scholarly journals Characters from the deciduous dentition and its interest for phylogenetic reconstruction in Hippopotamoidea (Cetartiodactyla: Mammalia)

2020 ◽  
Author(s):  
Helder Gomes Rodrigues ◽  
Fabrice Lihoreau ◽  
Maëva Orliac ◽  
Jean-Renaud Boisserie
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Reconstruction ◽  
Lower Degree ◽  
Parsimony Analysis ◽  
Deciduous Dentition ◽  
Mammal Species

Abstract Teeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.

scholarly journals Discovery of A New Mammal Species (Soricidae: Eulipotyphla) From Narcondam Volcanic Island, India

2021 ◽  
Author(s):  
Manokaran Kamalakannan ◽  
Chandrakasan Sivaperuman ◽  
Shantanu Kundu ◽  
Govindarusu Gokulakrishnan ◽  
Chinnadurai Venkatraman ◽  
...  
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Genetic Distances ◽  
External Morphology ◽  
Volcanic Island ◽  
Mammal Species ◽  
Molecular Approaches ◽  
Bayesian Phylogeny ◽  
Evolutionary Lineages

Abstract The present study discovered the existence of a new Crocidura species of shrew (Soricidae: Eulipotyphla) from Narcondam Island, India by using both morphological and molecular approaches. The new species, Crocidura narcondamica sp. nov. is medium-sized and has a distinct external morphology (darker-grey dense fur with a thick and darker tail) and craniodental (braincase is rounded and elevated with weak lambdoidal ridges) characters in comparison with other close congeners. This description illuminates the first discovery of soricid fauna (shrew) from this volcanic island and a total of 12 Crocidura species catalogued in the Indian checklist of mammals. The newly discovered species maintained sufficient genetic distances (12% to 16.6%) with other Crocidura species known from the Indian mainland, Andaman and Nicobar Archipelago, and Myanmar. Both Maximum-Likelihood and Bayesian phylogeny showed distinct clustering of all soricid species and exhibited congruence with the previous evolutionary hypothesis. The present phylogenetic analyses also furnished the oldest evolutionary lineages of this newly discovered species in comparison with other congeners, which assumed to be possible colonization of this species due to immature radiation in Narcondam Island.

Comparative variation of morphological and molecular evolution through geologic time: 28 S ribosomal RNA versus morphology in echinoids

1992 ◽  
Vol 338 (1286) ◽  
pp. 365-382 ◽  
Keyword(s):  
Molecular Evolution ◽  
Maximum Likelihood ◽  
Morphological Change ◽  
Rank Correlation ◽  
Morphological Data ◽  
Parsimony Analysis ◽  
Geological Time ◽  
Molecular Changes ◽  
Molecular Change ◽  
Rates Of Evolution

The comparatively good fossil record of post-Palaeozoic echinoids allows rates of morphological change to be estimated over the past 260 million years and com pared with rates of molecular evolution. Parsimony analysis of morphological data, based predominantly on skeletal characteristics, and parsimony, distance and maximum likelihood analyses of molecular data, from the first 380 bases from the 5' end of the 28 S rRNA molecule, for 10 species of echinoid produce congruent phylogenies. The m olecular sequence chosen is dem onstrably far from saturation and sister groups have divergence times ranging from about 15 to 260 Ma. Parsimony analysis allows the great majority of molecular and morphological apomorphies to be placed in one of 18 independent geological time intervals, providing a direct measure of rates of evolution for periods in the geological past. Because most molecular fixed point m utations in our sequences cannot be polarized unambiguously by outgroup comparison (making the outgroup states effectively random), distance and parsimony analyses both tend spuriously to root the echinoid tree on the longest internal branch. A topology identical to that derived from morphological data is, however, obtained using Maximum Likelihood and also parsimony analysis where outgroup rooting is restricted to more conserved regions. This is taken as the correct topology for assessing rates of evolution. Overall, both morphological and molecular changes show a m oderately strong correlation with time elapsed, but a weaker correlation with one another. Statistically significant differences in evolutionary rate are found between some, but not all, pair-wise comparisons of sister lineages for both molecular and morphological data. The molecular clock rate for echinaceans is three times faster than that for cidaroids and irregular echinoids. Spearm an’s rank correlation test, which requires only relative m agnitude of changes to be known, suggests that morphological change has a slightly better correlation with time than does molecular change, averaged over all ten species. However, when just echinaceans are considered an extremely good correlation is found between the num ber of molecular changes and time elapsed, whereas morphological change remains poorly correlated. Thus, molecular rates approxim ate to a clocklike model within restricted echinoid elades, but vary significantly between clades. Averaging results over all echinoids produces a correlation that is no better than the correlation between morphological change and time elapsed.

A broadly sampled 3-loci plastid phylogeny of Atraphaxis (Polygoneae, Polygonoideae, Polygonaceae) reveals new taxa: I. Atraphaxis kamelinii spec. nov. from Mongolia

Phytotaxa ◽  
2016 ◽  
Vol 268 (1) ◽  
pp. 1
Author(s):  
OLGA V. YURTSEVA ◽  
OXANA I. KUZNETSOVA ◽  
EVGENY V. MAVRODIEV
Keyword(s):  
Maximum Likelihood ◽  
New Taxa ◽  
Endemic Species ◽  
Phylogenetic Reconstruction ◽  
Morphological Data ◽  
The Novel ◽  
Bayesian Analyses

Maximum Likelihood (ML) and Bayesian analyses (BI) applied for 3-plastid loci (cpDNA trnL(UAA) intron, trnL–trnF IGS, and rpl32–trnL(UAG) IGS regions) / 65 tips matrix resulted in preliminary phylogenetic reconstruction of the genus Atraphaxis. In combination with the morphological data the obtained phylogeny appears sufficient for recognition of challenging taxonomic entities. We found that a collection of Atraphaxis from the Dzungarian Gobi, which appears to be phylogenetically related to A. pungens, is morphologically different from the latter by the predominantly dimerous perianth and gynoecium, shorter outer perianth segments, and the absence of the spiny shoots. It also differs from all other species of Atraphaxis that occur in Mongolia and neighboring countries. As a result, we described the novel endemic species Atraphaxis kamelinii O.V.Yurtseva sp. nov. More investigations are necessary to fully understand the origin of the newly described species.

scholarly journals Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018 ◽  
Vol 3 ◽  
pp. 33 ◽  
Author(s):  
John A. Lees ◽  
Michelle Kendall ◽  
Julian Parkhill ◽  
Caroline Colijn ◽  
Stephen D. Bentley ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Real Data ◽  
Tree Topology ◽  
Computational Time ◽  
Advantages And Disadvantages ◽  
Phylogenetic Reconstructions ◽  
Reconstruction Methods ◽  
True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined 'true tree' using a realistic evolutionary model. We  built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology.  We have publicly released our simulated data and code to enable further comparisons.

Phylogenetic Reconstruction of a Known HIV-1 CRF04_cpx Transmission Network Using Maximum Likelihood and Bayesian Methods

2004 ◽  
Vol 59 (5) ◽  
pp. 709-717 ◽  
Author(s):  
Dimitrios Paraskevis ◽  
Emmanouil Magiorkinis ◽  
Gkikas Magiorkinis ◽  
Vassilios G. Kiosses ◽  
Philippe Lemey ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Bayesian Methods ◽  
Phylogenetic Reconstruction ◽  
Transmission Network ◽  
Hiv 1

scholarly journals Additions to “The Cypriniformes Tree of Confusion”

Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 142 ◽  
Author(s):  
RALF BRITZ ◽  
KEVIN W. CONWAY
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Bayesian Analysis ◽  
Danio Rerio ◽  
Sister Group ◽  
Remarkable Difference ◽  
Maximum Likelihood Analysis ◽  
Parsimony Analysis ◽  
Life Project ◽  
Likelihood Analysis

Since the acceptance of our paper (Britz & Conway 2011), two publications have appeared that have relevance to the topic discussed and need to be mentioned. Mabee et al. (2011) is the first morphological phylogenetic analysis produced by the Cypriniformes Tree of Life project and covers 62 characters from gill arch, and hyoid osteology in 53 cypriniform taxa. Tang et al.’s (2011) molecular analysis of the cyprinid subfamily Gobioninae also included the three miniature taxa Sundadanio, Paedocypris and Danionella and was based on two mitochondrial and two nuclear genes. Their parsimony analysis recovered all three taxa in the cyprinid subfamily Danioninae, with Paedocypris and Danionella as sister groups, with this clade forming the sister group to a clade comprising Sundadanio and Esomus. Their maximum likelihood analysis confirmed their placement in danionines and found Paedocypris as the sister group to Sundadanio, and Danionella as the sister group of Danio rerio, Devario auropurpureus and Microrasbora rubescens. Their partitioned Bayesian analysis, however, recovered Sundadanio as the sister group of Leptobarbus, Danionella as the sister group to Danio, Devario and Microrasbora, and Paedocypris as the sister group to all other Cypriniformes, as did Mayden & Chen (2010). This remarkable difference in the position of the three taxa between the different trees was not even mentioned or discussed except in the brief remark relating only to Paedocypris (p. 11): “The Bayesian results agree on a monophyletic Cypriniformes, but recover a putative cyprinid (Paedocypris) as the sister group to all other cypriniform fishes.”

A Molecular Approach to the Circumscription and Evaluation of Some Genera Segregated from Parmelia S. Lat

1998 ◽  
Vol 30 (4-5) ◽  
pp. 369-380 ◽  
Author(s):  
Ana Crespo ◽  
Oscar F. Cubero
Keyword(s):  
Maximum Likelihood ◽  
Family Relationships ◽  
Type Species ◽  
Its Region ◽  
Maximum Parsimony Analysis ◽  
Molecular Approach ◽  
Parsimony Analysis ◽  
Distance Analysis ◽  
The Family ◽  
Flavoparmelia Caperata

AbstractNew sequences have been produced of the ITS rDNA region of twenty-nine species of Parmeliaceae and analysed by neighbour-joining maximum likelihood distance analysis, and maximum parsimony analysis. Twelve monophyletic groups have been identified, most of which correspond to proposed generic segregated from Parmelia s. lat. Parmelia and Parmelina, Melanelia, and Punctelia appear as independent monophyletic groups; the type species of the two latter genera were, however, not included in the analysis. The parsimony analysis does not support Xanthoparmelia as a monophyletic group separate from Neofuscelia, and Rimelia reticulate is nested within Parmotrema. Parmelinopsis horrescens is more closely related to Hypotrachyna revolute than to Parmelina. Genetic distance values suggest that Flavoparmelia caperata is closer to Parmotrema than to other taxa included, and that Platismatia glauca and Hypogymnia tubulosa are closer to Parmelia s. lat. than to the Physciaceae. However, there is no conclusive support for any of thelatter groupings in the parsimony analysis. We conclude that the ITS region contains valuable information for studying generic delimitations within the family Parmeliaceae, but our study suggests that this region will not conclusively resolve within-family relationships in this group.

scholarly journals Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018 ◽  
Vol 3 ◽  
pp. 33 ◽  
Author(s):  
John A. Lees ◽  
Michelle Kendall ◽  
Julian Parkhill ◽  
Caroline Colijn ◽  
Stephen D. Bentley ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Real Data ◽  
Tree Topology ◽  
Computational Time ◽  
Advantages And Disadvantages ◽  
Phylogenetic Reconstructions ◽  
Reconstruction Methods ◽  
True Tree

Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

scholarly journals Systematic implications from a robust phylogenetic reconstruction of the genus Helianthemum (Cistaceae) based on genotyping-by-sequencing (GBS) data

2021 ◽  
Vol 78 (2) ◽  
pp. e113
Author(s):  
Sara Martín-Hernanz ◽  
Mauricio Velayos ◽  
Rafael G. Albaladejo ◽  
Abelardo Aparicio
Keyword(s):  
Maximum Likelihood ◽  
Molecular Systematics ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Genotyping By Sequencing ◽  
New Combinations ◽  
Bayesian Analyses ◽  
Taxonomic Sampling ◽  
New Subgenus ◽  
Phylogenetic Framework

Molecular systematics requires the establishment of a robust phylogenetic framework including extensive geographical and taxonomic sampling. In this work, we proposed systematic changes in the genus Helianthemum based on phylogenetic trees obtained by both maximum likelihood and Bayesian analyses of GBS data. The implications of these phylogenetic results for the systematics of Helianthemum entail the establishment of a new subgenus and novel re-ascriptions of sections and species along with some nomenclatural novelties. The following new combinations are proposed: Helianthemum subg. Eriocarpum (Dunal) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. oelandicum subsp. conquense (Borja & Rivas Goday ex G.López) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. cantabricum (M.Laínz) Martín-Hernanz, Velayos, Albaladejo & Aparicio; H. nummularium subsp. tinetense (M.Mayor & Fern.Benito) Martín-Hernanz, Velayos, Albaladejo & Aparicio.

Molecular phylogeny of the pond skaters (Gerrinae), discussion of the fossil record and a checklist of species assigned to the subfamily (Hemiptera: Heteroptera: Gerridae)

2014 ◽  
Vol 45 (3) ◽  
pp. 251-281 ◽  
Author(s):  
Jakob Damgaard ◽  
Felipe Ferraz Figueiredo Moreira ◽  
Tom A. Weir ◽  
Herbert Zettel
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Species Group ◽  
28S Rrna ◽  
Parsimony Analysis ◽  
Dna Sequence Data ◽  
Genes Encoding ◽  
Future Revision

The phylogenetic relationships among selected species and genera of Gerrinae (Heteroptera: Gerridae) were investigated in a parsimony analysis of 2268 bp of DNA sequence data from the genes encoding COI + II, 16S rRNA and 28S rRNA. The taxa represented 12 of 15 recognized genera of Gerrinae and with outgroup taxa from all other subfamilies of Gerridae, including three of five recognized genera of Eotrechinae, which is considered the sister-group of Gerrinae. The resulting phylogeny shows that Gerrinae is not monophyletic, since a clade comprising Gerris, Aquarius, Limnoporus, Tachygerris, Eurygerris and Gigantometra is more closely related to representatives of the subfamily Eotrechinae than to a clade comprising Limnogonus, Neogerris, Limnometra, Tenagogerris and Tenagogonus. The two currently recognized gerrine tribes, Tachygerrini and Gerrini, were also paraphyletic, since Eurygerris was sister-group to Gigantometra, while Tachygerris was sister-group to Limnoporus + Aquarius + Gerris. Limnogonus and Neogerris were found to be strongly supported sister-taxa, and their sister-group was a clade comprising Limnometra, Tenagogerris and Tenagogonus, none of which were monophyletic. Finally, Aquarius chilensis (Berg, 1881) was sister-group to a clade comprising Aquarius amplus (Drake & Harris, 1938), A. remigis (Say, 1832) and A. remigoides (Gallant & Fairbairn, 1993), recognized as the A. remigis species group, and the entire clade was sister-group to Gerris. Based on the phylogenetic reconstruction, we outline possible diagnostic character combinations for a future revision of the Gerrinae and discuss the fossil record. While some of the relationships reinstate earlier ideas, e.g., Limnogonus and Neogerris being sister groups, many others are poorly supported and poorly diagnosed, and therefore, we retain from drawing taxonomic conclusions until data is available from the remaining genera, which can support a future generic revision of the Gerrinae. The updated checklist of species assigned to the subfamily is therefore based on the established taxonomy.

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