Phylogenetic analyses of some Egyptian genus of Lamiaceae family using rbcL sequences

Three chloroplast DNA (cpDNA) sequences [the rpl16 intron, the trnL-F, and atpB-rbcL intergenic spacer (IGS)] were employed to study phylogenetic relationships in the genus Rosa. Phylogenetic analyses using these three concatenated sequences were performed using maximum parsimony (MP) and Bayesian inference (BI) methods. Both analyses results suggest that the molecular phylogeny conforms closely to the conventional classification of botanical sections. Morphological similarities between R. sects. Synstylae and Chinenses, and R. sects. Rosa and Carolinae are corroborated on the molecular level in our analyses. Four taxa from R. sect. Pimpinellifoliae are further divided into two small clades, which reflect the morphological characters for these species on a molecular level. Whereas three accessions of R. foetida from R. sect. Pimpinellifoliae form a separate clade. R. ×fortuniana forms a clade with R. laevigata based on its maternal inheritance of cpDNA. R. ×cooperii is hypothesized to be a hybrid with seed parent from R. sects. Synstylae and Chinenses. And R. roxburghii should be classified as a section within the R. subgen. Rosa, rather than being treated as its own subgenus, based on molecular analyses.

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Discovery of Wilsonosiphonia fujiae (Rhodomelaceae, Rhodophyta) from the Maldives Islands and transfer of Polysiphonia rhizoidea from Hawaiʻi to Wilsonosiphonia

Phytotaxa ◽

10.11646/phytotaxa.451.1.5 ◽

2020 ◽

Vol 451 (1) ◽

pp. 63-72

Author(s):

GA HUN BOO ◽

TAE OH CHO ◽

ALISON R. SHERWOOD ◽

SUNG MIN BOO ◽

MUTUE TOYOTA FUJII

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Red Alga ◽

Species Level ◽

Mitochondrial Cox1 ◽

Upper Intertidal ◽

Algal Genus ◽

Marine Algal ◽

Cryptogenic Species ◽

Rbcl Sequences

Wilsonosiphonia is a newly described marine algal genus with three species. The genus was previously confused with the widely distributed taxon Polysiphonia, and because of this, the taxonomy and distribution of Wilsonosiphonia is likely underestimated. We report the discovery of a minute filamentous red alga, Wilsonosiphonia fujiae (Rhodophyta) in the Maldives Islands, a taxon which was considered endemic to Brazil. Specimens were collected at Fulhadoo, Goidhoo Atoll and Dhidhdhoo Islands, South Ari Atoll, which are ca. 160 km apart, during January and July, 2019, respectively. Thalli formed dense patches on the upper intertidal in regions of shaded rock. Both mitochondrial cox1 and plastid rbcL sequencing confirmed the occurrence of W. fujiae in the Maldives, which is also in agreement with morphological observations. Based on the low pairwise divergences of COI-5P and rbcL sequences between the Maldives and Brazil specimens, we suggest that W. fujiae is a recently introduced yet cryptogenic species in the Maldives. Additionally, as a result of our phylogenetic analyses, it became evident that sequences from the Hawaiian Islands, which were listed as members of the genus Polysiphonia, represent species-level diversity within the genus Wilsonosiphonia. Based on both morphological characteristics and the COI-5P phylogeny, we here reinstate Polysiphonia rhizoidea from Hawaiʻi and transfer it to Wilsonosiphonia, as W. rhizoidea comb. nov.

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Vulcanochloris (Trebouxiales, Trebouxiophyceae), a new genus of lichen photobiont from La Palma, Canary Islands, Spain

Phytotaxa ◽

10.11646/phytotaxa.219.2.2 ◽

2015 ◽

Vol 219 (2) ◽

pp. 118 ◽

Cited By ~ 13

Author(s):

Lucie Vančurová ◽

Ondřej Peksa ◽

Yvonne Němcová ◽

Pavel Škaloud

Keyword(s):

Geographical Distribution ◽

Canary Islands ◽

18S Rdna ◽

New Genus ◽

Phylogenetic Analyses ◽

Its Rdna ◽

Sister Relationship ◽

La Palma ◽

Chloroplast Morphology ◽

Rbcl Sequences

This paper describes a new genus of lichen photobionts, Vulcanochloris, with three newly proposed species, V. canariensis, V. guanchorum and V. symbiotica. These algae have been discovered as photobionts of lichen Stereocaulon vesuvianum growing on slopes of volcanos and lava fields on La Palma, Canary Islands, Spain. Particular species, as well as the newly proposed genus, are delimited based on ITS rDNA, 18S rDNA and rbcL sequences, chloroplast morphology, and ultrastructural features. Phylogenetic analyses infer the genus Vulcanochloris as a member of Trebouxiophycean order Trebouxiales, in a sister relationship with the genus Asterochloris. Our data point to the similar lifestyle and morphology of these two genera; however, Vulcanochloris can be well distinguished by a unique formation of spherical incisions within the pyrenoid. Mycobiont specificity and geographical distribution of the newly proposed genus is further discussed.

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Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences

Journal of Natural Medicines ◽

10.1007/s11418-009-0379-8 ◽

2010 ◽

Vol 64 (2) ◽

pp. 133-138 ◽

Cited By ~ 50

Author(s):

Haruka Asahina ◽

Junichi Shinozaki ◽

Kazuo Masuda ◽

Yasujiro Morimitsu ◽

Motoyoshi Satake

Keyword(s):

Phylogenetic Analyses ◽

Rbcl Sequences

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Ellipsomyxa ariusi sp. nov. (Myxosporea: Ceratomyxidae), a new myxosporean infecting the gallbladder of threadfin sea catfish Arius arius in India

Diseases of Aquatic Organisms ◽

10.3354/dao03529 ◽

2020 ◽

Vol 142 ◽

pp. 83-97

Author(s):

A Chandran ◽

PU Zacharia ◽

TV Sathianandan ◽

NK Sanil

Keyword(s):

Phylogenetic Analyses ◽

Type Specimen ◽

Ssu Rdna ◽

Fish Host ◽

Present Species ◽

Epithelial Layer ◽

Histopathological Changes ◽

Mucus Production ◽

High Bootstrap ◽

A New Species

The present study describes a new species of myxosporean, Ellipsomyxa ariusi sp. nov., infecting the gallbladder of the threadfin sea catfish Arius arius (Hamilton, 1822). E. ariusi sp. nov. is characterized by bivalvular, ellipsoid or elongate-oval myxospores with smooth spore valves and a straight suture, arranged at an angle to the longitudinal spore axis. Mature myxospores measured 10.1 ± 0.8 µm in length, 6.8 ± 0.5 µm in width and 7.7 ± 0.7 µm in thickness. Polar capsules are equal in size and oval to pyriform in shape. They are positioned at an angle to the longitudinal myxospore axis and open in opposite directions. Polar capsules measured 2.8 ± 0.3 µm in length and 2.5 ± 0.4 µm in width; polar filaments formed 4-5 coils, and extended to 32.2 ± 2.1 µm in length. Monosporic and disporic plasmodial stages attached to the wall of gallbladder. Molecular analysis of the type specimen generated a 1703 bp partial SSU rDNA sequence (MN892546), which was identical to the isolates from 3 other locations. In phylogenetic analyses, genus Ellipsomyxa appeared monophyletic and E. ariusi sp. nov. occupied an independent position in maximum likelihood and Bayesian inference trees with high bootstrap values. The overall prevalence of infection was 54.8% and multiway ANOVA revealed that it varied significantly with location, year, season, sex and size of the fish host. Histopathological changes associated with E. ariusi sp. nov. infection included swelling, vacuolation and detachment of epithelial layer, reduced mucus production and altered consistency and colour of bile. Based on the morphologic, morphometric and molecular differences with known species of Ellipsomyxa, and considering differences in host and geographic locations, the present species is treated as new and the name Ellipsomyxa ariusi sp. nov. is proposed.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Cultural evolution and cultural psychology

10.31234/osf.io/7k86h ◽

2018 ◽

Author(s):

Alex Mesoudi

Keyword(s):

Cultural History ◽

Cultural Evolution ◽

Cultural Transmission ◽

Cultural Psychology ◽

Phylogenetic Analyses ◽

Cultural Dimensions ◽

Human Cognition ◽

Cultural Variation ◽

Cultural Inheritance ◽

Human Psychology

Cultural evolution is a branch of the evolutionary sciences which assumes that (i) human cognition and behaviour is shaped not only by genetic inheritance, but also cultural inheritance (also known as social learning), and (ii) this cultural inheritance constitutes a Darwinian evolutionary system that can be analysed and studied using tools borrowed from evolutionary biology. In this chapter I explore the numerous compatibilities between the fields of cultural evolution and cultural psychology, and the potential mutual benefits from their closer alignment. First, understanding the evolutionary context within which human psychology emerged gives added significance to the findings of cultural psychologists, which reinforce the conclusion reached by cultural evolution scholars that humans inhabit a ‘cultural niche’ within which the major means of adaptation to difference environments is cultural, rather than genetic. Hence, we should not be surprised that human psychology shows substantial cross-cultural variation. Second, a focus on cultural transmission pathways, drawing on cultural evolution models and empirical research, can help to explain to the maintenance of, and potential changes in, cultural variation in psychological processes. Evidence from migrants, in particular, points to a mix of vertical, oblique and horizontal cultural transmission that can explain the differential stability of different cultural dimensions. Third, cultural evolutionary methods offer powerful means of testing historical (“macro-evolutionary”) hypotheses put forward by cultural psychologists for the origin of psychological differences. Explanations in terms of means of subsistence, rates of environmental change or pathogen prevalence can be tested using quantitative models and phylogenetic analyses that can be used to reconstruct cultural lineages. Evolutionary considerations also point to potential problems with current cross-country comparisons conducted within cultural psychology, such as the non-independence of data points due to shared cultural history. Finally, I argue that cultural psychology can play a central role in a synthetic evolutionary science of culture, providing valuable links between individual-oriented disciplines such as experimental psychology and neuroscience on the one hand, and society-oriented disciplines such as anthropology, history and sociology on the other, all within an evolutionary framework that provides links to the biological sciences.

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Faculty Opinions recommendation of Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718382559.793497569 ◽

2014 ◽

Author(s):

Deborah Charlesworth

Keyword(s):

Gene Conversion ◽

Sex Chromosomes ◽

Phylogenetic Analyses

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Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

Current HIV Research ◽

10.2174/1570162x18666200415140652 ◽

2020 ◽

Vol 18 (3) ◽

pp. 210-218

Author(s):

Guolong Yu ◽

Yan Li ◽

Xuhe Huang ◽

Pingping Zhou ◽

Jin Yan ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Reverse Transcriptase ◽

Phylogenetic Analyses ◽

Resistance Mutations ◽

Protease Inhibition ◽

Subtype B ◽

Primary Drug Resistance ◽

Hiv 1 ◽

Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

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