Phylogenetic studies on Didelphid marsupials i. introduction and preliminary results from nuclear IRBP gene sequences

Abstract

We report and analyze nucleotide sequence variation in the first exon (1158 bp) of the nuclear gene encoding the Interphotoreceptor Retinoid Binding Protein (IRBP) among 21 species representing all 15 currently recognized genera of living didelphids. Six previously published IRBP sequences representing five nondidelphimorph marsupial orders were also analyzed to test didelphid monophyly, and 12 published sequences representing ten placental orders were used as outgroups. No gaps (indels) are necessary to align didelphid sequences, but one short region (35 bp) is alignment-ambiguous among nondidelphids. Uncorrected pairwise sequence divergence ranges from 0.7 to 5.7% among nonconspecific didelphids, from 9.2 to 15.3% between didelphids and nondidelphid marsupials, and from 24.9 to 32.1% between marsupials and placentals. Neither transitions nor transversions exhibit saturation for any codon position at any level of taxonomic comparison. Parsimony analyses of these data provide strong support (bootstrap values >95%, Bremer values ≥7) for the monophyly of (1) Didelphidae ("caluromyines" + Didelphinae); (2) a group containing Caluromys and Caluromysiops; (3) Didelphinae; (4) a group of large opossums that includes Metachirus; (5) a group containing the remaining large opossums (with 2N = 22 chromosomes); (6) a group containing Marmosa and Micoureus; (7) a group containing Thylamys, Lestodelphys, and Gracilinanus; and (8) a group containing the last three genera plus a monophyletic Marmosops. In addition, we found moderate support (bootstrap values >80%, Bremer values ≥2) for the monophyly of Thylamys + Lestodelphys and for a sister-group relationship between Monodelphis and Marmosa + Micoureus. Sensitivity analysis suggests that all of these clades, together with their associated levels of bootstrap and Bremer support, are robust to alternative hypotheses of positional homology within the ambiguously alignable region. Although some of the relationships supported by IRBP are not consistent with the results of published morphological analyses, our reassessment of the morphological data suggests that many conflicts are more apparent than real.