phylogenetic relationships and classification of didelphid marsupials ...

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60 BULLETIN AMERICAN MUSEUM OF NATURAL HISTORY NO. 322 Fig. 25. Lingual views of right m2 and m3 illustrating taxonomic differences in entoconid size. Top, Thylamys pallidior (AMNH 262405) with a large entoconid (arrow). Bottom, Monodelphis peruviana (AMNH 272781) with an indistinct entoconid (arrow). which a diminutive crest (comprising a vestigial metacristid and part of the paracristid) curves anterolabially to abut the hypoconulid of m3. The entocristid on m1– m3 is a long crest that is deflected labially, away from the lingual margin of the tooth, and terminates deep inside the talonid basin. Summary The morphological observations described above provide evidence of taxonomic differences in many phenotypic attributes suitable for phylogenetic analysis, including unambiguously distinguishable aspects of pelage
2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 61 color and structure; sexually dimorphic skin glands and carpal tubercles; manual and pedal digital proportions; the presence, absence, and morphology of cutaneous shelters for nursing young; caudal modifications for prehensility and fat storage; the sizes and shapes of cranial bones and bony processes; the presence, absence, and ontogenetic persistence of cranial sutures; the number and occurrence of cranial foramina and fenestrae; auditory morphology; and the sizes, shapes and eruption sequences of teeth. Because the relevant literature on mammalian functional morphology is too extensive to review effectively in this report, we can only assert that such taxonomic differences are likely to reflect adaptations for such diverse functions as concealment, locomotion, reproduction, sense perception, and food reduction. Anatomical trait variation (together with published information about karyotypic differences that are not reviewed above) is formally described as qualitative characters in appendix 3, where we also explain the criteria used to score individual specimens and discuss the justification for ordering multistate transformation series. The resulting data are summarized in appendix 4. GENE SEQUENCES Of the many genes that have been sequenced to date from one or more didelphid marsupials (including the entire genome of Monodelphis domestica; Mikkelsen et al., 2007), only a few have been sequenced from enough taxa to be useful for phylogenetic inference. Below we summarize information about five protein-coding nuclear loci from which long (.900 bp) nucleotide sequences have now been obtained from numerous species representing almost all of the currently recognized genera (table 9). The following accounts describe the size, internal organization, and chromosomal location of each gene, as well as the tissues in which it is known to be active and the physiological activity of its translated protein product. We also provide a brief synopsis of previous analyses based on each gene in mammalian phylogenetic research before describing the sequence characteristics of the fragments we amplified from didelphids and other marsupials. Breast Cancer Activating 1 Gene The human BRCA1 gene consists of 22 coding exons distributed over ca. 100 kb of genomic DNA on the long arm of chromosome 17 (Miki et al., 1994). The gene is expressed in numerous tissues, but it is especially active in epithelial cells undergoing high levels of proliferation and differentiation (Miki et al., 1994; Casey, 1997). BRCA1 is a tumor suppressor gene whose unmutated product is a large (1863 amino acids) nuclearcytoplasmic-shuttling phosphoprotein of unknown structure but with apparently essential roles in transcriptional regulation and DNA repair, among other intracellular functions (Rodríguez and Henderson, 2000; Dimitrov et al., 2001; Venkitaraman, 2001). Nucleotide sequence data from BRCA1 exon 11 have been analyzed in several mammalian phylogenetic studies, usually in concatenated datasets with other genes (e.g., Adkins et al., 2001; Madsen et al., 2001; Delsuc et al., 2002; Douady et al., 2002; Raterman et al., 2006). Homology comparisons of the 2163 bp fragment that we amplified and sequenced for this study are consistent with the presence of a single fulllength copy in Monodelphis domestica, where the gene appears to be located on chromosome 2. BRCA1 sequence data are available from 48 terminals in our analyses, including 41 didelphids (Caluromysiops and Lestodelphys were not sequenced) and all 7 nondidelphid outgroups. All of the marsupial sequences that we obtained and others that we downloaded from GenBank translate to open reading frame. Twenty independent insertion-deletion events (indels) ranging in length from 3 to 39 bp were required to align didelphid BRCA1 sequences; of these, 9 were unique to single taxa and 11 were shared by two or more taxa. Dentin Matrix Protein 1 The human DMP1 gene (originally known as AG1; George et al., 1993) consists of six exons spanning about 14 kb of genomic DNA on the long arm of chromosome 4 (Hirst et al., 1997). DMP1 is an acidic calcium-binding secreted phosphoprotein of about 513 amino acids, most of which are
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PHYLOGENETIC RELATIONSHIPS AND CLAS
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CONTENTS Abstract .................
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ABSTRACT This report summarizes a d
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