Nuclear and concatenated phylogenies.
Topologies resulting from the Fgb-I7 and IRBP nuclear genes were
inconsistent with each other and with the cytb tree, showing low support
values for the ML and BI reconstruction methods. Neither of the nuclear
trees recovered the Aporodon species groups for the ML optimality
criteria, and most clades collapsed into polytomies (Appendix 3 and 4).
In the Fgb-I7 tree, individuals from R. mexicanus clade IIIB were
grouped within the R. mexicanus clade I, with generally low
support values (pP ≤ 0.50, UFB ≤ 50). Specimens of the R.
mexicanus clade II did not form a monophyletic group and their
relationships with the species with which they were grouped were mostly
poorly supported (pP ≤ 0.80, UFB ≤ 85). The IRBP tree showed minor
inconsistencies with the cytb tree, and relationships betweenAporodon species were, in general, better supported, compared to
the Fgb-I7 tree, at least for the BI analysis (Appendix 4).
Tree topologies obtained with the cytb + Fgb-I7 concatenated data were
almost identical to the cytb topology (Fig. 4). The only difference was
in the ML analysis, where specimens of R. gracilis from El
Salvador were grouped as the sister clade of R. mexicanus clade
I, but with low support values (UFB = 43, Appendix 5). Phylogenies
obtained with the cytb + IRBP concatenated data were generally congruent
with the cytb tree (Fig. 4). Minor differences were found with respect
to the tree resulting from the ML analysis, where R. garichensis+ R. sp. Volcan Poas were recovered as a sister clade to R.
microdon , although these relationships were not well supported (UFB =
44, Appendix 6).