogenetic affinity of Myotragus with the sheep (Ovis) and the takin (Budorcas). In each tree, the Myotragus branch is long in comparison with the other taxa, which may be evidence of a local change in the rate of evolution in cyt b. This rate change may be due to in part to an early age of first reproduction and short generation time in Myotragus, factors that are potentially related to the extreme reduction in size of the adult Myotragus as compared to the other Caprinae.     

Nucleotide sequence of the jaagsiekte retrovirus, an exogenous and endogenous type D and B retrovirus of sheep and goats.

The complete genome of the jaagsiekte sheep retrovirus (JSRV), the suspected etiological agent of ovine pulmonary carcinoma, has been cloned from viral particles secreted in lung exudates of affected animals and sequenced. The genome is 7,462 nucleotides long and exhibits a genetic organization characteristic of the type B and D oncoviruses. Comparison of the amino acid sequences of JSRV proteins with those of other retrovirus proteins and phylogenetic studies suggest that JSRV diverged from its type B and D lineage after the type B mouse mammary tumor virus but before the type D oncoviruses captured the env gene of a reticuloendotheliosislike virus. Southern blot studies show that closely related sequences are present in sheep and goat normal genomic DNA, indicating that JSRV could be endogenous in ovine and caprine species.     

Analysis of conserved microsatellite sequences suggests closer relationship between water buffalo Bubalus bubalis and sheep Ovis aries.

The distribution and evolutionary pattern of the conserved microsatellite repeat sequences (CA)n, (TGG)6, and (GGAT)4 were studied to determine the divergence time and phylogenetic position of the water buffalo, Bubalus bubalis. The mean allelic frequencies of these repeat loci showed a high level of heterozygosity among the euartiodactyls (buffalo, cattle, sheep, and goat). Genetic distances calculated from the allelic frequencies of these microsatellites were used to position Bubalus bubalis in the phylogenetic tree. The tree topology revealed a closer proximity of the Bubalus bubalis to the Ovis aries (sheep) genome than to other domestic species. The estimated time of divergence of the water buffalo genome relative to cattle, goat, sheep, pig, rabbit, and horse was found to be 21, 0.5, 0.7, 94, 20.3, and 408 million years (Myr), respectively. Although water buffaloes share morphological and biochemical similarities with cattle, our study using the microsatellite sequences places the bubaline species in an entirely new phylogenetic position. Our results also suggest that with respect to these repeat loci, the water buffalo genome shares a common ancestry with sheep and goat after the divergence of subfamily Bovinae (Bos taurus) from the family Bovidae.     

Mapping of mitochondrial DNA of individual sheep and goats: Rapid evolution in the D loop region

Mitochondrial DNA (mtDNA) from sheep and goat was compared by restriction endonuclease analysis and heteroduplex mapping in the electron microscope. The fragment patterns produced by endonuclease Hae III from three individual sheep and two goat mtDNAs all differed from each other. The three sheep mtDNAs had identical Eco RI and Hind III fragments, but the two goat mtDNA patterns differed from each other as well as from sheep mtDNA. We estimate that each sheep mtDNA differs from each other by 0.5–1% of its nucleotide sequences, the two goat mtDNAs by 1–2%, and there is a 6–11% sequence difference between sheep and goat mtDNAs. We have mapped the Eco RI and Hind III sites of goat and sheep mtDNA and determined the positions of the D loop, which marks the replication origin, relative to the restriction map. The D loops are at homologous positions on the mtDNAs from both species, but the goat D loop is only 75% as long as the sheep D loop. Regions with a high degree of sequence divergence occur at both ends of the D loop. We suggest that a duplication of about 150 base pairs has occurred in the region where the sheep and goat D loops differ in length. We discuss mtDNA evolution in terms of divergence of isolated “mitochondrial DNA clones.”     

Recombinant bovine interferon alpha causes only a temporary prolongation of the lifespan of the corpus luteum

Abstract

A method is described for developing a sheep‐ vs. goat‐specific DNA marker using sequence characterized amplified regions (SCARs) derived from a random amplified polymorphic DNA (RAPD) marker from sheep DNA samples. A sheep 645 bp DNA fragment that was absent in goat DNA was identified by analyzing pools of sheep and goat DNA with RAPD primers. This fragment was cloned and partially sequenced to design extended, strand‐specific 24‐mer oligonucleotide primers. Each primer contained the original 10 bases of the RAPD primer and the following 14 internal bases. The pair of primers resulted in the amplification of a single band of 645 bp when used to amplify sheep DNA, and in no amplification when used to amplify goat DNA. These SCAR primers successfully amplified the equivalent of DNA from one nucleated sheep cell in a sample of 5000 nucleated goat cells. This level of sensitivity is especially desirable for research involving the detection of interspecific chimerism.     

Sequence of specific mitochondrial 16S rRNA gene fragment from Egyptian buffalo is used as a pattern for discrimination between river buffaloes,cattle, sheep and goats

Characterization of molecular markers and the development of better assays for precise and rapid detection of domestic species are always in demand. This is particularly due to recent food scares and the crisis of biodiversity resulting from the huge ongoing illegal traffic of endangered species. The aim of this study was to develop a new and easy method for domestic species identification (river buffalo, cattle, sheep and goat) based on the analysis of a specific mitochondrial nucleotide sequence. For this reason, a specific fragment of Egyptian buffalo mitochondrial 16S rRNA gene (422 bp) was amplified by PCR using two universal primers. The sequence of this specific fragment is completely conserved between all tested Egyptian buffaloes and other river buffaloes in different places in the world. Also, the lengths of the homologous fragments were less by one nucleotide (421 bp) in case of goats and two nucleotides (420 bp) in case of both cattle and sheep. The detection of specific variable sites between investigated species within this fragment was sufficient to identify the biological origin of the samples. This was achieved by alignment between the unknown homologous sequence and the reference sequences deposited in GenBank database (accession numbers, FJ748599–FJ748607). Considering multiple alignment results between 16S rRNA homologous sequences obtained from GenBank database with the reference sequence, it was shown that definite nucleotides are specific for each of the four studied species of the family Bovidae. In addition, other nucleotides are detected which can allow discrimination between two groups of animals belonging to two subfamilies of family Bovidae, Group one (closely related species like cattle and buffalo, Subfamily Bovinae) and Group two (closely related species like sheep and goat, Subfamily Caprinae). This 16S DNA barcode character-based approach could be used to complement cytochrome c oxidase I (COI) in DNA barcoding. Also, it is a good tool for identification of unknown sample belonging to one of the four domestic animal species of family Bovidae quickly and easily.     

A comparative study of G+C-rich satellite components of sheep and goat DNA.

Restriction fragment patterns of G+C-rich satellites of sheep and goat DNA were compared. The 1,712 g/cm3 satellites of both species appear homologous, consisting of repeats 760 base pairs long and showing coincidence of position of primary+ EcoRI, BamHI and most BspRI restriction target sites. The EcoRI and BamHI endonucleases produce mostly monomers of the repeating unit, while oligomers prevail in the A1uI and Bg1II digests. Species-specific differences in the frequency, position and mode of distribution of secondary+ restriction target sites for EcoRI, Bg1II and A1uI were observed. Unlike the 1,712 g/cm3 satellites, the 1,723 g/cm3 component of sheep DNA and the 1,719 g/cm3 material from goat DNA appear species--specific, since no homologous material could ever be detected in the DNA of the other species.     

Molecular phylogeny of Megaloceros giganteus--the giant deer or just a giant red deer?

Two fragments of mitochondrial DNA (mtDNA) of the cytochrome b gene (137 bp and 167 bp) were successfully isolated and sequenced from antlers and bones of five specimens of the Giant Deer (Megaloceros giganteus) to examine the phylogenetic position of Megaloceros giganteus within the family Cervidae. This is the first report on ancient DNA (aDNA) sequences from Megaloceros giganteus. A phylogenetic analysis based on parameter-rich models describes the evolutionary relationships between five individuals of fossil Megaloceros giganteus and 37 individuals of 11 extant species of the family Cervidae. The results support a "Cervus-Megaloceros" clade. The phylogenetic positions of sympatric Megaloceros and Cervus elaphus specimens in particular indicate either that the Megaloceros mtDNA gene pool did not evolve for a substantial time period as an entity distinct from Cervus elaphus until its extinction, or that Megaloceros contributed mtDNA to Cervus elaphus or vice versa. The results of this study allow the conclusion that the European Megaloceros giganteus is more related to its modern regional counterparts of the species of Cervus elaphus than recent claims have suggested.     

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。     

Phylogenetic relationships of the sea eagles (genus Haliaeetus): reconstructions based on morphology, allozymes and mitochondrial DNA sequences

The relationships of eight extant species of sea eagles (genus Haliaeetus ) and some potentially related Accipitrid genera were investigated. A phylogenetic hypothesis is developed based on morphological characters and allozyme data, which is then contrasted with a reconstruction based on 1071 nucleotides of mitochondrial DNA (cytochrome b and part of one tRNA gene). Phylogenies derived from the three data sets are largely congruent, although several aspects are supported by only one kind of evidence (but not contradicted by the others). Only with regard to the position of south-east Asian H. leucogaster and its closely related sister species H. sanfordi was there conflict between allozyme and mtDNA data. The position of H. pelagicus relative to H. leucoryphus or H. albicilla/leucocephalus could not be resolved with the mtDNA sequence data, suggesting that some speciation events occurred in relatively quick succession during the early Pliocene or late Miocene periods. Available evidence suggests that extant sea eagles originated at tropical latitudes, the northernmost species appearing most derived.     

Combining genetic and ecological data to assess the conservation status of the endangered Ethiopian walia ibex

Knowledge about the phylogenetic history, genetic variation and ecological requirements of a species is important for its conservation and management. Unfortunately, for many species this information is lacking. Here we use multiple approaches (phylogenetics, population genetics and ecological modelling) to evaluate the evolutionary history and conservation status of Capra walie , an endangered flagship species of wild goat endemic to Ethiopia. The analysis of mitochondrial cytochrome b and Y-chromosome DNA sequences suggests that C. walie forms a monophyletic clade with Capra nubiana , but potentially has been isolated for up to 0.8 million years from this closely related species. Microsatellite DNA analyses show that C. walie has very low genetic variation (mean heterozygosity=0.35) compared with other endangered mammals. This reduced variation likely derives from a prolonged demographic decline and small effective population size. Ecological niche modelling using the bioclimatic features of habitats occupied by C. walie , suggests ecological differences between C. walie and C. nubiana , and identifies the areas most suitable for future reintroductions of C. walie . The genetic and bioclimatic data suggest that C. walie is distinct and requires immediate conservation actions including genetic monitoring and reintroductions to establish independent populations. This study illustrates how combining noninvasive sampling along with genetic and ecological (bioclimatic) approaches can help assess conservation status of poorly known species.     

A Cladistic Analysis of Mitochondrial Ribosomal DNA from the Bovidae

There is a huge data base of genetic information for the domestic artiodactyl speciesBos taurus(cow),Ovis aries(sheep), andCapra hircus(goat). However, the phylogenetic relationships of these economically critical taxa and their close relatives, family Bovidae, remain for the most part unresolved. In this report, we aligned new mitochondrial (mt) 12S and 16S ribosomal (r) DNA sequences from 26 bovid taxa with published sequences. Phylogenetic analyses of the more than 64 kilobases of mt rDNA from 57 taxa support a basal division in the Bovidae that separatesBosand its close relatives fromCapra, Ovis,and their kin. As suggested by previous molecular and morphological studies, “antelopes” are a paraphyletic assemblage. Caprinae (sheep, goats, goat antelopes, and musk oxen) groups consistently with hippotragine and alcelaphine antelopes, while Bovini (cattle and buffaloes) clusters with tragelaphine and boselaphine antelopes. The traditional tribal subdivisions of Bovidae are supported in most cases, but there are exceptions within Caprinae and Antilopinae (gazelles and close relatives). The rDNA data consistently place the enigmatic generaPelea, Pantholops,andSaiga,but the origin ofAepyceros,the impala, remains obscure. Combined phylogenetic analyses of the rDNA data with the skeletal characters of Gentry (1992) were used to assess the stability of the molecular results.     

EVOLUTIONARY ORIGIN OF A PARTHENOFORM,THE AMAZON MOLLY POECILIA FORMOSA,ON THE BASIS OF A MOLECULAR GENEALOGY

The appearance of vertebrate species that reproduce without genetic recombination has been explained by their origin from a rare hybridization event between members of two distantly related species. For the first recognized vertebrate unisexual, the Amazon molly Poecilia formosa, mostly morphological and biochemical genetic information has been available so far with respect to its evolutionary origin. DNA sequence analyses of transcribed portions of the genome (tyrosine kinase proto-oncogenes) demonstrated its hybrid state unequivocally. Both alleles can be traced in a DNA sequence-based phylogenetic tree to extant species that represent the parental species or that are closely related to the corresponding extinct forms, namely P. mexicana limantouri and a so far taxonomically ill-defined north Mexican subspecies of the P. latipinna/P. velifera complex. A rough estimate from the mutation rates dates the hybridization event further back than would have been predicted on the basis of “Muller's ratchet” for an ecologically successful species.     

Five ovine mitochondrial lineages identified from sheep breeds of the near East

Archaeozoological evidence indicates that sheep were first domesticated in the Fertile Crescent. To search for DNA sequence diversity arising from previously undetected domestication events, this survey examined nine breeds of sheep from modern-day Turkey and Israel. A total of 2027 bp of mitochondrial DNA (mtDNA) sequence from 197 sheep revealed a total of 85 haplotypes and a high level of genetic diversity. Six individuals carried three haplotypes, which clustered separately from the known ovine mtDNA lineages A, B, and C. Analysis of genetic distance, mismatch distribution, and comparisons with wild sheep confirmed that these represent two additional mtDNA lineages denoted D and E. The two haplogroup E sequences were found to link the previously identified groups A and C. The single haplogroup D sequence branched with the eastern mouflon (Ovis orientalis), urial (O. vignei), and argali (O. ammon) sheep. High sequence diversity (K = 1.86%, haplogroup D and O. orientalis) indicates that the wild progenitor of this domestic lineage remains unresolved. The identification in this study of evidence for additional domestication events adds to the emerging view that sheep were recruited from wild populations multiple times in the same way as for other livestock species such as goat, cattle, and pig.     

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.     

Amelogenin cross-amplification in the family Bovidae and its application for sex determination

Sex-specific sequence variability of the amelogenin gene had been observed in a variety of mammalian species. In our study, the suitability of the amelogenin gene for sex determination in different species of the family Bovidae was examined. Based on a sequence insertion/deletion characteristic for X- and Y-specific amelogenin (AMELX and AMELY), PCR amplification on male and female genomic DNA from domestic and wild bovine species, sheep and goat, consistently displayed a sex-specific pattern. Thus, the amelogenin amplification by PCR proved to be a reliable method for sex determination not only in domestic and wild species of the tribe Bovini, but also in the related species sheep and goat. Sex determination using the amelogenin-based assay can be performed with at least 40 pg of genomic DNA. The assay enables the investigation of small amounts of DNA from meat, hair, bones, and embryo biopsies to identify species and sex for a number of applications in animal production, forensics, population research, and monitoring within the family Bovidae. Sequence comparison of the amplified amelogenin gene region specific for male and female animals from domestic and wild bovide species revealed further sequence variations within and between sexes as well as between species. Sequence variations in the AMELX gene can be applied to discriminate Bos and Bison individuals from other bovine species, and also from sheep and goat.     

藏绵羊GHR基因5′侧翼区序列特征分析

对欧拉型藏绵羊生长激素受体(GHR)基因5′侧翼区(包括P1启动子和外显子1A)进行了T-A克隆和序列测定(GenBank accession No. EF116490), 在分析其序列结构特征的基础上与GenBank中摩弗伦羊、山羊、普通牛、欧洲野牛进行了比较基因组学和系统进化研究, 结果表明: (1)欧拉型藏绵羊GHR基因启动子P1区存在C/EBP、C/EBPb、SP1、Cap、USF、HFH-2、HNF-3b、Oct-1等多个潜在的转录因子结合位点, 可能与GHR基因的转录调控和起始以及特异表达有关。在该非编码序列中, 重复序列所占比率为2.55%, 不存在SINEs、LINEs、LTR类反转录元件和DNA转座子元件, 而发现存在一(TG)11微卫星位点; (2)在启动子P1区, 藏绵羊与摩弗伦羊、山羊、普通牛、欧洲野牛各物种间同源性大小分别为99.7%、94.2%、85.9%、86.5%; 而在外显子1A区段, 藏绵羊与摩弗伦羊、山羊、普通牛、欧洲野牛各物种间同源性大小分别为 99.0%、97.0%、92.7%、94.6%。物种间欧拉型藏绵羊与摩弗伦羊同源性最高, 而欧拉型藏绵羊与普通牛最低。(3)邻接法(即NJ法)构建的分子系统进化树聚类结果表明, 欧拉型藏绵羊与摩弗伦羊先聚为一类, 再与山羊聚类形成一个大分支, 而普通牛和欧洲野牛先聚类形成另一大分支, 两大分支最后再聚为一起, 其聚类结果与线粒体DNA和动物学分类的研究结果一致。     

Evolution of RAG-1 in polyploid clawed frogs

Possible genetic fates of a gene duplicate are silencing, redundancy, subfunctionalization, or novel function. These different fates can be realized at the DNA, RNA, or protein level, and their genetic determinants are poorly understood. We explored molecular evolution of duplicated RAG-1 genes in African clawed frogs (Xenopus and Silurana) (1) to examine the fate of paralogs of this gene at the DNA level in terms of recombination, positive selection, and gene degeneration and in the absence of extensive recombination among alleles at different paralogs, (2) to test phylogenetic hypotheses about the origins of polyploid species. We found that recombination between different RAG-1 paralogs is infrequent, that degeneration of some paralogs has occurred via stop codons and frameshift mutations, and that this degeneration occurred in paralogs inherited from only one diploid progenitor species. Simulations and phylogenetic analyses of RAG-1 and mitochondrial DNA support one origin of extant tetraploids in Xenopus and at least one origin in Silurana, five allopolyploid origins of extant octoploids, and two allopolyploid origins of extant dodecaploids. In allopolyploid species, which inherit a complete genome from two different ancestors, genes inherited from the same ancestor have a longer period of coevolution than genes inherited from different ancestors. Because of this, gene ancestry could potentially influence gene fate: interacting paralogs derived from the same lower ploidy ancestor might have similar genetic destinies.     

Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene

Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T. granosa to distinguish it from other related species found in other parts of the world and to create a DNA database for the species. An approximately 585-nucleotide fragment of the mitochondrial DNA (cytochrome oxidase I, COI) was sequenced for 150 individual cockles, representing 10 populations: three from the north, four from the central part and three from the southern part of peninsular Malaysia. Phylogenetic analyses of the resulting dataset yielded tree topologies that not only showed the relationship between T. granosa and its closest relatives but its position in the evolutionary tree. Three mitochondrial clades were evident, each containing an individual genus. Using the mutation rate of the COI gene, the divergence time between T. granosa and its closest related species was estimated to be 460 thousand years ago. This study provides a phylogenetic framework for this ecologically prominent and commercially important cockle species.     

Out of Africa? Phylogenetic relationships between Falco biarmicus and the other hierofalcons (Aves: Falconidae)

The phylogeographic history of the lanner falcon ( Falco biarmicus ) and the phylogenetic relationships among hierofalcons ( F. biarmicus , Falco cherrug , Falco jugger and Falco rusticolus ) were investigated using mitochondrial (mt) DNA sequences. Of the two non-coding mt sections tested, the control region (CR) appeared more suitable as phylogenetic marker sequence compared with the pseudo control region (ΨCR). For the comprehensive analysis samples from a broad geographic range representing all four hierofalcon species and their currently recognized subspecies were included. Moreover, samples of Falco mexicanus were analysed to elucidate its phylogenetic relationships to the hierofalcons. The sequence data indicate that this species is more closely related to Falco peregrinus than to the hierofalcons. In the DNA-based trees and in the maximum parsimony network all hierofalcons appear closely related and none of the species represents a monophyletic group. The close relationships among haplotypes suggest that the hierofalcon complex is an assemblage of morphospecies not yet differentiated in the genetic markers used in the present study and that the radiation of the four hierofalcon species took place rather recently. Based on the high intraspecific diversity found within F. biarmicus we assume an African origin of the hierofalcon complex. The observed pattern of haplotype distribution in the extant species may be due to incomplete lineage sorting of ancestral polymorphisms, and interspecific gene flow through hybridization.