phylogenetic relationships and classification of didelphid marsupials ...

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62 BULLETIN AMERICAN MUSEUM OF NATURAL HISTORY NO. 322 TABLE 9 GenBank Accession Numbers for Molecular Sequences Analyzed in This Report a BRCA1 DMP1 IRBP RAG1 vWF Didelphidae Caluromys lanatus FJ159278 DQ083120 AF257690 DQ865883 FJ159328 Caluromys philander FJ159279 DQ083121 AY233766 DQ865884 FJ159329 Caluromysiops irrupta N/A N/A AF257675 N/A N/A Chironectes minimus FJ159280 DQ083122 AF257679 DQ865885 FJ159330 Cryptonanus chacoensis FJ159281 DQ083123 AY957494 DQ865886 FJ159331 Cryptonanus unduaviensis FJ159282 DQ083124 AY957492 DQ865887 FJ159332 Didelphis albiventris FJ159283 DQ083125 AF257683 DQ865888 FJ159333 Didelphis marsupialis FJ159284 DQ083126 AF257703 DQ865889 FJ159334 Didelphis virginiana FJ159285 DQ083127 AF257678 DQ865890 FJ159335 Glironia venusta FJ159286 DQ083128 AF257688 DQ865891 FJ159336 Gracilinanus aceramarcae FJ159287 DQ083129 AY957488 DQ865892 FJ159337 Gracilinanus agilis FJ159288 DQ083130 AY957487 DQ865893 FJ159338 Gracilinanus emiliae FJ159289 DQ083131 AY957486 DQ865894 FJ159339 Gracilinanus microtarsus FJ159290 DQ083132 AF257687 DQ865895 FJ159340 Hyladelphys kalinowski FJ159291 DQ112326 DQ112324 DQ865923 FJ159341 Lestodelphys halli N/A DQ083133 AF257710 N/A N/A Lutreolina crassicaudata FJ159292 DQ083134 AF257685 DQ865896 FJ159342 Marmosa demerarae b FJ159304 DQ083146 AF257693 DQ865908 FJ159354 Marmosa lepida FJ159293 DQ083135 AY233769 DQ865897 FJ159343 Marmosa mexicana FJ159294 DQ083136 AY233770 DQ865898 FJ159344 Marmosa murina FJ159295 DQ083137 AF257709 DQ865899 FJ159345 Marmosa paraguayana b FJ159305 DQ083147 AY233778 DQ865909 FJ159355 Marmosa regina b FJ159306 DQ083148 AY233780 DQ865910 FJ159356 Marmosa robinsoni FJ159296 DQ083138 AY233774 DQ865900 FJ159346 Marmosa rubra FJ159297 DQ083139 AY233776 DQ865901 FJ159347 Marmosops impavidus FJ159298 DQ083140 AF257695 DQ865902 FJ159348 Marmosops incanus FJ159299 DQ083141 AY233785 DQ865903 FJ159349 Marmosops noctivagus FJ159300 DQ083142 AF257704 DQ865904 FJ159350 Marmosops parvidens FJ159301 DQ083143 AF257680 DQ865905 FJ159351 Marmosops pinheiroi FJ159302 DQ083144 AF257677 DQ865906 FJ159352 Metachirus nudicaudatus FJ159303 DQ083145 AF257707 DQ865907 FJ159353 Monodelphis brevicaudata FJ159307 DQ083150 AY233782 DQ865912 FJ159357 Monodelphis emiliae FJ159308 DQ083151 AF257692 DQ865913 FJ159358 Monodelphis peruviana c FJ159309 DQ083149 AF257694 DQ865911 FJ159359 Monodelphis theresa FJ159310 DQ083152 AY233783 DQ865914 FJ159360 Philander frenatus FJ159312 DQ083153 AY233787 DQ865915 FJ159362 Philander mcilhennyi FJ159313 DQ083154 AF257706 DQ865916 FJ159363 Philander opossum FJ159314 DQ083155 AY233789 DQ865917 FJ159364 Thylamys macrurus FJ159317 DQ083156 AY957491 DQ865918 FJ159366 Thylamys pallidior FJ159318 DQ083157 AF257689 DQ865919 FJ159367 Thylamys pusillus FJ159319 DQ083158 AY957489 DQ865920 FJ159368 Thylamys venustus FJ159320 DQ083159 AY233791 DQ865921 FJ159369 Tlacuatzin canescens Caenolestidae FJ159321 DQ083160 AY233768 DQ865922 FJ159370 Caenolestes fuliginosus AF355794 N/A FJ159322 AY243384 AY243403 Rhyncholestes raphanurus Dasyuridae AY243454 N/A AY243440 AY243399 FJ159365 Murexia longicaudata FJ159311 N/A FJ159325 N/A FJ159361 Sminthopsis crassicaudata FJ159316 N/A FJ159327 N/A AY243413
2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 63 BRCA1 DMP1 IRBP RAG1 vWF Microbiotheriidae Dromiciops gliroides Peramelidae AY243446 N/A FJ159323 AY243389 AY243407 Echymipera kalubu AF355796 N/A FJ159324 AY243386 AY243405 Perameles gunnii AY243450 N/A FJ159326 AY243394 AY243411 a See table 2 for taxonomic conventions. N/A 5 not available (see text). b As Micoureus in GenBank. c Formerly Monodelphis adusta. encoded by exon 6 (Hirst et al., 1997). The protein is assumed to have some role in tissue mineralization based on its chemical properties and presence in the extracellular matrix of dentine and bone (Butler and Ritchie, 1995; Feng et al., 2003). However, mRNA transcripts and the protein itself have also been detected in a wide range of soft tissues, where the gene presumably has other functions (Terasawa et al., 2004). Nucleotide sequence data from DMP1 exon 6 have been analyzed in several previous studies of mammalian intraordinal relationships (e.g., Van Den Bussche et al., 2003; Reeder and Bradley, 2004; Jansa et al., 2006). Homology comparisons of the 1176 bp fragment that we amplified and sequenced for this study are consistent with the presence of a single full-length copy in Monodelphis domestica, where the gene appears to be located on chromosome 5. We obtained DMP1 sequences from 42 didelphids (none is available from Caluromysiops). Fourteen indels ranging in length from 3 to 18 bp are required to align didelphid DMP1 sequences, including 6 that are unique to single taxa and 8 that are shared by two or more taxa. Unfortunately, didelphid DMP1 sequences cannot be aligned unambiguously with sequences from nondidelphid marsupials, so no outgroups are available to root phylogenetic analyses of this gene (Jansa and Voss, 2005; Jansa et al., 2006). Interphotoreceptor Retinoid Binding Protein The human IRBP gene (also known as the Retinol Binding Protein 3 gene, RBP3) consists of four exons spanning about 9.5 kb TABLE 9 (Continued) of genomic DNA on the long arm of chromosome 10 (Liou et al., 1989; Fong et al., 1990; Pepperberg et al., 1993). The gene product is a large (1230 amino acids) secreted glycolipoprotein that is primarily found in the extracellular matrix between the retinal pigment epithelium (RPE) and the neural retina of the eye; the protein apparently functions as a two-way carrier of retinoid between the rod photoreceptors and the RPE, and therefore plays a critical role in visual pigment regeneration (Pepperberg et al., 1993). Nucleotide sequences from IRBP exon 1 were among the first molecular character data to provide convincing support for mammalian superordinal relationships (Stanhope et al., 1992, 1996; Springer et al., 1997b), and they have also been analyzed in several subsequent studies focused on lower-level relationships (e.g., Jansa and Voss, 2000; Mercer and Roth, 2003; Weksler, 2003; Jansa and Weksler, 2004). The 1158 bp fragment that we amplified and sequenced from didelphids is homologous with a single full-length copy in Monodelphis domestica, where the gene is apparently located on chromosome 1. IRBP sequences are available from 43 didelphid terminal taxa (including Caluromysiops and Lestodelphys) and 7 nondidelphid outgroups. No indels are required to align didelphid IRBP sequences, all of which translate to open reading frame (Jansa and Voss, 2000, 2005; Voss and Jansa, 2003). Recombination Activating 1 Gene The human RAG1 gene contains a single uninterrupted exon of 3.1 kb located on the short arm of chromosome 11 adjacent to the
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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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2009 VOSS AND JANSA: DIDELPHID MARS
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