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Taxonomic grouping based on shared evolutionary novelties (cladistic analysis) brings these correlations into focus.
To do this, we replace the previous prior specifying independent virus locations with a prior that incorporates covariance based on shared evolutionary history.
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Generally this required that groupings be "monophyletic," or based solely on shared evolutionary history, though exceptions could occur and were allowed.
See also [ 98] that explicitly proposes to model different evolutionary outcomes with different evolutionary patterns (one tree, one rNOL, disconnected genome networks based on shared sequences, etc).
RD, based on loci, helps to resolve ancestral polymorphism through allele length impinged by slow evolutionary processes, while SAD, based on shared alleles, helps to understand recent gene flow characterized by direct allelic exchange free from slow evolutionary process.
Recent research has found that the inclusion of synapomorphies can help support understanding of tree diagrams and that evolutionary relationships are based on shared characteristics (Novick et al. 2010a), making their relatively uncommon use in museum tree diagrams problematic in terms of supporting visitor understanding.
The first revolution was the surge of cladistics (Hennig 1966), a new method to reconstruct evolutionary relationships among organisms based on shared, derived biological characteristics ("synapomorphies").
We opted for the second alternative to recognize the separate evolutionary trajectory of this lineage based on shared morphological and life history traits.
Likewise any estimate of distance based on shared CLOGs is likely biased by genome size, which again reflects evolutionary distance as determined by 16S rRNA analysis.
We suggest that the learning processes involved in the early development of social cognition among hominoids (apes and humans) are based on largely shared evolutionary mechanisms (e.g. Bard, 2009; Gardner, 2005; Jablonka & Lamb, 2007).
Why? Common purpose based on shared values.
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