Figure 4B D shows several ancestral codon configurations (ACCs) that could underlie an extant codon configuration (ECC) that MP would infer as a single pu change in the m lineage.
Such an extant codon configuration will be abbreviated "ECC_uppppp" assuming all "p" states are identical.
Given the phylogenetic distances in the D. melanogaster subgroup, dup,pu inference biases under the mixed non-equilibrium simulation can be understood, to a large extent, by considering extant codon configurations consistent with both a single change or changes in two lineages (ECC_SD for extant codon configurations consistent with single or double hits).
Examples of extant and ancestral codon configurations illustrate some of the causes of these inference biases.
Examination of extant and ancestral codon configurations reveals differences in the causes of similar MP reconstruction biases under equilibrium and decreasing codon bias.
Modal digit configurations for extant species of Lerista were collated from data in the literature, verified and augmented by our own observations of specimens in the South Australian Museum and Western Australian Museum.
Moreover, in all instances, the ancestral states implying implausible digit configurations are not significantly more likely than alternative states implying configurations observed among extant species of Lerista (see Figure 1; this is not the case for ancestral states inferred under the maximum likelihood rate of digit gain).
Whereas ancestral states entailing repeated re-elaboration of the pes imply digit configurations for many internal nodes differing fundamentally from those displayed by extant species of Lerista, ancestral digit configurations implied by reconstructions entailing no reversals of pedal digit loss are nearly invariably represented among observed phenotypes.
The extant literature suggests network structures evolve from a bridging configuration to a bonding configuration without examining the details of how the evolution occurs within the network and its stage-by-stage impact on knowledge transfer.
For example, consider a case where a configuration [G, A, G, G, G, G] for extant nodes [m, s, t, y, e, o] gave inferred ancestral configurations [G, G, G, G] and [A, G, G, G] for ancestral nodes [ms, tyeo, ty, eo] with probabilities 0.9 and 0.1, respectively.
However, in natural settings, microbial growth and decay continually over as little as several years can alter the original microbe-mineral configuration making it difficult to identify a direct association between extant microbial life and precipitates.
