The phylogenetic distribution of resupinate forms ... - Clark University

keeping 10 trees per replicate) were performed. In the second
step, TBR branch swapping was performed on the shortest
trees found in the first step, keeping all trees up to the limit of
MAXTREES. A bootstrap analysis was also performed, using
100 replicates (MAXTREES = 1000, 1 random taxon addition
sequence per replicate, keeping 10 trees per replicate).
Equally weighted Parsimony Ratchet (PR) analyses
of the full dataset
Traditional heuristic searches are hill-climbing procedures and
are susceptible to being trapped in local optima. To improve
the chance of finding the global optimum, heuristic searches
typically use many replicate searches, each beginning with a
unique starting tree. This approach can be effective, but it is
time consuming, especially if each search attempts to recover
all equally most parsimonious trees. PR analysis (Nixon, 1999)
is a strategy for finding the most parsimonious tree(s) from
large datasets that is designed to address some of the limitations
of traditional heuristic searches. PR analysis is incorporated
in NONA (Goloboff, 1998) and can also be implemented
in PAUP* using the companion program PAUPRat (Sikes &
Lewis, 2001). The analytical settings of the PR in PAUPRat and
NONA differ slightly. This study used PAUPRat and PAUP*
to perform PR analyses.
A PR analysis begins like a traditional heuristic search,
with a single starting tree that is rearranged by branch swapping.
Initially, all characters are subject to a uniform weighting
regime. Periodically, a randomly selected subset of characters
are reweighted (from two-fold to five-fold in PAUPRat), and
branch swapping proceeds under this perturbed weighting regime
(starting with the best tree obtained with the original
weights). Following a period of branch swapping under the
perturbed weights, the characters are returned to the original
weights, which completes one iteration. The next iteration proceeds
using the best tree found under the perturbed weights,
which may be shorter, longer or equal in length to the best tree
obtained before the data were reweighted.
The branch swapping routines that are performed under
the original and perturbed character weights in each iteration
are each susceptible to being trapped in local optima
(tree ‘islands’), just like standard heuristic analyses. The critical
feature of PR analysis is that by periodically perturbing
the character weights, the parsimony surface of treespace is
distorted, which may make it possible (one hopes) to move
away from a topology that was a local optimum under the
original weighting regime. In this way, a PR search wanders
through treespace, occasionally crossing ‘valleys’ that a traditional
heuristic search cannot overcome. PR analyses are
faster than traditional heuristic searches because they do not
require that multiple starting trees be obtained by taxon addition
(or another method) and subsequently refined through
branch swapping. In addition, PR analysis does not attempt to
find and swap through all the trees in any given island.
PR analyses of the full dataset were performed in batch
mode using PAUP* and PAUPRat. Three sets of PR analyses
were performed: (1) 20 runs with 200 iterations each
(20 × 200) and 15% of the characters randomly reweighted in
Phylogenetic distribution of resupinate forms of mushroom-forming fungi 5
each iteration; (2) 20 × 200 iterations with 5% perturbation;
and (3) 20 × 200 iterations with 25% perturbation.
Six-parameter weighted PR analyses of the full dataset
A set of PR analyses was performed under a six-parameter
weighting regime (Stanger-Hall & Cunningham, 1998), which
obtains weights for parsimony analyses based on rates of
nucleotide substitutions estimated with maximum likelihood.
Nucleotide transformation rates were estimated in PAUP*
under a general time-reversible model, with equal rates of evolution
for all sites and empirical base frequencies, using a tree
and data matrix from Binder & Hibbett (2002) that includes
93 species, each with nuc-ssu, nuc-lsu, mt-ssu and mt-lsu
rDNA. Rate matrices were converted to step-matrices for parsimony
analysis using an Excel spreadsheet provided by Clifford
Cunningham (http://www.biology.duke.edu/cunningham/),
which takes the natural logarithm of the rates and converts
them to proportions. Rates and weights for nuc-rDNA and
mt-rDNA were estimated separately. For nuc-rDNA, the
step-matrix values were A-C = 3, A-G = 2, A-T = 2, C-G = 2,
C-T = 1, G-T = 3; for mt-rDNA, the step-matrix values were
A-C = 2, A-G = 1, A-T = 2, C-G = 3, C-T = 1, G-T = 2.
Six-parameter weighted PR analyses were performed with
PAUP* and PAUPRat, with ten batches of 200 iterations each,
with 15% of the characters reweighted in each iteration.
Results
Sequences and alignment
The nuc-ssu sequence of Piriformospora indica contained a
345 bp group I intron at position 1509 (Gargas et al., 1995b)
that was removed prior to alignment. Nuc-ssu rDNA sequences
of Lentinellus spp., Artomyces (Clavicorona) pyxidata and
Panellus stypticus have also been shown to contain group I
introns, but at a different position (Hibbett, 1996); sequences
of these taxa in this dataset have had the intron sequences removed.
Excluding the P. indica sequence, the nuc-ssu rDNA
sequences ranged from 1059 bp (an incomplete sequence) in
Coniophora puteana to 1790 bp in Physalacria inflata. The
nuc-lsu rDNA sequences ranged from 870 bp in Albatrellus
ovinus to 972 bp in Scytinostroma renisporum. The nuc-lsu
rDNA of Antrodia xantha had a 65 bp insertion at position
830, which was also removed prior to alignment. No other
major insertions or deletions were observed in the nuc-rDNA.
The mt-ssu rDNA sequences ranged from 418 bp in Cylindrobasidium
laeve to 613 bp in Hydnochaete olivacea. The mt-ssu
rDNA sequences were divided into three blocks (blocks 3, 5,
7) to exclude hypervariable regions (Bruns & Szaro, 1992;
Hibbett & Donoghue, 1995). The mt-lsu rDNA sequences
ranged from 376 bp in Dacryobolus sudans to 680 bp in
Repetobasidium mirificium.The5 ′ end of the mt-lsu fragment
is highly variable and was trimmed prior to alignment. The total
aligned length of all four regions is 3807 bp, distributed as follows:
nuc-ssu = 1859 bp, nuc-lsu = 1103 bp, mt-ssu = 485 bp
(block 3 = 137 bp, block 5 = 262 bp, block 7 = 86 bp), and mtlsu
= 360 bp. One hundred and three positions were considered