ArticlePDF Available

Phylogenetics and biogeography of Theaceae based on sequences of plastid genes

July 2013
Journal of Systematics and Evolution 51(4)

July 2013
51(4)

DOI:10.1111/jse.12017

Authors:

Mimi Li

Institute of Botany, Jiangsu Province and Chinese Academy Sciences

Jianhua Li

Hope College

Peter Del Tredici

Harvard University

Show all 5 authorsHide

Despite several morphological and molecular analyses of Theaceae, several outstanding issues remain in the phylogenetics and biogeography of the family including the disputed relationships among the tribes Gordonieae, Stewartieae, and Theeae, the controversial taxonomic status of Hartia and Stewartia, and the unclear biogeographic history of Gordonieae and Stewartieae. In this study we gathered DNA sequences of multiple plastid genes from 27 species of Theaceae representing all genera except Laplacea, conducted phylogenetic analyses using parsimony, likelihood, and Bayesian methods, and estimated divergence times within a Bayesian framework with fossil calibrations and molecular data. Our data provided further support for the three tribes in the family and for the sister-group relationship of Theeae to Stewartieae plus Gordonieae. Within Gordonieae, our study for the first time offered strong molecular support for the sister relationship of Franklinia and Schima. Within Stewartieae, our data supported the paraphyly of Stewartia including Hartia. Within Stewartia, our data for the first time suggested that North American (NA) species Stewartia ovata was more closely related to eastern Asian (EA) species than to the other NA species Stewartia malacodendron. Biogeographic analyses indicated that disjunct endemic species of Gordonieae might have originated from NA and those of Stewartieae from EA. Divergence times of the EA-NA disjunct pairs identified in this study (Franklinia and Schima in Gordonieae and S. ovata (NA) and Asian species of Stewartia) were estimated to be in the Mid-Miocene. Population exchanges in Gordonieae and Stewartieae may have occurred over the Bering land bridge prior to the Mid-Miocene.

Maximum likelihood tree (−ln likelihood = 22960.55) of Theaceae based on 10 plastid genes. Numbers at branches are bootstrap percentages of MP and ML and posterior probability of BI.

…

Divergence times of lineages in Theaceae estimated based on the plastid phylogeny and two fossil calibration points as shown by the shaded squares. The bars represent 95% range of the estimated times of divergence. Letters A (EA, eastern Asia), B (NA, North America), and C (West indies, Central and South America) indicate geographic distribution of extant species and inferred area of ancestral populations. C1 to C5 are nodes discussed in the text.

…

Figures - uploaded by Peter Del Tredici

Content may be subject to copyright.

Content uploaded by Peter Del Tredici

Content may be subject to copyright.

Research Article

Phylogenetics and biogeography of Theaceae based on

sequences of plastid genes

1,2

Mi‐Mi LI

3,4

Jian‐Hua LI

Peter DEL TREDICI

Jeffrey CORAJOD

Cheng‐Xin FU

(College of Life Sciences,Zhejiang University, Hangzhou 310058, China)

(Jiangsu Provincial Key Laboratory for Plant Ex Situ Conservation,Institute of Botany, Jiangsu Province and Chinese Academy of Sciences,

Nanjing 210014, China)

(Department of Biology,Hope College, MI 49423, USA)

(Arnold Arboretum,Harvard University, Jamaica Plain, MA 02130, USA)

Abstract Despite several morphological and molecular analyses of Theaceae, several outstanding issues remain in

the phylogenetics and biogeography of the family including the disputed relationships among the tribes Gordonieae,

Stewartieae, and Theeae, the controversial taxonomic status of Hartia and Stewartia, and the unclear biogeographic

history of Gordonieae and Stewartieae. In this study we gathered DNA sequences of multiple plastid genes from 27

species of Theaceae representing all genera except Laplacea, conducted phylogenetic analyses using parsimony,

likelihood, and Bayesian methods, and estimated divergence times within a Bayesian framework with fossil

calibrations and molecular data. Our data provided further support for the three tribes in the family and for the sister‐

group relationship of Theeae to Stewartieae plus Gordonieae. Within Gordonieae, our study for the ﬁrst time offered

strong molecular support for the sister relationship of Franklinia and Schima. Within Stewartieae, our data supported

the paraphyly of Stewartia including Hartia. Within Stewartia, our data for the ﬁrst time suggested that North

American (NA) species Stewartia ovata was more closely related to eastern Asian (EA) species than to the other NA

species Stewartia malacodendron. Biogeographic analyses indicated that disjunct endemic species of Gordonieae

might have originated from NA and those of Stewartieae from EA. Divergence times of the EA‐NA disjunct pairs

identiﬁed in this study (Franklinia and Schima in Gordonieae and S. ovata (NA) and Asian species of Stewartia) were

estimated to be in the Mid‐Miocene. Population exchanges in Gordonieae and Stewartieae may have occurred over the

Bering land bridge prior to the Mid‐Miocene.

Key words Gordonieae, plastid, small single copy, Stewartieae, Theaceae, Theeae.

Ericales as deﬁned by the angiosperm phylogeny

group (APG, 2009) consists of 23 families that have

been traditionally placed in Rosidae, Dilleniidae, or

Asteridae (Cronquist, 1981). Theaceae is one of the

families and has been recognized narrowly excluding

the genera of Pentaphylacaceae (Schonenberger et al.,

2005; APG, 2009). A possible synapomorphy of

Theaceae is the presence of specialized pseudopollen

(Tsou, 1997).

Several phylogenetic studies of Theaceae have

been published based on morphological (Luna &

Ochoterena, 2004) and molecular data (Prince &

Parks, 2001; Li et al., 2002; Prince, 2002; Yang

et al., 2004; Wang et al., 2006). Three major lineages or

tribes have been recognized including Gordonieae

(Gordonia J. Ellis, Franklinia W. Bartram ex H.

Marshall and Schima Reinwardt ex Blume), Stewar-

tieae (Stewartia L. and Hartia Dunn), and Theeae

(Camellia L., Laplacea Kunth, Apterosperma Chang,

Polyspora Sweet ex Don, and Pyrenaria Blume)

(Prince & Parks, 2001; Yang et al., 2004; Wang

et al., 2006). However, relationships among the three

tribes remained controversial. In Prince & Parks (2001)

study using plastid gene matK and ﬂanking region

(2118 sites), Gordonieae and Stewartieae were sister to

each other with 62% bootstrap support, while in Yang

et al.’s (2004) study, sequences from nrDNA ITS region

(756 sites) provided strong support (100% bootstrap)

for the sister relationship of Gordonieae and Theeae.

This sister relationship was also recognized by a

phylogenetic analysis based on a non‐molecular data set

of 47 characters (Wang et al., 2006); however, the

bootstrap support was <50%. Relationships within

tribes also remained either unresolved or debated in

previous studies (Prince & Parks, 2001; Yang

et al., 2004; Wang et al., 2006). Within Gordonieae,

Received: 4 November 2012 Accepted: 25 March 2013

* Author for correspondence. E‐mail: li@hope.edu. Tel.: 1‐616‐395‐

7460. Fax: 1‐616‐395‐7125.

Journal of Systematics and Evolution 51 (4): 396–404 (2013) doi: 10.1111/jse.12017

in Prince & Parks (2001) study, unweighted phyloge-

netic analyses of plastid genes matK and rbcL (3440

sites) did not resolve the relationships among the three

genera, while equally weighted analysis of the same

sequence data provided support for sister relationship of

Schima and Franklinia. In Yang et al.’s (2004) study,

none of the sequence data (nrDNA ITS: 756 sites,

plastid trnL‐F: 982 sites, or mitochondrial matR: 1727

sites) resolved the intergeneric relationships of Gordo-

nieae. However, in Wang et al.’s (2006) study, non‐

molecular data recognized the sister relationship of

Franklinia and Schima with 86–87% bootstrap support.

Within Stewartieae, based on non‐molecular characters,

some authors (Chun, 1934; Merrill, 1938; Wu, 1940;

Yan, 1981; Ye, 1982, 1990; Chang & Ren, 1998; Heo

et al., 2011) recognized the deciduous Stewartia and

evergreen Hartia, while others preferred to merge the

two genera (Airy‐Shaw, 1936; Spongberg, 1974;

Li, 1996). Phylogenetic studies based on molecular

data have also drawn different conclusions for the

generic status of Stewartia and Hartia. In Li et al.’s

(2002) study using nrDNA ITS data and Franklinia as

the outgroup to root parsimonious trees, Hartia and

Stewartia formed reciprocal monophyletic groups.

However, in Prince’s (2002) study using both nrDNA

ITS and plastid sequence data, and Apterosperma and

Gordonia as the outgroups, Hartia appeared to be

derived from within the paraphyletic Stewartia (boot-

strap ¼80%). Paraphyly of Stewartia was also shown

in the nrDNA ITS trees reconstructed using the maxi-

mum likelihood (ML) method (Xiang et al., 2004). Both

parsimony and ML analyses of nrDNA ITS data

suggested that the two North American (NA) Stewartia

malacodendron and Stewartia ovata formed a weakly‐

supported clade (Li et al., 2002; Xiang et al., 2004).

However, the NA clade was not recovered from either

nrDNA ITS or plastid data in Prince (2002) study.

All three tribes in Theaceae show a disjunct

distribution between eastern Asia (EA) and NA. In

Gordonieae, Franklinia, and Gordonia are monotypic,

NA taxa (Prince, 2007). The former is extinct in the wild

but has ﬂourished in cultivation (Fry, 2000). Schima has

a wide distribution in subtropical and tropical areas of

southern Asia. Species of Hartia in the Stewartieae

occur in central and southern China, whereas Stewartia

has two species in southeastern United States and the

remaining species in EA. Laplacea of Theeae occurs in

the West Indies, and Central and South Americas

(WCSA), while Polyspora,Pyrenaria, and Aptero-

sperma are found in Southeast Asia.

Although the biogeographic patterns of the

disjunction between EA and NA are complex and

vary across lineages (Wen, 1999; Donoghue et al.,

2001), there is a predominant direction of migration of

ancestral lineages from Asia to North America—an

“out of Asia”hypothesis (Donoghue & Smith, 2004).

Few disjunct lineages between EA and eastern NA

(ENA) showed the opposite direction of migration from

ENA to EA (Donoghue & Smith, 2004). A recent

biogeographic analysis indicated that most eastern and

western NA endemic lineages of inter‐continental

disjunct genera originated from widespread ancestral

areas (Harris et al., 2013). In Stewartieae, fossils of

Stewartia have been described in the Miocene of EA

and the Oligocene of Europe (Caspary, 1872; Mai &

Walther, 1985; Suzuki & Hirata, 1989), but not in NA.

This implies an Old World origin of the disjunct

lineage. The Asian origin hypothesis is also supported

by the paraphyly of Asian Stewartia including the two

NA species of Stewartia and Hartia (Prince, 2002).

Nevertheless, phylogenetic relationships of Stewartia

remain debated and the Asian origin hypothesis needs

further testing. In Gordonieae, however, the earliest

reliable fossils have been found in NA (Grote &

Dilcher, 1992). Previous phylogenetic analyses sug-

gested that Franklinia and Schima may be sister to each

other (Prince & Parks, 2001; Wang et al., 2006).

Therefore, Gordonieae may represent one of few

lineages with migration of ancestral populations from

ENA to EA.

Some fossil leaf remains in the Upper Cretaceous

and Eocene of North America have been assigned to

Theaceae (Berry, 1916, 1924, 1925; Taylor, 1990).

However, their identities have been questioned (Grote

& Dilcher, 1989). Nevertheless, Theaceae have been

suggested to have radiated at least since the early

Eocene (Grote & Dilcher, 1992). Detailed comparative

analyses of fossil fruits and seeds from the middle

Eocene Claiborne Formation in western Kentucky and

Tennessee (Grote & Dilcher, 1989) have shown that the

fossils are closely related to Gordonia lansianthus and

Franklinia of North America or to Polyspora of

Southeast Asia (Grote & Dilcher, 1989, 1992). Fossil

capsules similar to Asian Polyspora were found in the

upper Eocene of eastern Germany (Mai & Walther,

1985). These reliable fossils provide calibration points

in molecular phylogenetic trees to estimate the

divergence times of EA‐NA disjunct lineages.

Because previous phylogenetic studies have

produced different phylogenetic trees likely due to

limited data points and/or the use of different analytical

methods along with other unknown factors, we

gathered the largest DNA sequence data set to date

for Theaceae (>9000 sites) from the small single copy

region (SSC) of plastid genome and reconstruct

phylogenetic relationships of Theaceae utilizing

LI et al.: Phylogeny and biogeography of Theaceae 397

maximum parsimony (MP), ML, and Bayesian meth-

ods. Speciﬁc objectives of the study were (i) to further

evaluate relationships among the three major tribes of

Theaceae (Gordonieae, Stewartieae, and Theeae); (ii) to

clarify intergeneric relationships of Franklinia,Gordo-

nia, and Schima; (iii) to test relationships of Stewartia

and Hartia; and (iv) to infer the biogeographical history

of EA‐NA disjunct lineages in Gordonieae and

Stewartieae.

1 Material and methods

1.1 Materials

Twenty‐seven samples were included in this study

(see Appendix A) representing all seven genera of

Theaceae (Prince, 2007) except for Laplacea (unavail-

able for the study). One species from Symplocaceae and

one from Styracaceae were also sampled as outgroups

to root the phylogenetic trees because the families are

most closely related to Theaceae (Geuten et al., 2004).

Within Theaceae (Prince, 2007), our taxon sampling

represents morphological and geographic diversity of

the tribes and genera, with a focus on Gordonieae and

Stewartieae. In Gordonieae we sampled Gordonia

lasianthus (L.) Ellis from Gordonia (2 species in total),

Franklinia alatamaha Bartr. ex Marshall from Frank-

linia (monotypic), and three species of Schima, which

has been treated as a monotypic genus with a complex‐

polymorphous species (Bloembergen, 1952) or as a

genus with 20 species (Keng, 1994). In Stewartieae, we

included seven species of Stewartia (8 species)

(Ye, 1982) and four species of Hartia (15 species),

which is a monophyletic group based on nrDNA ITS

data of 11 species (Li et al., 2011, unpublished data).

1.2 Molecular techniques

Genomic DNAs were extracted from silica gel

dried leaves using a Plant DNeasy Mini Kit following

the manufacturer’s instructions (Qiagen, Valencia,

CA). Polymerase chain reactions (PCR) were per-

formed to amplify SSC regions of the plastid genome

using an MJ‐Research thermocycler or Eppendorf

Mastercycler and eight primer pairs designed by

Dhingra & Folta (2005), which amply a 9000‐bp

fragment containing 10 genes: rps12,ndhF,rpl32,

ccsA,ndhD,psaC,ndhE,ndhG,ndhI, and ndhA. Each

10‐mL PCR reaction contained 2 mL buffer (5),

20 mmol/L primers, Phusion polymerase (New Eng-

land Biolabs, Cat# F540L, Ipswich, MA, USA), and

50–100 ng genomic DNA. PCR products were gel

puriﬁed in 1% agarose gel with a Qiagen Gel Extraction

Kit and sequenced using the BigDye Terminator Ready

Reaction Kit and automated Genetic Analyzers (GA

3130 at Hope College or GA 3730 at Harvard

University). Sequences were edited in Sequencher

(version 4, Gene Coding, Ann Arbor, MI).

1.3 Sequence alignment and phylogenetic analysis

The sequences were aligned using the computer

program MUSCLE (Edgar, 2004). Gaps were treated as

missing data. Phylogenetic analyses were conducted

using MP, ML, and Bayesian inference (BI) methods.

MP analyses were carried out using a heuristic tree

search with the following options in MEGA 5.05

(Tamura et al., 2011): close‐neighbor interchange

(CNI) on random trees, 10 initial trees, and search

level set to 1. Characters were equally weighted and

character states were unordered. MODELTEST (Posa-

da & Crandall, 1998) was used to select the optimal

model of sequence evolution for the ML and BI

analyses. ML analyses were conducted using the

selected model (GTR þG) and implemented in

MEGA with number of discrete gamma categories set

to 4 and heuristic tree inference with NNI swapping and

automatic making of the initial tree (Tamura

et al., 2011). Bayesian analyses were performed with

GTR þGmodel using MrBayes (Ronquist et al., 2012)

with two runs, each with four chains and 10 million

generations. The split frequency was <0.01. Trees were

sampled every 1000th generation. The ﬁrst 250 000

generations were discarded as Burnin generations when

ML scores have stabilized. Majority consensus indices

of clades in the remaining trees were taken as the

posterior probability for individual clades. To assess

relative support for individual clades in both MP and

ML analyses we used nonparametric bootstrap analyses

(Felsenstein, 1985) with 10 000 replicates for MP and

500 replicates for ML, and the options were as in the MP

and ML analyses.

1.4 Biogeographic analysis

To gain insights into the geographic origin of

EA‐NA disjunct clades in Gordonieae and Stewartieae,

we used dispersal‐vicariance analysis (DIVA on RASP

by Y. Yu, A. J. Harris, and X. J. He available at http://

mnh.scu.edu.cn/soft/blog/RASP) to reconstruct the

ancestral distribution of the disjunct pairs. The 50%

consensus tree from BI analysis was used for the DIVA

analysis because the disjunct nodes and all nodes below

the disjunct nodes were well supported in MP, ML, and

BI analyses. The number of samples for species with

two or more individuals included in the reconstructed

phylogeny was reduced to one due to the requirement of

DIVA for a bifurcating tree. Because Laplacea from the

West Indies, and Central and South Americas (WCSA)

398 Journal of Systematics and Evolution Vol. 51 No. 4 2013

was not included in the phylogeny, the DIVA analyses

were then conducted in two ways: without this genus

and with this genus manually connected to the tree as

the sister of the Camellia‐Pyrenaria clade (double

arrow in Fig. 2) based on the phylogenetic study of

Prince & Parks (2001) using plastid sequence data. The

maxarea in DIVA was set to 3 (EA, NA, and WCSA).

Outgroups were removed from DIVA analysis because

it is not entirely clear about where their ancestral areas

might be and whether they are sister taxa to Theaceae.

1.5 Molecular dating

Fossils with known ages and the inferred

phylogeny were used to estimate the divergence times

of sister clades between EA and NA. Fossil capsules of

the early Eocene (ca. 49 mya) represent the minimal age

of the tribe Theeae because they are similar to Asian

Polyspora (Mai & Walther, 1985). Fossil fruits and

seeds of the middle Eocene (ca. 40.4 mya) assignable to

either Gordonia or Franklinia suggest the minimal age

of the tribe Gordonieae (Grote & Dilcher, 1992).

Placing the fossil ages to the crown clades generated

unreasonably old age for the Theaceae (>125 mya).

Therefore, we used the fossils as the ages of the stem

clades for both tribes Theeae and Gordonieae. The

molecular dating exercise was conducted using BEAST

program (Drummond et al., 2012) with the following

parameters: GTR þGmodel, estimated base frequen-

cies, gamma categories 4, uncorrelated lognormal

relaxed clock model, Yule speciation process with a

UPGMA starting tree, and lognormal prior of calibra-

tion points with the offsets of 40.4 and 49 mya for

Gordonieae and Theeae, respectively, and the log

standard deviations of 2.365 and 2.2474, respectively.

For both Gordonieae and Theeae, the standard

deviations put the 95% quantiles to 89.3 mya, which

is the estimated age of the entire Ericales (Martínez‐

Millán, 2010). The MCMC analyses in BEAST were

run for 50 million generations with 2 million

generations as burnin, as determined by Tracer 1.5

(Drummond et al., 2012), and trees were sampled every

1000th generation. Effective sample size (ESS) was

ensured to be over 100 as shown in Tracer 1.5. Means

and 95% range of the estimated divergence times were

calculated in TreeAnnotator of the BEAST software

package (Drummond et al., 2012).

2 Results

2.1 Phylogenetic analyses

Individual analyses of each plastid gene did not

produce phylogenetic trees with strongly supported

but conﬂicting clades, we therefore combined them in

a single data set, which had 9787 bp, 572 of which

were parsimony informative (5.8%). MP analysis

generated 65 parsimonious trees of 1685 steps (CI ¼

0.89, RI ¼0.92). Trees from ML (Fig. 1) and BI

showed congruent relationships as in the MP trees.

Within Theaceae all three tribes (Gordonieae, Stew-

artieae, and Theeae) received strong support. Theeae

was sister to the clade containing Stewartieae and

Theeae. This relationship was more strongly supported

in the MP tree (93%) than in both ML (56%)

and BI (0.68) trees. In Gordonieae, Gordonia was

sister to the clade containing Franklinia and Schima

with strong support (MP/ML/BI: 98%/97%/1), while

within Stewartieae, Stewartia malacodendron was

sister to the clade consisting of Hartia and remaining

species of Stewartia (99%/100%/1). Hartia formed

a robust clade (99%/99%/1), and so did Stewartia

(minus S. malacodendron) (99%/99%/1). EA‐NA

disjunct clades were Franklinia (NA)—Schima (EA)

(98%/97%/1) (C1 in Fig. 2) and Stewartia ovata

Fig. 1. Maximum likelihood tree (ln likelihood ¼22960.55) of

Theaceae based on 10 plastid genes. Numbers at branches are bootstrap

percentages of MP and ML and posterior probability of BI.

LI et al.: Phylogeny and biogeography of Theaceae 399

(NA)—Asian Stewartia species (87%/91%/1) (C2 in

Fig. 2).

2.2 Biogeographic analyses and divergence time

estimation

Biogeographic analyses with or without Laplacea

generated similar inferred ancestral areas for the EA‐

NA disjunct lineages. NA was inferred as the ancestral

area of Gordonieae (C3 in Fig. 2). Dispersal from NA to

EA and subsequent vicariance produced the disjunct

distribution in Gordonieae. In Stewartieae, however,

DIVA suggested that either NA or EA þNA is the

likely ancestral area of the disjunction between S. ovata

and Asian species of Stewartia (C4 in Fig. 2).

Results of divergence time estimation using

BEAST showed that Franklinia and Schima diverged

at 9.9 mya (95% CI: 5–17 mya) (C1 in Fig. 2),

Stewartia malacodendron and the remaining species

of Stewartia (including Hartia) at 18.7 mya (95% CI:

11.3–29.1 mya, C5 in Fig. 2), and S. ovata and the

Asian Stewartia species at 9.3 mya (95% CI: 5.2–

15.1 mya) (C2 in Fig. 2).

Fig. 2. Divergence times of lineages in Theaceae estimated based on the plastid phylogeny and two fossil calibration points as shown by the shaded

squares. The bars represent 95% range of the estimated times of divergence. Letters A (EA, eastern Asia), B (NA, North America), and C (West indies,

Central and South America) indicate geographic distribution of extant species and inferred area of ancestral populations. C1 to C5 are nodes discussed in

the text.

400 Journal of Systematics and Evolution Vol. 51 No. 4 2013

3 Discussion

3.1 Phylogenetic relationships and systematic

implications

Several classiﬁcation systems have been proposed

in the past century for Theaceae (Melchior, 1925; Airy‐

Shaw, 1936; Sealy, 1958; Keng, 1962; Prince &

Parks, 2001). Recent phylogenetic analyses using

molecular data have provided strong support for three

clades or tribes (Gordonieae, Stewartieae, and Theeae)

in Theaceae (Prince & Parks, 2001; Yang et al., 2004;

Prince, 2007). Morphologically, Theeae differs from

the other two tribes in having multiple bracteoles on

pedicels, sepal to petal gradation, three capsule valves,

and lack of endosperm (Keng, 1962). Gordonieae is

unique in seeds with thin layers of endosperm, while

Stewartieae shows a few unique features including

seeds with copious endosperm and ovaries without a

central column (Keng, 1962). Our sequence data from

the plastid genome of all genera except for Laplacea

further support the three clades (Fig. 1).

Phylogenetic relationships among the three tribes

have been in debate over decades (Airy‐Shaw, 1936;

Keng, 1962). Airy‐Shaw (1936) included Stewartieae

in Gordonieae indicating their close afﬁnity. Keng

(1962), however, considered Gordonieae to be more

closely related to Theeae than Stewartieae. Cladistic

analysis of morphological characters did not provide

resolution for the generic relationships (Luna &

Ochoterena, 2004; Wang et al., 2006). Molecular

studies have also offered conﬂicting insights (Prince &

Parks, 2001; Yang et al., 2004). Prince & Parks (2001)

provided weak support (bs ¼62% and decay index

¼1) for the sister relationship of Gordonieae and

Stewartieae, whereas Yang et al.’s (2004) nrDNA ITS

data suggested a closer relationship of Gordonieae with

Theeae than to Stewartieae with strong support

(bs ¼100%). However, it is unclear whether their

ML analysis of the ITS data also provided support for

the closer relationship of Gordonieae with Theeae. In

addition, the combined analyses of ITS, trnL‐F, and

matR data sets did not show >50% bootstrap support

for the sister relationship of Gorodineae and Theeae

(Yang et al., 2004). In this study, results from all

analyses are consistent with Airy‐Shaw (1936) and

Prince & Parks (2001). However, the support is weak

from both ML (56%) and BI (0.68) analyses. Therefore,

tribal relationships of Theaceae remain unclear, and

genome‐wide data are needed to provide further

resolution to the problem.

Generic relationships of Gordonieae have not been

fully resolved by previous molecular studies (Prince &

Parks, 2001; Yang et al., 2004; Wang et al., 2006). Our

study with more plastid DNA sequence data provides

strong support for the sister‐group relationship of

Gordonia to the remaining Gordonieae (Wang

et al., 2006), and for the sister relationship of Franklinia

and Schima (Fig. 1). Although it is not clear what

morphological characters support the close relationship

of Franklinia and Schima, successful artiﬁcial crossing

of the two genera may lend further support for their

close afﬁnity (Ranney et al., 2003).

One of the long‐lasting debates in the systematics

of Theaceae concerns the taxonomy of Hartia and

Stewartia (Chun, 1934; Airy‐Shaw, 1936; Merrill,

1938; Wu, 1940; Spongberg, 1974; Yan, 1981; Ye,

1982, 1990; Li, 1996; Chang & Ren, 1998). Many

authors (Chun, 1934; Merrill, 1938; Wu, 1940; Yan,

1981; Ye, 1982, 1990; Chang & Ren, 1998) recognized

the deciduous Stewartia and evergreen Hartia, while

several authors (Airy‐Shaw, 1936; Spongberg, 1974;

Li, 1996) suggested the combination of the two genera.

Parsimony analyses of the nuclear sequence data from

nrDNA ITS region supported the separation of the two

genera (Li et al., 2002), while ML analyses of the same

data set placed Hartia within Stewartia (Xiang et al.,

2004). In the tree (Fig. 1), species of Hartia form a

robust clade nested within Stewartia with strong

support. Thus, the plastid data support the taxonomic

treatment combining the two genera (Li, 1996). Another

taxonomic option is to recognize a new genus for

Stewartia malacodendron so that each genus represents

a separate lineage in the phylogenetic tree. However,

there are no distinct morphological or ecological charac-

ters to distinguish S. malacodendron from the remaining

species of Stewartia (Li, 1996). Therefore, we do not

advocate the further split of Stewartia into three genera.

Stewartia ovata has been taxonomically separated

as a subgenus or section (Gray, 1849; Li, 1996) from the

remaining species of Stewartia because of its unique-

ness in having a single bract (vs. two in the rest of

species) subtending a ﬂower and free styles (vs. fused

styles). Parsimony analysis of the DNA sequence data

from the nrDNA ITS region provided weak support for

the sister relationship of S. ovata and S. malacodendron

(Li et al., 2002). In Prince’s (2002) study using plastid

gene data sets, S. ovata and S. malacodendron did not

form a clade; however, together they were in a clade

with Hartia species. Our plastid sequence data in this

study provide strong support for the distant relationship

of S. ovata and S. malacodendron (Fig. 1), and the latter

species appears to have diverged much earlier at 11.3–

29.1 mya from the remaining species of Stewartia

including Hartia (Fig. 2). Therefore, out data do not

support the recognition of S. ovata as a separate

subgenus or section.

LI et al.: Phylogeny and biogeography of Theaceae 401

3.2 Biogeographic implications

Our phylogenetic study has identiﬁed two EA‐NA

disjunctions: Franklinia (NA)‐Schima (EA) in Gordo-

nieae and S. ovata (NA)‐Asian Stewartia species in

Stewartieae. DIVA analyses based on the well‐resolved

phylogeny and molecular dating exercises using

BEAST suggest that the ancestral populations of

Gordonieae may have migrated from NA to EA in

the Mid‐Miocene producing a widespread distribution

(C1 in Fig. 2), which was subsequently interrupted by a

vicariant forming the EA‐NA disjunction. In the

Stewartieae, however, the migratory direction is

unresolved; the ancestral populations of the EA‐NA

disjunct lineage may be in EA or EA þNA (C4 in

Fig. 2). Nevertheless, this suggests that EA was

probably involved in the formation of the lineage,

which is dated at the mid‐Miocene. The fossil record

has shown that EA and NA exchanged ﬂora before the

Mid‐Miocene, that is, 15 mya (Manchester, 1999).

Declining temperatures since then may have resulted in

differential survival and extinction of lineages in the

two continents, thus forming the current disjunct

distribution (Milne & Abbott, 2002). Our estimated

times of divergence between EA‐NA fall within the

range of divergent times estimated for many other EA‐

NA disjunct angiosperm clades (Wen, 1999; Xiang

et al., 2000; Milne & Abbott, 2002; Donoghue &

Smith, 2004). Two migratory pathways have been

suggested for the population exchanges between EA

and NA: the Bering and North Atlantic land bridges

(Tiffney, 1985a, 1985b). However, the latter bridge,

albeit as stepping stones available in the early Miocene,

might not be readily available in the Mid‐Miocene

(Tiffney, 1985b). Therefore, the widespread distribu-

tion of the stem lineage of the EA‐NA disjunction in

both Gordonieae and Stewartieae was more likely due

to the exchange via the Bering land bridge. Nonethe-

less, because species of both Gordonieae and Stew-

artieae occur in the temperate and subtropical regions, if

the ancestral populations of the disjunct lineages had

migrated via the Bering land bridge, they would have to

survive the cold and dark winters of the high latitude

area (Tiffney, 2000).

Based on the biogeographic reconstruction of

100 disjunct lineages in the Northern Hemisphere,

Donoghue & Smith (2004) concluded that most EA‐NA

disjuncts had an Asian origin. Recently, Harris et al.

(2013) used a Bayes‐DIVA approach to infer the

biogeographic origins of 185 endemic lineages within

23 inter‐continental disjunct genera, and their results

suggested that lineages in NA and Europe more

often originated from widespread ancestors than

EA. This study of Theaceae provides examples of

NA and EA origins of disjunct lineages in the two

areas.

In conclusion, our data support the three tribes of

Theaceae sensu Prince & Parks (2001), the sister

relationship of Theeae with the remaining Theaceae,

and the closer relationship of Franklinia and Schima

than either is to Gordonia, and the merger of Stewartia

and Hartia. Our molecular dating and DIVA analyses

suggest that Schima and Franklinia may have originat-

ed from the ancestral populations in NA, while the

ancestral area of S. ovata and Asian Stewartia species

may be EA, and that the EA‐NA disjunctions in both

Gordonieae and Stewartieae may have formed via

Bering land bridge in the Mid‐Miocene.

Acknowledgements The authors thank Richard

OLSEN of the United States Agricultural Research

Service in Washington DC, Arnold Arboretum,

Kunming Botanical Garden, Polly Hill Arboretum,

Quarryhill Botanical Garden, University of British

Columbia Botanical Garden, and Wenbo LIAO of

Zhongshan University for providing leaf material for

the study, and Arnold Arboretum, China Scholarship

Council, and Janine Luke and Mel Seiden for providing

ﬁnancial support for the project.

References

Airy‐Shaw HK. 1936. Notes on the genus Schima and on the

classiﬁcation of the Theaceae‐Camellioideae. Kew Bulletin

1936: 496–500.

APG (Angiosperm Phylogeny Group). 2009. An update of the

Angiosperm Phylogeny Group classiﬁcation for the orders

and families of ﬂowering plants: APG III. Botanical Journal

of the Linnean Society 161: 105–121.

Berry EW. 1916. The lower Eocene ﬂoras of southeastern North

America. U.S. Geological Survey Professional Paper 91:

1–481.

Berry EW. 1924. The middle and upper Eocene ﬂoras of south‐

eastern North America. U.S. Geological Survey Profes-

sional Paper 92: 1–206.

Berry EW. 1925. The ﬂora of the Ripley formation. U.S.

Geological Survey Professional Paper 136: 1–94.

Bloembergen S. 1952. A critical study in the complex‐

polymorphous genus Schima (Theaceae). Reinwardtia 2:

133–183.

Caspary R. 1872. Einige Pﬂanzenreste aus der Bernsteinzeit.

Schriften der Koniglichen Physikalisch‐Okonomischen

Gesellschaft zu Königsberg 13: 17–18.

Chang HT, Ren SX. 1998. Theaceae. In: Flora Reipublicae

Popularis Sinicae. Beijing: Science Press. 1–251.

Chun WY. 1934. Additions to the ﬂora of Kwantung and south‐

eastern China (2). Sunyatsenia 2: 49–87.

Cronquist A. 1981. An integreated system of classiﬁcation

of ﬂowering plants. New York: Columbia University

Press.

402 Journal of Systematics and Evolution Vol. 51 No. 4 2013

Dhingra A, Folta KM. 2005. ASAP: Ampliﬁcation, sequencing

& annotation of plastomes. BMC Genomics 6: 176.

Donoghue MJ, Bell CD, Li JH. 2001. Phylogenetic patterns in

Northern Hemisphere plant geography. International Jour-

nal of Plant Sciences 162: S41–S52.

Donoghue MJ, Smith SA. 2004. Patterns in the assembly of

termperate forests around the Northern Hemisphere

Philosophical Transactions of the Royal Society of London

B: Biological Sciences 359: 1633–1644.

Drummond AJ, Suchard MA, Xie Dong, Rambaut A. 2012.

Bayesian phylogenetics with BEAUti and the BEAST 1.7.

Molecular Biology and Evolution 29: 1969–1973.

Edgar RC. 2004. MUSCLE: Multiple sequence alignment with

high accuracy and high throughput. Nucleic Acids Research

32: 1792–1797.

Felsenstein J. 1985. Conﬁdence limits on phylogenies: An

approach using the bootstrap. Evolution 39: 783–791.

Fry JT. 2000. Franklinia alatamaha, a history of that ‘very

curious’shrub, Part 1: Discovery and naming of the

Franklinia.Bartram Broadside pp. 1–24.

Geuten K, Smets E, Schols P, Yuan YM, Janssens S, Küpfer P,

Pyck N. 2004. Conﬂicting phylogenies of balsaminoid

families and the polytomy in Ericales: Combining data in a

Bayesian framework. Molecular Phylogenetics and Evolu-

tion 31: 711–729.

Gray A. 1849. The genera of the plants of the United States. New

York: George P. Putnam.

Grote PJ, Dilcher DL. 1989. Investigations of angiosperms from

the Eocene of North America: A new genus of the Theaceae

based on fruit and seed remains. Botanical Gazette 152:

190–206.

Grote PJ, Dilcher DL. 1992. Fruits and seeds of tribe Gordonieae

(Theaceae) from the Eocene of North America. American

Journal of Botany 79: 744–753.

Harris AJ, Wen J, Xiang QY. 2013. Inferring the biogeographic

origins of inter‐continental disjunct endemics using a

Bayes‐DIVA approach. Journal of Systematics and Evolu-

tion 51: 117–133.

Heo KI, Lee S, Lee C, Kim SC. 2011. Generic delimitation

and infrageneric classiﬁcation of Stewartia and Hartia

(Theaceae; Stewartieae): Insight from pollen morphology.

Plant Systematics and Evolution 297: 33–50.

Keng H. 1962. Comparative morphological studies in Theaceae.

University of California Publications in Botany 33: 269–

384.

Keng H. 1994. Flora Malesianae prevursors LVIII, part 4: The

genus Schima (Theaceae) in Malesia. Gardens’Bulletin

(Singapore) 46: 77–87.

Li J. 1996. A systematic study on the genera Stewartia and

Hartia (Theaceae). Acta Phytotaxonomica Sinica 34: 48–67.

Li JH, Del Tredici P, Yang SX, Donoghue MJ. 2002.

Phylogenetic relationships and biogeography of Stewartia

(Camellioideae, Theaceae) inferred from nuclear ribosomal

DNA ITS sequences. Rhodora 104: 117–133.

Luna I, Ochoterena H. 2004. Phylogenetic relationships of the

genera of Theaceae based on morphology. Cladistics 20:

223–270.

Mai DH, Walther H. 1985. Die obereozänen Floren des

Weisselster‐Beckens und seiner Randgebiete. Leipzig:

Deutscher Verlag fur Grundstofﬁndustrie.

Manchester SR. 1999. Biogeographical relationships of North

American Tertiary ﬂoras. Annals of the Missouri Botanical

Garden 86: 472–522.

Martínez‐Millán M. 2010. Fossil record and age of the Asteridae.

Botanical Review 76: 83–135.

Melchior H. 1925. Theaceae. In: Engler A, Prantl E eds.

Die naturlichen pﬂanzenfamilien. 2nd ed. Leipzig: Wilhelm

Engelmann. 21: 109–154.

Merrill ED. 1938. New or noteworthy Indo‐Chinese plants.

Journal of Arnold Arboretum 19: 21–70.

Milne RI, Abbott RJ. 2002. The origin and evolution of Tertiary

relict ﬂoras. Advances in Botanical Research 38: 282–314.

Posada D, Crandall KA. 1998. MODELTEST: Testing the model

of DNA substitution. Bioinformatics Application Note 14:

817–818.

Prince LM. 2002. Circumscription and biogeographic patterns in

the eastern North American‐East Asian genus Stewartia

(Theaceae: Stewartieae): Insight from chloroplast and

nuclear DNA sequences data. Castanea 67: 290–301.

Prince LM. 2007. A brief nomenclatural review of genera and

tribes in Theaceae. Aliso 24: 105–121.

Prince LM, Parks CR. 2001. Phylogenetic relationships of

Theaceae inferred from chloroplast DNA sequence data.

American Journal of Botany 88: 2309–2320.

Ranney TG, Eaker TA, Fantz PR, Parks CR. 2003. xSchimlinia

ﬂoribunda (Theaceae): A new intergeneric hybrid between

Franklinia alatamaha and Schima argentea. HortScience

38: 1198–1200.

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A,

Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.

2012. MrBayes 3.2: Efﬁcient Bayesian phylogenetic

inference and model choice across a large model space.

Systematic Biology 61: 539–542.

Schonenberger J, Anderberg AA, Sytsma KJ. 2005. Molecular

phylogenetics and patterns of ﬂoral evolution in the

Ericales. International Journal of Plant Sciences 166:

265–288.

Sealy JR. 1958. A revision of the genus Camellia. London: Royal

Horticlutural Society.

Spongberg SA. 1974. A review of deciduous‐leaved species of

Stewartia (Theaceae). Journal of Arnold Arboretum 55:

182–214.

Suzuki M, Hirata C. 1989. Fossil wood ﬂora from the pumice tuff

of Yanagida Formation (Lower Miocene) at Mawaki, Noto

Peninsula (Japan). Annals of Science. Kanazawa University

26: 47–75.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

2011. MEGA5: Molecular evolutionary genetics analusis

using maximum likelihood, evolutionary distance, and

maximum parsimony methods. Molecular Biology and

Evolution 28: 2731–2739.

Taylor DW. 1990. Paleobiogeographic relationships of

angiosperms from the Cretaceous and early Tertiary of

the North America area. The Botanical Review 56: 279–

320.

Tiffney BH. 1985a. Perspectives on the origin of the ﬂoristic

similarity between Eastern Asia and eastern North America.

Journal of the Arnold Arboretum 66: 73–94.

Tiffney BH. 1985b. The Eocene North Atlantic land bridge: Its

importance in tertiary and modern phytogeography of the

LI et al.: Phylogeny and biogeography of Theaceae 403

northern hemisphere. Journal of the Arnold Arboretum 66:

243–273.

Tiffney BH. 2000. Geographic and climatic inﬂuence on the

Cretaceous and Tertiary history of Euramerican ﬂoristic

similarity. Acta Universitatis Carolinae Geologica (Prague)

44: 5–16.

Tsou CH. 1997. Embryology of the Theaceae—Anther and

ovule development of Camellia,Franklinia, and Schima.

American Journal of Botany 84: 369–381.

Wang YH, He H, Min TL, Zhou LH, Fritsch PW. 2006. The

phylogenetic position of Apterosperma (Theaceae) based

on morphological and karyotype characters. Plant System-

atics and Evolution 260: 39–52.

Wen J. 1999. Evolution of eastern Asian and eastern North

American disjunct distributions in ﬂowering plants. Annual

Review of Ecology and Systematics 30: 421–455.

Wu YC. 1940. Beiträge zur Kenntnis der Flora Süd‐Chinas.

Botanische Jahrbucher fur Systematik, Pﬂanzengeschichte

und Pﬂanzengeographie 71: 169–199.

Xiang QY, Soltis DE, Soltis PS, Manchester SR, Crawford DJ.

2000. Timing the eastern Asian‐eastern North American

ﬂoristic disjunction: Molecular clock corroborate paleonto-

logical estimates. Molecular Phylogenetics and Evolution

15: 462–472.

Xiang QY, Zhang WH, Ricklefs RE, Qian H, Chen ZD, Wen J,

Li J. 2004. Regional differences in rates of plant speciation

and molecular evolution: A comparison between eastern

asia and eastern north america. Evolution 58: 2175–2184.

Yan SZ. 1981. On the Chinese genera Stewartia Linn. and Hartia

Dunn. Acta Phytotaxonomica Sinica 19: 462–471.

Yang SX, Yang JB, Lei LG, Li DZ, Yoshino H, Ikeda T. 2004.

Reassessing the relationships between Gordonia and

Polyspora (Theaceae) based on the combined analyses of

molecular data from the nuclear, plastid and mitochondrial

genomes. Plant Systematics and Evolution 248: 45–55.

Ye CX. 1982. Systematic study of Stewartia and Hartia. Acta

Scientiarum Naturalium Universitatis Sunyatseni 21: 108–

116.

Ye CX. 1990. A discussion on relationship among genera

in Theoideae (Theaceae). Acta Scientiarum Naturalium

Universitatis Sunyatseni 29: 74–81.

Appendix A

Samples used in this study in the order of species

(in bold); family; voucher; source; SSC GenBank

accessions. A ¼Arnold Arboretum, KUN ¼Kunm-

ing Institute of Botany, Chinese Academy of Sciences,

NCSU ¼North Carolina State University, SYSU ¼

Zhongshan University, UBC ¼University of British

Columbia, ZJU ¼Zhejiang University.

Apterosperma oblata; Theaceae; 6423 (SYSU);

Guangdong, China; JX987783. Camellia obtusifolia;

Theaceae; Li, M. 8237 (ZJU); Hangzhou Botanical

Garden, Zhejiang, China; HM164083. Franklinia

alatamaha; Theaceae; Li, J. 4822 (A); Arnold Arbore-

tum, MA, USA; HM164089. Gordonia lasianthus;

Theaceae; Olsen, R. 4191 (NCSU); North Carolina,

USA; HM164088. Hartia crassifolia; Theaceae; Li, M.

8026 (ZJU); Mangshan, Hunan, China; HM164107.

Hartia sinensis; Theaceae; Li, M. 8000 (ZJU);

Kunming Botanical Garden, China; HM164105. Har-

tia sinii; Theaceae; Li, J. 4551 (ZJU); Laoshan,

Guangxi, China; HM164104. Hartia villosa; Theaceae;

Li, M. 8055 (ZJU); Heishiding, Guangdong, China;

HM164106. Polyspora chrysandra; Theaceae; Li, J.

3177 (A); Decanso Botanical Gardern, California,

USA; HM164084. Pyrenaria hirta; Theaceae; Li, M.

8247 (ZJU); Hangzhou Botanical Garden, Zhejiang,

China; HM164082. Schima argentea; Theaceae; Li, M.

8189 (ZJU); Lushan, Jiangxi, China; HM164086.

Schima khasiana; Theaceae; Li, J. 4809 (ZJU);

Yunnan, China; HM164087. Schima wallichii; The-

aceae; GLGS 18299; Li, J. 5891 (KUN); Gaoligong-

shan, Yunnan, China; HM164085. Stewartia

malacodendron; Theaceae; Li, J. 4827 (A); Polly

Hill Arboretum, MA, USA; HM164090. Stewartia

malacodendron; Theaceae; Del Tredici, P. and John-

son, J. 4e, 8277 (A); Alabama, USA; HM164091.

Stewartia malacodendron; Theaceae; Del Tredici, P.

and Johnson, J. 4c, 8278 (A); Alabama, USA;

HM164092. Stewartia monadelpha; Theaceae; Li, J.

6088; Quarryhill Botanical Garden, 1989.319B;

HM164096. Stewartia ovata; TheaceaeLi, J. 1601

(A); Arnold Arboretum 18847A; HM164101. Stew-

artia ovata; Theaceae; Li, J. 1602 (A); Arnold

Arboretum 18244B; HM164102. Stewartia ovata;

Theaceae; Del Tredici, P. and Johnson, J. 2–6, 8279

(A); South Carolina, USA; HM164103. Stewartia

ovata; Theaceae; Del Tredici, P. and Johnson, J. 4b,

8280 (A); Georgia, USA; HM164100. Stewartia

pseudocamellia; Theaceae; Li, J. 6090 (A); Quarryhill

Botanical Garden, 1989.071A, Japan; HM164094.

Stewartia rubiginosa; Theaceae; Li, M. 8025 (ZJU);

Ruyuan, Guangdong, China; HM164093. Stewartia

serrata; Theaceae; Li, J. 4821 (UBC); University of

British Columbia Botanical Garden, Canada;

HM164095. Stewartia sinensis; Theaceae; Li, M.

8078 (ZJU); Anhui, China; HM164098. Stewartia

sinensis; Theaceae; Li, M. 8190 (ZJU); Jiangxi, China;

HM164099. Stewartia sinensis; Theaceae; Li, M. 8267

(ZJU); Wuyishan, Jiangxi, China; HM164097. Styrax

obassia; Styracaceae; Li, J. 6156 (A); Arnold Arbore-

tum, MA, USA; HM164078. Symplocos paniculata;

Symplocaceae; Li, J. 6155 (ZJU); Arnold Arboretum,

MA, USA; HM164073.

404 Journal of Systematics and Evolution Vol. 51 No. 4 2013

Phylogenetics of global Camellia (Theaceae) based on three nuclear regions and its implications for systematics and evolutionary history

Article

Full-text available

Mar 2023

Camellia contains tea, oil camellia, and camellias which benefit people globally. Its infrageneric classification is, however, controversial and unstable, and former phylogenetic analyses failed to yield robust and consistent trees. Here, we aimed to reconstruct a robust phylogenetic tree, date all clades and discuss the evolutionary history of Camellia. Emphasising the taxonomically comprehensive sampling rather than more DNA data, orthologous nuclear RPB2 introns 11–15 and 23, and waxy were sequenced for 99 taxa of Camellia to reconstruct its phylogenetic history. Ten clades are identified in Camellia: Camellia II, Camelliopsis, Corallina, Furfuracea, Heterogenea, Paracamellia, Piquetia, Stereocarpus, Thea and Yellow camellias II. Camellia grijsii and C. shensiensis are not closely related with other oil camellias that form the clade Paracamellia. Sections Camelliopsis and Theopsis together form the clade Camelliopsis, while clade Furfuracea consists of sect. Furfuracea and C. hongkongensis. Camellia connata is separated from C. lanceolata but nested in the clade Heterogenea, and C. longissima is nested in the clade Thea, suggesting a new germplasm for tea breeding. Molecular dating using four fossil calibration points suggests that the crown age of Camellia is 39.5 Ma with clade Corallina probably the earliest infrageneric clade to diversify and the most widespread clade, Paracamellia, the latest. Our findings provide new insights into the phylogenetic relationships, systematics and evolutionary history of Camellia. This article is protected by copyright. All rights reserved.

Genetic diversity and population structure of a rare flowering tree endemic to Appalachia, Stewartia ovata

Article

Full-text available

Jun 2024

Stewartia ovata (cav.) Weatherby, commonly known as mountain stewartia, is an understory tree native to the southeastern United States (U.S.). This relatively rare species occurs in isolated populations in Virginia, Kentucky, Tennessee, North Carolina, South Carolina, Georgia, Alabama, and Mississippi. As a species, S. ovata has largely been overlooked, and limited information is available regarding its ecology, which presents obstacles to conservation efforts. Stewartia ovata has vibrant, large white flowers that bloom in summer with a variety of filament colors, suggesting potential horticultural traits prized by ornamental industry. However, S. ovata is relatively slow growing and, due to long seed dormancy, propagation is challenging with limited success rates. This has created a need to assess the present genetic diversity in S. ovata populations to inform potential conservation and restoration of the species. Here, we employ a genotyping‐by‐sequencing (GBS) approach to characterize the spatial distribution and genetic diversity of S. ovata in the southern Appalachia region of the eastern United States. A total of 4475 single nucleotide polymorphisms (SNPs) were identified across 147 individuals from 11 collection sites. Our results indicate low genetic diversity (He = 0.216), the presence of population structure (K = 2), limited differentiation (FST = 0.039), and high gene flow (Nm = 6.16) between our subpopulations. Principal component analysis corroborated the findings of STRUCTURE, confirming the presence of two distinct S. ovata subpopulations. One subpopulation mainly contains genotypes from the Cumberland Plateau, Tennessee, while the other consists of genotypes present in the Great Smoky Mountain ranges in Tennessee, North Carolina, and portions of Nantahala, Chattahoochee‐Oconee national forests in Georgia, highlighting that elevation likely plays a major role in its distribution. Our results further suggested low inbreeding coefficient (FIS = 0.070), which is expected with an outcrossing tree species. This research further provides necessary insight into extant subpopulations and has generated valuable resources needed for conservation efforts of S. ovata.

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea

Article

Full-text available

Mar 2023
J MOL EVOL

Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.

Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change

Article

Full-text available

Jun 2023

The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modeling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into accounts of studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 Ma), facilitated by the greenhouse warming. As a response to the cooling climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.

Incompatible pollen abortion and late-acting self-incompatibility in Schima superba

Article

Full-text available

Sep 2022

In angiosperms, self-incompatibility (SI) is a common and widespread mechanism for plant prevention of inbreeding, and late-acting self-incompatibility (LSI) may be ancestral in the group. In this work, we studied Schima superba, a species in Theaceae that is a commercially important timer and fire-resistant tree, and revealed its LSI mechanism. Hormones, enzymes, transcriptomes, and proteins were compared between self-pollination (SP) and outcross pollination (OP) in the styles and ovaries from 0 to 120 h after pollination. The self-pollen tubes grew to the bottom of the style and entered the ovary within 48 h but failed to penetrate the ovule. Meanwhile, the hormone and peroxidase levels dramatically changed. Transcriptome and proteome analyses explored the molecular mechanisms of LSI and candidate genes related to LSI in S. superba. Overall, 586.71 million reads were obtained, and 79,642 (39.08%) unigenes were annotated. KEGG and GO analysis showed that there were 4531 differentially expressed genes (DEGs) and 82 differentially expressed proteins (DEPs) at 48 h in self- (SP) versus outcross pollination (OP). Among these, 160 DEGs and 33 DEPs were involved in pollen–pistil interactions. “Pollen–pistil interaction,” “signal recognition,” and “component of membrane” were downregulated in SP, whereas “cell wall and membrane biosynthetic process,” and “oxidoreductase activity” were upregulated. The DEGs involved with S-RNases and SCF during SP suggested that the LSI occurred at 48 h in the ovary and that the LSI in S. superba was under gametophyte control. Calcium ion increase and release, mitochondrial function loss, and ROS disruption further aggravated PCD progress and cell death. The LSI of S. superba, which happened 48 h after pollination, was a key time point. The incompatibility PT ceased growth in the ovary because of S-RNase recognition and PCD in this organ. This study highlights the LSI molecular mechanism in S. superba and provides a reference to other species in Theaceae.

Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Article

Full-text available

Jul 2022

Plastid genome and nrDNA arrays, proposed recently as “super barcodes”, might provide additional discriminatory power and overcome the limitations of traditional barcoding loci, yet super barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes the genus a model for testing the efficacy of super barcodes. In this study, we generated multiple datasets comprising standard DNA barcodes (matK, rbcL, trnH‐psbA, nrITS) and super‐barcodes (plastid genome, nrDNA arrays) across 58 individuals from 12 out of 13 species of Schima from China. No samples were correctly assigned to species using standard DNA barcodes and nrDNA arrays, while only 27.27% of species with multiple accessions were distinguished using the plastid genome and its partitioned datasets—the lowest estimated rate of super barcode success in the literature so far. For Schima and other taxa with similarly recently divergence and low levels of genetic variation, incomplete lineage sorting, hybridization, or taxonomic oversplitting are all possible causes of the failure. Taken together, our study suggests that by no means are super barcodes immune to the challenges imposed by evolutionary complexity. We therefore call for developing multi‐locus nuclear markers for species discrimination in plant groups.

Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity

Article

Jul 2022

Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.

Using phylogenomics to untangle the taxonomic incongruence of yellow‐flowered Camellia species (Theaceae) in China

Article

Full-text available

Sep 2022

All yellow Camellia plants in China are threatened, but their classification is contentious. Here, we performed a phylogenetic reconstruction based on nuclear double‐digest restriction site‐associated DNA sequencing (ddRAD), transcriptomes, nuclear ribosomal internal transcribed spacer (nrITS), and the small single‐copy region of the chloroplast genome, in combination with morphological evidences to help resolve taxonomic ambiguity of those rare and threatened species. Conflicting relationships were derived from nuclear and chloroplast sequences. The strong hybridization/introgression signal detected suggests reticulate evolution mainly caused this discordance pattern. The nuclear‐ddRAD and RNA‐seq phylogenies fit better to the yellow camellias’ morphology, providing a clear resolution for inferring their relationships in China. Based on present phylogenetic analyses and morphological characters, we propose these taxonomic suggestions: (1) C. petelotii and C. nitidissima are distinct species; (2) C. ptilosperma, C. longruiensis, C. longgangensis and longgangensis var. grandis are conspecific with C. flavida; (3) C. multipetala and C. longgangensis var. patens are synonyms of C. quinqueloculosa, and C. quinqueloculosa should be recognized as an independent species; (4) C. wumingensis should be formally recognized as an independent species; (5) C. longzhouensis is synonyms of C. chrysanthoides; (6) C. xiashiensis and C. parvipetala should be treated as synonyms of C. micrantha; (7) C. achrysantha is a good species; (8) C. tunghinensis is an independent species (9) species status of C. huana is well‐supported; (10) C. pingguoensis var. terminals should be correctly identified to species level as C. terminalis. These results provide the basis for the recognition 20 yellow Camellia species in China. This article is protected by copyright. All rights reserved.

Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants

Article

May 2022

The Camellia includes more than 200 species of great diversity and has immense economic, ornamental, and cultural values. We here sequenced the transcriptomes of 116 Camellia plants from nearly all sections of the genus Camellia. We constructed a pan‐transcriptome of Camellia plants with 89,394 gene families and then well resolved the phylogeny of genus Camellia based on 405 high‐quality low‐copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We show strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavy accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web‐accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards breeding program of cultivated tea, camellia and oil‐tea plants.

Late-acting self-incompatibility (LSI) in Schima superba: pollen-ovary interactions and signaling to trigger PCD in incompatible pollen

Preprint

Full-text available

Mar 2022

Background In angiosperm, Self-incompatibility (SI) is a common and widespread mechanism for plant preventing inbreeding risk and late-acting self-incompatibility (LSI) is even more ancestral conserved. In this work, we worked on Schima superba, one species in Theaceae, commercially important timer and fire-resistant tree species and revealed its LSI mechanism. Results The self-pollen tubes grew to the bottom of the stylus and enter ovary until 48h, but failed to penetrate the ovule. Meanwhile, the hormone and peroxidase levels were dramatically changed. Transcriptome and proteome analysis explored the molecular mechanisms of LSI and candidate genes related to LSI in S.superba. Overall 586.71 million reads were obtained and 79,642 (39.08%) unigenes were annotated. KEGG and GO showed that 4531 differentially expressed genes (DEGs) and 82 differentially expressed proteins (DEPs) were at 48h in self- (SP) vs outcross-pollination (OP). Among these, 160 DEGs and 33 DEPs involved in pollen-pistil interaction. The “pollen-pistil interaction”, “signal recognition” and “component of membrane” were downregulated in SP whereas the “cell wall and membrane biosynthetic process”, “oxidoreductase activity” were upregulated. The DEGs involved with S-RNases and SCF during SP suggested that the LSI was happened at 48h ovary, and the LSI in S.superba was under gametophyte control. The calcium ion increase-releasement and F-actin depolymerization initiated metacaspases-1 activity and lead to PCD progress. Also, mitochondrial function loss and ROS disruption further aggravated the PCD progress and cell death. Cell wall biosynthetic progress upregulated and cellulose synthase downregulated could lead to ovary xylification and withering. Conclusions The LSI of S.superba which happened at 48h after pollination was key time point. The incompatibility PT ceased growth in ovary because of the S-RNase recognition and PCD happened in this organ. This study highlight the LSI molecular mechanism in S.superba and also gave a reference to other species in Theaceae.

A critical study in the complex-polymorphous genus Schima (Theaceae)

Article

Full-text available

Nov 2015

S. Bloembergen

1. The author considers the genus Schima monotypic. Its only species, Schimaviallichii (DC.) Korth., is subdivided into nine geographically separated subspecies andthree varieties. These may be recognised sometimes by one dominating character,mostly, however, by a complex of characters. Several new combinations are made.2. Yet the variability of most of the subspecies is still often enormous and atfirst sight appears complex. Thus we may often encounter the polymorphy of the wholespecies in its subspecies again. It was the striking different percentage-numbers of(phenotypically) about the same characters which turned the scale in favour ofthe recognition of the subspecies, besides their geographic separation.The attempts made by the author to divide certain resulting complex-polymorphoussubspecies into units of still lower rank and to trace correlations with peculiaritiesof environment such as different heights above sealevel, or with different stages inthe age of the trees, failed.3. On account of these negative results and the above mentioned different per-centage-numbers for phenotypically about the same characters, the author came tothe conclusion that the most probable explanation is that the variability within thesubspecies is just due to Mendel-segregation and nothing else. It looks very muchas if one is dealing here with the inheriting of striking characters, each caused byone or only a few polymeric factors, characters which hold their own, just as inpanmictically propagated populations (by cross-pollination). This explanation, too,makes the striking fact that in some subspecies we find back phenotypically thewhole, or part, of the polymorphy of the entire species more understandable, as wellas the fact that individuals of different subspecies may agree phenotypically, whereasgenotypically they belong to different races (subspecies). Moreover, all these phenomenastrongly support the monotypic conception of the genus.

Phylogenetic relationships and biogeography of Stewartia (Camellioideae, Theaceae) inferred from nuclear ribosomal DNA ITS sequences.

Article

Full-text available

Mar 2002

Sequences of the internal transcribed spacers of nuclear ribosomal DNA were used to estimate phylogenetic relationships within Stewartia. Eighteen samples were included representing two species of Hartia, seven species of Stewartia, and Franklinia alatamaha. Hartia sinensis and H. villosa form a clade that is the sister group of Stewartia. Within Stewartia the New World and the Old World species form well-supported clades. The sub-genera and sections of Stewartia proposed by previous authors are not supported by our ITS data. Two clades are recognized within the Old World lineage: S. serrata + S. rostrata and S. pseudocamellia + S. monadelpha + S. sinensis. Southeastern Asia and China may be a recent center of diversification of Stewartia based on the ITS phylogeny and fossil record.

A Review of Deciduous-Leaved Species of Stewartia (Theaceae)

Article

Jan 1974

Stephen A Spongberg

FRUITS AND SEEDS OF TRIBE GORDONIEAE (THEACEAE) FROM THE EOCENE OF NORTH AMERICA

Article

Jul 1992

A new genus and species Gordoniopsis polysperma and two new species of Gordonia (Gordonieae, Camellioideae, Theaceae) are described based on fossil fruit and seed remains. These specimens are part of a large flora consisting of various plant organs from the middle Eocene Claiborne Formation in western Kentucky and Tennessee. Gordoniopsis is a five-valved loculicidally dehiscent capsule similar to capsules of Gordonia but differing in having unwinged seeds and a greater number of seeds per locule. The two Gordonia species are among the earliest unequivocal records of the genus and two of only four fossil Gordonia species known with in situ seeds. Two extinct genera, Gordoniopsis and Andrewsiocarpon, and the extant genus Gordonia in the tribe Gordonieae are known from the middle Eocene Claiborne flora, suggesting an early radiation within the tribe. Based on a survey of Recent fruits and seeds we concur with Keng's proposal to merge Laplacea with Gordonia.

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

Article

Jul 1985
EVOLUTION

Joseph Felsenstein

The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

Einige Pflanzenreste aus der Bernsteinzeit

Article