Analyses were performed using both the default branch collapsing rule (collapse if maximum is zero) and amb- (collapse if minimum length is zero).
Two most parsimonious trees of 445 steps (CI = 0.613, RI = 0.789) were found in all replicates, using the collapsing rule 3 for zero-length branches [30], the strict consensus of which is shown in Figure 7 (see also Figure S4).
Phylogenetic analyses performed using WinClada, version 1.00.08 [38], spawning the matrix to NONA version 2.0 [39] were executed using heuristic search options hold10000, mult*100, max*, hold/10, and the default branch collapsing rule, amb-.
Under the default branch collapsing rule and simple sequence addition the number of equally parsimonious trees was very high (hitting the limit of 637.000 defined by memory allocation) and analyses without an upper limit for the number of saved trees could not be run to completion.
We set the collapsing rule to minimum length = 0 and random seed was set to "time".
We applied the USRDS 60-day collapsing rule to such changes, namely, that they must remain in place for at least 60 days to be considered stable [ 1].
Zero length branches in any of the recovered MPTs were collapsed (rule 1 of Coddington & Scharff [ 22]).
Collapsing rule was set to minimum length = 0. Jackknife branch support values were produced in TNT using random addition of sequences, 1000 search replicates, and cut-off value of 50%.
Existing carbon markets have been plagued with volatile pricing – Europe's cost of carbon has basically collapsed – or rules that prevent carbon trading with developing countries.
