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1.
Despite the considerable research that has focused on the evolutionary relationships and biogeography of the genus Bufo, an evolutionary synthesis of the entire group has not yet emerged. In the present study, almost 4 kb of DNA sequence data from mitochondrial (12S, tRNAVal, and 16S) and nuclear (POMC; Rag-1) genes, and 83 characters from morphology were analysed to infer a phylogeny of South American toads. Phylogenies were reconstructed with parsimony and maximum likelihood and Bayesian model-based methods. The results of the analysis of morphological data support the hypothesis that within Bufo , some skull characters (e.g. frontoparietal width), correlated with the amount of cranial ossification, are prone to homoplasy. Unique and unreversed morphological synapomorphies are presented that can be used to diagnose recognized species groups of South American toads. The results of all phylogenetic analyses support the monophyly of most species groups of South American Bufo . In most DNA-only and combined analyses, the South American (minus the B. guttatus and part of the ' B. spinulosus ' groups), North American, Central American, and African lineages form generally well-supported clades: ((((((((South America) (North America + Central America)) Eurasia) Africa) Eurasia) South America) West Indies) South America). This result confirms and extends prior studies recovering South American Bufo as polyphyletic. The biogeographical results indicate that: (1) The origin of Bufo predates the fragmentation of Gondwana; (2) Central and North American species compose the sister group to a large, 'derived' clade of South American Bufo ; and (3) Eurasian species form the sister group to the New World clade.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 407–452.  相似文献   

2.
Over eight kilobases (kb) of sequence from eight genes including two mitochondrial loci, Cyt b and 12S, and six nuclear loci, B2m , Zp3 , Tcp1, Sry, Smcx and Smcy , were used to investigate phylogenetic relationships among 11 taxa representing eight species within the rodent genus Mus . Particular attention was given to discerning relationships among species within the subgenus Mus including members of a Palearctic clade ( M. musculus , M. spicilegus , M. macedonicus and M. spretus ) and members of an Asian clade ( M. caroli , M. cookii and M. cervicolor ), as previous studies using different datasets have produced different topologies for taxa within these two groups. While parsimony analyses of the combined eight-gene dataset yielded a single, fully resolved tree, support values were lower for nodes resolving relationships within the Palearctic and Asian clades than they were elsewhere in the tree. In addition, a maximum likelihood analysis of the same eight-gene dataset yielded different topologies for both the Palearctic and the Asian clades. Both observations are indicative of clade instability. The nature of this instability was explored through a comparison with our previous study in which we included the two mitochondrial loci and only four of the six nuclear genes, and through an analysis of partitioned data, specifically mitochondrial vs. nuclear genes. This study underscores the importance of considering among-site rate variation in phylogeny reconstruction. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 653–662.  相似文献   

3.
Most eastern North American cyprinid fishes belong to a clade known as the "open posterior myodome" (OPM) minnows, but phylogenetic relationships within this clade have been difficult to ascertain. Previous attempts to resolve relationships among the generally benthic "chubs" and the more pelagic "shiners", that constitute the majority of OPM minnows, have led to highly discordant phylogenetic hypotheses. To further examine relationships among the OPM minnows, we utilized both a concatenated Bayesian approach and a coalescent-based species tree method to analyze data from six protein coding nuclear loci (Enc1, Ptr, Ryr3, Sh3px3, Tbr1, and Zic1), as well as the mitochondrial locus (Cytb). We focused our analyses on the chub-like genus Phenacobius, a group that has drifted topologically between other benthic chubs and the more pelagic shiners, and also included exemplar taxa from 11 other OPM lineages. Individual gene trees were highly discordant regarding relationships within Phenacobius and across the OPM clade. The concatenated Bayesian analysis and coalescent-based species tree reconstruction recovered slightly different phylogenetic topologies. Additionally, the posterior support values for clades using the coalescent-based approach were consistently lower than the concatenated analysis. However, Phenacobius was resolved as monophyletic and as the sister lineage to Erimystax regardless of the combined data approach taken. Furthermore, Phenacobius+Erimystax was recovered as more closely related to the shiners we examined than to other chubs. Relationships within Phenacobius varied depending on the combined phylogenetic method utilized. Our results highlight the importance of multi-locus, coalescent-based approaches for resolving the phylogeny of diverse clades like the eastern North American OPM minnows.  相似文献   

4.
To help clarify controversial phylogenetic relationships within the family Emberizidae, we sequenced 1238 bp of mitochondrial DNA from the cytochrome b gene and a flanking portion of ND5. Although the longspurs ( Calcarius ) and the snow buntings ( Plectrophenax ) have been grouped with the Old World buntings ( Emberiza ) in traditional classifications, our molecular phylogenies constructed with maximum likelihood and maximum parsimony place these genera basal to a clade in which the Old World buntings and North American sparrows are sister groups. Contrary to the hypothesis that the radiation within Emberiza is recent following a westward expansion of emberizid stock into Eurasia from North America, we found that the level of genetic divergence among Old World buntings approximates those among different genera in North American sparrows. Thus the radiation of the Emberizidae seems to have occurred at roughly the same time in the Palaearctic and Nearctic. Our results are consistent with earlier analyses of allozymes, but sequences from multiple genes and new morphological analyses are required to fully resolve phylogenetic relationships within the Emberizidae.  相似文献   

5.
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   

6.
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   

7.
The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.  相似文献   

8.
Chironius is one of the most speciose genera of the South American colubrid snakes. Although the genus represents a well‐known radiation of diurnal racers, its monophyly, affinities with other Neotropical colubrid genera, and intrageneric relationships are open questions. Here, we present a phylogenetic analysis of Chironius based on a data matrix that combines one nuclear (c‐mos) and two mitochondrial (12S and 16S rRNA) genes with 37 morphological characters derived from scutellation, skull, and hemipenial features. Phylogenetic relationships were inferred using maximum parsimony (MP) and maximum likelihood (ML). Our combined morphological and molecular analyses strongly support the monophyly of the genus Chironius and its sister‐group relationship with a clade formed by the genera Dendrophidion and Drymobius. Phylogenetic relationships within the genus Chironius is still controversial, although five clades are retrieved with medium to strong support. © 2014 The Linnean Society of London  相似文献   

9.
Carex section Acrocystis currently includes 27 taxa in North America. Recent phylogenetic studies have suggested that the North American and some but not all of the Eurasian species form a clade. Relationships and biogeographic patterns among species in this core-Acrocystis group are explored here using nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS) and nrDNA external transcribed spacer region (ETS) sequence data. While maximum parsimony analysis of the ITS and ETS data provides only a moderately resolved branching structure for species relationships within the core-Acrocystis clade, maximum likelihood analysis provides a more resolved hypothesis of relationships in the section. The core-Acrocystis clade consists of a grade of Eurasian and primarily western North American species, with a well-supported clade of only eastern North American species nested within this grade. ITS and ETS types do not coalesce within many species or species complexes. Possible explanations for the non-coalescent nature of ITS and ETS copies in Acrocystis are explored, including lineage sorting, hybridization, and cryptic species.  相似文献   

10.
Plagiochila sect. Vagae is a large pantropical clade that is characterized morphologically by frequent terminal branching, vegetative distribution by propagules on the ventral surface of the leaves and a capsule wall with thickenings in all layers. Plagiochila corrugata from Brazil is characterized by strongly undulate, toothed leaf margins and represents the only known neotropical species of sect. Vagae with unispiral elaters. Plagiochila cambuena from Madagascar is distinguished by the same features. Maximum likelihood and parsimony analyses of 38 nrDNA ITS sequences of Plagiochila reveal P. corrugata and P. cambuena in a weakly (ML) to well (MP) supported monophyletic lineage within P.  sect.  Vagae . As an outcome of the morphological and molecular investigation, P. cambuena is relegated to the synonymy of P. corrugata. Plagiochila corrugata is placed in a Vagae -subclade with 11 further American species. The range of P. corrugata can be ascribed to long-range dispersal from the Neotropics rather than a Gondwanan distribution. Species from tropical Asia and Africa are placed at the base of the Vagae clade. Branch length within P.  sect.  Vagae points to a sudden radiation.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 469–481.  相似文献   

11.
The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum‐likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 686–710.  相似文献   

12.
The butterfly Pieris napi (L.) and relatives exemplify recently evolving taxa, exhibiting variation that makes their evolutionary dynamics interesting, but their systematics difficult. Wing-pattern characters commonly used to distinguish these Holarctic insects display both genetic polymorphism and environmentally-cued polyphenism. Often, these causes of variation are confounded, impairing the characters' phylogenetic usefulness. DNA sequences of four mitochondrial genes offer an independent view of pierine phylogeny. Sampling diverse relatives within family Pieridae assists resolution of the P. napi complex, suggests previous underestimation of clade diversity in subfamily Pierinae, and shows that other genera near Pieris also display confusions of wing-pattern-based phylogenetic inference. The European P. napi is sister to all North American taxa, and is well diverged from them all in sequences. The North American taxa comprise a northern subclade including Pieris oleracea , and questionably distinct Pieris ' angelika ', and a southern subclade including distinct Pieris virginiensis , Pieris marginalis , and Pieris macdunnoughii , and other regional entities yet to be clarified. Weak bootstrap support for some nodes in this group arises from a closeness of sequence identity rather than character conflict; more sequence data and denser geographical sampling may resolve these nodes more clearly. Evidence of reproductive isolation, from other experimental hybridization studies, agrees with the DNA results where these conflict with other divergent character sets. The system offers much promise for a deeper understanding of character evolution in relation to phyletic differentiation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 413–435.  相似文献   

13.
We studied phylogenetic relationships of the New World Jays (NWJs) based on DNA sequences from three mitochondrial and two nuclear loci. Sampling included at least two individuals from each of the seven NWJ genera and four outgroups of closely related corvids, as well as six of the 16 Cyanocorax species (including two representatives of the previously recognized "Cissilopha"). Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and a combined dataset. The combined phylogenetic analysis supports the basal position of Cyanolyca to all other NWJs, a (Cyanocorax (Calocitta, Psilorhinus)) clade, and a ((Cyanocitta, Aphelocoma) Gymnorhinus) clade that agrees with a novel morphological synapomorphy uniting Cyanocitta and Aphelocoma. Within Cyanocorax, C. yncas (former "Xanthoura") is basal to a split among former "Cyssilopha" species and the rest of the Cyanocorax species. To explore implications for the historical biogeography of the NJWs, we used Dispersal-Vicariance Analysis, which indicated that NWJs originated either in Mesoamerica or North America+Mesoamerica, with South American NWJs dispersing three times independently from Mesoamerica.  相似文献   

14.
The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeri Smith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [ Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade { Philautus odontotarsus Ye & Fei, 1993, [ Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma , so as to correct the paraphyly. Additionally, the monophyly of ' Aquixalus ' is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/ Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 733–749.  相似文献   

15.
Relationships among extant and fossil echimyids (Rodentia: Hystricognathi)   总被引:1,自引:0,他引:1  
The echimyid rodents are the most diverse group of Neotropical hystricognaths, with approximately 40 extant and fossil genera. Craniodental characters are proposed in order to formulate hypotheses of phylogenetic relationships within the Echimyidae. A data matrix of 54 taxa and 50 characters is constructed and submitted to parsimony analyses using PAUP and WinClada programs. Analysis of the complete data set results in 47 448 most parsimonious trees 107 steps long. These trees are summarized in a strict consensus tree, which is taken as the main phylogenetic hypothesis resulting from this study. The monophyly of several currently recognized supraspecific taxa is not corroborated. These are: the subfamilies Eumysopinae, Echimyinae, Myocastorinae and Adelphomyinae; and the genera Proechimys , Echimys and Makalata . Conversely, the monophyly of Dactylomyinae and Trinomys is supported. New associations are proposed: (1) a clade comprising the extant Carterodon , Clyomys and Euryzygomatomys and the fossil Pampamys and Theridomysops placed at the base of the crown-group Echimyidae; (2) a clade uniting Proechimys , Hoplomys and Trinomys , which is the sister-taxon of (3) a clade including Mesomys , Lonchothrix , Myocastor and a clade with extant dactylomyines and echimyines and associated fossil taxa. Based on this phylogenetic hypothesis, patterns of tooth evolution in Echimyidae are discussed, and minimum ages for the divergence events within the family are estimated.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 445–477.  相似文献   

16.
The complex evolutionary history of the Eurasian gastropod lineage Theodoxus reflects the evolution of marine basins following the breakup of the Tethys Sea. Today, this clade inhabits the lakes, rivers, streams, and estuaries of Europe, southwestern Asia, and North Africa. Here we present the first phylogenetic hypothesis for this clade. Based upon extensive geographic and taxonomic sampling, portions of the mitochondrial genes for cytochrome c oxidase subunit I and 16S rRNA were sequenced and analysed using maximum likelihood and maximum parsimony methods. Results from bootstrap analyses, Bayesian analysis, and sensitivity analyses lend support to six deep phylogenetic subdivisions within Theodoxus. These major clades are geographically associated with the major post-Tethyan marine basins. Estimates of divergence times using a penalized likelihood approach indicate that divergence of these major lineages occurred during the Miocene, simultaneous with the breakup of the Mediterranean and Paratethys Seas. The resulting major subclades later diversified during the Pliocene, primarily within geographic regions associated with the eastern and western Mediterranean Sea, the Pannonian Basin, and the Black Sea, thus producing the extant species assemblages. Finally, these phylogenetic results imply that much of the current taxonomy is flawed, therefore we offer recommendations for revising the classification of Theodoxus species based on phylogenetic systematics.  相似文献   

17.
18.
Although the temperate regions of South America are known to have a diverse daphniid fauna, there has been no genetic evaluation of the existing taxonomic system or of the affinities between the North and South American faunas. The present study analyses mitochondrial DNA sequences and allozyme variation to investigate species diversity in 176 Daphnia populations from Argentina. This work established the presence of at least 15 species in Argentina, six of which are either undescribed or are currently misidentified and two of which represent range extensions of North American taxa. Eleven of the Argentine species appear endemic to South America, while the remaining four also occur in North America. In the latter cases, the close genetic similarity between populations from North and South America indicates the recent exchange of propagules between the continents. While biological interactions and habitat availability have undoubtedly contributed to the observed species distributions, chance dispersal has apparently played a dominant role in structuring large-scale biogeographical patterns in this genus and probably in other passively-dispersed organisms.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 171−205.  相似文献   

19.
Shaw AJ 《Molecular ecology》2000,9(5):595-608
Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA (nrDNA) from 70 populations of Mielichhoferia elongata and M. mielichhoferiana, plus two outgroup species, was analysed using maximum parsimony and maximum likelihood methods. High levels of nucleotide substitution and numerous insertion-deletion events were detected within and between the two species. M. elongata is monophyletic with regard to nrDNA variation, but M. mielichhoferiana is paraphyletic. (M. elongata is nested within it.) A clade within M. mielichhoferiana provides evidence of vicariance, with North American and Scandinavian sister groups of populations. Two major clades are resolved in M. elongata by sequence data that are completely congruent with previous isozyme work. One clade includes populations from both North America and Europe whereas the other is strictly North American. These two clades, resolved by multiple independent loci, clearly represent cryptic species within the morphologically uniform M. elongata. Certain geographical areas, most notably southwestern Colorado in Ouray and San Juan Counties, harbour diverse populations of M. elongata with distinct phylogenetic and phylogeographical histories. Morphologically indistinguishable but phylogenetically distant populations were detected a few metres apart at one site. In contrast, all populations collected over hundreds of kilometres in California belong to a single clade. Arctic North American populations belong to a clade that includes disjunct populations in Alaska, northern Ellesmere Island, and the northeastern USA, but not subarctic Swedish populations, which are more closely related to plants from the Rocky Mountains. Morphological uniformity belies complex infraspecific phylogenetic patterns within M. elongata and M. mielichhoferiana.  相似文献   

20.
Phylogeography of Soboliphyme baturini , a nematode parasite in mustelids, is explored across Beringia. Sequences of the mitochondrial cytochrome c oxidase subunit I and nicotinamide adenine dinucleotide dehydrogenase subunit 4 genes were evaluated from 37 S. baturini , representing 19 localities throughout Alaska, Canada, and Siberia. A total of 30 haplotypes was recovered and maximum parsimony and Bayesian phylogenetic analyses support the recognition of a single species with a distribution extending from the Palearctic to the Nearctic. Within S. baturini , a host-specific partition in North America between Martes caurina and Martes americana was not identified. Instead, substantial geographic structure within S. baturini relates to the dynamic geological history of this northern region and especially the North Pacific Coast. Beringia and other coastal refugia along the western margin of North America played a large role during stadial maxima in the persistence and divergence of the parasite. Repeated events for biotic expansion and geographic colonization across the Bering Land Bridge and the Holarctic during glacial maxima in the Pleistocene appear to have facilitated at least two episodes of host-switching of this nematode among mustelids in populations now distributed in eastern Beringia.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 651–663.  相似文献   

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