scholarly journals Phylogenetic Analysis of Mandarin Landraces, Wild Mandarins, and Related Species in China Using Nuclear LEAFY Second Intron and Plastid trnL-trnF Sequence

2007 ◽  
Vol 132 (6) ◽  
pp. 796-806 ◽  
Author(s):  
Li Yingzhi ◽  
Cheng Yunjiang ◽  
Tao Nengguo ◽  
Deng Xiuxin
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Average Length ◽  
Hybrid Origin ◽  
Data Sets ◽  
Citrus Reticulata ◽  
F Region ◽  
Plausible Hypothesis

Nucleotide sequences of the second intron of the nuclear LEAFY gene (FLint2) and trnL-trnF region of the chloroplast genome were used to analyze the phylogenetic relationships among eight wild mandarins (Citrus reticulata Blanco), 19 mandarin landraces, and 19 related species of Citrus L. Forty-six trnL-trnF sequences and 111 FLint2 sequences were obtained from 46 ingroup accessions, with an average length of 1059.7 and 776.7 bp respectively. Phylogeny reconstructions were conducted separately for these two data sets using maximum parsimony and maximum likelihood criteria. Monophyly of mandarins was supported by both of these data sets, and in this clade, most mandarin landraces formed an unresolved polytomy, whereas ‘Jiangyong 1’, ‘Chongyi A2’, ‘Chongyi A1’ (or ‘Jiangyong 4’ in FLint2 data), and ‘Daoxian 1’ wild mandarins formed a subclade. ‘Mangshan A1’ and ‘Daoxian 5’ wild mandarins were sisters to this mandarin clade. A hybrid origin of five mandarin landraces and several mandarin-related species was suggested as a plausible hypothesis to explain the incongruence between the FLint2 and trnL-trnF data sets.

The problematic phylogenetic analysis of interlocus heteropolymer isozyme characters: a case study from sea snakes and cobras

1988 ◽  
Vol 66 (12) ◽  
pp. 2628-2633 ◽  
Author(s):  
Robert W. Murphy
Keyword(s):  
Phylogenetic Analysis ◽  
Lactate Dehydrogenase ◽  
Phylogenetic Relationships ◽  
Parallel Evolution ◽  
Taxonomic Group ◽  
Data Sets ◽  
Similar Data ◽  
Isozyme Patterns ◽  
Sea Snakes

Multiple cases of parallel advancement (isozyme silencing) of L-lactate dehydrogenase heterotetramer isozymes are encountered when the observed isozyme patterns are superimposed on a well-corroborated cladogram depicting the phylogenetic relationships of some sea snakes, cobras, and coral snakes. This finding may be common among similar data sets because of parallel evolution and the inability to discern transformation sequences. Thus, the utility of this isozyme character in phylogenetic investigations may be severely limited, depending on the taxonomic group or level of universality being investigated.

scholarly journals A molecular phylogenetic analysis of the genera of fruit doves and allies using dense taxonomic sampling

2019 ◽  
Vol 42 ◽  
pp. 2019001
Author(s):  
Jennifer Nowak ◽  
Andrew Sweet ◽  
Jason Weckstein ◽  
Kevin Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Large Fraction ◽  
Nuclear Gene ◽  
Data Sets ◽  
Foraging Mode ◽  
Biogeographic Patterns ◽  
Reconstruction Methods ◽  
Molecular Phylogenetic ◽  
History Of

Fruit doves and their allies are a diverse group within the pigeon and dove family (Aves: Columbidae). Progress towards subfamilial classification of Columbidae relies on identifying major groups and the phylogenetic relationships within these groups. One such recently proposed group is the Raphinae based on previous evidence that the extinct dodo is potentially within what was formerly recognized as the Treroninae (fruit doves and allies). Although several studies have explored the phylogenetic relationships within Columbidae, most have focused either on broad-scale, familial level relationships or finer scale, species level relationships. Here we use mitochondrial and nuclear gene sequences from a diverse taxonomic sample to identify relationships among the genera and species of fruit doves and their allies. In particular our goal is to identify which of these genera should be included within Raphinae (the name which has taxonomic priority over Treroninae), focusing on an inclusive, well-supported monophyletic group. We also use dense taxon sampling to explore relationships among genera and species in this group, expanding on previous studies. In addition, we use resulting phylogenetic hypotheses to reconstruct the ancestral evolutionary history of foraging mode and biogeographic patterns of dispersal within the group. We used two data sets for our phylogenetic analysis: the first consisting of novel sequences generated for this project and the second with additional, previously published sequences from the fruit dove genus (Ptilinopus). Our analyses found support for the monophyly of a clade that contains a large fraction of the genera currently classified within Raphinae and also found several well-supported clades within this group of pigeons and doves. Character reconstruction methods based on the resulting phylogeny recover multiple transitions from a terrestrial to an arboreal foraging mode and evidence for multiple dispersal events from Asia to Africa throughout the history of the clade.

Molecular phylogeny of the butterfly tribe Baorini Doherty, 1886 (Hesperiidae, Hesperiinae) in China

Zootaxa ◽  
2019 ◽  
Vol 4565 (1) ◽  
pp. 108 ◽  
Author(s):  
WEIBIN JIANG ◽  
HAIYAN HE ◽  
YUANYUAN LI ◽  
YING WANG ◽  
CHEN GE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Species Diversity ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Mitochondrial Genes ◽  
Nuclear Genes ◽  
Large Group ◽  
The Status

The butterfly tribe Baorini Doherty, 1886 is a large group of skippers. In this study, a total of 8 genera and 41 species of putative members of this tribe, which represent most of the generic diversity and nearly all the species diversity of the group in China, were sequenced for two mitochondrial genes and three nuclear genes (2084 bp). Phylogenetic relationships and subdivision of this tribe were investigated and the status of the genera are discussed. Partitioned maximum likelihood analyses were performed based on the combined dataset. Our results suggest that the data are split into two well-supported clades in the phylogeny tree. This analysis also represents the most complete phylogenetic analysis of the tribe Baorini in China to date, and includes several genera and species that have been previously excluded from published phylogenies of this group. 

Three new species of Entoloma subgenus Nolanea from India based on morphology and molecular phylogeny

Phytotaxa ◽  
2016 ◽  
Vol 286 (4) ◽  
pp. 232 ◽  
Author(s):  
K. N.ANIL RAJ ◽  
PATINJAREVEETTIL MANIMOHAN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Internal Transcribed Spacer Region ◽  
Three New Species ◽  
Kerala State

Three new species of Entoloma belonging to the subgenus Nolanea, E. brunneoumbonatum, E. luteodiscum and E. brunneoapplanatum, are described from Kerala State, India based on morphology and molecular phylogeny. Comprehensive descriptions, photographs, and comparisons with phenetically similar and phylogenetically related species are discussed. The nuclear ribosomal internal transcribed spacer region (ITS) of the three species was sequenced and analyzed. The ITS-based phylogenetic analysis, performed using Maximum Likelihood (ML) method, supported both the novelty of these species and their infrageneric placement within the subgenus Nolanea. A key to the ten species of Entoloma subgenus Nolanea known from India is also provided.

scholarly journals Structure, variation, and systematic implications of the hemipenes of liolaemid lizards (Reptilia: Liolaemidae)

2018 ◽  
Vol 96 (9) ◽  
pp. 987-995 ◽  
Author(s):  
M. Quipildor ◽  
A.S. Quinteros ◽  
F. Lobo
Keyword(s):  
Phylogenetic Analysis ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Proximal Region ◽  
Closely Related Species ◽  
Structure Variation ◽  
Phylogenetic Studies ◽  
Taxonomic Importance ◽  
Single Set

The structure of copulatory organs is widely used in systematics for both differentiating species and for studying phylogenetic relationships. We describe the hemipenes of 42 species belonging to the genus Liolaemus, representing most of their internal groups. We reported 42 characters, the majority not published previously. We constructed a metatree based on previously proposed phylogenetic studies and optimized the hemipenial characters in this topology. Among the most informative characters are presence or absence of flounces or calyces on the sulcate face, ornamentation of the apex, presence or absence of an asulcate face prominence, and presence of a thickening on the proximal region of the asulcate face. Furthermore, we performed a phylogenetic analysis exclusively with the hemipenial characters, not with the intention of making a phylogeny based on this single set of characters, but rather to demonstrate their significance for the reconstruction of relationships in Liolaemus. The obtained results show that the main clades are recovered. We also compared the hemipenial morphology between closely related species to evaluate its taxonomic importance. We conclude that in Liolaemus, the hemipenes can be used both for the differentiation of species and to provide additional evidence for establishing their phylogenetic relationships.

scholarly journals Phylogenetic analysis of lysine, threonine and butanol strain-producers

1970 ◽  
Vol 21 ◽  
pp. 288-292
Author(s):  
O. O. Tigunova ◽  
G. S. Andriiash ◽  
N. Ye. Beiko ◽  
S. M. Shulha
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Phylogenetic Relationships ◽  
Clostridium Acetobutylicum ◽  
Genomic Dna ◽  
Agarose Gel ◽  
Brevibacterium Flavum ◽  
Mutant Strains

Aim. Identify and confirm the taxonomic position of the obtained mutant strains Brevibacterium sp. IMB B-7447, Brevibacterium flavum IMB B-7446 and Clostridium acetobutylicum IMB B-7407 (IFBG C6H). Methods. A fragment of genomic DNA from agarose gel using «Macherey-Nagel NucleoSpin Extract» was isolated according to the instructions of the producer and sequenced. Comparative analysis using the program «BLAST-online» was done. Phylogenetic dendrograms using methods Neighbour joining and Maximum likelihood were created. Results. Dendrograms of phylogenetic relationships of studied strains and related strains of databases «GenBank» were constructed. Conclusions. Found that homology of Brevibacterium sp. 90 and Brevibacterium sp. IMB B-7447 is 98 %, and stains B. flavum TH7 and B. flavum IMB B-7446 classified to species C. glutamicum. Strain C. acetobutylicum IMB B-7407 (IFBG C6H) been reclassified to C. pasteurianum IFBG C6H. Keywords: genes 16S rRNA, dendrogram, stains-produsers.

A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa

Paleobiology ◽  
1998 ◽  
Vol 24 (4) ◽  
pp. 430-449 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Maximum Likelihood Method ◽  
Character Evolution ◽  
Likelihood Method ◽  
Data Sets ◽  
Data Set ◽  
Parsimony Tree ◽  
Tree Length

Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, L[hypothesized length | parsimony length] can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.

Phylogenetic relationships of Echeveria (Crassulaceae) and related genera from Mexico, based on three DNA barcoding loci

Phytotaxa ◽  
2019 ◽  
Vol 422 (1) ◽  
pp. 33-57 ◽  
Author(s):  
LUIS E. DE LA CRUZ-LÓPEZ ◽  
FRANCISCO VERGARA-SILVA ◽  
JERÓNIMO REYES SANTIAGO ◽  
GABRIELA ESPINO ORTEGA ◽  
PABLO CARRILLO-REYES ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Dna Barcoding ◽  
Phylogenetic Relationships ◽  
Consensus Trees ◽  
As Species ◽  
Tree Inference ◽  
Selection Of

Mexico is considered as diversification and endemism center of the genus Echeveria. Previous tree inference studies have shown the genus to be non-monophyletic in relation to other genera, but sampling for Echeveria has been poor, and has not allowed to understand the relationships within the genus. In this work, Bayesian and maximum likelihood phylogenetic analysis were performed, using a combined standard DNA barcoding loci matrix (rbcL, matK and ITS2) and GenBank ITS2 accessions for Graptopetalum, some Sedum and few Echeveria taxa. The selection of taxa encompasses all current infrageneric categories of the genus Echeveria, as well as species from genera previously associated with it. The inferred consensus trees suggested that Echeveria is paraphyletic. Instead, four main clades were retrieved within the “Echeveria group”: Clade I includes exclusively Pachyphytum species. Clade II is formed by the majority of series Urbiniae; Clade III encompasses series Chloranthae, Ciliatae, Echeveria, Mucronatae, Nudae, Racemosae, Thyrsiflorae, Pachyphytum cuicatecananum and Thompsonella; Clade IV contains series Angulatae, Gibbiflorae, Occidentales, Pruinosae, Secundae, some Urbiniae species, Valvatae. genera Cremnophila, Graptopetalum and Reidmorania. Pachyphytum and Thompsonella were retrieved as monophyletic groups, but the first outside Echeveria while the latter inside. Results of our study suggest that Echeveria and the Echeveria Group require a redefinition.

Two new species of Crepidotus (Basidiomycota, Agaricales) from peninsular India

Phytotaxa ◽  
2018 ◽  
Vol 372 (1) ◽  
pp. 67 ◽  
Author(s):  
A. MANOJ KUMAR ◽  
K.B. VRINDA ◽  
C.K. PRADEEP
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Maximum Likelihood ◽  
New Taxa ◽  
Related Species ◽  
Peninsular India ◽  
Phylogenetic Data ◽  
Two New Species ◽  
Kerala State

Two new species, Crepidotus volubilis and Crepidotus palodensis are described from Kerala State, India based on morphological and molecular (nrLSU) phylogenetic data. The new taxa were assigned to section Echinospori due to the verrucose basidiospores and presence of clamp connections in the hyphae. Comprehensive descriptions, photographs and comparisons with phenetically similar and phylogenetically related species are discussed. The nrLSU-based phylogenetic analysis performed using Maximum Likelihood (ML) method, supported the novelty of the species.

scholarly journals Molecular identification of stone loaches of Choman River system, Tigris Basin, based on the Cytochrome b gene with an overview of the Cobitoidea Superfamily

2017 ◽  
Author(s):  
Edris Ghaderi ◽  
Hamid Farahmand ◽  
Barzan Bahrami Kamangar ◽  
Mohammad A. Nematollahi
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Maximum Likelihood ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
River System ◽  
Distinct Species ◽  
Molecular Data ◽  
Genetic Distances ◽  
Molecular Phylogenetic

AbstractMolecular data and phylogenetic relationships of four Choman loaches species (Oxynoemacheilus chomanicus, O. zagrosensis, O. kurdistanicus and Turcinoemacheilus kosswigi) recently morphologically described from western Iran were evaluated with 64 species from the Cobitoidea superfamily based on their cytochrome b sequences to exhibit the placement of the Choman loaches species within the Cobitoidea superfamily. A comparative analysis of Kimura-2-parameter (K2P) distances was accomplished using sequence divergences of Cobitoidea to calculate intra and interspecific in superfamily, family and genus taxa. The average intraspecific K2P genetic distances of Choman loaches species was 0.005 whereas this value was 0.016 for the Cobitoidea superfamily. Molecular phylogenetic relationships were assessed using Maximum likelihood and Bayesian methods. Dendrograms obtained by these methods revealed all four Choman loaches species as distinct species among other reported Nemacheilidae Spp. These species were clustered with Oxynoemacheilus and Turcinoemacheilus genera within other species in the Nemacheilidae family. The phylogenetic analysis revealed that Cobitoidea superfamily consists of nine families ((Gyrinocheilidae + Botiidae) + ((Catostomidae + Vaillentellidae) + ((Nemacheilidae + Cobitidae) + ((Ellopostomidae + Gastromyzontidae) + Balitoridae)))) and indicated Nemacheilidae is a valid and distinct family from Balitoridae.

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