全 文 ：葱属 Amerallium亚属 (石蒜科) 的系统发生与性状进化*
李琴琴, 周颂东, 何兴金**, 魏先芹
(四川大学生命科学学院, 四川 成都摇 610064)
摘要: 运用贝叶斯和简约法对葱属 (Allium) Amerallium 亚属的核糖体 DNA 内转录间隔区 ( ITS) 进行了
分析, 对该亚属的系统发生进行了推测。 系统分析证实 Amerallium是单系的, 并表明该亚属由三个隔离的
地理群组成: 北美 Ameralliums, 地中海区 Ameralliums 和东亚 Ameralliums。 性状进化的重建表明鳞茎是原
始或祖先状态, 根状茎和肉质增粗的根是衍生状态且在 Amerallium 这个亚属的类群中独立进化发生了几
次。 重建也表明该亚属的原始染色体基数 x=7, 其它染色体基数 (x = 8, 9, 10, 11) 是由它转化而来的。
在北美类群中, 异基数性相当罕见, 而多倍性似乎是一个相对频繁的进化事件。 在地中海区类群和东亚类
群中, 异基数性和多倍性是染色体进化的两个主要驱动力。
关键词: 葱属; Amerallium; 性状进化; ITS; 系统发生
中图分类号: Q 948. 2, Q 942摇 摇 摇 摇 文献标识码: A摇 摇 摇 摇 摇 文章编号: 2095-0845(2012)02-107-13
Phylogeny and Character Evolution in Allium Subgenus
Amerallium (Amaryllidaceae)
LI Qin鄄Qin, ZHOU Song鄄Dong, HE Xing鄄Jin**, WEI Xian鄄Qin
(School of Life Sciences, Sichuan University, Chengdu 610064, China)
Abstract: Bayesian and parsimony analyses of the nuclear ribosomal DNA internal transcribed spacer ( ITS) were
used to infer the phylogeny of Allium subgenus Amerallium. Phylogenetic analyses corroborate that Amerallium is
monophyletic and the results indicate that Amerallium composed of three isolated geographical groups: North Ameri鄄
can Ameralliums, the Mediterranean region Ameralliums, and eastern Asian Ameralliums. Reconstruction of charac鄄
ter evolution suggests bulbs as a primitive or ancestral state, and rhizomes and thick fleshy roots as derived states
which have evolved and developed several times independently within the groups of Amerallium, and the basic chro鄄
mosome number x=7 is the primitive state and other basic chromosomes numbers ( x = 8, 9, 10, 11) are derived
from x=7. Within North American Ameralliums, dysploidy is a rather rare evolutionary event and polyploidy seems
to be a relatively frequent evolutionary event. Within the Mediterranean region and eastern Asian Ameralliums, both
dysploidy and polyploidy are two primary driving forces in their chromosome evolution.
Key words: Allium; Amerallium; Character evolution; ITS; Phylogeny
摇 The genus Allium L. consists of approximately
more than 800 species according to Fritsch et al.
(2010). To some extent, this is consistent with the
current online version of the World Checklist of Se鄄
lected Plant Families maintained by Royal Botanic
Gardens, KEW (UK, http: / / apps. kew. org / wcsp /
reportbuilder. do), which recognizes 881 species.
Allium is a member of order Asparagales, family
植 物 分 类 与 资 源 学 报摇 2012, 34 (2): 107 ~ 119
Plant Diversity and Resources摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 DOI: 10. 3724 / SP. J. 1143. 2012. 10259
*
**
基金项目: 国家自然科学基金资助项目 (31070166, 31100161); 教育部博士点基金资助项目 (20090181110064); 中国科学院
大科学装置开放研究项目 (2009鄄LSF鄄GBOWS鄄01) 资助; 科技部科技基础性工作专项重点项目 (2007FY110100)
Author for correspondence; E鄄mail: xjhe@ scu. edu. cn
Received date: 2011-04-29, Accepted date: 2012-01-25
作者简介: 李琴琴 (1983-) 女, 博士研究生, 主要从事葱属植物的系统发育与分子进化研究。 E鄄mail: liqq@ imnu. edu. cn
Amaryllidaceae J.St. 鄄Hil., subfamily Allioideae Herb.,
tribe Allieae Dumort. (Fay and Chase, 1996; APG,
2009; Chase et al., 2009). After Fay and Chase
(1996), Friesen et al. (2000) and Chase et al.
(2009), Allium (including Caloscordum Herb., Mi鄄
lula Prain and Nectaroscordum Lindl. ) is the only
genus in tribe Allieae. Previous molecular data sug鄄
gested that Allium evolution proceeded in three sepa鄄
rate evolutionary lines (Fritsch, 2001; Fritsch and
Friesen, 2002; Friesen et al., 2006; Li et al.,
2010) and Amerallium Traub is the largest subgenus
in the most ancient line comprising around 135 spe鄄
cies occurring in North America (New World), the
Mediterranean region and eastern Asia (Old World)
(Traub, 1968; Friesen et al., 2006). Members of
this subgenus are extremely diverse in ecology and
grow in dry stony slopes, Mediterranean garigues,
cliffs, river banks, prairies, mountains and subal鄄
pine meadows (Hanelt et al., 1992). The subgenus
is very diverse in cytology and contains all the basic
chromosome numbers in the genus Allium. The most
common basic chromosome number is x = 7, and yet
other numbers (x=8, 9, 10, 11) also exist (Traub,
1968; Sen, 1974; Yan et al., 1990; Huang et al.,
1995; Huang et al., 1996a, b; Xu et al., 1998;
Ni, 1999; Xu and Kamelin, 2000; Dale et al.,
2002; Zhang and Xu, 2002; Zhang et al., 2008,
2009; Wei et al., 2011).
Historically, Traub ( 1968, 1972 ) proposed
classifying the 600 or so Allium species under three
subgenera: Allium L. , Amerallium and Nectaroscor鄄
dum (Lindl. ) Asch. et Graebn. In Traub爷s classi鄄
fication, Allium siculum Ucria was the type species
of subgenus Nectaroscordum; subgenus Amerallium
united the North American species with the Mediter鄄
ranean Alliums classified under section Molium
Endl. and species that are now classified under sec鄄
tions Arctoprason Kirschl. and Briseis ( Salisb. )
Stearn (Hanelt et al., 1992); and the rest of the
species were lumped together in subgenus Allium.
Based on a multidisciplinary approach, Hanelt et al.
(1992) reassembled the species pooled by Traub in
subgenus Allium into six subgenera namely Allium,
Amerallium, Bromatorhiza Ekberg, Caloscordum
(Herb. ) R. M. Fritsch, Melanocrommyum (Webb
& Berth. ) Rouy and Rhizirideum (G. Don ex Koch)
Wendelbo, while excluded Nectaroscordum from
classifications of the genus Allium. Recently, molec鄄
ular approaches such as chloroplast DNA and nucle鄄
ar ribosomal DNA ( nrDNA) have been applied to
understand the evolutionary processes and taxonomic
relations within the genus Allium and also in subge鄄
nus Amerallium. A first approach to structuring the
genus Allium itself by molecular markers was pub鄄
lished by Linne von Berg et al. (1996). The resul鄄
ting phenogram largely confirmed the subgeneric
classification based on an integration of morphologi鄄
cal and other methods, but found that subgenus Am鄄
erallium and Bromatorrhiza could not be clearly dis鄄
tinguished. The subgenus Bromatorrhiza ( including
section Bromatorrhiza Ekberg, Coleoblastus Ekberg,
Cyathophora R. M. Fritsch), originally circumscribed
by Ekberg (1969) by the presence of fleshy roots as
storage organs and the lack of true storage bulbs or
rhizomes, again proved to be paraphyletic and had to
be cancelled in other studies ( Samoylov et al.,
1995, 1999; Mes et al., 1997, 1999; Friesen et
al., 2000). Later, Friesen et al. (2006) presented
a new classification of genus Allium consisting of 15
subgenera ( including Nectaroscordum ) based on
their phylogenetic study, in which they confirmed
the artificial character of subgenus Bromatorrhiza
and placed section Bromatorrhiza in subgenus Amer鄄
allium and other two sections in subgenus Cya鄄
thophora (R. M. Fritsch) R. M. Fritsch. Li et al.
(2010) again corroborated the artificial character of
subgenus Bromatorrhiza and agreed with their taxo鄄
nomic treatment. The distribution of Amerallium spe鄄
cies between Old World and New World was well re鄄
flected in the phylogenetic data (Dubouzet and Shi鄄
noda, 1999; Friesen et al., 2006; Nguyen et al.,
2008; Li et al., 2010), and the origin and migra鄄
tion about Amerallium has been long in dispute.
Hanelt et al. (1992) postulated that the Ameralliums
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had its origins in Asia and spread to North America
via the Bering Land Bridge, but they did not discuss
the origins of the Mediterranean Ameralliums. The
alternate hypothesis is a predominantly unidirectional
migration via the land bridges at Bering and North
Atlantic (Dubouzet and Shinoda, 1999). Nguyen et
al. (2008) investigated the evolutionary history of
Alliums in western North America (especially in Ca鄄
lifornia) and their adaptation to serpentine soils.
Their results also represent a first attempt at initia鄄
ting a more detailed study on the biogeography of
subgenus Amerallium in North America and imply
that two separate biogeographic patterns led to Ame鄄
rallium diversi覱cation in North America. Based on
those researches, Li et al. (2010) further examined
the migration route of the Ameralliums by the inclu鄄
sion of species endemic to eastern Asia that have of鄄
ten been excluded from previous analyses. They pro鄄
posed that the ancestor of Amerallium originated in
eastern Asia and one lineage of Amerallium likely
spread eastward to North America via the Bering
Land Bridges and expanded their range southward,
while the other lineage of Amerallium expanded its
range from east to west and ended up in the Mediter鄄
ranean region, not across the North Atlantic.
All the above鄄mentioned works have been useful
in understanding of Amerallium phylogeny and bioge鄄
ography, but the diversity of cytological data and other
character have not been tested in a phylogenetic
framework to date. In order to better understand the
character evolution of Amerallium, species endemic to
eastern Asia were again incorporated in the present
study, but we still lack samples of the Mediterranean
Amerallium which are also poorly sampled in the pre鄄
vious studies. Nevertheless, it seems appropriate now
to publish the results of our study, partly because
these are important for considerations of phylogeny
and character evolution of Amerallium and partly be鄄
cause we hope our results will stimulate further stu鄄
dies. The goals of the present study were to: (1) con鄄
struct phylogenetic relationships within Amerallium;
(2) elucidate possible patterns of underground stor鄄
age organs and chromosome numbers evolution in
Amerallium under the phylogenetic framework.
1摇 Materials and methods
1. 1摇 Taxon sampling
Our sampling scheme was designed to cover
those taxonomic and geographic Amerallium groups,
and 64 taxa from North America (47 out of about 81
species), the Mediterranean region (10 out of about
46 species), and eastern Asia (18 samples, repre鄄
senting 5 species and 2 varieties out of about 8 spe鄄
cies) were included in the present study. Allium
bulgaricum (Janka) Prod佗n, A. siculum Ucria, and
A. monanthum Maxim., were designated as outgroups
according to previous studies (Fritsch, 1988, 2001;
Fritsch and Friesen, 2002; Friesen et al., 2006;
Nguyen et al., 2008; Li et al., 2010). The sources
of ITS sequences obtained from original materials
and GenBank accession numbers for all other species
included in this investigation are listed in the Ap鄄
pendix 1. All accessions in the collection stem from
populations collected during field trips. Voucher
specimens were deposited in the herbarium of the Si鄄
chuan University (SZ).
1.2摇 DNA extraction, amplification and sequencing
Genomic DNA was extracted from silica gel鄄
dried or fresh leaves by using the method of Doyle
and Doyle (1987). The ITS region was amplified
with primers ITS4 and ITS5 (White et al., 1990).
The PCR parameters were as follows: 94益 for 5
min; 30 cycles of 94益 for 45 s, 55益 for 45 s,
72益 for 1 min; and 72益 for 7 min. PCR products
were separated by 1. 5% (w / v) agarose TAE gel
and purified using Wizard PCR preps DNA Purifica鄄
tion System (Promega, Madison, WI, USA) follow鄄
ing manufacturer爷s instructions. The purified PCR
products were analyzed in an ABI 310 Genetic Ana鄄
lyzer (Applied Biosystems Inc. ) in both directions
using the PCR primers.
1.3摇 Sequence comparisons and phylogenetic analyses
DNA sequences were initially aligned using the
default pairwise and multiple alignment parameters
9012 期摇 摇 摇 摇 摇 LI Qin鄄Qin et al. : Phylogeny and Character Evolution in Allium Subgenus Amerallium …摇 摇 摇 摇 摇 摇 摇
in Clustal X (Jeanmougin et al., 1998) and then re鄄
checked and adjusted manually as necessary using
MEGA 4 (Tamura et al., 2007). Gaps were posi鄄
tioned to minimize nucleotide mismatches and trea鄄
ted as missing data in phylogenetic analyses.
Phylogenetic analyses were conducted by emplo鄄
ying maximum parsimony (MP) criteria and Bayes鄄
ian Inference (BI), using the programs PAUP* ver鄄
sion 4. 0b10 (Swofford, 2003) and MrBayes version
3. 1. 2 (Ronquist and Huelsenbeck, 2003), respec鄄
tively. For MP, heuristic searches were carried with
1 000 random addition sequence replicates. One tree
was saved at each step during stepwise addition, and
tree鄄bisection鄄reconnection (TBR) was used to swap
branches, and the maximum number of trees was set
to 10 000. All characters were unordered and equal鄄
ly weighted. Gaps were treated as missing data.
Bootstrap values were calculated from 1 000 000 rep鄄
licate analyses using “fast冶 stepwise鄄addition of taxa
and only those values compatible with the majority鄄
rule consensus tree were recorded. Prior to a Bayes鄄
ian analysis, MrModeltest version 2. 2 ( Nylander,
2004) was used to select a best鄄覱t model of nucleo鄄
tide substitution, and the GTR+I+G model under the
AIC was selected. The Bayesian Markov Chain Monte
Carlo ( MCMC) algorithm was run for 2 000 000
generations with one cold chain and three heated
chains, starting from random trees and sampling
trees every 100 generations. The first 5 000 trees
were considered as the burn鄄in and discarded. A
50% majority鄄rule consensus tree of the remaining
trees was produced.
1. 4摇 Estimation of ancestral character states
Selected characters, namely underground sto鄄
rage organs and chromosome numbers, were defined
according to previous studies of these Alliums (Traub,
1968; Sen, 1974; Pastor and Vald佴s, 1988; Tza鄄
noudakis and Vosa, 1988; Yan et al., 1990; Huang
et al., 1995; Huang et al., 1996a, b; Ohri et al.,
1998; Xu et al., 1998; Ni, 1999; Xu and Kame鄄
lin, 2000; Dale et al., 2002; Zhang and Xu,
2002; Ricroch et al., 2005; Friesen et al., 2006;
Zhang et al., 2008, 2009; Wei et al., 2011 ).
Three states were chosen for underground storage or鄄
gans: bulbs (0), rhizomes (1), and thick fleshy
roots ( 2 ), and five states were chosen for basic
chromosome numbers: 7 (0), 8 (1), 9 (2), 10
(3) and 11 (4). To infer ancestral character states,
Parsimony optimizations were performed in the soft鄄
ware Mesquite v. 2. 01. (Maddison and Maddison,
2007). Considering all accessions of the same spe鄄
cies composed a well鄄supported clade, a reduced
taxonomic subset was obtained and then phylogenetic
analysis was conducted by employing BI with the
methods described above. Optimizations were run on
the 50% majority rule tree from Bayesian analysis
and the character states were treated as “unordered冶
(i. e., allow free transformation of a character state
to any other states).
2摇 Results
2. 1摇 Sequence analyses
The ITS region varied in length from 589 bp
(A. shevockii McNeal) to 661 bp (A. hoffmanii Own鄄
bey ex Traub ). After introducing the necessary
gaps, the ITS alignment was 706 bp in length and
resulted in 225 constant characters and 463 variable
characters of which 390 were parsimony鄄informative.
The mean GC content of the ITS region was 52. 5% .
2. 2摇 Phylogenetic analyses
Trees inferred from Bayesian analysis and maxi鄄
mum parsimony showed no significant difference in
their topologies, therefore here the Bayesian tree with
posterior probabilities ( PP) and bootstrap support
values (BS) is shown in Fig. 1. In all analyses, the
subgenus Amerallium proved to be monophyletic.
Within subgenus Amerallium, the New World Ameral鄄
lium clade is sister to the Old World Amerallium
clade (PP=1. 00, BS=99%). The New World Am鄄
erallium clade (PP=1. 00, BS=97% ) contains two
groups. One group ( PP = 0. 55, BS = 53% ) in鄄
cludes several subclades corresponding to sections
Amerallium Traub +Caulorhizideum Traub +Rhopeto鄄
prason Traub with species native to mid鄄western and
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Fig. 1摇 Phylogenetic tree resulting from a Bayesian analysis of the ITS sequences from species of Amerallium and three outgroup
species. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Fries鄄
en et al. (2006), Nguyen et al. (2008), and Li et al. (2010) is indicated on the right. Values along branches represent
Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively
1112 期摇 摇 摇 摇 摇 LI Qin鄄Qin et al. : Phylogeny and Character Evolution in Allium Subgenus Amerallium …摇 摇 摇 摇 摇 摇 摇
southwestern United States (with few exceptions, e.
g. , A. validum S. Watson). The other group (PP =
1. 00, BS = 66%) includes monophyletic section Lo鄄
phioprason Traub with species restricted to western
North America ( the only exceptions are A. cernuum
Roth and A. stellatum Ker Gawler). Within the Old
World Amerallium clade (PP = 0. 88, BS = 56%),
two sister subclades are evident: one with species
from the Mediterranean region; the other with species
from the Himalayas and South鄄West China. In the
Mediterranean subclade, section Narkissoprason
Kam. is sister to a clade containing sections Briseis
(Salisb. ) Stearn, Arctoprasum Kirschl., and Molium
G. Don ex Koch (PP=1. 00, BS=89%). In the Hi鄄
malayas and South鄄West China clade, A. wallichii
var. wallichii Kunth, A. wallichii var. platyphyllum
(Diels) J. M. Xu and A. macranthum Baker are sister
to a clade comprising A. omeiense Z. Y. Zhu, A. fas鄄
ciculatum Rendle, A. hookeri Thwaites var. hookeri
and A. hookeri var. muliense Airy Shaw (PP = 0. 58,
BS< 50%). The five accessions of A. macranthum
composed a well鄄supported clade (PP = 1. 00, BS =
100%) that was sister to a clade containing seven ac鄄
cessions of A. wallichii var. wallichii and one of A.
wallichii var. platyphyllum (PP=1. 00, BS =96%),
and these two clades constituted a weakly supported
clade (PP=0. 65, BS<50%). A. omeiense, A. hook鄄
eri var. hookeri and A. hookeri var. muliense form a
trichotomy (PP=1. 00, BS=99%) and this trichoto鄄
my is sister to A. fasciculatum ( PP = 1. 00, BS =
94%). the two accessions of A. omeiense formed a
strongly supported clade (PP=1. 00, BS=99%).
2. 3摇 Character state reconstruction
Two morphological characters, underground sto鄄
rage organs and basic chromosome numbers were op鄄
timized onto the 50% majority rule tree. Parsimoni鄄
ous optimization suggested that bulbs are primitive,
and rhizomes and thick fleshy roots are derived states
within Amerallium (Fig. 2A). Optimization of chro鄄
mosome numbers suggested x = 7 to be the ancestral
basic chromosome number and the chromosome num鄄
ber in Amerallium evolved from x = 7 to other basic
numbers (Fig. 2B).
3摇 Discussion
3. 1摇 Phylogeny within the subgenus Amerallium
Amerallium spp. are extremely diverse in mor鄄
phology, in which some produce mainly rhizomes
and poorly developed bulbs and others form distinct
bulbs and broad leaves similar to those common in
the subgenus Melanocrommyum, or very narrow
leaves as in the subgenus Allium (Kamenetsky and
Rabinowitch, 2006). However, morphological syna鄄
pomorphies for Amerallium include one row of vascu鄄
lar bundles, absence of palisade parenchyma and
subepidermal position of laticifers ( Traub, 1968,
1972; Fritsch, 1988). Furthermore, strong serolo鄄
gical affinities and the dominating basic chromosome
number of x = 7 strongly support its separate status.
The results presented here continue to support earlier
覱nding that Amerallium is monophyletic ( Samoylov
et al., 1995; Dubouzet and Shinoda, 1999; Friesen
et al., 2006; Nguyen et al., 2008; Li et al.,
2010). In accordance with studies of Dubouzet and
Shinoda (1999), our molecular data underline the
existence of two distinct biogeographic clades,
namely the Old World clade and the New World
clade. Both clades are a monophyletic unit, which
agrees with a uniform electrophoretic banding pattern
of salt鄄soluble seed storage proteins (Maass, 1992).
Furthermore, our results indicate that Amerallium
composed of three isolated geographical groups: one
comprising almost all Allium species native to North
America (New World) and the remainder containing
two smaller groups from the Mediterranean region
and eastern Asia (Old World). In the well鄄suppor鄄
ted North American Amerallium clade, the sister re鄄
lationship of section Lophioprason to sections Ameral鄄
lium+Caulorhizideum+Rhopetoprason is well suppor鄄
ted. Allium validum from section Caulorhizideum is
sister to a clade containing the remaining Caulorhiz鄄
ideum + Amerallium + Rhopetoprason. Thus, section
Caulorhizideum is found to be non鄄monophyletic.
Section Lophioprason which comprises species that
211摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 植 物 分 类 与 资 源 学 报摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 第 34 卷
are native to California or restricted to western North
America in their distributions was found to be mono鄄
phyletic. Within the Old World Amerallium clade,
the monophyletic section Bromatorrhiza Ekberg was
sister to a clade containing all other Mediterranean
region sections. In the Mediterranean region taxa the
species of section Molium show greater affinity to
each other than to those of other sections including
Narkissoprason, Briseis and Arctoprasum. Allium ur鄄
sinum, while sister to the Molium, is maintained as
a separate monotypic section Arctoprasum, which is
also supported by various unique characteristics such
as leaf morphology and anatomy, leaf sequence,
bulb morphology, secondarily reduced ovule number
and size, seedling morphology, cpDNA variability
(Pastor and Vald佴s, 1985; Fritsch, 1988; Drusel鄄
mann, 1992; Hanelt et al., 1992; Kruse, 1992;
Samoylov et al., 1995). Section Briseis was isolated
from Molium on the basis of distinctive structure of
filaments and style and the presence of elaiosomes on
the seeds (Stearn, 1946) and their relationship is al鄄
so reflected in our phylogenetic studies. According to
Li et al. (2010) and our present studies, within Bro鄄
matorrhiza, two sister groups are evident, one with
species A. wallichii var. wallichii, A. wallichii var.
platyphyllum and A. macranthum, and the other with
species A. omeiense, A. guanxianense J. M. Xu, A.
xiangchengense J. M. Xu, A. hookeri var. hookeri and
A. hookeri var. muliense, A. fasciculatum, A. chien鄄
chuanense J. M. Xu.
Fig. 2摇 Evolution of categorical characters on the Bayesian topology: A, underground storage organs (bulbs, rhizomes, and thick fleshy roots);
B, basic chromosome numbers (7, 8, 9, 10, and 11) . Colours are explained in the legend of each figure
3112 期摇 摇 摇 摇 摇 LI Qin鄄Qin et al. : Phylogeny and Character Evolution in Allium Subgenus Amerallium …摇 摇 摇 摇 摇 摇 摇
3. 2摇 Character evolution in Amerallium
3. 2. 1摇 Underground storage organs
Within the New World (North America) Amer鄄
allium, two sections, Caulorhizideum and Rhopheto鄄
prason with rhizomes and bulbs developed have a
southernmost distribution in the New World in
Mexico and Guatemala whereas sections with true
bulbs (Amerallium and Lophioprason) occur mainly
in mountains of western North America (Hanelt et
al., 1992; Pistrick, 1992; Ohri et al., 1998). In
the Mediterranean region Ameralliums, except for
section Narkissoprason, which also has rhizomes, all
the extra鄄Mediterranean sections have true bulbs.
Bulbs are dominant in these two regions, which may
represent an adaptation to environments with a Medi鄄
terranean type climate characterized by hot and dry
summers, but cool and moist winters favourable for
plant growth and development (McNeal and Own鄄
bey, 1973; Hanelt, 1990). Bulbs can float unim鄄
paired for a long time in salt water (De Wilde鄄Duy鄄
fjes, 1976; Stearn, 1978), which may also explain
the predominantly coastal distribution of Mediterra鄄
nean Moliums (Dubouzet and Shinoda, 1999). Sec鄄
tion Bromatorrhiza is a small insufficiently studied
group occurring in ecologically mesophytic high
mountain regions of western Himalaya and south鄄
west China as a component of moist grassy slopes,
rocks, and herb layer of forests ( Hanelt et al.,
1992). The special character of this group differing
from the other sections in the Amerallium is the pres鄄
ence of thick fleshy roots as storage organs, without
true bulbs or rhizomes, and this special character al鄄
so exists in sections Coleoblastus Ekberg and Cya鄄
thophora R. M. Fritsch which belong to subgenus
Cyathophora (R. M. Fritsch) R. M. Fritsch. Previ鄄
ous studies (Fritsch and Friesen, 2002; Friesen et
al., 2006; Li et al., 2010) have indicated that sub鄄
genus Cyathophora is one member of the third evolu鄄
tionary line in Allium evolution. This may suggest
the process of convergent evolution, in which those
two distinct lineages evolve a similar characteristic
(thick fleshy roots) independently of one another.
The reason may be that both lineages distributed in
the Himalaya and south鄄west china face similar envi鄄
ronmental challenges and selective pressures. Parsi鄄
monious optimization suggests bulbs as a primitive or
ancestral state, and rhizomes and thick fleshy roots
as derived states which have evolved and developed
several times independently within the groups of Am鄄
erallium (Fig. 2A).
3. 2. 2摇 Chromosome numbers
Former researchers have different views about
the evolution of basic chromosome numbers in the
genus Allium. Levan (1932, 1935) has suggested
their origin in the form of an ascending series. Men鄄
sinki (1940) has also put forward an alternative view
according to which the basic numbers seven and nine
have both arisen from eight. Brat (1965) considered
that the basic numbers in different taxonomic groups
of the genus Allium have arisen in independent or鄄
ders. Previous molecular studies have indicated that
Allium is monophyletic (Friesen et al., 2006; Nguy鄄
en et al., 2008; Li et al., 2010), so there should
be a single primitive basic chromosome number for
the entire genus although the primitive basic chromo鄄
some number may vary in different subgenera. It is
regrettable that one cannot, at present, deduce with
confidence the primitive state of the basic chromo鄄
some number and the direction of the basic chromo鄄
some numbers changes within the phylogeny of the
entire Allium spp. We just infer the primitive basic
chromosome number and the direction of the basic
chromosome number changes within the subgenus
Amerallium and the primitive basic chromosome
number of the entire Allium is out of the scope of the
present paper.
In the subgenus Amerallium, most species are
diploid with basic chromosome numbers of x=7, 8,
9, 10 or 11; x=7 being the most common. In addi鄄
tion to these differences in basic numbers,
polyploidy has proceeded on four basic series, 7, 8,
9 and 11. The reconstruction of ancestral state in the
present study suggested x = 7 being ancestral and
other basic numbers (x = 8, 9, 10, 11) being de鄄
411摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 植 物 分 类 与 资 源 学 报摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 第 34 卷
rived (Fig. 2B). Levan (1932, 1935) found arm鄄
length asymmetry is more pronounced in the “16冶
and “18冶 鄄chromosomes types and took this to mean
that the “ 14 冶 鄄chromosome types were the most
primitive and that the “16冶 and “18冶 鄄chromosome
types were derived from them. In subgenus Ameralli鄄
um, symmetrical chromosomes with median鄄subme鄄
dian centromeres are most common in species with
x = 7, while species with x = 8 have usually varying
numbers of asymmetrical chromosomes and species
with x= 9, 10, 11 have entirely asymmetrical chro鄄
mosomes with telocentric chromosomes (Brat, 1965;
Huang et al., 1995; Xu et al., 1998). According
to the general principles ( Stebbins, 1971; Hong,
1990) and minimum interaction hypothesis ( Imai et
al., 1986; Schubert, 2007) of karyotype evolution,
karyotype evolution in higher plants generally tends
to develop from symmetry to asymmetry and tends to鄄
wards an increasing number of acrocentric chromo鄄
somes, thereby minimising the risk of deleterious re鄄
arrangements, while the opposite tendency, the re鄄
duction of chromosome number and formation of
metacentric chromosomes, is considered to be the
result of ‘ rare back鄄eddies爷 that are generated at
random and tolerated or even favoured when they
provide short鄄term advantages. Based on the cytolo鄄
gical and molecular data, we propose that, in the
subgenus Amerallium, the basic chromosome number
x= 7 is the primitive state and other basic chromo鄄
somes number (x=8, 9, 10, 11) are derived from
it. The New World ( North America) Amerallium
clade displays a uniform basic chromosome number
with x = 7. Within the 47 species investigated, 40
species show a noteworthy constancy of chromosome
number represented by diploid populations only
(2x), and four species ( A. drummondii, A. am鄄
plectens, A. cratericola, A. campanulatum) contain
both diploid and polyploid (2x, 3x, or 4x) and
three species (A. canadense var. canadense L., A.
glandulosum Link & Otto and A. validum) exclusive鄄
ly polyploid populations (3x, 4x or 8x). So, the
basic chromosome number found so far is very stable
and no linking dysploid numbers are known within
North American Ameralliums, which indicate that
dysploidy is a rather rare evolutionary event in this
group. Compared with dysploidy, polyploidy origina鄄
ted via autoploidization or alloploidization occurs in
several North American Ameralliums and thus seems
to be a relatively frequent evolutionary event. Chro鄄
mosome structure, such as inversions and transloca鄄
tions, seems to have acted as an important cytoge鄄
netic mechanism in the evolution of the North Ameri鄄
can Amerallium, considering that 66 of the 81 Ame鄄
rallium species, i. e. 81. 48% , are represented in
North America by diploid populations only ( data
from the statistical results of the North American Flo鄄
ra for Allium). Considering all the available chro鄄
mosomal data, Mediterranean region Ameralliums
possess the abundant diversity for basic chromosome
numbers (x=7, 8, 9, and 11) in subgenus Ameral鄄
lium, in which sections Narkissoprason and Arctopra鄄
son with x=7, section Briseis with x = 7, 8, 9, and
section Molium with x= 7, 8, 9, and 11. The high
karyotypic diversity encountered in Briseis and Moli鄄
um might indicate rapid evolutionary episodes within
those two groups. Furthermore, polyploidy has taken
place in the three series of basic chromosome num鄄
bers, 7, 8 and 9. Thus, dysploidy and polyploidy
seem to have acted as important cytogenetic mecha鄄
nisms in the evolution of the Mediterranean region
Ameralliums. Karyotype reconstruction suggests x=7
as a possible ancestral basic number for Mediterra鄄
nean region Ameralliums and thus an ascending dys鄄
ploid series for this group. Yet, the mechanism of
the dysploidy is still not well understood. Meiosis in鄄
volving irregular segregation, unequal translocation,
and centric fission are all possible causes of dysploid
variations (Stebbins, 1971). Karyotype reconstruc鄄
tion indicates x = 7 being ancestral for sections
Narkissoprason, Arctoprason, and Molium. For Bri鄄
seis, species with x=7 are not included in the pre鄄
sent study, so karyotype reconstruction did not pro鄄
vide any valuable information for the primitive basic
number in this section. Overall, relatively poor rep鄄
5112 期摇 摇 摇 摇 摇 LI Qin鄄Qin et al. : Phylogeny and Character Evolution in Allium Subgenus Amerallium …摇 摇 摇 摇 摇 摇 摇
resentatives in this region, do not allow us to pro鄄
pose an unambiguous and credible scenario for kary鄄
otype evolution within every section. Detailed sam鄄
pling of Mediterranean region taxa would be necessa鄄
ry to elucidate the potential scenario. Section Bro鄄
matorrhiza is a small group restricted to the Himalayas
and South鄄West China and reveals three different
basic numbers ( x = 7, 10 and 11), in which two
species and one variety ( A. wallichii, A. wallichii
var. platyphyllum and A. macranthum) with x = 7,
one species (A. fasciculatum) with x = 10, and four
species and one variety ( A. guanxianense, A.
xiangchengense, A. chienchuanense, A. omeiense and
A. hookeri var. muliense) with x = 11. Basic num鄄
bers for A. hookeri var. hookeri is complex. Except
for few cytotypes recorded to have 33 (Huang et
al., 1996b; Zhang and Xu, 2002; Wei et al.,
2011) and 44 chromosomes ( Yan et al., 1990;
Huang et al., 1996b), twenty鄄two is the most com鄄
mon number on record for this taxon ( Sen, 1974;
Yan et al., 1990; Huang et al., 1996b; Zhang and
Xu, 2002). According to existing researches, 2n =
22 being off鄄types (trisomics) of segmental allotrip鄄
loids with x=7 (Sharma et al., 2011), 2n= 33 be鄄
ing triploid with x = 11 ( Huang et al., 1996b;
Zhang and Xu, 2002; Wei et al., 2011), and 2n=
44 being autoallohexaploid with x = 7 (Yan et al.,
1990) and tetraploid with x = 11 (Huang et al.,
1996b). Four ploidy levels (2x, 3x, 4x and 6x)
exist in this group, in which A. wallichii var. walli鄄
chii and A. macranthum are diploid and tetraploid,
A. hookeri var. hookeri is allotriploid, triploid, tetra鄄
ploid and autoallohexaploid, and the remaining spe鄄
cies contain diploids only. It is evident that A. hook鄄
eri var. hookeri has significant karyotype differentia鄄
tion, and detailed cytogenetic study for this taxon is
necessary for determining the ploidy level, type of
ploidy and its mechanism. Therefore, both dysploidy
and polyploidy are two primary driving forces in
chromosome evolution of Bromatorrhiza. Geological
history, unique ecological environment, and micro鄄
environmental diversity in this region could be rea鄄
sons for the diversity of basic chromosome number.
Optimization of the chromosomal data onto the mo鄄
lecular phylogenies reveals x=7 to be the most likely
ancestral type in Bromatorrhiza with other basic
numbers being derived mainly through ascending
dysploidy ( Fig. 2B). The probable mechanism in鄄
volved in the dysploid differentiation of chromosome
numbers in Bromatorrhiza is chromosome fission and
the subsequent loss of chromosomes.
4摇 Conclusions
Our present paper has provided insights into the
phylogeny and character evolution of Amerallium.
Despite relatively lack samples of the Mediterranean
region Ameralliums, we have established evolution鄄
ary patterns of underground storage organs and basic
chromosome numbers. However, a more detailed
phylogenetic study including a larger sample of spe鄄
cies, especially the Mediterranean region Ameralli鄄
ums and additional molecular markers and further
studies focusing on their morphological characters,
will be required to clarify the phylogeny and charac鄄
ter evolution of Amerallium.
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811摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 植 物 分 类 与 资 源 学 报摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 摇 第 34 卷
Appendix 1
Taxa, references, and GenBank accession numbers for all ITS sequences used in the present study. Sequences in bold are our
own accessions. 1Dubouzet and Shinoda (1998); 2Dubouzet and Shinoda (1999); 3Friesen et al. (2000); 4Ricroch et al.
(2005); 5Friesen et al. (2006); 6Nguyen et al. (2008). Subgenus Amerallium Traub: A. abramsii (Ownbey & Aase) McNeal
EU0961316; A. amplectens Torr. AF0550972; A. anceps Kellogg EU0961346; A. atrorubens S. Watson var. atrorubens
EU0961376; A. atrorubens var. cristatum (S. Watson) McNeal EU0961386; A. bolanderi S. Watson var. bolanderi EU0961396;
A. brevistylum S. Watson AJ4127635; A. burlewii Davidson EU0961426; A. campanulatum S. Watson EU0961436; A. canadense
L. var. canadense EU0961456; A. cernuum Roth AF0376221; A. chamaemoly L. AF0551092; A. cratericola Eastw. EU0961466;
A. crispum Greene EU0961476; A. denticulatum (Ownbey & Aase ex Traub) McNeal EU0961496; A. diabolense (Ownbey &
Aase) McNeal EU0961506; A. dichlamydeum Greene EU0961516; A. drummondii Regel AJ4119085; A. falcifolium Hook. &
Arn. EU0961536; A. fimbriatum S. Watson var. fimbriatum EU0961556; A. fimbriatum var. purdyi ( Eastw. ) McNeal
EU0961566; A. fasciculatum Rendle—GQ181068; Dazi, Xizang, China; Tu Y鄄L et al. 94鄄9; A. glandulosum Link & Otto
AJ4127465; A. goodingii Ownbey AF0550952; A. haematochiton S. Watson EU0961576; A. hickmanii Eastw. EU0961596; A.
hoffmanii Ownbey EU0961606; A. hookeri Thwaites var. hookeri AJ4127405; A. hookeri var. muliense Airy Shaw—GQ181071;
Xianggelila ,Yunnan, China; Xu J鄄M 93 鄄25; A. howellii Eastw. var. howellii EU0961616; A. hyalinum Curran EU0961626; A.
insubricum Boiss. & Reut. AJ2502913; A. jepsonii (Ownbey & Aase) S. S. Denison & McNeal EU0961636; A. lemmonii S. Wat鄄
son EU0961646; A. macranthum Baker 1—HQ690254; Daocheng, Sichuan, China; Li Q鄄Q 092303; A. macranthum Baker 2—
HQ690256; Mangkang, Xizang, China; Gao Y鄄D G2010081702; A. macranthum Baker 3—HQ690255; Litang, Sichuan, Chi鄄
na; Li Q鄄Q 092206; A. macranthum Baker 4—GQ181072; Xianggelila, Yunnan, China; Xu J鄄M 93鄄23; A. macranthum Baker
5—HQ690562; Taibai Mountain, Shanxi, China; Li Q鄄Q 09080901; A. membranaceum Ownbey ex Traub EU0961656; A. moly
L. AF0551082; A. monanthum Maxim. AJ4127455; A. neapolitanum Cirillo AF0551042; A. obtusum Lemmon EU0961666; A.
omeiense Z. Y. Zhu 1—GQ181076; Emei Mountain, Sichuan, China; Xu J鄄M 91鄄01; A. omeiense Z. Y. Zhu 2—HQ690567;
Emei Mountain, Sichuan, China; Hu H鄄Y em鄄20100626鄄2; A. paradoxum (M. Bieb. ) G. Don AJ4127415; A. parvum Kellogg
EU0961696; A. peninsulare Lemmon ex Greene var. peninsulare EU0961706; A. platycaule S. Watson EU0961716; A. praecox
Brandegee EU0961736; A. punctum L. F. Hend. EU0961746; A. roseum L. AF0551052; A. sanbornii Alph. Wood var. sanbornii
EU0961776; A. serra McNeal & Ownbey EU0961786; A. sharsmithiae (Ownbey & Aase) McNeal EU0961796; A. shevockii Mc鄄
Neal EU0961806; A. siculum Ucria AJ2502993; A. siskiyouense Munz & Keck ex Ownbey EU0961816; A. stellatum Nutt. ex Ker
Gawl. EU0961836; A. subhirsutum L. AF0551062; A. tribracteatum Torr. EU0961846; A. triquetrum L. AJ4127425; A. tuolum鄄
nense (Ownbey & Aase) S. S. Denison & McNeal EU0961856; A. unifolium Kellogg EU0961866; A. ursinum L. AJ4127445; A.
validum S. Watson EU0961886; A. wallichii Kunth var. wallichii 1—HQ690253; Wenbi Mountain, Lijiang, Yunan, China;
Liu S & Gao P 20100903鄄02; A. wallichii Kunth var. wallichii 2—HQ690251; Hou shan, Yicun, Xianggelila, Yunan, China;
Li Q鄄Q YC09072907; A. wallichii Kunth var. wallichii 3—HQ690250; Mountain near Potatso National Park, Xianggelila, Yu鄄
nan, China; Li Q鄄Q BT09072818; A. wallichii Kunth var. wallichii 4—GQ181091; Kangding, Sichuan, China; Li Q鄄Q
2008081203; A. wallichii Kunth var. wallichii 5—HQ690252; Jilong, Xizang, China; Yu Y yy10080905; A. wallichii Kunth
var. wallichii 6—HQ690249; Mahuangba, Lijiang, Yunan, China; Li Q鄄Q MH09072515; A. wallichii Kunth var. wallichii 7—
HQ690566; Yulong Snow Mountain, Lijiang, Yunan, China; Li Q鄄Q YL09072630; A. wallichii var. platyphyllum (Diels) J.
M. Xu—GU566624; Lijiang, Yunnan, China; Li Q鄄Q 09072503; A. yosemitense Eastw. EU0961896; A. zebdanense Boiss. &
No觕 AY4275524; Subgenus Microscordum (Maxim. ) N. Friesen: A. monanthum Maxim. AJ4127455; Subgenus Nectaroscordum
(Lindl. ) Asch. et, Graebn. : A. bulgaricum (Janka) Prodan AJ4127475; A. siculum Ucria AJ2502993
9112 期摇 摇 摇 摇 摇 LI Qin鄄Qin et al. : Phylogeny and Character Evolution in Allium Subgenus Amerallium …摇 摇 摇 摇 摇 摇 摇