phylogenetic relationships and classification of didelphid marsupials ...

2009 VOSS AND JANSA: DIDELPHID MARSUPIALS 65
Location b
TABLE 10
Biological Properties of Genetic Loci Sequenced for This Study a
GC (versus AT) content, is now widely
recognized as a potential problem for phylogenetic
inference (see literature reviewed by
Gruber et al., 2007). Of the five genes
analyzed herein, BRCA1 and DMP1 exhibit
the lowest overall GC content (fig. 26). For
BRCA1, GC content at all codon positions is
remarkably consistent across taxa. However,
GC content at third codon positions (GC 3)of
DMP1 is substantially higher in two taxa
(Hyladelphys and Tlacuatzin) than it is in
other didelphids (Jansa and Voss, 2005). As
reported elsewhere, third codon positions of
RAG1 are so highly variable in GC content
among didelphids that plausible phylogenetic
results cannot be recovered from datasets
that include these positions (Gruber et al.,
2007); therefore, only first and second codon
positions of RAG1 are analyzed below. The
GC content of vWF is most similar to that of
RAG1, but vWF does not exhibit the
exceptionally high taxonomic variation in
GC 3 seen in the latter gene. Compared to the
other loci, IRBP has relatively high GC
content at all codon positions, with one
taxon (Cryptonanus chacoensis) exhibiting
elevated GC content at first and second
codon positions.
Additional sequence characteristics can be
effectively summarized in the context of
model fitting (Posada and Crandall, 1998).
The best-fitting model of nucleotide substitution
for each gene is either a general-timereversible
(GTR) model or a modification
thereof (TVMef) that assumes equal base
frequencies and equal transition rates (table
11). In addition, the best-fitting model for
each gene includes among-site rate heterogeneity
as approximated by a gamma distribu-
Gene Protein product
Active in Location Primary function
BRCA1 chr 2 many tissues nucleus & cytoplasm tumor suppression
DMP1 chr 5 dentine & bone extracellular mineralization
IRBP chr 1 retina extracellular photoreception
RAG1 chr 5 developing B & T lymphocytes nucleus immune response
vWF chr 8 endothelium & megakaryocytes extracellular blood clotting
a As indicated primarily by research on humans and other placental taxa (see references cited in text).
b Chromosome number in Monodelphis domestica genome.
tion (C), and a proportion of invariant sites
(p inv) applies to three genes. Fitted basecompositional
parameters (pA, pC, pG, pT)
for GTR-modeled loci are relatively even for
IRBP, slightly skewed towards A for the
RAG1 partition, strongly skewed towards A
for BRCA1, and strongly biased towards A
and G for DMP1. All five genes exhibit
higher rates of transitions than transversions;
in addition, first and second positions of
RAG1 exhibit a relatively high rate of A-to-C
transversions. The degree of among-site rate
heterogeneity was lowest for BRCA1 (a
51.48), and highest for the RAG1 partition
(a 5 0.41).
PHYLOGENETIC RELATIONSHIPS
The six data partitions recognized herein
(nonmolecular characters plus nucleotide
sequences from five loci) were analyzed
separately and in combination to explore
relevant patterns of support for monophyletic
groups. To assess the sensitivity of our
results to missing data and to different
analytic methods, we conducted MP and
Bayesian analyses of the nonmolecular data
with and without Chacodelphys (4 analyses);
MP, ML, and Bayesian analyses of each
single-gene dataset (15 analyses); MP, ML,
and Bayesian analyses of a concatenatedgene
dataset (3 analyses); and MP, ML, and
Bayesian analyses of a combined (nonmolecular
+ molecular) dataset with and without
Chacodelphys (6 analyses). Given the complexity
of these results (a total of 28 separate
analyses), the following accounts are focused
on issues of generic monophyly and on
higher-level (intergeneric) relationships among