Functional Constraints and rbcL Evidence for Land Plant Phylogeny

34 Pages·1994·13.1 MB·

by  Victor A Albert

FUNCTIONAL
CONSTRAINTS
Victor A. Albert, 2 3 Anders Backlund,
- 2 Kare
AND Mark
EVIDENCE FOR Bremer, 2 W. Chase*
rbcL
James R. Manhart,5 Brent
D. Mishler,6
LAND PLANT PHYLOGENY
1
and Kevin Nixon7
C.
Abstract
DNA
Although
the proportion of "functional" in eukaryotic genomes is both debatable and subject to definition,
most sequences gathered
for phylogenetic purposes are indisputably functional. For example, patterns of variation
are likely to be strongly constrained in ribosomal RNAs because of their structural and catalytic roles in protein
and
translation, in protein-coding genes, because of protein function Although seemingly obvious, these concerns
itself.
We
are usually ignored by workers producing gene have examined
trees. the extent of functional constraints in land-
plant r6cL sequences. Not only do rbcL sequences appear to change with essentially clocklike regularity, but nucleotide-
based cladograms imply that approximately 97.5% of codon changes on internal branches are functionally neutral
(i.e., synonymous or functionally labile). From this perspective, rbcL evolution appears to be strongly constrained by
function. Transforming
nucleotide data into ad hoc string recognitions alters the size of the unit character sufficiently
to highlight "blocks" of conservative information that may or may not be functionally constrained. Simultaneous
cladistic analysis of available evidence
all will highlight the proportion of congruent information, despite diverse
among We
functional constraints the characters analyzed. demonstrate the strength of this approach using different
forms of the same rbcL evidence
(i.e., nucleotides, strings, or amino acids) in combination with the seed-plant data
of Nixon
et al.
Diversification of the major
clades of extant land phenotypic gaps. In particular, the plastid rbcl
plants probably dates from
the Silurian to Creta- gene (which encodes the large subunit of RuBisCO:
ceous. During the Silurian- Devonian,
liverworts, ribulose- ,5-bisphosphate carboxylase/oxygenase,
1
hornworts, mosses, and
tracheophytes formed dis- a primary enzyme carbon fixation) has been
in
tinct lineages. Differentiation of the tracheophyte emphasis on
sequenced primary
extensively, with
clades, notably angiosperms and
other seed plants, the angiosperms (Clegg, 1993; Chase et al, 1993).
began by the Devonian. The
estimation of land- Arguing from expected synonymous substitutions
plant phylogeny, a research goal spanning over per site under a particular rate assumption, Clegg
400
million years of cladogenesis and extinction, (1993) suggested rbcL sequences should be
that
no
is simple task. For example, many
groups lack phylogenetically informative for the time interval
strong morphological We
similarities that might suggest 400-100 million years before present. argue
patterns of relationship.
incomplete.
here that this and similar assertions are
Recent years have seen an explosion of interest From direct estimation of total substitutions (as
in molecular information, with promise l"y
its of easily optimized on cladograms; see Albert et al.,
interpreted similarities for bridging & 1993)
otherwise large 1993; Albert Mishler, 1992 Albert et al.,
T
Bo^ch
nS and
PetCr EngStr6m BruneUa
for ideas advice and Diana Lipscomb,
zndZil >K / discussion,
and Mick KRichardson for comments on an ' ' an*Ufcniuj
earlier draft of the manuscript, Crepet, Else Marie Friis,
Bill
Stevenson for permission to use unpublished versions of their data matrix produced collaboration with KCN, and
in
Anderson o*n.
Bill for last-m.nute our
discussion of Malpighiaceae biogeography. All interpretations are, of course,
The program
for constructing random Support Iron
strings was written by Karl-Konig KSnigsson and Rolf Staflin.
™
mJ «onlin/ tUrti^en e ReSearch C°Uncil to VAA AB d ™) and the U.S. National Science Found* •
BSR-8906496 MWC, S < ' > VAA
BSR-8906126
t to JRM, BSR-9107484 BDM) Lastly,
to acknowledged.
to gratefully
is
thanks the sympos.um Garden lor
organizers, travel arrangement staff, and editorial office of the Missouri Botanical
their courteous and
patient
assistance.
Department ^^
of Systematic
Botany, Uppsala University, Villavagen S-752 36 Uppsala, Sweden. -
6, 9
J 5
a C eSPO
Department Villavagen
of Physiological Botany, Uppsala University, 6,
36 Uppsda Swe -
d°en
M
3101"7 °f °leCU,ar Systema*cs, Royal Botanical Gardens, Kew, Richmond, Surrey TW9 3AB, United
Kingdom'
Department A&M
of Biology, Texas
University, College Texas 77843, U.S.A. u
Station,
| _.
.
"^ Berkele
r "
Department
California,
ST" of Integrative Biology, University of
Califorr U
94720
7
L. H. Bailey Hortorium,
Cornell University, New
Ithaca, York 14853, U.S.A.
Ann. mn.
Missouri Rot. Carh
«i- rsa-cj;-?
Number
Volume 81 3 Albert et 535
al.
,
1994 Functional Constraints and rbcL Evidence
we will demonstrate that divergence-time asym- al. (1992) and in the relative-rate tests of Gaut et
metries among taxa restrict rfccL-based hypotheses al. (1992), but absolute rate estimates do not differ
of land-plant phylogeny far more than do rate substantially from our own findings. Thus, whereas
asymmetries. rbch data cannot be considered perfectly ultra-
We
have examined the internal stability of land- metric (i.e., satisfying a clock assumption), the
plant rbcL evidence through conversion of nucle- small range of absolute variation suggests that some
otide information into different data forms, includ- predictions of the clock hypothesis apply. For
still
ing presence/absence of ad hoc nucleotide strings. example, the relationship between time and the
may
Cladograms produced from nucleotide, string, and accumulation of nucleotide substitutions be
We
translated amino acid data are only partially con- nearly linear. term this condition, apparently
gruent. Character optimization on both nucleotide characterizing rbcL sequence data, "quasi-ultra-
and string trees reveals extensive functional con- metric."
servation through the predominance of Quasi-ultrametricity has several important im-
silent
changes and labile (function-conserving) amino acid plications. One is that the extent of sequence di-
replacements. Hence, r&cL nucleotides are no less vergence in a given taxon sampling should roughly
functionally constrained than morphological char- reflect the timing of underlying cladogenetic events.
sequence
acters (contra Olmstead, 1989;Sytsmaetal., 1991; such events are ancient, extensive
If all
Clegg, 1993). differences among taxa are to be expected (Fig.
all
&
Although the separation of protein-functional 1; cf. Donoghue Sanderson, 1992, fig. 15.3).
from cladogenetic history may not be entirely pos- If some cladogenetic events are ancient whereas
much more expected sequence
sible, the extent to which functional history reflects others are recent,
phylogeny might be assessed through congruence divergence in a data set would be prominently
become
studies with characters expected to carry diverse skewed (Fig. 2). As these properties ex-
patterns of functional constraints. As such, we have treme, parsimony analysis will be hampered by the
among
performed changes
total-evidence analyses at the seed-plant increased probability of parallel
divergence-time-asym-
level using, as a "constant," a new matrix of pri- either anciently diverged or
&
Donoghue
marily morphological data (Nixon et al., 1994, this metric sequences (Figs. 1, 2; cf.
issue). It emerges that combination of rbcL nucle- Sanderson, 1992: 347-349). Given that A, T, G,
otide, amino acid, or string data with this matrix and C are the only character-state alternatives,
produces produce patterns of
highly compatible hypotheses. either scenario likely to
cladistic is
Ihese may nonhomologous and there-
be
studies point to the commonality of in- similarity that
(i)
formation in different data forms representing the fore cladograms that are ahistorical. This is pre-
same by
evidence, and the power of simultaneous cisely the "long branches attract" issue raised
(ii)
evaluation of available evidence and weakness Felsenstein (1978) and others.
all
of further production of rbcL gene trees Kluge, Although asymmetrical rates of sequence change
(cf.
1989; Barrett et 1991; Donoghue & Sander- are often invoked to explain branch attraction be-
al.,
son. 1992; Jones et 1993; Mishler, 1994). havior (see Clegg and Zurawski, 1992: 10, with
al.,
reference to rbcL), the problem is better defined
and divergence time as their
terms of both rate
The in
Rate
"Problem"
per-character change: the X of Albert et
product,
&
As 1992;
has been (1992a, 1993; Albert Mishler, cf.
pointed out several recent papers,
in al.
&
sequence With quasi-ultrametric
change Hendy Penny, 1989).
in the rbcL gene not strictly
is
clocklike asymmetry unimportant in this regard:
(Albert et al., 1992a; Bousquet et al., data, rate is
19 becomes
92; Gaut et al., 1992; Clegg, 1993). Here, we time through which a branch exists the
provide a number of new comparisons (Table central factor. As such, our expectation of the
1)
based on parsimony analysis on rbcL data
patristic distances between woody taxon performance of
Pairs from Search of Chase (1993). must include our ability to estimate both the ab-
II et al. It is
c'ear that our own estimates and those of other solute and relative timing of cladogenetic events
w
Of
course,
orkers data matrices.
all fall within a very narrow range of inherent to particular
absolutely low values. The mean rate per taxon this may not always be possible.
10'" quasi-ultrametricity
Pair An implication of
investigated here approximately 2 x additional
is
A
total substitutions per site per million years; Wen- is the near satisfaction of selective neutrality.
d el & Albert 5-7 x 10"' molecular clock predicted by the neutral theory
(1992) estimated for is
and
mutation
""ee herbaceous-pair comparisons. Lineage-spe- of molecular evolution; equal rates of
«C Kirnura, 1983;
( rate differences were found by Bousquet et fixation are the expectation (see
536 Annals of the
Missouri Botanical Garden
Table "Phylogenetic" estimation of total substitution rate for 1 9 woody-taxon pairs. The rate of sequence
1
.
D
divergence was calculated as per-site divergence (the patristic distance, divided by the number of nucleotides
,
p
compared) divided by time since cladogenesis (Albert et al., 1992a). Average rates for individual taxa are half of the
values shown. Data are from Search II of Chase et al. (1993); systematic error associated with that analysis can be
expected to affect all calculations equally. Divergence time assumptions are based upon geologic dates associated with
vicariant disjunctions (with the exception of Arecaceae comparisons, which follow from the arguments of Wilson
all
1990).
et al.,
Divergence Divergence
rate
time (subst./site-
D
Taxon pair Area assumption taxon pair)
Callitris rhomboidea R. Br. ex Rich. Australia 100 My* 55 3.85 x 10'"'
iddringtonia cedarbcrgcnsis Marsh Africa
//
(Cupressareae)
Weta&equoia glyptostroboides Hu & Asia 40 My" 16 2.80 x 10-"'
W.
Chang
C.
Sequoiadendron giganteum (Lindl.) N. America
Buchholz
J.
(Taxodiaceae)
My
Hlicium parviflorum Michx. ex Vent N. America/ Asia 200 54 1.89 x 10 -in
Austrobaileyn scandens C. T. White Australia
(Illiciaceae/Austrobaileyaceae)
"
&
Drimys hi uteri J. R. G. Forst. S. America 100 My 21 1.47 x 10
New
lirlliolum sp. Caledonia
(Winteraceae)
& 10-'"
Drimys My x
winter R. G. Forst. America 100 14 0.98
i J. S.
Tasmannia insipida DC. Tasmania
interaceae)
(\\
-10
Canella winteriana (L.) Gaertn. N. America 200 My 78 2.73 x 10
Belliolum sp. New
Caledonia
(Canellaeeae Winteraceae)
-Mi
Canella winteriana (L.) Gaertn. N. America 200 My 67 2.35 x 10
Tasmannia
insipida DC.
Tasmania
iant'llaceae/ Winteraceae)
((
-Mi
Liriodendron tulipifera L. N. America 40 My 10 1.75 x 10
Liriodendron chinense
(Hemsl.) Sarg. Asia
(Magnoliaceae)
-H<
Calycanthus vhinensis Cheng & Asia/ N. America 200 My 28 0.98 x 10
Chang
S. T.
Idiospermum
australiense
(Diels) Australia
S. T. Blake
(Calycanthaceae
Idiospermaceae)
-
Chimonanthus praecox (L.) Link Asia 200 My 24 0.84 x 10 !••
Idiospermum
australiense
(Diels) Australia
S. T. Blake
'.alycanthaceae/ Idiospermaceae)
{(.
-Hi
Chamaedorea My x 10
costaricana 1.75
Oerst. Americas 60 15
1
Drymophloeus
subdistickus
S. Pacific
(H. E. Moore) E. Moore
II.
(Arecaceae)
Chamaedorea
costarieanu Oerst. Americas 60 My 20 2.33 x 10
Vr/W
frutienns Wurb.
S. Pacific India
(Arecaceae)
Serenoa repens (Bertram) Small Americas 60 My 18 2.10 x 10
Drymophloeus
subdistickus
S. Pacific
(H. E. Moore) H. Moore
E.
(Arecaceae)
Number 3
Volume 81 Albert et 537
al.
,
Functional Constraints and rbcL Evidence
1994
Table Continued.
1.
Divergence Divergence rate
time (subst./site-
Taxon
pair Area assumption D, taxon pair)
Serenoa repens (Bartram) Small Americas 60 My 23 2.68 x 10 '"
Wurb.
Vy/wi fruticans S. Pacific/ India
(Arecaceae)
llct u la nigra L. N. Hemisphere 200 My 35 1.23 x 10 '«
CustHirina litorca L. Australia
(bVtulaceae Casuarinaceae)
My
Sothofagus dombeyi (Mirb.) Oerst. S. America 100 30 2.10 x 10 '"
New
\othofagus balansae (Baill.) Steenis Caledonia
(Nothofagaceae)
My
Galphimia gracilis Bartl. S.-N. America" 00 34 2.38 x 10 M>
1
kridocarpus natalitius A. Juss. Africa/ Madagascar/
New
(Malpighiaceae) Caledonia
Oicella nucifera Chodat America 100 My 33 2.31 x 10 '"
S.
kridocarpus
natalitius A. Juss. Africa/Madagascar/
Malpighiaceae) New
Caledonia
Watcagnia stannea (Griseb.) Nied. S.-N. America 00 My 34 2.38 x 10-' ii
1
kridocarpus
natalitius A. Juss. Africa/ Madagascar/
Malpighiaceae) New
Caledonia
"
Range 3.01 x 10
Mean 2.05 x 10 "'
10 -"•
5.D. 0.75 x
My
Standard time figure used to represent the breakup of Gondwana (rounded to the nearest 100 (million year-)
&
from 130 My, as estimated using Terra Mobilis® 2.1 by C. R. Denham and C. R. Scotese; see Wendel Albert,
1992:
137).
Standard interchange between
time figure (ca. early Oligocene) used to represent disruption of the boreotropical
North America &
and
Eurasia (see Lavin Luckow, 1993).
Standard time figure used to represent separation of the Northern and Southern Hemispheres upon the breakup
W
Denham
Pangaea (rounded to the nearest 100 My from 160 My, as estimated using Terra Mobilis® 2.1 by C. R.
andC. &
R. Scotese; see Wendel Albert, 1992: 137).
Divergence
date used by Wilson et al. (1990), based on the fossil record.
^•>rth American Malpighiaceae are here interpreted as representing range expansion from South America.
ei, 1987). Quasi-ultrametric data may imply se- Unit Characters and Finctional Constraints
lection
coefficients very Re-
close to neutrality.
Dumber
membering that the underlying premise of selective As recently reviewed by Clegg(1993), a
have
neutrality and evolutionary studies relied
is the neutral effect of point mutations, of systematic
Such analyses
nearly clocklike sequence evolution should involve solely on rbcL sequence variation.
rbcL nucleotides
a ,a rge make assumption that
proportion of such changes, fixed as effec- the implicit
mark-
informative
neutral independent and potentially
Jroeiy Such would are
substitutions. substitutions
As discussed above with
expected events.
to be mainly synonymous ers of cladogenetic
silent (i.e.,
*ith change, branching
respect to amino acid8 and, with regard to respect to total rates of if all
),
amino are relatively recent.
acid replacements, functionally conservative events under consideration
aD may be expected to proceed
«le). parsimony analysis
Quasi-ultrametricity in rbcL nucleotide se-
branch
quences of spuriou at-
is thus an expected manifestation of strong with a reduced probability
lower expected
constraints on because of the absolutely
protein 9 traction
function.
are relevant to cfedittk
aegg<i993) on anonymous note that or.lv total institution rates
•S«J rates for rl><\-
"**t tods because
Assuming all informative variation is considered. protein function and t,hat Jf i.s t,he tr_r_a_ctt .- onn
that purifying selection eliimnates mutations deleterious to
s uch
°» mutations, may reformulated as
the neutral theory be
-/>
S-(l
Q 41
*Here S i« tk. »«.„i „..u_.:...»: u- ~~a e tk» mutation rate (after Nei, 1 87: 52, 1).
.. ;
Annals of the
538
Garden
Missouri Botanical
A B c D E A B C D E
6
Yrs
•
1
(1)
(2)
FIGURES and 2. Patterns of historical versus spurious similarity resulting from symmetrically ancient and
1
asymmetrical time-samples. In both cases, time-sample refers to the nodes on these imaginary trees. In (1), all nodes
are essentially time-coincident at 400 My, so the "true tree*' appears polytomous. In (2), the cladogenetic even!
My
indicated occur asymmetrically with respect to time, ranging from 400 to 50 since divergence. Possible patterns
of nucleotide change are indicated by the filled and open rectangles; the former represent unadulterated markers ot
from multiple
cladogenetic history, whereas the latter represent spurious character-state similarity resulting, e.g.,
nucleotide substitutions. In these patterns of similarity are approximately equal in extent (because of ncarh
(1),
may
clocklike substitutional behavior) but are in partial conflict with each other; parsimony analysis include resolution-
In*
containing some proportion of ahistorical evidence or even alternatives comprising totally spurious patterns.
might be the expectation if taxa A through E were, e.g., Isoetes, Selaginella, Psilotum, Equisetum, and Angioptens.
In (2), which approximates the situation in simultaneous studies of sporing and seed plants, the problems of (1) are
mos
only partially alleviated. Patterns of convergent similarity between the oldest taxa, A and B, will result in
*
parsimonious reconstructions that pair these taxa spuriously. As divergence time becomes shallower, the redu(
likelihood of multiple changes at sites will insure that D and E are paired historically. Although C is linked with {11
E) by "true" similarity, this relationship may be broken by false similarities between B and C as well as between b\
(C, D, E). In summary, comparing only anciently diverged lineages with rbch may suggest patterns of relations ip
o
comparison
that represent a hopelessly even mixture of historically reliable and nonreliable similarity. Likewise,
more consisten
ancient and recently diverged clades may have the same problem near the base while being relatively
near the tips. This condition may characterize the /"6cL-based results shown in this paper.
base
studies
sequence divergence and relatively lower associ- however, are in conflict with cladistic
Ribosoma
ated likelihood of character-state parallelism. This on morphological characters (see below).
roles in
"time-sampling" and catalytic
strategy has been employed in RNAs, with their structural
enormou--
under
circumscribed studies ranging from particular an- protein translation, are obviously
rDNAs may also
giosperm groups (e.g., Conti et al., 1993; Kron & functional constraints. Like rbcU
w
tehavior
Rodman
Chase, 1993; 1993) substitutional
et al., to seed plants exhibit nearly clocklike
vary,
as a whole (Chase et al., 1993). Here, a "time those positions that are "free" to
ir-
low
sample" refers to the nodes rather than change approximate the
the ter- absolute rates of
corresponds
minals on an imaginary tree; as such, a time sam- on estimated for rbcU analysis of
result in «>^
pling is the collection of absolute and relative tim- time samples might be expected to
dra
and
ings of underlying cladogenetic events in a data responding patterns of homologous P ^
matrix. Of course, the nodes of a cladogram are and therefore similar hieTaTC V^
similarity,
Q :
& 1992:
not discernible a priori to analysis, but their ab- structions Donoghue Sanderson,
(cf.
solute and relative timing may be estimated by
349).
* of
*
external criteria (e.g., the fossil record; cf. Norell To gain insight into the topological efl
&
h
Novacek, 1992). samples (see Fig-
asymmetrical time
vastly
from r
Initial attempts to analyze time samples beyond have combined rbch information
J
"gymnosperms,
angiosperms and other seed plants including phytes," "pteridophytes,"
(i.e.,
pro
rbcL sequences from substitutional
sporing plants; Albert et al., angiosperms (Table 2). If the
1 992b) resulted in cladistic patterns familiar from effectively clocklike among these taxa,
is
DNA land-plant r
studies based on ribosomal (rDNA) constraints in
variation effects of functional
spun
may be
(e.g., monophyletic gymnosperms or combinations evolution should be discernible (as
tu. "Problem,
gymnosperm Ratp
of lineages, a seed-plant "root" ibrancih • see ne naie ^
at attractions;
I
bo
from
the Gnetales, an angiosperm
"root" at the mon- above); we explore this cladistically
eo
nuc
hoc
ocots; see Troitsky et al., 1991; Zimmer et primary nucleotide data as well as ad
al., ^
a
Hamby &
1989; Zimmer, examined also
1992). These The r&cL data are
results, strings.
Volume 81 Number 3 Albert et al. 539
,
Functional Constraints and rbcL Evidence
1994
Table 2. rbcL sequences used for data transformation and cladistic analysis. These are listed by taxon and by
GenBank accession number and/or literature reference where sequence data appeared. Voucher information,
first
where available, given by these sources.
is
Taxon GenBank. accession or literature reference
Conoeephalum eonivum (L.) Lindb. Mishler et al., 1994
Lophocolea heterophylla (Schrad.) Dumort. Mishler et al., 1994
Anthoceros pu netatus L. Mishler et al., 1994
&
Andreaeobryum macrosporum
Steere
Murray 1994
B. Mishler et
al.,
Ophioglossum engelmannii Prantl LI 1058 R. Manhart, n press)
(J.
Psilotum nudum (L.) P. Beauv. LI 1059 R. Manhart, n press)
(J.
&
Isoetes melanopoda Gay Durieu LI 1054 R. Manhart, n press)
J. (J.
Lycopodium digit a turn A. Br. LI 1055 R. Manhart, n press)
(J.
ingiopteris evecta (G. Forst.) Hoffm. LI 1052 (J. R. Manhart, in press)
Equisetum arvense L. LI 1053 R. Manhart, n press)
(J.
Selaginella sp. LI 1280 R. Manhart, n press)
(J.
Botrychium biternatum (Sav.) Underwood LI 3474 R. Manhart, n press)
(J.
Tuxus x media Chase 1993
et al.,
Taxodium 1992
distichum
(L.) Rich. Soltis et al.,
Podocarpus X58135 1992)
gracilior Pilg. (Bousquet et al.,
Ginkgo 1993
biloba Chase
L. et al.,
W.
(Wras, revoluta Schutzman, FLAS, (M. Chase, unpublished)
L. B. s.n.,
Stangeria 1993
eriopus (Kunze) Chase
Baill. et al.,
Zamia &
inermis Vovides, D. Reese
J.
M. Vasquez-Torres LI 2683 (Chase et al., 1993)
Ephedra tueediana C. A. Mey. L12677 (Chase et al., 1993)
U'lwitschia mirabilis Hook. Chase et al., 1993 (G. R. Furnier)
f.
m
(>netu gnemon L. LI 2680 (Chase et al., 1993)
Chloranthus japonicus Siebold LI 2640 (Chase et al., 1993)
Piper
betle L. LI 2660 (Chase et al., 1993)
{Drimys) Tasmannia L01957 1992c)
insipida DC. (Albert et al.,
Cafycanthus chinensis Cheng & S. T. Chang LI 2635 (Chase et al., 1993)
Eupomatia 2644 1993)
bennettii F. Muell. LI (Chase et al.,
Magnolia 1990
macrophylla L. Golenberg et al.,
Per me
sen a can a Golenberg 1990
ri Mill. et al.,
Trochodendron & L01958 1992c)
aralioides Siebold Zucc. (Albert et al.,
-1428
184 from
Ceratophyllum demersum L. M77030 (Les et al., 1991) plus nucleotides 1
1993
Qiu
et al.,
-1428
184 from
Vymphaea odor M77035 1991) plus nucleotides
at a Aiton (Les et al., 1
1993
Qiu
et al.,
lilwm
superbum 2682 1992a)
L. LI (Albert et al.,
Plateaus 1992c)
L01943
occidentalis L. (Albert et al.,
Caltha 1992c)
palustris L. L02431 (Albert et al.,
DUknia
1992c)
indica L. L01903 (Albert et al.,
rysolepis
(Castanopsis) sempervirens
Kellogg) 1993
Hjelmq. Chase
< et al.,
Betula 1992c)
nigra L01889
L. (Albert et al.,
Ca*uarina 1992c)
L01893
litorea L. (Albert et al.,
Hamametti 1992c)
mollis Oliv. L01922 (Albert et al.,
becomes
X (= rate time),
amino changes per site,
acid ber of
level for hierarchic compatibility with
characters, nu-
some morphological
the Unlike
nucleotide and large.
string evidence.
with
analyzed cladistically
data are usually
cleotide
nonadditive
no assumed transformation series (i.e.,
NUCLEOTIDES
Albert
For such procedures,
1971).
Fitch,
steps;
spurious
The examined the potential for
(1993)
nucleotide the smallest unit character et al.
is
(1978) sim-
DNA under Felsenstein's
available
in information. With only four states branch attraction
State-change probabil-
P^ible scenario.
any four-taxon
at given nucleotide data are sub- plified
site,
&
Cantor, 1969)
(Jukes
ject to parallelism among sequences when the num- ities with Jukes-Cantor
I
540 Annals of the
Missouri Botanical Garden
and Kimura 2-parameter (Kimura, 1980) correc- retention indices (C and R, respectively; Kluge &
tions for multiple changes at sites were considered Farris, 1 969; Farris, 1 989a) were also calculated.
in addition to observed changes only because of Five hundred fifteen nucleotide positions showed
among
the prospect of reducing character-state parallel- patterns of similarity taxa.
isms. All calculations indicated a very small pa- Eight equally parsimonious cladograms were
=
R =
rameter region under which branch attraction could found (C 0.362 (including all data), 0.523).
be expected, provided that X values remained small The strict and combinable component consensus
less than approximately 0.1; see Albert et trees (Bremer, 1990) were identical (see Fig.
(i.e., al., 3).
1992a). For quasi-ultrametric data, differences in All trees indicate that (i) hornworts are nested inside
X values must principally result from divergence the tracheophyte clade, lycopods rather than
(ii)
time differences. ferns plus Equisetum represent the sister group to
The bryophyte lineages examined here could seed plants, Gnetales represent the sister group
(iii)
easily be pre-Silurian; the pteridophytes no later of all other seed plants, (iv) conifers, Ginkgo, and
than Devonian; the seed-plants appearing by the cycads form the monophyletic sister group to an-
Carboniferous; the angiosperms by the Cretaceous, giosperms, and (v) monocots are basalmost in the
followed by their diversification through the Ter- angiosperms, followed by Piper. Characteristics
(iii)
—
500-5 rDNA
tiary a time range potentially spanning and are shared with the analysis of
(iv)
&
million years before present. Thus, even without a Hamby Zimmer (1992) but not with the mor
&
knowledge Crane Doyle Don
priori of precise divergence times, phological analyses of (1985),
it is
&
reasonable to approximate upper and lower X-bounds oghue(1986, 1992), Loconte Stevenson 1 990).
(
from this range and our estimates of total sequence and Nixon et al. (1994). Characteristic (i) is in
divergence. The mean rate for woody taxa (Table conflict with both morphological and molecular cla-
&
1), averaged for single lineages by halving the distic studies (Mishler Churchill, 1985; Mishler
divergence value, is approximately 1.0 x 10 -10 et al., 1994, this issue). Characteristic (ii) contrasts
nucleotide substitutions per site per year. Similarly, both with morphological data (Bremer, 1985) and
&
of
the estimates for herbaceous taxa (Wendel Al- with the chloroplast genome structural findings
&
bert, 1992) range between 2.5-3.5 x 10 10 As- Raubeson Jansen (1992) that link all tracheo-
.
suming that bryophytes and pteridophytes phytes except the lycopods, which have the ple-
into
fall
the range 1.0-3.5 x lO" 10 as well, X values are siomorphic liverwortlike) state. Characteristic
(i.e.,
(Don-
estimated to lie between 0.05-0.175 (500 My) (v) contrasts with the results of morphological
&
& 1991:
and 0.0005-0.00175 (5 My). On a four-taxon oghue Doyle, 1989; Loconte Stevenson,
tree, some combinations of these values would yield Taylor & Hickey, 992) and some rDNA (Hambv
1
spurious branch attractions (see Albert et al., 1993). & Zimmer, 1992; cf. Zimmer et al., 1989) anal-
Here, we are working with 40 taxa and a greater yses.
potential for inconsistent Penny
results (see
et
al.,
Needless to say.
Function and phylogeny.
1991).
the
can represent
not of the above observations
all
found
Data The groups
analysis. Nucleotide sequences (un- truth about land-plant history.
ambiguously aligned by sight and excluding the 30 in the nucleotide-based parsimony analysis (1 ig-
nature
5' -most which may but the
positions, incorporated only primer well reflect historical reality,
phy
information for some taxa; Table 2) were analyzed of that reality could be other than strictly
oo-
PAUP
cloc
with nearly
3.1.1 (Swofford, 1993) using the Fitch genetic. From our argument about
may r0
criterion (Fitch, 1971; cf. Albert et al., 1993) with rates and the functional constraints that P
ACCTRAN som^^
that
suppose
(accelerated transformation) optimi- duce them, reasonable to
it is
& Fl ur
zation (Farris, 1970; Swofford Maddison, 1987). or even of the branchings depicted in &
all
j^
The ra
heuristic search option was used with 100 may reflect primarily spurious similarities
We
random have as
replicates of data addition sequence, COL- than phylogenetic homologies.
LAPSE, MULPARS, TBR exa
by
and (tree bisection-re- possible constraints on r be L evolution
connection) branch-swapping. The on the in
consistency and the amino acid changes implied
^
of fbi
FIGURES 3-5. analyses
Combinable component parsimony
consensus trees summarizing the results of ^
evidence tor
as (3) nucleotide, (4) sMtrinMg, and (5) amino acid data. For (3), the strict consensus is identical: \
(•jV tn** Sintrl#> rninlnn-iLln M*m«» «l4 *_ ~-~ ' J* ,. _ 1 I .1 r ' mnmtl that TCSOl
opologies
o
CD
Conocephalum Conocephalum -Conocephalum ^
* CO
Androaeobryum Lophocolea
Lophocolea 3
Androaeobryum
Andreaeobryum Equisetum
oo
-Lycopodium
Equisetum Lophocolea
Anthoceros Selaginella
Angiopteris
n
Isoetes
Psilotum
Psilotum
3
Angiopteris
Ophioglossum Angiopteris
CD
Anthoceros
Ophioglossum
Botrychium
CO
Psilotum
Anthoceros Botrychium
Equisetum
Lycopodium Selaginella
phfogbssum
Isoetes
Isoetes
Botrychium
Lycopodium
Selaginella
r~~ Ephedra Podocarpus
Ephedra
|r~ Ephedra
Welwitschia Welwitschia
^-Gnetum
Gnetum Welwitschia
netum
Podocarpus Piper
Nymphaea Ginkgo
Taxus
Taxus
Taxodium Ceratophyllum
Taxodium
Ginkgo
Lilium
Cycas
Cycas Podocarpus
[r~
tangeria
Stangeria i— Taxus
*— Zamia
*—Zamia Taxodium
Nymphaea
Ginkgo o
Lilium CD
3-
Chloranthus
Piper Cycas o
CD
Piper
Chloranthus Stangeria
0)
Trochodendron
Drimys Zamia O
o
Caltha
Ceratophyllum Calycanthus
rimys
r~ Calycanthus Chloranthus CD
Persea Drimys Ceratophyllum 3
Eupomatia
r-Eupomatia [_j—Eupomatia
0>
^—Magnolia agnolia
*— Magnolia
Nymphaea Platanus
Persea
Q.
rL— Platanus Trochodendron Calycanthus
_
Persea
Caltha Platan us
Hamamelis
Trochodendron
Caltha
m
Hamamelis ilium <
Dillenia
a.
Hamamelis
Dillenia illenia
CD
Betula
|— Chrysolepis Chrysolepis
M— (4) (5)
(3)
8
Betu hrysolepis
la Betula
asuarina
*—Casuarina Casuarina
CJ1
542 Annals of the
Garden
Missouri Botanical
minimum
have homoplasy
branches of one of the eight equally most-parsi- if optimized as three
monious trees (Appendix As summarized in Ta- autapomorphies). Additionally, direct analysis
I). of
84%
sequences from
ble 3, over of the inferred nucleotide substi- nucleotide protein-coding genes ig-
tutions on internal branches are silent with regard nores constraints imposed both by the genetic code
to amino acid identity. The percentage of nucle- and protein function; codon positions may be both
&
amino and
otide changes incurring functionally labile intra- inter -correlated (Fitch Markowitz,
AM-
acid replacements (judged using the P 250 log- 1970; Fitch, 1986).
A may
odds matrix of Dayhoffet 1978: 352; see Table data transformation that overcome these
al.,
«
3) amount to an additional 13%. Viewed as a shortcomings stems from the early comparison of
whole, 97.5% percent of synapomorphous nu- oligonucleotide catalogues (and even whole chro-
all
cleotide changes are expected to have little or no mosomes; see Farris, 1978; Fox et al., 1980; Bre-
& DNA
effect on protein function. With a maximum of mer Bremer, 989) prior to the sequencing
1
only 2.5% of these changes incurring non-labile revolution: production of ad hoc nucleotide strings.
amino acid replacements of potential structural/ Our procedure (analogous to generating mapped
may
functional distinction (see Table 3), rbch sequences restriction site data) be outlined thus: (i) gen-
C
appear heavily burdened by forces leading to func- erate strings of random A, T, G, and content
tional conservation." 1 Thus, the challenge for land- varying randomly in size between 6 and 21 base
plant cladistics to determine how strongly func- pairs (so that a minimum and maximum of two and
is
tionally constrained variation may also reflect phy- seven codons are included), scan rbcL sequence
(ii)
logenetic patterns. data for the presence/ absence of given strings, (iii)
and
record recognitions by both base position tax-
by a
STRINGS on, treat multiple positional recognitions
(iv)
given search string separately, (v) treat all rec-
The
ideal "unit" character in phylogenetic anal-
ognitions found in two or more taxa as binary
ysis one that truly evolves as an independent
is
(sequences that
characters for cladistic analysis
unit, meaning one that independently undergoes
position are
have missing information at a string
transformations from one
condition to another that
pro-
coded Another procedure for
accordingly).
are hierarchically correlated congruent;
(i.e., cf.
sequences has
ducing string data from nucleotide
Farris, 1969) with those of other such characters.
(unpublished); se-
been developed by Farris
S.
J.
For molecular may
data, this often be the individual
number
quences are subdivided into a prespecified
nucleotide, but possibly also a contiguous length of
which
each of
DNA of string characters ("supersites"),
an
in insertion/deletion event, several non-
explain
many necessary to
assigned as states as
is
contiguous nucleotide
positions that are function-
both
method guarantees
observed variation. Farris's
RNA
ally associated (e.g., because of higher order
sequence
a complete transformation of the entire
or protein structure), a unique codon
for a func-
characters,
as well as the non-overlap of string
tionally constrained amino acid, or a whole chro-
and Ap-
below
approach used here (see
unlike the
mosome
in a karyological change. of course
It is
pendix
II).
difficult to assess such possibilities a priori, but
it sequences into
The transforming
net effect of
is nonetheless important to begin to develop meth-
more mfor-
incorporates
strings twofold:
ods examine is (i) it
to the issue empirically.
spann
codons
We mation terms of nucleotides or
(in
have thus examined some means
by which
e
decreases
and I
in a larger unit character, (ii)
the functional/phylogenetic
evidence manifest
in
sai*
of the
gains
independent
probability that
a given set of rbcL sequences might man
be represented
data
character-state are represented in
by
data forms other than
nucleotide and
positions
charac-
binary
parsimony analyses,
(although,
in
their character The
states. nucleotide indeed the
is
branch attrac i
more spurious
ters are subject to
smallest unit character rbcL
in evidence, but
it is *^
characters;
than are nonadditive multistate
not necessarily the most informative nor most con-
site to
As mapped restriction
et 1993). with
al.,
sistent. First, nonadditive optimization of multistate i^
recogni
a
of
may the probabilities of gain versus loss
characters
restrict potential topological
res- ga^-
paraile
with
string are highly asymmetrical, 1
olution a
(e.g., 4-state, nonadditive character can
Tern L
P
the least likely transformation series ( J
H*
& aL,
1983; DeBry 1985; Albert et
Slade,
ma^
may historical
contain
Therefore, string data
10
Patterns of codon usage ^
intrinsic to the primary
branch attr
much engage in
nucleotide matrix are ers less likely to
also suggestive of functional con-
para e
accumulated
straints; these are discussed (which occurs because of
in a separate paper _
(Albert,
&
Backlund &
Bremer, Penny,
in press). 1978; Hendy
Felsenstein,
cf.
Volume 81 Number 3 Albert et al. 543
,
Functional Constraints and rbcL Evidence
1994
#1
Table 3. Analysis of character support for internal branches of tree (of 8) from the nucleotide analysis.
"#
"Node" refers to the node numbers on the reference tree of Appendix I. changes" refers to the total number
of nucleotide changes optimized onto a branch. "Constant" indicates that the nucleotide site belongs in a codon
position that codes for the same amino acid throughout the entire matrix. "No change" indicates that the nucleotide
belongs in a codon position that codes for two or more amino acids throughout the matrix, but that the particular
site
change indicated at this node does not cause a change in amino acid sequence. "Labile" means that the inferred
change in amino acid due to the observed change in nucleotide sequence likely to happen by random chance or
is
PAM-250
better (according to the log-odds matrix of Dayhoff et al., 1978: 352). "Potentially nonlabile" indicates
that at least one of the potential amino acid changes inferred from a particular nucleotide position is not likely to
happen by random, but that there also are some changes in the same character that are likely to happen by random
rhance or better. "Nonlabile" means that inferred acid changes (often only one) occur at less than random chance.
all
Potentially
#
Node No
changes Constant change Labile nonlabile Nonlabile
78-77
42 22 4 8 5 3
77 76 24 13 6 4
1
76-71
27 13 9 3 2
71 70 29 19 9
1
70-42
40 24 5
11
42-41
33 26
5 1
1
70-69
42 17 16 8 1
69-66
29 21 8
66-48
34 15 13 5 1
48-44
25 10 12 2 1
44-43
29 19 8 2
48-47
15 8
7
47-46
24 14 7 3
46-45
11 4 4 3
66-65
56 34 15 7
65-64
26 13 10 3
64-63
18 11 6 1
63-54
5 2 3
54-53
4 3
1
53-51
10 3 5 1
1
51-49
9 4 2 3
51-50
8 5
2
1
53-52
4
11 5 2
63-62
16 5
11
62-61
14 6 7
1
61-59
8 2 4 2
59-58
4
17 8 5
58-57
13 6 4 3
57-56
33 20 6 7
56-55
6 3 2 1
6] 60
8 5 2 1
69 68 8 3
58 29 18
68 67
45 24 17 4
3
76 75
34 20 4
7
75 74
38 23 12 2
1
74 73
45 28 14 3
73- 72
65 43 12 9 1
2 13 11
951 529 272 126
1.37% 1.16
100.00% 55.63% 28.60% 13.25%
84 .23%
97.48%