Cleaning a taxonomic dustbin: placing the European Hypnum species in a phylogenetic context!

2018 ◽  
Vol 40 (2) ◽  
pp. 37 ◽  
Author(s):  
SASKIA SCHLESAK ◽  
LARS HEDENÄS ◽  
MARTIN NEBEL ◽  
DIETMAR QUANDT
Keyword(s):  
18Th Century ◽  
Morphological Evolution ◽  
Phylogenetic Reconstruction ◽  
Moss Species ◽  
New Family ◽  
Pleurocarpous Mosses ◽  
Tree Topologies ◽  
Molecular Information ◽  
Pleurocarpous Moss ◽  
Rps4 Gene

The pleurocarpous moss genus Hypnum s.l. is a species-rich (> 40 species) cosmopolitan genus, of which 21 taxa occur in Europe. Although several of these species show high morphological resemblance there are strong indications that the genus is highly paraphyletic, which may be masked by convergent morphological evolution. Using molecular information, we analyse whether the morphological similarity of gametophytes of the European Hypnum taxa is explained by common ancestry or convergence. We provide a phylogenetic reconstruction of the relationships of the currently recognized European Hypnum taxa in a broad pleurocarpous moss context (192 taxa) using the nuclear ITS1-5.8S-ITS2, the plastid rps4 gene and trnL-F, and the mitochondrial nad5 intron. Bayesian tree topologies show that the genus is polyphyletic, and we retain only the Hypnum cupressiforme complex within Hypnum. The genus originally represented half of the moss species diversity, as it accommodated basically all pleurocarpous mosses; here we retain only seven species and one variety. The remainder of the species where resolved either within the three families Amblystegiaceae, Entodontaceae, and Pylaisiaceae, or in an independent clade that we describe as the new family Stereodontaceae. The Stereodontaceae includes five European species, all in the genus Stereodon, where they were already placed in the 18th century. In addition, we describe the four new genera Aquilonium, Insomniella, Jochenia, and Lignocariosa, and make new combinations for several Hypnum species.

Back to the Future? Molecules Take Us Back to the 1925 Classification of the Lembophyllaceae (Bryopsida)

2009 ◽  
Vol 34 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Dietmar Quandt ◽  
Sanna Huttunen ◽  
Ray Tangney ◽  
Michael Stech
Keyword(s):  
Single Species ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
New Family ◽  
Morphological Studies ◽  
The Family ◽  
Family Level ◽  
Plastid Markers ◽  
Pleurocarpous Moss

Although the Lembophyllaceae has undergone considerable revision during the last century, the generic and familial level relationships of this pleurocarpous moss family are still poorly understood. To address this problem, a generic revision of the Lembophyllaceae based on molecular data was undertaken. We analyzed two plastid markers, the trnL-trnF and the psbT-psbH region in combination with the ITS2 of nuclear ribosomal DNA. The molecular data reveal that the current circumscription of the family is too narrow and that several genera previously placed in the Lembophyllaceae should be reincluded. The family includes: Bestia, Camptochaete, Dolichomitra, Dolichomitriopsis, Fallaciella, Fifea, Isothecium, Lembophyllum, Looseria stat. nov., Pilotrichella, Rigodium, Tripterocladium, and Weymouthia. Looseria contains a single species: Looseria orbiculata comb. nov. Acrocladium is excluded and provisionally accommodated in the Lepyrodontaceae. Generic limits supported by the molecular data support a return to the early twentieth century family concept of Brotherus. The analyses indicate that the segregate genus Orthostichella is distinct from its parent genus Pilotrichella, probably at the family level. Whereas Pilotrichella is resolved within the Lembophyllaceae, Orthostichella clusters with Porotrichum and Porothamnium forming a clade (OPP-clade) sister to the remaining Neckeraceae and Lembophyllaceae. Hence, the Neckeraceae is paraphyletic. Recognition of the OPP-clade as a new family is desirable but awaits the results of detailed ongoing morphological studies.

scholarly journals Pleurocarpous mosses of Bangladesh: family - Sematophyllaceae

1970 ◽  
Vol 36 (1) ◽  
pp. 69-80
Author(s):  
Hamida Khatun ◽  
Syed Hadiuzzaman
Keyword(s):  
Key Words ◽  
Pleurocarpous Mosses ◽  
Pleurocarpous Moss

A taxonomic account of eight species of pleurocarpous mosses from different localities of Bangladesh has been made. These are new addition to the pleurocarpous moss flora reported earlier. Key words : Pleurocarpous mosses, Hypnobryales, Sematophyllaceae, Bangladesh doi:10.3329/bjb.v36i1.1551 Bangladesh J. Bot. 36(1): 69-80, 2007 (June)

scholarly journals Pleurocarpous mosses of Bangladesh : Meteoriaceae and Pterobryaceae

1970 ◽  
Vol 12 (1) ◽  
pp. 53-57 ◽  
Author(s):  
Hamida Khatun ◽  
Syed Hadiuzzaman
Keyword(s):  
Key Words ◽  
New Records ◽  
Pleurocarpous Mosses ◽  
Plant Taxon ◽  
Pleurocarpous Moss

Barbella rufifolia (Thwait & Mitt.) Broth. (Family Meteoriaceae) and Pterobryopsis auriculata Dix. (Family Pterobryaceae) of Isobryales are described as new records for Bangaldesh. Key words: Pleurocarpous moss; Isobryales; Meteoriaceae; Pterobryaceae; Bangladesh DOI: 10.3329/bjpt.v12i1.611 Bangladesh J. Plant Taxon. 12(1): 53-57, 2005 (June)

scholarly journals Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eudald Pascual-Carreras ◽  
Carlos Herrera-Úbeda ◽  
Maria Rosselló ◽  
Pablo Coronel-Córdoba ◽  
Jordi Garcia-Fernàndez ◽  
...  
Keyword(s):  
Cell Death ◽  
Phylogenetic Reconstruction ◽  
Single Copy ◽  
Schmidtea Mediterranea ◽  
Functional Studies ◽  
New Family ◽  
Gene Diversification ◽  
Fox Genes ◽  
Key Aspects

AbstractThe forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.

A taxonomic revision and phylogenetic reconstruction of the Jahnulales (Dothideomycetes), and the new family Manglicolaceae

2011 ◽  
Vol 51 (1) ◽  
pp. 163-188 ◽  
Author(s):  
Satinee Suetrong ◽  
Nattawut Boonyuen ◽  
Ka-Lai Pang ◽  
Jureerat Ueapattanakit ◽  
Anupong Klaysuban ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Taxonomic Revision ◽  
New Family

Size matters: the effects of ontogenetic disparity on the phylogeny of Trematopidae (Amphibia: Temnospondyli)

2020 ◽  
Vol 190 (1) ◽  
pp. 79-113
Author(s):  
Bryan M Gee
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Inference ◽  
Type Specimens ◽  
Directional Bias ◽  
Skull Length ◽  
Size Disparity ◽  
Tree Topologies

Abstract Trematopids are a clade of terrestrial Permo-Carboniferous temnospondyl amphibians. The intrarelationships of this clade are poorly known. This is largely attributable to a substantial disparity in size between type specimens, which range from the small-bodied lectotype of Mattauschia laticeps (< 4 cm skull length) to the large-bodied holotype of Acheloma cumminsi (> 15 cm skull length). Inferred correlation of size disparity with ontogenetic disparity has led previous workers either to omit taxa in phylogenetic analyses or to forgo an analysis altogether. Here, I take a specimen-level approach and multiple subsampling permutations to explore the phylogeny of the Trematopidae as a case study for assessing the effects of ontogenetic disparity on phylogenetic reconstruction in temnospondyls. The various analyses provide evidence that ontogenetic disparity confounds the phylogenetic inference of trematopids but without a directional bias. Tree topologies of most permutations are poorly resolved and weakly supported, reflecting character conflict that results from the inability of the analyses to differentiate retained plesiomorphies from juvenile features. These findings urge caution in the interpretation of phylogenetic analyses for which ontogenetic disparity exists, but is unaccounted for, and provide a strong impetus for more directed exploration of the interplay of ontogeny and phylogeny across Temnospondyli.

scholarly journals Pleurocarpous mosses of Bangladesh : Symphyodontaceae and Amblystegiaceae

1970 ◽  
Vol 13 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Hamida Khatun ◽  
Syed Hadiuzzaman
Keyword(s):  
Key Words ◽  
Pleurocarpous Mosses ◽  
Plant Taxon ◽  
Pleurocarpous Moss

A taxonomic account of six species of Pleurocarpous mosses of Bangladesh of the families Symphyodontaceae and Amblystegiaceae under the order Hookeriales and Hypnobryales respectively are given. Key words: Pleurocarpous moss, Hookeriales, Hypnobryales, Symphyodontaceae, Amblystegiaceae, Bangladesh DOI: 10.3329/bjpt.v13i1.591 Bangladesh J. Plant Taxon. 13(1): 29-40, 2006 (June)

scholarly journals Phylogenetic reconstruction based on synteny block and gene adjacencies

2019 ◽  
Author(s):  
Guénola Drillon ◽  
Raphaël Champeimont ◽  
Francesco Oteri ◽  
Gilles Fischer ◽  
Alessandra Carbone
Keyword(s):  
Chromosomal Rearrangements ◽  
Phylogenetic Reconstruction ◽  
Simulated Data ◽  
Synteny Block ◽  
Reconstruction Method ◽  
Reconstruction Methods ◽  
Wide Range ◽  
Genomic Markers ◽  
Tree Topologies ◽  
Almost All

AbstractGene order can be used as an informative character to reconstruct phylogenetic relationships-between species independently from the local information present in gene/protein sequences.PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches.PhyChro performance isevaluatedon two datasets of 13 vertebrates and 21 yeast genomes by using up to 130 000 and 179 000 breakpoints respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared to other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in less than 15 min.AvailabilityPhyChro will be freely available under the BSD license after [email protected]

scholarly journals Use of Continuous Traits Can Improve Morphological Phylogenetics

2017 ◽  
Author(s):  
Caroline Parins-Fukuchi
Keyword(s):  
Morphological Evolution ◽  
Phylogenetic Reconstruction ◽  
Continuous Measurements ◽  
Extant Species ◽  
Discrete Character ◽  
Significant Step ◽  
Biological Interpretation ◽  
Feasible Alternative ◽  
Character Coding ◽  
Continuous Traits

ABSTRACTThe recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modelling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modelling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers’ subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behaviour is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximise phylogenetic information in morphological datasets by preserving larger variation in state space compared to many discretisation schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.

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