基于Adhl基因分析高粱属的系统进化关系

高粱属中有重要的粮食作物和优良牧草,也有农业生产上的重要杂草.文章旨在进一步从分子水平阐明高粱属种间的系统进化关系,为有效利用种质资源进行分子育种改良作物品质提供理论依据,并明确检疫性杂草的分类地位.根据二色高粱(Sorghum bicolor)的Adhl全基因序列(GenBank登录号:AF050456)设计引物,扩增并测定黑高粱(S.almum),假高粱(S.halepense)、丝克高粱(S.silk)和苏丹草(S.sudanense)共计8个植物材料约2 000 bp的Adhl基因部分序列,结合GenBank中其他24个Sorghum属的同源序列.以Cleistachne sorghoides的对应序列为外群,进行了高粱属的亲缘关系分析,用MP、ML和NJ法分别构建了分子进化树,得到了基本相同的拓扑结构.结果显示:(1)高粱属可明显分为三大支,一支是蒴柄高粱(Chaetosorghum)和异高粱(Heterosorghum)个亚属,一支是优高粱亚属(Eusorghum),这两个分支包含2n=20、40,染色体较小的种类,另一分支包括拟高粱(Parasorghum)和有柄高粱(Stiposorghum)两个亚属,包含2n=10的种类和它们的多倍体近缘种,染色体相对较大;(2)S.almum的Adhl基因表现出明显的地理分化;(3)Parasorghum亚属的S.pur-pureosericeum和多色高粱(S.versicolor)、光高粱(S.nitidum)和S.leiocladum聚在一起,而该亚属中的S.mata-rankense、S.grande、S.timorense却与亚属Stiposorghum的种聚在一起,表现出更近的亲缘关系;(4)S.mac-rospermum和S.laxiflorum之间具有比其他高粱属种更近的亲缘关系.     

基于Adh1基因分析高粱属的系统进化关系

高梁属中有重要的粮食作物和优良牧草, 也有农业生产上的重要杂草。文章旨在进一步从分子水平阐明高梁属种间的系统进化关系, 为有效利用种质资源进行分子育种改良作物品质提供理论依据, 并明确检疫性杂草的分类地位。根据二色高粱(Sorghum bicolor)的Adh1全基因序列(GenBank登录号: AF050456)设计引物, 扩增并测定黑高粱(S. almum)、假高粱(S. halepense)、丝克高粱(S. silk)和苏丹草(S. sudanense)共计8个植物材料约2 000 bp的Adh1基因部分序列, 结合GenBank中其他24个Sorghum属的同源序列, 以Cleistachne sorghoides的对应序列为外群, 进行了高梁属的亲缘关系分析, 用MP、ML和NJ法分别构建了分子进化树, 得到了基本相同的拓扑结构。结果显示: (1) 高梁属可明显分为三大支, 一支是蒴柄高梁(Chaetosorghum)和异高梁(Heterosorghum)二个亚属, 一支是优高梁亚属(Eusorghum), 这两个分支包含2n=20、40, 染色体较小的种类, 另一分支包括拟高梁 (Parasorghum)和有柄高梁(Stiposorghum)两个亚属, 包含2n=10的种类和它们的多倍体近缘种, 染色体相对较大; (2) S. almum的Adh1基因表现出明显的地理分化; (3) Parasorghum亚属的S. pur-pureosericeum和多色高粱(S. versicolor)、光高粱(S. nitidum)和S. leiocladum聚在一起, 而该亚属中的S. mata-rankense、S. grande、S. timorense却与亚属Stiposorghum的种聚在一起, 表现出更近的亲缘关系; (4) S. mac-rospermum和S. laxiflorum之间具有比其他高梁属种更近的亲缘关系。     

Molecular phylogenetic relationships among species of the Malagasy-Comoran gecko genus Paroedura (Squamata: Gekkonidae)

We use approximately 3100bp of mitochondrial (ND2, ND4) and nuclear (RAG1, phosducin) DNA sequence data to recover phylogenetic relationships among 14 of the 16 recognized taxa of the lizard genus Paroedura as well as two undescribed forms. These geckos are endemic to Madagascar and the Comores and are popularly kept and bred by herpetoculturalists. The closest relative of Paroedura is another Indian Ocean leaf-toed gecko, Ebenavia. Both Bayesian inference and maximum parsimony strongly support the monophyly of two major clades within Paroedura that conflict with existing species group assignments based on scale characteristics. Our well-resolved tree elucidates a biogeographic pattern in which eastern Paroedura are most basal and western and south-western species form a monophyletic group. Our data demonstrate the phylogenetic utility of phosducin, a novel marker in squamate phylogenetics, at the intrageneric level.     

Pollen morphology and phylogenetic relationships in neotropical Phyllanthus (Euphorbiaceae)

In order to provide new insights into phylogenetic relationships among the neotropical taxa of Phyllanthus , 28 illustrations are provided of the pollen grains of 22 selected species studied from 11 sections of the subgenera represented in the neotropics. Special attention has been given to subgenus Conami because of its variability in pollen morphology: of eight species illustrated, the apertures are diploporate colpi in three species and pores in five species; exine ornamentation is vermiculate in two species and pilate in the other six species. The six species in the neotropical sections Pityrocladus and Microglochidion (subgenus Emblica ) are characterized by prolate grains with an increased number of colpi (4–8). Of particular interest are species in which the pollen exine is clypeate (with exine shields); clypeate pollen grains are illustrated in two species of subgenus Xylophylla and in one species of section Cyclanthera that has unique exine shields with single central pila. The pollen of the one Brazilian phylloclade-bearing species illustrated (in section Choretropsis ) has 3-colporate grains with reticulate exine, typical for subgenus Phyllanthus , and very different from the clypeate grains of the West Indian phylloclade-bearing species in section Xylophylla . This pollen evidence clearly demonstrates homoplasy in the origin of phylloclades in Phyllanthus . Pollen morphological data suggest that the neotropical taxa of Phyllanthus have arisen following colonization from Africa (subgenus Kirganelia ) and Asia (subgenus Emblica ). © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 325–338.     

A multigenic perspective on phylogenetic relationships in the largest family of salamanders, the Plethodontidae

Despite several recent studies, the phylogeny of plethodontid salamanders is not yet fully resolved and the phylogenetic positions of several key genera, especially Aneides, Hemidactylium, Hydromantes and Karsenia, are contentious. Here we present a combined dataset of complete mitochondrial genomes and three nuclear loci for 20 species (16 genera) of plethodontids, representing all major clades in the family. The combined dataset without mitochondrial third codon positions provides a fully resolved, statistically well-supported tree. In this topology two major clades are recovered. A northern clade includes Aneides, Desmognathus, Ensatina, Hydromantes, Karsenia, Phaeognathus and Plethodon, with Plethodon being the sister taxon to the rest of the clade. Hydromantes and Karsenia are sister taxa, and Aneides is recovered as the sister taxon to Ensatina. Desmognathus+Phaeognathus form the sister taxon to Aneides+Ensatina. An eastern/southern clade comprises two subclades. One subclade, the spelerpines (Eurycea, Gyrinophilus, Pseudotriton, Stereochilus, Urspelerpes) is the sister taxon to a subclade comprising Hemidactylium, Batrachoseps and the tropical plethodontids (represented by Bolitoglossa, Nototriton and Thorius). In this topology Hemidactylium is well-supported as the sister taxon to Batrachoseps. Only when mitochondrial third codon positions are included using maximum likelihood analysis is Hemidactylium recovered as the sister taxon to Batrachoseps+tropical genera. Hypothesis testing of alternative topologies supports these conclusions. On the basis of these results we propose a conservative taxonomy for Plethodontidae.     

Mitochondrial gene variation and phylogenetic relationships in the genus Beta

Restriction fragment length polymorphisms (RFLPs) for three mitochondrial genes, coxI, coxII and atpA, were used to determine mitochondrial (mt) DNA diversity in 21 accessions of the genus Beta representing wild and cultivated species. On the basis of distribution of the RFLP patterns these Beta genotypes were assigned into six distinct chondriome groups. A high degree of heterogeneity was found to exist between the mitochondrial genomes of the sugarbeet cultivar and the wild species of Procumbentes section. The polymorphic fragments from wild Beta species were cloned and subjected to fine mapping. We found that most of the RFLPs are due to sequence rearrangements rather than point mutations. Our data also suggest that the close linkage between coxII and coxI is taxonomically localized to an evolutionary lineage that led to Vulgares and Corollinae species but not to Procumbentes species. This linkage is most likely to have arisen via the mutation(s) that inserted the DNA segment containing coxI downstream of coxII in the common ancestor of Vulgares and Corollinae species. The results are discussed with regard to the taxonomic and phylogenetic relationships of the Beta species.     

Molecular phylogenetic relationships of the deep-sea fish genus Coryphaenoides (Gadiformes: Macrouridae) based on mitochondrial DNA

In order to characterize the phylogenetic relationship and deep-sea adaptation process of the deep-sea fish genus Coryphaenoides, the nucleotide sequences of the mitochondrial (mt) 12 S rRNA and COI gene sequences for seven Coryphaenoides species were analyzed. Our molecular phylogenetic tree shows a new arrangement of seven Coryphaenoides species, which form two distinct groups, abyssal and nonabyssal species, and differs from the results of previous taxonomic studies. Using the mutation rate of mitochondrial genes, the divergence time between abyssal and nonabyssal Coryphaenoides was found to be 3.2-7.6 million years ago. Our study suggests that hydraulic pressure plays an important role in the speciation process in the marine environment.     

Molecular phylogenetic analysis of the genus Strongyloides and related nematodes

Strongyloides spp., parasitic nematodes of humans and many other terrestrial vertebrates, display an unusual heterogonic lifecycle involving alternating parasitic and free-living adult reproductive stages. A number of other genera have similar lifecycles, but their relationships to Strongyloides have not been clarified. We have inferred a phylogeny of 12 species of Strongyloides, Parastrongyloides, Rhabdias and Rhabditophanes using small subunit ribosomal RNA gene (SSU rDNA) sequences. The lineage leading to Strongyloides appears to have arisen within parasites of terrestrial invertebrates. Inferred lifecycle evolution was particularly dynamic within these nematodes. Importantly, the free-living Rhabditophanes sp. KR3021 is placed within a clade of parasitic taxa, suggesting that this species may represent a reversion to a non-parasitic lifecycle. Species within the genus Strongyloides are very closely related, despite the disparity of host species parasitised. The highly pathogenic human parasite Strongyloides fuelleborni kelleyi is not supported as a subspecies of the primate parasite S. fuelleborni fuelleborni, but is most likely derived from a local zoonotic source.     

Molecular phylogenetic position of Schistosoma sinensium in the genus Schistosoma

The status of Schistosoma sinensium (samples from Thailand and from Sichuan, China) relative to other species of the genus Schistosoma was investigated using DNA sequences from the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene (partial) and the nuclear ribosomal DNA second internal transcribed spacer 2 (ITS2). Trees inferred from these sequences place S. sinensium as sister to the S. japonicum group and suggest a basal position in the clade utilizing snails of the family Pomatiopsidae. The sequence differences between specimens of S. sinensium from China and Thailand are at least as great as between S. malayensis and S. mekongi. Schistosoma sinensium is probably best regarded as a species complex.     

Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data

Phylogenetic relationships among salamander families illustrate analytical challenges inherent to inferring phylogenies in which terminal branches are temporally very long relative to internal branches. We present new mitochondrial DNA sequences, approximately 2,100 base pairs from the genes encoding ND1, ND2, COI, and the intervening tRNA genes for 34 species representing all 10 salamander families, to examine these relationships. Parsimony analysis of these mtDNA sequences supports monophyly of all families except Proteidae, but yields a tree largely unresolved with respect to interfamilial relationships and the phylogenetic positions of the proteid genera Necturus and Proteus. In contrast, Bayesian and maximum-likelihood analyses of the mtDNA data produce a topology concordant with phylogenetic results from nuclear-encoded rRNA sequences, and they statistically reject monophyly of the internally fertilizing salamanders, suborder Salamandroidea. Phylogenetic simulations based on our mitochondrial DNA sequences reveal that Bayesian analyses outperform parsimony in reconstructing short branches located deep in the phylogenetic history of a taxon. However, phylogenetic conflicts between our results and a recent analysis of nuclear RAG-1 gene sequences suggest that statistical rejection of a monophyletic Salamandroidea by Bayesian analyses of our mitochondrial genomic data is probably erroneous. Bayesian and likelihood-based analyses may overestimate phylogenetic precision when estimating short branches located deep in a phylogeny from data showing substitutional saturation; an analysis of nucleotide substitutions indicates that these methods may be overly sensitive to a relatively small number of sites that show substitutions judged uncommon by the favored evolutionary model.     

Novel insights into the phylogenetic relationships of the endangered marsupial genus Potorous

The three extant potoroo species of the marsupial genus Potorous -Potorous tridactylus, P. longipes and P. gilbertii - are all of conservation concern due to introduced predators and habitat loss associated with the European settlement of Australia. Robust phylogenies can be useful to inform conservation management, but past phylogenetic studies on potoroos have been unable to fully resolve relationships within the genus. Here, a multi-locus approach was employed, using three mitochondrial DNA (mtDNA): NADH dehydrogenase subunit 2, cytochrome c oxidase subunit 1 and 12S rRNA and four nuclear DNA (nuDNA) gene regions: breast and ovarian cancer susceptibility gene, recombination activating gene-1, apolipoprotein B and omega globin. This was coupled with widespread geographic sampling of the broadly distributed P. tridactylus, to investigate the phylogenetic relationships within this genus. Analyses of the mtDNA identified five distinct and highly divergent lineages including, P. longipes, P. gilbertii and three distinct lineages within P. tridactylus (northern mainland, southern mainland and Tasmanian). P. tridactylus was paraphyletic with the P. gilbertii lineage, suggesting that cryptic taxa may exist within P. tridactylus. NuDNA sequences lacked the resolution of mtDNA. Although they resolved the three currently recognised species, they were unable to differentiate lineages within P. tridactylus. Current management of P. tridactylus as two sub-species (mainland and Tasmania) does not recognise the full scope of genetic diversity within this species, especially that of the mainland populations. Until data from more informative nuDNA markers are available, we recommend this species be managed as the following three subspecies: Potorous tridactylus tridactylus (southern Queensland and northern New South Wales); Potorous tridactylus trisulcatus (southern New South Wales and Victoria) Potorous tridactylus apicalis (Tasmania). Molecular dating estimated that divergences within Potorous occurred in the late Miocene through to the early Pliocene.     

RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon

Summary Forty single-copy, nuclear probes of known chromosomal position were used to examine restriction fragment length polymorphism in the tomato genus Lycopersion. The probes were from three libraries: one cDNA, and two genomic libraries ne genomic made with EcoRI and the other with PstI. Total DNA from 156 plants representing eight species was cut with five different restriction enzymes and scored in 198 probe-enzyme combinations. Genetic distances between accessions (populations) and species were calculated from the resultant restriction patterns and proportion of shared bands. Accessions belonging to the same species largely clustered together, confirming their current classification. However, one mountain accession, classified as L. peruvianum var. humifusum (LA2150), was sufficiently distinct from the other accessions of L. peruvianum that it may qualify as a separate species L. esculentum and L. pimpinellifolium were the least clearly differentiated, possibly reflecting introgressive hybridization, known to have been promoted by man in recent history. Dendrograms constructed from cDNA versus genomic clones were nearly identical in their general grouping of species. The dendrograms revealed two major dichotomies in the genus: one corresponding to mating behavior [self-compatible (SC) versus self-incompatible (SI) species] and the other corresponding to fruit color (red versus green-fruited species). The ratio of withinversus between-accession diversity was much lower for SC species, indicating that most of the diversity within these species exists between populations, rather than within populations. Overall, the amount of genetic variation in the SI species far exceeded that found in SC species. This result is exemplified by the fact that more genetic variation could be found within a single accession of one of the SI species (e.g., L. peruvianum) than among all accessions tested of any one of the SC species (e.g., L. esculentum or L. pimpinellifolium). Results from this study are discussed in relationship to germ plasm collection/utilization and with regard to the use of RFLPs in tomato breeding and genetics.     

Biochemical identification and phylogenetic relationships in free-living amoebas of the genus Naegleria

Using isoelectric focusing, the zymograms of 23 pathogenic and nonpathogenic Naegleria strains were studied for the activity of 16 enzymes. Certain enzymes (lactate dehydrogenase, L-threonine dehydrogenase, superoxide dismutase, acid phosphatase, malic enzyme, and leucine aminopeptidase) proved particularly useful from a practical point of view as they allow easy and reliable identification of pathogenic N. fowleri and N. australiensis as well as nonpathogenic N. lovaniensis strains. Genetic interpretation of these zymograms gave estimates of genetic distances that largely confirmed the taxonomic position of the Naegleria species. In addition, the genetic data suggest that there are two main phylogenetic groups in the genus Naegleria.     

PCR derived molecular markers and phylogenetic relationships in theSecale genus

DNA from 22 different species, accessions, cultivars and lines included in theSecale genus were analyzed by the polymerase chain reaction (PCR), using as primers five pairs of oligonucleotides derived from specific sequences. A total of 42 amplified bands were considered, and some of them appeared to be potentially useful as molecular markers for some of the analyzed groups. These amplified bands were used to generate molecular phenograms inside theSecale genus.     

Morphological variation and phylogenetic relationships in the genus Anginon (Apiaceae)

The variation in habit and morphology of the twelve species of Anginon, a poorly known southern African genus of woody Apiaceae, is discussed and illustrated. The genus Glia is shown to be the obvious outgroup, sharing with Anginon two convincing synapomorphies: 1, the reduction or partial reduction of the laminar part of the leaves, and 2, the heavily cutinized outer walls of the fruit epidermis. Several characters of the internal structure of the fruit, together with other morphological characters, have been analysed by the cladistic method. Our interpretation of character evolution within the genus and a first hypothesis of phylogenetic relationships, showing three distinct infrageneric groups, is presented.     

The meiotic structure and behavior of the strongly heteromorphic X/Y sex chromosomes of neotropical plethodontid salamanders of the genus Oedipina

Plethodontid salamanders in the genus Oedipina are characterized by a strongly heteromorphic sex-determining pair of X/Y chromosomes. The telocentric X chromosome and the subtelocentric Y chromosome are clearly distinguished from the autosomes and their behavior during meiosis can be sequentially followed in squash preparations of spermatocytes. In Oedipina the sex chromosomes are not obscured by an opaque sex vesicle during early meiotic stages, making it possible to observe details of sex bivalent structure and behavior not directly visible in other vertebrate groups. The sex chromosomes can first be distinguished from autosomal bivalents at the conclusion of zygotene, with X and Y synapsed only along a short segment at their non-centromeric ends, forming a bivalent that contrasts sharply with the completely synapsed autosomes. During pachytene, the XY bivalent becomes progressively shortened and more compact, disappearing as a visible structure when pachytene progresses into the diffuse stage of male meiosis. Diplotene bivalents gradually emerge from the diffuse nuclei, presumably by the return of the loops of chromatin into their respective chromomeres. During early diplotene, the X/Y bivalent is clearly visible with a single chiasma within the synapsed segment. This chiasma is terminalized by first meiotic metaphase with the X and Y appearing either in end-to-end synaptic contact or as univalents separated at opposite poles relative to the equatorially distributed autosomal bivalents. In C-banded preparations, the Y is entirely heterochromatic while the X contains a large centromeric C-band and another block of heterochromatin located at the telomeric end, in the region of synapsis with the Y. We find no cytological evidence of dosage compensation, such as differential staining of the X chromosomes or Barr bodies, in mitotic or interphase cells from female animals.     

Molecular phylogenetic relationships among seven Japanese species of Cercopithifilaria

DNA sequences from a portion of the mitochondrial COI gene were used to clarify phylogenetic relationships among Japanese species in the genus Cercopithifilaria. Sequences were determined from seven Japanese species, five (C. shohoi, C. multicauda, C. minuta, C. tumidicervicata and C. bulboidea) from the serow (Capricornis crispus F. Bovidae) and two (C. longa and C. crassa) from the sika deer (Cervus nippon nippon F. Cervidae). No base substitutions were observed between C. bulboidea and C. longa, suggesting that recent host switching of a lineage of C. bulboidea between bovid and cervid hosts gave rise to C. longa. In phylogenetic trees inferred using a variety of methods, the morphologically ancestral type, C. bulboidea, appeared as a derived species. C. multicauda was found to be basal in the analyses. It seems therefore that C. multicauda is the most primitive out of the seven species.     

Molecular phylogeny of the genus Pieris (Ericaceae) with special reference to phylogenetic relationships of insular plants on the Ryukyu Islands

Phylogenetic relationships within the genus Pieris (Ericaceae) were investigated based on the rbcL and matK genes along with five spacer sequences of chloroplast DNA to address questions regarding the phylogeography of the genus in association with insular plants on the Ryukyu Islands. The most parsimonious trees indicated that P. floribunda from eastern North America is a sister taxon to the remaining taxa examined, and suggested that the East Asian taxa examined are monophyletic. A morphologically cohesive group, section Pieris, was revealed to be paraphyletic. Within the East Asian clade, insular endemics from the Ryukyu Islands, Taiwan, and mainland Japan formed a sister group to P. formosa from the Himalayas and southern China. Our data suggest that the insular endemics of the Ryukyu Islands and Taiwan arose via allopatric divergence as a result of a paleogeographical land configuration of a landbridge during the early–middle Pleistocene in the Quaternary Period.     

分子系统进化关系分析的一种新方法--贝叶斯法在硬蜱属中的应用

距离矩阵邻接法、最大简约法和最大似然法是重建生物系统关系的3种主要方法。普遍认为最大似然法在原理上优于前二种方法，但其计算复杂费时。由于现行计算机的能力尚达不到其要求而实用性差，特别是在处理大数据集样本(即大于25个分类单元)时，用此方法几乎不可能。新近提出的贝叶斯法(Bayesianmethod)既保留了最大似然法的基本原理，又引进了马尔科夫链的蒙特卡洛方法，并使计算时间大大缩短。本文用贝叶斯法对硬蜱属(Ixodes)19个种的线粒体16S rDNA片段进行了系统进化分析。从总体上看，分析结果与现有的基于形态学的分类体系基本吻合。但与现存的假说相反，莱姆病的主要宿主蓖籽硬蜱复合种组并非单系。通过比较贝叶斯法与其它三种方法的结果，我们认为贝叶斯法是一种系统进化分析的好方法，它既能根据分子进化的现有理论和各种模型用概率重建系统进化关系，又克服了最大似然法计算速度慢、不适用于大数据集样本的缺陷。贝叶斯法根据后验概率直观地表示系统进化关系的分析结果，不需要用自引导法进行检验。可以预料，贝叶斯法将会被广泛地应用到系统进化分析上[动物学报49(3)：380—388，2003]。