phylogenetic relationships and classification of didelphid marsupials ...

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8 BULLETIN AMERICAN MUSEUM OF NATURAL HISTORY NO. 322 TABLE 2 Marsupial Terminal Taxa Scored for Phylogenetic Analysis a Percent complete character data b Nonmolecular Molecular Combined INGROUP: Didelphidae Caluromys lanatus 99.2 100 100 Caluromys philander 99.2 100 100 Caluromysiops irrupta 93.7 16.5 17.8 Chacodelphys formosa 86.0 0 1.5 Chironectes minimus 99.2 99.8 99.8 Cryptonanus chacoensis 98.4 95.2 95.3 Cryptonanus unduaviensis 93.0 99.8 99.7 Didelphis albiventris 100 99.1 99.1 Didelphis marsupialis 100 99.1 99.1 Didelphis virginiana 100 100 100 Glironia venusta 93.0 100 99.9 Gracilinanus aceramarcae 93.0 99.8 99.7 Gracilinanus agilis 95.3 99.7 99.6 Gracilinanus emiliae 95.3 99.8 99.7 Gracilinanus microtarsus 95.3 95.1 95.1 Hyladelphys kalinowskii 95.3 100 99.9 Lestodelphys halli 97.6 30.4 31.6 Lutreolina crassicaudata 99.2 100 100 Marmosa (Marmosa) lepida 96.1 100 99.9 Marmosa (Marmosa) mexicana 99.2 98.8 98.8 Marmosa (Marmosa) murina 99.2 98.6 98.6 Marmosa (Marmosa) robinsoni 99.2 98.8 98.8 Marmosa (Marmosa) rubra 92.2 99.7 99.6 Marmosa (Micoureus) demerarae c 99.2 98.5 98.5 Marmosa (Micoureus) paraguayana c 96.1 95.7 95.7 Marmosa (Micoureus) regina c 99.2 100 100 Marmosops impavidus 98.4 98.0 98.0 Marmosops incanus 96.8 99.0 99.0 Marmosops noctivagus 98.4 100 100 Marmosops parvidens 95.3 98.8 98.7 Marmosops pinheiroi 95.3 99.7 99.6 Metachirus nudicaudatus 98.4 98.9 98.9 Monodelphis brevicaudata 97.7 100 100 Monodelphis emiliae 96.1 100 99.9 Monodelphis peruviana d 92.3 100 99.9 Monodelphis theresa 89.9 100 99.8 Philander frenatus 97.7 100 100 Philander mcilhennyi 100 99.2 99.2 Philander opossum 99.2 99.1 99.1 Thylamys macrurus 96.1 99.8 99.7 Thylamys pallidior 96.1 98.3 98.3 Thylamys pusillus 98.4 95.7 95.7 Thylamys venustus 96.1 99.5 99.4 Tlacuatzin canescens OUTGROUPS: Caenolestidae 99.2 97.5 97.5 Caenolestes fuliginosus 86.9 63.3 63.7 Rhyncholestes raphanurus 85.3 62.5 62.9
2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 9 presence and absence were both commonly observed for a given taxon). However, whereas we formerly (Voss and Jansa, 2003) treated such polymorphism as a separate state intermediate to the two fixed conditions, with transformations to and from the polymorphic state weighted as half-steps (the ‘‘scaled’’ option discussed by Wiens, 2000), we here conform with the prevailing custom of coding polymorphisms as taxonomic ambiguities (e.g., as ‘‘0/1’’ for a binary character). This coding change has minimal impact on our results (only weakly supported relationships are affected, even in separate analyses of morphology) but it facilitates likelihood modeling of morphological character evolution (Lewis, 2001) in Bayesian analyses of our combined datasets (see below). MOLECULAR SEQUENCING AND HOMOLO- GY COMPARISONS: The laboratory procedures we used for DNA amplification and sequencing (including the names and locations of primers used in PCR reactions) have already been described for three of the protein-coding nuclear loci analyzed in this report: IRBP (Jansa and Voss, 2000), Dentin Matrix Protein 1 (DMP1; Jansa et al., 2006), and Recombination Activating 1 Gene (RAG1; Gruber et al., 2007). In addition, we sequenced two other protein-coding nuclear genes as described below. TABLE 2 (Continued) Percent complete character data b Nonmolecular Molecular Combined Dasyuridae Murexia longicaudata 95.3 57.9 58.5 Sminthopsis crassicaudata Microbiotheriidae 96.1 42.1 43.0 Dromiciops gliroides Peramelidae 99.2 63.3 63.9 Echymipera kalubu 95.3 63.2 63.8 Perameles gunnii 93.0 63.3 63.8 a Nomenclature follows Wilson and Reeder (2005) and Gardner (2008) except as noted. b Number of filled (total minus empty) cells in the corresponding row of each data matrix, divided by the total number of cells (N5 129, 7320, and 7449 for nonmolecular, molecular, and combined data, respectively) 3 100. For the nonmolecular data, empty cells include those scored as missing (‘‘?’’) and those scored as inapplicable (‘‘-’’). For the molecular data, only unsequenced base pairs were counted as missing (‘‘?’’); gaps (‘‘-’’) were counted as filled data cells. c Micoureus was formerly treated as a full genus. d Formerly identified as Monodelphis adusta (e.g., by Jansa and Voss, 2000; Voss and Jansa, 2003), our material is referable to M. peruviana, a distinct species recently resurrected from synonymy by Solari (2007). We amplified 2.1 kb of BRCA1 exon 11 from genomic DNA in two fragments using the primers listed in table 3. The first fragment, comprising the upstream 1.2 kb of the exon, was amplified using primers F1 paired with R1218 or F47 paired with R1343. The second, downstream fragment (ca. 1 kb) was amplified with primers F1163 or F1163a paired with R2078 or R2151. These amplification products were then used in a second round of PCR to generate smaller pieces of suitable size for sequencing. For the upstream fragment, either F1 or F47 was paired with R743, and F593 was paired with either R1218 or R1343. For the downstream fragment, F1163 or F1163a was paired with R1780, and F1697 was paired with either R2078 or R2151. A single fragment of ca. 1 kb was amplified from vWF exon 28 using either F104 or F120 paired with R1141. This product was then used in a second round of PCR in which F1 or F47 was paired with either R665 or R742, and F557 was paired with R1141. Initial amplifications using genomic DNA as template were performed as 20 ml reactions using Ampli-Taq Gold polymerase (Perkin-Elmer Corp.) and recommended concentrations of primers, nucleotides, buffer, and MgCl 2. These genomic amplifications were performed using a four-stage touch-
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