Phylogenetic relationships within the lizard clade Xantusiidae: Using trees and divergence times to address evolutionary questions at multiple levels

2013 ◽  
Vol 69 (1) ◽  
pp. 109-122 ◽  
Author(s):  
Brice P. Noonan ◽  
Jennifer B. Pramuk ◽  
Robert L. Bezy ◽  
Elizabeth A. Sinclair ◽  
Kevin de Queiroz ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Multiple Levels

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

scholarly journals Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)

2017 ◽  
Vol 181 (2) ◽  
pp. 471-483 ◽  
Author(s):  
Sofya Dolotovskaya ◽  
Juan Torroba Bordallo ◽  
Tanja Haus ◽  
Angela Noll ◽  
Michael Hofreiter ◽  
...  
Keyword(s):  
Southern Africa ◽  
Phylogenetic Relationships ◽  
Phylogenetic Reconstruction ◽  
Divergence Times ◽  
Mtdna Sequences ◽  
East Division ◽  
North Eastern ◽  
Statistical Support ◽  
Green Monkeys ◽  
Complete Mtdna

Abstract Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west–east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.

Phylogenetic relationships and divergence times among dormice (Rodentia, Gliridae) based on three nuclear genes

2007 ◽  
Vol 36 (6) ◽  
pp. 537-546 ◽  
Author(s):  
Mitsuo Nunome ◽  
Shumpei P. Yasuda ◽  
Jun J. Sato ◽  
Peter Vogel ◽  
Hitoshi Suzuki
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Genes ◽  
Divergence Times

Phylogenetic relationships and divergence times among New World monkeys (Platyrrhini, Primates)

2006 ◽  
Vol 40 (1) ◽  
pp. 274-280 ◽  
Author(s):  
Juan C. Opazo ◽  
Derek E. Wildman ◽  
Tom Prychitko ◽  
Robert M. Johnson ◽  
Morris Goodman
Keyword(s):  
Phylogenetic Relationships ◽  
New World ◽  
Divergence Times ◽  
New World Monkeys

Phylogenetic relationships and divergence times of the family Araucariaceae based on the DNA sequences of eight genes

2009 ◽  
Vol 54 (15) ◽  
pp. 2648-2655 ◽  
Author(s):  
Nian Liu ◽  
Yong Zhu ◽  
ZongXian Wei ◽  
Jie Chen ◽  
QingBiao Wang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Divergence Times ◽  
The Family

scholarly journals Phylogenetic relationships among Callosciurus squirrels in the Indochina Peninsula: phylogenetic position of C. pygerythrus from Myanmar

2021 ◽  
Vol 67 (1) ◽  
pp. 87-98
Author(s):  
Tatsuo Oshida ◽  
Wynn Than ◽  
Thida Oo ◽  
Khin Yu Yu Swe ◽  
Hiroaki Saito ◽  
...  
Keyword(s):  
Cytochrome B ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Divergence Times ◽  
Phylogenetic Position ◽  
Mitochondrial Cytochrome ◽  
Indochina Peninsula ◽  
Mitochondrial Cytochrome B ◽  
Global Cooling ◽  
Mitochondrial Cytochrome B Gene

The phylogenetic relationships among seven Callosciurus species from the Indochina Peninsula, including the C. honkhoaiensis which is endemic to Hon Khoai Island, were studied using complete mitochondrial cytochrome b gene sequences (1140 bases). We primarily focused on the phylogenetic position of C. pygerythrus, which is distributed in the western part of the peninsula. We identified two main lineages: 1) C. caniceps, C. honkhoaiensis, C. inornatus, C. phayrei and C. pygerythrus, and 2) C. erythraeus and C. finlaysonii. Estimated divergence time between the two lineages was at the junction of the Zanclean and Piacenzian in the Pliocene. Within the first linage, the divergence time of sub-lineages corresponded to the Pliocene-Pleistocene boundary, although phylogenetic relationships were unclear. These two divergence times estimated in the present study correspond to episodes of global cooling, suggesting that climate may have contributed to the divergence of these Callosciurus squirrels.

scholarly journals An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)

2019 ◽  
Vol 286 (1895) ◽  
pp. 20182076 ◽  
Author(s):  
Dominic A. Evangelista ◽  
Benjamin Wipfler ◽  
Olivier Béthoux ◽  
Alexander Donath ◽  
Mari Fujita ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Sister Group ◽  
Divergence Times ◽  
Sister Group Relationship ◽  
Time Analysis ◽  
The Social ◽  
History Of ◽  
Egg Care ◽  
Phylogenomic Study

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

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