Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations

Genomics ◽  
2021 ◽  
Author(s):  
Peng-Bin Dong ◽  
Ruo-Nan Wang ◽  
Nawal Afzal ◽  
Mi-Li Liu ◽  
Ming Yue ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Relationships ◽  
Nuclear Gene ◽  
Forest Tree

scholarly journals Molecular Evolution of Large Virulence Plasmid inShigella Clones and EnteroinvasiveEscherichia coli

2001 ◽  
Vol 69 (10) ◽  
pp. 6303-6309 ◽  
Author(s):  
Ruiting Lan ◽  
Brad Lumb ◽  
David Ryan ◽  
Peter R. Reeves
Keyword(s):  
Escherichia Coli ◽  
Molecular Evolution ◽  
Phylogenetic Relationships ◽  
Shigella Flexneri ◽  
The Other ◽  
Lateral Transfer ◽  
Virulence Plasmid ◽  
Main Body ◽  
Chromosomal Genes ◽  
Cluster 2

ABSTRACT Three genes, ipgD, mxiC, and mxiA,all in the invasion region of the Shigella virulence plasmid, were sequenced from strains representing a range ofShigella serotypes and from two enteroinvasiveEscherichia coli (EIEC) isolates. The plasmids can be classified into two relatively homogeneous sequence forms which are quite distinct. pINV A plasmids are found in Shigella flexneri strains F6 and F6A, S. boydii strains B1, B4, B9, B10, B14, and B15, S. dysenteriae strains D3, D4, D6, D8, D9, D10, and D13, and the two EIEC strains (M519 and M520). pINV B plasmids are present in S. flexneristrains F1A, F2A, F3A, F3C, F4A, and FY, two S. boydiistrains (B11 and B12), and S. sonnei. The D1 pINV plasmid is a recombinant with ipgD gene more closely related to those of pINV A but with mxiA andmxiC genes more closely related to those of pINV B. The phylogenetic relationships of the plasmid and those of the chromosomal genes of Shigella strains are largely consistent. The cluster 1 and cluster 3 strains tested (G.M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567–10572, 2000) have pINV A and pINV B plasmids, respectively. However, of the three cluster 2 strains (B9, B11, and B15), B9 and B15 have pINV A while B11 has a pINV B plasmid. Those Shigella (D8 and D10 and S. sonnei) and EIEC strains which do not group with the main body of Shigella strains based on chromosomal genes were found to have plasmids belonging to one or the other of the two types and must have acquired these by lateral transfer.

scholarly journals Phylogenetic relationships of Atractylodes lancea, A. chinensis and A. macrocephala, revealed by complete plastome and nuclear gene sequences

PLoS ONE ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. e0227610 ◽  
Author(s):  
Liqiang Wang ◽  
Hui Zhang ◽  
Xi Wu ◽  
Ziyue Wang ◽  
Weiwei Fang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Gene ◽  
Gene Sequences ◽  
Atractylodes Lancea

Genetic evidence supports Sylvilagus mansuetus (Lagomorpha: Leporidae) as a subspecies of S. bachmani

Zootaxa ◽  
2016 ◽  
Vol 4196 (2) ◽  
pp. 289
Author(s):  
SERGIO TICUL ÁLVAREZ-CASTAÑEDA ◽  
CONSUELO LORENZO
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Traits ◽  
Nuclear Gene ◽  
Sister Group ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
The Other ◽  
Cyt B ◽  
San Jose ◽  
Allopatric Distribution

Since Sylvilagus bachmani (Lagomorpha: Leporidae) from the Baja California Peninsula and S. mansuetus from San Jose Island, Mexico, display an allopatric distribution and are closely related, their taxonomy is unclear. The phylogenetic relationships among specimens of both species were evaluated using two mitochondrial genes (Cyt b, COI) and the beta-fibrinogen nuclear gene intron 7 (β-fib I7). The genetic analyses revealed that S. mansuetus was included within the S. bachmani clade as the sister-group of S. b. cerrosensis. The genetic distances among S. b. cerrosensis and mansuetus were relatively low (1.3% with Cyt b), similar to intraspecific distances observed within other species of Sylvilagus. We consider mansuetus to be a subspecies of S. bachmani, and the morphological traits previously used to differentiate the two taxa should be used to distinguish S. b. mansuetus from the other subspecies of S. bachmani. 

Phylogenetic relationships of Combretoideae (Combretaceae) inferred from plastid, nuclear gene and spacer sequences

2002 ◽  
Vol 115 (6) ◽  
pp. 475-481 ◽  
Author(s):  
Fengxiao Tan ◽  
Suhua Shi ◽  
Yang Zhong ◽  
Xun Gong ◽  
Yuguo Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Gene

scholarly journals PHYLOGENETIC RELATIONSHIPS WITHIN FAMILIES MYRTACEAE IN TRIPA PEAT SWAMP FOREST USING INTERNAL TRANSCRIBED SPACER (ITS)

2018 ◽  
Vol 18 (2) ◽  
pp. 65-71
Author(s):  
Ardhana Yulisma ◽  
Zairin Thomy ◽  
Essy Harnelly
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Forest Tree ◽  
Sequencing Data ◽  
Swamp Forest ◽  
Peat Swamp Forest ◽  
Peat Swamp ◽  
Aceh Province ◽  
Experimental Laboratory

The Tripa peat swamp forest is located on the west coast of Aceh province and falls administratively under the two districts of Nagan Raya and Aceh Barat Daya. Tripa peat swamp forest has a high diversity of plants. The previous research discovered that Myrtaceae is one of the dominant families in the forest. This study aimed to predict phylogenetic relationships among trees species within families Myrtaceae that live in the Tripa peat swamp forest using Internal Transcribed Spacer (ITS). The research was conducted at Laboratory of Forest Genetics and Molecular Forestry, Faculty of Forestry, IPB from June 2015 to December 2016. The methods were conducted with an experimental laboratory of molecular identification consisting of DNA extraction, amplification, and sequencing. Data was analyze using BioEdit, Clustal X, Mega 6, and BLAST. The morphology identification reported that there were four trees species within families Myrtaceae, i.e., Syzygium sp 1, Syzygium garciniifolium, Syzygium leptostemon and Tristaniopsis whiteana. Reconstruction of phylogenetic tree using the Neighbor-Joining (NJ) method 1000x showed that the ITS region was successfully to predict phylogenetic relationships within genus Syzygium and Tristaniopsis.Keywords: tripa peat swamp forest, tree species, phylogenetic, myrtaceae, internal transcribed spacer

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.

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