Cytochrome b phylogeny and molecular species delimitation.
The cytb gene trees produced identical topologies using both the BI and
ML reconstruction methods (Fig. 2). The Aporodon major clade
recovered the R. mexicanus (R. brevirostris , R.
mexicanus , R. darienensis , R. garichensis, R.
gracilis, and R. spectabilis ) and R. tenuirostris(represented here by R. microdon , R. tenuirostris , andR. cherrii ) species groups. Specimens from Costa Rica identified
as R. sp. by Miller and Engstrom (2008) were recovered as closely
related to R. garichensis . R. mexicanus specimens split
into three clades that were well-supported in the BI method, but weakly
supported by ML. Clade I included individuals with geographical
distribution in the Sierra Madre Oriental and northern Oaxaca, Mexico.
This clade was sister to the R. mexicanus and R.
tenuirostris species groups (pP = 1). Clade II corresponded to
specimens distributed in Mexico, Guatemala, and El Salvador, and was
recovered as the sister group to R. brevirostris from Costa Rica
(pP = 1). The remaining individuals of R. mexicanus were grouped
into a clade III with distribution in Colombia and Ecuador and sister toR. darienensis from Panama (pP = 1).
The results of the species delimitation methods were not congruent with
each other (Fig. 2). For the R. mexicanus group, the mPTP method
identified 15 putative species while 11 were delimited by the bGMYC. The
multi-locus method STACEY suggested 10 species for both datasets (cytb +
Fgb-I7 and cytb + IRBP), excluding species that were not successfully
sequenced. The three methods supported the recognition of R.
darienensis , R . sp. from Volcan Poas, Alajuela, Costa
Rica, and R. garichensis (including the R . sp .
individual from La Carpentera, Cartago, Costa Rica), as species. In
addition, R. gracilis from Yucatán and R. spectabilis were
considered the same species, excluding specimens of R. gracilisdistributed in El Salvador, which were delimited as a distinct species.
For R. brevirostris , each delimitation method proposed different
numbers of possible species (from 1 to 3), although bGMYC and K2P
genetic distances were congruent in delimiting only one species.
Within the R. mexicanus species complex, the R. mexicanusclade I was supported at the species level by all three delimitation
methods. Within the R. mexicanus clade I, STACEY (cytb + Fgb-I7)
demarcated four possible species, while the other methods delimited only
two. Following the recognition of two species, one of them is formed of
samples from Mexico and Guatemala (R. mexicanus clade IIA),
whereas the other corresponded to individuals from El Salvador, which
were considered a distinct species under all the methods (R.
mexicanus clade IIB). Within clade III, the mPTP identified 5 species,
whereas bGMYC 2, and STACEY 3 (cytb + Fgb-I7). In this clade, the
consensus between methods demarcated two putative species: R.
mexicanus clade IIIA and R. mexicanus clade IIIB. The cytb
genetic distance values between the species delimitation consensus
ranged from 4.96 to 18.18, with the highest value generally betweenR. mexicanus clade I and the other identified species. The cytb
genetic distance values between delimited taxa in the R.
mexicanus species group are shown in Table 2 and Appendix 2.