scholarly journals Venation patterns of neotropical blueberries (Vaccinieae: Ericaceae) and their phylogenetic utility

Phytotaxa ◽  
2013 ◽  
Vol 96 (1) ◽  
pp. 1 ◽  
Author(s):  
PAOLA PEDRAZA-PEÑALOSA ◽  
NELSON R. SALINAS ◽  
WARD C. WHEELER
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Operational Definition ◽  
Phylogenetic Framework

The description of venation patterns in neotropical Vaccinieae has been problematic because of the lack of an operational definition. Moreover, the underlying homologies remain unknown across and within lineages, thus precluding the use of venation characters in phylogenetic analyses. Venation patterns are often obscured in herbarium and living specimens due to the characteristic coriaceous and thick nature of Ericaceae leaves. Therefore, to obtain an unobstructed view of the veins, leaf clearings of 16 putative generic lineages of Vaccinieae were prepared and described. The main venation patterns were then defined and traditional definitions of venation were discussed in the light of the observed patterns. Selected characters were scored and the evolution of venation characters was discussed using a phylogenetic framework derived from molecular data analyzed under Maximum Likelihood. Venation descriptions and photographs are provided for 33 species.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

scholarly journals Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

2018 ◽  
Vol 285 (1893) ◽  
pp. 20181632 ◽  
Author(s):  
Robin M. D. Beck ◽  
Charles Baillie
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Ancestral State ◽  
Case Scenario ◽  
State Reconstruction ◽  
Consensus View

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record—specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus—may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 125-138
Author(s):  
Sohrab Mirzaei ◽  
Ebrahim Pourjam ◽  
Majid Pedram
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Morphological Variation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
28S Rdna ◽  
Molecular Characterisation ◽  
Morphometric Data ◽  
Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

Phlebia nigrodontea sp. nov. in Meruliaceae (Polyporales) with a black hymenial surface

Phytotaxa ◽  
2020 ◽  
Vol 458 (3) ◽  
pp. 195-206
Author(s):  
RUO-XIA HUANG ◽  
KAI-YUE LUO ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Molecular Data ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
Phlebioid Clade ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungus, Phlebia nigrodontea, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by a grandinioid hymenophore with vinaceous brown to black colour, a monomitic hyphal system with clamped generative hyphae and ellipsoid, colourless, thin-walled, smooth basidiospores (3.9–4.9 × 2.3–3.1 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses carried out using maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on the molecular data of ITS+nLSU sequences showed that P. nigrodontea nested within the phlebioid clade. A further investigation of more representative taxa from Phlebia, based on ITS+nLSU sequences, demonstrated that the species P. nigrodontea formed a monophyletic lineage with strong support (100% BS, 100% BT, 1.00 BPP) and closely grouped with P. chrysocreas.

Ascomal evolution of filamentous ascomycetes: evidence from molecular data

1995 ◽  
Vol 73 (S1) ◽  
pp. 811-815 ◽  
Author(s):  
Joseph W. Spatafora
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Small Subunit ◽  
Filamentous Ascomycete ◽  
Group 4 ◽  
Nucleotide Data ◽  
Group 2 ◽  
Parsimony Trees

Phylogenetic analyses of nucleotide data from partial sequences (1150 bp) of the small subunit ribosomal DNA (SSU rDNA) were performed on 30 taxa representing several orders of Hymenoascomycetes and Loculoascomycetes. These analyses detected four major groups of filamentous ascomycetes: group 1, pyrenomycetes (Hypocreales, Microascales, Diaporthales, Sordariales) and loculoascomycetes (Pleosporales); group 2, operculate discomycetes (Pezizales); group 3, inoperculate discomycetes (Geoglossaceae); and group 4, plectomycetes (Eurotiales, Onygenales) and loculoascomycetes (Chaetothyriales). Well-supported clades, which correspond to groupings based on ascomal morphology, were resolved; however, the monophyly of the classes Hymenoascomycetes and Loculoascomycetes was rejected. The placement of the root on the filamentous ascomycete ingroup proved more problematic than resolving the ingroup relationships. Three alternative rooting possibilities, which were identified in suboptimal parsimony trees, were not significantly less likely in maximum likelihood ratio tests. Nonetheless, the most likely topology obtained from fastDNAml was identical to the most parsimonious tree. Key words: filamentous ascomycetes, Hymenoascomycetes, Loculoascomycetes, parsimony, maximum likelihood, ribosomal DNA.

Taxonomy and phylogeny of Chara (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2017 ◽  
Vol 302 (2) ◽  
pp. 101 ◽  
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Molecular Markers ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
American Studies ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
South American ◽  
Bayesian Analyses ◽  
Sem Analyses

South American studies on the genus Chara are relatively scarce, most consisting of floristic surveys and using only traditional morphological characters. This study is a first approach to the systematics of the genus Chara applying modern techniques (DNA sequences and oospore SEM analyses) in addition to the alpha-taxonomy investigations that have been conducted in Brazil. Twelve populations of Chara were analyzed from the midwest and southeast regions of Brazil. Sequences of three molecular markers were applied to infer phylogenies. The ultrastructure of the oospore wall and currently used morphological characters were analyzed for Chara populations. Maximum likelihood and Bayesian analyses of sequences of rbcL, ITS2, and matK were congruent in that they grouped the species in six clades, each representing one species: Chara braunii C.C. Gmelin, C. foliolosa C.L.Willdenow, C. guairensis R.Bicudo, C. haitensis M.P.J.F. Turpin, C. hydropitys H. Reichenbach and C. rusbyana M. Howe. Morphological characters, including ultrastructure of oospore wall, provided good evidences to characterize each species. Molecular data supported the recent view that some traditional infra-generic taxa (e.g. subgenus Charopsis and subsection Willdenowia) are not supported in phylogenetic analyses, whereas some species (e.g. C. foliolosa, C. haitensis, C. hydropitys and C. rusbyana previously considered as varieties and forms of C. zeylanica) were consistently distinguished in the analyses for the three molecular markers.

Phylogenetic Relationships in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (Chenopodiaceae) Clade and a Clarification of the Phylogenetic Position of Bienertia and Alexandra Using Multiple DNA Sequence Datasets

2006 ◽  
Vol 31 (3) ◽  
pp. 571-585 ◽  
Author(s):  
Maxim V. Kapralov ◽  
Hossein Akhani ◽  
Elena V. Voznesenskaya ◽  
Gerald Edwards ◽  
Vincent Franceschi ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Kranz Anatomy ◽  
Statistical Support ◽  
Chloroplast Dna Regions

The Chenopodiaceae includes taxa with both C3 and C4 photosynthesis with diverse kinds of Kranz anatomy and single-celled C4 species without Kranz anatomy; thus, it is of key importance for understanding evolution of C4 photosynthesis. All of the C4 genera except Atriplex, which belongs to Chenopodioideae, are in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (including Camphorosmeae and Sclerolaeneae) clade. Our study focused on the relationships of the main lineages within this clade with an emphasis on the placement of the single cell functioning C4 genus Bienertia using maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of the nuclear ribosomal ITS and five chloroplast DNA regions (atpB-rbcL, matK, psbB-psbH, rbcL, and trnL-trnF). Further we provide a detailed phylogeny of Alexandra and Suaeda based on ITS, atpB-rbcL, and psbB-psbH. Our molecular data provide strong statistical support for the monophyly of: (1) a Salicornioideae / Suaedoideae / Salsoloideae s.l. clade; (2) a Salicornioideae / Suaedoideae clade; (3) the subfamilies Salicornioideae, Suaedoideae (including Bienertia) and Salsoloideae s.l.; (4) the tribes Suaedeae, Salsoleae, and Camphorosmeae; (5) the Salicornieae if Halopeplideae is included; and (6) Suaeda if Alexandra is included. Alexandra lehmannii is therefore reclassified as Suaeda lehmannii and a new section of Suaeda is created, section Alexandra. There are four independent origins of C4 photosynthesis within the Suaedoideae including two parallel origins of Kranz C4 anatomy (in Suaeda sections Salsina s.l. and Schoberia) and two independent origins of C4 systems without Kranz anatomy (in Bienertia and in Suaeda section Borszczowia).

Neoalbatrellus odorus sp. nov. (Albatrellaceae, Russulales) from Southwest China

Phytotaxa ◽  
2017 ◽  
Vol 309 (3) ◽  
pp. 217 ◽  
Author(s):  
YUAN-YUAN CHEN ◽  
MIN WANG ◽  
BO ZHANG ◽  
BAO-KAI CUI
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Southwest China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Pore Surface ◽  
Rdna Sequences ◽  
Dark Violet ◽  
28S Rdna Sequences

We describe herein the Neoalbatrellus odorus sp. nov. accounting on its peculiar morphological features and molecular data. It is characterized by fleshy basidiomata with a deep violet to dark violet pileal surface, which turns blackish blue and glossy after drying. It also has a white pore surface, light violet to bluish violet stipe, simple septate generative hyphae, and thick-walled, non-amyloid basidiospores. The phylogenetic analyses, based on ITS and 28S rDNA sequences of Neoalbatrellus and its related genera, were performed using Maximum Parsimony, Maximum Likelihood and Bayesian Inference, confirming the affiliation of the new species to Neoalbatrellus.

scholarly journals Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12104
Author(s):  
Bastian Bentlage ◽  
Allen G. Collins
Keyword(s):  
Maximum Likelihood ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Life Cycles ◽  
Tree Topologies ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Inference Methods

Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.

scholarly journals Morphological and phylogenetic evidence for two new species of Russula subg. Heterophyllidia from Guangdong Province of China

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 139-157
Author(s):  
Bin Chen ◽  
Jie Song ◽  
Yanliu Chen ◽  
Jinhua Zhang ◽  
Junfeng Liang
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Morphological Characters ◽  
Molecular Data ◽  
Terminal Cell ◽  
Two New Species ◽  
Long Chains

Two new species of Russula subg. Heterophyllidia from Guangdong Province of China were described and illustrated based on morphological characters, and their identity supported by molecular phylogeny. R. luofuensis is morphologically characterized by a grayish yellow to brownish orange pileus center with a purplish gray to grayish magenta margin, a surface that is cracked and broken into small golden-brown patches, subglobose to broadly ellipsoid basidiospores with warts fused in short or long chains and a suprapellis composed of hyphal extremities with inflated, ellipsoid or globose cells and attenuated terminal cell. R. subbubalina is distinguished by the blanched almond to dark salmon pileus that is cracked with age, subglobose to broadly ellipsoid basidiospores with wart fused in short or long chains and frequently connected by line connections, a suprapellis with hyphal ends composed of inflated or ellipsoid cells and attenuated terminal cell, and pileocystidia that are mainly clavate and sometimes with round or ellipsoid appendage. The phylogenetic analyses based on ITS-nrLSU-mtSSU-TEF1 dataset were performed using maximum likelihood and Bayesian analysis. In terms of morphological features and molecular data, the former species belongs to subsect. Virescentinae, whereas the latter comes under subsect. Heterophyllinae.

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