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Based on the distribution of family presence in the leaf taxa, we assign creations to specific branches of the tree using a parsimony rule where: if two branches share a family, a creation is assigned to the MRCA of those branches.
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Bootstrapping was performed using a parsimony criterion (1000 replicates).
The partition homogeneity test was run on PAUP* 4.0a109 using a parsimony criterion for four genes and 1000 replicates [70].
The degree of homoplasy of each dataset both with and without indels was assessed on a Maximum Parsimony (MP) tree that was obtained using a parsimony ratchet approach.
We also performed maximum parsimony bootstrap analyses on the 3-gene and 5-gene data sets using a parsimony ratchet search strategy [ 57] implemented in PAUP* [ 58].
Paraphyly of H. melpomene, as found by Brower [ 23] using a parsimony analysis, is however strongly rejected by equal-weighted parsimony bootstrapping on our data.
Analyses of genetic differentiation among species using a 95% parsimony limit reconstruction criterion [ 52] suggest that biological species often form unconnected parsimony networks.
Secondly, we dated lincRNAs according to appearance of homologs using parsimony rules.
We analyzed the C. elegans DUF23 family using a maximum parsimony phylogenetic method.
Haplotypes were connected using a 95% parsimony limit.
The tree was constructed with MEGA 5.1 software using a maximum parsimony method.
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