Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Ecology and Evolutionary Biology (4)
- Other Ecology and Evolutionary Biology (3)
- Bioinformatics (2)
- Computational Biology (2)
- Alternative and Complementary Medicine (1)
-
- Bacteria (1)
- Biochemistry (1)
- Biochemistry, Biophysics, and Structural Biology (1)
- Biodiversity (1)
- Biology (1)
- Botany (1)
- Environmental Microbiology and Microbial Ecology (1)
- Evolution (1)
- Genetics (1)
- Immunity (1)
- Immunology and Infectious Disease (1)
- Medicine and Health Sciences (1)
- Microbiology (1)
- Molecular Genetics (1)
- Organisms (1)
- Other Genetics and Genomics (1)
- Plant Biology (1)
- Plant Sciences (1)
- Plants (1)
- Systems Biology (1)
- Terrestrial and Aquatic Ecology (1)
- Keyword
-
- AMY (1)
- Algae (1)
- Amylase (1)
- Ancestral state reconstruction (1)
- Catarrhines (1)
-
- Coalescence (1)
- Evolution (1)
- Freshwater (1)
- Gene flow (1)
- Genetics (1)
- Genome (1)
- Immunomodulatory herbs (1)
- Lipid A (1)
- Lipopolysaccharide (1)
- Medicinal Plants (1)
- Next Generation Sequencing (1)
- Phylogenetic signal (1)
- Phylogenetics (1)
- Phylogenomics (1)
- Phylogeny (1)
- Primates (1)
- Probiotics (1)
- Reticulations (1)
- Species network (1)
- Species tree (1)
- Starch (1)
- Starry stonewort (1)
- Publication
- Publication Type
Articles 1 - 5 of 5
Full-Text Articles in Genomics
Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He
Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He
Publications and Research
With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).
Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané
Phylogenetic Trees And Networks Can Serve As Powerful And Complementary Approaches For Analysis Of Genomic Data, Christopher Blair, Cécile Ané
Publications and Research
Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point-of-view we highlight some of the strengths and limitations …
Distribution And Population Structure Of The Invasive Nitellopsis Obtusa (Desv. In Loisel.) J. Groves And Native Species Of Characeae In The Northeast U.S.A., Robin Sleith
Dissertations, Theses, and Capstone Projects
Freshwater ecosystems are some of the most biologically diverse environments on Earth. Billions of humans rely on functioning freshwater ecosystems for drinking water and many other services. These ecosystems are increasingly threatened by human impacts including nutrient pollution, invasive species, and climate change. Here I contribute four research chapters that investigate freshwater diversity and ecosystem threats using the Characeae, a family of freshwater green macroalgae, as a study system. Characeae are a diverse and ancient group with more than 500 extant species and a fossil history spanning at least 250 million years. These algae are macrophytes in freshwater ecosystems, and …
Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon
Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon
Theses and Dissertations
This study phylogenetically analyzed 30 AMY-related genes from 11 primates. The results show the gradual expansion of the AMY gene family which could have allowed primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity.
Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana
Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana
Dissertations, Theses, and Capstone Projects
Medicinal plants are one of the biggest sources of natural products with therapeutic importance. There are currently over 28,000 plants with putative medicinal values. Plant-derived compounds have been explored extensively for various biological activities ranging from anti-cancer, immune-boosting to anti-inflammatory and anti-oxidant. Some of the most important therapeutic agents are of plant-origin, such as paclitaxel from Pacific yew (Taxus brevifolia) and artemisinin from qinghao su (a Chinese medicinal herb; a.k.a. Artemisia annua) to name a few.
The study presented in this thesis started out as classical pharmacognosy research, which focused on the identification of immunostimulatory factors in …