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1.
Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.  相似文献   

2.
Many phylogenetic analyses, particularly morphological studies, use higher taxa (e.g., genera, families) rather than species as terminal taxa. This general approach requires dealing with interspecific variation among the species that make up the higher taxon. In this paper, I review different parsimony methods for coding and sampling higher taxa and compare their relative accuracies using computer simulations. Despite their widespread use, methods that involve coding higher taxa as terminals perform poorly in simulations, relative to splitting up the higher taxa and using species as terminals. Among the methods that use higher taxa as terminals, coding a taxon based on the most common condition among the included species (majority or modal coding) is generally more accurate than other coding methods, such as coding taxa as missing or polymorphic. The success of the majority method, and results of further simulations, suggest that in many cases "common equals primitive" within variable taxa, at least for low and intermediate rates of character change. The fixed-only method (excluding variable characters) performs very poorly, a result that is indirectly supported by analyses of published data for squamate reptiles. Sampling only a single species per higher taxon also yields low accuracy under many conditions. Along with recent studies of intraspecific polymorphism, the results of this study show the general importance of (1) including characters despite variation within taxa and (2) using methods that incorporate detailed information on the distribution of states within variable taxa.  相似文献   

3.
Li B  Liu Z  Zheng ZM 《ZooKeys》2011,(148):209-255
The grasshopper family Catantopidae is a well-known group, whose members include some of the most notorious agricultural pests. The existing classifications of the family are mostly utilitarian rather than being based on phylogenetic analysis and therefore unable to provide the stability desired for such an economically important group. In the present study, we present the first comprehensive phylogenetic analysis of the family based on morphology. By extensively sampling from the Chinese fauna, we included in the present analysis multiple representatives of each of the previously recognized tribes in the family. In total, we examined 94 genera represented by 240 species and evaluated 116 characters, including 84 for external morphology and 32 for male genitalia. The final matrix consists of 86 ingroup taxa and 88 characters. Our phylogenetic analyses resulted in a high resolution of the basal relationships of the family while showed considerable uncertainty about the relationships among some crown taxa. We further evaluated the usefulness of morphological characters in phylogeny reconstruction of the catantopids by examining character fit to the shortest trees found, and contrary to previous suggestions, our results suggest that genitalia characters are not as informative as external morphology in inferring higher-level relationship. We further suggest that earlier classification systems of grasshoppers in general and Catantopidae in particular most probably consist of many groups that are not natural due the heavy reliance on genitalia features and need to be revised in the light of future phylogenetic studies. Finally, we outlined a tentative classification scheme based on the results of our phylogenetic analysis.  相似文献   

4.
Character coding entails assumptions that may be problematic within the context of parsimony analysis using current computer algorithms. The example discussed here involves a character-variable (e.g., tail color) that is inapplicable in some taxa in the analysis because the part (e.g., tail) with which it is associated is lacking in those taxa. The part and character-variable can be coded as separate characters, or they can be fused into a single character. If the part and character-variable are coded as separate characters there is transformational independence between the part and the character-variable, but the logical dependence inherent to the hierarchical relationship between the part and its character-variable is only partly accounted for. Fusing the part and character-variable into one multistate character fully accounts for the logical dependence, but it is equivocal regarding the transformational independence. Separate coding is consistent with the primary homology statement that the part is homologous in all taxa possessing it, whereas fused coding is equivocal regarding this hypothesis of primary homology. As a result fused coding involves a loss of phylogenetic information. Use of a stepmatrix or other mechanisms associated with fused coding that preserve this phylogenetic information involves weighting schemes or ordered characters that have other assumptions that may also be difficult to justify.  相似文献   

5.
6.
Contemporary molecular phylogenetic analyses often encompass a broad range of taxonomic diversity while maintaining high levels of sampling within each major taxon. To help maximize phylogenetic signal in such studies, one may analyse multiple levels of characters simultaneously. We test the performance of both the original and the modified versions of non‐redundant coding of dependent characters (NRCDC) relative to commonly applied alternative character‐sampling strategies using codon‐based simulations under a range of conditions. Both original and modified NRCDC generally outperformed other character‐sampling strategies that only sampled characters at one level (nucleotides or amino acids) over a broader range of simulation parameters than any of the alternative character‐sampling strategies with respect to both overall success of resolution and averaged overall success of resolution in the parsimony‐based analyses. Based on theoretical considerations and the results of our simulations, we encourage application and further testing of modified NRCDC in parsimony‐based molecular phylogenetic analyses that sample exons of protein‐coding genes. We expect that modified NRCDC will generally increase both accuracy and branch‐support over commonly applied alternative character‐sampling strategies when analysed using the same phylogenetic inference method, particularly in studies that sample both closely and distantly related taxa with clades representing both ancient and recent divergences. © The Willi Hennig Society 2010.  相似文献   

7.
Variable characters are ubiquitous in hominoid systematics and present a number of unique problems for phylogenetic analyses that include extinct taxa. As yet, however, few studies have quantified ranges of variation in complex morphometric characters within extant taxa and then used those data to assess the consistency with which discrete character states can be applied to poorly represented fossil species. In this study, ranges of intrageneric morphometric variation in the shape of the hominoid orbital aperture are estimated using exact randomization of average pairwise taxonomic distances (ATDs) derived from size-adjusted centroid, height-width, and elliptic Fourier (EF) variables. Using both centroid and height-width variables, 19 of the 21 possible ATDs between individuals representing seven extinct catarrhine taxa (Aegyptopithecus, Afropithecus, Ankarapithecus, Ouranopithecus, Paranthropus, Sivapithecus and Turkanapithecus) can be observed within a single extant hominoid subspecies, although generally with low probabilities. A resampling study is employed as a means for gauging the effect that this intrataxonomic variation may have on the consistency with which discrete orbital shape character states can be delimited given the small sample sizes available for most Miocene catarrhine taxa preserving this feature (i.e., n=1). For each type of morphometric variable, 100 cluster (UPGMA) analyses of pairwise ATDs are performed in which a single individual is randomly selected from each hominoid genus and analyzed alongside known extinct taxa; consensus trees are computed in order to obtain the frequencies with which different shape clusters appeared in each of the three analyses. The two major clusters appearing most frequently in all three consensus trees are found in only 57% (centroid variables), 49% (height-width variables), and 36% (EF variables) of these trees. If ranges of variation within represented extinct taxa could also be estimated, these frequencies would certainly be far lower. Hominoids clearly exhibit considerable intrageneric, intraspecific, and even intrasubspecific variation in orbit shape, and substantial morphometric overlap exists between taxa; consequently, discrete character states delimiting these patterns of continuous variation are likely to be highly unreliable in phylogenetic analyses of living and extinct species, particularly as the number of terminal taxa increases. Morphological phylogenetic studies of extant catarrhines that assess the effect of different methods (e.g., use of objective a priori weighting or frequency coding of variable characters, inclusion vs. exclusion of variable characters, use of specific vs. supraspecific terminal taxa) on phylogenetic accuracy may help to improve the techniques that systematists employ to make phylogenetic inferences about extinct taxa.  相似文献   

8.
The result of a phylogenetic analysis of the Sepsidae based on larval characters is presented. It is shown that cyclorrhaphan larvae can be as rich a source of characters as Nematocera immatures when investigated using an SEM. The cladistic analysis comprised fifty-two species in sixteen genera of the Sepsidae and five outgroup species and used fifty-seven morphological characters. It found seven parsimonious trees which only differed with respect to the arrangement of some species within the genus Themira. The basal dichotomies of the phylogenetic trees are particularly well supported, indicating the conservative nature of larval characters. Orygma is confirmed as the sister group of all the remaining sepsids, the Sepsinae. There is good larval evidence that Ortalischema is the sister group of all remaining Sepsinae and that the Toxopodinae constitute an early radiation within the Sepsidae. According to larval data, some genera are paraphyletic ( Themira, Palaeosepsis ), but adult characters appear to contradict these findings. Among the traditionally recognized higher taxa within the Sepsidae, Hennig's Themira species-group and Steysbal's Sepsini have to be rejected as polyphyletic. However, Hennig's Sepsis species-group is confirmed as monophyletic and will probably constitute one major element of a future phylogenetic system of the Sepsidae. States of the strongly modified fore-legs of some adult sepsid males are mapped onto the phylogenetic tree, largely confirming Šulc's ideas about the evolution of these features. The origin and evolution of male sternites with brushes and a gland on the tibiae of the males ('osmeterium') are discussed. Whereas adult characters point to a sister-group relationship between the Sepsidae and the Ropalomeridae, larval characters appear to indicate a sister-group relationship between the Coelopidae and the Sepsidae. The evidence for both hypotheses is critically evaluated.  相似文献   

9.
Abstract— Miniaturization, which results in the presence of numerous apparently paedomorphic characters associated with reduced size, is a common phenomenon among neotropical fishes, with over 85 miniature species distributed among the five major ordinal groups. Eleven species are recognized as miniatures within the Characidiinae, a monophyletic subunit of Characiformes. A reconstruction of characidiin phylogeny is used to analyze the history of miniaturization events. Former hypotheses of origin of miniaturization among characidiins are rejected, underscoring the need for phylogenetic frameworks in the study of ontogenetic changes associated with the phenomenon of miniaturization. The 11 instances of miniature species can be most parsimoniously attributed to three independent miniaturization events within the Characidiinae.
Reductive characters comprise a large proportion of phylogenetically informative characters within the Characidiinae. In the largest group of miniatures, reductive characters represent more than half of the character state transformations affecting supraspecific relationships among Elachocharax, Klausewitzia, Odontocharacidium and Microcharacidium . An analysis of patterns of character state distributions fails to reject the null hypothesis of character independence. A distinction is made between the concepts of character independence, defined as the origination of character states from different (non-simultaneous) evolutionary events, and character correlation, defined as the association of character states in terminal taxa. Character correlation is not a sufficient criterion to reject Hennig's auxiliary principle, according to which the "presence of apomorphous characters in different species is always reason for suspecting kinship, and their origin by convergence should not be assumed a priori". High values of character correlation are the expected result of congruent patterns of character distribution.  相似文献   

10.
A morphometric study of Potentilla nivea, P unijlora, and P hookeriana, as well as the close relative of the latter, P furcata, has been carried out, and the quantitative data subjected to Canonical Discriminant Analysis. The four taxa belong to the arctic-alpine section Niveae of Potentilla, and material for the analysis was collected in Alaska, U. S. A. The a priori defined groups are based on petiole hair type, the qualitative, and only, character traditionally used to distinguish taxa within Potentilla sect. Niveae. The hair types recognized previously by taxonomists have been vaguely defined, and the intraspecific variation of other morphological characters has never been discussed. Ordination by canonical discriminant analysis was performed to characterize mean differences among species, to obtain insight into group differences, and to estimate character weights from correlations between canonical variates and original variables. The four taxa differ significantly in the canonical analysis of six quantitative characters. Leaflet length, incision depth (length of leaflet teeth), and ovule number are shown to be the most important discriminators. A key to the four taxa, taking into account the intra- vesus interspecific variation, as well as character weights, is provided.  相似文献   

11.
Phylogenetic relationships within the Pentatomoidea are investigated through the coding and analysis of character data derived from morphology and DNA sequences. In total, 135 terminal taxa were investigated, representing most of the major family groups; 84 ingroup taxa are coded for 57 characters in a morphological matrix. As many as 3500 bp of DNA data are adduced for each of 52 terminal taxa, including 44 ingroup taxa, comprising the 18S rRNA, 16S rRNA, 28S rRNA, and COI gene regions. Character data are analysed separately and in the form of a total evidence analysis. Major conclusions of the phylogenetic analysis include: the concept of Urostylididae is restricted to that of earlier authors; the Saileriolinae is raised to family rank and treated as the sister group of all Pentatomoidea exclusive of Urostylididae sensu stricto; a broadly conceived Cydnidae, as recognized by Dolling, 1981 , is not supported; the placement of Thaumastellidae within the Pentatomoidea is affirmed and the taxon is recognized at family rank rather than as a subfamily of Cydnidae, although its exact phylogenetic position within the Pentatomoidea remains equivocal; the Parastrachiinae is treated as also including Dismegistus Amyot & Serville and placed within a broadly conceived Corimelaenidae, the latter group being treated at family rank; the family‐group taxa Dinidoridae and Tessaratomidae probably represent a monophyletic group, but the recognition of monophyletic subgroups will benefit from additional representation in the sequence data set; and the Lestoniidae is treated as the sister group of the Acanthosomatidae. The Acanthosomatidae and Scutelleridae are consistently recovered as monophyletic. The monophyly of the Pentatomidae appears unequivocal, inclusive of the Aphylinae and Cyrtocorinae, on the basis of morphology, the latter two taxa not being represented in the molecular data set. © The Willi Hennig Society 2008.  相似文献   

12.
The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.  相似文献   

13.
14.
The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.  相似文献   

15.
The pill millipedes of the order Glomerida are a moderately diverse group with a classical Holarctic distribution pattern. Their classification is based on a typological system utilizing mainly a single character complex, the male telopods. In order to infer the apomorphies of the Glomerida, to elucidate its position in the Pentazonia, and to test the monophyly of its families and subfamilies, we conduct the first phylogenetic analysis of the order. To provide additional characters, we comparatively analyze the mandible using scanning electron microscopy. The final character matrix consists of 69 characters (11 mandible characters) and incorporates 22 species from 20 of the 34 pill millipede genera, representing all families and subfamilies, except the monotypic Mauriesiinae. Two species from each of the two other Pentazonian orders Sphaerotheriida and Glomeridesmida, as well as two Spirobolida, are included as outgroup taxa. The Glomerida are recovered as monophyletic and are supported by five apomorphies. Within the Pentazonia, the Glomeridesmida are recovered as the sister group to the classical Oniscomorpha (Sphaerotheriida + Glomerida) with weak support. The analysis provides little resolution within the Glomerida, resulting in numerous polytomies. Further morphological characters and/or the addition of molecular analyses are needed to produce a robust phylogenetic classification of the Glomerida.  相似文献   

16.
New information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.  相似文献   

17.
Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.  相似文献   

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Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.  相似文献   

20.
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