Phylogenetic reconstructions in the genus <Emphasis Type="Italic">Capra</Emphasis> (Bovidae,Artiodactyla) based on the mitochondrial DNA analysis

Mitochondrial genome fragments were examined in all species of the genus Capra (Bovidae, Artiodactyla). Phylogenetic analysis was carried out using 59 cytochrome b gene sequences (392 bp), and 22 sequences of the mtDNA variable fragment (402 bp). In the control region, two unique deletions were revealed. One of the deletions was found only in Capra cylindricornis (17 bp), while another one grouped C. caucasica with C. aegagrus (1 bp). The group of Caucasian wild goats splits into two clades, and furthermore, the sequences of C. caucasica demonstrate remarkable similarity to the sequences of C. aegagrus, while C. cylindricornis seems to have evolved independently for a long period of time. It was demonstrated that C. pyrenaica and C. ibex were extremely close to one another. Capra sibirica formed an outer group relative to the other species, and according to our data, was the most ancient species of the genus. On the contrary, genetic distance separating C. falconeri (the most independent species of the genus related to its morphology) from the other species is small.     

Systematics of the genus Capra inferred from mitochondrial DNA sequence data

Traditional classification in the genus Capra is based mainly on horn morphology. However, previous investigations based on allozyme data are not consistent with this classification. We thus reexamined the evolutionary history of the genus by analyzing mitochondrial DNA (mtDNA) sequence variation. We collected bone samples from museums or dead animals found in the field. Thirty-four individuals were successfully sequenced for a portion of the mtDNA cytochrome b gene and control region (500 bp in total). We obtained a star-like phylogeny supporting a rapid radiation of the genus. In accordance with traditional classification, mtDNA data support the presence of two clades in the Caucasus and the hypothesis of a domestication event in the Fertile Crescent. However, in conflict with morphology, we found that C. aegagrus and C. ibex are polyphyletic species, and we propose a new scenario for Capra immigration into Europe.     

中国部分家养山羊mtDNA D环区遗传多样性与进化

对我国10个家养山羊品种140只个体的mtDNA D-loop区进行测序分析, 测得结果: 整个D-loop区为 1 211~1 213 bp, 共检测到84种单倍型, 171个多态位点。其中核苷酸多样性(Nucleotide diversity, Pi)为: 0.02063 ± 0.00225, 单倍型多样性(Haplotype gene diversity, Hd)为: 0.988 ± 0.003, 平均核苷酸差异数(Average number of nucleotide differences) k为: 24.896。表明我国家养山羊品种遗传多样性丰富。通过构建NJ网络进化树, 得出中国家养山羊主要分为两大支系, 并且其中一支与角骨羊(Capra aegagrus)聚在一起, 而旋角野山羊(Capra fal-coneri)单独聚为一支, 说明角骨羊对中国家养山羊贡献较大。     

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies

The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.     

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.     

Comparison of nucleotide sequences of ribosomal DNA of the mosquito genera Aedes and Ochlerotatus (Diptera: Culicidae: Aedini)

Morphological study allowed identifying 9 species of mosquitoes of the genus Ochlerotatus and 2 species of the genus Aedes. Sequencing of the rDNA region was performed for all these speciemens. The sequences of rDNA were the following: A. cinereus -868 bp, A. vexans--889 bp, Och. cantans--803 bp, O. excrucians--801 bp, O. euedes--794 bp, Och. cyprius--777 bp, O. diantaeus--758 bp, O. intrudens--817 bp, Och. punctor--783 bp, O. dorsalis--748 bp, O. species--767 bp. On average, the size of Aedes rDNA fragments exceeds rDNA of Ochlerotatus by 90-100 bp. The sequences are characterized by a high number of insertions and deletions, and also by point substitutions of nucleotides. It is important to notice that interspecific differences include not only different regions of the internal transcribed spacers, but also the conservative site which is represented by the 5.8S gene. Among four substitutions in this gene, one (C/A) represents the difference between Aedes and Ochlerotatus, the next (T/A) distinguishes A. cinereus from Ochlerotatus speciment and A. vexans, and two substitutions (A/C, T/G) testify the similarity between O. dorsalis and O. species and specimens of Aedes. Besides, two more deletions are typical for O. dorsalis and O. species. One deletion is com- mon, it distinguishes them from the other examined species, and another one is typical only for O. dorsalis. When analyzing morphological characteristics and comparing nucleotide rDNA sequences of O. species with the database, the similarity to O. caspius has been revealed. On the whole, phylogenetic relationships among Ochlerotatus species correspond to subdivision into groups based on morphological characters. Probably, examination of the larger number of specimens will change the morphological division into groups.     

用ITS序列研究杨属各组之间的系统发育关系

杨树是重要的工业用材树种。我国杨树遗传资源丰富 ,分布范围广泛 ,不少种为我国特有。开展杨属系统发育和分子进化研究 ,对丰富的杨树遗传资源保存和利用有着重大意义。杨属 (Ｐｏｐｕｌｕｓ)全世界约 10 0余种 ,属下通常分 5个组[1] 。胡志昂等[2 ] 对杨属不同组间的过氧化物酶同工酶进行了研究 ;李宽钰等[3] 利用ＲＡＰＤ标记技术对白杨组、青杨组、黑杨组 2 0个种作了遗传分析。但是在杨属系统分类上还存在着许多混乱 ,同物异名、同名异物现象相当普遍。本文以杨属 5个派主要代表种为材料 ,用ＰＣＲ产物直接测序法测定杨树ＩＴＳ序列 ,…     

用ITS序列研究杨属各组之间的系统发育关系

ITS sequences of 15 representative species of five sections inthe genus Populus L. were determined. By using direct sequencing of PCR product, it was found that the fragments of internal transcribed spacers (ITS) are about 594 bp in length. The length of ITS-1 and ITS-2 is about 220 bp and 210 bp, respectively, while that of 5.8s is 164 bp. Its G+C content is about 69.0%. The number of phylogenetically informative loci is higher in ITS-2 than in ITS-1. Transversion and transition are two main factors that drive the ITS evolution, and more insertions and deletions occurred in ITS-2. Taking Salix matsudana Koidz. and Salix suchowensis Cheng as outgroups, phylogenetic analysis of ITS sequences using PAUP 4.0 software indicated that Populus is monophyletic group and can be divided into two main clades. One is the section Leuce, and the other is the remaining sections.     

Phylogenetic Relationship ofPopulusSections by ITS Sequence Analysis

ITS sequences of 15 representative species of five sections in the genus Populus L. were determined. By using direct sequencing of PCR product, it was found that the fragments of internal transcribed spacers (ITS) are about 594 bp in length. The length of ITS-1 and ITS-2 is about 220 bp and 210 bp, respectively, while that of 5.8s is 164 bp. Its G+C content is about 69.0%. The number of phylogenetically informative loci is higher in ITS-2 than in ITS-1. Transversion and transition are two main factors that drive the ITS evolution, and more insertions and deletions occurred in ITS-2. Taking Salix matsudana Koidz. and Salix suchowensis Cheng as outgroups, phylogenetic analysis of ITS sequences using PAUP 4.0 software indicated that Populus is monophyletic group and can be divided into two main clades. One is the section Leuce , and the other is the remaining sections.     

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。     

Mitochondrial DNA diversity of Pakistani goats

Pakistan contains numerous domestic goat breeds, but until now there has been no comprehensive study on genetic diversity or a phylogenetic analysis of Pakistani goats. In this study, we analysed the complete mitochondrial DNA D-loop and the cytochrome b gene of 13 Pakistani domestic goat breeds (Capra hircus) and one wild goat, the Sindh Ibex (Capra aegagrus blythi). The phylogenetic analyses and sequence divergence (SD) established four distinct mt-lineages termed as A, B and C (previously reported) and a new lineage D. The Sindh Ibex appeared as an outgroup of domestic goats. The estimated divergence times between the most recently evolved mt-lineages A and D were from 260,483 to 371,052 YA. This suggested that at least four different strains of wild Capra might have been the source of the modern domestic goats. The new mt-lineage D revealed high SD from mt-lineage A and may be the oldest branch under domestication, while mt-lineages B and C showed lower SD and might have been domesticated during an advanced stage of the domestication process.     

A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices

The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.     

Molecular Phylogeny of Nicotiana (Solanaceae) Based on the Nucleotide Sequence of the matK Gene

Abstract: Intrageneric relationships in the genus Nicotiana were investigated by comparison of DNA sequences of the matK gene of the chloroplast genome. A total of 40 taxa were examined in this study, representing 39 of the approximately 70 wild species of this genus. We obtained the full sequences of the 1530 bp matK ORFs; no variations in length due to insertions or deletions were found. The phylogenetic trees obtained from maximum parsimony (MP) and neighbour-joining (NJ) methods were fundamentally consistent. The genus Nicotiana formed a clade in these trees. The traditional classification of this genus was mostly in agreement with the molecular phylogeny. However, all three subgenera and some sections did not form a monophyletic group. Character-state mappings were used to infer a centre of origin, biogeographic history, and transition of chromosome number. The results support the previous hypothesis that this genus originated in South America and subsequently spread to other continents. The suggestion that the ancestral basic chromosome number is x = 12 and that polyploidy and aneuploidy have occurred independently several times during the evolution of Nicotiana species is also discussed.     

Genetic Variations of 13 Indigenous Chinese Goat Breeds Based on Cytochrome b Gene Sequences

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F _st=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.     

Bezoar (Capra aegagrus) Is a Matriarchal Candidate for Ancestor of Domestic Goat (Capra hircus): Evidence from the Mitochondrial DNA Diversity

The leading hypothesis on the ancestor of domestic goats (Capra hircus) is that it is the wild goat called the bezoar or pasang (Capra aegagrus). To verify this hypothesis, we sequenced and compared the cytochrome b gene of mitochondrial DNA from six domestic goats and a bezoar. A further sequence for the markhor was taken from the database. In total we detected 51 nucleotide substitutions among the domestic goats, bezoar and markhor. However, only one specific nucleotide substitution was found between the domestic goats and the bezoar. On the other hand, 43 nucleotide substitutions were specific for the markhor. This result suggested a close relationship between the domestic goats and the bezoar. A neighbor-joining and parsimony phylogenetic tree constructed using the sequences showed that the domestic goats and the bezoar belong to the same cluster, while the markhor showed a distinct cluster separate from that of the domestic/bezoar cluster. This result was confirmed by trees based on the sequence of the mitochondrial displacement loop regions. These results suggest that the strongest candidate for a matriarchal ancestor of domestic goats is the bezoar.     

Toward the phylogeny of Caucasian rock lizards: implications from mitochondrial DNA gene sequences (Reptilia: Lacertidae)

A maximum parsimony phylogeny of 14 Caucasian species of rock lizards, genus Ijicerta , subgenus Archaeolacerta , was constructed from mitochondrial cytochrome b and ATPase 6 partial gene sequences. Congruence analyses were carried out between the two genes. A synthesis of the data sets reveals three well supported monophyletic groups: (1) the caucasica group including ( Lacerta derjugini (( Lalpina, L. clarkorum ) ( L. caucasica, L. daghestanica ))); (2) the rudis group including ( L. parvula ( L. portschinskii ( L. vakntini, L. rudis ))); and (3) the saxicola group including ( L. mixta ( L. nairensis ( L. saxicola, L. raddeijj ). Despite the diagnosis of three groups, the placement of L. praticola as a basal taxon is uncertain, as are the relationships among the three groups. The mitochondrial DNA sequence data suggested prior hybridization between L. mixta and L. alpina and possibly between L. saxicola and L. nairensis. Lacerta raddei was resolved as a paraphyletic species on the mtDNA tree; this may result from either hybridization or random gene sorting.     

The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

On the origin of Darwin's finches

Darwin's finches comprise a group of 15 species endemic to the Galápagos (14 species) and Cocos (1 species) Islands in the Pacific Ocean. The group is monophyletic and originated from an ancestral species that reached the Galápagos Archipelago from Central or South America. Descendants of this ancestor on the Archipelago then colonized Cocos Island. In the present study, we used sequences of two mitochondrial (mt) DNA segments (922 bp of the cytochrome b gene and 1,082 bp of the control region), as well as two nuclear markers (830 bp of numt2, consisting of 140 bp of mtDNA control region and 690 bp of flanking nuclear DNA; and 740 bp of numt3, consisting of 420 bp of mt cytochrome b sequence flanked by 320 bp of nuclear DNA) to identify the species group most closely related to the Darwin's finches. To this end, we analyzed the sequences of 28 species representing the main groups (tribes) of the family Fringillidae, as well as 2 outgroup species and 13 species of Darwin's finches. In addition, we used mtDNA cytochrome b sequences of some 180 additional Fringillidae species from the database for phylogeny reconstruction by maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods. The study identifies the grassquit genus Tiaris, and specifically the species Tiaris obscura, as the nearest living relative of Darwin's finches among the species surveyed. Darwin's finches diverged from the Tiaris group shortly after the various extant species of Tiaris diverged from one another. The initial adaptive radiation of the Tiaris group apparently occurred on the Caribbean islands and then spread to Central and South America, from where the ancestors of Darwin's finches departed for the Galápagos Islands approximately 2.3 MYA, at the time of the dramatic climatic changes associated with the closure of the Panamanian isthmus and the onset of Pleistocene glaciation.     

Pleistocene effects on the European freshwater fish fauna: double origin of the cobitid genus Sabanejewia in the Danube basin (Osteichthyes: Cobitidae)

Biogeographical hypotheses of European freshwater fishes were inferred using phylogeographic analysis of the complete cytochrome b and ATP synthase 8 and 6 mitochondrial genes (1982bp). To test the relative importance of drainage origin versus Pleistocene glaciations in the origin of primary freshwater fishes in Europe, we reconstructed the phylogenetic relationships of the genus Sabanejewia which is distributed in European waters. The phylogenetic relationships recovered for the genus Sabanejewia (n=75) provide support for the monophyly of six main evolutionary mtDNA lineages: Sabanejewia larvata, Sabanejewia romanica, Sabanejewia aurata/Sabanejewia caucasica, Sabanejewia kubanica, Sabanejewia baltica, and the Danubian-Balkanian complex. The Caucasian-Caspian mtDNA lineages, S. kubanica, S. aurata/S. caucasica, and the Northern European S. baltica represents the sister group of the Danubian-Balkanian complex mtDNAclade, supporting a Caucasian-Northern European origin of most of mtDNA lineages of the Central European freshwater fish fauna. The mtDNA divergence observed between the Danubian Sabanejewia species is too dissimilar to support their contemporary origin. Rather, the mtDNA data suggest that the Danubian Sabanejewia lineages most likely have a double origin, indicating that the European Sabanejewia lineages have experienced different historical processes for the following reasons. First, the origin of the S. larvata and S. romanica mtDNA clades predates the origin of the Danubian-Balkanian complex, and our results showed that the completion of the Alps and the origin of the Danube drainage seem to have promoted the speciation of the earliest Sabanejewia clades in the Miocene. Second, small genetic distances and the geographical pattern found within the Danubian-Balkanian complex clade indicate that the lineages included in this clade spread recently across the Danube and Greek river drainages. The inclusion of the S. balcanica species within all mtDNA lineages suggests that cyclical cold periods during the Pleistocene glaciations have favoured its rapid expansion and genetic homogenisation across Central European and Greek waters.     

MONOPHYLY OF THE GENUS CLOSTERIUM AND THE ORDER DESMIDIALES (CHAROPHYCEAE, CHLOROPHYTA) INFERRED FROM NUCLEAR SMALL SUBUNIT rDNA DATA

We newly sequenced the nuclear-encoded small subunit (SSU) rDNA coding region for 21 taxa of the genus Closterium. The new sequences were integrated into an alignment with 13 known sequences of conjugating green algae representing six traditional families (i.e. Zygnemataceae, Mesotaeniaceae, Gonatozygaceae, Peniaceae, Closteriaceae, and Desmidiaceae) and five known charophycean sequences as outgroups. Both maximum likelihood and maximum parsimony analyses supported with high bootstrap values one large clade containing all placoderm desmids (Desmidiales). All the Closterium taxa formed one clade with 100% bootstrap support, indicating their monophyly, but not paraphyly, as suggested earlier. As to the taxa within the genus Closterium , we found two clades of morphologically closely related taxa in both maximum likelihood and maximum parsimony trees. They corresponded to the C. calosporum species complex and the C. moniliferum-ehrenbergii species complex. It is of particular interest that the homothallic entity of C. moniliferum v. moniliferum was distinguished from and ancestral to all other entities of the C. moniliferum-ehrenbergii species complex. Superimposing all 50 charophycean sequences on the higher order SSU rRNA structure model of Closterium , we investigated degrees of nucleotide conservation at a given position in the nucleotide sequence. A characteristic "signature" structure to the genus Closterium was found as an additional helix at the tip of V1 region. In addition, eight base deletions at the tip of helix 10 were found to be characteristic of the C. calosporum species complex, C. gracile , C. incurvum , C. pleurodermatum , and C. pusillum v. maius. These taxa formed one clade with an 82% bootstrap value in maximum parsimony analysis.