Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Noncoalescent Genes
Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.
- GCG: Displaying Restriction Sites and Possible Translations in a DNA Sequence
- Quantifying Interactions Between G-Quadruplex DNA and Transition-Metal Complexes
- PC/GENE: Translation and Searches for Protein Coding Regions
- Integrative Food Grade Expression System for Lactic Acid Bacteria
- Subtractive cDNA Cloning Using Magnetic Beads and PCR
- Sedimentation and Immunoprecipitation Assays for Analyzing Complexes that Repress Transcription
- Adenoviral Vectors: Production and Purification
- Generation of Multiple Site-Specific Mutations by Polymerase Chain Reaction
- Nearest-Neighbor Analysis
- Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)