1. 1654
Mol. Biol. Evol. 18(9):1654–1667. 2001
᭧ 2001 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
A Structural and Phylogenetic Analysis of the Group IC1 Introns in the
Order Bangiales (Rhodophyta)
Kirsten M. Mu¨ller,*1 Jamie J. Cannone,† Robin R. Gutell,† and Robert G. Sheath*
*Department of Botany and Dean’s Office, University of Guelph, Guelph, Ontario, Canada; and †Institute of Cellular and
Molecular Biology, University of Texas at Austin
Our previous study of the North American biogeography of Bangia revealed the presence of two introns inserted
at positions 516 and 1506 in the nuclear-encoded SSU rRNA gene. We subsequently sequenced nuclear SSU rRNA
in additional representatives of this genus and the sister genus Porphyra in order to examine the distribution,
phylogeny, and structural characteristics of these group I introns. The lengths of these introns varied considerably,
ranging from 467 to 997 nt for intron 516 and from 509 to 1,082 nt for intron 1506. The larger introns contained
large insertions in the P2 domain of intron 516 and the P1 domain of intron 1506 that correspond to open reading
frames (ORFs) with His-Cys box homing endonuclease motifs. These ORFs were found on the complementary
strand of the 1506 intron in Porphyra fucicola and P. umbilicalis (HG), unlike the 516 intron in P. abbottae, P.
kanakaensis, P. tenera (SK), Bangia fuscopurpurea (Helgoland), and B. fuscopurpurea (MA). Frameshifts were
noted in the ORFs of the 516 introns in P. kanakaensis and B. fuscopurpurea (HL), and all ORFs terminated
prematurely relative to the amino acid sequence for the homing endonuclease I-Ppo I. This raises the possibility
that these sequences are pseudogenes. Phylogenies generated using sequences of both introns and the 18S rRNA
gene were congruent, which indicated long-term immobility and vertical inheritance of the introns followed by
subsequent loss in more derived lineages. The introns within the florideophyte species Hildenbrandia rubra (position
1506) were included to determine relationships with those in the Bangiales. The two sequences of intron 1506
analyzed in Hildenbrandia were positioned on a well-supported branch associated with members of the Bangiales,
indicating possible common ancestry. Structural analysis of the intron sequences revealed a signature structural
feature in the P5b domain of intron 516 that is unique to all Bangialean introns in this position and not seen in
intron 1506 or other group IC1 introns.
Introduction
Many eukaryotic genes have their coding regions
interrupted by intervening sequences or introns. Group
I introns represent a family of RNA molecules with a
specific higher-order structure and the ability to catalyze
their own excision by a common splicing mechanism
(Cech 1990). Group I introns are divided into 11 sub-
groups based on conserved primary- and secondary-
structure elements (Michel and Westhof 1990) and have
been reported in the 18S rRNA genes of numerous or-
ganisms (Johansen, Muscarella, and Vogt 1996), such as
fungi (Takashima and Nakase 1997), amoebae (De Jonck-
heere 1994; Schroeder-Diedrich, Fuerst, and Byers 1998),
and green algae (Wilcox et al. 1992; VanOppen, Olsen,
and Stam 1993; Bhattacharya et al. 1994, 1996; Bhatta-
charya 1998). Group I introns have also been reported in
several red algae, including Hildenbrandia rubra (Ragan
et al. 1993) and particularly members of the order Ban-
giales (Porphyra spiralis var. amplifolia and Bangia fus-
copurpurea [as Bangia atropurpurea] [Oliveira and Ra-
gan 1994]; Porphyra miniata, P. purpurea, P. linearis
[Oliveira et al. 1995]; Bangia spp. [Mu¨ller et al. 1998]).
Stiller and Waaland (1993) reported cryptic diversity in
a number of species of Porphyra after finding large in-
sertions in the nuclear SSU rRNA genes of a number of
taxa. Oliveira et al. (1995) speculated that these introns
1 Present address: Department of Biology, University of Waterloo,
Waterloo, Ontario, Canada.
Key words: Group IC1 introns, Bangiales, phylogeny.
Address for correspondence and reprints: Robert G. Sheath,
Dean’s Office and Department of Botany, University of Guelph,
Guelph, Ontario, Canada N1G 2W1. E-mail: rsheath@uoguelph.ca.
may be a means to differentiate among geographic en-
tities within the genus Porphyra. During the course of
a study of the biogeography of Bangia in North Amer-
ica, we reported the presence of two introns in positions
516 and 1506 (Escherichia coli numbering) in the nu-
clear SSU rRNA gene (Mu¨ller et al. 1998). Subsequent
analysis of additional nuclear SSU rRNA gene sequenc-
es of Bangia and Porphyra revealed a rich source of
these introns, which are also variable in occurrence. Var-
iable occurrence of group I introns can be simply ex-
plained by two models: intron insertion or intron dele-
tion (Burke 1988). The first model, intron insertion, is
hypothesized to have begun with a gene devoid of in-
trons followed by subsequent insertion of one or more
introns (Burke 1988). The deletion model proposes a
gene initially containing one or more introns, after
which precise deletion of these introns occurs; that is,
nonmobile introns are destined to be lost over time if
they cannot reinfect homologous sites. Burke (1988)
proposed that the variable occurrence of introns in genes
may be the result of a combination of these two models.
High sequence similarity between introns is consistent
with descent from an ancestral intron that was initially
acquired and vertically inherited (Schroeder-Diedrich,
Fuerst, and Byers 1998). In addition, congruent intron
and rRNA gene phylogenies would provide support for
this theory (Bhattacharya et al. 1994, 1996; Friedl et al.
2000). The present study provides a large data set that
will allow us to test these hypotheses in context with
the phylogeny of the rhodophyte order the Bangiales.
Materials and Methods
Collections of Bangia and Porphyra collected for
molecular analyses and obtained from GenBank for the

2. Group IC1 Introns in the Bangiales 1655
present study are listed in table 1 Filaments collected
for DNA analysis were cleaned of visible epiphytes, ba-
ses were removed to prevent contamination, and the
specimens were stored atϪ20ЊC. Samples were ground
in liquid nitrogen, and the DNA was extracted according
to the protocol outlined by Saunders (1993) with mod-
ifications given in Vis and Sheath (1997). Amplification
and sequencing of the nuclear SSU rRNA gene for both
genera are as outlined in Mu¨ller et al. (1998).
Intron Amplification
The intron in position 516 was amplified in the
large fragment of the nuclear SSU rRNA gene as de-
scribed in Mu¨ller et al. (1998) using the primers G02.1
(5Ј-CGA TTC CGG AGA GGG AGC CTG-3Ј) and
G15.1 (5Ј-CTT GTT ACG ACT TCT CCT TCC-3Ј).
These fragments were then sequenced in both directions
using internal primers flanking the intron. The intron in
position 1506 was amplified using primers GO6 (5Ј-
GTT GGT GGT GCA TGG CCG TTC-3Ј) and G07 (5Ј-
TCC TTC TGC AGG TTC ACC TAC-3Ј) from Saun-
ders and Kraft (1994) as follows: initial denaturation at
95ЊC for 2 min, 35 cycles of denaturation for 1 min at
93ЊC, primer annealing at 50ЊC for 1 min, and extension
for 2 min at 72ЊC, followed by a final extension time of
3 min at 72ЊC. This intron was sequenced in both di-
rections using an internal primer at the 5Ј end of the
intron and the primer G07 (sequences for internal prim-
ers can be obtained from R.G.S.). All products were
prepared for sequencing and sequenced using the pro-
tocols outlined in Mu¨ller et al. (1998).
RNA Extraction/cDNA Production in the Bangiales
RT-PCR was used to determine if introns were pre-
sent in mature RNA or excised from all collections of
Bangia and Porphyra listed in table 1 and the Bangia
collections utilized in Mu¨ller et al. (1998). RNA was
extracted following the procedure previously outlined
for DNA extraction. Following this, 12 ␮l of extract was
placed in a clean tube, to which 3 ␮l of 25 mM MgCl2
and 1 ␮l of DNAase was added. This mixture was then
left at room temperature for 2 h, after which 5 ␮l was
loaded in a 0.5% agarose gel to determine if all DNA
had been digested within the extract. If this was the case,
the extract was then immediately placed in the freezer
at Ϫ20ЊC. RT-PCR using Titan by Boehringer Mann-
heim was used to amplify the RNA. The primers G02.1
and G09 (5Ј-ATC CAA GAA TTT CAC CTC TG-3Ј)
and G15.R (5Ј-GGA AGG AGG AGT CGT AAC AAG-
3Ј) and G07 were used to amplify the region containing
the intron in positions 516 and 1506, respectively (Saun-
ders and Kraft 1994; Mu¨ller et al. 1998). Following the
protocols for RT-PCR outlined by Boehringer Mann-
heim, the reaction consisted of master mix 1 (1 ␮l of
RNA template; 20 ␮M of each primer; 40 mM of dNTP;
2.5 ␮l DTT solution; dH2O) and master mix 2 (14 ␮l
dH2O; 5 ϫ RT-PCR buffer with MgCL2; 1 ␮l enzyme
mix). These two master mixes were combined and
placed in a 0.5-␮l thin-walled PCR tube on ice. Ampli-
fication was performed as follows: initial denaturation
at 94ЊC for 2 min; 10 cycles of denaturation at 94ЊC for
30 s, primer annealing at 50ЊC for 30 s, and extension
for 2 min at 68ЊC; 25 cycles of denaturation at 94ЊC for
30 s, primer annealing at 50ЊC for 30 s, extension for 2
min at 68ЊC, plus cycle elongation for 5 s for each cycle;
and a final extension of 7 min at 68ЊC. Sequencing of
the amplified regions was carried out as previously
outlined.
Alignment of Nuclear SSU rRNA Genes and Group
IC1 Introns
The nuclear SSU rRNA gene and group IC1 intron
sequences in the present study were incorporated into
large alignments that spanned a large taxonomic range
in order to ensure optimum alignment. The new se-
quences were manually aligned with the alignment ed-
itor AE2 (developed by T. Macke; see Larsen et al.
1993) on the basis of sequence similarity and a previ-
ously established eukaryotic secondary-structure model
(Gutell 1993). The alignments were then subjected to a
process of comparative sequence analysis (Gutell et al.
1985). This process consisted of searching for compen-
sating base changes using computer programs developed
within the Gutell Laboratory (University of Texas at
Austin, http://www.rna.icmb.utexas.edu/; discussed in
Gutell et al. 1985) and using the subsequent information
to infer additional secondary-structural features. This re-
fined alignment was reanalyzed and the entire process was
repeated until the proposed structures were entirely com-
patible with the alignment. Secondary-structure diagrams
were generated with the computer program XRNA (de-
veloped by B. Weiser and H. Noller, University of Santa
Cruz). Individual secondary-structure diagrams will be
available at http://www.rna.icmb.utexas.edu/, and align-
ments can be obtained from K.M.M.
Analysis of Nuclear SSU rRNA Gene and Group I
Intron Sequences
All analyses on both the nuclear SSU rRNA gene
and the group I introns were carried out using only well-
aligned regions of the sequences. Parsimony analyses on
the two introns were carried out with PAUP 3.1.1 (Swof-
ford 1993) with a heuristic search under the constraints
of random sequence addition (100 replicates), steepest
descent, and tree bisection-reconnection (TBR) branch
swapping. The data were then subjected to bootstrap re-
sampling (1,000 replicates). Analyses of the introns
were carried out as follows: (1) the alignment gaps were
treated as missing data, and (2) the alignment gaps were
coded as independent single evolutionary events (inser-
tion or deletion) based on secondary-structure models
(Damberger and Gutell 1994). Group IC1 introns in
Chlorella ellipsoidea (GenBank accession number A:
X63520, B: D13324) were used as outgroups in the phy-
logenetic analyses. Parsimony trees could not be deter-
mined for the nuclear SSU rRNA gene due to the large
number of taxa and limited computational capacity;
however, neighbor-joining trees were calculated for this
data set. PHYLIP (Felsenstein 1993) was used to con-
struct neighbor-joining trees for both the introns and the

3. 1656 Mu¨ller et al.
Table 1
Specimens of Porphyra and Bangia Utilized in the Present Study, Including GenBank Accession Numbers for 18S
rRNA Gene and Intron Sequences
COLLECTION COLLECTION INFORMATION/REFERENCE
GENBANK ACCESSION NOS.
18S rRNA Intron 516 Intron 1506
Bangia atropurpurea (BI12)
(BI ϭ British Isles) . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043365 AF172565 —a
B. atropurpurea (GL) (GL ϭ Great Lakes)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043365 AF172566 —
B. atropurpurea (IR) (IR ϭ Ireland) . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043365 AF172563 —
B. atropurpurea (IT) (IT ϭ Italy) . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043365 AF172564 —
B. atropurpurea (NL) (NL ϭ Netherlands) Mu¨ller et al. (unpublished) for 18S rRNA gene AF169341 AF172562 —
Bangia fuscopurpurea (1) . . . . . . . . . . . . . . . . Oliveira et al. (1995) (as B. atropurpurea) L36066 — L36066
B. fuscopurpurea (2) . . . . . . . . . . . . . . . . . . . . Shimomura et al. (unpublished)
(as B. atropurpurea)
D88387 D88387 D88387
B. fuscopurpurea (Antarctic) . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175530 — —
B. fuscopurpurea (AK) (AK ϭ Alaska) . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043355 — —
B. fuscopurpurea (Australia) . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175531 AF172557 —
B. fuscopurpurea (BC2)
(BC ϭ British Columbia) . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043359 AF172567 AF172591
B. fuscopurpurea (BC1) . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043360 — —
B. fuscopurpurea (CA) (CA ϭ California) . . Mu¨ller et al. (1998) for 18S rRNA gene AF043356 AF172568 AF172590
B. fuscopurpurea (GLD)
(GLD ϭ Greenland) . . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043355 — —
B. fuscopurpurea (Greece) . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175533 AF172558 AF172587
B. fuscopurpurea (Helgoland) . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175532 AF172560 AF172585
B. fuscopurpurea (IR) . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175534 AF172569 AF172593
B. fuscopurpurea (MA)
(MA ϭ Massachusetts) . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043362 AF172561 —
B. fuscopurpurea (Mexico) . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF169334 — AF172582
B. fuscopurpurea (NC)
(NC ϭ North Carolina) . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043363 AF172559 AF172586
B. fuscopurpurea (NF)
(NF ϭ Newfoundland) . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043357 AF172570 AF172592
B. fuscopurpurea (NF-F) . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF169338 — —
B. fuscopurpurea (NH)
(NH ϭ New Hampshire) . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043353 — —
B. fuscopurpurea (Nice, France) . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175535 AF172556 AF172584
B. fuscopurpurea (NJ) (NJ ϭ New Jersey) . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF169335 AF172555 AF172583
B. fuscopurpurea (NWT) . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043355 — —
B. fuscopurpurea (OR) (OR ϭ Oregon) . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043358 AF172572 AF172589
B. fuscopurpurea (RI) (RI ϭ Rhode Island)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043354 — —
B. fuscopurpurea (TX) . . . . . . . . . . . . . . . . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043361 — —
B. fuscopurpurea (WA) (WA ϭ Washington)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF169336 — —
Bangia sp. (VIS7) (VI ϭ Virgin Islands) . . . Mu¨ller et al. (1998) for 18S rRNA gene AF043364 AF172578 —
Porphyra abbottae . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175545 AF172581 AF172596
Porphyra acanthophora . . . . . . . . . . . . . . . . . . Ragan et al. (1994) L26197 — —
Porphyra amplissima . . . . . . . . . . . . . . . . . . . . Oliviera et al. (1995) L36048 — —
Porphyra dentata (KF) . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013183 AB013183 AB013183
Porphyra fallax ssp. fallax . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175541 — —
Porphyra fucicola . . . . . . . . . . . . . . . . . . . . . . Stiller and Waaland (1993) (Pfu 1646) — ?b AF172595
Porphyra haitenensis (YE) . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013181 — AB013181
Porphyra kanakaensis . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175556 AF172580 —
Porphyra katadae (KY) . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013184 AB013184 AB013184
Porphyra leucosticta . . . . . . . . . . . . . . . . . . . . Ragan et al. (1994) L26199
P. leucosticta (UTEX) . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175557 AF172576 AF172598
P. cf. leucosticta (NF) . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175538 — —
Porphyra linearis (CCAP 1379/1) . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175539 — —
Porphyra miniata . . . . . . . . . . . . . . . . . . . . . . . Ragan et al. (1994) L26200 — —
P. miniata (CCAP 1379/2) . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175547 — —
P. miniata (NF) . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175540 — —
Porphyra nereocystis . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175542 AF172577 —
Porphyra cf. plocamiesteris . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175555 — —
Porphyra pseudolinearis (TT) . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013185 AB013185 AB013185
Porphyra pseudolanceolata . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175543 — AF172599
Porphyra purpurea (Avonport, NS) . . . . . . . . Ragan et al. (1994) L26201 — —
P. purpurea (NLbr)
(NLbr ϭ Netherlands brown) . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175550 — —
P. purpurea (NLgr) (NLgr ϭ Netherlands
gray) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175551 AF172575 AF172588

4. Group IC1 Introns in the Bangiales 1657
Table 1
Continued
COLLECTION COLLECTION INFORMATION/REFERENCE
GENBANK ACCESSION NOS.
18S rRNA Intron 516 Intron 1506
Porphyra rediviva . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175544 — AF172600
Porphyra spiralis var. amplifolia B . . . . . . . . Oliveira and Ragan (1994) — — L26175
P. spiralis var. amplifolia D . . . . . . . . . . . . . . Oliveira and Ragan (1994) — — L26176
P. spiralis var. amplifolia R . . . . . . . . . . . . . . Oliveira and Ragan (1994) L26177 — L26177
Porphyra suborbiculata (KY) . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013180 AB013180 —
Porphyra tenera (KK) . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013176 AB013176 AB013176
P. tenera (SK) . . . . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013175 AB013175 AB013175
P. tenera (T-1) . . . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D86237 D86237 —
P. tenera (TU-3) . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D86236 D86236 —
P. tenera (T8) . . . . . . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) AB000964 AB000964 —
Porphyra torta . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175552 AF172579 ?
Porphyra umbilicalis (HF) . . . . . . . . . . . . . . . Ragan et al. (1994) L26202 — —
P. umbilicalis (HG) (HG ϭ Hallig Gro¨de,
Germany) . . . . . . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175549 — AF172602
P. umbilicalis (NJ) . . . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175553 AF172573 —
P. umbilicalis (NM) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013179 — —
Porphyra yezoensis . . . . . . . . . . . . . . . . . . . . . Yamazaki et al. (unpublished) D79976 D79976 —
P. yezoensis (HH) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013177 AB013177 —
P. yezoensis (OM) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013178 AB013178 AB013178
P. yezoensis (OG-1) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017078
P. yezoensis (OG-4) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017081
P. yezoensis narawaensis . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017083
P. yezoensis (NA-2) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017075
P. yezoensis (NA-4) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) (ITS) — ? AB017076
Porphyra sp. (Brest) . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175548 — AF172601
Porphyra sp. (Marseille) . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175546 — AF172597
Porphyra sp. (SHH) . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) — ? AB017077
Porphyra sp. (SY) . . . . . . . . . . . . . . . . . . . . . . Kunimoto et al. (unpublished) AB013182 AB013182 AB013182
Porphyra sp. (Wales) . . . . . . . . . . . . . . . . . . . . Mu¨ller et al. (unpublished) for 18S rRNA gene AF175554 AF172574 —
NOTE.—The abbreviations UTEX, CCAP, and CCMP are for culture collections. Other abbreviations for taxa not noted were obtained from the GenBank file
and represent those assigned by the original authors or the collector of the material.
a Intron not present.
b Intron not sequenced, or presence or absence unknown.
nuclear SSU rRNA genes using a matrix of distance val-
ues estimated according to the Kimura two-parameter
model (Kimura 1980) with a transition/transversion ratio
of 2.0 and a single-category substitution rate, as well as
the Jukes and Cantor (1969) model (intron data set
only). These data sets were also subjected to bootstrap
resampling. Maximum-likelihood analysis was carried
out using the puzzle function in PAUP (version 4.0 beta
2a) as described by Strimmer and von Haeseler (1996)
with 1,000 puzzling steps. The nuclear SSU rRNA gene
sequence analyses of the Bangiales were run using Er-
ythrotrichia carnea (L26189) and Erythrocladia sp.
(L26188) as outgroups. These taxa were determined to
be basal to the Bangiales and have been previously used
as outgroup taxa for this order (Ragan et al. 1994; Oliv-
eira et al. 1995; Mu¨ller et al. 1998).
Results
Sequence data for all intron sequences were sub-
mitted to GenBank, and accession numbers are given in
table 1. Presence and absence of introns within the nu-
clear SSU rRNA gene Bangiales is depicted in figure 4.
Letters and numbers behind taxonomic names refer to
various collections that are listed in table 1, of which
some represent standard state, provincial, or country
codes, whereas others are arbitrary numbers or initials
of the author of the particular sequence. Due to the dif-
ficulty in delineating species in Bangia (Mu¨ller et al.
1998) and the lack of a definitive global key for Por-
phyra species, identification of species that are used in
the molecular analyses should be considered tentative.
Thus, many of the analyses in the present study will
focus more on the relationship among the intron se-
quences and nuclear SSU rRNA gene within the two
genera than on morphological species within each ge-
nus, other than for characters that would not be disputed
(e.g., monostromatic vs. distromatic). With respect to
Bangia, based on the findings in Mu¨ller et al. (1998),
all freshwater collections (AT22, BI12, GL, IR, IT, and
NL) should be classified as B. atropurpurea, while col-
lections from marine locations have provisionally been
given the name B. fuscopurpurea until they can be dif-
ferentiated morphologically.
Using RT-PCR it was determined that neither in-
tron is present in the mature rRNA, indicating that these
introns are excised (not shown). Thirty-three nuclear
SSU rRNA gene sequences from Bangia and 52 from
Porphyra were examined for the presence of either in-
tron in position 516 (intron 516) (E. coli numbering sys-
tem) and position 1506 (intron 1506). Of these 52 Por-
phyra specimens, there were 39 complete sequences of
the nuclear SSU rRNA gene; the remainder consisted of

5. 1658 Mu¨ller et al.
FIG. 1.—Phylogenetic conservation of Rhodophyta (Bangiophy-
ceae) group I (IC1) introns (18S rRNA positions 516 and 1506) su-
perimposed onto the Bangia sp. (IR) group I (IC1) intron secondary
structure (18S rRNA position 1506). Positions with a nucleotide in
Ͼ95% of sequences are shown: ACGU—95ϩ% conserved; acgu—
90%–95% conserved; ●—80%–90% conserved; o—Ͻ80% conserved.
Otherwise, the regions are represented by arcs. Positions shown in
small square boxes and arcs with dashed lines represent features that
distinguish the 516 and 1506 introns (described in table 3). The exon
sequences that flank the intron are indicated with x’s.
species for which the nuclear SSU rRNA gene could not
be obtained (difficulty in obtaining sequences, or sample
was not sequenced) but sequences of some introns were
available. Among the 33 collections of Bangia, 21 were
determined to have intron 516 (64%), and 13 were ob-
served to have intron 1506 (39%). Only 10 (30%) col-
lections contained neither intron, and 11 (33%) collec-
tions had both introns (fig. 4). Within Porphyra, 20
(40%) of 50 nuclear SSU rRNA gene sequences were
determined to have intron 516, and 26 (52%) contained
intron 1506. Only 14 (28%) Porphyra sequences had
either intron, and 10 (20%) contained both introns (fig.
4).
Structural Characteristics of Group IC1 Introns in the
Bangiales
All of the rRNA introns in Bangia and Porphyra
were determined to belong to the CI subgroup of the
group I introns based on characteristic primary- and sec-
ondary-structure features (fig. 1) (Michel and Westhof
1990; Damberger and Gutell 1994). The lengths of these
introns within the Bangiales varied considerably, rang-
ing from 467 to 998 nt for intron 516 and ranging from
509 to 1,082 nt for intron 1506 (table 1). Figure 1 is a
consensus diagram of all of the group IC1 introns in the
Bangiales. Both introns were observed to have large in-
sertions within the P1 (12–567 nt), P2 (62–553 nt), P5
(3–91 nt), P6b (10–84 nt), and P9.2 (5–53 nt) domains
(fig. 1). The large insertions in the P1 and P2 domains
were found in introns 1506 and 516, respectively (fig.
1), whereas the other insertions (P5, P6b, and P9) were
similar in size between both the 516 and the 1506 in-
trons. The majority of the base pairs in the P4 and P7
helices are highly conserved (Ͼ95%) between both sets
of introns, whereas the remaining helices are less con-
served. The single positions and base pair ‘‘signatures’’
that distinguish the 516 and 1506 introns are shown as
square boxes and dashed lines in figure 1 and detailed
in table 3. Approximately half of these nucleotides and
the 5Ј positions of the base pairs noted in table 3 (and
depicted in fig. 1) are purines (A, G) in the 516 intron
and are pyrimidines (C, U) in intron 1506 (positions 2,
25, 26, 97:277, 216:257, 217:256, 262:312, 322:326,
and 335:364 [relative to Tetrahymena thermophila]). All
of these positions are highly conserved (Ͼ95%) with the
exception of base pair 97:277 (Ͼ90%, Ͻ95%). Position
172 and the 322:326 base pair have no homologous po-
sition with respect to T. thermophila. These three posi-
tions are highly conserved in both introns (Ͼ95%). Fig-
ure 2 highlights the differences between the 516 and
1506 introns in the P5b and P8 domains. The P5b helix
(fig. 2a) is one of the most distinct features of the 516
intron. This bifurcated helix, present in all of the Ban-
giales 516 introns, replaces the typical single helix pre-
sent in all IC1 introns, including the Bangialean 1506
introns (fig. 2a). The P8 domain (fig. 2b) is also distinct,
primarily on the basis of helix length. In the 516 version
of this structure, the 3-bp helix is capped by a tetraloop,
while the 1506 structure has a longer helix capped by a
variable-length hairpin loop.
Haugen et al. (1999) determined that P. spiralis var.
amplifolia (R) appeared to contain an open reading
frame (ORF) corresponding to a 149-amino-acid His-
Cys box protein within the P1 extension of the 1506
intron, as does P. tenera (KK) within the P2 extension
of the 516 intron. Johansen, Embley, and Willassen
(1993) noted that the His-Cys box motif is a hallmark
of nuclear homing endonucleases. Examination of these
domains in the bangialean introns within the present
study revealed that this ORF is present in those taxa
containing large extensions within the P1 or P2 domain
for 1506 and 516 introns, respectively. Table 2 high-
lights the sizes of the P2 domain (516 intron) and the
P1 domain (1506 intron) for all collections examined in
the study and the presence or absence of the His-Cys
box motif. The size of the P2 domain in the 516 intron
ranged from 62 to 552 nt, with only those Ͼ414 nt con-
taining an ORF and His-Cys box motif. This motif has
not previously been reported in the 516 intron for the
following taxa: B. fuscopurpurea (Helgoland), B. fus-
copurpurea (MA), P. abbottae, P. kanakaensis, and P.
tenera (SK). The P1 domain in the 1506 intron ranged
from 53 to 521 nt, and the His-Cys box motif was found
only in those with larger insertions in this region: P.
fucicola and P. umbilicalis (previously unreported).

6. Group IC1 Introns in the Bangiales 1659
FIG. 2.—Gallery highlighting differences between introns 516 and 1506 using consensus diagrams and individual secondary-structure
diagrams. a, P5b region of intron 516, showing bangialean consensus and differences among specific taxa. b, P5b region of intron 1506, showing
a bangialean consensus and differences specific among taxa. c, Consensus of the P8 regions of introns 516 and 1506 in the Bangiales. For
consensus diagrams, positions with a nucleotide in Ͼ95% of sequences are shown: ACGU—95ϩ% conserved; acgu—90%–95% conserved;
●—80%–90% conserved; o—Ͻ80% conserved. Otherwise, the regions are represented by arcs.
Haugen et al. (1999) noted that the ORF within the
P1 extension for intron 1506 was determined to be on
the complementary strand to that encoding the SSU
rRNA, and this was also the case for the ORF in the
previously unreported taxa (P. fucicola and P. umbili-
calis). However, this was not true for the ORF in the P2
extensions for the 516 introns, which were found on the
same strand as that encoding the SSU rRNA. Figure 3
depicts an amino acid alignment of the His-Cys box
motif region in the P1 domain of the 1506 intron and
the P2 domain of the 516 intron. As noted by Haugen
et al. (1999), P. spiralis var. amplifolia (R) and the en-
donuclease I-Ppo I were identical in 16 out of the 29
amino acids. The two new additional amino acid se-
quences, P. fucicola and P. umbilicalis (HG), were iden-
tical in 13 amino acids to the I-Ppo I endonuclease.
However, the amino-acid sequence for the His-Cys box
in the 516 introns was identical in only 9 or 10 amino
acids (fig. 3). Haugen et al. (1999) also noted frame-
shifts in the ORF of P. spiralis var. amplifolia (R) and
B. fuscopurpurea (1). Frameshifts were noted in the
ORF of the 516 introns in P. kanakaensis and B. fus-
copurpurea (HL); however, the remaining sequences
were not found to have frameshifts, although they all
terminated prematurely relative to the amino acid se-
quence for the homing endonuclease I-Ppo I (fig. 3).
This raises the possibility that these sequences are pseu-
dogenes; however, endonuclease activity in the Bangi-
ales was not tested in this study and needs to be inves-
tigated in further detail.
Phylogenetic Analysis of Introns
Figure 4 depicts a neighbor-joining tree derived
from the analysis of the nuclear SSU rRNA genes (par-
simony analyses were unobtainable due to the very long
computation time required) upon which the presence
(ϩ) and absence (Ϫ) of both introns have been mapped.
From these analyses, there appear to be multiple losses
of both introns. For example, the first major clade of
Bangia and Porphyra at the bottom of the tree contains
three smaller clusters in which there have been at least
two losses of the 1506 intron along each lineage (fig.
4). This same trend is even more evident in the larger
Bangia-Porphyra clade, where taxa possessing an intron
are intermingled with those that do not. There does not
appear to be any consistent trend with respect to pres-
ence or absence of either intron; however, it does appear
that the more derived a taxon is, the more likely the
intron will be absent (e.g., P. miniata (CCAP 1379/2),
P. amplissima, P. miniata, and P. miniata (NF)) (fig. 4).
Sequences of collections of B. atropurpurea were de-
termined to have identical nuclear SSU rRNA gene se-
quences, and all collections contained only intron 516.
Interestingly, some collections of B. fuscopurpurea
that were identical with regard to nuclear SSU rRNA
gene sequences were variable with regard to possession
of either or both introns. For example, the collection
from Greece contained both introns 516 and 1506; how-
ever, the other collection from Australia, with which it
was identical, did not contain the 1506 intron. In addi-

7. 1660 Mu¨ller et al.
Table 2
Sizes (nt) of Bangialean Nuclear Group I Introns in SSU rDNA, Sizes of P1 and P2 Regions, and Presence (؉)
or Absence (Ϫ) of His-Cys Box Motif (HC) Within Introns Inserted at Positions 516 and 1506, Respectively
TAXON/COLLECTION
POSITION 516
Intron Size P2 Size HC
POSITION 1506
Intron Size P1 Size HC
Bangia atropurpurea (AT17) . . . . . . . . . . . 531 108 Ϫ /a / /
B. atropurpurea (AT 22) . . . . . . . . . . . . . . . 531 108 Ϫ / / /
B. atropurpurea (BI12) . . . . . . . . . . . . . . . . 531 108 Ϫ / / /
B. atropurpurea (GL) . . . . . . . . . . . . . . . . . 532 108 Ϫ / / /
B. atropurpurea (IR) . . . . . . . . . . . . . . . . . . 531 108 Ϫ / / /
B. atropurpurea (IT) . . . . . . . . . . . . . . . . . . 531 108 Ϫ / / /
B. atropurpurea (NL) . . . . . . . . . . . . . . . . . 531 108 Ϫ / / /
Brangia fuscopurpurea (1) . . . . . . . . . . . . . / / / 1,038 514b ϩb
B. fuscopurpurea (2) . . . . . . . . . . . . . . . . . . 504 113 Ϫ 668 103 Ϫ
B. fuscopurpurea (Australia) . . . . . . . . . . . . 467 62 Ϫ / / /
B. fuscopurpurea (BC2) . . . . . . . . . . . . . . . 546 174 Ϫ 652 99 Ϫ
B. fuscopurpurea (CA) . . . . . . . . . . . . . . . . 552 174 Ϫ 652 99 Ϫ
B. fuscopurpurea (Greece) . . . . . . . . . . . . . 470 62 Ϫ 524 53 Ϫ
B. fuscopurpurea (Helgoland) . . . . . . . . . . . 997 527 ϩ 524 53 Ϫ
B. fuscopurpurea (IR) . . . . . . . . . . . . . . . . . 497 108 Ϫ 610 115 Ϫ
B. fuscopurpurea (MA) . . . . . . . . . . . . . . . . 998 528 ϩ / / /
B. fuscopurpurea (Mexico) . . . . . . . . . . . . . / / / 524 53 Ϫ
B. fuscopurpurea (NC) . . . . . . . . . . . . . . . . 470 62 Ϫ 523 53 Ϫ
B. fuscopurpurea (NF) . . . . . . . . . . . . . . . . 495 108 Ϫ 603 115 Ϫ
B. fuscopurpurea (Nice) . . . . . . . . . . . . . . . 467 62 Ϫ 523 53 Ϫ
B. fuscopurpurea (NJ) . . . . . . . . . . . . . . . . . 467 62 Ϫ 524 53 Ϫ
B. fuscopurpurea (OR) . . . . . . . . . . . . . . . . 531 143 Ϫ 578 61 Ϫ
Bangia sp. (VIS7) . . . . . . . . . . . . . . . . . . . . 502 86 Ϫ / / /
Porphyra abbottae . . . . . . . . . . . . . . . . . . . . 996 552 ϩ 699 239 Ϫ
Porphyra dentata (KF) . . . . . . . . . . . . . . . . 630 158 Ϫ 572 52b Ϫb
Porphyra fucicola . . . . . . . . . . . . . . . . . . . . ?c ? ? 976 (?) 514 Ϫ
Porphyra haitenensis (YE) . . . . . . . . . . . . . / / / 554 61b Ϫb
Porphyra kanakaensis . . . . . . . . . . . . . . . . . 904 414 ϩ / / /
Porphyra katadae (KY) . . . . . . . . . . . . . . . . 601 162 Ϫ 588 83b Ϫb
Porphyra leucosticta (UTEX) . . . . . . . . . . . 560 154 Ϫ 567 97 Ϫ
Porphyra nereocystis . . . . . . . . . . . . . . . . . . 606 145 Ϫ / / /
Porphyra pseudolinearis (TT) . . . . . . . . . . 567 135 Ϫ 581 108b Ϫb
Porphyra pseudolanceolata . . . . . . . . . . . . . / / / 573 93 Ϫ
Porphyra purpurea (Nlgr) . . . . . . . . . . . . . . 529 70 Ϫ 660 72 Ϫ
Porphyra rediviva . . . . . . . . . . . . . . . . . . . . / / / 596 85 Ϫ
Porphyra spiralis var. amplifolia B . . . . . . / / / 744 170b Ϫb
P. spiralis var. amplifolia D . . . . . . . . . . . . / / / 908 235b ϩb
P. spiralis var. amplifolia R . . . . . . . . . . . . / / / 1,056 482b ϩb
Porphyra suborbiculata (KY) . . . . . . . . . . . 494 105 Ϫ / / /
Porphyra tenera (KK) . . . . . . . . . . . . . . . . . 992 550 ϩb 783 342b ϩb
P. tenera (SK) . . . . . . . . . . . . . . . . . . . . . . . 972 550 ϩ 960 518b ϩb
P. tenera (T-1) . . . . . . . . . . . . . . . . . . . . . . . 517 128 Ϫ / / /
P. tenera (TU-3) . . . . . . . . . . . . . . . . . . . . . 517 71 Ϫ / / /
P. tenera (T8) . . . . . . . . . . . . . . . . . . . . . . . . 509 125 Ϫ / / /
Porphyra torta . . . . . . . . . . . . . . . . . . . . . . . 555 116 Ϫ ? ? ?
Porphyra yezoensis . . . . . . . . . . . . . . . . . . . 517 128 Ϫ / / /
Porphyra umbilicalis (HG) . . . . . . . . . . . . . / / / 1,082 570 ϩ
P. umbilicalis (NJ) . . . . . . . . . . . . . . . . . . . . 517 128 Ϫ / / /
Porphyra yezoensis (HH) . . . . . . . . . . . . . . 517 128 Ϫ / / /
P. yezoensis (OM) . . . . . . . . . . . . . . . . . . . . 517 128 Ϫ 509 77b Ϫb
P. yezoensis (OG-1) . . . . . . . . . . . . . . . . . . . ? ? ? 525 77b Ϫb
P. yezoensis (OG-4) . . . . . . . . . . . . . . . . . . . ? ? ? 514 79b Ϫb
P. yezoensis narawaensis . . . . . . . . . . . . . . ? ? ? 526 80b Ϫb
P. yezoensis (NA-2) ? ? ? 526 81 Ϫ
P. yezoensis (NA-4) . . . . . . . . . . . . . . . . . . . ? ? ? 526 81 Ϫ
Porphyra sp. (Brest) . . . . . . . . . . . . . . . . . . / / / 595 85 Ϫ
Porphyra sp. (Marseilles) . . . . . . . . . . . . . . / / / 565 98 Ϫ
Porphyra sp. (SHH) . . . . . . . . . . . . . . . . . . . ? ? ? 967 521b ϩb
Porphyra sp. (SY) . . . . . . . . . . . . . . . . . . . . 529 85 Ϫ 654 150b Ϫb
Porphyra sp. (Wales) . . . . . . . . . . . . . . . . . . 529 70 Ϫ / / /
a Intron not present.
b Reported in Haugen et al. (1999).
c Intron not sequenced, or presence or absence unknown.

8. Group IC1 Introns in the Bangiales 1661
Table 3
Differences Between the 516 and 1506 Introns at Single
Positions or Base Pairs Using Tetrahymena thermophila
Position Numbering
T. thermophila Intron 516 Intron 1506
2 . . . . . . . . . . . . . .
25 . . . . . . . . . . . . .
26 . . . . . . . . . . . . .
97:277 . . . . . . . . .
98 . . . . . . . . . . . . .
160 . . . . . . . . . . . .
172a . . . . . . . . . . .
205 . . . . . . . . . . . .
216:257 . . . . . . . .
217:256 . . . . . . . .
262:312 . . . . . . . .
272 . . . . . . . . . . . .
281 . . . . . . . . . . . .
304 . . . . . . . . . . . .
313:413 . . . . . . . .
322:326a . . . . . . .
335:364 . . . . . . . .
G
A
G
A:U
C
A
U
U
G:C
G:C
G:C
U
C
G
A:U
G:C
A:U
U
U
U
u:g
U
G
C
C
C:G
C:G
C:G
G
U
A
G:C
C:G
C:G
NOTE.—Each position number shown is the nearest T. thermophila nucleo-
tide. Uppercase letters indicate that nucleotides are conserved in at least 95% of
the sequences. Lowercase letters indicate conservation between 90% and 95%.
a No homologous position exists in the T. thermophila sequence.
FIG. 3.—Alignment of open reading frames (ORFs) coding for
endonuclease-like amino acid sequences highlighting the His-Cys box
motif from the 516 and 1506 introns in the Bangiales. A, 516 introns:
Porphyra abbottae (P. abb.), Porphyra kanakaensis (P. kana.), Por-
phyra tenera (KK) (P. ten. (KK)), P. tenera (SK) (P. ten. (SK)), Ban-
gia fuscopurpurea (Helgoland) (B. fusc. (HL)), and B. fuscopurpurea
(MA) (B. fusc. (MA)). B, 1506 introns: Porphyra spiralis var. ampli-
folia (R), Porphyra umbilicalis (HG) (P. umb. (HG)), Porphyra fuci-
cola, and B. fuscopurpurea (1) (B. fusc. (1)). Identical positions are
indicated by dots, alignment gaps are indicated by dashes, and residues
inferred from reading frameshift corrections are shown in bold low-
ercase letters. Conserved residues proposed to be directly involved in
zinc binding (C100, C105, H110, C125, C132, H134, C138) and the
active site (H98, N119) of the I-PpoI endonuclease (Flick et al. 1998)
are indicated. The His-Cys box motif and frameshifts for P. tenera
(KK), P. tenera (SK), B. fuscopurpurea (1), and P. spiralis var. am-
plifolia (R) were previously noted by Haugen et al. (1999).
tion, the collection from Ireland (IR) contained both in-
trons 516 and 1506, whereas the other collections (WA
and TX), with which it was nearly identical (differing
by 8 bp) contained neither intron. A similar pattern oc-
curred in B. fuscopurpurea from Massachussetts (MA),
which did not contain the intron 1506, yet it was present
in the other collections with nearly identical sequences
(Helgoland and Nice, differing by 5 bp). Within Por-
phyra, this was only seen in one case: Porphyra ye-
zoensis (HH) did not contain intron 1506, whereas P.
yezoensis (OM) did.
Well-supported clades are along biogeographic
lines with few exceptions, but the presence or absence
of introns does not appear to be consistent based on
geographic locations. For example, the well-supported
clade (100% bootstrap) of B. fuscopurpurea containing
primarily collections from the Atlantic and Mediterra-
nean (NC, NJ, Greece, Helgoland, Nice, MA [with the
exception of the Pacific samples from Australia and
Mexico]) all contained intron 516, except the sample
from Mexico, and the samples from Massachusetts and
Australia did not contain intron 1506. Distromatic taxa
(subgenus Diploderma) of Porphyra, P. miniata (CCAP
1379/2, NF) and P. amplissima (2), contained neither
intron, whereas other species of Porphyra belonging to
the subgenera Diplastida and Porphyra were variable in
containing either intron.
Introns occur frequently within the Chlorophyta,
but within the Rhodophyta, Bangia, Porphyra, and Hil-
denbrandia are the only genera currently known to con-
tain introns (Ragan et al. 1993). This trend raises the
question of whether the introns within Hildenbrandia
and the Bangiales might be related. Hence, figure 5 also
includes the two 1506 introns from H. rubra and one
chlorophyte algae, C. ellipsoidea (A, B). This figure pre-
sents the one most-parsimonious tree based on analysis
of 1,025 parsimony-informative characters of well-
aligned positions of the group IC1 intron in positions
516 and 1506. This tree has a length of 4,589 steps and
a consistency index (CI) (a measure of the amount of
homoplasy exhibited by the set of characters: for no
homoplasy, CI ϭ 1) of 0.4988. This data set was also
analyzed by coding the gaps as single evolutionary
events (e.g., 10 consecutive gaps are treated as one event
rather than 10 separate events), whereas in the previous
analysis, they were treated as missing data. This analysis
depicted little change in the topologies of the trees; in
fact, the resolution was much lower than when the gaps
were treated as missing characters.

9. 1662 Mu¨ller et al.
FIG. 4.—Presence (ϩ) and absence (Ϫ) of group IC1 introns in positions 516 (first symbol) and 1506 (second symbol) mapped on an 18S
rRNA gene neighbor-joining tree. Lengths of branches in tree correspond to sequence divergence calculated using the Kimura (1980) two-
parameter model.
Figure 5 clearly depicts the 516 and 1506 intron
sequences as two separate clades that are generally well
supported (516: 100% maximum-parsimony [MP] boot-
strap; 50% quartet puzzling values [QPS]; 100% neigh-
bor-joining [NJ] bootstrap; 1506: 98% MP bootstrap;
Ͻ50% QPS; 99% NJ bootstrap). The two introns in H.
rubra are well associated with each other (100% MP
bootstrap; 88% QPS; 95% NJ bootstrap) and are well
positioned within the 1506 intron sequence clade of the
Bangiales (89% MP bootstrap; 89% QPS; 99% NJ boot-
strap). The introns in P. spiralis var. amplifolia (position
1506) are positioned on a branch that is basal to the
cluster containing the 1506 intron sequences from the
Bangiales and H. rubra.
Both the nuclear SSU rRNA gene NJ tree (fig. 4)
and the phylogenetic tree using intron sequences (fig. 5)
show similar trends. For example, the well-supported
(100% bootstrap support; fig. 5) cluster containing B.
fuscopurpurea from New Jersey (NJ), Nice, Australia,
Greece, North Carolina (NC), Helgoland, and Massa-
chusetts (MA) is also present in the intron phylogenetic
tree for both the 1506 (100% MP bootstrap; 99% QPS;
92% NJ bootstrap) and 516 introns (98% MP bootstrap;
Ͻ50% QPS; 70% NJ bootstrap) (fig. 5). In addition, the
collections from Ireland, Newfoundland (NF), and B.
fuscopurpurea (2) also cluster together within the nu-
clear SSU rRNA gene analysis (93% bootstrap) and the
intron phylogeny for both intron insertion sites. This re-
lationship is fairly well supported for the 1506 intron
sequences (72% MP bootstrap; 94% QPS; 83% NJ boot-
strap) but not for the 516 intron sequences (61% MP
bootstrap; Ͻ50% QPS; Ͻ50% NJ bootstrap) (fig. 5).
Similarly, the 516 intron sequences within the
freshwater taxon B. atropurpurea from the British Isles
(BI12), Netherlands (NL), Great Lakes (GL), Italy (IT),
and Ireland (IR) are positioned in a well-supported clade
(100% MP bootstrap; 57% QPS; 85% NJ bootstrap), as
are the sequences of the nuclear SSU rRNA gene for
these collections. In addition, none of the freshwater col-
lections contained intron 1506. The relationship of the

10. Group IC1 Introns in the Bangiales 1663
FIG. 5.—The one most-parsimonious tree based on analysis of 1,025 phylogenetically informative characters of well-aligned positions of
the group IC1 intron in positions 516 and 1506 in the order Bangiales (length ϭ 4,589, consistency index ϭ 0.4988). The first number above
a branch represents bootstrap support (1,000 replicates) for maximum parsimony, the second value is the percentage of times that a particular
cluster was found among the 1,000 intermediate steps (QPS) using quartet puzzling, and the final value represents bootstrap resampling for
distance analysis (1,000 replicates). Numbers below branches represent Bremer indices or decay values.
marine collection from the Virgin Islands (VIS7) was
unresolved (Ͻ55% bootstrap support) in both the intron
analyses, and it is only weakly associated (62% boot-
strap) with one of the main clades in the NJ nuclear
SSU rRNA gene tree.
The relationship among the introns in Porphyra is
not as well resolved as that in Bangia. However, some
groupings are evident in all three analyses. For example,
Porphyra sp. (SY) and P. pseudolinearis (TT) are close-
ly associated in the nuclear SSU rRNA gene phylogeny
(75% bootstrap), and the 516 intron sequences for these
two taxa are also well associated (99% MP bootstrap;
Ͻ50% QPS; 99% NJ bootstrap) (fig. 5). In addition, the
clade consisting of P. tenera (T1, TU-3), P. umbilicalis
(NJ), P. yezoensis, and P. yezoensis (HH, OM) is present
in the nuclear SSU rRNA gene phylogeny (although not
well supported), and this cluster is also seen for the 516
introns for these taxa in figure 5 (100% MP bootstrap;
97% QPS; 76% NJ bootstrap). A close relationship
among Porphyra rediviva, Porphyra sp. (Brest), and P.
umbilicalis (HG) is reflected in both the nuclear SSU
rRNA gene tree (100% bootstrap) and the 1506 portion
of the intron phylogeny, with the relationship between
P. rediviva and Porphyra sp. (Brest) being well sup-
ported (100% MP bootstrap; 100% QPS; 75% NJ boot-
strap) and the 1506 intron sequence being only weakly
associated with the previous clade (Ͻ50% MP boot-
strap; 64% QPS; Ͻ50% NJ bootstrap). A grouping of
Porphyra 1506 intron sequences consisting primarily of
collections from Japan (P. yezoensis (OM, OG-1, OG-
4, NA-2, NA-4), P. yezoensis narawaenis, P. tenera
(KK, SK), P. pseudolinearis (TT), Porphyra sp. (SHH))
is moderately supported (82% MP bootstrap; 83% QPS;
Ͻ50% NJ bootstrap). This trend is not, however, reflect-

11. 1664 Mu¨ller et al.
ed in the nuclear SSU rRNA gene tree, where the rela-
tionship among many of the Japanese taxa is close but
unresolved (Ͻ50% support). Many of the other relation-
ships seen in the nuclear SSU rRNA gene NJ tree are
similar to those in the intron trees, but most are not well
supported by bootstrap analysis (Ͻ60%). The sequence
divergence in the intron at position 516 varied consid-
erably, ranging from 0% to as high as 31.0%. The se-
quence divergence for the intron in position 1506 was
higher than that for the 516 intron (31.0% vs. 44.3%).
Interestingly, the 1506 introns in P. spiralis var. ampli-
folia (Oliveira and Ragan 1994) were quite distant from
all other Porphyra and Bangia taxa, ranging from 30.3%
to 44.3% sequence divergence.
Discussion
Introns within the nuclear SSU rRNA gene from
members of the Bangiales have been reported several
times within the past few years (Stiller and Waaland
1993; Oliveira and Ragan 1994; Oliveira et al. 1995;
Mu¨ller et al. 1998). The presence and absence of these
introns presents us with an opportunity to examine lat-
eral intron transfer events and the evolutionary history
of introns within the order Bangiales. Oliveira et al.
(1995) speculated that these introns could also be used
to discern biogeographic or specific entities within the
genus Porphyra, as they determined that variants of the
group IC1 intron were present in different geographic
populations of this alga. Due to the considerable number
and variation (as high as 40%) in the introns in Por-
phyra and Bangia, this system is well suited to address-
ing some of these issues. In addition, group I introns
that lack endonuclease coding regions appear to be non-
mobile and provide a potentially valuable tool for trac-
ing the evolutionary history of these sequences (Bhat-
tacharya 1998).
The similarity in phylogenies between the 516 and
1506 introns and their nuclear SSU rRNA genes sug-
gests that these introns have not been mobile during the
evolution of the Bangiales. Introns have been docu-
mented in the nuclear-encoded rRNA genes of different
Naegleria species. The majority of these occur at the
516 position of the nuclear SSU rRNA gene. A more
extensive analysis of the Naegleria nuclear SSU rRNA
genes revealed that this intron is absent in the majority
of the species’ nuclear SSU rRNA genes (De Jonckheere
1994). De Jonckheere (1994) hypothesized that since
there was probably no selective advantage arising from
the presence of these introns, they were eliminated in
many of the descendants. In the case of the Bangiales,
it appears that after initial acquisition of the introns in
the ancestor of these taxa, there was subsequent vertical
inheritance and evolution within the order (and species)
and in some cases loss of the introns in either insertion
site, as the intron phylogenies are very similar to that
of the host gene. An alternative and less favorable hy-
pothesis is that frequent lateral transfers within the order
may have taken place, but this would result in intron
phylogenies that would be widely discordant with the
nuclear SSU rRNA gene phylogenies (Bhattacharya et
al. 1994).
The similarity among group I intron and nuclear
SSU rRNA gene phylogenies has also been reported for
other eukaryotic taxa. Takashima and Nakase (1997)
noted that introns had been transferred horizontally to
distinct insertion sites in the yeast-like fungus Tilletiop-
sis flava and then inherited vertically. Similarly, introns
1506 and the nuclear SSU rRNA gene sequences share
similar phylogenies in members of the green algal order
Zygnematales (Bhattacharya et al. 1994). Wilcox et al.
(1992) also postulated that the distribution of introns
within other green algal taxa could be explained by in-
heritance of these sequences along with the gene. How-
ever, VanOppen, Olsen, and Stam (1993) concluded that
nuclear group I introns in green algae have arisen sev-
eral times and do not appear to be lineage-specific and
disagreed that the distribution of introns could be ex-
plained by vertical inheritance within the green algae as
postulated by Wilcox et al. (1992). In the case of the
Bangiales, the latter scenario appears to be possible. For
instance, the intron phylogenies appear to be in accor-
dance with the gene phylogenies, indicating long-term
immobility and vertical inheritance.
The evolutionary history of the Bangiales is quite
long, as bangiophyte taxa have been reported in the fos-
sil record from the Proterozoic (1,200 MYA) (Butter-
field, Knoll, and Swett 1990), and the conchocelis stage
of Porphyra has been reported in fossils up to 425 MYA
(Campbell 1980). In terms of utilizing the introns within
the Bangiales as specific or geographic markers as spec-
ulated by Oliveira and Ragan (1994), the present study
does not appear to indicate this possibility. In fact, anal-
yses of the group I introns appear to provide further
evidence for the synonymy of these two genera, as in-
tron phylogenies are congruent with those of the nuclear
SSU rRNA gene. This is not surprising, as other molec-
ular studies using nuclear and chloroplast genes have
indicated that these taxa are not monophyletic genera
(Mu¨ller et al. 1998). Thus, attempts at constructing a
phylogenetic classification within the order based on
morphology, life histories, and molecular analyses, and,
in this case, intron sequences, have been problematic.
The observation that similar group I introns are dis-
tributed across different genomes and phylogenetically
distant taxa is taken as evidence that intron transfer is
relatively common (Burke 1988). The clustering of
group I introns in phylogenetic trees from distinct in-
sertion sites suggests that these introns may be traced
back to one or more events in which the introns were
inserted into rRNA and vertically inherited or lost (Bhat-
tacharya et al. 1994; Bhattacharya 1998). Within the
Zygnematales, bootstrap analyses yielded little support
for the single origin of all group I introns at different
insertion sites within rRNA (Bhattacharya et al. 1994).
It is difficult to determine if this is the case with the
introns within the Bangiales due to the lack of a suitable
outgroup. Nonetheless, all of the 516 and 1506 introns
form two separate clades distinct from each other. High
sequence similarity between introns is consistent with
descent from an ancestral intron that was initially ac-

12. Group IC1 Introns in the Bangiales 1665
quired and vertically inherited (Schroeder-Diedrich,
Fuerst, and Byers 1998). In the protist Acanthamoeba,
low sequence identity (highly variable) among introns
in four different positions suggests that the intron ac-
quisition occurred independently at the four positions
after divergence of the taxa within the tree (Schroeder-
Diedrich, Fuerst, and Byers 1998). There is high se-
quence identity (0% sequence divergence in some cases)
among many of the introns sequenced within the Ban-
giales; however, there is also considerable variability.
For example, the 1506 introns in P. spiralis var. ampli-
folia (B, D, R) differ from all other intron sequences by
30%–44% sequence divergence. Despite this, P. spiralis
var. amplifolia is well supported as grouping with the
remaining 1506 introns.
Homing-Endonuclease Pseudogenes in the Bangiales
The mobility of nuclear group I introns may depend
on homing through the expression of intron-encoded
homing endonucleases (Belfort and Roberts 1997). The
His-Cys box is one of several types of homing endo-
nucleases that is restricted to group I introns (Johansen,
Embley, and Willassen 1993). Haugen et al. (1999) de-
scribed unusual P1 extensions within the nuclear SSU
rRNA introns of Bangia and Porphyra. Their analysis
showed that the intron sequences contained His-Cys box
reading frames within the P1 extension and that these
may represent homing-endonuclease pseudogenes. They
also demonstrated that the ORF in the 1506 intron of P.
spiralis var. amplifolia occurred on the strand comple-
mentary to that encoding the SSU rRNA gene and group
I intron. The present study also observed this phenom-
enon for the P1 domain in the introns at position 1506
for P. fucicola and P. umbilicalis (HG), both of which
also contained the His-Cys box motif noted in P. spiralis
var. amplifolia. The introns in the 516 position that con-
tained an ORF as well as a His-Cys box motif were
within the P2 domain and not on the complementary
strand, as seen in the 1506 introns. Haugen et al. (1999)
also noted frameshifts in the 3Ј end of the P. spiralis
var. amplifolia intron ORF which resulted in a truncated
C-terminal end and would explain the lack of cleavage
activity in the in vitro translated protein. Haugen et al.
(1999) suggested that the truncation and frameshifts
seen in the Bangialean intron ORFs may be the result
of selection against endonuclease expression which
would lethally cleave chromosomal DNA. Only two of
the new sequences in this study had frameshifts, P. kan-
akaensis and B. fuscopurpurea (Helgoland), and all se-
quences were found to terminate prematurely. This may
indicate that these ORFs are no longer functional; how-
ever, endonuclease activity has not been studied in these
sequences and needs to be investigated.
Secondary-Structure Signatures of the Group IC1
Introns in the Bangiales
In 1987, Woese rationalized that the examination
of higher-order structure from a phylogenetic perspec-
tive would enable us to examine the stages of evolution
of rRNA structure and aid in extrapolating the signifi-
cance of changes and variation in rRNA. Subsequently,
Winker and Woese (1991) delineated the three primary
domains using structural characteristics of 16S rRNA.
They defined two types of signature characters: (1) ho-
mologous positions whose compositions are (very near-
ly) constant (present in at least 94% of the representative
sequences) within each of the domains or kingdoms and
are characteristic of at least one, and (2) nonhomologous
structures that characterize and distinguish the various
groupings (e.g., structures that are present in one group
and absent in another and/or structural units that differ
strikingly from one group to another). Within these two
types there are different examples of phylogenetically
constrained elements ranging from single nucleotides
and base pairs to hairpin loops, noncanonical pairing,
insertions, deletions, and combinations of these ele-
ments, along with coaxial stacked helices or differences
in numbers between homologous structures (Gutell
1992).
In the present study, the Bangiales were observed
to have sequence and structural elements, or ‘‘signa-
tures,’’ that differentiate these introns from each other
as well as from other available intron sequences. As
noted previously, the P5b domain in the 516 introns of
the Bangiales contains a bifurcated helix that distin-
guishes these introns from all other group IC1 introns
(fig. 2a). This element is not present in the P5b domain
in the 1506 bangialean introns and is an example of a
nonhomologous signature. The variation in length in the
P8 domain of the 1506 introns is also unique to the
Bangiales and is not seen in the bangialean 516 introns.
In addition to these structural elements, the introns in
the Bangiales can be differentiated based on nonhomol-
ogous and homologous single-nucleotide and base pair
signatures (table 3). For example, nucleotide 172 and
base pair 322:326 have no homologous positions with
respect to T. thermophila and can be considered non-
homologous signatures defining these introns. The two
introns can be differentiated based on nucleotide and
base pair signatures. For example, position 205 is a U
in intron 516 (conserved in Ͼ95% of the sequences) and
a C in intron 1506 (conserved in Ͼ95% of the sequenc-
es). These unique structural and sequence signatures
provide further evidence that the introns in positions 516
and 1506 are probably the result of a single (although
separate from each other) lateral transfer event and sub-
sequent vertical inheritance. In addition, these structural
signatures may provide a means for determining the pos-
sible origin of the Bangialean 516 and 1506 introns if
an ancestral intron still exists. This information also
yields a basis for utilizing introns to differentiate dif-
ferent phyla/organisms or to determine the origin of in-
trons based on structural characteristics.
Acknowledgments
This research was supported by NSERC grant RGP
0183503 to R.G.S., NIH grant GM 48207 to R.R.G., and
an OGS Scholarship to K.M.M. Technical assistance in
DNA sequencing by Angela Holliss is gratefully ac-
knowledged. We thank John Stiller, Alison Sherwood,

13. 1666 Mu¨ller et al.
Ron Deckert, Blair Brace, Wilson Freshwater, Mary Ko-
ske, and John West for help in collecting or providing
samples for this study.
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DAVID IRWIN, reviewing editor
Accepted April 10, 2001