scholarly journals Phylogenetic analysis of Bangiadulcis atropurpurea (A. Roth) W.A. Nelson and Bangia fuscopurpurea (Dillwyn) Lyngbye (Bangiales, Rhodophyta) in Taiwan

2015 ◽  
Vol 67 (2) ◽  
pp. 445-454 ◽  
Author(s):  
Jui-Yu Chou ◽  
Shao-Lun Liu ◽  
Yu-Der Wen ◽  
Wei-Lung Wang
Keyword(s):  
New Record ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Marine Species ◽  
Rbcl Gene ◽  
Algal Flora ◽  
Red Algal ◽  
Ecological Conservation ◽  
Freshwater Red Algae ◽  
Bangia Fuscopurpurea

Samples of the freshwater red algae, Bangiadulcis atropurpurea, collected from the mountain waterfalls and its close species, Bangia fuscopurpurea, collected from coasts, were phylogenetically analyzed. The sequences of the rbcL gene and RuBisCO spacer region of the freshwater Bangiadulcis atropurpurea species were identical or similar to those of B. atropurpurea from Japan, North America and Europe. This result indicated that the freshwater Bangiadulcis species from Taiwan shared a common ancestor with the three above-mentioned populations and formed a distinct clade from the marine Bangia species in the phylogenetic trees. It is suggested that all the previous records on marine Bangia species should be revised and the name B. fuscopurpurea be used for the marine species in Taiwan. In this study, the freshwater alga B. atropurpurea presents a new record in the algal flora of Taiwan. This finding is important for the protection of the biodiversity of red algal flora, and provides useful information on the ecological conservation of the species in Taiwan.

scholarly journals New record of endangered red alga Bangia atropurpurea (A. Roth) C. Agardh (Bangiales, Rhodophyta) in the Nisava river, Serbia

2010 ◽  
Vol 62 (4) ◽  
pp. 1239-1243 ◽  
Author(s):  
Jelena Andrejic ◽  
M. Cvijan ◽  
Snezana Simic
Keyword(s):  
New Record ◽  
Red Alga ◽  
Algal Flora ◽  
Ecological Preferences ◽  
New Findings ◽  
Red Algal ◽  
New Localities ◽  
Bangia Atropurpurea

Bangia atropurpurea was found at two new localities in the Nisava River (Southern Serbia). In Serbia, this species is endangered. It has been found so far in the Trgoviski Timok River, the Gvozdovacka River and the Raska River. With the two new localities in the Nisava River, at present Bangia occupies four rivers (five localities). New findings are important for the protection of the biodiversity of red algal flora in the region, and provide useful information on the ecological preferences of the species in Serbia.

scholarly journals Role of the Digestive Gland in Ink Production in Four Species of Sea Hares: An Ultrastructural Comparison

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Jeffrey S. Prince ◽  
Paul Micah Johnson
Keyword(s):  
Digestive Gland ◽  
Common Ancestor ◽  
Aplysia Californica ◽  
Digestive Cell ◽  
Digestive Cells ◽  
Sea Hare ◽  
Red Algal ◽  
The Common ◽  
Algal Chloroplast

The ultrastructure of the digestive gland of several sea hare species that produce different colored ink (Aplysia californicaproduces purple ink,A. julianawhite ink,A. parvulaboth white and purple ink, whileDolabrifera dolabriferaproduces no ink at all) was compared to determine the digestive gland’s role in the diet-derived ink production process. Rhodoplast digestive cells and their digestive vacuoles, the site of digestion of red algal chloroplast (i.e., rhodoplast) inA. californica, were present and had a similar ultrastructure in all four species. Rhodoplast digestive cell vacuoles either contained a whole rhodoplast or fragments of one or were empty. These results suggest that the inability to produce colored ink in some sea hare species is not due to either an absence of appropriate digestive machinery, that is, rhodoplast digestive cells, or an apparent failure of rhodoplast digestive cells to function. These results also propose that the digestive gland structure described herein occurred early in sea hare evolution, at least in the common ancestor to the generaAplysiaandDolabrifera. Our data, however, do not support the hypothesis that the loss of purple inking is a synapomorphy of the white-ink-producing subgenusAplysia.

scholarly journals RootDigger: a root placement program for phylogenetic trees

2020 ◽  
Author(s):  
Ben Bettisworth ◽  
Alexandros Stamatakis
Keyword(s):  
Phylogenetic Analysis ◽  
Markov Model ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Markov Models ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Root Position ◽  
Confidence Value ◽  
Root Location

AbstractSummaryIn phylogenetic analysis, it is common to infer unrooted trees. Thus, it is unknown which node is the most recent common ancestor of all the taxa in the phylogeny. However, knowing the root location is desirable for downstream analyses and interpretation. There exist several methods to recover a root, such as midpoint rooting or rooting the tree at an outgroup. Non-reversible Markov models can also be used to compute the likelihood of a potential root position. We present a software called RootDigger which uses a non-reversible Markov model to compute the most likely root location on a given tree and to infer a confidence value for each possible root placement.Availability and implementationRootDigger is available under the MIT licence at https://github.com/computations/root_digger

scholarly journals PHYLOGENETIC ANALYSIS ON FOUR SPECIES OF TILAPIA (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron) IN NIGERIA

2017 ◽  
Vol 16 (2) ◽  
pp. 61-68
Author(s):  
O. T. AGBEBI ◽  
J. ECHEFU
Keyword(s):  
Oreochromis Niloticus ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Clarias Gariepinus ◽  
Evolutionary Relationship ◽  
Pcr Amplification ◽  
Fta Cards ◽  
Loop Region ◽  
Sarotherodon Galilaeus ◽  
Sarotherodon Melanotheron

An investigation into evolutionary history of four species of Tilapia species was carried out as a taxonomy tool to relate most tilapia species found within the Nigerian waters. These species are (Oreochromis niloticus, Tilapia zilli, Sarotherodon galilaeus, Sarotherodon melanotheron). Blood samples from the four species of tilapia were collected and preserved on Fast Technology for Analysis (FTA) cards for DNA extraction and PCR amplification. The various nucleotide sequences of the four Tilapia species found in the Mitochondria D-loop region were copied and aligned with the use of BioEdit and Mega 6.0 softwares. Three phylogenetic trees were drawn to show the evolutionary relationship amongst the four species of tilapia. The results indicated that Sarotherodon galilaeus and Sarotherodon melanotheron are sister texa and share a common ancestor with Oreochromis niloticus. Tilapia zilli is an out group which is the most distantly related to the three species (Oreochromis niloticus, Sarotherodon galilaeus Sarotherodon melanotheron). Tilapia zilli (Israel) and Tilapia zilli are sister texa and share a common ancestor in Tilapia sparmanii. The study also revealed ancestry relationship among other species of fish Cyprinus caprio and Clarias gariepinus formed a clade with the three tilapia species (Tilapia zilli, Tilapia zilli (Israel) and Tilapia sparmanii), which share an unknown but common ancestor.

scholarly journals Algae Diversity and Ecology during a Summer Assessment of Water Quality in the Abraham Lincoln Birthplace National Historical Park, USA

Diversity ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 206 ◽  
Author(s):  
Sophia Barinova ◽  
Thomas Smith
Keyword(s):  
Water Quality ◽  
Algal Species ◽  
Benthic Algae ◽  
Water Quality Assessment ◽  
Abraham Lincoln ◽  
Algal Flora ◽  
Diatom Algae ◽  
Class 1 ◽  
Red Algal ◽  
The Usa

There were 88 species of algae and cyanobacteria observed from seven sites in the Abraham Lincoln Birthplace National Historical Park (Hodgenville, Kentucky, USA). This was the first algal investigation study in the park. There were 21 samples collected, during the summer, on 16 July 2008. Algal flora, dominated by diatoms was represented by 54 species identified (61.4% of the total), 20 species of cyanobacteria, 11 green and two charophyte algal species, and one red algal species (22.7%, 12.5%, 2.2%, and 1.1%, respectively). Benthic diatoms dominated the aquatic system with 14 species of Navicula and 12 species of Nitzschia identified, which was 15.7% and 13.5% of the total, respectively. Species tended to be site specific and 78.6% of the species were only found in two or less sites. The bioindicator methods for water quality assessment were based on species autoecology. This method was used for the first time in the USA during this study. This demonstrated that benthic and planktonic-benthic algae preferred temperate temperatures, middle-oxygenated mesotrophic waters, low-to-middle enriched by chlorides. The waters were well oxygenated, sometimes saturated by sulfides, low-alkaline, low-to-middle organic enriched, and of class 1–3 water quality with high self-purification capacity. This is very important for habitat protection and cannot be easily accomplished strictly through chemical analysis. The diversity of diatom algae not only plays a major role in the formation of algal communities and their uniqueness, but diatom algae can be a good indicator of environmental assessments and change.

Sheathia jinchengensis (Batrachospermales, Rhodophyta), a new freshwater red algal species described from North China

Phytotaxa ◽  
2018 ◽  
Vol 367 (1) ◽  
pp. 63 ◽  
Author(s):  
JIN-FEN HAN ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
...  
Keyword(s):  
New Species ◽  
North China ◽  
Cold Water ◽  
Sequence Data ◽  
Algal Species ◽  
Point Of View ◽  
Shanxi Province ◽  
Water Stream ◽  
Red Algal ◽  
Freshwater Red Algae

A new species of freshwater red algae, Sheathia jinchengensis, is described based on material collected from rocks in a clean and cold-water stream from the Jincheng region of Shanxi province in North China. Molecular sequences of rbcL and psbA genes were used to evaluate the phylogenetic relationship among samples of S. jinchengensis and other Sheathia species from several regions of the world. The results showed that S. jinchengensis formed an independent branch and separated from the previously published sequence data of other Sheathia taxa. From a morphological point of view, this new species differs also from other species of the genus by the smaller diameter of whorls (167.0–312.5 μm) and larger carpogonium diameter (17.0–29.0 μm). Comparison of sequence variation and thallus morphology with other Sheathia taxa resulted in the proposal of the new species—S. jinchengensis. Additionally, two endemic Batrachospermum species described earlier from China i.e., B. hongdongense and B. longipedicellata are now transferred to the genus Sheathia based on the present study as S. hongdongensis (S.L.Xie & J.Feng) Han, Nan, Feng, Lv, Liu, Kociolek et Xie comb. nov. and S. longipedicellata (Hua & Shi) Han, Nan, Feng, Lv, Liu, Kociolek et Xie comb. nov.

scholarly journals The Common Ancestor of Deinococcus Species was Rod-Shaped

2018 ◽  
Vol 11 (1) ◽  
pp. 252-258 ◽  
Author(s):  
Yusuke Morita ◽  
Hiromi Nishida
Keyword(s):  
Horizontal Transfer ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Thermus Thermophilus ◽  
Spherical Shape ◽  
Evolutionary Relationships ◽  
The Common ◽  
Formation System

Background:The genusDeinococcusconsists of species in rod-shape (Bacilli) and spherical shape (Cocci).Objective:In this study, we aimed to determine whether the common ancestor ofDeinococcusspecies was rod-shaped or spherical.Methods:We compared the homologs of the proteins related to the rod-shape in bacteria (MreB, MreC, MreD, MrdA, RodA, and RodZ) in variousDeinococcusspecies andThermus thermophilus.Results:The phylogenetic trees based on each protein and the homologs reflected the evolutionary relationships of the species, indicating that the Horizontal transfer of the genes did not occur during theDeinococcusevolution.Conclusion:The ancestor of the genusDeinococcuswas rod-shaped, and the spherical forms appeared when the rod-shaped formation system was lost during evolution and diversification within the genus.

scholarly journals The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome

2022 ◽  
Vol 66 (6) ◽  
pp. 409-416
Author(s):  
T. E. Sizikova ◽  
V. N. Lebedev ◽  
S. V. Borisevich
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Infectious Agent ◽  
Global Public Health ◽  
The Common ◽  
Epidemiological Characteristics ◽  
Severe Fever

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

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