Molecular Phylogenetics and Evolution 59 (2011) 489–509
Contents lists available at ScienceDirect
Molecular Phylogenetics and Evolution
journal homepage: www.elsevier.com/locate/ympev
A multi-locus molecular phylogeny of the Lepidoziaceae: Laying
the foundations for a stable classification
Endymion D. Cooper a,b,⇑, A. Jonathan Shaw c, Blanka Shaw c, Murray J. Henwood a,
Margaret M. Heslewood b, Elizabeth A. Brown b
a
b
c
School of Biological Sciences, University of Sydney, NSW 2006, Australia
National Herbarium of New South Wales, Mrs Macquaries Road, Sydney NSW 2000, Australia
Department of Biology, Duke University, Durham, NC 27708, USA
a r t i c l e
i n f o
Article history:
Received 10 November 2010
Revised 31 January 2011
Accepted 2 February 2011
Available online 18 February 2011
Keywords:
Lepidoziaceae
Jungermanniopsida
Molecular phylogeny
Classification
Neogrollea
Zoopsidioideae
a b s t r a c t
The Lepidoziaceae, with over 700 species in 30 genera, is one of the largest leafy liverwort families.
Despite receiving considerable attention, the composition of subfamilies and genera remains unsatisfactorily resolved. In this study, 10 loci (one nuclear 26S, two mitochondrial nad1 and rps3, and seven chloroplast atpB, psbA, psbT-psbH, rbcL, rps4, trnG and trnL-trnF) are used to estimate the phylogeny of 93
species of Lepidoziaceae. These molecular data provide strong evidence against the monophyly of three
subfamilies; Lepidozioideae, Lembidioideae and Zoopsidoideae, and seven of the 20 sampled genera;
Lepidozia, Telaranea, Kurzia, Zoopsis, Lembidium, Paracromastigum and Chloranthelia. Several robust clades
are recognised that might provide the basis for a revised subfamily circumscription including a narrower
circumscription of the Lepidozioideae and a more inclusive Lembidioideae. Neogrollea notabilis is
returned to the Lepidoziaceae and Megalembidium insulanum is placed in the Lembidioideae.
Ó 2011 Elsevier Inc. All rights reserved.
1. Introduction
The Lepidoziaceae is one of the largest families of leafy liverworts (Jungermanniales) with over 2200 published binomials, but
perhaps as few as 720 accepted species, in 30 genera (CrandallStotler et al., 2009; Müller, 2007). With a cosmopolitan distribution,
the family has its greatest species diversity in the southern hemisphere leading some to postulate a Gondwanan origin (Schuster,
2000), which is consistent with an early to mid-cretaceous origin
of the family (Heinrichs et al., 2007). Unrivalled in the breadth of
gametophyte morphological diversity, the Lepidoziaceae are united
by conserved sporophyte morphology and isophyllous gynoecial
branches (Schuster, 2000). Nevertheless, the morphological contrast between the robust leafy shoots of Bazzania and Lepidozia
and the lax-celled, pseudo-thalli of Zoopsis and Zoopsidella, was sufficient for some authors to divide the taxa amongst six families
(Evans, 1939; Fulford, 1963a, 1966, 1968; Nakai, 1943). Furthermore, the degree of gametophyte polymorphism within genera of
the Lepidoziaceae is at times greater than that exhibited by entire
families of Jungermanniales (Schuster, 2000). This morphological
diversity is accompanied by an equally broad range of ecological
⇑ Corresponding author. Address: Rm 409 Heydon-Laurence Building (A08),
School of Biological Sciences, University of Sydney, NSW 2006, Australia. Fax: +61 2
9351 4119.
E-mail address: endymion.cooper@sydney.edu.au (E.D. Cooper).
1055-7903/$ - see front matter Ó 2011 Elsevier Inc. All rights reserved.
doi:10.1016/j.ympev.2011.02.006
differentiation, with plants occurring in habitats ranging from sandy alpine soils to lowland tree trunks.
Recent treatments of the Marchantiophyta (Crandall-Stotler
and Stotler, 2000; Crandall-Stotler et al., 2009) provide a conservative precis of the Lepidoziaceae and do not propose a structure
below family level. Crandall-Stotler et al. (2009) noted in their
review of liverwort classification, based on a decade of phylogenetic analyses, that broader sampling within the Lepidoziaceae
would be necessary before a revision of its internal classification
could be presented. The most recent and complete subfamilial
classification is that of Schuster (2000), an account that largely follows Schuster (1969), but places Drucella integristipula, Neogrollea
notabilis and Protocephalozia ephemeroides in monotypic subfamilies. In the absence of robust modern phylogenetic hypotheses,
extensive taxonomic study of the family has not provided stable
subfamily, generic or subgeneric delimitations. For example, the
monotypic genus Neogrollea was recently removed from the
Lepidoziaceae to its own monotypic suborder Neogrollineae (Engel
and Braggins, 2001) and Megalembidium insulanum was transferred
from Lepidozioideae to a monotypic Megalembidioideae (Engel
and Braggins, 2005). The delimitation of genera has followed often
geographically restricted traditional morphological treatments and
as a result generic limits remain fluid (Engel and Merrill, 1994,
2004; Engel and Schuster, 2001; Evans, 1934; Grolle, 1964;
Hodgson, 1955; Schuster, 1980).
490
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Despite their significance in biological systematics, modern
phylogenetic methods have only been applied to the Lepidoziaceae
in the last decade (Engel and Merrill, 2004; Heslewood and Brown,
2007; Renner et al., 2006). A cladistic study of Telaranea, based on
32 morphological characters, led to a reinterpretation of the genus
and its synonymisation with Arachniopsis (Engel and Merrill, 2002,
2004). A second study also indicated the paraphyly of Zoopsis and
Zoopsidella, but the authors suggested that limitations of morphological cladistics might have hampered their attempt to recover an
accurate phylogeny (Renner et al., 2006).
Several molecular phylogenetic studies of liverworts have
included representatives of the Lepidoziaceae (Davis, 2004; Forrest
et al., 2006; He-Nygrén et al., 2006; Heinrichs et al., 2007; Hendry
et al., 2007) but the few taxa included therein have been sufficient
only to indicate monophyly of the family. Heslewood and Brown
(2007) provided the first explicit test of Schuster’s (2000) classification. Their analyses of Australasian representatives of the family
using two chloroplast loci (trnL-trnF and rbcL) and one mitochondrial gene (nad5) revealed extensive paraphyly of subfamilies and
genera, suggested possible polyphyly of the family, and contradicted
the works of Engel and Braggins (2001, 2005). They emphasised the
need for further taxonomic sampling, including greater representation of the Lembidioideae and morphologically reduced Telaranea
species in the molecular phylogeny (Heslewood and Brown, 2007).
In this paper, we use a large molecular dataset (10 loci) and a
broad taxonomic sample (93 species from 20 genera) to investigate
phylogenetic relationships between species belonging to the Lepidoziaceae. We aim to test the monophyly of the family and evaluate
the phylogenetic basis for removing Neogrollea to the Neogrollineae.
By testing the monophyly of subfamilies and genera we aim to provide a phylogenetic foundation for future taxonomic revisions.
2. Materials and methods
2.1. Taxonomic sample
Species were sampled haphazardly from available material in
order to encompass as much taxonomic and geographic diversity
as possible. We sampled 93 species from 20 genera, in seven subfamilies. Zoopsis leitgebbiana, Lembidium nutans, Arachniopsis major
and Hygrolembidium rigidum were represented by multiple accessions because preliminary data (E.D. Cooper, unpublished) suggested that these species are not monophyletic. We included
nine outgroup taxa based on the phylogenies of Forrest et al.
(2006) and He-Nygrén et al. (2006) (see Appendix A for complete
accession information).
2.2. Molecular methods
DNA extraction was performed using a modification of the CTAB
protocol (Doyle and Doyle, 1987) or using a DNeasy Plant Minikit
as previously described (Heslewood and Brown, 2007). One nuclear, two mitochondrial and seven chloroplast markers were sequenced (Table 1). All PCR reactions were completed under
standard conditions. Each 10 ll reaction contained 1 PCR Buffer,
0.16 mM dNTPs, 2 mM MgCl2, 0.5 lm each primer, 0.75 mg/ml BSA
and 0.2 units Taq polymerase. Genomic DNA was added as 0.5 ll to
each reaction without standardising concentration. A standard
temperature profile was used: 95 °C for 1 min, then 30 cycles of
95 °C for 1 min, 50 °C for 1 min and 72 °C for 1 min, followed by
a final extension step of 72 °C for 10 min. The same primers were
used for sequencing (Table 1).
2.3. Sequence alignment and phylogenetic analyses
Initial sequence alignments were produced using MUSCLE
(Edgar, 2004) on the European Bioinformatics Institute web server
(www.ebi.ac.uk) and then manually edited in Mesquite v2.72
(Maddison and Maddison, 2009). Coding sequences were aligned
to Marchantia polymorpha sequences from Genbank (chloroplast
genome X04465 and mitochondrial genome M68929) and translated to check for premature stop codons.
Maximum parsimony (MP) analyses were run using PAUP⁄ v4.0
(Swofford, 2002) as implemented on the University of Oslo bioportal (www.bioportal.uio.no). Branch swapping was performed using
TBR and 500 random sequence addition replicates, and the strict
Table 1
Details of markers used in this study.
a
b
c
Marker
Genome
Primer [sequence 50 –30 ]
References
nr26S
Nuclear
nad1
Mitochondrial
rps3
Mitochondrial
atpB
Chloroplast
psbA
Chloroplast
psbT-psbH
Chloroplast
rbcL
Chloroplast
rps4
Chloroplast
trnG
Chloroplast
trnL-trnF
Chloroplast
LS0F [ACCCGCTGTTTAAGCATAT]
LS12R [ATCGCCAGTTCTGCTTACCA]
Mp-nad1-1 [ATGAGAATTTATCTAATTGG]
Mp-nad1-966 [TTAAGGRAGCCATTCAAAGGCT]
rps3F1 [TCGTAGTTCAGATTCCAGTTG]
rps3R2 [CCAAAACGTACAAAATTTCG]
atpB672F [TTGATACGGGAGCYCCTCTWAGTGT]
atpE384R [GAATTCCAAACTATTCGATTAGG]
trnK2F [GACGAGTTCCGGGTTCGA]
psbA576R [TGGAATGGGTGCATAAGG]
psbA501F [TTTCTCAGACGGTATGCC]
trnHR [GAACGACGGGAATTGAAC]
psbT [ATGGAAGCWTTAGTWTATACWTT]
psbH [GTHCCCCARCCDGGDRVHACTTTWCC]
mtrnRR [GCTCTAATCCACTGAGCTAC]
nm34 [GTTGTTGGATTTAAAGCTGGTGTT]
rbcL1 [GGGATTTATGTCACCACAAACAGA]
rbcL2 [GATCTCCTTCCATACTTCACAAGC]
rps5 [ATGTCCCGTTATCGAGGACCT]
trnas [TACCGAGGGTTCGAATC]
trnGF [ACCCGCATCGTTAGCTTG]
trnGR [GCGGGTATAGTTTAGTGG]
trnF [ATTTGAACTGGTGACACGAG]
trnC [CGAAATCGGTAGACGCTACG]
Shaw (2000)
Shaw (2000)
Dombrovska and Qiu (2004)
Dombrovska and Qiu (2004)
This studya
This studya
Forrest and Crandall-Stotler (2004)b
Forrest and Crandall-Stotler (2004)b
Forrest and Crandall-Stotler (2004)c
Forrest and Crandall-Stotler (2004)c
Forrest and Crandall-Stotler (2004)c
Forrest and Crandall-Stotler (2004)c
Krellwitz et al. (2001)
Krellwitz et al. (2001)
Cox et al. (2000)
Cox et al. (2000)
Gadek and Quinn (1993)
Gadek and Quinn (1993)
Nadot et al. (1994)
Souza-Chies et al. (1997)
Pacak and Szweykowska-Kuliñska (2000)
Pacak and Szweykowska-Kuliñska (2000)
Taberlet et al. (1991)
Taberlet et al. (1991)
Designed for the Liverwort Tree of Life (LiToL: www.biology.duke.edu/bryology/LiToL).
Source given as P. Wolf (http://bioweb.usu.edu.wolf/atpB%20primer%20map.htm).
Source given as C. Cox, pers. comm.
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
consensus of most parsimonious trees was computed. Autapomorphic and constant characters were excluded prior to the analysis.
Clade support was assessed by conducting 10,000 bootstrap replicates with five random sequence addition replicates per bootstrap
replicate. Clades are considered supported if found in P70% of the
bootstrap replicates and strongly supported if found in P90% of
replicates.
Rapid maximum likelihood (ML) analyses were run using RAxML v7.2.6 (Stamatakis, 2006) provided on the CIPRES portal (Miller
et al., 2010). Analyses used the GTRGAMMA model and 10,000
bootstrap replicates were run. Clade support is assessed using
the same thresholds as for maximum parsimony bootstrapping.
Prior to Bayesian analysis, model selection was completed using
jModeltest (Posada, 2008). The highest ranked model according to
the Akaike information criterion (AIC, Akaike, 1973; Burnham and
Anderson, 2004) was used for Bayesian analyses. Where the highest ranked model was not the GTR + C + I model, analyses were
also performed with the GTR + C + I model and their performance
compared using Bayes Factors (Kass and Raftery, 1995).
Bayesian inference (BI) was run using a hybrid version (Pratas
et al., 2009) of Mr. Bayes (Huelsenbeck and Ronquist, 2001) as
implemented on the CIPRES Portal (Miller et al., 2010). Two independent metropolis coupled MCMC runs were run for five million
generations, using one heated and three cold chains, and sampling
every 1000 generations. After plotting log likelihood values and
calculating the standard deviation of split frequencies to check
convergence, the first 1001 samples were discarded as burnin.
The 10 loci were analysed separately and then concatenated by
genome. A concatenated 10 locus dataset was also analysed. For BI
analyses of concatenated datasets, a homogeneous analysis (single
partition) using the GTR + C + I model and a heterogeneous analysis (partitioned by marker, using the best model per partition)
were run. Clades with a posterior probability P0.9 are considered
supported and those with posterior probability P0.95 are considered strongly supported.
3. Results
3.1. Sampling
We sampled 93 species, representing seven subfamilies and 20
genera, for an average of eight out of ten markers each. The number
of sequences per marker ranged from 66 (atpB) to 89 (psbA). A total
of 784 new sequences were generated for this study (Appendix A).
3.2. Model selection
The AIC universally preferred the general time reversible model
(GTR) with gamma distributed rates and, in all but two cases, a
proportion of invariant sites (Table 2). For rps3 the GTR + C model
was preferred, but the DAIC between it and the next best GTR +
C + I model was within the interval of strongly supported models
(Burnham and Anderson, 2004). For trnG, the GTR + C + I model
had considerably less support than the GTR + G model (DAIC 7.98)
but was still within the approximate cut off for supported models
of 10 AIC units (Burnham and Anderson, 2004). Despite this,
analyses under the GTR + C + I model resulted in better marginal
likelihoods for these markers than the GTR + C model. For the combined analyses, partitioning by marker always improved model fit.
3.3. Phylogenetic analyses
Support values from individual BI, ML and MP analyses of the 10
loci are summarised in Table 2. Maximum likelihood and MP boot-
491
strap percentages for analyses of concatenated datasets are shown
on the Bayesian topologies (Figs. 1–3 and 5). All trees are available
as online Supplementary material (Appendix B).
3.3.1. Nuclear data
The single nuclear marker (26S) was the least variable of the ten
regions used. Of 1009 aligned base pairs, 77 (8%) were parsimony
informative (Table 2). Sequences were available for 76 of the 98
ingroup accessions. Little incongruence is observed between the
three methods of analysis, which yield largely unresolved phylogenetic estimates with few supported nodes (Fig. 1). The family is
strongly supported in MP, ML and BI analyses of 26S (pp 1,
ML-BS 100, MP-BS 100) and is separated by a long branch from
the outgroup (phylogram not shown). Additionally, the family is
characterised by a four base pair deletion at position 662 and a
three base pair insertion at position 917. Four species of Zoopsidoideae are resolved as sister to the rest of the family at node B, which
is supported in BI and ML analyses (pp 0.96, ML-BS 77). An unsupported clade comprised of Lepidozia and some Telaranea species is
recovered in all analyses. Eight out of nine Bazzania species are
consistently resolved as a clade with strong support in BI analysis
(pp 0.95). The two Paracromastigum species are sisters (pp 0.99), as
are the two Pseudocephalozia species (pp 1, ML-BS 99, MP-BS 99).
3.3.2. Mitochondrial data
The concatenated mitochondrial dataset had 89 ingroup accessions of which 70 had data for both nad5 and rps3. We were unable
to obtain nad1 sequences for Telaranea meridiana and T. pulcherrima var. mooreana. The concatenated alignment had 2119 positions of which 246 (12%) were parsimony informative. The
resolution, support values and topology are consistent across BI,
ML and MP analyses, and are largely congruent with topologies
from the individual marker analyses (Fig. 2, Table 2). Monophyly
of the family is supported (pp 0.92, ML-BS 94, MP-BS 90). Node
B, which places Zoopsids I and II sister to the remainder of the
family, has weak support (pp 0.9). Bazzania (pp 0.99, ML-BS 89,
MP-BS 80) and Acromastigum (pp 0.96) are always recovered as
sister clades, but are separated by relatively long branches (phylogram not shown). The Lembidioid/Kurzia clade is consistently
recovered without support, and Pseudocephalozia is separated from
the remainder of this clade (node iv) by a long branch. The Lepidozia clade is also recovered without support but has minimal internal
resolution. Unlike the individual analyses, the combined mitochondrial topologies always recover an unsupported monophyletic
Zoopsids III. Relationships amongst these clades are unresolved, as
are the relationships of Paracromastigum, Hyalolepidozia, Drucella
and Neogrollea.
3.3.3. Chloroplast data
The combined chloroplast alignment had 6569 positions of
which 1951 (30%) were parsimony informative. A total of 552
sequences for 98 ingroup accessions represents a 80% complete
sequence set. The Lepidoziaceae are strongly supported (pp 0.99,
ML-BS 100, MP-BS 99) and several early divergent nodes are resolved and supported in Bayesian analyses (nodes A–E, Fig. 3).
Six clades corresponding approximately to current generic concepts are recovered, Hygrolembidium, Pseudocephalozia, Bazzania,
Acromastigum, Kurzia, and Lepidozia with varying support (Table
2). Zoopsis and Telaranea are dispersed throughout the tree, and
three clades containing these genera are labelled in Fig. 3 (Zoopsids
I–III). Three clades of Telaranea (i.e. Telaranea I–III) form consecutive sister relationships with Lepidozia. The monotypic genera
Neogrollea, Psiloclada, Sprucella, Megalembidium and Isolembidium
have supported relationships with other taxa. Drucella, however,
occupies a phylogenetically isolated position.
492
Table 2
Summarised support values for major clades of interest from all individual and combined analyses (pp/ML-BS/MP-BS). Clade names follow Figs. 1–5. The aligned length, proportion of parsimony informative (PI) sites and best fit model
(the number of partitions are indicated) are shown for each dataset. Where insufficient representation is available for a particular clade, the support values are labelled not available (n/a). The following abbreviations are used when
nodes are unsupported: ns = recovered but not supported, nr = not recovered, cn = topological incongruence not supported, and cs = topological incongruence with support.
nr26S
nad1
rps3
atpB
psbA
psbT-psbH
rbcL
rps4
trnG
trnL-trnF
770
33%
GTR + C + I
Concatenated
mitochondrial
2119
12%
2 GTR + C + I
Concatenated
chloroplast
6569
30%
7 GTR + C + I
Total evidence
(all markers)
9697
23%
10 GTR + C + I
Aligned length
PI sites
Best model
1009
8%
GTR + C + I
943
12%
GTR + C + I
1176
12%
GTR + C
1143
27%
GTR + C + I
1151
26%
GTR + C + I
541
26%
GTR + C + I
1386
26%
GTR + C + I
612
41%
GTR + C + I
966
42%
GTR + C
Lepidoziaceae
Node A
Node B
Node C
Node D
Node E
Node F
Bazzanioideae
Lembidioid/Kurzia clade
Lepidozia clade
Zoopsids I
Zoopsids II
Zoopsids III
Paracromastigum clade
Node i
Acromastigum
Bazzania
Pseudocephalozia
Lembidioids
Node ii.
Node iii.
Kurzia
Node iv.
Node v.
Telaranea II
Node vi.
Lepidozia
Telaranea III
Node vii.
1/100/100
cn/cn/cn
0.96/77/ns
cn/cn/nr
cn/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
nr/ns/nr
ns/ns/ns
n/a
nr/nr/cn
cs/cn/cn
n/a
n/a
cs/cn/cn
nr/cn/nr
1/99/99
nr/cn/nr
nr/cn/nr
nr/cn/nr
nr/cn/nr
nr/cn/nr
nr/cn/nr
cn/cn/nr
cn/cn/nr
cn/cn/cn
cn/cn/cn
cn/cn/cn
1/97/89
nr/cn/cn
nr/ns/cn
nr/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
nr/cn/cn
1/ns/ns
ns/ns/ns
1/97/98
nr/cn/nr
nr/ns/cn
cn/cn/cn
0.93/76/70
ns/ns/nr
ns/ns/nr
1/100/ns
nr/ns/nr
ns/80/nr
0.99/ns/ns
nr/cn/cn
0.96/ns/ns
n/a
cn/cn/nr
nr/ns/nr
cn/ns/nr
cn/cn/nr
cn/ns/ns
1/100/99
cn/cn/nr
0.94/ns/ns
cn/cn/nr
cn/cn/nr
cn/cn/nr
cn/cn/nr
0.93/ns/ns
1/94/96
ns/ns/nr
1/100/100
1/100/100
cn/cn/nr
cn/cn/nr
1/99/99
1/86/76
0.91/81/ns
1/100/100
ns/ns/ns
0.98/98/ns
1/92/89
ns/ns/ns
1/100/100
n/a
ns/ns/nr
0.95/ns/ns
ns/ns/ns
n/a
1/87/81
1/98/94
n/a
n/a
ns/ns/nr
cn/cn/nr
cn/cn/nr
nr/cn/nr
ns/ns/nr
1/100/100
1/99/100
n/a
n/a
cn/cn/nr
1/75/ns
1/100/100
1/96/89
1/100/99
1/100/100
1/85/76
1/94/97
1/99/98
0.96/ns/nr
0.99/79/ns
0.92/85/nr
0.99/92/77
1/98/95
ns/ns/nr
n/a
1/99/96
1/89/ns
cn/ns/ns
cn/cn/cn
cn/cn/cn
cn/cn/nr
cs/cn/nr
cn/cn/nr
ns/ns/nr
1/87/ns
1/96/82
0.93/ns/ns
0.99/ns/ns
cs/cn/nr
cn/cn/nr
1/98/89
1/98/89
1/91/94
1/100/100
0.99/90/87
1/92/92
cn/ns/nr
cs/cn/cn
0.99/78/nr
nr/ns/nr
0.98/74/ns
0.9/ns/nr
cn/cn/cn
cn/cn/nr
ns/ns/ns
0.99/74/ns
nr/ns/cn
ns/ns/cn
nr/ns/cn
nr/ns/cn
nr/ns/cn
nr/cn/cn
nr/ns/nr
1/92/87
1/76/nr
0.99/75/ns
1/97/93
nr/ns/ns
nr/cn/cn
1/93/93
1/76/ns
0.94/ns/nr
1/100/100
ns/cn/nr
1/99/98
nr/cn/nr
nr/ns/nr
nr/ns/nr
0.94/ns/nr
0.96/ns/ns
nr/ns/nr
ns/ns/nr
n/a
1/78/75
1/96/75
cs/cn/ns
cs/cn/nr
cs/cn/cn
cs/cn/nr
cs/cn/nr
nr/cn/cn
ns/cn/nr
1/98/86
1/98/91
1/100/100
n/a
1/71/ns
nr/cn/cn
1/100/100
1/96/84
1/100/100
1/100/100
0.97/ns/ns
1/81/83
1/93/90
nr/cn/ns
0.97/cn/nr
0.98/83/75
nr/cn/cn
ns/ns/ns
0.99/78/79
ns/ns/ns
1/90/80
1/99/98
nr/cn/nr
0.91/ns/ns
cn/cn/cn/
nr/cn/nr
nr/cn/nr
cn/cn/cn
cn/cn/cn
1/88/76
1/78/85
n/a
1/100/100
nr/ns/nr
0.93/ns/nr
1/100/100
0.98/ns/nr
1/99/100
1/100/100
1/92/95
1/99/99
1/91/91
nr/ns/nr
0.99/76/81
n/a
1/89/ns
nr/cn/cn
nr/cn/cn
n/a
1/99/97
1/91/84
cn/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
0.91/ns/nr
1/97/98
1/100/98
1/100/97
1/98/96
0.97/ns/nr
cn/cn/cn
1/100/99
1/99/96
1/99/100
1/100/100
0.99/75/nr
1/98/97
0.99/74/70
nr/cn/cn
ns/cn/ns
1/99/99
1/99/96
1/100/97
ns/ns/ns
cn/cs/cn
1/98/95
1/99/97
nr/cn/ns/
0.95/ns/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
cn/cn/cn
nr/cn/cn
1/95/86
1/94/93
1/96/86
0.99/86/87
0.99/71/ns
cn/cn/cn
1/99/99
1/95/82
1/100/100
1/100/100
1/85/80
1/89/93
1/99/94
cn/cn/nr
ns/72/ns
cn/cn/nr
cs/cn/cn
cn/cn/nr
cn/cn/nr
cn/cn/nr
1/98/95
0.92/94/90
nr/cn/nr
0.9/ns/ns
nr/cn/ns
nr/cn/cn
nr/cn/cn
nr/cn/cn
ns/ns/ns
ns/ns/ns
ns/ns/ns
99/96/99
nr/cn/nr
ns/ns/ns
nr/cn/cn
1/98/98
0.96/ns/ns
0.99/89/80
1/99/100
0.95/75/72
0.99/93/82
1/91/88
nr/cn/nr
ns/ns/ns
na
cn/cn/nr
cn/cn/nr
cn/cn/nr
cn/cn/nr
ns/ns/nr
0.99/100/99
ns/ns/ns
0.99/ns/ns
0.91/ns/ns
0.97/ns/cn
0.97/ns/cn
nr/nr/ns
0.99/92/ns
0.99/100/100
0.99/100/100
0.99/100/100
0.99/100/100
0.99/92/ns
0.99/86/ns
1/100/100
1/100/100
1/100/100
1/100/100
1/100/100
1/100/100
1/100/100
cn/cn/cn
0.99/100/100
0.99/100/100
0.99/100/97
1/100/99
0.99/84/86
ns/ns/nr
1/100/100
0.99/100/100
nr/cn/75
0.99/96/76
ns/ns/ns
ns/ns/ns
ns/ns/cn
ns/cn/ns
0.99/95/ns
0.99/100/100
0.99/100/100
1/100/100
1/100/100
0.98/93/70
0.99/83/ns
1/100/100
1/100/100
0.99/100/100
1/100/100
1/100/100
1/100/100
1/100/100
nr/ns/nr
0.99/100/100
0.99/100/99
0.99/99/95
0.99/100/100
0.99/85/86
ns/ns/nr
1/100/100
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Alignment
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
493
Fig. 1. Majority rule consensus tree from Bayesian analysis of the nuclear 26S dataset. Numbers above branches are posterior probabilities >0.9, maximum likelihood
bootstraps >70%, and maximum parsimony bootstraps >70% (pp/ML/MP). Node B is discussed in the text and support values for all analyses given in Table 2.
494
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Fig. 2. Majority rule consensus tree from Bayesian analysis of the concatenated mitochondrial dataset partitioned by marker. Numbers above branches are posterior
probabilities >0.9, maximum likelihood bootstraps >70%, and maximum parsimony bootstraps >70% (pp/ML/MP). Nodes B and (i)–(iv) are discussed in the text and support
values for all analyses presented in Table 2.
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
495
Fig. 3. Majority rule consensus tree from Bayesian analysis of the concatenated chloroplast dataset partitioned by marker. Numbers above branches are posterior
probabilities >0.9, maximum likelihood bootstraps >70%, and maximum parsimony bootstraps >70% (pp/ML/MP). Nodes A–E and (i)–(vii) are discussed in the text and
support values are given in Table 2.
496
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Fig. 4. Majority rule consensus tree from Bayesian analysis of the concatenated chloroplast dataset partitioned by marker. Branch lengths are drawn proportional to the
average number of substitutions per site. The topology is identical to that shown in Fig. 3.
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
497
Fig. 5. Majority rule consensus tree from Bayesian analysis of the concatenated 10 locus (total evidence) dataset partitioned by marker. Numbers above branches are
posterior probabilities >0.9, maximum likelihood bootstraps >70%, and maximum parsimony bootstraps >70% (pp/ML/MP). Nodes B–F and (i)–(vii) are discussed in the text.
498
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Three large clades frequently recovered in individual analyses,
and strongly supported in the combined analyses, are illustrated
in Fig. 3. These are, the clade containing Bazzania and Acromastigum (Bazzanioideae; pp 0.99, ML-BS 92), the clade containing the
lembidioid species, Kurzia, and Pseudocephalozia (Lembidioid/Kurzia clade; pp 0.99, ML-BS 100, MP-BS 100), and the clade containing Lepidozia and some Telaranea species (Lepidozia clade; pp 0.99,
ML-BS 100, MP-BS 100). Branch lengths corresponding to early
divergences (i.e. subtending nodes A–E) are relatively short, as is
the branch that subtends the Bazzanioideae and those that separate Telaranea I–III and Lepidozia (Fig. 4).
3.3.4. Total evidence
The 10 locus, three genome, concatenated dataset had 778
sequences for 98 ingroup accessions (79%) and a total of 9697
alignment positions of which 2274 (23%) were parsimony informative. Of the 2274 parsimony informative characters, 1951 (86%)
were contributed by the seven chloroplast loci. The Lepidoziaceae
are strongly supported (pp 0.99, ML-BS 100, MP-BS 100; Fig. 5).
Maximum parsimony analysis provides support for node A, which
places Zoopsids I sister to the remainder of the Lepidoziaceae, but
this node is not recovered in BI analysis (MP-BS 75). Node A, however, is contradicted by an unsupported sister relationship
between Zoopsids I and II in the ML analysis. The Paracromastigum
clade is an unsupported sister to the Bazzanioideae in BI and MP
analyses (node F) but this is incongruent with the ML topology,
in which the Paracromastigum clade is sister to the other clades
resolved at node C. With the exception of nodes A and F, the topology and support values are largely the same as the chloroplast tree.
4. Discussion
Biological classification aims to facilitate communication. In
order to serve this aim well, classification should be maximally
predictive. A widely held belief, frequently applied in practise, is
that maximally predictive classifications are those based on the
theory of descent with modification. In addition, communication
is best served by stability of classification. We take the view that
predictive content and stability are promoted by naming monophyletic groups such that the least nomenclatural change is required. By monophyletic we mean groups that contain all, and
only, descendants of a common ancestor (monocladistic, sensu
Podani, 2010).
4.1. Incongruence between the molecular phylogeny and the
subfamilial and generic classification of the Lepidoziaceae
The currently accepted broad definition of the Lepidoziaceae
(Schuster, 2000) is corroborated by the monophyly of the family
in individual and concatenated analyses of ten molecular markers
across three genomic compartments. The strong evidence for a
monophyletic Lepidoziaceae, gives some support to Schuster’s
(1969) choice of morphological characters as reliable predictors
of phylogeny, i.e. a wide array of branching modes including general retention of lateral-terminal and ventral-intercalary branches;
distinct, usually large, underleaves with rhizoids restricted to the
basal sector; strictly isophyllous gynoecial branches of determinate length; long, usually slender, trigonous perianths; flagelliform/stoloniferous branches; sporophytes with the seta having a
fixed number of cortical cell rows (usually 8 or 16 ± 1) and numerous rows of much smaller, medullary cells; and a capsule wall that
undergoes a two-phase development.
The molecular phylogeny strongly supports placement of N.
notabilis within the Lepidoziaceae. Engel and Braggins (2001), pro-
viding the first description of its sporophyte, considered Neogrollea
morphologically distinct from the remainder of the Lepidoziaceae
and erected a monotypic family Neogrolleaceae. They listed nine
morphological characters which they consider preclude placing
the new family in the Lepidoziineae. Only one of these characters,
baculate spore ornamentation, strictly distinguish Neogrollea from
the Lepidoziaceae. Of the remaining characters, Neogrollea is
simply at the extreme end of the range or variation seen in the
Lepidoziaceae. Engel and Braggins (2001) are incorrect in their
statement that reddish pigments are not produced in the Lepidoziaceae. Several species of Paracromastigum and Hyalolepidozia
microphylla produce reddish to brown pigments. Indeed, the morphology of Neogrollea fits within the diagnostic criteria given by
Schuster (1969), suggesting that focussing attention on perceived
differences in typical expressions of character states, rather than
similarity in general morphological trends, might obscure phylogenetic relatedness. Given that Neogrollea shares character similarity
with several distantly related members of the Lepidoziaceae, we
hypothesise that a pleisiomorphic morphology is retained in this
species.
In contrast to the strong support for a monophyletic Lepidoziaceae, is the lack of support, and often evidence against, the monophyly of several subfamilies and genera. Of the five polytypic
subfamilies, only Bazzanioideae are monophyletic. Lembidioideae
are paraphyletic by the exclusion of Megalembidium and Kurzia
dendroides. Lepidozioideae and Zoopsidoideae are polyphyletic.
Neither Micropterygium nor Mytilopsis were sampled and monophyly of Micropterygioideae remains untested. Furthermore, the
subfamily status of two of the three sampled monotypic genera,
Neogrollea and Megalembidium, is brought into question.
Seven of the 20 genera sampled are not monophyletic. The
monophyly of five genera, Sprucella, Hygrolembidium, Amazoopsis,
Hyalolepidozia and Zoopsidella, remains untested as only one representative of each was sampled. Monophyly is supported for only
three genera, Acromastigum, Bazzania and Pseudocephalozia. The
five remaining genera, Psiloclada, Drucella, Neogrollea, Isolembidium
and Megalembidium, are monotypic (Engel and Glenny, 2008;
Schuster, 2000).
4.2. Unresolved early divergence
Despite a dataset containing over 2000 parsimony informative
sites, only the Bayesian analysis of the concatenated chloroplast
data provides support for early divergent relationships. It is possible that resolving the sequence of early divergence is hampered by
missing lineages. However, phylograms show a clustering of short
branches around these basal nodes and in analyses of individual
markers alternative, unsupported arrangements were recovered
(Appendix B Supplementary figures). Thus, an alternative explanation is that this pattern of incongruent but unsupported gene trees,
with relatively short basal branch lengths is the result of rapid
divergence of main lineages. Unresolved basal relationships are
also found in ferns (Schneider et al., 2006), mosses (Buck et al.,
2000) and other liverworts (Hentschel et al., 2009; Wilson et al.,
2007a). Few attempts have been made to date liverwort divergence
but rapid establishment of main lineages of Lejeuneaceae in the
cretaceous (Wilson et al., 2007b) is consistent with the hypothesis
that spore producing plants diversified following, or concurrently
with, the establishment of angiosperm forests (Newton et al.,
2007; Schneider et al., 2004). The chronogram of Heinrichs et al.
(2007) is consistent with rapid basal diversification in Lepidoziaceae at this time. The extent of this pattern needs to be empirically
tested and the conceptual basis for reflecting such information in
classification schemes needs consideration.
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
4.3. Zoopsids I and II
The entire suite of gametophyte morphologies observed in the
Jungermanniales can be found within the Zoopsidioideae (Schuster, 2000). Given this degree of polymorphism, it is not surprising
that this subfamily is polyphyletic. Zoopsids I and Zoopsids II, are
resolved sister to the remainder of the family (node B), whereas
Zoopsids III, is sister to the Lembidioid/Kurzia clade. Zoopsids I contains Telaranea major, Zoopsidella caledonica and Zoopsis ceratophylla. Little can be concluded about the relationships of Zoopsidella
because only Z. caledonica was included in this analysis and morphological data indicate a closer relationship to Z. ceratophylla than
to other Zoopsidella species (Renner et al., 2006). In resolving T. major with species of Zoopsis, Heslewood and Brown (2007) took this
as evidence supporting Schuster’s (2000) concept of Arachniopsis
and Telaranea. In doing so they emphasised the need for further
representation of morphologically reduced Telaranea species in
the molecular phylogeny. Our results place these species in three
different clades, namely Zoopsids I, the Lembidioid/Kurzia clade,
and the Zoopsids III, lending support to the suggestion that morphological convergence is at play (Heslewood and Brown, 2007).
These genera are discussed further under the relevant clades.
The Zoopsids II clade is comprised of Zoopsis argentea, Z. leitgebiana, and Z. macrophylla. The later two species are similar in their
morphology, sharing succubous leaf insertion and characteristically asymmetric bilobed leaves. However, their morphological
connection with Z. argentea, which is more similar to Z. liukiuensis
(Schuster, 2000), is unclear and it is separated from the rest of the
clade by a long branch. In our analyses, and the earlier analyses of
Heslewood and Brown (2007), Z. liukiuensis is resolved sister to Z.
setulosa (Zoopsid III clade in this study).
The unsupported early divergent node A separates the Zoopsids
I and Zoopsids II clades. However, in several individual marker
analyses these clades are either resolved as a polytomy or as sister
taxa. Consequently, a sister relationship between these two clades
cannot be ruled out. Although Z. argentea, the nomenclatural type
of Zoopsis, is placed in Zoopsids II, further molecular sampling is required before clade membership can be determined and an appropriate taxonomic treatment provided.
4.4. Drucella integristipula
The monotypic Drucella is placed in an isolated position
amongst the early diverging nodes of the family. Only in BI analysis
of rbcL was a supported placement sister to Zoopsids I recovered
(pp 0.98), but a conflicting relationship with Neogrollea is weakly
supported in BI analysis of psbA (pp 0.9). Neither placement reflects previous taxonomic treatments of D. integristipula, which
was first described as a Lepidozia (Stephani, 1909) and was until recently retained in the Lepidozioideae. The phylogenetic isolation of
Drucella was anticipated by Schuster (1980) on the basis of gametophyte morphology and this notion gained further support when
sporophytes were discovered (Boesen, 1982). In contrast to the
molecular analysis of Heslewood and Brown (2007), we consistently resolved Drucella within the family. Our phylogeny supports
retention of a monotypic subfamily for this taxon.
4.5. Paracromastigum clade
Paracromastigum, currently assigned to the Zoopsidoideae, has a
complex taxonomic history (Fulford, 1968; Fulford and Taylor,
1961; Schuster, 2000; Schuster and Engel, 1996). We recover two
species of Paracromastigum in a clade with H. microphylla, Chloranthelia denticulata and N. notabilis. This clade is not recovered in the
analyses of nuclear and concatenated mitochondrial datasets, but
499
it is supported in the analysis of chloroplast and total evidence
datasets. A subclade containing Paracromastigum microstipum, H.
microphylla and C. denticulata is always supported, confirming the
conclusion of Heslewood and Brown (2007) that it is unlikely that
C. denticulata belongs with the lembidioids. Paracromastigum, Hyalolepidozia and Chloranthelia bergrennii were not included in their
study, and they resolved a sister relationship with Z. leitgebbiana.
Our analyses do not support an association between C. denticulata
and Z. leitgebbiana, and place Chloranthelia bergrenii within the lembidioid clade. Several authors have speculated that C. bergrenii,
with its strongly lembidioid appearance, would show different
phylogenetic affinities to those of C. denticulata, the type of the diatypic genus (Engel and Glenny, 2008; Heslewood and Brown, 2007;
Schuster, 2000; Schuster and Engel, 1987).
The placement of H. microphylla sister to P. microstipum supports
Schuster’s (2000) suggestion that Hyalolepidozia should be reduced
to a subgenus of Paracromastigum. However, the type species of the
diatypic genus, Hyalolepidozia bicuspidata, was not sampled. Morphologically these species are distinguished from Paracromastigum
by their bifid leaves and their highly reduced stems, which consist
of only six cortical cell rows (Schuster, 2000). Similar reduction in
leaf and stem size occurs in unrelated lineages of Lepidoziaceae
and does not always indicate phylogenetic relationships. Although
the phylogeny supports transfer of H. microphylla to Paracromastigum, the generic status of Hyalolepidozia remains untested.
The monotypic Neogrollea was recently removed from the Lepidoziaceae and placed in a monotypic suborder, Neogrollineae (Engel and Braggins, 2001), but phylogenies based on molecular data
(Hendry et al., 2007; Heslewood and Brown, 2007) have consistently placed it within the Lepidoziaceae. Schuster (1972) placed
it tentatively in the Lembidioideae but recently moved it to its
own subfamily and suggested possible links to the Bazzanioideae
(Schuster, 2000). In the analyses of the concatenated total evidence
dataset Neogrollea is sister to the rest of the Paracromastigum clade,
a position that better reflects its morphological uniqueness than
placement within Paracromastigum as suggested by the chloroplast
analyses. The two Paracromastigum species and H. microphylla are
all from New Zealand and inclusion of south American representatives would be desirable. The phylogeny supports transfer of C.
denticulata, and H. microphylla to Paracromastigum and suggests
subfamily status for the clade comprised of Paracromastigum and
Neogrollea would be appropriate.
4.6. Bazzanioideae
Morphologically the best defined subfamily, Bazzanioideae are
monophyletic but with little support. A close relationship between
Bazzania and Acromastigum has long been hypothesised based on
shared pseudo-dichotomous terminal branching and formation of
frequent geotropic, flagelliform ventral branches (Evans, 1934,
1939; Fulford, 1963b; Schuster, 2000).
Bazzania is a genus of between 100 (Schuster, 2000) and 450
species (Stephani, 1909) and its internal classification is widely
viewed as unsatisfactory (Engel and Glenny, 2008; Meagher,
2008; Schuster, 1969, 2000). The placement of Bazzania nitida sister to the rest of the genus is in agreement with Heslewood and
Brown (2007) who resolve two other members of sect. Vittatae, B.
monilinervis and B. tayloriana, in this position. Whilst this indicates
that there might be support for some morphologically defined subgeneric groupings, sampling is currently insufficient to evaluate
the competing hypotheses (Fulford, 1963a; Schuster, 2000). Acromastigum exile from the phylogenies of Davis (2004) and Forrest
et al. (2006) was included in the analyses. It is consistently nested
in the Bazzania clade (Bazzania sp. Mb28). Following examination of
the voucher we are of the opinion that the specimen, which has
500
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
shallowly tridentate falcate leaves, ventral intercalary stolons and
lacks ventral terminal (Acromastigum-type) branches, is a Bazzania.
Acromastigum is a smaller genus and our resolution of three
clades agrees with the results of Heslewood and Brown (2007)
and has some similarities with the current subgeneric classification. We resolve the elobate nearly isomorphic A. stellare and A.
caevifolium from subg. Acromastigum as sister to the remainder of
the genus. A clade of small, wiry, pigmented species, A. mooreanum,
A. anisostomum and A. furcatifolium, from subg. Inaequilaterae, and
the small wiry A. filum from subg. Subcomplicatae, form an unsupported clade. The third clade consists of Bazzania-like species from
subgenus Inaequilaterae. The phylogeny indicates that morphologically circumscribed subgeneric groups exist within this genus.
4.7. Zoopsids III
The Zoopsids III clade is comprised of Psiloclada clandestina,
Amazoopsis diplopoda, two species of Zoopsis, and four species of
Telaranea. These small plants share reduced stems and leaves, often
without a disk present, and a preference for sheltered microhabitats (Schuster, 2000). Of the four Telaranea species, T. diacantha
and T. herzogii were previously assigned to Arachniopsis, which is
currently considered a synonym of Telaranea (Engel and Merrill,
2002, 2004). Telaranea maorensis was recently described (Pócs,
2006) and closely resembles T. pectin, also previously an Arachniopsis. The fourth, T. pseudozoopsis, has not been previously assigned to
the genus Arachniopsis.
It is possible that the nomenclatural types of Telaranea and Arachniopsis belong within the Zoopsids III clade and not with the bulk of
Telaranea species, here placed with Lepidozia. The type of Telaranea,
Telaranea chaetophylla, has been the subject of persistent nomenclatural confusion; sometimes considered a synonym of Telaranea nematodes (e.g. Howe, 1902; Schuster, 1969, 2000) or a synonym of
Telaranea (Arachniopsis) sejuncta (Fulford, 1963b), but on recent
revision it was recognised as a distinct species (Engel and Merrill,
2004). It is morphologically similar to T. herzogii, which is placed
in the Zoopsids III. Telaranea coactilis, the type of Arachniopsis, was
considered a synonym of Telaranea (Arachniopsis) diacantha (Pócs,
1984). Although, it is morphologically similar to T. diacantha, Engel
and Merrill (2004) recognise T. coactilis as a separate species. We
were unable to obtain sequence data for either T. chaetophylla or
T. coactilis and cannot confirm their phylogenetic placement. Nevertheless, it is clear from the current phylogeny that Telaranea species
with reduced stem and leaf anatomy exhibit a convergent morphology and more complete taxonomic sampling will be necessary before taxonomic changes are made.
4.8. Lembidioid/Kurzia clade
The Lembidioid/Kurzia clade is comprised of Kurzia, some
Telaranea species, the Lembidioideae, Megalembidium and Pseudocephalozia. A subclade at node iv, containing taxa of the Lembidioideae and Kurzia was recovered by Heslewood and Brown
(2007), and is strongly supported in our analyses. Within this clade
a further subclade, which contains species mostly referable to
Lembidioideae, is strongly supported. However, two additional
species are resolved within this clade, M. insulanum (Megalembidioideae) and K. dendroides. The placement of M. insulanum with the
lembidioids is in contradiction to its placement in the Lepidozioideae (Schuster, 2000) and its placement in a monotypic subfamily
(Engel and Braggins, 2005). The molecular data presented here provide very strong support for a sister relationship with Isolembidium.
The association of these elements, namely Megalembidium, the
lembidioids, and Kurzia, is hinted at in the controversy surrounding
K. dendroides which has been variously placed in Lembidium, Kurzia
or Dendrolembidium (Heslewood and Brown, 2007; Schuster, 2000).
The results presented here clearly show that this species is not a
Kurzia and provide support for recognition of a separate genus.
However, the paraphyly of Lembidium indicates that generic limits
need to be revisited in this clade. The placement of C. bergrenii
within the Lembidioid/Kurzia clade demonstrates that it has no
phylogenetic affinity with the type, C. denticulata, of the diatypic
genus and perhaps should be returned to Lembidium (Herzog,
1952; Schuster and Engel, 1987). However, in analyses of concatenated mitochondrial and total evidence datasets, C. bergrenii is sister to Hygrolembidium with which it shares a lack of terminal
branching. Furthermore, Lembidium is paraphyletic to the exclusion of Hygrolembidium and Chloranthelia, and re-evaluation of
the morphological characters separating these genera is necessary.
It is possible that a broader generic concept for Lembidium should
be applied to encapsulate these various elements. The lack of support for a monophyletic Kurzia suggests that the delimitation of
this genus also needs revision. Nevertheless, strong support for
the clade containing Kurzia and the lembidioids demonstrates that
the recent transfer of Kurzia species with reduced leaf and stem
anatomy to Telaranea (Engel and Merrill, 2004) is not compatible
with the phylogeny.
4.9. Lepidozia clade
Lepidozia is paraphyletic to the exclusion of Sprucella. However,
Sprucella has often been considered a synonym of Lepidozia (Pócs,
1994; Vanden Berghen, 1983) and the phylogeny indicates that it
should not be retained as a separate genus. Lepidozia is placed in
a clade with several subclades of Telaranea (i.e. Telaranea I–III).
These three clades contain the Lepidozia-like members of Telaranea,
which were included in Lepidozia until Fulford and Taylor (1959)
erected the genus Neolepidozia to accommodate them. Common
to these species are the deeply lobed leaves, except in Sprucella,
with a distinct disc present. Telaranea centipes, which is resolved
sister to the remainder of the clade, is placed in Telaranea sect. Ceraceae (Engel and Merrill, 2004) with other glaucous Telaranea species. This monophyletic section (E. D. Cooper, unpublished data) is
not phylogenetically associated with Lepidozia subg. Glaucophylla
as represented by L. bisbifida, implying multiple origins of waxy
cuticle. Telaranea II contains taxa with a reduced leaf disc and elongated to ±filiform lobes. The form of the lobes and short disc are
similar to the reduced leaves seen in Telaranea species placed in
the Zoopsids I, Zoopsids III and Lembidioid/Kurzia clades, and are
in some species, accompanied by a similar preference for damp
niches. Telaranea III is resolved as sister to Lepidozia (node vi) in
many analyses, often with strong support. Given that the clade
contains the most Lepidozia-like of the Telaranea species, this association is not surprising. Taxa placed in this clade (i.e., of Lepidozia
and Telaranea III) have 3–4 lobed leaves and a distinct disc. In Lepidozia these leaves are asymmetric. The association between the
four components of the Lepidozia clade recovered in all but two
analyses (Table 2) indicates strong support for the clade. The morphological similarity of these four clades suggests that returning to
a broader concept of this genus might be appropriate. Our analysis
included only 33 species from this clade and internal relationships
are not consistently resolved. A study focussing on this clade is
underway and aims to provide the phylogenetic background for a
taxonomic revision.
4.10. Perspectives and conclusions
Our data from 93 species, representing 20 genera in seven subfamilies, significantly improves upon previous phylogenetic studies of the Lepidoziaceae (Engel and Merrill, 2004; Heslewood and
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Brown, 2007; Renner et al., 2006). The extent of incongruence between the current classification and the phylogeny indicates that
reassessment of morphological homologies and, in some groups,
intensive taxonomic sampling are necessary. Consequently, a fully
revised classification is not presented here but several preliminary
taxonomic conclusions can be made:
1. Neogrollea notabilis belongs within Lepidoziaceae and subfamily
status is not warranted. This change is formalised below.
2. Megalembidium insulanum should not be retained in a monotypic subfamily and this change is formalised below.
3. Drucella integristipula is phylogenetically isolated, and retention
of a monotypic Drucelloideae reflects this.
4. Despite weak support, Bazzanioideae are likely to be monophyletic and no changes to the classification are required at this
time.
5. Expanding the definition of Lembidioideae to encompass all
members of the Lembidioid/Kurzia clade is appropriate.
6. Delimitation of Lembidium and Kurzia need to be revised, but
provisional transfer of C. bergrenii back to Lembidium and resurrection of Dendrolembidium for K. dendroides are justified.
7. The definition of Lepidozioideae should be restricted to include
only Telaranea I, II and III and Lepidozia. Sprucella is not an
autonomous genus and should be accommodated within
Lepidozia.
8. The Zoopsidioideae are a polyphyletic assemblage of morphologically convergent taxa. Until adequate taxonomic sampling
is completed, the Zoopsids I–III, and the Paracromastigum clade
should be considered unaligned. The phylogeny suggests that
recognition of three or four subfamilies and significant revision
of generic boundaries are required.
9. Transfer of H. microphylla and C. denticulata to Paracromastigum
is warranted and this change will be made elsewhere.
Several phylogenetically important taxa remain unsampled or
under-sampled. The Micropterygioideae, for example, are yet to
be included in phylogenetic studies of the family. The phylogenetic
incongruence in Zoopsis and Telaranea indicate that a more thorough taxonomic sampling within these groups is desirable before
a stable, unequivocal classification is possible. In particular, inclusion of South and Central American species is necessary to improve
the geographically biased sampling within Pseudocephalozia, Zoopsidella, Hygrolembidium, and Paracromastigum. Nevertheless, the
phylogeny presented here provides a solid foundation for evaluating and revising the classification.
4.11. Taxonomic changes
Lepidoziaceae Limpr., in Cohn, Krypt.-Fl. Schlesien 1: 310
(1877).
501
Lepidozieae Limpr., in Cohn, Krypt.-Fl. Schlesien 1: 310 (1877).
Zoopsidaceae Nakai, in Ogura, Ord. Fam. Trib. Gen. Sect. . . . nov.
ed. 199. 1943.
Bazzaniaceae Nakai, in Ogura, Ord. Fam. Trib. Gen. Sect. . . . nov.
ed. 200. 1943.
Hyalolepidoziaceae Fulford, Mem. New York Bot. Gard. 11: 376.
1968.
Regredicaulaceae Fulford, Mem. New York Bot. Gard. 11: 358.
1968.
Paracromastigaceae Fulford, Mem. New York Bot. Gard. 11: 384.
1968.
Neogrolleaceae (R.M.Schust.) J.J.Engel & Braggins, J. Hattori Bot.
Lab. 91: 195. 2001. syn. nov.
Type: Lepidozia (Dumort.) Dumort., Recueil Observ. Jungerm.
19, 1835.
Lepidoziaceae subfamily Lembidioideae R.M.Schust., Hepat.
Anthocerotae N. Amer. 2: 11, 1969.
Lepidoziaceae subfamily Megalembidioideae J.J.Engel, in J.J.Engel and Braggins, J. Hattori Bot. Lab. 97: 88. 2005. syn. nov.
Type: Lembidium Mitt., in Hook.f., Handb. N. Zeal. Fl. 2: 751, 754.
1867.
Acknowledgments
We would like to thank the New Zealand Department of Conservation/Te Papa Atawhai, and people of Te Roroa, Piki te Aroha
Marae and Te Rünanga for permission to collect specimens from
their land. We thank John Braggins for his invaluable assistance
in the field. Matt von Konrat and John Engel (F), and Jochen Heinrichs (GOET) provided specimens. Sandy Boles and Carolyn Porter
provided E.D.C. with technical assistance for laboratory work. We
thank Matthew Renner for useful comments on an earlier draft of
this manuscript.
An Australian Biological Resources Study, student travel bursary
(to E.D.C.) partially funded field work in New Zealand. The Hermon
Slade Foundation supported DNA extraction at NSW (Grant HSF
03-14 to E.A.B.). This research was supported by US National Science Foundation Grant EF-0531730-002 (to A.J.S.).
Appendix A.
List of taxa, voucher information and accession numbers. Ingroup taxa are listed alphabetically before outgroup taxa (also
alphabetically). Accession numbers in bold indicate sequences generated for this study. Superscripts following accession numbers
indicate place of publication as follows: aForrest et al. (2006);
b
Heslewood and Brown (2007).
Source
nr26S
nad1
Acromastigum
adaptatum Hürl.
Acromastigum
anisostomum (Lehm.
et Lindenb.) A.Evans
Acromastigum
cavifolium
R.M.Schust.
Acromastigum
cunninghamii
(Steph.) A.Evans
Acromastigum
divaricatum (Nees)
A.Evans
Acromastigum filum
(Steph.) A.Evans
Acromastigum
furcatifolium (Steph.)
E.A.Br. ms
Acromastigum
mooreanum (Steph.)
E.A.Hodgs.
Acromastigum stellare
N.Kitag.
Amazoopsis diplopoda
(Pócs) J.J.Engel et
G.L.Merr.
Bazzania sp. Mb28
E.A.Brown, 06/
137, NSW
E.C.Davis, NZ40,
DUKE
New
Caledonia
New
Zealand
JF315899
JF316100 JF316378 JF315966 JF316167
JF315905
JF316097 -
E.A.Brown, 08/
278, NSW
New
Zealand
-
JF316102 JF316373 -
J.J.Engel 23662,
F
New
Zealand
JF315888
JF316096 -
E.A.Brown 04/
84e, NSW
Papua
New
Guinea
New
Caledonia
Australia
-
JF316098 -
Bazzania affinis
(Lindenb. et
Gottsche) Trevis.
Bazzania intermedia
(Lindenb. et
Gottsche) Trevis.
Bazzania involuta
(Mont.) Trevis.
Mastigobryum
[Bazzania]
lenormandii Steph.
Mastigobryum
[Bazzania] limbatum
Steph.
Bazzania nitida
(F.Weber) Grolle
E.A.Brown 03/
139, NSW
E.A.Brown 02/
100, NSW
rps3
rps4
trnG
JF316259 JF316320
-
JF316541 JF316589
JF316263 JF316321
JF316457
JF316545 JF316588
JF316143
JF316264 JF316302
JF316437
JF316540 JF316585
-
JF316168
JF316268 -
JF316459
JF316542 JF316590
-
JF316169
-
-
JF316460
JF316543 JF316591
JF315901
JF316101 JF316376 JF316001 JF316166
-
EF1009752
-
JF316544 EF1010822
-
-
-
JF316165
-
EF1009772
JF316456
JF316547 EF1010842
JF316164
-
JF316318
JF316455
JF316546 JF316587
-
atpB
psbA
JF316002 JF316163
psbTpsbH
rbcL
trnL- trnF
B.Shaw 6407,
DUKE
Australia
JF315904
JF316103 JF316377 -
E.A.Brown 03/
184, NSW
A.Szabo 9607/
CB,
New
Caledonia
Reunion
Island
-
JF316099 JF316375 JF315972 JF316148
JF316198 EF1009782
-
JF316528 EF1010852
-
-
-
-
-
-
-
-
JF316499 JF316582
Chua-Petiot
Mb28, NY
E.C.Davis, 146,
Duke
Kenya
AY6081921
-
-
-
AY6079191 -
-
AY6080411 JF316535 JF316636
Jamaica
AY6082001
JF316093 JF316386 JF316008 AY6079271 JF316272 DQ4396801 AY6080481 JF316497 JF316633
-
JF316089 JF316388 JF316006 JF316153
JF316275 -
JF316445
JF316537 -
JF315915
JF316095 JF316389 JF316012 JF316155
JF316277 JF316323
JF316448
JF316493 JF316631
JF315916
JF316092 JF316390 JF316003 JF316156
JF316278 EF1009892
JF316449
JF316534 EF1010962
JF315908
JF316091 JF316392 JF316005 JF316152
JF316274 EF1009902
JF316446
JF316536 EF1010972
JF315919
JF316088 JF316385 JF316004 JF316151
JF316276 JF316322
JF316444
JF316492 JF316630
E.A.Brown, 04/
67f, NSW
Papua
New
Guinea
J.J.Engel, 37
New
Tarn 1 (2006), F Zealand
E.A.Brown, 03/
New
140c, NSW
Caledonia
D.M.Crayn, 829,
NSW
Australia
J.J.Engel, Bearley New
36 (2006), F
Zealand
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Voucher
[Collector, date,
Herbarium]
502
Taxon
Kurzia brevicalycina
(Steph.) Grolle
Kurzia calcarata
(Steph.) Grolle
Kurzia compacta
(Steph.) Grolle
Kurzia dendroides
(Carrington et
Pearson) Grolle
Kurzia gonyotricha
(Sande Lac.) Grolle
Kurzia helophila
R.M.Schust.
Kurzia hippurioides
G.P.Rothero,
11022, E
D.Long, 34721,
E
D.Kosma, SIU
culture IV
T.Yamaguchi,
29079, F
Scotland
-
JF316080 -
JF316010 JF316154
JF316269 JF316282
JF316447
JF316494 JF316632
China
JF315877
JF316094 JF316381 JF316009 JF316157
JF316271 JF316310
JF316451
JF316498 JF316635
U.S.A.
JF315876
JF316090 JF316387 JF316007 JF316113
JF316273 -
JF316453
JF316496 JF316634
Japan
JF315878
JF316081 JF316391 JF316011 JF316158
JF316270 -
JF316452
JF316495 JF316637
E.A.Brown, 08/
282, NSW
E.A.Brown, 03/
147, NSW
New
Zealand
New
Caledonia
JF315931
JF316035 JF316354 JF315960 JF316126
JF316248 JF316296
JF316423
JF316520 JF316601
-
JF316085 JF316382 -
JF316266 EF1009912
-
-
E.A.Brown, 08/
219, NSW
E.A.Brown, 08/
301, NSW
New
Zealand
New
Zealand
JF315897
JF316075 JF316380 JF315999 JF316147
JF316197 JF316287
JF316436
JF316502 JF316576
-
JF316087 JF316384 JF315968 JF316149
JF316267 JF316304
JF316435
JF316527 JF316629
E.A.Brown, 08/
310
New
Zealand
JF315932
JF316033 JF316355 -
JF316131
JF316252 JF316299
JF316422
JF316522 JF316602
J.J.Engel, 28134,
F
New
Zealand
JF315928
JF316032 JF316358 JF315957 JF316129
JF316250 JF316297
JF316420
-
E.A.Brown, 08/
283, NSW
New
Zealand
JF315930
JF316031 JF316357 JF315958 JF316130
JF316251 JF316298
JF316421
JF316521 JF316603
E.A.Brown,
08286, NSW
New
Zealand
JF315926
JF316041 JF316345 JF315962 JF316123
JF316244 JF316294
JF316416
JF316517 JF316600
E.A.Brown, 03/
140a, NSW
E.A.Brown, EAB
03/131, NSW
E.D.Cooper, 330,
NSW
M.A.M.Renner,
02102, AK
E.A.Brown, 04/
02, NSW
New
Caledonia
New
Caledonia
New
Zealand
New
Zealand
Australia
JF315890
JF316029 JF316342 -
JF316237 JF316292
JF316415
JF316508 JF316595
JF315918
JF316047 JF316349 JF315963 JF316112
JF316239 EF1009932
JF316427
JF316511 EF1011022
JF315921
JF316043 JF316347 JF315965 JF316121
JF316240 JF316301
JF316428
JF316513 JF316596
-
-
-
-
JF316512 EF1011042
JF315920
JF316039 JF316341 JF315956 JF316124
JF316246 EF1009962
JF316418
JF316518 EF1011052
M.von Konrat,
6/8-8b, F
E.D.Cooper, 383,
NSW
E.A.Brown, 04/
Fiji
-
JF316046 JF316348 -
-
JF316426
JF316510 JF316604
New
Zealand
Australia
JF315923
JF316042 JF316350 JF315964 JF316133
JF316241 JF316300
JF316431
JF316515 JF316597
JF315924
JF316044 JF316346 JF315951 JF316132
JF316243 EF1009972
-
JF316514 -
-
-
JF316109
JF316117
JF316120
-
EF1009952
-
EF1011002
-
503
(continued on next page)
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Bazzania pearsonii
Steph.
Bazzania tricrenata
(Wahlenb.) Lindenb.
Bazzania trilobata (L.)
Gray
Bazzania yoshinagana
(Steph.) Steph. ex
Yoshin.
Chloranthelia berggrenii
(Herzog) R.M.Schust.
Chloranthelia
denticulata (Steph.)
R.M.Schust.
Drucella integristipula
(Steph.) E.A.Hodgs.
Hyalolepidozia
microphylla
R.M.Schust. ex
J.J.Engel
Hygrolembidium
rigidum R.M.Schust.
et J.J.Engel
Hygrolembidium
rigidum R.M.Schust.
et J.J.Engel
Hygrolembidium
rigidum R.M.Schust.
et J.J.Engel
Isolembidium
anomalum (Rodway)
Grolle
Kurzia sp.
504
Appendix A (continued)
Voucher
[Collector, date,
Herbarium]
(Hook.f. et Taylor)
Grolle
Kurzia trichoclados
(Müll.Frib.) Grolle
Lembidium longifolium
R.M.Schust.
Lembidium nutans
(Hook.f. et Taylor)
Mitt. ex A.Evans
Lembidium nutans
(Hook.f. et Taylor)
Mitt. ex A.Evans
Lepidozia sp. 1
42, NSW
Lepidozia sp. 2
Source
nr26S
nad1
rps3
atpB
psbA
psbTpsbH
rbcL
rps4
trnG
trnL- trnF
JF316319
JF316430
-
-
G.P.Rothero,
11014, E
M.A.M.Renner,
2530, F
E.A.Brown, 02/
322, NSW
UK
JF315875
JF316045 JF316351 JF315955 -
-
New
Zealand
New
Zealand
JF315927
JF316037 JF316352 -
JF316128
JF316253 -
JF316425
-
JF315922
JF316034 JF316353 -
JF316125
JF316247 EF1009922
JF316419
JF316519 EF1010462
J.J.Engel, 28415,
F
New
Zealand
JF315929
JF316036 JF316356 JF315959 JF316127
JF316249 JF316295
JF316424
-
-
M.von Konrat,
6/20-4, F
B.Shaw, 5789,
DUKE
E.D.Cooper, 430,
NSW
D.G.Long,
29184, E
T.Yamaguchi,
29076, F
E.A.Brown, 04/
08, NSW
Fiji
JF315909
JF316068 JF316408 JF315996 JF316180
JF316219 JF316325
JF316478
-
-
China
JF315934
JF316062 JF316405 JF315991 JF316189
JF316218 JF316307
JF316477
-
-
JF315940
JF316060 JF316410 JF315995 JF316193
JF316223 JF316305
JF316480
JF316560 JF316627
-
JF316063 JF316403 JF315992 JF316191
JF316220 -
JF316474
JF316556 JF316623
JF315933
JF316066 JF316406 JF315988 JF316187
JF316214 -
JF316476
JF316551 JF316620
JF315906
JF316067 JF316409 JF315994 JF316192
JF316224 EF1010002
JF316472
JF316559 EF1011092
JF315871
JF316055 -
-
-
JF316210 -
-
JF316555 JF316622
JF315938
JF316048 -
-
JF316185
JF316215 -
JF316475
-
-
AY6082291
JF316064 JF316404 JF315990 AY6079621 JF316217 JF316327
AY6080831 -
-
JF315907
JF316059 JF316402 JF315998 JF316110
JF316221 JF316326
JF316471
JF316552 JF316625
JF315935
JF316061 JF316407 JF315989 JF316188
JF316216 EF1010022
-
JF316554 EF1011112
JF315898
JF316058 -
-
JF316479
JF316558 JF316624
Lepidozia bisbifida
New
Steph.
Zealand
UK
Lepidozia cupressina
(Sw.) Lindenb.
Lepidozia fauriana
Japan
Steph.
Australia
Lepidozia laevifolia
(Hook.f. et Taylor)
Gottsche, Lindenb. et
Nees
N.J.M.Gremmen, Gough
Lepidozia laevifolia
2000-0385, F
Island
(Hook.f. et Taylor)
Gottsche, Lindenb. et
Nees
Lepidozia microphylla
J.J.Engel, 23699, New
(Hook.) Lindenb.
F
Zealand
Lepidozia reptans (L.)
Sargent living
Dumort.
culture
collection,
Berkeley, UC
Lepidozia setigera Steph. J.J.Engel, 41 Bog New
20, F
Zealand
Lepidozia spinosissima
M.A.M.Renner,
New
(Hook.f. et Taylor)
MR810, NSW
Zealand
Mitt.
Papua
Lepidozia trichodes
E.A.Brown, 04/
New
(Reinw. ex Blume et 67g, NSW
JF315997 JF316179
JF316324
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Taxon
Telaranea sp. 2
Telaranea centipes
(Taylor ex Gottsche,
Lindenb. et Nees)
R.M.Schust.
Telaranea chaetocarpa
(Pearson) Grolle
Telaranea diacantha
(Mont.) J.J.Engel et
G.L.Merr.
Telaranea herzogii
(E.A.Hodgs.)
E.A.Hodgs.
Telaranea heterotexta
(Steph.) J.J.Engel et
G.L.Merr.
Telaranea lawesii
(Steph.) Grolle
E.A.Brown, 08/
273, NSW
M.A.M.Renner,
02100a, NSW
Guinea
New
Zealand
New
Zealand
E.A.Brown, 08/
312, NSW
E.A.Brown, 08/
315, NSW
New
Zealand
New
Zealand
E.A.Brown, 08/
218, NSW
JF315939
JF316065 JF316411 JF315993 JF316190
JF316222 JF316306
JF316473
JF316557 JF316626
JF315925
JF316040 JF316344 JF315961 JF316122
JF316245 EF1010052
JF316417
JF316516 EF1011152
JF315891
JF316104 JF316394 JF315948 JF316114
JF316254 JF316288
JF316443
JF316523 JF316605
JF315887
JF316079 JF316393 JF316000 JF316170
JF316234 JF316283
JF316461
JF316532 JF316586
New
Zealand
JF315874
JF316086 JF316383 JF315967 JF316150
JF316265 JF316303
JF316434
JF316526 JF316628
E.A.Brown, 08/
216, NSW
New
Zealand
JF315893
JF316027 JF316365 JF315949 JF316144
JF316235 JF316289
JF316413
JF316505 JF316593
E.A.Brown, 08/
293, NSW
New
Zealand
JF315894
JF316028 JF316366 JF315950 JF316145
JF316236 JF316290
JF316414
JF316506 JF316594
E.A.Brown, 03/
131c, NSW
T.Pocs, 97108/D,
F
J.J.Engel,
18Apr08, F
M.von Konrat,
6/7-9, F
D.A.Meagher,
4237, NSW
New
Caledonia
Uganda
JF315868
JF316084 JF316379 JF315971 JF316159
JF316262 EF1017002
JF316458
JF316533 EF1011162
-
-
-
-
JF316173
JF316211 -
JF316470
JF316550 JF316617
Fiji
-
-
-
-
JF316111
JF316232 -
-
JF316563 JF316614
Fiji
JF315896
JF316073 -
JF315980 JF316177
JF316231 -
-
JF316562 JF316613
Australia
JF315895
-
JF315974 JF316172
JF316205 JF316311
-
JF316549 JF316616
-
E.A.Brown, 03/
146a, NSW
T.Pocs, 03156/N,
F
New
JF315886
Caledonia
Dominican JF315902
Republic
JF316049 JF316367 JF315973 JF316171
JF316206 EF1010112
JF316462
JF316548 EF1011202
JF316106 JF316363 -
JF316160
-
-
JF316454
-
J.J.Engel, 23927,
F
New
Zealand
JF315903
JF316108 JF316364 -
JF316162
-
JF316309
JF316440
JF316539 JF316639
E.A.Brown, 03/
129, NSW
New
Caledonia
JF315910
JF316071 JF316398 JF315979 JF316175
JF316229 EF1010122
JF316464
JF316564 EF1011212
E.A.Brown, 04/
84h, NSW
Papua
New
Guinea
JF315885
JF316053 JF316374 JF315977 JF316195
JF316207 JF316332
JF316469
-
-
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Nees) Gottsche
Lepidozia ulothrix
(Schwägr.) Lindenb.
Megalembidium
insulanum (W.Martin
et E.A.Hodgs.)
R.M.Schust.
Neogrollea notabilis
E.A.Hodgs.
Paracromastigum drucei
(R.M.Schust.)
R.M.Schust.
Paracromastigum
macrostipum (Steph.)
R.M.Schust.
Pseudocephalozia
lepidozioides
R.M.Schust.
Pseudocephalozia
paludicola
R.M.Schust.
Psiloclada clandestina
Mitt.
Sprucella succida (Mitt.)
Steph.
Telaranea sp. 1
JF316606
(continued on next page)
505
506
Appendix A (continued)
Taxon
Voucher
[Collector, date,
Herbarium]
nr26S
nad1
New
Zealand
JF315884
JF316054 -
Fiji
-
JF316023 JF316335 -
New
Caledonia
Comoros
JF315873
JF316024 JF316336 -
rps3
atpB
psbA
rps4
trnG
JF316209 JF316316
JF316482
JF316570 JF316608
-
-
-
JF316500 -
JF316116
JF316204 JF316333
-
JF316501 JF316583
-
JF316025 JF316339 JF315947 JF316115
JF316203 JF316284
-
-
New
Zealand
JF315936
-
-
-
JF316484
JF316571 JF316615
New
Zealand
-
-
JF316399 -
JF316226 -
JF316466
JF316566 JF316610
New
Zealand
JF315872
JF316030 -
-
-
-
New
Zealand
Australia
JF315914
JF316072 JF316400 JF315987 JF316184
JF316228 JF316317
JF316468
JF316568 JF316612
JF315867
JF316069 JF316401 JF315985 JF316181
JF316225 EF1010162
JF316465
JF316565 EF1011252
Chile
JF315889
JF316056 JF316337 -
JF316176
-
JF316312
JF316483
-
Chile
JF315900
JF316107 -
JF316161
-
JF316308
-
JF316538 JF316638
New
Zealand
JF315883
-
JF316485
JF316573 JF316619
Australia
AY6082561
JF316050 JF316396 JF315983 AY6079931 JF316212 DQ4397041 AY6081141 JF316572 JF316618
Australia
-
JF316052 -
JF315978 -
-
JF316331
-
-
Chile
JF315937
JF316057 -
-
-
JF316315
-
JF316553 JF316621
Australia
JF315879
JF316026 JF316340 JF315952 JF316146
JF316238 JF316285
-
JF316507 JF316592
JF315976 JF316194
JF315982 -
JF316182
JF315953 JF316118
-
JF316397 JF315984 JF316174
JF316186
psbTpsbH
rbcL
-
JF316330
-
JF316213 -
trnL- trnF
-
JF316598
-
-
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
J.J.Engel, 23605,
Telaranea lindenbergii
NSW
(Gottsche) J.J.Engel
et G.L.Merr.
Telaranea major Herzog M.von Konrat,
6/26-15, F
Telaranea major Herzog E.A.Brown, 03/
180, NSW
Telaranea maorensis
T.Pocs, 05090/B,
F
Pócs
Telaranea martinii
J.J.Engel, 24903,
(E.A.Hodgs.)
F
R.M.Schust.
J.J.Engel, 24863,
Telaranea meridiana
F
(E.A.Hodgs.)
E.A.Hodgs.
J.J.Engel, 23623,
Telaranea pallescens
F
(Grolle) J.J.Engel et
G.L.Merr.
Telaranea palmata
M.A.M.Renner,
J.J.Engel et G.L.Merr. 2522, NSW
Telaranea patentissima
E.A.Brown, 03/
(Hook.f. et Taylor)
61, NSW
E.A.Hodgs.
J.J.Engel, 26422,
Telaranea plumulosa
F
(Lehm. et Lindenb.)
Fulford
Telaranea pseudozoopsis J.J.Engel, 25743,
(Herzog) Fulford
F
M.A.M.Renner,
Telaranea pulcherrima
01-100, F
var. mooreana
(Steph.) J.J.Engel et
G.L.Merr.
Telaranea pulcherrima
H.Streimann,
var. pulcherrima
59554, NY
(Steph.) R.M.Schust.
D.A.Meagher,
Telaranea quadriseta
1064, F
(Steph.) J.J.Engel et
G.L.Merr.
Telaranea seriatitexta
J.J.Engel, 25953,
(Steph.) J.J.Engel
F
M.A.M.Renner,
Telaranea tasmanica
1954, NSW
(Steph.) J.J.Engel et
G.L.Merr.
Source
Outgroup species
Calypogeia muelleriana
(Schiffn.) Müll.Frib.
Chiloscyphus semiteres
(Lehm.) Lehm. &
Lindenb.
Herbertus sakurai
S.Hatt.
Lepicolea attenuata
(Miit.) Steph.
Lepicolea rara (Steph.)
Grolle
Mastigophora woodsii
(Hook.) Nees
D.G.Long,
29502, E
UK
-
JF316051 -
JF315975 -
JF316208 -
JF316481
JF316569 JF316607
J.J.Engel, 24292,
F
New
Zealand
JF315913
JF316074 -
JF315986 JF316183
JF316227 JF316329
JF316467
JF316567 JF316611
E.A.Brown, 08/
250, NSW
New
Zealand
JF315917
JF316038 JF316343 JF315954 JF316119
JF316242 JF316293
JF316429
JF316509 JF316599
E.A.Brown, 04/
829, NSW
Papua
New
Guinea
New
Caledonia
New
Zealand
JF315892
JF316070 JF316395 JF315981 JF316178
JF316230 JF316328
JF316463
JF316561 JF316609
-
-
-
-
-
JF316233 EF1010222
-
-
JF315880
JF316105 -
-
JF316141
JF316255 -
-
JF316504 JF316577
E.A.Brown, 03/
179, NSW
J.J.Engel, 23962,
F
EF1011312
E.A.Brown, 08/
320, NSW
R.Coveny, sn,
NSW [614795]
New
Zealand
Australia
-
JF316022 -
-
JF316142
JF316199 JF316314
JF316412
JF316503 JF316584
-
JF316078 JF316368 -
JF316134
JF316256 EF1010232
JF316432
JF316529 EF1011322
B.Shaw, 6319,
DUKE
Australia
JF315881
JF316077 JF316369 -
JF316135
JF316258 -
-
JF316530 -
E.A.Brown, 03/
132, NSW
E.A.Brown, 08/
212, NSW
E.A.Brown, 04/
39, NSW
New
Caledonia
New
Zealand
Australia
JF315911
JF316082 JF316371 JF315969 JF316137
JF316260 EF1010242
JF316441
JF316524 EF1011342
JF315882
JF316076 JF316370 -
JF316257 JF316286
JF316433
JF316531 JF316574
JF315912
JF316083 JF316372 JF315970 JF316138
JF316261 EF1010252
JF316442
JF316525 EF1011352
E.C.Davis, 130,
DUKE
J.J.Engel, 24780,
F
USA
AY6082031
JF316013 -
New
Zealand
JF315869
JF316014 JF316338 JF315942 JF316139
Steere,
74(2)882, NY
R.Stotler, 4586,
ABSH
D.Norris, 66575,
DUKE
Alaska
AY6082161
JF316017 JF316361 JF315945 AY6079491 JF316201 AY6080311
New
Zealand
Papua
New
Guinea
China
DQ2688881 JF316020 JF316360 -
AY5074941 JF316280 AY5074101
AY6082271
JF316021 -
AY6079601 JF316281 DQ4396911 AY6080811 JF316488 JF316579
JF315870
JF316019 JF316362 JF315946 JF316140
D.Long, 33696,
E
JF316136
JF315941 AY6079311 JF316196 JF316291
-
-
JF316334
JF316200 JF316313
AY6080521 JF316438
-
JF316487 -
AY6080761 -
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Telaranea tetradactyla
(Hook.f. et Taylor)
E.A.Hodgs.
Telaranea tetrapila
(Hook.f. et Taylor)
J.J.Engel et G.L.Merr.
Telaranea trilobata
(R.M.Schust.)
J.J.Engel et G.L.Merr.
Telaranea wallichiana
(Gottsche)
R.M.Schust.
Zoopsidella caledonica
(Steph.) R.M.Schust.
Zoopsis argentea
(Hook.f. et Taylor)
Gottsche, Lindenb. et
Nees
Zoopsis ceratophylla
(Spruce) Hamlin
Zoopsis leitgebiana
(Carrington et
Pearson) Bastow
Zoopsis leitgebiana
(Carrington et
Pearson) Bastow
Zoopsis liukiuensis
Horik.
Zoopsis macrophylla
R.M.Schust.
Zoopsis setulosa Leitg.
-
AY5074521 JF316491 JF316578
JF316439
JF316486 JF316581
(continued on next page)
507
508
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
AY6081181 JF316016 JF316359 JF315944 AY6079971 JF316279 AY6080401
AY6082611
Ecuador
E.C.Davis, 368,
DUKE
JF315943 AY6079961 JF316202 DQ4397061 AY6081171 JF316490 JF316580
JF316018 AY6082591
Venezuela
Ricardi, 9730/T,
F
-
AY6079951 JF316015 AY608257
New
Zealand
J.E.Braggins, 92/
87, F
Temnoma pulchellum
(Hook.) Mitt. ex
Bastow
Triandrophyllum
subtrifidum (Hook. &
Taylor) Fulford &
Hatcher
Trichocolea tomentosa
(Sw.) Gottsche
rps3
atpB
psbA
psbTpsbH
rbcL
nad1
nr26S
Source
DQ4397051 AY6081151 JF316489 JF316575
References
Voucher
[Collector, date,
Herbarium]
Appendix A (continued)
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.ympev.2011.02.006.
Taxon
rps4
trnG
trnL- trnF
Appendix B. Supplementary material
Akaike, H., 1973. Information theory as an extension of the maximum likelihood
principle. In: Petrov, B.N., Csaki, F. (Eds.), Second International Symposium on
Information Theory. Akademiai Kiado., Budapest, pp. 267–281.
Boesen, D.F., 1982. The taxonomy of Drucella Hodgs. and Druceleae, trib. nov. and
their position within Lepidozioideae Limpr. Lindbergia 8, 77–88.
Buck, W.R., Goffinet, B., Shaw, A.J., 2000. Testing morphological concepts of orders of
pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on
trnL–trnF and rps4 sequences. Mol. Phylogenet. Evol. 16, 180–198.
Burnham, K.P., Anderson, D.R., 2004. Multimodel inference. Understanding AIC and
BIC in model selection. Social. Methods Res. 33, 261–304.
Cox, C.J., Goffinet, B., Newton, A.E., Shaw, A.J., Hedderson, T.A., 2000. Phylogenetic
relationships among the Diplolepideous-alternate mosses (Bryidae) inferred
from nuclear and chloroplast DNA sequences. Bryologist 103, 224–241.
Crandall-Stotler, B., Stotler, R.E., 2000. Morphology and classification of the
Marchantiophyta. In: Shaw, A.J., Goffinet, B. (Eds.), Bryophyte Biology.
Cambridge University Press, Cambridge, pp. 21–70.
Crandall-Stotler, B., Stotler, R.E., Long, D.G., 2009. Phylogeny and classification of the
Marchantiophyta. edinb. J. Bot. 66, 155–198.
Davis, E.C., 2004. A molecular phylogeny of leafy liverworts (Jungermaniidae:
Marchantiophyta). In: Goffinet, B., Hollowell, V., Magill, R. (Eds.), Molecular
Systematics of Bryophytes. Missouri Botanic Garden Press, St. Louis, Missouri,
pp. 61–86.
Dombrovska, O., Qiu, Y.-L., 2004. Distribution of introns in the mitochondrial gene
nad1 in land plants phylogenetic and molecular evolutionary implications. Mol.
Phylogenet. Evol. 32, 246–263.
Doyle, J.J., Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of
fresh leaf tissue. Phytochem. Bull. 19, 11–15.
Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and
high throughput. Nucl. Acids Res. 32, 1792–1797.
Engel, J.J., Braggins, J.E., 2001. Austral Hepaticae 34. The sporophyte of Neogrollea
Hodgs. and the taxonomic position of Neogrolleaceae (Schust.) Engel & Braggins
Comb, & Stat. Nov. J. Hattori Bot. Lab. 91, 337–421.
Engel, J.J., Braggins, J.E., 2005. Austral Hepaticae 37. The sporophyte of
Megalembidium Schust., together with a re-evaluation of the taxonomic
position of the genus. J. Hattori Bot. Lab. 97, 81–96.
Engel, J.J., Glenny, D., 2008. A Flora of the Liverworts and Hornworts of New Zealand
Volume 1. Monographs in Systematic Botany from the Missouri Botanical
Garden 110, pp. 1–897.
Engel, J.J., Merrill, G.L.S., 1994. Studies of the New Zealand Hepaticae. 8–13. Bazzania
and Acromastigum. Bryologist 97, 313–320.
Engel, J.J., Merrill, G.L.S., 2002. Proposal to conserve the name Telaranea against
Arachniopsis (Hepaticae). Taxon 51, 571–572.
Engel, J.J., Merrill, G.L.S., 2004. Austral hepaticae. 35. A taxonomic and phylogenetic
study of Telaranea (Lepidoziaceae), with a monograph of the genus in temperate
Australasia and commentary on extra-Australasian taxa. Fieldiana Bot. 44, 1–
265.
Engel, J.J., Schuster, R.M., 2001. Austral Hepaticae. 32. A revision of the genus
Lepidozia (Hepaticae) for New Zealand. Fieldiana Bot. 42, 1–107.
Evans, A.W., 1934. A revision of the genus Acromastigum. Ann. Bryol. Suppl. 3, 1–
178.
Evans, A.W., 1939. The classification of the Hepaticae. Bot. Rev. 5, 49–96.
Forrest, L.L., Crandall-Stotler, B.J., 2004. A molecular phylogeny of the simple
thalloid liverworts (Jungermanniopsida, Metzgeriidae) inferred from five
chloroplast genes. In: Goffinet, B., Hollowell, V., Magill, R. (Eds.), Molecular
Systematics of Bryophytes. Missouri Botanic Garden Press, St. Louis, Missouri,
pp. 61–86.
Forrest, L.L., Davis, E.C., Long, D.G., Crandall-Stotler, B.J., Clark, A., Hollingsworth,
M.L., 2006. Unraveling the evolutionary history of the liverworts
(Marchantiophyta): multiple taxa, genomes and analyses. Bryologist 109,
303–334.
Fulford, M., 1963a. Manual of the leafy Hepaticae in Latin America. Part I. Mem. N. Y.
Bot. Garden 11, 1–172.
Fulford, M., 1963b. Segregate genera of the Lepidozia complex (Hepaticae). Part 4.
Telaranea and a review of the Lepidoziaceae. Brittonia 15, 65–86.
Fulford, M., 1966. Manual of the leafy Hepaticae in Latin America. Part II. Mem. N. Y.
Bot. Garden 11, 1–172.
Fulford, M., 1968. Manual of the leafy Hepaticae in Latin America. Part III. Mem. N.
Y. Bot. Garden 11, 1–172.
Fulford, M., Taylor, J., 1959. The segregate genera of the Lepidozia complex
(Hepaticae). Part 1. Sprucella Steph. and Neolepidozia gen. nov. Brittonia 11,
77–85.
Fulford, M., Taylor, J., 1961. Segregate genera of the Lepidozia complex (Hepaticae).
Part 2. Two new genera, Bonneria and Paracromastigum. Brittonia 13, 334–339.
Gadek, P.A., Quinn, C.J., 1993. An analysis of relationships within Cupressaceae
sensu stricto based on rbcL sequences. Ann. Missouri Bot. Garden 80, 581–586.
Grolle, R., 1964. Notulae hepaticologicae XV. Neue Notizen über Kurzia v. Mart. und
Verwandte. J. Jpn. Botany 39, 79–81.
E.D. Cooper et al. / Molecular Phylogenetics and Evolution 59 (2011) 489–509
Heinrichs, J., Hentschel, J., Wilson, R., Feldberg, K., Schneider, H., 2007. Evolution of
leafy liverworts (Jungermanniidae, Marchantiophyta): estimating divergence
times from chloroplast DNA sequences using penalized likelihood with
integrated fossil evidence. Taxon 56, 31–44.
Hendry, T.A., Wang, B., Yang, Y., Davis, E.C., Braggins, J.E., Schuster, R.M., Qui, Y.-L.,
2007. Evaluating phylogenetic positions of four liverworts from New Zealand,
Neogrollea notabilis, Jackiella curcata, Goebelobryum unguinculatum, and
Herzogianthus vaginatus using three chloroplast genes. Bryologist 110, 738–
751.
Hentschel, J., von Konrat, M.J., Pócs, T., Schäfer-Verwimp, A., Shaw, A.J., Schneider,
H., Heinrichs, J., 2009. Molecular insights into the phylogeny and subgeneric
classification of Frullania Raddi (Frullaniaceae, Porellales). Mol. Phylogenet.
Evol. 52, 142–156.
He-Nygrén, X., Juslén, A., Ahonen, I., Glenny, D., Piippo, S., 2006. Illuminating the
evolutionary history of liverworts (Marchantiophyta)—towards a natural
classification. Cladistics 22, 1–31.
Herzog, T., 1952. Revision der Lebermoosgattung Lembidium Mitt. Arkiv Bot. N.S. 1,
471–503.
Heslewood, M.M., Brown, E.A., 2007. A molecular phylogeny of the leafy liverwort
family Lepidoziaceae Limpr. in Australasia. Plant Syst. Evol. 265, 193–219.
Hodgson, E.A., 1955. New Zealand Hepaticae (Liverworts)—IX a review of the New
Zealand species of the genus Lepidozia. Trans. R. Soc. N. Z. 83, 589–620.
Howe, M.A., 1902. Notes on American Hepaticae. Bull. Torrey Bot. Club 29, 281–
289.
Huelsenbeck, J.P., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogeny.
Bioinformatics 17, 754–755.
Kass, R.E., Raftery, A.E., 1995. Bayes factors. J. Am. Stat. Assoc. 90, 773–795.
Krellwitz, E.C., Kowallik, K.V., Manos, P.S., 2001. Molecular and morphological
analyses of Bryopsis (Bryopsidales, Chlorophyta) from the western North
Atlantic and Caribbean. Phycologia 40, 330–339.
Maddison, W.P., Maddison, D.R., 2009. Mesquite: a modular system for evolutionary
analysis. Version 2.72. <http://www.mesquiteproject.org>.
Meagher, D., 2008. Studies on Bazzania 1. Some new and little known species from
Australia. Nova Hedwig. 86, 477–495.
Miller, M.A., Holder, M.T., Vos, R., Midford, P.E., Liebowitz, T., Chan, L., Hoover, P.,
Warnow, T., 2010. The CIPRES Portals. <http://www.phylo.org>.
Müller, F., 2007. Meinungeria mouensis (Lepidoziaceae), a new genus and species
from New Caledonia. Bryologist 110, 494–499.
Nadot, S., Bajon, R., Lejeune, B., 1994. The chloroplast gene rps4 as a tool for the
study of Poaceae phylogeny. Plant Syst. Evol. 191, 27–38.
Nakai, T., 1943. A list of Prof. Nakai’s Papers with Indices to Names of Plants and
Plant-Groups Published as New to Science by Him, Tokyo.
Newton, A.E., Wiksrtöm, N., Bell, N., Forrest, L.L., Ignatov, M.S., 2007. Dating the
diversification of the pleurocarpous mosses. In: Newton, A.E., Tangney, R.S.
(Eds.), Pleurocarpous Mosses: Systematics and Evolution. CRC Press, Boca Raton,
pp. 337–366.
Pacak, A., Szweykowska-Kuliñska, Z., 2000. Molecular data concerning alloploid
character and the origin of chloroplast and mitochondrial genomes in the
liverwort species Pellia borealis. J. Plant Biotech. 2, 101–108.
Pócs, T., 1984. Synopsis of the African Lepidozioideae K. Müll. In: Vána, J. (Ed.),
Proceedings of the Third Meeting of Bryologists from Central and Eastern
Europe. Univerzita Karlova, Praha.
Pócs, T., 1994. Taxonomic results of the BRYOTROP expedition to Zaïre and Rwanda.
Trop. Bryol. 9, 123–130.
509
Pócs, T., 2006. East African Bryophytes, XXI. Two new species of Telaranea, sect.
Tenuifoliae and records on Amazoopsis (Lepidoziaceae) from the Indian Ocean
Islands. Acta Bot. Hung. 48, 119–138.
Podani, J., 2010. Monophyly and paraphyly: a discourse without end? Taxon 59,
1011–1015.
Posada, D., 2008. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25,
1253–1256.
Pratas, F., Trancoso, P., Stamatakis, A., Sousa, L., 2009. Fine-grained parallelism using
Multi-core, Cell/BE, and GPU systems: Accelerating the Phylogenetic Likelihood
Function. In: Proceedings of the ICPP, Vienna, Austria.
Renner, M.A.M., Brown, E.A., Glenny, D., 2006. Two new Zoopsis species and their
relationships to other zoopsids (Jungermanniopsida: Lepidoziaceae). J. Bryol.
28, 331–334.
Schneider, H., Schuettpelz, E., Pryer, K.M., Cranfill, R., Magallón, S., Lupia, R., 2004.
Ferns diversified in the shadow of angiosperms. Nature 428, 553–557.
Schneider, H., Kreier, H.-P., Wilson, R., Smith, A.R., 2006. The Synammia enigma:
evidence for a temperate lineage of polygrammoid ferns (Polypodiaceae,
Polypodiidae) in southern South America. Syst. Bot. 31, 31–41.
Schuster, R.M., 1969. The Hepaticae and Anthocerotae of North America. Columbia
University Press, New York.
Schuster, R.M., 1972. Phylogenetic and taxonomic studies on Jungermaniidae. J.
Hattori Bot. Lab. 36, 321–405.
Schuster, R.M., 1980. Studies on Hepaticae, LIV–LVII. Kurzia v.Mart [Microlepidozia
(Spr.) Joerg.], Megalembidium Schust., Psiloclada Mitt., Drucella Hodgs. and
Isolembidium Schust. J. Hattori Bot. Lab. 48, 337–421.
Schuster, R.M., 2000. Austral Hepaticae Part 1. Nova Hedwig. 118, 1–542.
Schuster, R.M., Engel, J.J., 1987. A monograph of Lepidoziaceae subfam.
Lembidioideae (Hepaticae). J. Hattori Bot. Lab. 63, 247–350.
Schuster, R.M., Engel, J.J., 1996. Austral Hepaticae. XXI. Paracromastigum fiordlandiae
(sp. nov.) and the Delimitation of Paracromastigum and Hyalolepidozia
(Lepidoziaceae). Brittonia 48, 165–173.
Shaw, A.J., 2000. Phylogeny of the Sphagnopsida based on chloroplast and nuclear
DNA sequences. Bryologist 103, 277–306.
Souza-Chies, T.T., Bittar, G., Nadot, S., Carter, L., Besin, E., Lejeune, B., 1997.
Phylogenetic analysis of Iridaceae with parsimony and distance methods using
the plastid gene rps4. Plant Syst. Evol. 204, 109–123.
Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–
2690.
Stephani, F., 1909. Species Hepaticarum, Geneva.
Swofford, D.L., 2002. PAUP⁄. Phylogenetic Analysis Using Parsimony (⁄and Other
Methods). Sinauer Associates, Sunderland, Massachusetts.
Taberlet, P., Gielly, L., Pautou, G., Bouvet, J., 1991. Universal primers for
amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol.
17, 1105–1109.
Vanden Berghen, C., 1983. Lepidozia Dum. emend. Joerg. subgen Sprucella (Steph.)
Vanden Berghen comb. et stat. nov. (Hepaticae). Bull. Jard. Bot. Nat. Belg. 53,
321–330.
Wilson, R., Gradstein, S.R., Schneider, H., Heinrichs, J., 2007a. Unravelling the
phylogeny of Lejeuneaceae (Jungermanniopsida): Evidence for four main
lineages. Mol. Phylogenet. Evol. 43, 270–282.
Wilson, R., Heinrichs, J., Hentschel, J., Gradstein, S.R., Schneider, H., 2007b. Steady
diversification of derived liverworts under Tertiary climatic fluctuations. Biol.
Lett. 3, 566–569.