phylogenetic relationships and classification of didelphid marsupials ...

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