The Tupí-Guaraní language family

Diachronica ◽  
2021 ◽  
Author(s):  
Fabrício Ferraz Gerardi ◽  
Stanislav Reichert
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Stochastic Algorithm ◽  
Language Family ◽  
Historical Sources ◽  
Bayesian Phylogenetic Analysis

Abstract Attempts to classify Tupí-Guaraní languages have so far been inconsistent with archaeological evidence and ignored information from historical sources. The case of Tupinambá is most illustrative in this regard. Using both Bayesian phylogenetic analysis and a stochastic algorithm that reconstructs phylogenetic trees by relying on maximum likelihood estimation, we suggest a new internal classification of the Tupí-Guaraní branch. The results of the analyses are in accordance with the most recent genetic research on Tupían populations and challenge previous classifications by suggesting, among others, that Tupinambá should not be considered a ‘Guaraní’ language.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

scholarly journals A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)

Phytotaxa ◽  
2014 ◽  
Vol 159 (4) ◽  
pp. 241 ◽  
Author(s):  
Yu-lan Peng ◽  
Yu Zhang ◽  
Xin-fen Gao ◽  
Lin-jing Tong ◽  
Liang Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Chloroplast Dna ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Likelihood Inference ◽  
Nuclear Its ◽  
Chloroplast Dna Regions

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

scholarly journals A Bayesian Phylogenetic Classification of Tupí-Guaraní

2015 ◽  
Vol 15 (2) ◽  
pp. 193 ◽  
Author(s):  
Lev Michael ◽  
Natalia Chousou-Polydouri ◽  
Keith Bartolomei ◽  
Erin Donnelly ◽  
Sérgio Meira ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Structure ◽  
Character Table ◽  
Loss Model ◽  
Phylogenetic Classification ◽  
Bayesian Phylogenetic Analysis ◽  
Binary Coding ◽  
Semantic Shift ◽  
Lexical Data

This paper presents an internal classification of Tupí-Guaraní based on lexical data from 30 Tupí-Guaraní languages and 2 non-Tupí-Guaraní Tupian languages, Awetí and Mawé. A Bayesian phylogenetic analysis using a generalized binary cognate gain and loss model was carried out on a character table based on the binary coding of cognate sets, which were formed with attention to semantic shift. The classification shows greater internal structure than previous ones, but is congruent with them in several ways.

scholarly journals Taxonomic Revisiting and Phylogenetic Placement of Two Endangered Plant Species: Silene leucophylla Boiss. and Silene schimperiana Boiss. (Caryophyllaceae)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 740
Author(s):  
Ahmed EL-Banhawy ◽  
Iman H. Nour ◽  
Carmen Acedo ◽  
Ahmed ElKordy ◽  
Ahmed Faried ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Epidermal Cells ◽  
Phylogenetic Study ◽  
Endangered Plant ◽  
Sinai Peninsula ◽  
Phylogenetic Placement ◽  
Bayesian Phylogenetic Analysis ◽  
Genus Silene ◽  
Sectional Classification

The genus Silene L. is one of the largest genera in Caryophyllaceae, and is distributed in the Northern Hemisphere and South America. The endemic species Silene leucophylla and the near-endemic S. schimperiana are native to the Sinai Peninsula, Egypt. They have reduced population size and are endangered on national and international scales. These two species have typically been disregarded in most studies of the genus Silene. This research integrates the Scanning Electron Microscope (SEM), species micromorphology, and the phylogenetic analysis of four DNA markers: ITS, matK, rbcL and psb-A/trn-H. Trichomes were observed on the stem of Silene leucophylla, while the S. schimperiana has a glabrous stem. Irregular epicuticle platelets with sinuate margin were found in S. schimperiana. Oblong, bone-shaped, and irregularly arranged epidermal cells were present on the leaf of S. leucophylla, while Silene schimperiana leaf has “tetra-, penta-, hexa-, and polygonal” epidermal cells. Silene leucophylla and S. schimperiana have amphistomatic stomata. The Bayesian phylogenetic analysis of each marker individually or in combination represented the first phylogenetic study to reveal the generic and sectional classification of S. leucophylla and S. schimperiana. Two Silene complexes are proposed based on morphological and phylogenetic data. The Leucophylla complex was allied to section Siphonomorpha and the Schimperiana complex was related to section Sclerocalycinae. However, these two complexes need further investigation and more exhaustive sampling to infer their complex phylogenetic relationships.

Maximum likelihood estimation of phylogeny using stratigraphic data

Paleobiology ◽  
1997 ◽  
Vol 23 (2) ◽  
pp. 174-180 ◽  
Author(s):  
John P. Huelsenbeck ◽  
Bruce Rannala
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimator ◽  
Phylogenetic Trees ◽  
Likelihood Estimation ◽  
Likelihood Estimator ◽  
Fossil Species ◽  
True Tree ◽  
Phylogeny Estimation ◽  
Fossil Preservation ◽  
Preservation Rate

The stratigraphic distribution of fossil species contains potential information about phylogeny because some phylogenetic trees are more consistent with the distribution of fossils in the rock record than others. A maximum likelihood estimator of phylogeny is derived using an explicit mathematical model of fossil preservation. The method assumes that fossil preservations within lineages follow an independent Poisson process, but can be extended to include other preservation models. The performance of the method was examined using Monte Carlo simulation. The performance of the maximum likelihood estimator of topology increases with an increase in the preservation rate. The method is biased, like other methods of phylogeny estimation, when the rate of fossil preservation is low; estimated trees tend to be more asymmetrical than the true tree. The method appears to perform well as a tree rooting criterion even when preservation rates are low. We suggest several possible extensions of the method to address other questions about the nature of fossil preservation and the process of speciation and extinction over time and space.

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