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1.
Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among these clades. A dataset of 93 species that represent all eight previously recognized clades was assembled, with 3800 bp of sequence data from nuclear and mitochondrial large and small subunit rDNAs for each taxon. Parsimony and maximum-likelihood analyses support the monophyly of the eight major clades recognized by Hibbett and Thorn. Most groups are strongly supported in bootstrapped parsimony analyses, but the polyporoid clade remains weakly supported. For the first time, the sister-group relationship of the euagarics clade and bolete clade is strongly supported, and the Hygrophoraceae is strongly supported as the sister group of the rest of the euagarics clade. Nevertheless, the backbone of the homobasidiomycete phylogeny, and the internal structure of several clades, remain poorly resolved.  相似文献   

2.
It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.  相似文献   

3.
A cladistic analysis that includes representatives of all recent genera of mysticetes and several fossil species that were previously referred to the family Cetotheriidae, with tooth-bearing mysticetes and an archaeocete as an outgroup, is presented here. The result of this analysis forms the base of a revised classification of Mysticeti. Cetotheriidae is redefined as a monophyletic family, which includes the genera Cetotherium , Piscobalaena , and a new subfamily Herpetocetinae, including Herpetocetus , Nannocetus , Metopocetus , and Cephalotropis . Eschrichtiidae is the closest sister taxon to Cetotheriidae. A few species are referred to Eomysticetoidea, whereas the remaining species that were previously referred to Cetotheriidae appear in four clades that branch off from the lineage leading to Balaenopteridae. These are a Mauicetus clade and three clades that are named as new families Aglaocetidae, Pelocetidae, and Diorocetidae.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 875–894.  相似文献   

4.
We performed the first combined‐data phylogenetic analysis of ictalurids including most living and fossil species. We sampled 56 extant species and 16 fossil species representing outgroups, the seven living genera, and the extinct genus ?Astephus long thought to be an ictalurid. In total, 209 morphological characters were curated and illustrated in MorphoBank from published and original work, and standardized using reductive coding. Molecular sequences harvested from GenBank for one nuclear and four mitochondrial genes were combined with the morphological data for total evidence analysis. Parsimony analysis recovers a crown clade Ictaluridae composed of seven living genera and numerous extinct species. The oldest ictalurid fossils are the Late Eocene members of Ameiurus and Ictalurus. The fossil clade ?Astephus placed outside of Ictaluridae and not as its sister taxon. Previous morphological phylogenetic studies of Ictaluridae hypothesized convergent evolution of troglobitic features among the subterranean species. In contrast, we found morphological evidence to support a single clade of the four troglobitic species, the sister taxon of all ictalurids. This result holds whether fossils are included or not. Some previously published clock‐based age estimates closely approximate our minimum ages of clades.  相似文献   

5.
Computational methods for estimating diversification rates from extant species phylogenetic trees have become abundant in evolutionary research. However, little evidence exists about how their outcome compares to a complementary and direct source of information: the fossil record. Furthermore, there is virtually no direct test for the congruence of evolutionary rates based on these two sources. This task is only achievable in clades with both a well‐known fossil record and a complete phylogenetic tree. Here, we compare the evolutionary rates of ruminant mammals as estimated from their vast paleontological record—over 1200 species spanning 50 myr—and their living‐species phylogeny. Significantly, our results revealed that the ruminant's fossil record and phylogeny reflect congruent evolutionary processes. The concordance is especially strong for the last 25 myr, when living groups became a dominant part of ruminant diversity. We found empirical support for previous hypotheses based on simulations and neontological data: The pattern captured by the tree depends on how clade specific the processes are and which clades are involved. Also, we report fossil evidence for a postradiation speciation slowdown coupled with constant, moderate extinction in the Miocene. The recent deceleration in phylogenetic rates is connected to rapid extinction triggered by recent climatic fluctuations.  相似文献   

6.
7.
X Liu  Y Wang  C Shih  D Ren  D Yang 《PloS one》2012,7(7):e40345
Fishflies (Corydalidae: Chauliodinae) are one of the main groups of the basal holometabolous insect order Megaloptera, with ca. 130 species distributed worldwide. A number of genera from the Southern Hemisphere show remarkably disjunctive distributions and are considered to be the austral remnants or "living fossils" of Gondwana. Hitherto, the evolutionary history of fishflies remains largely unexplored due to limited fossil record and incomplete knowledge of phylogenetic relationships. Here we describe two significant fossil species of fishflies, namely Eochauliodes striolatus gen. et sp. nov. and Jurochauliodes ponomarenkoi Wang & Zhang, 2010 (original designation for fossil larvae only), from the Middle Jurassic of Inner Mongolia, China. These fossils represent the earliest fishfly adults. Furthermore, we reconstruct the first phylogenetic hypothesis including all fossil and extant genera worldwide. Three main clades within Chauliodinae are recognized, i.e. the Dysmicohermes clade, the Protochauliodes clade, and the Archichauliodes clade. The phylogenetic and dispersal-vicariance (DIVA) analyses suggest Pangaean origin and global distribution of fishflies before the Middle Jurassic. The generic diversification of fishflies might have happened before the initial split of Pangaea, while some Gondwanan-originated clades were likely to be affected by the sequential breakup of Pangaea. The modern fauna of Asian fishflies were probably derived from their Gondwanan ancestor but not the direct descendents of the Mesozoic genera in Asia.  相似文献   

8.
The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the existing phylogenetic trees of the Alexandrium tamarense species complex from large subunit rDNA sequences has confirmed that geographic distribution is consistent with the molecular clades but not with the three morphologically defined species that constitute the complex. In addition, a new clade has been discovered, representing Mediterranean nontoxic strains. The dinoflagellates fossil record was used to calibrate a molecular clock: key dates used in this calibration are the origins of the Peridiniales (estimated at 190 MYA), Gonyaulacaceae (180 MYA), and Ceratiaceae (145 MYA). Based on the data set analyzed, the origin of the genus Alexandrium was estimated to be around late Cretaceous (77 MYA), with its earliest possible origination in the mid Cretaceous (119 MYA). The A. tamarense species complex potentially diverged around the early Neogene (23 MYA), with a possible first appearance in the late Paleogene (45 MYA). A paleobiogeographic scenario for Alexandrium is based on (1) the calculated possible ages of origination for the genus and its constituent groups; (2) paleogeographic events determined by plate movements, changing ocean configurations and currents, as well as climatic fluctuations; and (3) the present geographic distribution of the various clades of the Alexandrium tamarense species complex.  相似文献   

9.
The phylogeny of the living and fossil Sphenisciformes (penguins)   总被引:4,自引:1,他引:3  
We present the first phylogenetic analysis of the Sphenisciformes that extensively samples fossil taxa. Combined analysis of 181 morphological characters and sequence fragments from mitochondrial and nuclear genes (12S, 16S, COI, cytochrome b, RAG‐1) yields a largely resolved tree. Two species of the New Zealand Waimanu form a trichotomy with all other penguins in our result. The much discussed giant penguins Anthropornis and Pachydyptes are placed in two clades near the base of the tree. Stratigraphic and phylogenetic evidence suggest that some lineages of penguins attained very large body size rapidly and early in the clade's evolutionary history. The only fossil taxa that fall inside the crown clade Spheniscidae are fossil species assigned to the genus Spheniscus. Thus, extant penguin diversity is more accurately viewed as the product of a successful radiation of derived taxa than as an assemblage of survivors belonging to numerous lineages. The success of the Spheniscidae may be due to novel feeding adaptations and a more derived flipper apparatus. We offer a biogeographical scenario for penguins that incorporates fossil distributions and paleogeographic reconstructions of the Southern continent's positions. Our results do not support an expansion of the Spheniscidae from a cooling Continental Antarctica, but instead suggest those species that currently breed in that area are the descendants of colonizers from the Subantarctic. Many important divergence events in the clade Spheniscidae can instead be explained by dispersal along the paths of major ocean currents and the emergence of new islands due to tectonic events. © The Willi Hennig Society 2006.  相似文献   

10.
Peintner U  Moncalvo JM  Vilgalys R 《Mycologia》2004,96(5):1042-1058
Research on the molecular systematics of Cortinarius, a species-rich mushroom genus with nearly global distribution, is just beginning. The present study explores infrageneric relationships using rDNA ITS and LSU sequence data. One large dataset of 132 rDNA ITS sequences and one combined da-taset with 54 rDNA ITS and LSU sequences were generated. Hebeloma was used as outgroup. Bayesian analyses and maximum-likelihood (ML) analyses were carried out. Bayesian phylogenetic inference performed equally well or better than ML, especially in large datasets. The phylogenetic analysis of the combined dataset with species representing all currently recognized subgenera recovered seven well-supported clades (Bayesian posterior probabilities BPP > 90%). These major clades are: /Myxacium s.l., /subg. Cortinarius, the /phlegmacioid clade (including the subclades /Phlegmacium and /Delibuti), the /calochroid clade (/Calochroi, /Ochroleuci and /Allutus), the /telamonioid clade (/Telamonia, /Orellani, /Anomali), /Dermocybe s.l. and /Myxotelamonia. Our results show that Cortinarius consists of many lineages, but the relationships among these clades could not be elucidated. On one hand, the low divergence in rDNA sequences can be held responsible for this; on the other hand, taxon sampling is problematic in Cortinarius phylogeny. Because of the incredibly high diversity (~2000 Cortinarius species), our sampling included <5% of the known species. By choosing type species of subgenera and sections, our sampling is strongly biased toward Northern Hemisphere taxa. More extensive taxon sampling, especially of species from the Southern Hemisphere, is essential to resolve the phylogeny of this important genus of ectomycorrhizal fungi.  相似文献   

11.
12.
Rock-dwelling gastropods are usually patchily distributed in limestone habitats, presumably have low active and passive dispersal ability and often represent narrow-ranged endemic taxa. Their current taxonomy is predominantly shell morphology based, and it remains unknown whether the morphologically differentiated and geographically separated populations represent phylogenetic clades. In this study, we analysed the hyperdiverse, terrestrial door snail genus Montenegrina. Based on the current taxonomy defined by shell morphology, it contains 29 species and 106 subspecies distributed in the Balkan region. The constructed phylogenetic tree using three mitochondrial markers was used to test whether it agrees with the current taxonomy. In this comprehensive tree, about half of the species and subspecies are monophyletic. Some of the paraphylies could be reasonably resolved by taxonomic changes; that is, some subspecies should be reassigned or raised to species level. Other incongruencies probably arose due to introgression even between distant clades. The histone genes turned out to be unsuitable for elucidating the phylogeny of Montenegrina. In the species-delimitation tests, considerably more molecular operational taxonomic units were delimited than the number of presently described species. The present data indicate that (a) shell morphology-based taxonomy and taxon recognition can be problematic in such a large and morphologically highly variable genus; (b) the potential error due to incomplete sampling presents a problem in a genus as variable as Montenegrina; (c) multi-locus analyses should be conducted to arrive at a better basis for species delimitation; and (d) integrative approaches including genetic as well as morphological/anatomical data from a comprehensive geographic sample are necessary.  相似文献   

13.
Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature   总被引:2,自引:0,他引:2  
An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.  相似文献   

14.
Abstract: The fossil record of the two primary subclades of softshell turtles (Trionychidae) is exceedingly asymmetric, as a result of a ghost range of total clade Cyclanorbinae that is estimated at 80 Ma. Herein, we present the first phylogenetic analysis of Trionychidae that includes a representative of the poorly studied taxon Plastomenidae, which is known from the Campanian to Eocene of North America. The analysis reveals that plastomenids are stem cyclanorbines, thus significantly reducing the apparent ghost range of total group Cyclanorbinae to approximately 30 Ma. Plastomenids are either an early branching clade of stem Cyclanorbinae, or they represent a paraphyletic grade that gave rise to modern cyclanorbines. Although abundant, the fossil record is still too poorly understood to distinguish between these two primary hypotheses. The previously persistent extremely long ghost range of total clade Cyclanorbinae appears to have been the result of a research bias.  相似文献   

15.
? Premise of the study: Fossil leaves of Menispermaceae were previously described from the Paleocene of Colombia. Because of strong homoplasy of leaf characters, the fossils could not be placed more specifically within recognized clades, and additional data were needed to specify intrafamilial and paleogeographic relationships during the Paleocene. ? Methods: Fossil endocarps of Menispermaceae were collected from the Cerrejón Formation, the recently discovered Bogotá flora, and Wyoming (~60 Ma). We surveyed the endocarp morphology of almost all extant genera, conducted character optimization, a molecular scaffold analysis, and critically reviewed the related fossil genera. ? Key results: Parallel syndromes of fruit characters have appeared in unrelated clades of the family according to current phylogenetic reconstructions. However, mapping selected endocarp characters across those clades that contain horseshoe-shaped endocarps facilitates identification and phylogenetic assessment of the fossils. Three fossil species are recognized. One of them belongs to the extant genus Stephania, which today grows only in Africa and Australasia. Palaeoluna gen. nov. is placed within the pantropical clade composed of extant Stephania, Cissampelos, and Cyclea; this morphogenus is also recognized from the Paleocene of Wyoming. Menispina gen. nov. shows similarity with several unrelated clades. ? Conclusions: The new fossils from Colombia reveal a complex paleobiogeographic history of the recognized clades within Menispermaceae, suggesting a more active exchange among neotropical, paleotropical, North American, and European paleoforests than previously recognized. In addition, the new fossils indicate that neotropical forests were an important biome for the radiation and dispersal of derived lineages in Menispermaceae after the Cretaceous-Paleogene boundary.  相似文献   

16.
Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.  相似文献   

17.
Sun P  Clamp J  Xu D  Kusuoka Y  Miao W 《Protist》2012,163(1):129-142
Recent phylogenetic analyses of the peritrich genus Vorticella have suggested that it might be paraphyletic, with one Vorticella species - Vorticella microstoma grouping with the swimming peritrichs Astylozoon and Opisthonecta in a distant clade. These results were based on very limited taxon sampling and thus could not be accepted as conclusive evidence for revising the generic classification. We tested paraphyly of the genus Vorticella by making a new analysis with a broad range of samples from three continents that yielded 52 new sequences of the gene coding for small subunit rRNA. Our results, together with the available sequences in Genbank, form a comprehensive set of data for the genus Vorticella. Analyses of these data showed that Vorticella microstoma morphotypes, Astylozoon, and Opisthonecta form a well-supported, monophyletic clade, that is distinct from and basal to the family Vorticellidae containing other species of Vorticella. Paraphyly of the genus Vorticella and family Vorticellidae was strongly confirmed by these results. Furthermore, the two clades of Vorticella identified by the SSU rRNA gene are so genetically diverse whereas the genetic distances within the one containing Vorticella microstoma morphotypes, Astylozoon, and Opisthonecta were so slight, which marked it as a separate family that must be defined by molecular characters in the absence of unifying morphological and morphogenetic characters. An emended characterization and status of the genus Vorticella, the families Vorticellidae and Astylozoidae are presented and discussed.  相似文献   

18.
19.
基于细胞色素b的鸫亚科部分鸟类的系统进化   总被引:8,自引:0,他引:8  
采用分子系统学方法对鸫亚科(Turdinae)16属35种鸟类的线粒体细胞色素b基因进行系统发生分析。所测序列经对位排列后共983bp,包含变异位点399个,简约信息位点349个。以太平鸟(Bombycillagarrulus)和雪松太平鸟(Bombycillacedrorum)为外群,采用邻接法、最大简约法、最大似然法和贝叶斯法分别构建鸫亚科的系统发生树。研究结果表明:构建的系统树将所研究鸫亚科鸟类分为2个支系。第1个支系包括鸫属(Turdus)、地鸫属(Zoothera)和宽嘴鸫属(Cochoa);第2个支系包括歌鸲属(Luscinia)、鸲属(Tarsiger)、鹊鸲属(Copsychus)、薮鸲属(Cercotrichas)、红尾鸲属(Phoenicurus)、水鸲属(Rhyacornis)、燕尾属(Enivurus)、啸鸫属(Myiophoneus)、石属(Saxicola)、属(Oenanthe)、溪鸲属(Chaimarrornis)、矶鸫属(Monticola)和欧亚鸲属(Erithacus)。其中地鸫属并非单系类群;红尾鸲属为并系发生,水鸲属和溪鸲属归并到这一支系;石属与矶鸫属互为姐妹群,再与属聚合构成另一支系;然后上述两个支系构成姐妹群;歌鸲属和鸲属聚成姐妹群。对于鹊鸲属、薮鸲属、啸鸫属、欧亚鸲属、宽嘴鸫属和燕尾属,本研究结果并没有完全解决它们在大分支内与其它属间的亲缘关系  相似文献   

20.
The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus , Phyllastrephus and Chlorocichla . We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus , Thescelocichla, Baeopogon and Chlorocichla , although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A . importunus and A . gracilirostris , which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love ( Pyrrhurus scandens ) is placed within Phyllastrephus . We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.  相似文献   

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