From 18S ribosomal sequence data to evolution of morphology among the fungi

1995 ◽  
Vol 73 (S1) ◽  
pp. 677-683 ◽  
Author(s):  
Mary L. Berbee ◽  
John W. Taylor
Keyword(s):  
Sequence Data ◽  
Morphological Evolution ◽  
Strong Support ◽  
Morphological Characters ◽  
Geological Time ◽  
Data Set ◽  
Dna Sequence Data ◽  
Sequence Of Events ◽  
History Of ◽  
Time Of Divergence

From ribosomal DNA sequence data we can estimate ascomycete relationships, the time of divergence of major ascomycete lineages, and the history of morphological evolutionary change. Groups long accepted by mycologists such as the filamentous ascomycetes with fruiting bodies, (the plectomycetes and pyrenomycetes) are supported by 18S rDNA sequence data. After generating a phylogenetic tree showing relationships, the geological time of divergence of major fungal lineages may be estimated, inferring elapsed time using the calibrated percent substitutions between sequences. Determining the pathway of evolution of morphological characters is more difficult than inferring the relationships among these taxa. To establish the history of morphological evolution, we need accurate trees receiving strong support from our data set. We also need taxa with the intermediate characters to reveal the sequence of events in morphological evolution. Soon, however, we may be able to take a more direct approach to evolution of morphological characters, sequencing the genes that code for the character. Key words: fungus evolution, ascomycete phylogeny.

Perssoniella and the genera of Schistochilaceae: a new classification based on molecular phylogenies

2010 ◽  
Vol 23 (4) ◽  
pp. 229 ◽  
Author(s):  
Xiaolan He ◽  
David Glenny
Keyword(s):  
Dna Sequence ◽  
New Caledonia ◽  
Sequence Data ◽  
Strong Support ◽  
Morphological Characters ◽  
Monotypic Genus ◽  
New Classification ◽  
Dna Sequence Data ◽  
The Family ◽  
Molecular Phylogenies

The monotypic genus Perssoniella with P. vitreocincta Herzog, endemic to New Caledonia, possesses a series of unique morphological characters and it has been assumed that the genus, assigned to the family Perssoniellaceae and suborder Perssoniellineae, is very isolated but sister to the family Schistochilaceae. The systematic identity of Perssoniella vitreocincta was studied using DNA sequence data for the chloroplast rbcL, rps4 and trnL-F regions. Our analyses placed Perssoniella vitreocincta within the family Schistochilaceae, and within Schistochila itself, with strong support. It suggests that retaining Perssoniella as an independent genus is untenable and we transfer it to the genus Schistochila. Our results indicate that Perssoniella vitreocincta is not an archaic species, as presupposed earlier. The differentiating characters in Perssoniella are mostly probably later derived, rather than ancestral. Our analyses also placed Pachyschistochila and Paraschistochila within Schistochila, again with strong support. We also transfer these two genera to Schistochila.

The phylogeny, biogeography and morphological evolution of Gaultheria (Ericaceae) from Australia and New Zealand

2009 ◽  
Vol 22 (4) ◽  
pp. 229 ◽  
Author(s):  
Catherine M. Bush ◽  
Steven J. Wagstaff ◽  
Peter W. Fritsch ◽  
Kathleen A. Kron
Keyword(s):  
New Zealand ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Morphological Characters ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Biogeographical Analysis ◽  
Dispersal Events ◽  
South American Origin

Phylogenetic relationships within Gaultheria L. from Australia and New Zealand were examined by using DNA sequence data from matK, ndhF, nrITS, waxy and lfy. In the combined parsimony and maximum likelihood analyses, all Australia/New Zealand species form a clade that is sister to a clade of temperate South American species. Optimisation of morphological characters that have been emphasised in classifications of Gaultheria onto the molecular phylogeny revealed that, within the Australia/New Zealand clade, non-fleshy fruiting calyces, berries and solitary-flowered inflorescences each evolved twice, from fleshy fruiting calyces, capsules and multiple-flowered inflorescences, respectively. A historical biogeographical analysis that included the temperate southern hemisphere element in Gaultheria supports a South American origin of the Australia/New Zealand clade, followed by three dispersal events from New Zealand to Australia. Whether the origin is from temperate or tropical South America is ambiguous in our analysis.

scholarly journals Early-branching euteleost relationships: Areas of congruence between concatenation and coalescent model inferences

2017 ◽  
Author(s):  
Matthew A Campbell ◽  
Michael E Alfaro ◽  
Max Belasco ◽  
J. Andres Lopez
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Strong Support ◽  
Supporting Evidence ◽  
Gene Trees ◽  
Data Set ◽  
Dna Sequence Data ◽  
Tree Estimation ◽  
Analytical Frameworks ◽  
High Support

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted both in concatenated and joint gene trees and species tree estimation frameworks. Both analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the two analysis types receiving high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are apparent within the Ostarioclupeomorpha and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

scholarly journals Seasonal Migration, Speciation, and Morphological Convergence in the Genus Catharus (Turdidae)

The Auk ◽  
2006 ◽  
Vol 123 (4) ◽  
pp. 1052-1068 ◽  
Author(s):  
Kevin Winker ◽  
Christin L. Pruett
Keyword(s):  
Sequence Data ◽  
Morphological Evolution ◽  
Morphological Characters ◽  
Seasonal Migration ◽  
Species Flock ◽  
Hylocichla Mustelina ◽  
Base Pairs ◽  
Long Distance ◽  
Dna Sequence Data ◽  
Traditional Taxonomy

Abstract The effects of seasonal migration on evolutionary change within lineages is poorly understood, in terms of both differentiation (cladogenesis) and specialization (anagenesis). Regarding differentiation, two contradictory hypotheses exist: Seasonal migration counters differentiation; or it can stimulate differentiation by exposing lineages to new environments. Regarding specialization, the morphological consequences of a migratory life history have not been well explored. We examined these issues by reconstructing morphological and molecular phylogenies of the genus Catharus (Turdidae), a group of forest-dwelling, New World thrushes traditionally considered to include a small “species flock” of Nearctic-Neotropic migrants. DNA sequence data (2,920–3,027 base pairs) do not support traditional taxonomy, and morphological characters conflicted with these data. Results suggest that long-distance seasonal migration arose independently four times in Catharus sensu lato (including Hylocichla mustelina). Correlated morphological evolution occurred among several characters in these lineages, and these shared traits may stem from ecological conditions in Nearctic forests. Migración Estacional, Especiación y Convergencia Morfológica en el Género Catharus (Turdidae)

scholarly journals Early-branching euteleost relationships: Areas of congruence between concatenation and coalescent model inferences

2017 ◽  
Author(s):  
Matthew A Campbell ◽  
Michael E Alfaro ◽  
Max Belasco ◽  
J. Andres Lopez
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Strong Support ◽  
Supporting Evidence ◽  
Gene Trees ◽  
Data Set ◽  
Dna Sequence Data ◽  
Tree Estimation ◽  
Analytical Frameworks ◽  
High Support

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted both in concatenated and joint gene trees and species tree estimation frameworks. Both analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the two analysis types receiving high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are apparent within the Ostarioclupeomorpha and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

scholarly journals Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3548 ◽  
Author(s):  
Matthew A. Campbell ◽  
Michael E. Alfaro ◽  
Max Belasco ◽  
J. Andrés López
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Strong Support ◽  
Species Tree ◽  
Supporting Evidence ◽  
Gene Trees ◽  
Data Set ◽  
Dna Sequence Data ◽  
Tree Estimation ◽  
Analytical Frameworks

Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny.

scholarly journals The Age of a Unique Event Polymorphism

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 401-409
Author(s):  
Lada Markovtsova ◽  
Paul Marjoram ◽  
Simon Tavaré
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Hypervariable Region ◽  
Data Set ◽  
Dna Sequence Data ◽  
Unique Event ◽  
Mitochondrial Data ◽  
Region I ◽  
History Of ◽  
Hypervariable Region I

Abstract We develop a Markov chain Monte Carlo approach for estimating the distribution of the age of a mutation that is assumed to have arisen just once in the history of the population of interest. We assume that in addition to the presence or absence of this mutation in a sample of chromosomes, we have DNA sequence data from a region completely linked to the mutant site. We apply our method to a mitochondrial data set in which the DNA sequence data come from hypervariable region I and the mutation of interest is the 9-bp region V deletion.

Molecular systematics of the ascomycete genus Farrowia (Chaetomiaceae)

2001 ◽  
Vol 79 (3) ◽  
pp. 321-333 ◽  
Author(s):  
Wendy A Untereiner ◽  
Valérie Débois ◽  
Françoise A Naveau
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Strong Support ◽  
Morphological Characters ◽  
Rrna Gene ◽  
Generic Level ◽  
Data Set ◽  
Close Relationship ◽  
Relationship Of

The genus Farrowia D. Hawksworth was established for members of the Chaetomiaceae with Botryotrichum-like anamorphs and long-necked ascomata, but the separation of Farrowia from Chaetomium Kunze has been questioned by mycologists who did not consider these characters to be significant at the generic level. The recent description of a species of Chaetomium with an aleurioconidial anamorph and long-necked ascomata prompted us to explore this question employing molecular characters. We sequenced a portion of the nuclear large ribosomal subunit rRNA gene (28S) of members of the Sordariales including species of Chaetomium, Farrowia and Thielavia. Phylogenetic analyses confirmed the monophyly of the Sordariales and the close relationship of Aporothielavia leptoderma to the genus Chaetomium. A sequence-based phylogeny identified a well-supported clade that included Chaetomium floriforme, Chaetomium sphaerale, members of the genus Farrowia, and longicollous species of Chaetomium with aleurioconidial anamorphs. A clade containing Chaetomium brevipilium, Chaetomium cuyabenoensis, Chaetomium homopilatum and species of Farrowia was inferred from the analysis of morphological characters, but this data set was found to be incongruent with the 28S sequence data. While these results are in agreement with the hypothesis that species of Farrowia comprise a group of closely related taxa, they do not provide strong support for the recognition of the genus Farrowia.Key words: anamorph, aleurioconidia, Botryotrichum, Chaetomium, 28S ribosomal RNA gene sequences.

Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)

Phytotaxa ◽  
2013 ◽  
Vol 146 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER B. HEENAN ◽  
ROB D. SMISSEN
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Papua New Guinea ◽  
New Genus ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
New Combinations ◽  
Southern South America ◽  
Dna Sequence Data

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera.        Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

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