Posted on 1 May 2023 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.168295740.05040250/v1 — This a preprint and has not been peer reviewed. Data may be preliminary.
Phylogenomic time tree of bryophytes resolves 500 million years of
diversification
Julia Bechteler1 , Gabriel Peñaloza-Bojacá1 , David Bell1 , Gordon Burleigh1 , Stuart F.
McDaniel1 , Christine Davis1 , Emily Sessa1 , Alexander Bippus1 , Christine Cargill1 , Salut
Chantanaorrapint1 , Isabel Draper1 , Gaik Ee Lee1 , Lorena Endara1 , Laura L. Forrest1 ,
Ricardo Garilleti1 , Sean Graham1 , Sanna Huttunen1 , Javier Jauregui Lazo1 , Francisco
Lara1 , Juan Larraı́n1 , Lily Lewis1 , David Long1 , Dietmar Quandt1 , Karen S. Renzaglia1 ,
Alfons Schäfer-Verwimp1 , Adriel Michel Sierra Pinilla1 , Matt von Konrat1 , Charles
Zartman1 , Bernard Goffinet1 , and Juan Carlos Villarreal A.1
1
Affiliation not available
May 8, 2023
1
April 28, 2023
Phylogenomic time tree of bryophytes resolves 500 million years of
diversification
Author list:
Julia Bechteler1 *, Gabriel Peñaloza-Bojacá2*, David Bell3, Gordon Burleigh4*, Stuart
McDaniel4, Christine Davis4, Emily Sessa4 5, Alexander Bippus6, D. Christine Cargill7,
Sahut Chantanoarrapint8, Isabel Draper9, Lorena Endara4, 10, Laura L. Forrest3,
Ricardo Garilleti11, Sean W. Graham12, Sanna Huttunen13, Javier Jauregui Lazo14,
Francisco Lara9, Juan Larraín15, Lily Lewis4, David Long3, Dietmar Quandt1, Karen
Renzaglia16, Alfons Schäfer-Verwimp17, Gaik Ee Lee18 Adriel Sierra Pinilla19, Matt
von Konrat20, Charles Zartman21, Bernard Goffinet 22 *& Juan Carlos Villarreal A. 19 *
1
Nees-Institute for Plant Biodiversity, University of Bonn, Meckenheimer Allee 170,
53115 Bonn, Germany. 2Laboratório de Sistemática Vegetal, Departamento de
Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais.
3
Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, United
Kingdom. 4Department of Biological Sciences, 220 Bartram Hall, University of
Florida, Gainesville, FL 32611, USA. 5 Present address: The New York Botanical
Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA. 6California State
Polytechnic University, Humboldt, Arcata, CA 95521. 7Australian National
Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1700,
Canberra. ACT. 2601. 8PSU Herbarium, Division of Biological Science, Faculty of
Science Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand. 9
1
April 28, 2023
Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid,
28049 Madrid, Spain / Centro de Investigación en Biodiversidad y Cambio Global,
Universidad Autónoma de Madrid, Madrid, Spain. 10 Present address: Department of
Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA.
11
Departamento de Botánica y Geología. Universidad de Valencia, Avda. Vicente
Andrés Estelles s/n, 46100 Burjassot, Spain. 12Department of Botany, University of
British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4,
Canada. 13Herbarium (TUR), Biodiversity Unit, 20014 University of Turku, Finland.
14
Department of Plant Biology and Genome Center, University of California Davis,
451 Health Sciences Drive, Davis, 95616, USA. 15Centro de Investigación en
Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins,
Avenida Viel 1497, Santiago, Chile. 16Southern Illinois University, IL 62901,
Carbondale, USA. 17Mittlere Letten 11, 88634 Herdwangen-Schönach, Germany. 18
Faculty of Science and Marine Environment/Institute of Tropical Biodiversity and
Sustainable Development, Universiti Malaysia Terengganu, 21020 Kuala Nerus,
Terengganu, Malaysia. 19Department de Biologie, Université Laval, Québec, QC,
Canada. 20Gantz Family Collections Center, Field Museum, 1400 S. DuSable Lake
Shore Drive, Chicago, IL 60605, U.S.A. 21 Instituto Nacional de Pesquisas da
Amazônia, Departamento de Biodiversidade, Avenida André Araújo, 2936, Aleixo,
CEP 69060-001, Manaus, AM (Brazil) f 22Ecology and Evolutionary Biology, 75
NorthEagleville road, University of Connecticut, Storrs CT, 06269-3043, USA.
2
April 28, 2023
Abstract – 200 words
Bryophytes are emerging as the sister-group to extant vascular plants, and their
current diversity highlights that their life cycle characterized by a dominating
vegetative gametophyte and an unbranched sporophyte composes a successful
alternative to that of vascular plants and their dominating sporophyte. The
evolutionary history of hornworts, liverworts and mosses remains, however, poorly
resolved, due in part to the small character space from which to draw shared
ancestry. Our understanding of the diversification of these lineages has been
significantly reshaped by inferences from molecular data, highlighting extensive
homoplasy in various traits and repeated bursts of diversification. Here, we present
the first bryophyte time-tree based on 228 nuclear genes sampled via target capture
for 531 species with divergence times estimated based on a comprehensive set of
fossil calibrations. Our phylogenetic trees reflect a robust backbone, highlight novel
ordinal relationships and circumscriptions, and the recognition of 13 new orders of
liverworts and mosses. Our time-tree reveals that most orders originated prior to the
Cretaceous, confirms the Cretaceous radiation of the hyperdiverse hypnalean
mosses and species-rich liverwort clades. This comprehensive resource provides a
robust and expandable phylogenomic framework for evolutionary analyses across
lineages in this diverse and important group of land plants.
Keywords: Community resource, Cretaceous diversification, Hornworts, Land
plants, Liverworts, Mosses, Phylogenomic, Rapid diversification.
3
April 28, 2023
Introduction
The emerging consensus that bryophytes, which comprise hornworts,
liverworts, and mosses (Fig. 1), form the sister group to extant vascular plants1,2
raises important questions about the morphology and life cycle of the first land
plants3. Key elements of land plant development, including meristem function4,
stomatal development5, and hormone responses6,7, are built from a conserved
genomic blueprint5, and bryophytes hold signatures of divergence and reduction
from an ancestor with at least a morphologically more complex sporophyte8.
Bryophytes are important components of various ecological communities and
contribute to local nutrients fluxes and global biogeochemical cycles9–11. Broad
evolutionary analyses are key for assessing the significance of vegetative
gametophyte trait in these roles. Reconstructing the history of bryophytes and hence
of character transformations are therefore critical for understanding the
transformations of developmental, physiological and functional morphological traits
across land plants1,8,12.
Unraveling the relationships and time of divergence among major lineages of
bryophytes has been hampered by the putative low morphological character space,
the high homoplasy in the evolution of these traits, the shortage of phylogenetically
informative ontogenetic data, the paucity of fossil taxa and the difficulty in reliably
assigning these to lineages defined by extant taxa. Furthermore, phylogenetic
inferences suffer from insufficient signal, especially across major lineages, due
perhaps to their old divergence, and hence substitutional saturation or their rapid
diversification. All prior reconstructions rely on either a few loci sampled for perhaps
many species, or many markers sampled for a few bryophyte taxa8,13–16.
4
April 28, 2023
We present the first comprehensive phylogeny of bryophytes based on 228
markers sampled for 531 species from across all orders, using the GoFlag 408 probe
set. We then calibrated this phylogeny based on the most recent assessments of the
affinities of liverwort17 and moss18 fossils to estimate divergence times. We acquired
homologous sequences for virtually all samples and recovered strong support for
many relationships between classes and orders. We confirm the persisting
phylogenetic ambiguity for others and propose three new liverwort and ten new moss
orders. As in vascular plants, significant conflict among genes both within rapidly
diversifying groups of bryophytes and among the oldest nodes is likely due to
incomplete lineage sorting, ancient hybridization, and lack of signal in explosive
radiations. We have unraveled the macroevolutionary history of this key group of
land plants using the GoFlag 408 probe set, which emerged as a powerful tool to
tackle the complexity of the diversification process at multiple phylogenetic scales
across the bryophytes19.
Results and Discussion
We sampled 533 samples representing 531 species from 499 genera distributed
among 72% of families from all 69 orders of bryophytes (Figs 1–3; Extended Data
Figs. 1–7; Supplementary Figs. S1–S9; Supplementary Tables S1–S11). The
alignment of sequences from 228 targeted nuclear genes varies in length, variable
sites, potentially parsimony informative sites and GC content (Supplementary Table
S4). The average alignment length was 339.74 bp (min=120, max=1459) with most
5
April 28, 2023
(n=146) over 200 bp long. Parsimony informative sites were correlated with
alignment length (R² = 0.9593) with a mean of 238.42 sites per alignment (min=66,
max=1065) and a low percentage of missing data (8.61%, SD=0.43).
Coalescent-based (ASTRAL) and maximum likelihood (ML) concatenated
super-matrix analyses (IQ-TREE) of nucleotide and amino-acid data yielded similar
results (Extended Data Figs. 1-7). In the following sections, we present the results
from the ASTRAL analyses of nucleotide and amino-acid data including quartet
values and gene concordance factors (gCF) and site concordance factors (sCF). We
refer to a majority of gene trees when more than 50% of these share a given signal,
and a plurality of gene trees when the proportion of trees supporting the topology is
higher than 33% but less than 50%. The gene concordance factor (gCF) and site
concordance factor (sCF) represent the percentage of decisive gene trees and sites
containing a specific branch20. ASTRAL quartet values and IQ-TREE concordance
factors for nucleotide and amino-acid analyses are presented in the Supplementary
information (Supplementary Figs. S1–S8; Supplementary Tables S5–S8).
Phylogenetic relationships within hornworts: The circumscription and
relationships of classes and orders within the hornworts, Anthocerotophyta (Fig. 2
and Extended Data Figs. 1 and 4) reflect those inferred from organellar markers and
a broad taxon sampling13 except for the affinities of the monotypic
Leiosporocerotales. The monophyly of subclasses and orders is typically supported
by a large majority of loci, whether inferences are based on nucleotides (Extended
Data Fig. 1; Supplementary Figs. S1 and S2) or amino-acid data (Extended Data
Fig. 4). By contrast, the relationship of Leiosporoceros is ambiguous, as it is resolved
6
April 28, 2023
as sister to Anthocerotales (i.e., Anthoceros) based on nucleotide gene trees
(ASTRAL) (Fig. 2 and Extended Data Fig. 1) or to all hornworts based on
concatenated nucleotide data (Supplementary Fig. S5) or with ambiguous affinities
based amino-acid gene trees (Extended Data Fig. 4).
The position of Leiosporoceros as sister to all other hornworts was previously
proposed based on few organellar loci sampled for a large set of taxa21–23 and from
over 400 loci sequenced for selected hornwort placeholders19,24. The novel
phylogenetic hypothesis in the ASTRAL analysis would impact ancestral state
reconstructions for the hornwort pyrenoid: if Leiosporoceros is sister to all hornworts,
the pyrenoid-less state would be predicted as the ancestral condition in hornworts13,
whereas under the alternative topology the presence of the pyrenoid may be
ancestral in hornworts with subsequent losses in Leiosporoceros. Under either
scenario, pyrenoids have been independently lost in all hornwort orders, and gained
in the derived Dendrocerotales13.
Phylogenetic relationships within liverworts: The earliest split within
liverworts segregates the Haplomitriopsida (21 spp.) from the ancestor to the
Marchantiopsida (mostly complex thalloid taxa, ca. 543 spp.) and the
Jungermanniopsida (simple thalloid and leafy liverworts, over 6870 spp.), a topology
supported by a small majority of loci (Fig. 2; Extended Data Figs. 2 and 5). Within the
three classes, ordinal circumscriptions and relationships generally reflect prevailing
interpretations14,25–28, with most backbone nodes supported by a majority of loci and
high posterior probabilities (Fig. 2 and Fig. 3; Extended Data Figs. 2 and 5).
7
April 28, 2023
The Haplomitriopsida comprise plants with leaf-like appendages, stems
secreting copious mucilage and one primary androgonial initial in early ontogeny29.
The earliest split in the Marchantiopsida segregates the Marchantiidae (complex
thalloids) from the Blasiidae, a lineage of two simple thalloid species with endophytic
cyanobacteria30,31. The Marchantiidae typically develop a complex thallus with air
chambers, four primary androgonial initials in early ontogeny, and unlobed
sporocytes29. The ordinal relationships within the Marchantiidae vary in support (Fig.
2 and Fig. 3; Extended Data Figs. 2 and 5). The Neohodgsoniales comprise a single
species from New Zealand, diagnosed by a uniquely branched carpocephalum, and
mark another deep split in the subclass27. The Sphaerocarpales comprise mostly
taxa with leafy-like gametophytes and are sister to the Marchantiales, although not
supported by most gene trees (Fig. 2 and Fig. 3; Extended Data Figs. 2 and 5). The
Marchantiales contain the majority of the species of the class (ca. 497 spp.),
including the model species Marchantia polymorpha32.
The Jungermanniopsida include species developing simple thalloid or leafy
vegetative bodies, all with antheridia developed from two primary androgonial initials
in early ontogeny and with lobed sporocytes29. The Jungermanniopsida are typically
accommodated in three subclasses, whose monophyly and relationships are not
consistently resolved (Figs. 2 and 3) perhaps due to ancient introgression31. The
Pelliidae comprise two robustly monophyletic orders (i.e., Pallaviciniales and
Pelliales) and the Fossombroniales, which are supported by most nucleotide gene
trees but only a small plurality of amino-acid loci (Extended Data Figs. 2 and 5). The
relationships among the three orders are congruent only among a plurality of gene
trees (Extended Data Figs. 2 and 5), with the paraphyly of the subclass caused by
the resolution of the Pelliales sister to all other Jungermanniopsida based on
8
April 28, 2023
nucleotide data23 (Figs. 2 and 3; Extended Data Fig. 2) versus sister to other
Pelliidae based on amino-acid data with ambiguous signal (Extended Data Fig. 5).
Such conflicting topologies were previously recovered based on nucleotide-based
nuclear transcriptome and mitochondrial data24, and plastid data28,33, respectively,
and may reflect a rapid divergence of the Pelliidae, ancient introgression, incomplete
lineage sorting and subsequent saturation in nucleotide data.
The Metzgeriidae compose a robustly monophyletic group comprising the
Metzgeriales and Pleuroziales (Fig. 2; Extended Data Figs. 2 and 5), as previously
resolved based on a few DNA loci25,34,35, and genomic, transcriptomic and organellar
data28,33. The monophyly of the Metzgeriidae is supported by the unique shared
lenticular apical cell giving rise to the bilaterally symmetric and thalloid body of the
Metzgeriales and the leafy stem of the Pleuroziales23.
The vast majority of liverworts (ca. 6160 spp.) belong to the well supported
clade Jungermanniidae or true leafy liverworts (Figs. 2 and 3; Extended Data Figs. 2
and 5). A shared ancestry of the Ptilidiales and Porellales sensu lato, as inferred
from nuclear nucleotide data (Fig. 2; Extended Data Fig. 2) was recently argued for
based on phylotranscriptomic and plastid evidence33. By contrast, our amino-acid
data resolve the Ptilidiales as sister to the Jungermanniales s. lato (Extended Data
Fig. 5), a hypothesis also supported by mitochondrial data23,33 and prior plastidbased inferences25,28. A majority of genes recover the monophyly of the Porellales s.
lato, which we propose to accommodate into three resurrected and two new orders
(Table 1), each of pre-Cretaceous origin: Frullaniales, Jubulales, Lejeuneales
Porellales, and Radulales (Fig. 2; Extended Data Figs. 2 and 5). The Frullaniales
(ca. 599 spp.) and Lejeuneales (ca. 1900 spp.) comprise two of the most species-
9
April 28, 2023
rich families of liverworts characteristic of epiphytic communities, particularly in
tropical rainforests15.
Within the Jungermanniales s. lato, the deepest splits giving rise to the main
lineages are estimated to have occurred in or prior to the Triassic, and we therefore
propose to recognize these at the ordinal level, resurrecting Perssoniellales36,
Lepidoziales and Lophoziales and erecting Myliales (Table 1). The Perssoniellales
(ca. 88 spp.) emerged from the earliest split (Fig. 2) in the Carboniferous (Fig. 3) and
are sister to the common ancestor shared by the remaining others. The Myliales (5
spp.) mark the next split based on nucleotide data (Figs. 2 and 3; Extended Data Fig.
2) or are sister to the Lophoziales only, based on amino-acid data, although with low
support (Extended Data Fig. 5). Either resolution is incongruent with Mylia sister to
the Jungermanniales s. str. based on nuclear transcriptomic and organellar data33, a
hypothesis based, however, on a mislabeled specimen (Y. Liu, pers. com. March
2023).
A majority of nucleotide, and at least a plurality of amino-acid, gene trees
resolve the remaining orders of the Jungermanniales s. lato, i.e., the Lophoziales
(ca. 611 spp.), Lepidoziales (ca. 1943 spp.) and Jungermanniales s. str. (ca. 565
spp.) as monophyletic (Extended Data Figs. 2 and 5, respectively). All three
suborders are highly heterogenous in terms of leaf morphology (2–4 lobes),
branching patterns, form, and position of gametangia37. The sister-group relationship
of the latter two suborders most recently supported by nuclear transcriptomic and
organellar data33, emerges here also from a near majority of nucleotide loci but only
a weak plurality of amino-acid loci (Extended Data Figs. 2 and 5, respectively). The
resolution within suborders seems to vary, especially within species-rich families
10
April 28, 2023
(e.g., Lepidoziaceae) and may point to a period of rapid diversification (Extended
Data Figs. 2 and 5).
Phylogenetic relationships within mosses: The phylogenetic structure in
mosses (Fig. 2; Extended Data Figs. 3 and 6) is congruent with most current
supraordinal circumscriptions and ordinal relationships and shaped primarily by
innovations in sporangial dehiscence, peristome architecture and development, and
by vegetative body plant organization relative to sex organ position29,38. The
circumscription and relationships of classes and subclasses sensu29,38,39 are typically
supported by a majority or a plurality of loci (Fig. 2; Extended Data Fig. 3) or their
amino-acid translations (Extended Data Fig. 6), while concordance among
nucleotide loci is typically low for clades following the initial splits within the
Bryophyta (Fig. 2; Supplementary Tables S5 and S7).
The current classification11 accommodates mosses into four subdivisions,
which are here recovered as emerging from the deepest splits, with the
Takakiophytina sister to all other extant mosses, followed by the Sphagnophytina
and the Andreaeophytina, which comprise the two lineages of lantern mosses (i.e.,
Andreaeales and Andreaeobryales) and are sister to the remaining mosses
composing the Bryophytina (Fig. 2; Extended Data Figs. 3 and 6). The latter
comprise species potentially developing stomata on their sporangia and a peristome,
a set of teeth lining the sporangial mouth and controlling spore dispersal12. Thus, the
lack of stomata in the other subdivisions is considered to result from independent
losses5, which given the topology occurred independent in all three bryophyte
lineages.
11
April 28, 2023
Mosses developing peristome teeth made of whole cells (i.e., nematodontous
peristome, Fig. 1K) compose a monophyletic group, the Polytrichopsida s. str., as
previously suggested38. The monospecific Oedipodiales were resolved either as
sister to all peristomate mosses in a small plurality of nucleotide gene trees (Fig. 2,
Extended Data Fig. 3) and congruent with signal from organellar loci38, or only to the
Polytrichopsida in a small plurality of amino-acid gene trees40 (Extended Data Fig.
6). The ambiguous placement of the Oedipodiales from nucleotide data likely
emerges from a combination of a relatively rapid divergence (Fig. 3) and saturation
in nucleotide substitution, as the more conserved amino-acid data more robustly
resolve the Oedipodiales as sister to the Polytrichales and Tetraphidales, similarly to
inferences from a distinct set of hundred nuclear loci38.
The remaining mosses (i.e., Bryopsida) typically develop a peristome
composed solely of cell plates rather than whole cells (Fig. 1L). Such joined and
hence articulate teeth lining the sporangial or capsule mouth upon dehiscence likely
constitute a key innovation that optimizes and controls spore release and is
developed by the vast majority of mosses. Several arthrodontous peristome types
arise from distinct developmental sequences12 and these largely define monophyletic
groups38. However, the resolution of Catoscopium as sister to most Dicranidae may
call for an amendment of Dicranum-peristome type diagnosis41. Although mature
peristomes may be variably reduced, especially along environmental gradients42, the
fundamental architecture and ontogeny seem highly conserved during the
diversification of mosses.
The vast majority of mosses belong to the Bryidae, a lineage diagnosed by its
double peristome of alternating inner and outer teeth43. The subclass comprises the
12
April 28, 2023
most speciose superorder of mosses, the Hypnanae or pleurocarpous mosses (ca.
4903 spp.), which are characterized by a homogenous anatomy of their midrib, the
lateral development of female sex organs, and hence of the sporophyte on the
maternal gametophyte44,45. The Hypnanae comprise five orders (i.e.,
Hypnodendrales, Ptychomniales, Hypopterygiales, Hookeriales and Hypnales),
whose relationships match those previously recovered38 but are here, too only
supported by a plurality of loci (Fig. 2; Extended Data Figs. 3 and 6). While a lateral
shift of the sex organs and the associated shift to monopodial growth has occurred in
other moss lineages46, such as the Orthotrichales, the persistence of lateral female
sex organs in all Hypnanae suggest that this trait is either under strong genetic
constraint or selection (see 47,48). Within the Hypnales, the most diverse order of
mosses49 the backbone relationships are typically shared only by a plurality of gene
trees (Fig. 2; Extended Data Figs. 3 and 6), likely reflecting a rapid early radiation of
the order50. The recurrent phylogenetic pattern of species-rich families being either
paraphyletic due to the inclusion of additional, morphologically distinct lineages, or
polyphyletic following their phylogenetic fragmentation, and the resolution of various
species poorer lineages across the backbone phylogeny, reveals that morphological
traits, and primarily the vegetative ones, are evolutionarily highly labile within the
Hypnales. Transformations of putative homologous traits appear highly
homoplasious, and potentially correlated, yielding morphologically highly
heterogenous clades. Such homoplasy may even span across subclasses, as
reflected by Sorapilla, the sole member of Sorapillaceae, and which was originally
placed in Dicranidae, but was then moved to the Hypnales51. Based on the first DNA
sequences obtained for this genus, we resolve the family in the Dicranidae as
proposed earlier52,53 but in an isolated position within the Dicranalean grade (Fig. 2;
13
April 28, 2023
Extended Data Figs. 3 and 6), prompting the proposal for a new order, Sorapillales
(Table 1).
The Hypnanae emerged from the acrocarpous Bryidae that typically develop
terminal sex organs. The Bryidae are consistently recovered as paraphyletic across
all present (Fig. 2; Extended Data Figs. 3 and 6) and prior38 analyses. While all
orders are recovered with strong support, the relationships among them are typically
supported only by a plurality of loci (Fig. 2; Extended Data Figs. 3 and 6). The
relationships among the Rhizogoniales, Orthotrichales, Orthodontiales and
Aulacomniales inferred here from nucleotide data (Fig. 2; Extended Data Fig. 3)
match those previously proposed38 based on amino-acid sequences. However, the
present protein-based topology (Extended Data Fig. 6) differs in that a clade
comprising some members of the Rhizogoniales, along with Hymenodontopsis, a
member of the Aulacomniaceae, are sister to the Hypnanae, whereas the
Orthotrichales, Orthodontiales and Aulacomniales, and Goniobryum (a member of
the Rhizogoniaceae) compose a single lineage sister to the Rhizogoniales and
Hypnanae (Extended Data Fig. 6). The relationships of these orders are in all cases
supported only by a small plurality of loci. Furthermore, inferences from nucleotide
versus amino-acid data resolve incongruent circumscriptions of the Rhizogoniales.
Calomnion, a genus of a few South Pacific Island species54 is reconstructed as sister
to the Hypnanae except Hypnodendrales or all Hypnanae based on nucleotide
versus amino-acid data, respectively (Fig. 2; Extended Data Figs. 3 and 6). In none
of the alternative topologies are the relationships supported by a majority of loci, and
hence the circumscription of the Rhizogoniales remains uncertain. The early
diversification of the Bryidae gave rise to the Bartramiales, Bryales, Hedwigiales, and
Splachnales, which compose robust lineages but of uncertain relationship. The
14
April 28, 2023
Helicophyllaceae (Hedwigiales), diagnosed by plagiotropic shoots and dimorphic
leaves55, are robustly resolved as sister to the Bartramiaceae (Figs. 2 and 3;
Extended Data Figs. 3 and 6; see also 56).
Within the Dicranidae, the sister group to the Bryidae, the relationships are
congruent with previous hypotheses33 and strengthen the hypothesis of a broadly
polyphyletic Dicranales. The earliest splits within the subclass gave rise to the
Catoscopiales, followed by the here erected Distichiales and Flexitrichales (Table 1).
The later holds only the Flexitrichaceae, a family here formally recognized (Table 1),
and is likely sister to a here not sampled Scouleriales (sensu 57; Fig. 2). The next
split yields the Grimmiales, sister to the clade composed of the Archidiales, the
dicranalean grade and the Pottiales (Fig. 2; Extended Data Figs. 3 and 6). The
circumscription of the Archidiales Limpr. is here broadened to include the
Micromitriaceae and Leucobryaceae, as the Archidiaceae are nested between the
latter two families (Fig. 2; Extended Data Figs. 3 and 6)58.
The Dicranales are consistently resolved as a grade leading to the well
supported Pottiales (Fig. 2; Extended Data Figs. 3 and 6), a hypothesis congruent
with prior phylogenetic studies38,58,59. To integrate the phylogenetic resolution of the
dicranalean grade into the current classification, we propose to restrict the
Dicranales (Fig. 2) to only the Dicranaceae, Calymperaceae, Fissidentaceae and
Octoblepharaceae, and accommodate the remaining families, which all have an
origin no later than the Jurassic (Fig. 3), in the Amphidiales, Bruchiales, Ditrichales,
Erpodiales, Eustichiales, Pleurophascales and Rhabdoweisiales (Table 1). Despite
these systematic novelties, various families of the Dicranales s. lato remain
unassigned (e.g., Amphidiaceae, Distichiaceae, etc.) awaiting further study.
15
April 28, 2023
Our phylogenomic inferences confirm that the Timmiidae, restricted to Timmia
characterized by a unique peristomial architecture60, compose the sister lineage to
the ancestor of the Dicranidae and Bryidae38. The Funariidae, which include the
model taxon Physcomitrium patens61 along with the Diphysciidae and Buxbaumiidae,
each with a distinct peristome type compose the basal grade within the Bryopsida.
Thus, the main transformations of the arthrodontous peristome, yielding the various
fundamental types, occurred during the Permian or even late Carboniferous (Fig. 3)
rather than in the first half of the Paleozoic as previously proposed (Laenen et al.
2014).
500 million years of bryophyte diversification
Divergence time estimates of the first comprehensive phylogenomic
reconstructions of bryophytes confirm that they arose in the Ordovician16. Speciose
lineages arose during the diversification of angiosperms in the Cretaceous (Fig. 3;
Extended Data Figs. 7, 10). The common ancestor to extant lineages of mosses and
liverworts is traced to 420 [416–424] Ma and 447 [444–450] Ma, respectively, which
is consistent with recent estimates8,13,15,16,44. The lineage through time plots (Fig. 3B)
suggest a rather steady diversification of both lineages over the last 400 My with a
higher net moss diversification near mid Cretaceous. The average crown age of
orders as recognized here across all three bryophyte lineages is 150.5 Ma (SD 70
Ma) (Fig. 3C; Supplementary Table S10). The crown age of the most species rich
bryophyte order, the Hypnales (491 genera, ca. 4150 species) is 129 [78–173] Ma,
and thus younger than previously estimated62. The origin of mosses and liverworts
(419–447 Ma, crown group Setaphyta) seem to be slightly older than that of extant
lycophytes and their sister group, the euphyllophytes16. The age of most bryophyte
16
April 28, 2023
orders coincides with the diversification of angiosperms during the Late Jurassic and
Cretaceous63.
Our estimates of family stem ages suggest that most bryophyte families (63%
of families, n=166) originated during the Cretaceous (65 families) and Jurassic (40
families). Extant bryophyte families (crown ages, n=80) diversified predominantly
during the Late Cretaceous (66–102 Ma, 27 families) and the early Cretaceous
(103–145 Ma, 18 families) and the Cenozoic (–65 Ma, 26 families). The average
crown age of bryophyte families is 98 Ma (SD 51 Ma) (Extended Data Fig. 10;
Supplementary Table S10; Supplementary Fig. S9). In mosses, the crown age of the
Pottiaceae (77 genera, ca. 1,209 species) is estimated at 133.3 [115–150] Ma and
the Orthotrichaceae (24 genera, ca. 900 species) started to diversify around 139.6
[106–169] Ma. Within liverworts, the diversification of the hyperdiverse Lejeuneaceae
(ca. 88 genera, ca. 1900 species) began around 149 [116–188] Ma while that of the
Lepidoziaceae (31 genera, ca. 703 species) dates to 121 [114–166] Ma. As
previously suggested for bryophyte genera14, bryophyte diversity may have accrued
during the Cretaceous and Cenozoic14 (Fig. 3C). Our analyses support the
Cretaceous terrestrial revolution63,64 wherein the majority of bryophyte families
diversified during this period (Fig. 3; Extended Data Fig. 10; Supplementary Table
S10; Supplementary Fig. S9) contributing to an explosive radiation of life. The
Cretaceous expansion of the angiosperm canopy and diversification of
leptosporangiate ferns65 potentially provided novel habitats for bryophytes to
diversify in tropical and subtropical areas. In addition, global and local extinctions,
and the climatic fluctuations during the Cretaceous and Cenozoic may explain the
burst of diversity in lineages occupying new niches in arid regions (e.g., Pottiales,
17
April 28, 2023
Marchantiales) or open areas (e.g., Funariales, Polytrichales) before the explosive
diversification of angiosperms and ferns.
Conclusions
Bryophytes are the second-most diverse group of land plants, compose the sister
group to extant vascular plants8,24 and contribute significant ecosystem functions in
communities where they are abundant. Bryophytes are thus critical to understand the
polarity of character transformations early in the evolution of land plants, and
contemporary ecological processes, in particular, local and global nutrient flows. In
parallel to the loss of complexity of the vascular plant gametophyte, this puts
renewed importance on comparative studies of gametophyte morphology and
function. The ordinal-level phylogeny of the bryophytes, based on the GoFlag408
probe set, provides an expandable resource upon which to build such studies.
Our results are largely consistent with previous efforts based on fewer loci or
representative taxon sampling, with some interesting exceptions (Fig. 2) suggesting
that the bryophyte phylogenetic studies are converging on a relatively stable set of
relationships. The incongruence found in several nodes along the backbone implies
that different genes coalesce to variable and conflicting topologies, especially in
recent radiations (e.g., Hypnales), or are remnants of potential ancient
introgressions33 (Fig. 3; Extended Data Figs. 8 and 9) or incomplete lineage sorting.
The current challenge facing the community is to fill in unsampled genera, species,
or populations of focal taxa. At shallower phylogenetic depth, the data could be
expanded to the flaking intron and spacer regions that are generally more variable
18
April 28, 2023
than the exonic regions, and hence suitable for resolving population genomic
problems within or between populations of single species, or groups of closely
related species. The growing GoFlag 408 database of sequences used here, and in
other studies, provides a sturdy scaffold in which to place more focused studies.
Methods
Taxon sampling
We sampled in total 531 bryophyte species belonging to 499 genera (Supplementary
Table S3), comprising 362 moss species representing 338 genera (34 %); 159
liverwort species that can be assigned to 151 genera (37 %), and 12 hornwort
species from 10 genera (100 %).Sampling percentage values were calculated using
recent checklists and classification literature66–68. Hornworts were assumed to be the
sister group of the other two bryophyte clades based on 24.
DNA Extraction
We used the modified cetyltrimethylammonium bromide (CTAB) extraction protocol69
described in 19 for most of the samples. This includes lysing the cells by centrifuging
them and performing two rounds of chloroform/isoamyl 24:1 wash followed by cold
isopropanol precipitation and an ethanol 70% wash. Finally, we added 2 μl of 10
mg/Ml ml RNase A (QIAGEN, Valencia, California, United States) to remove RNA
contamination between chloroform washes. For a few specimens (Lejeuneaceae)
19
April 28, 2023
the Invisorb Spin Plant Mini Kit (Stratec Molecular GmbH, Berlin, Germany) was
used following the kit protocol.
Target Enrichment and Sequencing Assembly
We generated a multi-locus nuclear sequence dataset with a target enrichment
approach using the GoFlag probe sets. We assembled published data from 36
samples generated using the GoFlag 451 probe set and generated new data from
497 samples using the GoFlag 408 probe set, an optimized subset of the GoFlag
451 probe set consisting of 53,306 probes covering 408 exons from single or low
copy nuclear loci. The library preparation, target enrichment, and sequencing were
done by RAPiD Genomics (Gainesville, FL USA) using protocols described in 19, with
the enriched, pooled libraries sequenced on an Illumina HiSeq 3,000 platform
(Illumina; 2 × 100 bp).The paired end raw reads are available in the NCBI SRA
database. We assembled phylogenetic sequence alignments for each locus using
the iterative baited assembly pipeline19. In some loci, the pipeline retains more than
copy per sample, where the Bridger70 assembler interprets greater than simple allelic
variation. To control this, we removed all copies of a sample in a locus alignment
(script "rmall.pl"). Second, we removed any columns in the alignments that had
nucleotide data from fewer than ten samples in all output PHYLIP files. We also
pruned out sequences associated with excessively long branches in the locus trees.
First, we inferred maximum likelihood (ML) trees from the locus alignments using
RAxML using the GTR CAT model, and we rooted the resulting gene trees with
Newick Utilities71 using the hornworts as the outgroup. We eliminated one locus for
which hornworts were not monophyletic. For the others, we calculated the root to tip
20
April 28, 2023
distance for each taxon and pruned out any sequences that had a root to distance
>3 standard deviations more than the average for that locus. This removed 750 out
of 178,650 sequences. We then for each locus examined the trees with branch
lengths >1 and removed 35 additional long branch sequences. All loci correspond to
exons, and some which are part of the same gene19. Thus, to create gene
alignments, we concatenated any loci found in the same gene, resulting in 228 gene
alignments that were used in our analyses. We also created amino-acid alignments
for each gene. To do this, we took the original locus alignments and removed any
columns sequence alignments with only one nucleotide, most likely representing
sequencing error. We used AliView72 to make edits by hand to put the alignments in
frame; usually this required minimal editing to getting the alignments in line. We then
saved the corresponding amino-acid alignments and concatenated the loci from the
same gene.
Phylogenomic analyses
We performed Maximum Likelihood phylogenetic inferences of the concatenated
nucleotide dataset implemented in IQ-TREE v.2.173. Loci located within the same
gene were concatenated and the dataset was partitioned by genes (228 genes) and
were used for nucleotide and amino-acid analyses. The best-scoring ML tree and a
rapid bootstrap analysis with 100 replicates was run. In all cases a GTRGAMMA
model of sequence evolution was chosen. Moreover, we used IQ-TREE v.2.173 for
phylogenetic inference on the translated matrix dataset (into amino-acids), with “-S
option” that load all alignment files within the directory. We performed auto model
21
April 28, 2023
selection (ModelFinder) and tree inference separately for each gene. Branch support
was assessed using ultrafast bootstrapping (1000 replicates)74.
We conducted species tree analyses using ASTRAL-III v.5.7.775. Gene trees were
estimated in RAxMLv.8.2.976,77 under the following settings for the nucleotide
dataset: the default RAxML tree search algorithm (-f d) was implemented and a
GTRGAMMA model selected. The loci belonging to the same gene were combined
prior to the gene tree estimation, resulting in 228 unrooted gene trees. For aminoacids dataset gene trees were estimated in IQ-TREE v.2.1, with “-S option” (see
above). ASTRAL-III was employed for species tree inference on both gene tree
datasets using the default settings and computing local posterior probabilities78 as
well as quartet scores for all three resolutions per branch (-t 8). The resulting
ASTRAL topologies were annotated with quartet support values78 for the main
topology (q1), the first alternative topology (q2), and the second alternative topology
(q3). We also used the built-in functionality of ASTRAL to compute the percentage of
gene trees that agreed with each branch in the species tree, by finding the average
number of gene-tree quartets defined around the branch (choosing one taxon from
each side) that were congruent with the species tree. Similar phylogenetic analyses
were conducted on the translated matrix (into amino-acids). We used DiscoVista79 to
visualize the results.
In addition to bootstrap (IQ-TREE) and local posterior probabilities (ASTRAL), we
implemented the gene (gCF) and site (sCF) concordance factors to investigate
topological conflict around each branch of the species tree for the nucleotide and
amino-acid datasets in IQ-TREE, using the “–gcf and –scf ” options20, particularly for
22
April 28, 2023
the backbone nodes. Likewise, we compared the species and gene trees generated
with ASTRAL (gCGAst, sCFAst, sDFPAst) and IQ-TREE (maximum likelihood,
gCGmL, sCFmL, gDFPmL) to evaluate possible divergences. These analyses
measured every branch of the species tree; the gCF and sCF represents the
percentage of decisive gene trees and sites. The program also estimates gDFP
(gene discordant factor due to paraphyly) or the gene discordance factor due to lack
of information in the genes or paraphyly of the quartet. For measures of support
gene concordance factor/site concordance factor (gCF/sCF) was categorized as
follows” weak < 33, moderate 33–50, strong > 50 (following 20,80). Using the ASTRAL
output, we analyzed whether the discordance among gene trees or sites regarding
the neutral ILS model implemented in IQ-TREE. We carried out χ2 tests comparing
the number of trees or sites supporting discordant topologies with roughly equal
quartet values. Under the assumption of ILS, the discordant topologies should be
supported by an equal number of gene trees or sites (Supplementary Table 12).
Equal quartets, gcf or scf (~33%) for the tree quartets point out to incomplete lineage
sorting or ancient introgression20. We performed correlation analyses between
branch lengths, divergence times (see below) and concordance factor values using
linear regressions.
Divergence time estimation
Divergence time estimation was performed in treePL81 according to the analysis
guidelines of
82
. The best-ML tree as input for treePL was selected from the
maximum likelihood analysis (see above). In order to be able to infer node bars on
the dated tree, a set of bootstrap replicates were run through the
23
April 28, 2023
“Bootstrap+Consensus” workflow of RAxML-HPC2 on XSEDE on the CIPRES
Science Gateway83, whereby the best ML tree served as constraint, the option to
print branch lengths on the BS replicates was selected, a partition scheme by genes
(i.e., loci were grouped together according to their relatedness to genes) was
implemented as well as a GTR+G substitution model and 1000 bootstrap iterations.
All trees were rooted with hornworts set to be the sister group of other bryophytes,
using the program pxrr in phyx84 that was also used in the dating analysis. We
calibrated 16 liverwort and 13 moss nodes stemming from fossil evidence
(Supplementary Table S2) and implemented a maximum age constraint of the root of
515 Ma16. Priming and cross-validation analyses were performed using the best-ML
tree and all 29 calibrations. Best optimization parameters were indicated as the
follows: opt = 2, optad = 2, optcvad = 5. Cross-validation used these parameters and
was done four times, indicating stable values of a smoothing parameter = 10. To
obtain confidence intervals on the dated tree, we ran the treePL analysis with the
bootstrap replicates using the same calibration, optimization and cross-validation
values as outlined above. The set of trees was summarized in TreeAnnotator
v.2.6.685; (part of the BEAST package) with mean node heights and 0% of burnin.
Trees were visualized in FigTree v.1.4.386. Lineage-through-time plots were
conducted on the treePL chronogram for all bryophyte taxa together, as well as
liverworts and mosses separated using the R-package “ape”87,88. We visualized the
temporal distribution of order and family ages using the average stem and crown
age. Monotypic families or orders were excluded from the calculations
(Supplementary Table S10). Bryophyte species number were obtained from 66–68.
Absolute rates were estimated with the same calibrations and targeted ML
trees using r8s89. Among-lineage rate variation, as expected across such a dataset,
24
April 28, 2023
is high. The lowest absolute substitution rate in mosses characterizes the
Orthodontiales (1.34 × 10-04 subst/site/Ma) and the highest the Polytrichales (5.44 ×
10-04 subst/site/Ma). In liverworts, the variation spans from 3.53 × 10-04 subst/site/Ma
in the simple thalloid Pallaviciniales to 7.85 × 10-04 subst/site/Ma in the complex
thalloids (Marchantiopsida,) (Fig. 3; Supplementary Table S9). The rate variation
observed in our dataset set the stage to test specific hypotheses correlating natural
history traits (e.g., perennial vs annual taxa) and molecular rates across genes and
all bryophyte groups.
Data Availability Section
All bryophyte gene sequences, alignments for each gene and concatenated
alignments will be available from FigShare.
Acknowledgements
We thank all the herbaria that provided specimens. Funding was provided by the
NSF collaborative project “Building a Comprehensive Evolutionary History of
Flagellate Plants” (DEB #1541506 to JG Burleigh, EC Davis, S McDaniel, and EB
Sessa, and #1541545 to M von Konrat). A.A. acknowledges the financial support by
the University of Padova (BIRD 173749/17). BG acknowledges DEB-1753811. JCVA
acknowledges the Canada Research Chair (950-232698); the CRNSG- RGPIN
05967–2016 and the Canadian Foundation for Innovation (projects 36781, 39135)
25
April 28, 2023
Author contributions
G.B., S.M., D.B., G.P.-B., J.B., B.G., J.C.V.A. conceptualized the study.
B.G, J.C.V.A. wrote the first draft.
G.B., S.G., K.S.R., D.Q., J.L., F.L., I.D., E.S., J.B., D.B., G.P.-B., B.G., J.C.V.A.
participated in the final reviewing and editing.
A.B, A.M.S.P., A.S.-V., C.Z., C.D., D.C.C., I.D., J.J.L., J.L., L.L., M.v.K., S.C., S.H.,
D.L., L.E., L.L.F., P.L., R.G., G.E.L., K.F., J.B., G.P.-B., S.M., D.B., J.B., J.C.V.A.
participated in the specimen collections.
L.L., L.E., G.E.L., J.B., J.C.V.A. participated in data collection and laboratory work.
G.B., J.B., G.P.-B., A.M.S.P., B.G., J.C.V.A. performed the analyses.
G.B., C.D., E.S., S.M., J.C.V.A. procured funding.
Additional Information
References
1.
Puttick, M. et al. The interrelationships of land plants and the nature of the
ancestral embryophyte. Curr. Biol. 28, 733-745.e2 (2018).
2.
Sousa, F., Foster, P., Donoghue, P., Schneider, H. & Cox, C. Nuclear protein
phylogenies support the monophyly of the three bryophyte groups (Bryophyta
Schimp.). New Phytol. 222, 565–575 (2019).
26
April 28, 2023
3.
Rich, M. & Delaux, P.-M. Plant evolution: when Arabidopsis is more ancestral
than Marchantia. Curr. Biol. 30, R642–R644 (2020).
4.
Cammarata, J., Morales Farfan, C., Scanlon, M. & Roeder, A. Cytokinin–
CLAVATA cross-talk is an ancient mechanism regulating shoot meristem
homeostasis in land plants. Proc. Natl. Acad. Sci. 119, 1–11 (2022).
5.
Harris, B. J., Harrison, C. J., Hetherington, A. M. & Williams, T. A.
Phylogenomic Evidence for the Monophyly of Bryophytes and the Reductive
Evolution of Stomata. Curr. Biol. 30, 1–12 (2020).
6.
Bennett, T. et al. Plasma membrane-targeted pin proteins drive shoot
development in a moss. Curr. Biol. 24, 2776–2785 (2014).
7.
Lavy, M. et al. Constitutive auxin response in Physcomitrella reveals complex
interactions between Aux/IAA and ARF proteins. Elife 5, 1–22 (2016).
8.
Harris, B. J. et al. Divergent evolutionary trajectories of bryophytes and
tracheophytes from a complex common ancestor of land plants. Nat. Ecol.
Evol. (2022) doi:10.1038/s41559-022-01885-x.
9.
Porada, P., Weber, B., Elbert, W., Pöschl, U. & Kleidon, A. Estimating impacts
of lichens and bryophytes on global biogeochemical cycles. Global
Biogeochem. Cycles 28, 71–85 (2014).
10.
Stuart, J. et al. Host identity as a driver of moss-associated N2 fixation rates in
Alaska. Ecosystems 24, 530–547 (2021).
11.
Porada, P., Weber, B., Elbert, W., Pöschl, U. & Kleidon, A. Estimating global
27
April 28, 2023
carbon uptake by lichens and bryophytes with a process-based model.
Biogeosciences 10, 6989–7033 (2013).
12.
Goffinet, B., Buck, W. & Shaw, J. Morphology, anatomy, and classification of
the Bryophyta. in Bryophyte biology 55–138 (Cambridge University Press,
2009).
13.
Villarreal, J. C. & Renner, S. Hornwort pyrenoids, carbon-concentrating
structures, evolved and were lost at least five times during the last 100 million
years. Proc. Natl. Acad. Sci. 109, 18873–18878 (2012).
14.
Laenen, B. et al. Extant diversity of bryophytes emerged from successive postMesozoic diversification bursts. Nat. Commun. 5, 5134 (2014).
15.
Feldberg, K. et al. Epiphytic leafy liverworts diversified in angiospermdominated forests. Sci. Rep. 4, 5974 (2014).
16.
Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl. Acad.
Sci. 115, E2274–E2283 (2018).
17.
Feldberg, K. et al. Checklist of fossil liverworts suitable for calibrating
phylogenetic reconstructions. Bryophyt. Divers. Evol. 43, 14–71 (2021).
18.
Ignatov, M. S. & Maslova, E. V. Fossil mosses: What do they tell us about
moss evolution? Bryophyt. Divers. Evol. 43, 72–97 (2021).
19.
Breinholt, J. W. et al. A target enrichment probe set for resolving the flagellate
land plant tree of life. Appl. Plant Sci. 9, 1–28 (2021).
20.
Minh, B. Q., Hahn, M. W. & Lanfear, R. New Methods to Calculate
28
April 28, 2023
Concordance Factors for Phylogenomic Datasets. Mol. Biol. Evol. 37, 2727–
2733 (2020).
21.
Duff, J., Villarreal, J. C., Cargill, C. & Renzaglia, K. Progress and challenges
toward developing a phylogeny and classification of the hornworts. Bryologist
110, 214–243 (2007).
22.
Villarreal, J. C., Cusimano, N. & Renner, S. Biogeography and diversification
rates in hornworts: The limitations of diversification modeling. Taxon 64, 229–
238 (2015).
23.
Bell, D. et al. Organellomic data sets confirm a cryptic consensus on
(unrooted) land-plant relationships and provide new insights into bryophyte
molecular evolution. Am. J. Bot. 107, 91–115 (2020).
24.
Leebens-Mack, J. et al. One thousand plant transcriptomes and the
phylogenomics of green plants. Nature 574, 679–685 (2019).
25.
Forrest, L. L. et al. Unraveling the evolutionary history of the liverworts
(Marchantiophyta): Multiple taxa, genomes and analyses. Bryologist 109, 303–
334 (2006).
26.
Dong, S. et al. Plastid genomes and phylogenomics of liverworts
(Marchantiophyta): Conserved genome structure but highest relative plastid
substitution rate in land plants. Mol. Phylogenet. Evol. 161, 107171 (2021).
27.
Villarreal, J. C., Crandall-Stotler, B., Hart, M., Long, D. & Forrest, L.
Divergence times and the evolution of morphological complexity in an early
land plant lineage (Marchantiopsida) with a slow molecular rate. New Phytol.
29
April 28, 2023
209, 1734–1746 (2016).
28.
Yu, Y. et al. Chloroplast phylogenomics of liverworts: a reappraisal of the
backbone phylogeny of liverworts with emphasis on Ptilidiales. Cladistics 36,
184–193 (2020).
29.
Crandall-Stotler, B. J., Stotler, R. E. & Long, D. G. Morphology and
classification of the Marchantiophyta. in Bryophyte Biology (eds. Shaw, B. &
Goffinet, A. J.) 1–54 (Cambridge University Press, 2009).
30.
Liaimer, A., Jensen, J. & Dittmann, E. A genetic and chemical perspective on
symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant
Blasia pusilla L. Front. Microbiol. 7, 1–16 (2016).
31.
Renzaglia, K. S. & Duckett, J. G. Spermatogenesis in Blasia pusilla: from
young antheridium through mature spermatozoid. Bryologist 90, 419 (1987).
32.
Bowman, J. L. et al. Insights into Land Plant evolution garnered from the
Marchantia polymorpha Genome. Cell 171, 287-304.e15 (2017).
33.
Dong, S., Yu, J., Zhang, L., Goffinet, B. & Liu, Y. Phylotranscriptomics of
liverworts: revisiting the backbone phylogeny and ancestral gene duplications.
Ann. Bot. 1–13 (2022) doi:10.1093/aob/mcac113.
34.
Davis, E. C. A molecular phylogeny of leafy liverworts (Jungermanniidae:
Marchantiophyta). in Molecular systematics of bryophytes: progress, problems
and perspectives vol. 98 (eds. Goffinet, B., Hollowell, V. C. & Magill, R. E.) 61–
86 (Missouri Botanical Garden, 2004).
30
April 28, 2023
35.
He-Nygrén, X., Ahonen, I., Juslén, A., Glenny, D. & Piippo, S. Phylogeny of
liverworts-beyond a leaf and a thallus. in Molecular systematics of bryophytes:
progress, problems and perspectives vol. 98 (eds. Goffinet, B., Hollowell, V. C.
& Magill, R. E.) 87–118 (Missouri Botanical Garden, 2004).
36.
Schljakov, R. N. On the higher taxa of liverworts—class Hepaticae s. str. Bot.
Zhurnal 57, 496–508. (1972).
37.
Crandall-Stotler, B., Stotler, R. E. & Long, D. G. Phylogeny and classification
of the Marchantiophyta. Edinburgh J. Bot. 66, 155–198 (2009).
38.
Liu, Y. et al. Resolution of the ordinal phylogeny of mosses using targeted
exons from organellar and nuclear genomes. Nat. Commun. 10, 1–11 (2019).
39.
Goffinet, B., Buck, W. & Shaw, J. Addenda to the classification of mosses. I.
Andreaeophytina stat. nov. and Andreaeobryophytina stat. nov. Bryologist 112,
856–857 (2009).
40.
Chang, Y. & Graham, S. W. Patterns of clade support across the major
lineages of moss phylogeny. Cladistics 30, 590–606 (2014).
41.
Ignatov, M. S., Spirina, U. N., Ignatova, E. A., Krug, M. & Quandt, D. On the
systematic position of the moss genus Catoscopium, with a new approach to
the peristome reduction study. Arctoa 24, 389–415 (2015).
42.
Vitt, D. Adaptive modes of the moss sporophyte. Bryologist 84, 166–186
(1981).
43.
Goffinet, B. & Shaw, A. J. Bryophyte biology. (Cambridge University Press,
31
April 28, 2023
2009).
44.
Bell, N. E., Quandt, D., O’Brien, T. J. & Newton, A. E. Taxonomy and
phylogeny in the earliest diverging pleurocarps: Square holes and bifurcating
pegs. Bryologist 110, 533–560 (2007).
45.
Huttunen, S., Bell, N. & Hedenäs, L. The Evolutionary Diversity of Mosses –
Taxonomic Heterogeneity and its Ecological Drivers. CRC. Crit. Rev. Plant Sci.
37, 128–174 (2018).
46.
Farge-England, C. La. Growth Form, Branching Pattern, and Perichaetial
Position in Mosses: Cladocarpy and Pleurocarpy Redefined. Bryologist 99, 170
(1996).
47.
Coudert, Y., Bell, N., Edelin, C. & Harrison, C. Multiple innovations
underpinned branching form diversification in mosses. New Phytol. 215, 840–
850 (2017).
48.
Coudert, Y. et al. Three ancient hormonal cues co-ordinate shoot branching in
a moss. Elife 4, 1–26 (2015).
49.
Crosby, M. R., Magill, R. E., Allen, B. & He, S. A checklist ofthe mosses.
Missouri Bot. Gard. (1999).
50.
Shaw, A., Cox, C., Goffinet, B., Buck, W. & Boles, S. Phylogenetic evidence of
a rapid radiation of pleurocarpous mosses (Bryophyta). Evolution (N. Y). 57,
2226–2241 (2003).
51.
Meagher, D., Cairns, A., Seppelt, R. & Grixti, M. A re-evaluation of the
32
April 28, 2023
morphology of Sorapilla (Bryophyta: Sorapillaceae) based on Sorapilla
papuana. Aust. Syst. Bot. 33, 427–435 (2020).
52.
Lin, S. H. A taxonomic revision of Phyllogoniaceae (Bryopsida). part I J.
Taiwan Mus. 臺灣省立博物館半年刊 37, 1–54 (1983).
53.
Vitt, D. H. Classification of the Bryopsida. New Man. Bryol. 696–759 (1984).
54.
Vitt, D. H. The genus Calomnion (Bryopsida): taxonomy, phylogeny, and
biogeography. Bryologist 98, 338 (1995).
55.
Vitt, D. H. The New Zealand species of the pantropical genus Macromitrium
(Orthotrichaceae Musci) taxonomy, phylogeny and phytogeography. J. Hattori
Bot. Lab. 1–94 (1983) doi:10.18968/jhbl.54.0_1.
56.
Buchbender, V. et al. Phylogenetic reconstructions of the Hedwigiaceae reveal
cryptic speciation and hybridisation in Hedwigia. Bryophyt. Divers. Evol. 36, 1
(2014).
57.
Fedosov, V. E., Fedorova, A. V., Fedosov, A. E. & Ignatov, M. S. Phylogenetic
inference and peristome evolution in haplolepideous mosses, focusing on
Pseudoditrichaceae and Ditrichaceae s. l . Bot. J. Linn. Soc. 181, 139–155
(2016).
58.
Bonfim Santos, M. et al. Phylogenetic inferences reveal deep polyphyly of
Aongstroemiaceae and Dicranellaceae within the haplolepideous mosses
(Dicranidae, Bryophyta). Taxon 70, 246–262 (2021).
59.
Fedosov, V. E. et al. Unity in diversity: phylogenetics and taxonomy of
33
April 28, 2023
Rhabdoweisiaceae (Dicranales, Bryophyta). Bot. J. Linn. Soc. 195, 545–567
(2021).
60.
Budke, J., Jones, C. & Goffinet, B. Development of the enigmatic peristome of
Timmia megapolitana (Timmiaceae; Bryophyta). Am. J. Bot. 94, 460–467
(2007).
61.
Rensing, S. A., Goffinet, B., Meyberg, R., Wu, S.-Z. & Bezanilla, M. The moss
Physcomitrium ( Physcomitrella ) patens : A model organism for non-seed
plants. Plant Cell 32, 1361–1376 (2020).
62.
Newton, A. E., Wikström, N., Bell, N., Forrest, L. L. & Ignatov, M. S. Dating the
diversification of the pleurocarpous mosses. in Pleurocarpous Mosses (eds.
Newton, A. E. & Tangney, R. S.) 337 (Systematics and Evolution, 2007).
63.
Lloyd, G. T. et al. Dinosaurs and the Cretaceous Terrestrial Revolution. Proc.
R. Soc. B Biol. Sci. 275, 2483–2490 (2008).
64.
Benton, M. J., Wilf, P. & Sauquet, H. The Angiosperm Terrestrial Revolution
and the origins of modern biodiversity. New Phytol. 233, 2017–2035 (2022).
65.
Schuettpelz, E. & Pryer, K. M. Evidence for a Cenozoic radiation of ferns in an
angiosperm-dominated canopy. Proc. Natl. Acad. Sci. 106, 11200–11205
(2009).
66.
Söderström, L. et al. World checklist of hornworts and liverworts. PhytoKeys
59, 1–828 (2016).
67.
Brinda, J. C. & Atwood, J. J. Bryophyte nomenclator. Catalogue of life checklist
34
April 28, 2023
(Jan 2023) (2023). doi:10.48580/dfqt-8zmp.
68.
Goffinet, B. & Buck, W. R. Classification of the Bryophyta. http://bryology.
uconn. edu/classification/ (2020).
69.
Doyle, J. & Doyle, J. A rapid DNA isolation procedure for small quantities of
fresh leaf tissue. Phytochem Bull. 19, 11–15 (1987).
70.
Chang, Z. et al. Bridger: a new framework for de novo transcriptome assembly
using RNA-seq data. Genome Biol. 16, 30 (2015).
71.
Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic
tree processing in the Unix shell. Bioinformatics 26, 1669–1670 (2010).
72.
Larsson, A. AliView: a fast and lightweight alignment viewer and editor for
large datasets. Bioinformatics 30, 3276–3278 (2014).
73.
Nguyen, L.-T., Schmidt, H., von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast
and Effective Stochastic Algorithm for Estimating Maximum-Likelihood
Phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
74.
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L.
UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 35,
518–522 (2017).
75.
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time
species tree reconstruction from partially resolved gene trees. BMC
Bioinformatics 19, 153 (2018).
76.
Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post35
April 28, 2023
analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
77.
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–
2690 (2006).
78.
Sayyari, E. & Mirarab, S. Fast Coalescent-Based Computation of Local Branch
Support from Quartet Frequencies. Mol. Biol. Evol. 33, 1654–1668 (2016).
79.
Sayyari, E., Whitfield, J. B. & Mirarab, S. DiscoVista: Interpretable
visualizations of gene tree discordance. Mol. Phylogenet. Evol. 122, 110–115
(2018).
80.
Cooper, B. J. et al. Target Enrichment and Extensive Population Sampling
Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus.
Syst. Biol. 0, 1–15 (2022).
81.
Smith, S. & O’Meara, B. treePL: divergence time estimation using penalized
likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).
82.
Maurin, K. J. L. An empirical guide for producing a dated phylogeny with
treePL in a maximum likelihood framework. arXiv 2008.07054 (2020)
doi:10.48550/arXiv.2008.07054.
83.
Miller, M., Pfeiffer, W. & Schwartz, T. The CIPRES science gateway. in
Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery 1–8
(ACM, 2011). doi:10.1145/2016741.2016785.
84.
Brown, J., Walker, J. & Smith, S. Phyx: phylogenetic tools for unix.
36
April 28, 2023
Bioinformatics 33, 1886–1888 (2017).
85.
Bouckaert, R. et al. Beast 2: a software platform for bayesian evolutionary
analysis. PLoS Comput. Biol. 10, e1003537 (2014).
86.
Rambaut, A. FigTree-version 1.4. 3, a graphical viewer of phylogenetic trees.
http://tree.bio.ed.ac.uk/software/figtree/. (2017).
87.
Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics
and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).
88.
R Core Team, R. R: A language and environment for statistical computing.
Foundation for Statistical Computing https://www.r-project.org/ (2020).
89.
Werness, S. A. & Anderson, D. J. r8s, version 1.70 User’s Manual. at (2004).
37
April 28, 2023
Table 1: Description of novel families and orders of liverworts and mosses.
MARCHANTIOPHYTA (LIVERWORTS)
Lejeuneales Bechteler, A.M. Sierra, D. Bell & D.G. Long ord. nov.
Leaves mostly 2-lobed, the ventral lobule forming a Lejeunea-type water sac,
gynoecia with 1 archegonium and a single series of bracts and bracteoles, seta 4
cells in diameter, commonly articulate; Type: Lejeuneaceae Rostovzev, New
Phytol. 9: 291. 1910; Lejeuneaceae.
Frullaniales D. Bell & D.G. Long ord. nov.
Leaves 3-lobed, the median lobule forming a Frullania-type water sac, underleaves
bifid, gynoecia with multiple archegonia, bracts and bracteoles in 3 or 4 series,
seta up to 12 cells in diameter, non-articulate; Type: Frullaniaceae Lorch in
G.Lindau, Krypt.-Fl. Anf. 6: 174. 1914; Frullaniaceae.
Myliales D.G. Long & D. Bell ord. nov.
Leaves unlobed, branching mostly terminal, rhizoids numerous, leaves succubous,
simple, gemmiferous, with reduced underleaves, dioicous, sporophyte enclosed in
shoot calyptra and perianth; Type: Myliaceae Schljakov, Novosti Sist. Nizsh. Rast.
12: 308. 1975; Myliaceae.
BRYOPHYTA (MOSSES)
Amphidiales D. Bell & Goffinet ord. nov.
Plants acrocarpous, forming dense cushions, leaves crisped when dry, capsules
gymnostomous, emergent to shortly exserted; Type: Amphidiaceae M. Stech,
Nova Hedwigia 86: 14, 2008; Amphidiaceae.
38
April 28, 2023
Bruchiales Goffinet ord. nov.
Plants erect, acrocarpous, capsule with well-developed neck, peristome
haplolepideous; Type: Bruchiaceae Schimp., Coroll. Bryol. Eur.: 6, 1856;
Bruchiaceae.
Distichiales D. Bell & Goffinet ord. nov.
Plants acrocarpous, leaves distichous, spreading from broad sheathing base,
costa excurrent, monoecious, peristome haplolepideous; Type: Distichiaceae
Schimp., Syn. Musc. Eur. 135. 1860; Distichiaceae.
Ditrichales D. Bell & Goffinet ord. nov.
Plants erect, acrocarpous, with costate and mostly lanceolate leaves, sporangium
exserted with haplolepideous peristome, or immersed and cleistocarpous. Type:
Ditrichaceae Limpr., Laubm. Deutschl. 1: 482, 1887; Ditrichaceae.
Erpodiales Goffinet ord. nov.
Plants small, plagiotropic, leaves ecostate, cladocarpous, peristome
haplolepideous; Type: Erpodiaceae Broth., Nat. Pflanzenfam. I(3): 706. 1905;
Erpodiaceae.
Eustichiales Goffinet ord. nov.
Plants erect, leaves single costate, distichous with sheathing laminae, with lateral
sporophytes and erect capsules; Type: Eustichiaceae Broth., Nat. Pflanzenfam.
(ed. 2) 10: 420, 1924; Eustichiaceae.
Flexitrichaceae Ignatov & Fedosov ex Goffinet fam. nov. for Flexitrichaceae Ignatov
& Fedosov invalid
39
April 28, 2023
Plants acrocarpous; leaves straight to flexuose, from sheathing bases, dioecious,
peristome haplolepideous; Type: Flexitrichum Ignatov & Fedosov, Bot. J. Linn.
Soc. 181(2): 152. 2016; Flexitrichum.
Flexitrichales D. Bell & Goffinet ord. nov.
Plants acrocarpous; leaves straight to flexuose, from sheathing bases, dioecious;
Type: Flexitrichaceae Ignatov & Fedosov ex D. Bell & Goffinet; Flexitrichaceae.
Pleurophascales Goffinet ord. nov.
Plants robust, stems plagiotropic, branches erect, leaves acostate, sporophyte
exserted, capsule globose, cleistocarpous; Type: Pleurophascaceae Broth. Nat.
Pflanzenfam. I(3): 774, 1906; Pleurophascaceae.
Rhabdoweisiales D. Bell & Goffinet ord. nov.
Plants small, erect, acrocarpous, leaves unicostate, unistratose, peristome
haplolepideous; Type: Rhabdoweisiaceae Limpr. Laubm. Deutschl. 1: 271, 1886;
Rhabdoweisiaceae52 and Rhachitheciaceae.
Sorapillales Goffinet ord. nov.
Plants monopodial, vaginant leaves distichous, complanate, sporophyte lateral,
immersed, peristome haplolepideous with vestigial exostome; Type: Sorapillaceae
M. Fleisch, Musci Buitenzorg 3: 847, 1908; Sorapillaceae.
40
April 28, 2023
Figure 1. Representatives of major lineages of bryophytes and examples of traits unique to
hornworts, liverworts and mosses. A. Hornwort with longitudinally dehiscing sporophyte: Anthoceros
neesii. B. Pyrenoid (arrowheads) of the hornwort Phaeoceros perpusillus. C. Complex thalloid
liverwort: Marchantia paleacea. D. Simple thalloid liverwort: Metzgeria conjugata. E. Leafy liverwort:
Leiocolea badensis. F. Liverwort sporophyte before (left) and after (right) dehiscence: Fossombronia
pusilla. G. Oil bodies of Gymnocolea inflata. H. Polytrichopsida moss: Atrichopsis trichodon. I.
Acrocarpous moss: Orthotrichum anomalum. J. Pleurocarpous moss: Exsertotheca intermedia. K.
Nematodontous peristome of Polytrichum ohioense. L. Arthrodontous peristome of Bryum capillare.
Pictures kindly shared by Štěpán Koval (A, D, E, F & I), Sahut Chantanaorrapint (B), Des Callaghan
(C, J & L), Bernard Goffinet (H), Jerry Jenkins (K) and David Wagner (G).
41
April 28, 2023
CF DFP
DF1 DF2
SCF
48
35
93
29
63
94
37
70
29
95
50
71
53
96
53
82
72
30
97
26
94
31
68
84
69
45
36
46
56
47
43
44
48
40
73
44
98
48
25
74
23
99
45
50
44
75
28
100
56
51
63
76
42
101
22
52
76
77
32
102
50
53
35
78
53
103
29
42
79
31
104
57
55
45
80
46
105
42
56
28
81
46
106
33
57
39
82
78
107
35
58
61
83
91
108
47
59
78
84
32
109
37
60
37
85
60
110
40
61
32
86
39
111
52
62
45
87
51
63
23
88
29
64
24
89
71
65
61
90
40
93
66
94
91
64
55
30
28
11
35
31
64
38
41
33
36
33
34
56
15
42
35
48
16
42
36
38
17
47
37
42
18
52
38
49
40
13
14
19
30
39
82
Sorapillales*
Rhabdoweisiales*
61
74
76
Dicranales s. str.
Amphidiales*
73
72
Eustichiales*
Pleurophascales*
70
Archidiales
68
71
60
Grimmiales
69
64
67
Scouleriales
63 65
Flexitrichales*
66
62
Distichales*
56
Catoscopiales
Timmiales
Funariales
59
55
57
Encalyptales
58
Disceliales
Gigaspermales
75
54
48
Dicranales s. lato
Bryophyta
Polytrichales
52
50
Tetraphidales
Oedipodiales
51
Andreaeales
47
46
42
78
Diphysciales
Buxbaumiales
49
Andreaeobryales
Sphagnales
44
39
37
S
e
t
a
p
h
y
t
a
8
34
20
36
40
49
21
51
41
34
22
30
1
NA
23
44
2
35
24
36
25
34
26
30
27
68
28
25
Anthocerotophyta
83
Takakiales
32
12
Ditrichales* s. str.
Bruchiales*
Erpodiales*
85
81
79
Pottiales
86
77
53
Marchantiophyta
29
Splachnales
Hedwigiales
91
84
45
47
Bryales
Bartramiales
89
43
44
Rhizogoniales
96
94
87
48
9
Orthotrichales
98
88 92
Setaphyta
10
Aulacomniales
Orthodontiales
97 100
95
80
54
8
104
99 102
90
49
Calomnion
Hypnodendrales
103
101
Ptychomniales
107
105
92
67
44
Hypopterygiales
106
Bryophyta
42
Hypnales
Hookeriales
111
109
108 110
q3 q1
q2
23
82
4
52
5
44
6
48
7
51
24
17
14
6
2
Marchantiophyta
Pelliales
Marchantiales
16
Sphaerocarpales
15
Neohodgsoniales
Blasiales
Calobryales
13
12
10
1
Porellales s. lato
Radulales
Porellales
Ptilidiales
Metzgeriales
Pleuroziales
Pallaviciniales
18
4
Jubulales**
Frullaniales*
Fossombroniales
20
9
Lejeuneales*
34
21
11
3
29
27
19
Jungermanniales s. lato
Myliales*
Perssoniellales**
33
32
30
28
31
22 26
40
38
36
35
25
Lepidoziales**
Jungermanniales s. str.
Lophoziales**
41
Dendrocerotales
7
Phymatocerotales
5
Notothyladales
3
Anthocerotales
Leiosporocerotales
Anthocerotophyta
Figure 2. Phylogenetic inferences for 531 species from 499 genera belonging to orders from all three
bryophyte groups (mosses, liverworts and hornworts) based on ASTRAL analysis of 228 single-copy
nuclear genes (Supplementary Tables S1 and S3). The phylogram shows internal branch lengths
relative to coalescent unites between branching events, as estimated by ASTRAL-III v.5.7.7. The
nodes of interests have been numbered to illustrate quartet values from ASTRAL analyses presented
as pie-charts (right) and quartet values from concordance factor values (left), while the number in the
center is the site concordance factor (sCF). ASTRAL pies are divided into q1 (blue), q2 (orange) and
q3 (grey) with the percentage for q1 included in the pie diagram; see Supplementary Fig. S1 and Fig.
S2 for quartet values for all other nodes and local posterior probabilities. Pies for quartet values from
concordance factor values: CF (topology shown) and alternative options (DF1, DF2, DFP); see
Supplementary Tables S4-S6 for the concordance factors for all nodes. * marks newly proposed order
and ** resurrected order.
42
April 28, 2023
A
Bryanae*
100 200
500
B
bryophytes
50
liverworts
Mosses
Bryopsida
Bryidae
Hypnanae
C
Cam Ord Sil Dev
500
Car
Per
300
400
Tri
Jur
200
Cre
100
Dicranidae
1
2
5
10
N
20
mosses
Pal N
0 Ma
Liverworts
Metzgeriidae
Pelliidae
Jungermanniopsida
Jungermanniidae
Timmiidae Gigaspermidae
Funariidae Diphysciidae
Buxbaumiidae
Polytrichopsida
Andreaeopsida
Sphagnopsida
Takakiopsida
Marchantiopsida
Haplomitriopsida
Hornworts
Cambrian
500
Ordovician Silurian
450
Devonian
400
Carboniferous
350
300
Triassic
Permian
250
Cretaceous
Jurassic
200
150
100
Paleogene
50
Neo
0 Ma
Figure 3. A. Divergence time estimates for bryophytes inferred by penalized likelihood using 29 fossil
calibrations. The three bryophyte groups (hornworts, liverworts, mosses) are included with their major
suprafamilial taxonomic ranks including classes, subclasses, orders and suborders. Black dots
scattered in the tree represent calibration points (Supplementary Table S2). Detailed chronograms
with mean node ages including confidence intervals are reported in three parts: liverworts and
hornworts in Extended Data Figure 7-1, mosses Extended Data Figure 7-2 and Extended Data Figure
7-3. B. Lineage through time plots of all bryophytes (black line), liverworts (orange line) and mosses
(green line), reflecting the slowdown in diversification in liverworts during the Late Cretaceous when
43
April 28, 2023
compared to mosses. C. Histogram of the frequency of orders and families estimated from crown age
divergences of all bryophytes (hornworts, liverworts, and mosses). Kernel density plots depict the
probability distribution (95% confidence interval) of crown age divergences. The green dotted line
represents the average of family crown ages and orange dotted line represents the average of order
crown ages. See also Extended Data Fig. 10, Supplementary Table S10 and Supplementary Fig. S9.
44
Extended data
Phylogenomic 2me tree of bryophytes resolves 500 million years of
diversifica2on
Table of content
Extended Data Figure 1. Annotated ASTRAL phylogeny of hornworts inferred from nucleo:de
data, highligh:ng (supra-)ordinal rela:onships.
Extended Data Figure 2. Annotated ASTRAL phylogeny of liverworts inferred from nucleo:de
data, highligh:ng suprafamilial rela:onships.
Extended Data Figure 3. Annotated ASTRAL phylogeny of mosses inferred from nucleo:de data,
highligh:ng suprafamilial rela:onships.
Extended Data Figure 4. Annotated ASTRAL phylogeny of hornworts inferred from amino acid
data, highligh:ng (supra)ordinal rela:onships.
Extended Data Figure 5. Annotated ASTRAL phylogeny of liverworts inferred from amino acid
data, highligh:ng suprafamilial rela:onships.
Extended Data Figure 6 Annotated ASTRAL phylogeny of mosses inferred from amino acid data,
highligh:ng suprafamilial rela:onships.
Extended Data Figure 7. Divergence :mes es:mates for bryophytes inferred by penalized
likelihood using 29 fossil calibra:ons.
Extended Data Figure 8. Correla:on between gene concordance factor inferred by IQ-TREE and
number of genes in the nucleo:de dataset suppor:ng a node.
Extended Data Figure 9. Correla:on between gene concordance factor inferred by IQ-TREE and
mean divergence :mes for backbone nodes (between 130-450 Ma) inferred from the nucleo:de
data.
Extended Data Figure 10. Histogram of the frequency of orders and families (A) stem and (B)
crown es:mated age divergences of three bryophyte phyla (Anthocerotophyta, Bryophyta, and
Marchan:ophyta).
Extended Data Figure 1. Annotated ASTRAL phylogeny of hornworts inferred from nucleo:de
data, highligh:ng (supra-)ordinal rela:onships. Quartet values from ASTRAL analyses are
presented as pie-charts (q1:blue; q2:orange; q3:grey) for selected nodes with the percentage for
the first quartet (q1) included in the pie diagram; see Fig. S1 for quartet values for all other nodes.
Branches with maximum local posterior probability (lpp) are represented as solid black lines;
those with a lpp below 0.80 as a grey dashed line; see Fig. S2 for detailed lpp for all branches.
Telaranea blepharostoma
Tricholepidozia tetradactyla
Lepidozia reptans
Kurzia trichoclados
Amazoopsis diplopoda
Bazzania pearsonii
Herbertus aduncus
Lepidoziales**
Herbertus sendtneri
Triandrophyllum sp.
Mastigophora woodsii
Lepicolea rigida
Chiloscyphus pallescens
Protosyzygiella sp.
Lophocolea fragrans
Leptoscyphus cuneifolius
Plagiochila punctata
Plagiochila carringtonii
Pedinophyllopsis abdita
Acrochila biserialis
Leiomitra elegans
60
Trichocolea tomentella
Temnoma pilosum
Blepharostoma trichophyllum
Gymnomitrion obtusum
Marsupella sprucei
Nardia geoscyphus
Solenostoma obovatum
Saccogyna viticulosa
Harpanthus scutatus
Liochlaena lanceolata
47
Jungermannia pumila
Mesoptychia rutheana
Anthelia julacea
Jungermanniales
Hygrobiella laxifolia
Southbya tophacea
Gongylanthus ericetorum
Geocalyx graveolens
Calypogeia muelleriana
Balantiopsis splendens
Blepharidophyllum densifolium
88
Goebelobryum unguiculatum
Acrobolbus wilsonii
Saccogynidium vasculosum
Scapania nimbosa
J
Scapania irrigua
Douinia ovata
u
Diplophyllum obtusifolium
n
Saccobasis polita
Schistochilopsis opacifolia
g J
58
Tritomaria quinquedentata
Lophozia excisa
e U
Cephaloziella hampeana
Cephaloziopsis intertexta
r N
Chonecolea doellingeri
m G
Pisanoa sp.
Orthocaulis attenuatus
a E
Sphenolobus donnianum
Anastrepta orcadensis
Lophoziales**
n R
Anastrophyllum saxicola
Gymnocolea inflata
n M
Sphenolobopsis pearsonii
i A
Chandonanthus hirtellus
85
Tetralophozia setiformis
i N
Barbilophozia lycopodioides
Biantheridion undulifolium
d N
Isopaches bicrenatus
I
Odontoschisma denudatum
a
Odontoschisma portoricensis
87
65
e O
Fuscocephaloziopsis albescens
Cephalozia bicuspidata
P
Syzygiella sonderi
S
Perdusenia sp.
Pseudomarsupidium
decipiens
upidium decipie
I
Myliales*
Mylia
My
Myl
lia anomala
Schistochila acuminata
acuminat
acumina
Perssoniellales**
D
Microlejeunea ulicina
Harpalejeunea stricta
A
Lejeunea adpressa
Lepidolejeunea cuspidata
Luteolejeunea herzogii
Ceratolejeunea cubensis
Colura tortifolia
Cololejeunea clavatopapillata
Diplasiolejeunea replicata
Drepanolejeunea hamatifolia
Leptolejeunea epiphylla
Cheilolejeunea xanthocarpa
Pictolejeunea sprucei
Acanthocoleus aberrans
Brachiolejeunea laxifolia
65
Neurolejeunea seminervis
Symbiezidium transversale
Lejeuneales*
Ptychanthus striatus
Spruceanthus semirepandus
Dibrachiella auberiana
96
Mastigolejeunea auriculata
Thysananthus repletus
Frullanoides densifolia
Lopholejeunea nigricans
Acrolejeunea sandvicensis
49
M
Archilejeunea crispistipula
Achilejeunea badia
e
Caudalejeunea lehmaniana
Bryopteris filicina
66
t
40
Marchesinia mackaii
Jubulales**
Jubula bogotensis
z
43
Frullania tamarisci
Frullaniales*
g
Radula retroflexa
Radula voluta
Radulales**
e
47
Radula complanata
Lepidolaena taylorii
r
Gackstroemia schwabei
Porellales
39
Porella canariensis
i
Ptilidium ciliare
37
Ptilidiales
i
Neotrichocolea bissetii
41
94
Aneura pinguis
d
Riccardia multifida
Metzgeriales
73
Metzgeria pubescens
a
75
Pleurozia purpurea
Pleuroziales
Jensenia decipiens
0.87
e
76
Pallavicinia lyellii
Pallaviciniales
87
Moerckia blyttii
Fossombronia angulosa
P
Petalophyllum ralfsii
48
Fossombroniales
e
Makinoa crispata
Pellia epiphylla
l
Pelliales
Apopellia endiviifolia
80
Sauteria alpina
50
l
Athalamia pinguis
Clevea hyalina
i M
Peltolepis quadrata
Wiesnerella denudata
M i A
Targionia hypophylla
Cronisia fimbriata
a d R
Exormotheca bischleri
r a C
Corsinia coriandrina
Riccia glauca
50
c e H
Riccia fluitans
Riccia crustata
A
h
Marchantiales
Oxymitra cristata
N
Conocephalum conicum
a
Monoclea forsteri
n B T
Dumortiera hirsuta
Plagiochasma wrightii
t l I
Reboulia hemisphaerica
Asterella tenella
i a O
Mannia triandra
Cryptomitrium tenerum
i s P
Cyathodium tuberosum
81
d i S
Preissia quadrata
Bucegia romanica
a
i I
Marchantia polymorpha
46
Sphaerocarpos texanus
e d D
Monocarpus sphaerocarpus
81
Sphaerocarpales
55
Riella parisii
a A
Neohodgsonia mirabilis
70
Neohodgsoniales
Blasia pusilla
e
Blasiales
Apotreubia nana
Haplomitrium blumei
66
HAPLOMITRIOPSIDA
q3 q1
q2
lpp = 1.00
1.00 < lpp ≥ 0.80
lpp < 0.80
87
3.0
Extended Data Figure 2. Annotated ASTRAL phylogeny of liverworts inferred from nucleo:de
data, highligh:ng suprafamilial rela:onships. Quartet values from ASTRAL analyses are presented
as pie-charts (q1:blue; q2:orange; q3:grey) for selected nodes with the percentage for the first
quartet (q1) included in the pie diagram; see Fig. S1 for quartet values for all other nodes.
Branches with maximum local posterior probability (lpp) are represented as solid black lines;
those with a lpp between 0.8 and 1.0 as a solid grey line and those with a lpp below 0.80 as a grey
dashed line; see Fig. S2 for detailed lpp for all branches. Asterisk marks novel order, and double
Asterisk resurrected order.
40
q3 q1
q2
lpp = 1.00
1.00 < lpp ≥ 0.80
lpp < 0.80
49
35
41
56
35
35
34
36
85
Homalothecium sericeum
Brachytheciastrum velutinum
Eurhynchiastrum pulchellum
Brachythecium rivulare
Myuroclada maximowiczii
Sciuro-hypnum plumosum
Kindbergia praelonga
Rhynchostegiella tenella
Helicodontium capillare
Cirriphyllum piliferum
Microeurhynchium pumilum
Oxyrrhynchium hians
Squamidium brasiliense
Palamocladium leskeoides
Pseudoscleropodium purum
Rhynchostegium riparioides
Rhynchostegium confertum
Eurhynchium striatum
Scorpiurium circinatum
Claopodium whippleanum
Floribundaria flaccida
Meteoriopsis squarrosa
Pseudospiridentopsis horrida
Aerobryopsis longissima
Aerobryidium subpiligerum
Pseudobarbella attenuata
Toloxis imponderosa
Meteorium polytrichum
Papillaria crocea
Hyocomium armoricum
Ctenidium molluscum
Myurium hochstetteri
Exsertotheca crispa
Leptodon smithii
Alleniella complanata
Neckera pennata
Porothamnium fasciculatum
Echinodiopsis hispida
Porotrichodendron superbum
Homalia trichomanoides
Pseudanomodon attenuatus
Taiwanobryum crenulatum
Shevockia inunctocarpa
Pinnatella minuta
Neckeropsis disticha
Homaliodendron flabellatum
Lembophyllum divulsum
Isothecium myosuroides
Nogopterium gracile
Heterocladium heteropterum
Orthostichella pachycastrella
Limbella tricostata
Anomodon longifolius
Callicladium imponens
Hypnum cupressiforme
Isopterygium albescens
Isocladiella surcularis
Taxithelium nepalense
Trachyphyllum inflexum
Platygyrium repens
Hageniella micans
Sematophyllum demissum
Donnellia commutata
Macrohymenium muelleri
Piloecium pseudorufescens
Trismegistia calderensis
Clastobryum cuculligerum
Lescuraea incurvata
36
Lescuraea patens
Lescuraea plicata
Schwetschkeopsis fabronia
Conardia compacta
Hylocomium splendens
Loeskeobryum brevirostre
33
Pleurozium schreberi
Hypnales
Hylocomiastrum pyrenaicum
Rhytidiadelphus squarrosus
Pleuroziopsis ruthenica
Climacium dendroides
Antitrichia curtipendula
Sarmentypnum exannulatum
Warnstorfia fluitans
Straminergon stramineum
Calliergon cordifolium
Leskea polycarpa
Haplocladium microphyllum
Rauiella scita
Abietinella abietina
Pelekium chenagonii
Thuidium tamariscinum
Ptilium crista-castrensis
Pseudoleskeella catenulata
Rhytidium rugosum
Lindbergia patentifolia
Entodon schleicheri
Homomallium incurvatum
Pylaisia polyantha
Buckia vaucheri
48
Ectropothecium perrotii
Vesicularia galerulata
Pseudostereodon procerrimus
Elmeriobryum philippinense
Gollania turgens
Chryso-hypnum elegantulum
Calliergonella cuspidata
Breidleria pratensis
Palustriella commutata
Cratoneuron curvicaule
Kandaea elodes
Amblystegium serpens
Hygroamblystegium tenax
Vittia pachyloma
Cratoneuropsis chilensis
38
Drepanocladus aduncus
39
Pseudocalliergon trifarium
Serpoleskea confervoides
Pseudoamblystegium subtile
Hygrohypnum luridum
Campylium stellatum
Campylophyllum calcareum
Leptodictyum riparium
Tomentypnum nitens
Sanionia uncinata
Scorpidium scorpioides
41
34
Hamatocaulis vernicosus
Herpetineuron toccoae
Phyllodon truncatulus
Henicodium geniculatum
Orthostichopsis tortipilis
Phyllogonium viscosum
Pterobryopsis
orientalis
35
Leucodon sciuroides
Cryphaea heteromalla
Pterigynandrum filiforme
Orthothecium rufescens
Myurella julacea
Platydictya jungermannioides
Dichelyma capillaceum
Fontinalis antipyretica
55
Habrodon perpusillus
Rectithecium piliferum
Plagiothecium denticulatum
44
Isopterygiopsis muelleriana
Herzogiella striatella
Pseudotaxiphyllum elegans
Pilosium chlorophyllum
36
Stereophyllum leucostegum
37
Entodontopsis nitens
Ischyrodon lepturus
Fabronia pusilla
Acrocladium auriculatum
Lepyrodon lagurus
Catagonium nitens
56
Rutenbergia madagassa
Neorutenbergia usagarae
Pseudocryphaea domingensis
Benitotania elimbata
39
Adelothecium bogotense
Bryobrothera crenulata
Daltonia splachnoides
Hookeriales
Cyclodictyon laetevirens
73
Lepidopilidium nitens
85
Leucomium lignicola
50
Hookeria lucens
Hypopterygium didictyon
Hypopterygiales
Ptychomnion aciculare
47
Garovaglia elegans
Ptychomniales
Cladomniopsis crenato-obtusa
Orthorrhynchium elegans
52
Calomnion schistostegiellum
31
Franciella spiridentoides
50
Bescherellia elegantissima
Hypnodendron comosum
Hypnodendrales
Pterobryella vieillardii
38
Racopilum tomentosum
74
Racopilum cuspidigerum
Aulacomnium heterostichum
Aulacomniales
Aulacomnium androgynum
Hymenodontopsis
mnioides
42
Leptotheca gaudichaudii
Orthodontiales
Orthodontium lineare
45
Pulvigera lyellii
Pulvigera lyellii
Plenogemma phyllantha
45
Lewinskya striata
Orthotrichales
Nyholmiella obtusifolia
Orthotrichum anomalum
Zygodon rupestris
Zygodon conoideus
68
Macromitrium saddleanum
80
Macrocoma abyssinica
Leratia obtusifolia
Pyrrhobryum medium
Rhizogoniales
Goniobryum subbasilare
50
Mnium thomsonii
Mnium lycopodioides
Rhizomnium punctatum
Pseudobryum cinclidioides
Plagiomnium undulatum
Cinclidium stygium
67
Plagiomnium cuspidatum
Mielichoferia elongata
Pohlia elongata
Pohlia cruda
Roellobryon roellii
Phyllodrepanium falcifolium
Bryales
Mniomalia viridis
Plagiobryum zieri
Ptychostomum pseudotriquetrum
Gemmabryum vinosum
Imbribryum alpinum
70
Bryum argenteum
37
Anomobryum julaceum
Brachymenium nepalense
Rosulabryum perlimbatum
Leptostomopsis systylia
Rhodobryum roseum
Rhodobryum ontariense
Leptostomum menziesii
47
Conostomum tetragonum
Breutelia integrefolia
Philonotis fontana
Bartramiales
Bartramia pomiformis
Bartramia ithyphylla
66
Helicophyllum torquatum
Amblyodon dealbatus
Meesia triquetra
Paludella squarrosa
Tayloria dubyi
Splachnales
Splachnum vasculosum
Tetraplodon mnioides
Leptobryum pyriforme
96
Neomeesia paludella
Pararhacocarpus patagonicus
Rhacocarpus purpurascens
Hedwigiales
Braunia imberbis
94
Hedwigia ciliata
Willia austroleucophaea
H
y
p
n
a
n
a
e
=
p
l
e
u
r
o
c
a
r
p
o
u
s
m
o
s
s
e
s
B
r
y
i
d
a
e
B
r
y
a
n
a
e
B
r
y
o
p
s
i
d
a
B
R
Y
O
P
H
Y
T
I
N
A
67
34
75
43
73
44
62
98
Willia austroleucophaea
Sagenotortula quitoensis
Syntrichia ruralis
Streptopogon erythrodontus
Calyptopogon mnioides
Hennediella macrophylla
Tortula truncata
Dolotortula mniifolia
Chenia leptophylla
Acaulon muticum
Microbryum davallianum
Aloina aloides
Cinclidotus fontinaloides
Dialytrichia saxicola
Barbula unguiculata
Bryoerythrophyllum recurvirostrum
Pottiales
Saitobryum lorentzii
Didymodon rigidulus
Leptodontium flexifolium
Weissia controversa
Trichostomum brachydontium
Chionoloma hibernicum
Tortella fragilis
Ephemerum serratum
Eucladium verticillatum
Molendoa warburgii
Anoectangium aestivum
Gymnostomum calcareum
Gyroweisia tenuis
Hyophila apiculata
68
53
Streblotrichum convolutum
Scopelophila cataractae
Pseudephemerum nitidum
Pleuridium subulatum
Ditrichum subulatum
Ditrichales*
50
Ditrichum cornubicum
Ceratodon purpureus
Trichodon cylindricus
45
Trematodon longicollis
Bruchiales*
Bruchia brevifolia
Erpodium domingense
Erpodiales*
Venturiella coronata
50
Sorapilla papuana
Sorapillales*
Kiaeria starkei
Cynodontium tenellum
46
Rhabdoweisiales*
Glyphomitrium daviesii
Oncophorus virens
Dicranoweisia cirrata
Rhabdoweisia fugax
Rhachithecium perpusillum
Platyneuron praealtum
Chorisodontium aciphyllum
Dicranum scoparium
Dicranum flagellare
53
Holomitrium seticalycinum
Dicranales Dicranales
Dicranoloma billarderi
Leucoloma molle
sensu stricto sensu lato
Syrrhopodon ligulatus
47
Calymperes lonchophyllum
Octoblepharum albidum
Fissidens exilis
44
Fissidens bryoides
Dicranella heteromalla
35
Aongstroemia longipes
46
Dichodontium pellucidum
Amphidiales*
Amphidium mougeotii
Eustichiales*
Eustichia longirostris
Pleurophascum globosum
46
Dicranodontium denudatum
Atractylocarpus subporodictyon
43
Leucobrym glaucu m
Campylopus flexuosus
Archidiales
Archidium alternifolium
Micromitrium tenerum
70
Bucklandiella heterosticha
Codriophorus acicularis
Niphotrichum canescens
77
Grimmia anomala
Dryptodon trichophyllus
Schistidium maritimum
Coscinodon cribrosus
41
Grimmiales
Ptychomitrium polyphyllum
Brachydontium trichodes
59
Campylostelium saxicola
Blindiadelphus recurvatus
82
41
Blindia acuta
Seligeria pusilla
Holodontium strictum
Scouleriales
Hymenoloma crispulum
Flexitrichum gracile
Flexitrichales*
43
Flexitrichum flexicaule
65
Distichium capillaceum
Distichales*
80
Catoscopium nigritum
Catoscopiales
Timmia norvegica
Physcomitrium patens
Physcomitrium pyriforme
Funariales
Entosthodon attenuatus
100
Funaria hygrometrica
68
Encalyptales
Encalypta ciliata
53
Discelium nudum
Disceliales
69 Gigaspermum mouretii
Diphyscium foliosum
Buxbaumia aphylla
Pogonatum aloides
Polytrichales
Polytrichum commune
Oligotrichum hercynicum
Atrichum undulatum
Dendroligotrichum squamosum
Notoligotrichum trichodon
100
Dawsonia beccarii
Tetraphis pellucida
Tetraphidales
89
Tetrodontium brownianum
Oedipodiales
Oedipodium griffithianum
Andreaea wilsonii
Andreaea wilsonii
Andreaea rupestris
Andreaea rothii
Andreaeobryum macrosporum
Sphagnum strictum
Sphagnum girgensohnii
Sphagnum palustre
Sphagnum cuspidatum
Sphagnum falcatulum
99
Eosphagum inretortum
D
i
c
r
a
n
i
d
a
e
Timmiidae
Funariidae
Gigaspermidae
Diphysciidae
Buxbaumiidae
Polytrichopsida
ANDREAEOPHYTINA
SPHAGNOPHYTINA
85
Takakia lepidozioides
TAKAKIOPHYTINA
Extended Data Figure 3. Annotated ASTRAL phylogeny of mosses inferred from nucleo:de data,
highligh:ng suprafamilial rela:onships. Quartet values from ASTRAL analyses are presented as
pie-charts (q1:blue; q2:orange; q3:grey) for selected nodes with the percentage for the first
quartet (q1) included in the pie diagram; see Fig. S1 for quartet values for all other nodes.
Branches with maximum local posterior probability (lpp) are represented as solid black lines;
those with a lpp between 0.8 and 1.0 as a solid grey line and those with a lpp below 0.80 as a grey
dashed line; see Fig. S2 for detailed lpp for all branches. Asterisks mark novel orders.
95/2/3
lpp = 1.00
lpp < 0.80
Dendroceros aff. crispus
46/22/32
53/21/26
73/10/18
61/19/20
Megaceros austronesophilus
Nothoceros endiviifolius
Phaeomegaceros fimbriatus
Phymatoceros sp.
78/12/10
Dendroceros tubercularis
Dendrocerotales
Phymatocerotales
D
E
N
D
R
O
C
E
R
O
T
I
D
A
E
Notothylas levieri
q: 35/29/36
lpp: 33/12/55
94/2/4
Phaeoceros himalayensis
67/19/14
70/22/7
96/2/2
Phaeoceros engelii
Folioceros fuciformis
Anthoceros punctatus
Leiosporoceros dussii
NOTOTHYLATIDAE
Notothyladales
A
N
T
H
O
C
E
R
O
T
O
P
S
I
D
A
ANTHOCEROTIDAE
Anthocerotales
LEIOSPOROCEROTOPSIDA
Leiosporocerotales
Extended Data Figure 4. Annotated ASTRAL phylogeny of hornworts inferred from amino acid
data, highligh:ng (supra)ordinal rela:onships. Quartet values for the three possible topologies
are presented as percentages near the node. Branches with maximum local posterior probability
(lpp) are represented as solid black lines; those with a lpp below 0.80 as a grey dashed line; see
Fig. S7 for detailed lpp for all branches.
41/27/32 Telaranea blepharostoma
51/25/24
Lepidozia reptans
Tricholepidozia tetradactyla
Kurzia trichoclados
Amazoopsis diplopoda
40/31/29
Herbertus aduncus
80/8/11
44/33/23
Herbertus sendtneri
60/21/18
Triandrophyllum sp.
36/33/31
Mastigophora woodsii
38/33/29
Lepicolea rigida
Temnoma pilosum
Leiomitra elegans
68/15/18
Trichocolea tomentella
34/37/28
41/30/29 Pedinophyllopsis abdita
64/18/18
41/29/31
Acrochila biserialis
46/28/26
53/24/23
Plagiochila punctata
60/18/22
Plagiochila carringtonii
Leptoscyphus cuneifolius
54/24/22
Lophocolea fragrans
67/19/15
Protosyzygiella sp.
40/24/36 Chiloscyphus pallescens
Blepharostoma trichophyllum
46/32/22 Balantiopsis splendens
Blepharidophyllum densifolium
Calypogeia muelleriana
34/34/31
39/29/32
Geocalyx graveolens
Southbya tophacea
60/18/21
41/24/35
Gongylanthus ericetorum
50/25/25
65/12/23
Anthelia julacea
Hygrobiella laxifolia
Mesoptychia rutheana
49/22/28
Liochlaena
lanceolata
40/34/26
59/18/23
Jungermannia
pumila
38/33/29
45/31/24
Harpanthus scutatus
37/33/30 Saccogyna viticulosa
Solenostoma obovatum
36/31/33
Marsupella sprucei
48/33/19
Nardia geoscyphus
37/33/30
46/29/25 Gymnomitrion obtusum
Acrobolbus wilsonii
52/26/23
Saccogynidium vasculosum
36/32/32 Goebelobryum unguiculatum
Bazzania pearsonii
61/21/19
Fuscocephaloziopsis albescens
Cephalozia bicuspidata
57/20/23
42/31/27
65/19/15
lpp = 1.00
1.00 < lpp ≥ 800
lpp < 800
37/32/32
1
q: 39/26/35
lpp: 84/2/13
2
q: 48/37/015
lpp: 92/7/0.01
66/17/17
2
48/37/15
Lepidoziales**
Jungermanniales
Odontoschisma denudatum
Odontoschisma portoricensis
Cephaloziopsis intertexta
Cephaloziella hampeana
41/37/23 Chonecolea doellingeri
88/5/6
77/16/7
47/41/11
Pisanoa sp.
Lophozia excisa
Tritomaria quinquedentata
Schistochilopsis opacifolia
40/26/34
Saccobasis polita
36/35/29
Diplophyllum obtusifolium
37/28/35
Douinia ovata
50/28/23
46/24/30
Scapania irrigua
42/26/31
44/34/22 Scapania nimbosa
Isopaches bicrenatus
Biantheridion undulifolium
Barbilophozia
lycopodioides
46/31/22
35/33/33
Tetralophozia setiformis
44/27/29
Sphenolobopsis pearsonii
39/27/34
49/28/23
Chandonanthus hirtellus
40/27/33
Orthocaulis attenuatus
35/31/34 Gymnocolea inflata
Anastrepta orcadensis
36/35/30
Anastrophyllum donnianum
36/35/29
37/33/30 Sphenolobus saxicola
Pseudomarsupidium decipiens
Syzygiella sonderi
76/10/14
Perdusenia sp.
40/27/32
61/23/16
43/30/27
57/26/17
40/23/37
36/35/29
1
52/23/25
Mylia anomala
Schistochila acuminata
Ptilidium ciliare
75/14/11
Neotrichocolea bissetii
Microlejeunea ulicina
Lejeunea adpressa
Harpalejeunea stricta
Lepidolejeunea cuspidata
53/28/19
Luteolejeunea herzogii
her ogii
herz
37/38/25
Ceratolejeunea cubensis
Leptolejeunea epiphylla
47/32/21
39/30/30 Diplasiolejeunea replicata
Drepanolejeunea
hamatifolia
hamatifol
f
fol
ia
45/25/29
Colura tortifolia
tortifol
f ia
fol
39/29/32
47/21/32
48/33/19 Cololejeunea clavatopapillata
Cheilolejeunea xanthocarpa
xanthocarp
hocar a
hocarp
Pictolejeunea
Pictolej
e eunea sprucei
ej
Acanthocoleus aberrans
84/7/8
40/26/34
laxifolia
Brachiolejeunea laxifol
f ia
fol
37/30/33
Neurolejeunea seminervis
seminervi
vs
vi
Symbiezidium transversale
transvers
ver ale
vers
39/25/35 Ptychanthus
Pty
t chanthus striatus
ty
45/29/26
Spruceanthus semirepandus
49/24/27
Dibrachiella auberiana
Mastigolejeunea auriculata
41/32/26
T sananthus repletus
Thy
47/28/25 Thysananthus
38/24/38
47/30/22
Acrolejeunea sandvicensis
36/29/36
Frullanoides densifolia
densifol
f ia
fol
63/12/25
Lopholejeunea nigricans
38/34/28
Marchesinia mackaii
Bryopteris
Bry
r opteri
ry
r s filicina
ri
f icina
fil
38/32/29
Caudalejeunea lehmaniana
55/24/22
75/11/14
Archilejeunea crispistipula
Achilejeunea
chilejeunea badia
Lophoziales**
J
u
n
g
e J
r U
N
m G
a E
n R
n M
i A
i N
d N
a OI
e P
S
I
D
A
Myliales*
Perssoniellales**
Ptilidiales
37/30/32
46/29/25
39/24/37
43/25/33
40/30/30
83/9/8
43/27/30
42/25/33
54/26/20
32/
32/
36
Jubula bogotensis
Frullania tamarisci
90/7/3
43/24/33
69/19/12
75/14/11
44/26/31
57/23/20
60/21/19
64/14/22
Radula retroflexa
r tro
re
r fle
ro
f xa
Radula complanata
Radula voluta
Gackstroemia schwabei
Lepidolaena taylorii
taylor
ylori
ylor
lori i
37/31/32
Porella canariensis
Pleurozia purpurea
Metzgeria pubescens
54/21/25
Riccardia multifida
43/23/34 Aneura pinguis
Pellia epiphylla
Apopellia endiviifolia
Moerckia blyttii
38/33/29
39/28/33
36/32/32
Jubulales**
Frullaniales*
Radulales**
Porellales
Pleuroziales
Metzgeriales
Pelliales
Jensenia decipiens
Pallavicinia lyellii
81/10/9
Lejeuneales*
Makinoa crispata
Fossombronia angulosa
Petalophyllum ralfsii
Pallaviciniales
Fossombroniales
45/27/28
Cryptomitrium tenerum
Mannia triandra
58/23/19
Asterella tenella
45/28/26
49/23/28 Plagiochasma wrightii
Reboulia hemisphaerica
45/32/23
Corsinia coriandrina
92/3/5
Cronisia fimbriata
Exormotheca bischleri
56/24/20
Oxymitra cristata
53/23/24
Riccia crustata
58/17/25
40/35/25
Riccia glauca
38/32/29 Riccia fluitans
Dumortiera hirsuta
35/32/33
57/19/24
Wiesnerella denudata
Targionia hypophylla
39/34/27
44/28/28 Clevea hyalina
37/35/27
Peltolepis quadrata
57/20/24
65/19/16
Sauteria alpina
37/30/33
Athalamia pinguis
Conocephalum conicum
40/27/33 Monoclea forsteri
Cyathodium tuberosum
Marchantia polymorpha
84/6/9
Preissia quadrata
Bucegia romanica
62/21/17
41/21/38
54/33/13
84/11/5
56/16/28
64/16/20
62/19/19
Neohodgsonia mirabilis
Riella parisii
37/31/32
Sphaerocarpos texanus
37/35/29
46/27/27 Monocarpus sphaerocarpus
Blasia pusilla
Apotreubia nana
Haplomitrium blumei
64/13/24
51/21/28
Marchantiales
M
e
t
z
g
e
r
i
i
d
a
e
P
e
l
l
i
i
d M
Ma A
a e R
C
r
H
c
A
h
N
a
n B TI
t l O
i a P
i s S
d i I
a i D
e d A
a
e
Neohodgsoniales
Sphaerocarpales
Blasiales
HAPLOMITRIOPSIDA
Extended Data Figure 5. Annotated ASTRAL phylogeny of liverworts inferred from amino acid
data, highligh:ng suprafamilial rela:onships. Quartet values for the three possible topologies are
presented as percentages near the node. Branches with maximum local posterior probability (lpp)
are represented as solid black lines; those with a lpp between 0.8 and 1.0 as a solid grey line and
those with a lpp below 0.80 as a grey dashed line; see Fig. S7 for detailed lpp for all branches.
Asterisk marks novel order, and double Asterisk resurrected order.
Sanionia uncinata
Scorpidium scorpioides
Hamatocaulis vernicosus
Tomentypnum nitens
Hygroamblystegium tenax
Amblystegium serpens
Kandaea elodes
Palustriella commutata
Cratoneuron curvicaule
Leptodictyum riparium
Drepanocladus aduncus
Pseudocalliergon trifarium
35/34/30
Vittia pachyloma
Cratoneuropsis chilensis
Campylium stellatum
Campylophyllum calcareum
Hygrohypnum luridum
Pseudoamblystegium subtile
Serpoleskea confervoides
Lindbergia patentifolia
Breidleria pratensis
Chryso-hypnum elegantulum
35/34/31
Elmeriobryum philippinense
Gollania turgens
Ectropothecium perrotii
Vesicularia galerulata
Calliergonella cuspidata
36/32/33
Buckia vaucheri
Pseudostereodon procerrimus
Homomallium incurvatum
Pylaisia polyantha
Entodon schleicheri
Ptilium crista-castrensis
Pseudoleskeella catenulata
Rhytidium rugosum
Pelekium chenagonii
Thuidium tamariscinum
Rauiella scita
35/34/31
Abietinella abietina
Leskea polycarpa
Haplocladium microphyllum
Herpetineuron toccoae
Calliergon cordifolium
Straminergon stramineum
Sarmentypnum exannulatum
Warnstorfia fluitans
Conardia compacta
Callicladium imponens
Hypnum cupressiforme
Schwetschkeopsis fabronia
Anomodon longifolius
Lescuraea plicata
Lescuraea incurvata
Lescuraea patens
Porotrichodendron superbum
Nogopterium gracile
Lembophyllum divulsum
35/32/33
Isothecium myosuroides
Heterocladium heteropterum
Orthostichella pachycastrella
Limbella tricostata
Neckeropsis disticha
Homaliodendron flabellatum
Shevockia inunctocarpa
Taiwanobryum crenulatum
Pinnatella minuta
Porothamnium fasciculatum
Echinodiopsis hispida
Homalia trichomanoides
Pseudanomodon attenuatus
Neckera pennata
Leptodon smithii
Alleniella complanata
Exsertotheca crispa
Pleuroziopsis ruthenica
Climacium dendroides
34/32/34
Rhytidiadelphus squarrosus
Antitrichia curtipendula
Pleurozium schreberi
Hylocomiastrum pyrenaicum
Loeskeobryum brevirostre
Hylocomium splendens
Myurium hochstetteri
Hyocomium armoricum
Ctenidium molluscum
Claopodium whippleanum
35/31/34
Papillaria crocea
Meteorium polytrichum
Toloxis imponderosa
Pseudobarbella attenuata
40/29/30
Aerobryopsis longissima
Aerobryidium subpiligerum
Pseudospiridentopsis horrida
Floribundaria flaccida
Meteoriopsis squarrosa
39/30/32
Sciuro-hypnum plumosum
Kindbergia praelonga
Brachythecium rivulare
38/31/31
Myuroclada maximowiczii
Brachytheciastrum velutinum
Eurhynchiastrum pulchellum
Homalothecium sericeum
39/33/29
Squamidium brasiliense
Oxyrrhynchium hians
Microeurhynchium pumilum
Cirriphyllum piliferum
Rhynchostegiella tenella
Helicodontium capillare
Scorpiurium circinatum
Palamocladium leskeoides
Eurhynchium striatum
Pseudoscleropodium purum
36/36/28
Rhynchostegium riparioides
Rhynchostegium confertum
Clastobryum cuculligerum
Trismegistia calderensis
Piloecium pseudorufescens
Donnellia commutata
Macrohymenium muelleri
51/26/23
Sematophyllum demissum
Platygyrium repens
36/31/33
Hageniella micans
Trachyphyllum inflexum
Taxithelium nepalense
Isopterygium albescens
Isocladiella surcularis
Phyllodon truncatulus
Leucodon sciuroides
Pterigynandrum filiforme
34/34/33
Cryphaea heteromalla
Pterobryopsis orientalis
Phyllogonium viscosum
Henicodium geniculatum
Orthostichopsis tortipilis
Platydictya jungermannioides
Orthothecium rufescens
41/27/32
Myurella julacea
Pseudotaxiphyllum elegans
Isopterygiopsis muelleriana
Herzogiella striatella
34/33/33
Rectithecium piliferum
Plagiothecium denticulatum
Habrodon perpusillus
Dichelyma capillaceum
38/32/30
57/17/25 Fontinalis antipyretica
Catagonium nitens
Acrocladium auriculatum
Lepyrodon lagurus
Ischyrodon lepturus
41/33/26
Fabronia pusilla
Entodontopsis nitens
Pilosium chlorophyllum
Stereophyllum leucostegum
Neorutenbergia usagarae
40/30/30
Rutenbergia madagassa
47/36/17
Pseudocryphaea domingensis
Hookeria lucens
Leucomium lignicola
Cyclodictyon laetevirens
47/29/24
Lepidopilidium nitens
47/28/25
Daltonia splachnoides
Bryobrothera crenulata
44/27/29
Benitotania elimbata
Adelothecium bogotense
Hypopterygium didictyon
Orthorrhynchium elegans
84/6/10 Cladomniopsis crenato-obtusa
33/33/34 41/29/31
Ptychomnion aciculare
Garovaglia elegans
Racopilum tomentosum
Racopilum cuspidigerum
38/31/31 46/30/24
Pterobryella vieillardii
Hypnodendron comosum
Franciella spiridentoides
35/32/33
Bescherellia elegantissima
Hymenodontopsis mnioides
q: 28/31/42
Calomnion schistostegiellum
lpp: 3/4/93
Pyrrhobryum medium
44/29/27
Aulacomnium heterostichum
Aulacomnium androgynum
38/31/31
Goniobryum subbasilare
Orthodontium lineare
38/36/26
Leptotheca gaudichaudii
Leratia obtusifolia
35/32/34
Macromitrium saddleanum
Macrocoma abyssinica
50/25/25
Zygodon rupestris
Zygodon conoideus
Orthotrichum anomalum
Nyholmiella obtusifolia
40/27/33
Lewinskya striata
Plenogemma phyllantha
Pulvigera lyellii
Pulvigera lyellii
Rhodobryum roseum
Rhodobryum ontariense
82/10/8
Leptostomopsis systylia
Rosulabryum perlimbatum
Brachymenium nepalense
59/16/25
Gemmabryum vinosum
Plagiobryum zieri
Ptychostomum pseudotriquetrum
Anomobryum julaceum
42/31/27
Imbribryum alpinum
Bryum argenteum
36/27/37
Leptostomum menziesii
89/4/7
Phyllodrepanium falcifolium
Mniomalia viridis
39/30/31
Roellobryon roellii
Pohlia cruda
49/28/24
Mielichoferia elongata
59/22/19
Pohlia elongata
Rhizomnium punctatum
Plagiomnium cuspidatum
Plagiomnium undulatum
Cinclidium stygium
Pseudobryum cinclidioides
Mnium thomsonii
Mnium lycopodioides
57/18/25
Helicophyllum torquatum
55/21/24
Bartramia pomiformis
Bartramia ithyphylla
Conostomum tetragonum
37/34/29
Breutelia integrefolia
Philonotis fontana
Tetraplodon mnioides
Tayloria dubyi
43/32/25
Splachnum vasculosum
Amblyodon dealbatus
48/39/12
Paludella squarrosa
Leptobryum pyriforme
78/12/10
Meesia triquetra
Neomeesia paludella
Pararhacocarpus patagonicus
37/32/30
74/13/14
Rhacocarpus purpurascens
Braunia imberbis
Hedwigia ciliata
34/33/34
43/26/31
lpp = 1.00
1.00 < lpp ≥ 800
lpp < 800
1
1
H
y
p
n
a
n
a
e
=
p
l
e
u
r
o
c
a
r
p
o
u
s
Hypnales
m
o
s
s
e
s
B
r
y
i
d
a
e
Hookeriales
Hypopterygiales
Ptychomniales
Hypnodendrales
Rhizogoniales
Aulacomniales
Rhizogoniales
Orthodontiales
Orthotrichales
Bryales
Bartramiales
Splachnales
Hedwigiales
Willia austroleucophaea
B
r
y
a
n
a
e
B
r
y
o
p
s
i
d
a
B
R
Y
O
P
H
Y
T
I
N
A
Hedwigia ciliata
Willia austroleucophaea
Syntrichia ruralis
Sagenotortula quitoensis
Streptopogon erythrodontus
Tortula truncata
Hennediella macrophylla
Chenia leptophylla
Acaulon muticum
Calyptopogon mnioides
Microbryum davallianum
Dolotortula mniifolia
Dialytrichia saxicola
Cinclidotus fontinaloides
Barbula unguiculata
Bryoerythrophyllum recurvirostrum
Saitobryum lorentzii
Pottiales
Aloina aloides
Didymodon rigidulus
Leptodontium flexifolium
Eucladium verticillatum
Ephemerum serratum
Chionoloma hibernicum
61/21/18
Tortella fragilis
Weissia controversa
Trichostomum brachydontium
Gyroweisia tenuis
Gymnostomum calcareum
40/31/29
Molendoa warburgii
Anoectangium aestivum
Hyophila apiculata
36/26/38
Streblotrichum convolutum
Scopelophila cataractae
53/27/20
Ceratodon purpureus
30/35/35
Trichodon cylindricus
Ditrichum cornubicum
Ditrichales*
Ditrichum subulatum
36/30/33
Pseudephemerum nitidum
30/45/25
41/28/31
Pleuridium subulatum
Sorapilla papuana
Sorapillales*
75/12/13 Trematodon longicollis
Bruchiales*
Bruchia brevifolia
30/38/32
Rhachithecium perpusillum
Dicranoweisia cirrata
Rhabdoweisiales*
Rhabdoweisia fugax
45/32/23
38/28/34
Kiaeria starkei
Cynodontium tenellum
Glyphomitrium daviesii
Oncophorus virens
Erpodium domingense
Erpodales*
Venturiella coronata
Dicranum scoparium
Dicranum flagellare
Platyneuron praealtum
40/29/31
Holomitrium seticalycinum
Dicranoloma billarderi
Chorisodontium aciphyllum
Dicranales Dicranales
Leucoloma molle
sensu stricto sensu lato
Octoblepharum albidum
Syrrhopodon ligulatus
34/34/32
34/32/33
Calymperes lonchophyllum
37/34/28
Dicranella heteromalla
Fissidens exilis
Fissidens bryoides
41/23/35
37/30/33
Aongstroemia longipes
Dichodontium pellucidum
37/32/31
Amphidium mougeotii
Amphidiales*
Eustichia longirostris
Eustichiales*
Dicranodontium denudatum
Atractylocarpus subporodictyon
Leucobrym glaucum
Archidiales
Campylopus
flexuosus
53/24/24
Archidium alternifolium
Micromitrium tenerum
44/35/22
Niphotrichum canescens
Bucklandiella heterosticha
Codriophorus acicularis
Grimmia anomala
Dryptodon trichophyllus
Schistidium maritimum
46/23/31
Coscinodon cribrosus
43/39/19
Ptychomitrium polyphyllum
Grimmiales
Brachydontium trichodes
Campylostelium saxicola
Seligeria pusilla
53/21/25
Blindia acuta
Blindiadelphus recurvatus
Pleurophascum globosum
Pleurophascales*
Distichium capillaceum
Distichiales*
Catoscopium nigritum
Catoscopiales
Flexitrichum gracile
60/15/25
38/32/30
Flexitrichales*
Flexitrichum flexicaule
35/34/30
Holodontium strictum
38/30/31
Scouleriales
Hymenoloma crispulum
Timmia norvegica
Encalyptales
Encalypta ciliata
48/22/30
50/26/23 Discelium nudum
Disceliales
Funaria hygrometrica
47/23/30
90/5/5
Entosthodon attenuatus
Funariales
51/20/29
Physcomitrium pyriforme
q: 45/27/28
Physcomitrium patens
Gigaspermum mouretii
lpp: 100/0/0
Diphyscium foliosum
Buxbaumia aphylla
Pogonatum aloides
58/16/26
Polytrichales
Polytrichum commune
Oligotrichum hercynicum
Atrichum undulatum
Dendroligotrichum squamosum
90/5/5
Notoligotrichum trichodon
Dawsonia beccarii
65/12/23
70/14/16
Tetraphis pellucida
Tetraphidales
Tetrodontium brownianum
Oedipodiales
37/30/33 Oedipodium griffithianum
84/6/10
Andreaea wilsonii
51/15/34
Andreaea wilsonii
82/15/4
Andreaea rupestris
49/27/23
44/20/36
Andreaea rothii
Andreaeobryum macrosporum
Sphagnum strictum
Sphagnum girgensohnii
75/11/14
Sphagnum palustre
69/21/10
Sphagnum cuspidatum
97/2/1
Sphagnum falcatulum
Eosphagum inretortum
Takakia lepidozioides
D
i
c
r
a
n
i
d
a
e
Timmiidae
Funariidae
Gigaspermidae
Diphysciidae
Buxbaumiidae
2
2
Polytrichopsida
ANDREAEOPHYTINA
SPHAGNOPHYTINA
T
TAKAKIOPHYTINA
Extended Data Figure 6 Annotated ASTRAL phylogeny of mosses inferred from amino acid data,
highligh:ng suprafamilial rela:onships. Quartet values for the three possible topologies are
presented as percentages near selected nodes; see Fig. S6 for quartet values for all other
branches. Branches with maximum local posterior probability (lpp) are represented as solid black
lines; those with a lpp between 0.8 and 1.0 as a solid grey line and those with a lpp below 0.80 as
a grey dashed line; see Fig. S7 for detailed lpp for all branches. Asterisks mark novel orders.
15,39
61] Sphagnum palustre
ED Fig. 7A
93 [89-98]
103 [99-108]
121 [115-128]
166 [160-173]
54 [51-56]
57 [54-60]
17 [15-19]
74 [67-80]
92 [85-99]
155 [147-162]
mosses
53 [51-56]
64 [61-66]
189 [184-194]
ED Fig. 7B
H
124 [122-126]
199 [194-205]
86 [83-88]
178 [175-183]
43 [41-45]
49 [47-51]
103 [100-108]
184 [178-190]
62 [57-67]
68 [63-73]
76 [71-82]
103 [98-108]
219 [213-225]
100 [94-105]
106 [101-112]
80 [76-85]
87 [83-92]
63 [59-66]
115 [110-121]
126 [120-132]
67 [63-70]
G
152 [144-159]
119 [113-124]
160 [153-168]
123 [116-131]
110 [103-117]
101 [93-107]
I
44 [41-46]
48 [44-51]
59 [53-65]
61 [54-67]
64 [57-70]
67 [59-73]
231 [225-238]
109 [102-116]
49 [45-52]
F
105 [98-112]
E
116 [108-123]
40 [29-40]
44 [37-52]
254 [250-259]
181 [173-190]
D
23 [21-25]
119 [111-126]
75 [70-81]
38 [34-41]
131 [123-139]
486 [485-487]
30 [24-36]
38 [40-59]
49 [31-46]
5 1 [42-61]
75 [66-84]
147 [139-155]
35 [29-41]
3 4 [35-46]
64 [46-85]
M
94 [68-125]
103 [74-136]
58 [40-80]
108 [79-142]
68 [49-90]
86 [63-115]
98 [71-129]
116 [85-152]
121 [90-158]
126 [95-164]
143 [110-181]
146 [113-184]
26 [20-34]
C
131 [101-166]
O
60 [48-75]
75 [60-92]
90 [72-110]
97 [77-118]
27 [21-34]
149 [116-188]
P
122 [96-151]
262 [239-288]
14 [10-19]
72 [56-90]
125 [99-155]
284 [265-307]
364 [360-369]
115 [89-144]
313 [298-329]
117 [107-128]
131 [121-144]
324 [310-338]
329 [317-342]
339 [330-349]
374 [371-376]
J
190 [181-199]
225 [217-235]
289 [280-298]
B
N
107 [102-111]
238 [230-244]
358 [352-362]
287 [277-294]
326 [317-335]
282 [275-288]
27 [26-29]
44 [41-46]
227 [221-233]
260 [256-264]
141 [131-151]
163 [151-172]
266 [262-270]
94 [87-100]
195 [188-201]
424 [422-426]
272 [269-276]
276 [272-279]
185 [179-190]
K
252 [249-254]
269 [266-273]
235 [230-241]
280 [276-283]
303 [299-307]
447 [444-450]
A
74 [66-80]
93 [84-100]
103 [94-112]
53 [50-56]
332 [328-336]
391 [387-395]
178 [169-186]
L
251 [243-260]
280 [272-287]
325 [303-346]
132 [111-156]
60 my
184 [160-212]
308 [283-339]
341 [317-369]
128 [110-149]
7 [5-9]
63 [51-77]
74 [60-91]
83 [68-103]
30 [24-37]
59 [53-66]
Telaranea blepharostoma
Tricholepidozia tetradactyla
Lepidozia reptans
Kurzia trichoclados
Amazoopsis diplopoda
Bazzania pearsonii
Herbertus sendtneri
Herbertus aduncus
Triandrophyllum sp.
Mastigophora woodsii
Lepicolea rigida
Acrochila biserialis
Pedinophyllopsis abdita
Plagiochila punctata
Plagiochila carringtonii
Protosyzygiella sp.
Chiloscyphus pallescens
Lophocolea fragrans
Leptoscyphus cuneifolius
Leiomitra elegans
Trichocolea tomentella
Blepharostoma trichophyllum
Temnoma pilosum
Marsupella sprucei
Gymnomitrion obtusum
Nardia geoscyphus
Solenostoma obovatum
Harpanthus scutatus
Saccogyna viticulosa
Liochlaena lanceolata
Jungermannia pumila
Mesoptychia rutheana
Hygrobiella laxifolia
Anthelia julacea
Southbya tophacea
Gongylanthus ericetorum
Geocalyx graveolens
Calypogeia muelleriana
Balantiopsis splendens
Blepharidophyllum densifolium
Goebelobryum unguiculatum
Acrobolbus wilsonii
Saccogynidium vasculosum
Scapania nimbosa
Scapania irrigua
Douinia ovata
Diplophyllum obtusifolium
Saccobasis polita
Schistochilopsis opacifolia
Tritomaria quinquedentata
Lophozia excisa
Cephaloziopsis intertexta
Cephaloziella hampeana
Chonecolea doellingeri
Pisanoa sp.
Gymnocolea inflata
Sphenolobus saxicola
Orthocaulis attenuatus
Anastrophyllum donnianum
Anastrepta orcadensis
Chandonanthus hirtellus
Sphenolobopsis pearsonii
Tetralophozia setiformis
Biantheridion undulifolium
Barbilophozia lycopodioides
Isopaches bicrenatus
Odontoschisma portoricensis
Odontoschisma denudatum
Cephalozia bicuspidata
Fuscocephaloziopsis albescens
Syzygiella sonderi
Perdusenia sp.
Pseudomarsupidium decipiens
Mylia anomala
Schistochila acuminata
Microlejeunea ulicina
Harpalejeunea stricta
Lejeunea adpressa
Lepidolejeunea cuspidata
Luteolejeunea herzogii
Ceratolejeunea cubensis
Colura tortifolia
Cololejeunea clavatopapillata
Diplasiolejeunea replicata
Drepanolejeunea hamatifolia
Leptolejeunea epiphylla
Cheilolejeunea xanthocarpa
Pictolejeunea sprucei
Symbiezidium transversale
Acanthocoleus aberrans
Brachiolejeunea laxifolia
Neurolejeunea seminervis
Spruceanthus semirepandus
Ptychanthus striatus
Dibrachiella auberiana
Mastigolejeunea auriculata
Thysananthus repletus
Frullanoides densifolia
Lopholejeunea nigricans
Acrolejeunea sandvicensis
Archilejeunea crispistipula
Achilejeunea badia
Caudalejeunea lehmaniana
Marchesinia mackaii
Bryopteris filicina
Jubula bogotensis
Frullania tamarisci
Radula complanata
Radula voluta
Radula retroflexa
Porella canariensis
Gackstroemia schwabei
Lepidolaena taylorii
Ptilidium ciliare
Neotrichocolea bissetii
Riccardia multifida
Aneura pinguis
Metzgeria pubescens
Pleurozia purpurea
Jensenia decipiens
Pallavicinia lyellii
Moerckia blyttii
Petalophyllum ralfsii
Fossombronia angulosa
Makinoa crispata
Pellia epiphylla
Apopellia endiviifolia
Cronisia fimbriata
Exormotheca bischleri
Corsinia coriandrina
Cyathodium tuberosum
Clevea hyalina
Peltolepis quadrata
Athalamia pinguis
Sauteria alpina
Targionia hypophylla
Wiesnerella denudata
Riccia fluitans
Riccia glauca
Riccia crustata
Oxymitra cristata
Conocephalum conicum
Monoclea forsteri
Dumortiera hirsuta
Reboulia hemisphaerica
Plagiochasma wrightii
Asterella tenella
Mannia triandra
Cryptomitrium tenerum
Preissia quadrata
Bucegia romanica
Marchantia polymorpha
Monocarpus sphaerocarpus
Sphaerocarpos texanus
Riella parisii
Neohodgsonia mirabilis
Blasia pusilla
Haplomitrium blumei
Apotreubia nana
Dendroceros aff. crispus
Dendroceros tubercularis
Megaceros austronesophilus
Nothoceros endiviifolius
Phaeomegaceros fimbriatus
Phymatoceros sp.
Phaeoceros himalayensis
Phaeoceros engelii
Notothylas levieri
Anthoceros punctatus
Folioceros fuciformis
Leiosporoceros dussii
mosses ED
continued
Fig. 7C39 29[30-47]
[22-35]
2 [1-3]
Pulvigera lyellii
Pulvigera lyellii
Plenogemma phyllantha
Lewinskya striata
Nyholmiella obtusifolia
Orthotrichum anomalum
187 [143-225]
Zygodon rupestris
140 [105-169]
Zygodon conoideus
40 [29-50]
Macromitrium saddleanum
101 [77-124]
Macrocoma abyssinica
Leratia obtusifolia
Calomnion schistostegiellum
170
Pyrrhobryum medium
[125-209]
Goniobryum subbasilare
14 [8-19]
Mnium thomsonii
Mnium lycopodioides
70 [44-93]
Rhizomnium punctatum
72 [46-96]
Pseudobryum cinclidioides
211 [179-238]
26 [16-36]
Plagiomnium undulatum
Cinclidium stygium
88 [58-116] 52 [33-70]
Plagiomnium cuspidatum
17 [9-23]
Mielichoferia elongata
27 [16-37]
Pohlia elongata
133 [101-159]
Pohlia cruda
71 [44-96]
Roellobryon roellii
18 [13-22]
Phyllodrepanium falcifolium
Mniomalia viridis
18 [15-20]
Ptychostomum pseudotriquetrum
22 [18-24]
Plagiobryum zieri
179 [146-207]
40 [34-45]
Gemmabryum vinosum
231 [210-248]
Bryum
argenteum
31 [27-35]
52 [45-50]
35 [30-39] Imbribryum alpinum
Anomobryum julaceum
Rosulabryum perlimbatum
25 [21-29]
74 [62-84]
Brachymenium nepalense
38 [32-44]
Leptostomopsis systylia
10 [7-12]
Rhodobryum roseum
167 [135-194]
Rhodobryum ontariense
Leptostomum menziesii
102 [62-136]
Breutelia integrefolia
113 [70-150]
Conostomum tetragonum
158 [111-198]
Philonotis fontana
2 5 1 186 [153-213]
Bartramia pomiformis
Bartramia ithyphylla
Helicophyllum torquatum
57 [49-64]
Tayloria dubyi
60 [52-67]
Splachnum vasculosum
68 [59-76]
Tetraplodon mnioides
Meesia
triquetra
45
[37-52]
72 [63-81]
Amblyodon dealbatus
56 [47-63]
105 [95-113]
Paludella squarrosa
Leptobryum pyriforme
234 [229-237]
Neomeesia paludella
63 [58-69]
Pararhacocarpus patagonicus
93 [85-99]
Rhacocarpus purpurascens
Hedwigia ciliata
72 [66-77]
Braunia imberbis
25 [20-30]
Calyptopogon mnioides
26 [21-31]
Syntrichia ruralis
27 [22-32]
Willia austroleucophaea
29 [25-34]
Sagenotortula quitoensis
36 [32-42]
Streptopogon erythrodontus
28 [24-33] Hennediella macrophylla
39 [34-44]
34 [29-39] Dolotortula mniifolia
42 [38-47]
Tortula truncata
Chenia leptophylla
46 [41-51]
Acaulon muticum
50 [45-54]
Microbryum davallianum
Aloina aloides
52 [48-57] 12 [10-13]
Dialytrichia saxicola
26 [23-29]
Cinclidotus fontinaloides
57 [53-60]
Barbula unguiculata
45 [41-50]
recurvirostrum
31 [27-35] Bryoerythrophyllum
63 [60-65]
Saitobryum lorentzii
Didymodon rigidulus
Leptodontium flexifolium
24 [23-25]
Tortella fragilis
27 [26-28]
Chionoloma hibernicum
83 [79-86]
33 [31-34]
Weissia controversa
21[20-22]Trichostomum
brachydontium
35 [33-36]
Ephemerum
serratum
58 [56-60]
Eucladium verticillatum
88 [83-92]
Hyophila apiculata
63 [61-66]
Molendoa warburgii
28 [27-29] 25[24-26] Anoectangium aestivum
133 [115-150]
Gymnostomum calcareum
44 [42-50]
Gyroweisia tenuis
160 [133-182]
Streblotrichum convolutum
Scopelophila cataractae
162 [135-186]
98 [76-118]
Ceratodon purpureus
Trichodon cylindricus
164 [137-188]
Ditrichum cornubicum
30 [20-40]
Pseudephemerum nitidum
37 [25-48]
Pleuridium subulatum
269 [264-273]
178 [147-204]
Ditrichum subulatum
58 [47-69]
Venturiella coronata
Erpodium domingense
143 [116-166]
Sorapilla papuana
21 [16-26]
159 [131-184]
Trematodon longicollis
187 [155-213]
Bruchia brevifolia
Cynodontium tenellum
117 [92-139]
Kiaeria starkei
Oncophorus virens
134 [106-159]
106 [83-127]
Glyphomitrium daviesii
151 [122-175]
Dicranoweisia cirrata
103 [79-123]
Rhabdoweisia fugax
Rhachithecium perpusillum
12 [8-16]
Dicranum scoparium
22 [16-28]
Dicranum flagellare
196 [164-222]
6
30 [22-37]
Chorisodontium aciphyllum
[2-8]
Platyneuron praealtum
46 [35-56]
Holomitrium seticalycinum
Dicranoloma billarderi
159 [132-183]
Leucoloma molle
Calymperes lonchophyllum
84 [70-97]
Syrrhopodon
ligulatus
172
[143-197]
120 [100-138]
202 [171-227]
Octoblepharum albidum
12 [9-15]
Fissidens bryoides
179
Fissidens exilis
[148-205] 161 [133-186]
Dicranella heteromalla
189
Pleurophascum globosum
[157-216]
61 [47-73]
Dichodontium pellucidum
273 [268-277]
211 [182-233]
Aongstroemia longipes
Amphidium mougeotii
28 [24-31]
Dicranodontium denudatum
Atractylocarpus subporodictyon
128 [125-130]
Campylopus flexuosus
Leucobrym glaucum
178 [162-192]
Archidium alternifolium
186 [166-202]
Micromitrium tenerum
205 [178-227]
Eustichia
longirostris
216 [190-237]
31 [25-36]
Codriophorus acicularis
39 [32-44]
Bucklandiella heterosticha
115 [106-121]
Niphotrichum canescens
70 [61-78]
Dryptodon trichophyllus
Grimmia anomala
81 [77-86]
Coscinodon cribrosus
165 [153-176]
Schistidium maritimum
234 [210-251]
276 [271-280]
Ptychomitrium
polyphyllum
127 [108-142]
134
Brachydontium trichodes
180
[115-149]
Campylostelium saxicola
[163-193]
78 [63-90]
Blindia
acuta
237 [215-255]
107 [88-121]
Blindiadelphus recurvatus
Seligeria pusilla
28 [24-32]
Hymenoloma crispulum
242 [222-258]
Holodontium strictum
40 [25-58]
Flexitrichum
gracile
248[230-261]
282 [277-286]
Flexitrichum flexicaule
Distichium capillaceum
Catoscopium nigritum
Timmia norvegica
19 [17-20]
Physcomitrium patens
22 [20-24]
303 [297-307]
Physcomitrium pyriforme
77 [73-79]
Entosthodon attenuatus
252
Funaria hygrometrica
182 [172-191]
[245-258]
317 [312-322]
Discelium nudum
Encalypta ciliata
Gigaspermum mouretii
Diphyscium foliosum
Buxbaumia aphylla
334 [329-339]
72 [70-74]
Atrichum undulatum
Oligotrichum hercynicum
93 [92-94]
Polytrichum commune
68 [66-70]
103 [102-105]
Pogonatum aloides
337 [332-343]
Dendroligotrichum squamosum
Notoligotrichum trichodon
342 [337-347]
Dawsonia beccarii
169 [161-177]
Tetraphis pellucida
60 my
Tetrodontium brownianum
372 [367-377]
Oedipodium griffithianum
3.5 [3-4]
Andreaea wilsonii
37 [35-39]
Andreaea wilsonii
58 [55-60]
Andreaea rupestris
282 [269-297]
Andreaea rothii
403 [398-406]
Andreaeobryum macrosporum
4 [2-5]
Sphagnum falcatulum
14 [12-15]
Sphagnum cuspidatum
15 [13-17]
420 [416-423]
Sphagnum palustre
Sphagnum girgensohnii
75 [73-79]
17 [15-19]
Sphagnum strictum
Eosphagum inretortum
Takakia lepidozioides
183 [138-221]
54 [42-65]
58 [45-70]
86 [66-104]
28 [21-34]
ED Fig. 7B
j
i
g
h
f
e
d
c
b
a
liverworts
43 [15-70]
47 [17-76]
52 [19-83]
55 [20-87]
ED Fig. 7C
74 [27-116]
46 [15-75]
77 [29-122]
26 [9-43]
31 [11-51]
53 [19-86]
74 [27-117]
46 [16-75]
55 [20-89]
85 [32-132]
53 [19-85]
67 [24-106]
79 [29-125]
87 [34-135]
90 [36-139]
99 [46-146]
60 [31-87]
74 [37-107]
79 [39-114]
80 [40-117]
72 [35-105]
10 [6-15]
14 [8-19]
85 [42-125]
99 [46-146]
52 [27-74]
76 [38-110]
96
[45-142]
m
38 [16-60]
44 [18-69]
50 [21-77]
55 [24-85]
40 [17-62]
58 [25-89]
62 [27-94]
100 [47-148]
67 [29-102]
78 [34-119]
84 [37-127]
13 [5-20]
39 [16-61]
41 [17-64]
42 [17-65]
44 [18-69]
75 [32-114]
100 [47-148]
38 [18-58]
40 [18-60]
42 [19-64]
47 [21-71]
59 [26-90]
27 [11-43]
38 [15-60]
41 [17-65]
46 [19-71]
30 [12-48]
59 [25-91]
63 [27-97]
43 [17-67]
50 [21-78]
56 [24-87]
101 [47-149]
52 [20-81]
32 [12-52]
94 [42-140]
97 [44-145]
52 [18-84]
77 [28-121]
79 [29-125]
84 [31-132]
71 [25-113]
78 [28-123]
81 [30-127]
61 [27-93]
66 [30-100]
71 [32-106]
80 [36-120]
42 [19-64]
59 [27-89]
84 [38-126]
55 [23-86]
79 [35-119]
86 [39-129]
27 [12-42]
64 [29-97]
75 [35-111]
102 [48-150] 90 [42-134]
77 [36-115]
93 [43-138]
81 [38-120]
83 [39-123]
66 [31-97]
29 [14-43]
31 [15-46]
20 [10-30]
37 [20-54]
47 [25-67]
26 [13-38]
53 [28-77]
21 [11-30]
36 [19-51]
14 [7-21]
55 [29-79]
28 [15-40]
32 [17-45]
58 [30-84]
38 [20-54]
41 [22-59]
81 [39-120]
96 [45-141]
105 [49-155]
99 [46-146]
92 [43-136]
59 [25-90]
65 [28-100]
100 [47-149]
96 [45-142]
107 [50-157]
50 [21-78]
15 [6-24]
18 [7-28]
97 [45-144]
61 [27-92]
73 [32-110]
90 [40-135]
98 [44-146]
91 [40-136]
100 [45-149]
68 [23-111]
75 [16-120]
107 [51-158]
112 [58-160]
60 my
118 [65-166]
95 [36-148]
99 [37-153]
91 [34-142]
102 [40-156]
57 [30-81]
96 [50-137]
72 [40-101]
96 [52-135]
105 [56-147]
123 [70-169]
51 [29-72]
57 [31-81]
129 [78-173]
94 [47-136]
63 [38-86]
84 [51-114]
148 [106-184]
99 [74-121]
152 [110-189]
50 [38-61]
78 [59-95]
121 [89-149]
92 [69-113]
62 [46-76]
65 [49-81]
165 [121-203]
53 [40-66]
78 [56-98]
64 [45-92]
114 [91-137]
178 [133-219]
23 [15-32]
l
180 [135-220]
169 [124-210]
mosses
continued
39 [29-48]
147 [108-182]
175 [129-214]
154 [109-195]
k
Taiwanobryum crenulatum
Pinnatella minuta
Shevockia inunctocarpa
Neckeropsis disticha
Homaliodendron flabellatum
Pseudoanomodon attenuatus
Homalia trichomanoides
Exsertotheca crispa
Alleniella complanata
Leptodon smithii
Neckera pennata
Porothamnium fasciculatum
Porotrichodendron superbum
Echinodiopsis hispida
Isothecium myosuroides
Lembophyllum divulsum
Nogopterium gracile
Heterocladium heteropterum
Orthostichella pachycastrella
Limbella tricostata
Isocladiella surcularis
Isopterygium albescens
Taxithelium nepalense
Hageniella micans
Platygyrium repens
Trachyphyllum inflexum
Donnellia commutata
Sematophyllum demissum
Macrohymenium muelleri
Piloecium pseudorufescens
Trismegistia calderensis
Dicnemon cuspidatum
Hypnum cupressiforme
Callicladium imponens
Homalothecium sericeum
Brachytheciastrum velutinum
Eurhynchiastrum pulchellum
Brachythecium rivulare
Myuroclada maximowiczii
Sciuro-hypnum plumosum
Kindbergia praelonga
Cirriphyllum piliferum
Helicodontium capillare
Rhynchostegiella tenella
Microeurhynchium pumilum
Oxyrrhynchium hians
Squamidium brasiliense
Rhynchostegium confertum
Rhynchostegium riparioides
Palamocladium leskeoides
Scorpiurium circinatum
Pseudoscleropodium purum
Eurhynchium striatum
Claopodium whippleanum
Floribundaria flaccida
Meteoriopsis squarrosa
Pseudospiridentopsis horrida
Aerobryidium subpiligerum
Aerobryopsis longissima
Pseudobarbella attenuata
Toloxis imponderosa
Meteorium polytrichum
Papillaria crocea
Ctenidium molluscum
Hyocomium armoricum
Myurium hochstetteri
Lescuraea patens
Lescuraea incurvata
Lescuraea plicata
Schwetschkeopsis fabronia
Anomodon longifolius
Climacium dendroides
Pleuroziopsis ruthenica
Antitrichia curtipendula
Pleurozium schreberi
Hylocomium splendens
Loeskeobryum brevirostre
Rhytidiadelphus squarrosus
Hylocomiastrum pyrenaicum
Abietinella abietina
Rauiella scita
Haplocladium microphyllum
Leskea polycarpa
Thuidium tamariscinum
Pelekium chenagonii
Ptilium crista-castrensis
Rhytidium rugosum
Pseudoleskeella catenulata
Lindbergia patentifolia
Entodon schleicheri
Homomallium incurvatum
Pylaisia polyantha
Buckia vaucheri
Ectropothecium perrotii
Vesicularia galerulata
Pseudostereodon procerrimus
Calliergonella cuspidata
Gollania turgens
Elmeriobryum philippinense
Chryso-hypnum elegantulum
Breidleria pratensis
Pseudoamblystegium subtile
Serpoleskea confervoides
Hygrohypnum luridum
Campylophyllum calcareum
Campylium stellatum
Drepanocladus aduncus
Pseudocalliergon trifarium
Vittia pachyloma
Cratoneuropsis chilensis
Palustriella commutata
Kandaea elodes
Cratoneuron curvicaule
Amblystegium serpens
Hygroamblystegium tenax
Leptodictyum riparium
Tomentypnum nitens
Sanionia uncinata
Scorpidium scorpioides
Hamatocaulis vernicosus
Phyllodon truncatulus
Herpetineuron toccoae
Straminergon stramineum
Sarmentypnum exannulatum
Warnstorfia fluitans
Calliergon cordifolium
Conardia compacta
Henicodium geniculatum
Orthostichopsis tortipilis
Phyllogonium viscosum
Pterobryopsis orientalis
Cryphaea heteromalla
Leucodon sciuroides
Pterigynandrum filiforme
Orthothecium rufescens
Myurella julacea
Platydictya jungermannioides
Isopterygiopsis muelleriana
Herzogiella striatella
Plagiothecium denticulatum
Rectithecium piliferum
Pseudotaxiphyllum elegans
Dichelyma capillaceum
Fontinalis antipyretica
Habrodon perpusillus
Stereophyllum leucostegum
Pilosium chlorophyllum
Entodontopsis nitens
Fabronia pusilla
Ischyrodon lepturus
Acrocladium auriculatum
Lepyrodon lagurus
Catagonium nitens
Rutenbergia madagassa
Neorutenbergia usagarae
Pseudocryphaea domingensis
Lepidopilidium nitens
Cyclodictyon laetevirens
Leucomium lignicola
Hookeria lucens
Adelothecium bogotense
Benitotania elimbata
Bryobrothera crenulata
Daltonia splachnoides
Hypopterygium didictyon
Ptychomnion aciculare
Garovaglia elegans
Cladomniopsis crenato-obtusa
Orthorrhynchium elegans
Bescherellia elegantissima
Franciella spiridentoides
Hypnodendron comosum
Racopilum cuspidigerum
Racopilum tomentosum
Pterobryella vieillardii
Aulacomnium androgynum
Aulacomnium heterostichum
Hymenodontopsis mnioides
Leptotheca gaudichaudii
Orthodontium lineare
Extended Data Figure 7. Divergence :mes es:mates for bryophytes inferred by penalized
likelihood using 29 fossil calibra:ons. Mean node ages (in bold) including confidence intervals (in
brackets) reported in millions of years are stemming from a treePL analysis. Le]ers in red circles
indicate fossil calibra:ons as outlined in Table S2. The figure is divided in three parts: liverworts
and hornworts: Extended Data Figure 7A, mosses Extended Data Figures 7B & C.
Number of genes
Concordance factor
Extended Data Figure 8. Correla:on between gene concordance factor inferred by IQ-TREE and
number of genes in the nucleo:de dataset suppor:ng a node. For details on the concordance
values see Table S5
Concordance factor
Time (Ma)
Extended Data Figure 9. Correla:on between gene concordance factor inferred by IQ-TREE and
mean divergence :mes for backbone nodes (between 130-450 Ma) inferred from the nucleo:de
data. For details on the concordance values see Table S5.
Extended Data Figure 10. Histogram of the frequency of orders and families (A) stem and (B)
crown es:mated age divergences of three bryophyte phyla (Anthocerotophyta, Bryophyta, and
Marchan:ophyta). Kernel density plots depict the probability distribu:on (95% confidence
interval) of the es:mated divergence :me of orders and families. Boxplots at the bo]om show
the distribu:on of the es:mated age divergences of orders and families separated for
Anthocerotophyta, Bryophyte, and Marchan:ophyta.
Alfons Schäfer-Verwimp