Molecular Data in Phylogenetic Analysis

• molecular data


  DNA or protein sequences, allozymes, microsatellites
• molecular data number of characters is near unlimited compared to morphological data
• hypervariable markers can show variation down to the level of individual
• morphological data can't really differentiate between bacteria and archaebacteria
• morphological data limited at the low taxonomic level by a lack of variable data
• molecular data shows the +/- independent of neutral history, often selectively neutral
• morphological show convergence to similar to natural history
• molecular data would not be affected by direct environmental induction but morphological data will be
• direct environmental induction includes that of temperature and nutrition
• genetic basis shows molecular data dealing with the genetic code in terms of sequence
• purine and pyridmines can switch by methods of transversion
• travnsversion is more rare than transitions
• each position in a sequence is a character, each base is a character state
• types of models of sequence evolution

  likelihood and bayesian
• maximum likelihood and Bayesian methods use explicit models of sequence evolution
• model postulates a probability for any particular substitution
• Calculates probability for any given tree under model of sequence evolution
• Most likely tree retained as optimal
• Increasingly complex models allow increased resolving power
• molecular data give at least appropriate idea of lineage splits
• molecular clock hypothesis

  tracing lineage by molecular data
• comparisons of sequences should give time of divergence
• calibration in molecular clocks requires fossils
• precision of molecular clocks is affected by substitution rates between lineages