• Reliability analysis of reconstructing phylogenies under long branch attraction conditions

      Dissanayake, Ranjan; Allman, Elizabeth; McIntyre, Julie; Short, Margaret; Goddard, Scott (2018-05)
      In this simulation study we examined the reliability of three phylogenetic reconstruction techniques in a long branch attraction (LBA) situation: Maximum Parsimony (M P), Neighbor Joining (NJ), and Maximum Likelihood. Data were simulated under five DNA substitution models-JC, K2P, F81, HKY, and G T R-from four different taxa. Two branch length parameters of four taxon trees ranging from 0.05 to 0.75 with an increment of 0.02 were used to simulate DNA data under each model. For each model we simulated DNA sequences with 100, 250, 500 and 1000 sites with 100 replicates. When we have enough data the maximum likelihood technique is the most reliable of the three methods examined in this study for reconstructing phylogenies under LBA conditions. We also find that MP is the most sensitive to LBA conditions and that Neighbor Joining performs well under LBA conditions compared to MP.
    • Testing multispecies coalescent simulators with summary statistics

      Baños Cervantes, Hector Daniel; Allman, Elizabeth; Rhodes, John; Goddard, Scott; McIntyre, Julie; Barry, Ron (2018-12)
      The Multispecies coalescent model (MSC) is increasingly used in phylogenetics to describe the formation of gene trees (depicting the direct ancestral relationships of sampled lineages) within species trees (depicting the branching of species from their common ancestor). A number of MSC simulators have been implemented, and these are often used to test inference methods built on the model. However, it is not clear from the literature that these simulators are always adequately tested. In this project, we formulated tools for testing these simulators and use them to show that of four well-known coalescent simulators, Mesquite, Hybrid-Lambda, SimPhy, and Phybase, only SimPhy performs correctly according to these tests.