AToL: Phylogeny of Lepidoptera: A genomicsinspired, community collaboration

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Topic of presentation Phylogenetic consequences
of base compositional heterogeneity
Jerome Regier Michael Cummings Andreas
Zwick University of Maryland Univ. MD Biotech.
Inst.
AToL Phylogeny of Lepidoptera A
genomics-inspired, community collaboration --
PIs Michael Cummings, Don Davis, Charles
Mitter, Cyndy Parr, Jerome Regier, Susan Weller
Biocomplexity in the Environment Deep arthropod
phylogeny from 100 targeted nuclear coding-region
sequences -- PIs Cliff Cunningham, Jody Martin,
Jerome Regier, Jeff Shultz, Jeff Thorne
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• What are the concerns with inclusion of sites
  with synonymous change?
• frequently heterogeneous in base composition
• higher frequency of polymorphisms (inferred from
  sequencing total cDNA). This suggests that some
  character states at synonymous sites are likely
  to be missing because the population has been
  poorly sampled, e.g., typically a single specimen
  is sequenced. Note that the consequence of
  partially missing characters states would be
  different from completely missing characters.
• A comparison of results with and without
  synonymous change provides an assessment of the
  potential problem.