A 10-gene phylogeny ofSolanumsectionHerpystichum(Solanaceae) and a comparison of phylogenetic methods

2011 ◽  
Vol 98 (8) ◽  
pp. 1356-1365 ◽  
Author(s):  
Eric J. Tepe ◽  
Frank T. Farruggia ◽  
Lynn Bohs
Keyword(s):  
Gene Phylogeny ◽  
Phylogenetic Methods

Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333-gene phylogeny and resolves tribal level Moraceae taxonomy

Phytotaxa ◽  
2019 ◽  
Vol 388 (4) ◽  
pp. 253 ◽  
Author(s):  
NYREE J.C. ZEREGA ◽  
ELLIOT M. GARDNER
Keyword(s):  
Single Layer ◽  
Morphological Characters ◽  
Nuclear Genes ◽  
Target Enrichment ◽  
Gene Phylogeny ◽  
Genus Level ◽  
Phylogenetic Methods ◽  
The Family ◽  
New Tribe

Here we describe the new tribe, Parartocarpeae, within the Moraceae (mulberry family). The tribe comprises two small Malesian genera, Parartocarpus and Hullettia, and brings the total number of Moraceae tribes to seven. Evidence for this new designation comes from a phylogeny based on 333 nuclear genes sequenced using target enrichment via hybridization (hybseq). Morphological characters that set Parartocarpeae apart from other Moraceae tribes include the combination of the following characters: lateral nonamplexicaul stipules, spirally arranged leaves without annulate stipule scars, the presence of a single layer of involucral inflorescence bracts, and the lack of perianth tissue, wherein flowers are embedded in cavities of the receptacle. With the designation of Parartocarpeae, the tribe-level circumscription of Moraceae is now well-supported by phylogenetic methods. Because the phylogenetic markers employed here work well throughout Moraceae, they can facilitate much needed work at the genus level in the family.

scholarly journals A Six Nuclear Gene Phylogeny of Citrus (Rutaceae) Taking into Account Hybridization and Lineage Sorting

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e68410 ◽  
Author(s):  
Chandrika Ramadugu ◽  
Bernard E. Pfeil ◽  
Manjunath L. Keremane ◽  
Richard F. Lee ◽  
Ivan J. Maureira-Butler ◽  
...  
Keyword(s):  
Nuclear Gene ◽  
Lineage Sorting ◽  
Gene Phylogeny

scholarly journals Novel metric for hyperbolic phylogenetic tree embeddings

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Hirotaka Matsumoto ◽  
Takahiro Mimori ◽  
Tsukasa Fukunaga
Keyword(s):  
Phylogenetic Tree ◽  
Hyperbolic Space ◽  
Nearest Neighbor ◽  
Cancer Genomics ◽  
Geometric Approach ◽  
Artificial Intelligence Research ◽  
Phylogenetic Methods ◽  
Novel Approach ◽  
Multiple Trees ◽  
Euclidean Embeddings

Abstract Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.

scholarly journals A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL.

1994 ◽  
Vol 91 (15) ◽  
pp. 7281-7285 ◽  
Author(s):  
D. W. Freshwater ◽  
S. Fredericq ◽  
B. S. Butler ◽  
M. H. Hommersand ◽  
M. W. Chase
Keyword(s):  
Red Algae ◽  
Gene Phylogeny

Incongruence between molecules and morphology: A seven-gene phylogeny of Dacini fruit flies paves the way for reclassification (Diptera: Tephritidae)

2018 ◽  
Vol 121 ◽  
pp. 139-149 ◽  
Author(s):  
Michael San Jose ◽  
Camiel Doorenweerd ◽  
Luc Leblanc ◽  
Norman Barr ◽  
Scott Geib ◽  
...  
Keyword(s):  
Fruit Flies ◽  
Gene Phylogeny ◽  
The Way

Performance of Phylogenetic Methods in Simulation

1995 ◽  
Vol 44 (1) ◽  
pp. 17-48 ◽  
Author(s):  
John P. Huelsenbeck
Keyword(s):  
Phylogenetic Methods
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