scholarly journals Phylogeny of the Neotropical element of the Randia clade (Gardenieae, Rubiaceae, Gentianales)

2021 ◽  
Vol 154 (3) ◽  
pp. 458-469
Author(s):  
Rodrigo Lopes Borges ◽  
Sylvain G. Razafimandimbison ◽  
Nádia Roque ◽  
Catarina Rydin
Keyword(s):  
Maximum Likelihood ◽  
Evolutionary History ◽  
Sequence Data ◽  
Bayesian Analyses ◽  
The Core ◽  
Close Affinity ◽  
History Of ◽  
Geographic Distributions ◽  
Future Work

Background and aims – Generic limits of the tropical tribe Gardenieae (Ixoroideae, Rubiaceae) have partly remained unsettled. We produced a new phylogeny of the Randia clade, with emphasis on its Neotropical clade comprising five genera (Casasia, Randia, Rosenbergiodendron, Sphinctanthus, and Tocoyena). The result was subsequently used to evaluate and discuss: a) the respective monophyly of the above-mentioned genera and their interrelationships; b) relationships within Tocoyena and the evolutionary relevance of its subgeneric classification; and c) the monophyly of the morphologically variable T. formosa.Material and methods – We examined the phylogeny of the Randia clade based on maximum likelihood and Bayesian analyses of sequence data from two nuclear (ETS and Xdh) and two plastid (petB-petD and trnT-F) DNA regions from 59 individuals (including seven representatives from the remaining Ixoroideae).Key results – The Neotropical clade of the Randia clade comprises three major lineages, the Randia armata subclade, the Randia-Casasia subclade and the Rosenbergiodendron subclade. Neither Casasia nor Randia is monophyletic. Tocoyena is sister to Rosenbergiodendron + Sphinctanthus and is subdivided into three lineages: the Tocoyena pittieri group, the Tocoyena guianensis group, and the core Tocoyena. Tocoyena williamsii is paraphyletic with respect to T. pittieri. Tocoyena formosa is polyphyletic and should be re-circumscribed.Conclusions – Our results demonstrate the monophyly of each of the relatively species-poor genera Rosenbergiodendron, Sphinctanthus, and Tocoyena, and confirm their close affinity. The serial classification of Tocoyena does not reflect the evolutionary history of the genus. The paraphyly of T. williamsii with respect to T. pittieri, together with their morphological similarities and geographic distributions, support the inclusion of the former in the latter. Our study calls for additional phylogenetic work on Casasia and the more species-rich genus Randia. While the respective monophyly of both genera is rejected here, future work with a broader representation of Randia is needed.

“The Art or Mystery of Physick” – Asante Medicinal Plants and the Western Ordering of Botanical Knowledge

2016 ◽  
Vol 44 ◽  
pp. 27-62 ◽  
Author(s):  
Tom C. McCaskie
Keyword(s):  
Medicinal Plants ◽  
West African ◽  
Tabular Form ◽  
The West ◽  
Global Expansion ◽  
The Core ◽  
Botanical Knowledge ◽  
History Of ◽  
Longue Duree

Abstract:This paper deals with aspects of the still relatively neglected history of African medicinal plants. The core of the paper is a discussion in tabular form of the plants collected in the West African forest kingdom of Asante in 1817 by Henry Tedlie, a member of the well known English mission led by Thomas Bowdich. More generally, the paper considers episodes in the accumulation of Akan, Asante, and African plant specimens by Europeans, and the eventual classification of these in a western authorized botanical taxonomy that is now in worldwide use. The gathering of potentially medicinal plants is a little studied facet of European global expansion, from exploration to colonialism and beyond, and of the sovereign scientific orthodoxy that became established alongside it. The paper frames and discusses relevant details of this process over thelongue durée, from pre-Linnaean taxonomies to current controversies over bioprospecting.

scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

Generic delimitation and phylogenetic uncertainty: an example from a group that has undergone an explosive radiation

2005 ◽  
Vol 18 (1) ◽  
pp. 41 ◽  
Author(s):  
L. A. Orthia ◽  
L. G. Cook ◽  
M. D. Crisp
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Relationships ◽  
Recent Proposal ◽  
Generic Delimitation ◽  
Dna Sequence Data ◽  
Single Genus ◽  
Phylogeny Estimation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.

The shared evolutionary history of kinship classifications and language

2010 ◽  
Vol 33 (5) ◽  
pp. 402-403 ◽  
Author(s):  
Robert M. Seyfarth ◽  
Dorothy L. Cheney
Keyword(s):  
Human Evolution ◽  
Evolutionary History ◽  
The Other ◽  
History Of ◽  
System Maps

AbstractAmong monkeys and apes, both the recognition and classification of individuals and the recognition and classification of vocalizations constitute discrete combinatorial systems. One system maps onto the other, suggesting that during human evolution kinship classifications and language shared a common cognitive precursor.

scholarly journals Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16751 ◽  
Author(s):  
Adam C. Silver ◽  
David Williams ◽  
Joshua Faucher ◽  
Amy J. Horneman ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Aeromonas Veronii ◽  
Host Interaction ◽  
History Of ◽  
Complex Evolutionary History

Insights into the evolutionary history of Indo-Pacific bloodfeeding terrestrial leeches (Hirudinida:Arhynchobdellida:Haemadipisdae)

2010 ◽  
Vol 24 (5) ◽  
pp. 456 ◽  
Author(s):  
Elizabeth Borda ◽  
Mark E. Siddall
Keyword(s):  
Pacific Islands ◽  
Sequence Data ◽  
Indian Subcontinent ◽  
Tropical Rainforests ◽  
Mitochondrial Coi ◽  
Biogeographic Patterns ◽  
History Of ◽  
Volcanic Islands ◽  
South Pacific Islands

Haemadipsidae is a clade of notorious bloodfeeding annelids adapted to tropical and sub-tropical rainforests found throughout the Indo-Pacific. This family traditionally includes duognathous (two-jawed) endemics, each placed in their own genus, from continental and volcanic islands including: Australia, Indonesia, Madagascar, Papua New Guinea, Philippines, Seychelles, and South Pacific islands, while trignathous (three-jawed) Tritetrabdella species and the speciose Haemadipsa are exclusive to the Indian subcontinent ranging into east and south-east Asia. One of the more compelling aspects of haemadipsids is their distribution on post-Gondwanan landmasses. In this study, the phylogenetic relationships, taxonomy and biogeographic patterns of Haemadipsidae were examined. Over 5 kb of sequence data from three genes (nuclear 18S rDNA and 28S rDNA and mitochondrial COI) for 37 haemadipsid exemplars, representing 12 of the 15 recognised genera, were analysed under the criteria of maximum parsimony and Bayesian inference. The results show that widespread duognathous species form a monophyletic group derived from trignathous ancestry and are sister to a new trignathous clade for Haemadipsidae. This phylogenetic hypothesis rejected Gondwanan vicariance as an explanation for the diversification of haemadipsids. Haemadipsidae is accepted as the formal name for these Indo-Pacific leeches. Whereas the subdivisions Haemadipsinae and Domanibdellinae are clarified, there is a need to establish a new subfamily, Tritetrabdellinae, for the newly identified trignathous clade that is sister to Domanibdellinae. This study provides a basis for continued elucidation of the evolutionary relationships and classification of these terrestrial annelids.

An Analysis of the Sectional Classification of Anthurium (Araceae): Comparing Infrageneric Groupings and Their Diagnostic Morphology with a Molecular Phylogeny of the Genus

2019 ◽  
Vol 104 (1) ◽  
pp. 69-82 ◽  
Author(s):  
Mónica M. Carlsen ◽  
Thomas B. Croat
Keyword(s):  
Molecular Phylogeny ◽  
Evolutionary History ◽  
Morphological Characters ◽  
Taxon Sampling ◽  
Species Relationships ◽  
History Of ◽  
Sectional Classification

This study presents an evaluation of the currently accepted sectional classification of the genus Anthurium Schott (Araceae) in light of a recently published molecular phylogeny for the group. In general, disagreements between these two occur because many diagnostic morphological characters used in the sectional classification turned out to be highly homoplasious within Anthurium, with multiple independent gains or losses of seemingly similar morphologies in distantly related clades. A new sectional classification of Anthurium that more accurately represents species relationships and the evolutionary history of the genus is much needed, and here we propose the first steps toward it. Results from this study suggest that out of the 18 sections and two series recognized in Anthurium, only seven of these groups are monophyletic (i.e., sections Andiphilum (Schott) Croat, Calomystrium (Schott) Engl., Dactylophyllium (Schott) Engl., Leptanthurium (Schott) Engl., Polyphyllium Engl., Tetraspermium (Schott) Engl., and the newly recognized section Multinervia (Croat) Carlsen & Croat, previously a series within section Pachyneurium (Schott) Engl.). All other sections are either not monophyletic or their monophyly could not be accurately tested. A complete revision of the sectional classification of Anthurium will require a more comprehensive taxon sampling and a better supported molecular phylogeny.

scholarly journals Detecting Bottlenecks and Selective Sweeps From DNA Sequence Polymorphism

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 981-987 ◽  
Author(s):  
Nicolas Galtier ◽  
Frantz Depaulis ◽  
Nicholas H Barton
Keyword(s):  
Maximum Likelihood ◽  
Selective Sweep ◽  
Sequence Data ◽  
Likelihood Method ◽  
Recent History ◽  
Selective Sweeps ◽  
Gene Trees ◽  
Dna Sequence Polymorphism ◽  
History Of ◽  
Likelihood Approach

Abstract A coalescence-based maximum-likelihood method is presented that aims to (i) detect diversity-reducing events in the recent history of a population and (ii) distinguish between demographic (e.g., bottlenecks) and selective causes (selective sweep) of a recent reduction of genetic variability. The former goal is achieved by taking account of the distortion in the shape of gene genealogies generated by diversity-reducing events: gene trees tend to be more star-like than under the standard coalescent. The latter issue is addressed by comparing patterns between loci: demographic events apply to the whole genome whereas selective events affect distinct regions of the genome to a varying extent. The maximum-likelihood approach allows one to estimate the time and strength of diversity-reducing events and to choose among competing hypotheses. An application to sequence data from an African population of Drosophila melanogaster shows that the bottleneck hypothesis is unlikely and that one or several selective sweeps probably occurred in the recent history of this population.

Multi-locus phylogeny reveals Phaeodothis mori sp. nov. (Didymosphaeriaceae, Pleosporales) from dead leaves of Morus australis

Phytotaxa ◽  
2020 ◽  
Vol 428 (3) ◽  
pp. 241-254
Author(s):  
DANUSHKA S. TENNAKOON ◽  
CHANG-HSIN KUO ◽  
KEVIN D. HYDE
Keyword(s):  
New Species ◽  
Type Species ◽  
Sequence Data ◽  
Comprehensive Description ◽  
Bayesian Analyses ◽  
Natural Classification ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities ◽  
A New Species

In order to establish the phylogenetic relationships and to resolve the natural classification of species in Dothideomycetes, it is necessary to use multi-gene phylogeny as well as morphology. Phaeodothis mori is a new species collected from dead leaves of Morus australis from Chiayi, Taiwan. Maximum parsimony, maximum likelihood and Bayesian analyses were performed based on multi-locus phylogenies of ITS, LSU, SSU and tef1-α to clarify the phylogenetic affinities of the species. Phaeodothis mori is distinguished from the other Phaeodothis species based on distinct size differences in ascomata, asci, ascospores and base pair differences in DNA sequence data. Remarkably, this is the first Phaeodothis species recorded from Morus australis. The new species was compared with the type species of Phaeodothis and a comprehensive description and micrographs were provided.

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