Phylogenetic Analyses of a Combined Data Set Suggest that the Attheya Lineage is the Closest Living Relative of the Pennate Diatoms (Bacillariophyceae)

Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae, Arundinarieae) genus from Sri Lanka, is recognized based on chloroplast sequence data from five markers (coding: ndhF 3’ end; non-coding: rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). This genus represents the twelfth major lineage of temperate woody bamboos and is characterized by pachymorph culm bases with short necks, unicaespitose clumps, culm leaf girdles ca. 1 mm wide, usually abaxially hispid culm leaves with non-irritating hairs, persistent foliage leaf sheaths, complete branch sheathing and acute to biapiculate palea apices. Maximum Parsimony, Bayesian Inference and Maximum Likelihood analyses of a combined data set consistently strongly supported the monophyly of this Sri Lankan temperate woody bamboo clade. Although the Kishino-Hasegawa test is unable to reject the alternative hypothesis of monophyly of the Sri Lankan clade plus Bergbambos tessellata from South Africa, Kuruna and Bergbambos are distinguishable by a combination of morphological characters. A few additional cpDNA markers not previously used in phylogenetic analyses of Arundinarieae were tested to evaluate their utility in this taxonomically difficult tribe.

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Mazzaella canaliculata comb. nov. based on Chondrus canaliculatus (Gigartinaceae, Rhodophyta) from Peru and Chile

Phytotaxa ◽

10.11646/phytotaxa.497.3.2 ◽

2021 ◽

Vol 497 (3) ◽

pp. 211-228

Author(s):

NATALIA ARAKAKI ◽

MARIA ELIANA RAMIREZ

Keyword(s):

Southern Hemisphere ◽

Phylogenetic Analyses ◽

The Other ◽

Red Seaweed ◽

Central Coast ◽

Data Set ◽

Anatomical Features ◽

Tubular Cells ◽

Coi Sequences ◽

Combined Data

Chondrus canaliculatus is a red seaweed endemic to Peru and Chile. The name currently represents the only species classified in Chondrus from the southern hemisphere. Based on previous phylogenetic analyses, C. canaliculatus is polyphyletic with respect to Chondrus and possesses unique morpho-anatomical features that distinguish it from other genera in the Gigartinaceae. In this study, expanded phylogenetic analyses using rbcL and COI sequences, a combined data set, and morphological details were further examined to address the taxonomy and evolutionary systematics of C. canaliculatus. Genetic analyses placed C. canaliculatus well within the genus Mazzaella and therefore Mazzaella canaliculata comb. nov. is proposed. Mazzaella canaliculata is distinguished from the other Mazzaella from the southern hemisphere by its dichotomous branching, secondary filaments that persist and leave a well-defined involucre, the absence of terminal tubular cells, and tetrasporangia that are borne from secondary filaments from inner cortical and outer medullary cells. The distributional range of M. canaliculata is extended from the central coast of Peru, Bahía de Pucusana, Lima (12° S) to Chiloé, Chile (41° S). This study contributes to the systematics of the Gigartinaceae and formally validates a problematic species based on a combined analysis of molecular, morphological and anatomical data using recently field collected specimens.

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Integration of morphological and molecular data sets in estimating fungal phytogenies

Canadian Journal of Botany ◽

10.1139/b95-307 ◽

1995 ◽

Vol 73 (S1) ◽

pp. 649-659 ◽

Cited By ~ 38

Author(s):

François Lutzoni ◽

Rytas Vilgalys

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Molecular Data ◽

Morphological Data ◽

Homogeneity Test ◽

Data Sets ◽

Data Set ◽

Sampling Statistics ◽

Combined Data

To provide a clearer picture of fungal species relationships, increased efforts are being made to include both molecular and morphological data sets in phylogenetic studies. This general practice in systematics has raised many unresolved questions and controversies regarding how to best integrate the phylogenetic information revealed by morphological and molecular characters. This is because phylogenetic trees derived using different data sets are rarely identical. Such discrepancies can be due to sampling error, to the use of an inappropriate evolutionary model for a given data set, or to different phylogenetic histories between the organisms and the molecule. Methods have been developed recently to test for heterogeneity among data sets, although none of these methods have been subjected to simulation studies. In this paper we compare three tests: a protocol described by Rodrigo et al., an adapted version of Faith's T-PTP test, and Kishino and Hasegawa's likelihood test. These tests were empirically compared using seven lichenized and nonlichenized Omphalina species and the related species Arrhenia lobata (Basidiomycota, Agaricales) for which nrDNA large subunit sequences and morphological data were gathered. The results of these three tests were inconsistent, Rodrigo's test being the only one suggesting that the two data sets could be combined. One of the three most parsimonious trees obtained from the combined data set with eight species is totally congruent with the relationships among the same eight species in an analysis restricted to the same portion of the nrDNA large subunit but extended to 26 species of Omphalina and related genera. Therefore, the results from phylogenetic analyses of this large molecular data set converged on one of the three most parsimonious topologies generated by the combined data set analysis. This topology was not recovered from either data set when analysed separately. This suggests that Rodrigo's homogeneity test might be better suited than the two other tests for determining if trees obtained from different data sets are sampling statistics of the same phylogenetic history. Key words: data sets heterogeneity, homogeneity test, lichen phylogeny, Omphalina, ribosomal DNA.

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Resurrection of the Family Grateloupiaceae Emend. (Halymeniales, Rhodophyta) Based on a Multigene Phylogeny and Comparative Reproductive Morphology

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.775627 ◽

2021 ◽

Vol 9 ◽

Author(s):

Su Yeon Kim ◽

Hyung Woo Lee ◽

Eun Chan Yang ◽

Sung Min Boo ◽

Juan Lopez-Bautista ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Complex Iii ◽

Outer Cortex ◽

Data Set ◽

Auxiliary Cell ◽

The Family ◽

Red Algal ◽

Fusion Cell ◽

The Many ◽

Combined Data

The marine red algal order Halymeniales currently includes two families, the Halymeniaceae and Tsengiaceae, and consist of 38 genera and about 358 species. Phylogenetic analyses on specific taxa of the order are common, but not comprehensive, leaving the many intra-ordinal relationships within the Halymeniales unresolved. To reassess the phylogeny of the Halymeniales, we conducted extensive phylogenetic analyses based on 207 rbcL sequences and multigene analyses (rbcL, psaA, psbA, cox1, and LSU) using 47 taxa from the order. The combined data set fully supports the monophyly of the Grateloupia sensu lato clade. Phylogenetic assessment of the reproductive structures in the order using the type of auxiliary cell ampullae, pericarp origin, and tetrasporangial development characters, supports a Grateloupia sensu lato clade distinct from the Halymeniaceae exemplified by the generitype Halymenia. As a result, we propose to reinstate the family Grateloupiaceae Schmitz based on the Grateloupia sensu lato clade and including Grateloupia and eight other genera: Dermocorynus, Mariaramirezia, Neorubra, Pachymeniopsis, Kintokiocolax, Phyllymenia, Prionitis, and Yonagunia. The emended Grateloupiaceae is distinguished from the Halymeniaceae by the following three characteristics; (i) simple unbranched and unilateral type of auxiliary cell ampullae, (ii) pericarp formed densely by the fusion of secondary medullary filaments from subcortical cells and lateral ampullary filaments from a fusion cell complex, (iii) tetrasporangia originating laterally from the outer cortex. The Halymeniales comprises the monophyletic Grateloupiaceae, Halymeniaceae sensu lato (which requires further study), and the Tsengiaceae.

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A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)

Zootaxa ◽

10.11646/zootaxa.4559.2.8 ◽

2019 ◽

Vol 4559 (2) ◽

pp. 349 ◽

Cited By ~ 3

Author(s):

KATHERINE SGOUROS ◽

LAWRENCE M. PAGE ◽

SARAH A. ORLOFSKE ◽

ROBERT C. JADIN

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Genes ◽

Data Set ◽

The Third ◽

D Loop ◽

Taxonomic Changes ◽

Taxonomic Implications ◽

Species Groups ◽

Combined Data

There is a general consensus that the genus Schistura (Nemacheilidae), currently with 241 species, is not monophyletic. However, weak morphological synapomorphies and a lack of genetic data for most species of Schistura and their presumptive relatives have prevented meaningful diagnoses of species groups within this genus. To aid in deciphering evolutionary relationships, sequence data from two mitochondrial genes (cytochrome b and D-loop) were implemented in phylogenetic analyses for species of Schistura and other nemacheilids for which data from earlier studies and recently collected material were available. This analysis of 67 nemacheilid species, including 28 species of Schistura, provides the most comprehensive phylogeny of Nemacheilidae to date. In the phylogenetic tree for the combined data set, species of Schistura clustered in three clades. One clade contained 14 species of Schistura and Sectoria heterognathos and was sister to Homatula. A second clade of 11 species of Schistura was in a larger clade with Turcinoemacheilus kosswigi and Nemacheilus corica. The third clade contained three species, all from the Mae Khlong basin of Thailand. Taxonomic implications of these results are discussed; however, a more taxon-rich dataset and nuclear sequence data are needed before making taxonomic changes.

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Acanthocorticium brueggemannii, a new corticioid genus and species related to cyphelloid fungi in the euagarics clade (Agaricales, Basidiomycota)

Botany ◽

10.1139/cjb-2015-0053 ◽

2015 ◽

Vol 93 (8) ◽

pp. 453-463 ◽

Cited By ~ 1

Author(s):

Juliano M. Baltazar ◽

Sergio P. Gorjón ◽

María Belén Pildain ◽

Mario Rajchenberg ◽

Rosa Mara B. da Silveira

Keyword(s):

Phylogenetic Analyses ◽

New Taxon ◽

Southern Brazil ◽

Data Set ◽

Hyphal System ◽

Microscopic Features ◽

Thin Walled ◽

Combined Data

Acanthocorticium brueggemannii gen. et sp. nov. is introduced based on specimens from Southern Brazil. This corticioid fungus is characterized by resupinate basidiomes with smooth to tuberculate hymenophore, a monomitic hyphal system with simple-septate hyphae, finely echinulate halocystidia, cylindrical to clavate, dextrinoid acanthophyses, and globose, hyaline, smooth, and thin-walled IKI– basidiospores. Phylogenetic analyses of a LSU data set and a combined data set of ITS and LSU were carried out and the new taxon was found to be related to cyphelloid fungi within the Agaricales. Descriptions and drawings of the microscopic features of A. brueggemannii are provided.

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Macrodiplodiopsis in Lophiostomataceae, Pleosporales

Phytotaxa ◽

10.11646/phytotaxa.176.1.19 ◽

2014 ◽

Vol 176 (1) ◽

pp. 192 ◽

Cited By ~ 11

Author(s):

NALIN N. WIJAYAWARDENE ◽

ERIO CAMPORESI ◽

D. JAYARAMA BHAT ◽

YU SONG ◽

K.W. THILINI CHETHANA ◽

...

Keyword(s):

Maximum Likelihood ◽

Type Species ◽

Posterior Probability ◽

Phylogenetic Analyses ◽

New Combinations ◽

Data Set ◽

Molecular Studies ◽

Close Relationship ◽

High Bootstrap ◽

Combined Data

Macrodiplodiopsis desmazieri, the type species of Macrodiplodiopsis, was collected from Italy, and morpho-molecular studies were carried out. Phylogenetic analyses (maximum-likelihood, maximum parsimony and Bayesian) using combined data set of LSU, SSU and EF1-α sequences showed our strain to group in Lophiostomataceae (Pleosporales) with Misturatosphaeria uniseriata and other Misturatosphaeria spp. Floricola striata, the type species of Floricola also groups in the same clade with a close relationship with Misturatosphaeria cruciformis. The Macrodiplodiopsis clade is well supported with high bootstrap and posterior probability. Floricola striata and nine species of Misturatosphaeria are transferred to the older name Macrodiplodiopsis as new combinations.

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Selection of children with ultra-severe traumatic brain injury for neurosurgical intervention

Journal of Neurosurgery Pediatrics ◽

10.3171/2019.1.peds18293 ◽

2019 ◽

Vol 23 (6) ◽

pp. 670-679

Author(s):

Krista Greenan ◽

Sandra L. Taylor ◽

Daniel Fulkerson ◽

Kiarash Shahlaie ◽

Clayton Gerndt ◽

...

Keyword(s):

Traumatic Brain Injury ◽

Brain Injury ◽

Decision Tree ◽

Prediction Model ◽

Severe Traumatic Brain Injury ◽

Pupillary Response ◽

Data Set ◽

Robust Model ◽

Gcs Score ◽

Combined Data

OBJECTIVEA recent retrospective study of severe traumatic brain injury (TBI) in pediatric patients showed similar outcomes in those with a Glasgow Coma Scale (GCS) score of 3 and those with a score of 4 and reported a favorable long-term outcome in 11.9% of patients. Using decision tree analysis, authors of that study provided criteria to identify patients with a potentially favorable outcome. The authors of the present study sought to validate the previously described decision tree and further inform understanding of the outcomes of children with a GCS score 3 or 4 by using data from multiple institutions and machine learning methods to identify important predictors of outcome.METHODSClinical, radiographic, and outcome data on pediatric TBI patients (age < 18 years) were prospectively collected as part of an institutional TBI registry. Patients with a GCS score of 3 or 4 were selected, and the previously published prediction model was evaluated using this data set. Next, a combined data set that included data from two institutions was used to create a new, more statistically robust model using binomial recursive partitioning to create a decision tree.RESULTSForty-five patients from the institutional TBI registry were included in the present study, as were 67 patients from the previously published data set, for a total of 112 patients in the combined analysis. The previously published prediction model for survival was externally validated and performed only modestly (AUC 0.68, 95% CI 0.47, 0.89). In the combined data set, pupillary response and age were the only predictors retained in the decision tree. Ninety-six percent of patients with bilaterally nonreactive pupils had a poor outcome. If the pupillary response was normal in at least one eye, the outcome subsequently depended on age: 72% of children between 5 months and 6 years old had a favorable outcome, whereas 100% of children younger than 5 months old and 77% of those older than 6 years had poor outcomes. The overall accuracy of the combined prediction model was 90.2% with a sensitivity of 68.4% and specificity of 93.6%.CONCLUSIONSA previously published survival model for severe TBI in children with a low GCS score was externally validated. With a larger data set, however, a simplified and more robust model was developed, and the variables most predictive of outcome were age and pupillary response.

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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Drought Propagation in Semi-Arid River Basins in Latin America: Lessons from Mexico to the Southern Cone

Water ◽

10.3390/w10111564 ◽

2018 ◽

Vol 10 (11) ◽

pp. 1564 ◽

Cited By ~ 7

Author(s):

Melanie Oertel ◽

Francisco Meza ◽

Jorge Gironás ◽

Christopher A. Scott ◽

Facundo Rojas ◽

...

Keyword(s):

Soil Moisture ◽

Drought Monitoring ◽

Moisture Index ◽

Data Set ◽

Basin Scale ◽

Soil Moisture Index ◽

Streamflow Data ◽

Governmental Institutions ◽

Negative Impacts ◽

Combined Data

Detecting droughts as early as possible is important in avoiding negative impacts on economy, society, and environment. To improve drought monitoring, we studied drought propagation (i.e., the temporal manifestation of a precipitation deficit on soil moisture and streamflow). We used the Standardized Precipitation Evapotranspiration Index (SPEI), Standardized Streamflow Index (SSI), and Standardized Soil Moisture Index (SSMI) in three drought-prone regions: Sonora (Mexico), Maipo (Chile), and Mendoza-Tunuyán (Argentina) to study their temporal interdependence. For this evaluation we use precipitation, temperature, and streamflow data from gauges that are managed by governmental institutions, and satellite-based soil moisture from the ESA CCI SM v03.3 combined data set. Results confirm that effective drought monitoring should be carried out (1) at river-basin scale, (2) including several variables, and (3) considering hydro-meteorological processes from outside its boundaries.

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