Lecture 13 Flashcards
supermatrix
- directly inferred from seq data through the construction of a large multiple seq alignment for simultaneous analysis of final data-matrix
- often sacrifice completeness in interest of size
supertree
compile many source trees w/partially overlapping taxa into single tree; strictly topological; do not rely directly on primary data (cant go back and reanalyze with other parameters)
issues with supertree methods
- data independence: some data can contribute to more than one souce tree
- signal enhancement: novel relationship in supertree contradicting source trees
- assessment of uncertainty/confidence
Pros of Sanger seq
PCR-based, dependable, easy to target specific genes, accurate
cons of Sanger seq
max ~1000 bases in single rxn, expensive, primers
pros of NGS
huge amount of seqs, cheap, do not need prior knowledge
cons of NGS
inaccurate (~99%), overkill to target particular region, short reads, seq random parts of genome
phylogenomics
integration of evolutionary reconstructions and genome seq analysis
metagenomics
1) catalogue diversity w/barcoding (OTUs)
2) true metagenome of genes present in environmental sample
- herbivores-> amino acid synthesis genes; carn-> aa degradation genes
Dinsdale (2008) metagenome study
found rel contribution of functional categories of genes differed but the total complement was similiar
Why is it difficult to use RAD to reconstruct a phylogeny?
- more difficult to dtmn homology
- restriction sites change as spp diverge
reciprocal translated BLAST
helps find homologous genes across spp, but paralogs make things complicated
phylogenetic informativeness profiles
Townsend (2007); determine most appropriate genes for resolving particular relationships; use genes evolving slower and help avoid saturation
access to numerous genomes can be informative how?
informative marker discovery, gene order and gene loss studies, influence of organelle genomes
minimum optimal # of genes needed for equivalency to entire genome?
20
