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1.
The arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) are among the most poorly known Neotropical rodents. We investigated species-level phylogenetic relationships among the seven described Habromys species using 1331 aligned bases from the mitochondrial ND3 and ND4 regions. Sequences were obtained from 30 specimens of the seven known species of Habromys and we performed maximum parsimony, maximum likelihood, and Bayesian probabilities analyses. The monophyly of the genus Habromys within the Neotomines was verified. The northernmost H. simulatus is sister to the remaining species of the group; within the latter, the southernmost clade (Oaxaca to Central America) is sister to the Transmexican Volcanic Belt clade. Four major clades are clearly distinguished: H. simulatus from the Sierra Madre Oriental and the closely associated Sierra Mazateca; H. delicatulus and H. schmidlyi from the Transmexican Volcanic Belt; H. lepturus, H. chinanteco, and H. ixtlani from the northern Oaxacan highlands; and H. lophurus from Nuclear Central America. Within species, the analyses suggest that H. simulatus and H. lophurus are each composed by two different taxa.  相似文献   

2.
GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.  相似文献   

3.
The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.  相似文献   

4.
Eight genes (nuclear: 18S, 28S, H3, CAD; mitochondrial: 12S, 16S, COI, COII) and morphology were used to infer the evolutionary history of Corylophidae, some of the smallest free‐living insects. The study included 36 corylophid exemplars, representing approximately 60% of the known generic diversity of the family and 16 cucujoid outgroup taxa. Multiple partitioning strategies, molecular datasets, combined datasets and different taxon sampling regimes using maximum likelihood and mixed‐model Bayesian inference were utilized to analyse these data. Most results were highly concordant across analyses. There was strong agreement across (i) partitioning strategies, (ii) maximum likelihood and Bayesian inference analyses of the molecular data, and (iii) Bayesian inference of the molecular data alone and Bayesian inference of the combined morphological and molecular data when all terminal taxa were included. When a strict taxon sampling protocol was employed so that only single generic exemplars were included, deep relationships were affected in the resulting phylogenetic hypotheses. Under such narrow sampling strategies, deep phylogenetic relationships were also sensitive to the choice of generic exemplars. Although it is often challenging to obtain single representatives for many taxa in higher‐level phylogenetic analyses, these results indicate the importance of using denser taxon sampling approaches even at the specific level for genera included in such studies. Molecular data alone support Anamorphinae (Endomychidae) strongly as the sister group of Corylophidae. In combined data analyses, Coccinellidae is recovered as the sister group to Corylophidae. In all analyses, Corylophidae and the subfamily Corylophinae are recovered as monophyletic. The monophyly of Periptyctinae was untested, as only a single species was included. All included corylophine tribes were recovered as monophyletic with the exception of Aenigmaticini; Aenigmaticum Matthews forms the sister group to Orthoperus Stephens and Stanus?lipiński et al. is recovered as the sister group of Sericoderus Stephens. Stanus tasmanicus?lipiński et al. is transferred to a new genus, Pseudostanus Robertson, ?lipiński & McHugh gen.n. incertae sedis. We propose a new tribe, Stanini Robertson, ?lipiński & McHugh trib.n. for Stanus bowesteadi?lipiński et al. and a new concept of Aenigmaticini sensu.n. to include only the nominate genus. Anatomical transitions associated with corylophid miniaturization are highlighted. Key phenotypic modifications and elevated rates of substitution in nuclear rRNA genes are evident in a subgroup of Corylophinae that includes the most diminutive species. Other taxonomic and evolutionary implications are discussed in light of the results.  相似文献   

5.
张蒙  黄敏 《昆虫分类学报》2012,34(3):509-519
测定了中国Singhardina亚属15个代表种的核糖体28S基因D2区和线粒体16S基因、COI基因部分序列,分别采用最大简约法、最大似然法和贝叶斯法构建分子系统树。系统发育树显示了相似的拓扑结构,明晰了各分支间的关系。首次探讨了中国Singhardina亚属4个种团间的系统发育关系。结果显示,Singhardina亚属构成了1个独立支系,代表1个单系群。本研究首次提出种团Eurhadina(Singhardina)rubra,并推测该种团可能是Singhardina亚属中最原始的种团。种团Eurhadina(Singhardina)robusta和E.(Singhardina)mamata为姐妹群。种团E.(Singhardina)vittata不能从种团E.(Singhardina)punjabensis中分出得到了分子数据的支持。  相似文献   

6.
Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.  相似文献   

7.
Phylogenetic relationships of genera Allograpta, Sphaerophoria and Exallandra (Diptera, Syrphidae) were analyzed based on sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The three genera are members of the subfamily Syrphinae, where nearly all members feed as larvae on soft-bodied Hemiptera and other arthropods. Phytophagous species have recently been discovered in two subgenera of Allograpta, sg Fazia and a new subgenus from Costa Rica. Phylogenetic analyses of the combined datasets were performed using parsimony, under static alignment and direct optimization, maximum likelihood and Bayesian inference. Congruent topologies obtained from all the analyses indicate paraphyly of the genus Allograpta with respect to Sphaerophoria and Exallandra. Exallandra appears embedded in the genus Sphaerophoria, and both genera are placed within Allograpta. The distribution of phytophagous taxa in Allograpta indicates that plant feeding evolved at least twice in this group.  相似文献   

8.
A phylogenetic analysis of 25 species, representing eight genera of theRubieae tribe (Rubiaceae), has been made using the DNA sequence of the chloroplastatp B-rbc L intergene region. Six tropical genera from other tribes ofRubiaceae have been used as outgroups. Whatever the method of analysis (distance, parsimony or maximum likelihood), five groups are clearly separated and described as informal clades. Their relative relationships are not clearly resolved by the parsimony analysis, resulting in eight equally parsimonious trees, 327 steps long, with a consistency index (CI) of 0.749 (excluding uninformative sites). TheRubieae tribe appears monophyletic from the data available. Some new and partly unexpected phylogenetic relationships are suggested. The genusRubia forms a separate clade and appears to be the relatively advanced sister group of the remaining taxa. TheSherardia clade also includes the generaCrucianella andPhuopsis. Galium sect.Aparinoides appears closely attached to theAsperula sect.Glabella clade. The remaining taxa ofGalium are paraphyletic:Galium sect.Platygalium (in theCruciata clade) is linked to the advanced generaCruciata andValantia; the more apomorphic groups ofGalium form theGalium sect.Galium clade, including the perennial sectionsGalium, Leiogalium, andLeptogalium as well as the annual (and possibly polyphyletic) sect.Kolgyda.  相似文献   

9.
Clitellata (earthworms, leeches, and allies) is a clade of segmented annelid worms that comprise more than 5000 species found worldwide in many aquatic and terrestrial habitats. According to current views, the first clitellates were either aquatic (marine or freshwater) or terrestrial. To address this question further, we assessed the phylogenetic relationships among clitellates using parsimony, maximum likelihood and Bayesian analyses of 175 annelid 18S ribosomal DNA sequences. We then defined two ecological characters (Habitat and Aquatic‐environment preferences) and mapped those characters on the trees from the three analyses, using parsimony character‐state reconstruction (i.e. Fitch optimization). We accommodated phylogenetic uncertainty in the character mapping by reconstructing character evolution on all the trees resulting from parsimony and maximum likelihood bootstrap analyses and, in the Bayesian inference, on the trees sampled using the Markov chain Monte Carlo algorithm. Our analyses revealed that an ‘aquatic’ ancestral state for clitellates is a robust result. By using alterations of coding characters and constrained analyses, we also demonstrated that the hypothesis for a terrestrial origin of clitellates is not supported. Our analyses also suggest that the most recent ancestor of clitellates originated from a freshwater environment. However, we stress the importance of adding sequences of some rare marine taxa to more rigorously assess the freshwater origin of Clitellata. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 447–464.  相似文献   

10.
Complete sequences for the 18S-rRNA gene of 22 bryophytes (12 completely new) were determined and used to construct phylogenetic trees. The evaluation of sequence data according to the maximum parsimony principle (PAUP 3.1.1) and the neighbor-joining method (MEGA) results in similar phylogenetic trees in which theBryopsida appear as a sister group to theJungermanniopsida, and both together as a sister group to theMarchantiopsida. Among theMarchantiopsida, theSphaerocarpales diverge early as a separate clade. TheMetzgeriales andJungermanniales are monophyletic. They belong to one clade and cannot be separated by either method of evaluation.  相似文献   

11.
Producing a robust phylogenetic reconstruction for Polychaeta using either morphological or molecular data sets has proven very difficult. There remain many conflicts between morphological analyses and hypotheses based on DNA data, the latter principally derived from 18S rRNA sequences. For the present study a data set covering a broad range of polychaete diversity was assembled, including 38 new sequences from 21 species. Besides available 18S rRNA data, five additional gene segments were examined: the D1 and D9-10 expansion regions of 28S rRNA, histone H3, snU2 RNA and cytochrome c oxidase subunit I. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted.Annelida and Mollusca were reciprocally monophyletic in maximum likelihood analyses, but Polychaeta included a cephalopod in maximum parsimony analyses, and a patellogastropod in Bayesian analyses. When rooted on the Mollusca, optimal topologies from maximum likelihood analyses showed a recognisable basal group of taxa, including Oweniidae, Chaetopteridae and Amphinomidae. The six studied phyllodocidan families plus Orbiniidae (as the sister group of the scale-worms) formed the next most basal group. All analyses support the inclusion of Echiura, Clitellata and Siboglinidae within polychaetes. Bayesian analyses show Echiura as the sister group of Capitellidae, in agreement with previous 18S rRNA results, In contrast, Echiura formed the sister group to Trichobranchidae in maximum likelihood and maximum parsimony analyses.Supra-familial groupings consistently recovered within Polychaeta in the analyses are: (i) Terebellida without Ampharetidae; (ii) Scolecida (excepting Orbiniidae); (iii) Eunicidae, Lumbrineridae and Clitellata; and (iv) “Cirratuliformia” (including Sternaspidae) plus Sabellidae, Serpulidae and Spionidae.  相似文献   

12.
A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004 ; PNAS, 101, 13820–13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the “Out of Appalachia” hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed. © The Willi Hennig Society 2005.  相似文献   

13.
Evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Caucalideae Spreng. and related taxa were inferred from maximum parsimony analyses of chloroplast DNA restriction sites andrps16 intron sequences and the results compared to an existing phylogeny for the group based on nuclear ribosomal DNA internal transcribed spacer sequences. While these three data sets were not similar in size or composition, the relationships among the shared taxa, with few exceptions, were concordant. Three major lineages are recognized, coinciding with the previously delimited Scandiceae subtribes Daucinae Dumort. (Agrocharis, Ammodaucus, Cuminum, Daucus, Orlaya, Pachyctenium, Pseudorlaya), Torilidinae Dumort. (Astrodaucus, Caucalis, Glochidotheca, Lisaea, Szovitsia, Torilis, Turgenia, Yabea), and Scandicinae Tausch (Anthriscus, Kozlovia, Myrrhis, Osmorhiza, Scandix). Included in Daucinae is representation from tribe Laserpitieae (Laser, Laserpitium, Melanoselinum, Monizia, Polylophium). Daucinae and Torilidinae arise as sister taxa in the chloroplast DNA-based phylogenies, whereas in the ITS trees relationships among the three major lineages are unresolved. Unexpectedly, three species ofFerula ally with Daucinae and Torilidinae. The position ofArtedia is equivocal, occurring either sister to Daucinae in the ITS trees, within Torilidinae in the intron trees, or sister to Torilidinae upon analysis of combined ITS and intron data.Chaetosciadium trichospermum emerges withinTorilis, and is recognized asTorilis trichosperma (L.) Spreng.  相似文献   

14.
15.
Phylogenetic relationships of (19) serpulid taxa (including Spirorbinae) were reconstructed based on 18S rRNA gene sequence data. Maximum likelihood, Bayesian inference, and maximum parsimony methods were used in phylogenetic reconstruction. Regardless of the method used, monophyly of Serpulidae is confirmed and four monophyletic, well-supported major clades are recovered: the Spirorbinae and three groups hitherto referred to as the Protula-, Serpula-, and Pomatoceros-group. Contrary to the taxonomic literature and the hypothesis of opercular evolution, the Protula-clade contains non-operculate (Protula, Salmacina) and operculate taxa both with pinnulate and non-pinnulate peduncle (Filograna vs. Vermiliopsis), and most likely is the sister group to Spirorbinae. Operculate Serpulinae and poorly or non-operculate Filograninae are paraphyletic. It is likely that lack of opercula in some serpulid genera is not a plesiomorphic character state, but reflects a special adaptation.  相似文献   

16.
The morphology of many hypogeous fungi converges on a homogeneous reduced form, suggesting that disparate lineages are subject to a uniform selection pressure. The primary goal of this study was to evaluate the morphology and infer the phylogeny of the Leucogastrales with Mycolevis siccigleba using a Bayesian methodology. A comprehensive morphological assessment was used for an a priori phylogenetic inference to guide the sequencing effort. All structures except spore ornamentation pointed to the Albatrellaceae as the most likely sister taxon. Polyporoletus sublividus, a close relative of Albatrellus, produces ornamented basidiospores with a similar structure to M. siccigleba basidiospores. The ITS from 30 taxa was used for the molecular phylogenetic analysis. P. sublividus was found sister to Mycolevis. Leucophleps spinispora and L. magnata formed a group sister to the Polyporoletus/Mycolevis group, whereas Leucogaster was polyphyletic with respect to the core of the Leucogastrales and sister to A. caeruleoporus. This relationship was expected as previously undescribed chlamydospores produced by members of Albatrellus had a similar morphology to the basidiospores of L. rubescens.  相似文献   

17.
To more confidently assess phylogenetic relationships among astome ciliates, we obtained small subunit (SSU) rRNA sequences from nine species distributed in six genera and three families: Almophrya bivacuolata, Eudrilophrya complanata, Metaracoelophrya sp. 1, Metaracoelophrya sp. 2, Metaracoelophrya intermedia, Metaradiophrya sp., Njinella prolifera, Paraclausilocola constricta n. gen., n. sp., and Paraclausilocola elongata n. sp. The two new species in the proposed new clausilocolid genus Paraclausilocola n. gen. are astomes with no attachment apparatus, two files of contractile vacuoles, and an arc-like anterior suture that has differentiations of thigmotactic ciliature on the anterior ends of the left kineties of the upper surface. Phylogenetic analyses were undertaken using neighbor-joining, Bayesian inference, maximum likelihood, and maximum parsimony. The nine species of astomes formed a strongly supported clade, showing the subclass Astomatia to be monophyletic and a weakly supported sister clade to the scuticociliates. There were two strongly supported clades within the astomes. However, genera assigned to the same family were found in different clades, and genera assigned to the same order were found in both clades. Thus, astome taxa appear to be paraphyletic when morphology is used to assign species to genera.  相似文献   

18.
The importance of identifying biological diversity accurately and efficiently is becoming more evident. It is therefore critical to determine the species boundaries between closely related taxa and to establish diagnostic characters that allow us to define species. This is not an easy task when species exhibit high intraspecific phenotypic plasticity or when distinct evolutionary lineages with an unusually large amount of genetic distinctiveness show no apparent morphological diversity (cryptic species). These phenomena appear to be common in the genus of fan worms Branchiomma (Sabellidae, Annelida), and consequently, taxonomic errors are widespread in the group. Moreover, some Branchiomma species have been unintentionally translocated outside the area where natural range extension is expected, increasing the taxonomic problems. We have performed a range of analytical methods including genetic distances, Bayesian inference, maximum likelihood, maximum parsimony, statistical parsimony analyses and general mixed Yule coalescent model to clarify the taxonomic status and assess the species boundaries of Branchiomma in Australia. This study shows that the traditional diagnostic morphological features are greatly homoplastic. Results also indicate that the diversity of Branchiomma in Australia is higher than previously reported and evidence some cases of high phenetic plasticity (in features previously considered as stable within species), high intraspecific genetic variability, cryptic species and several unexpected cases of translocations.  相似文献   

19.
The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.  相似文献   

20.
曲畅游  许崇梅 《广西植物》2015,35(6):848-852
两栖蓼是一种水陆两栖植物,植株在不同生态环境下外部形态差异较大,同时两栖蓼的系统位置存在争议,被归入春蓼组(sect.Persicaria)或提升为两栖蓼组(sect.Amphibium)。该文选取两栖蓼及春蓼组植物12种,以及刺蓼组、头状蓼组、神血宁组、拳参组、萹蓄组和外类群掌叶大黄共23种植物进行研究。植物总DNA的提取采用改进的CTAB法,所测序列以及从Genbank数据库下载的序列,以掌叶大黄为外类群,采用最大简约法和贝叶斯法对核糖体ITS序列和叶绿体trn L-F序列进行了系统发育分析。ITS序列对位排列的长度为735 bp,包括489个可变位点,272个位点是信息位点。简约法得到9个简约树,步长为1 084,CI指数为0.680,RI指数为0.614。trn L-F序列对位排列的长度为1 121 bp,包括427个可变位点,239个位点是信息位点。简约法寻找到9个简约树,步长为551(CI=0.911,RI=0.910)。贝叶斯法和简约法得到的树基本一致。分子序列分析结果显示,trn L-F序列树类似于ITS序列树。ITS序列构建的发育树上,两栖蓼与刺蓼组植物、春蓼组其他植物形成3个并列的分支;在trn L-F序列树上,两栖蓼则与其他春蓼组植物形成两个并列的分支。由此可见,两栖蓼与春蓼组其他植物的亲缘关系较远,成一独立的分支。两个分子证据支持将两栖蓼提升为两栖蓼组的处理意见。此外,两栖蓼的花粉具散沟,与典型的春蓼组的具散孔花粉不一致。再加上两栖蓼水陆两栖的特性,因此支持把两栖蓼提升为两栖蓼组的观点。两栖蓼组的界定为多年生草本,水陆两栖,根状茎横生,生于水中茎漂浮,叶长圆形或椭圆形,生于陆地茎直立,叶披针形或长圆状披针形,托叶鞘为筒状、薄膜质,总状花序穗状,瘦果近圆形,花粉具散沟。  相似文献   

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