Communications in Plant Sciences (January-June 2015), Volume 5, Issues 1-2, Pages 1-8
Commun. Plant Sci. (ISSN 2237-4027)
www.complantsci.wordpress.com
Manuscript received on July 29, 2014, and published on October 16, 2014
Species delimitation in congenerics of Genus Daemonorops
from India using DNA barcodes
1,2
1
3
4
Senthilkumar Umapathy , Narasimhan Duvuru , Sanjappa Munivenkatappa , Uma Shaanker Ramanan ,
2*
and Ravikanth Gudasalamani
1
Center for Floristic Research, Department of Botany, Madras Christian College, East Tambaram, Chennai, Tamil Nadu, INDIA-600 059.
Conservation Genetics Lab, Ashoka Trust for Research in Ecology and the Environment (ATREE), Srirampura, Jakkur PO, Bangalore,
Karnataka, INDIA-560 064.
3
Department of Botany, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, INDIA-560 065.
4
School of Ecology and Conservation, Department of Crop physiology, University of Agricultural Sciences, GKVK, Bangalore, Karnataka,
INDIA-560 065.
2
ABSTRACT
Daemonorops is one of the largest genus of palms, widely distributed in tropical evergreen forests
of South and Southeast Asia and especially abundant in peninsular Malaysia. It shares the
phylogenetic clade with genus Calamus, but distinctly characterized by the presence of the
prophyllar bracts in subtribe Calaminae of family Arecaceae (Palmae). However, the species of
Daemonorops are highly variable and homoplasious in their morphological characters. Indian
Daemonorops has six species, of which five distributed in Andaman group of islands and one in
Indo-China. The study mainly focused on the species of Indo-Myanmar (Andaman Islands) because
they have showed uncertainty in their stand as distinct species. Hence it was attempted to test the
species delimitation in congenerics using phylogenetic and character analysis of the nuclear genes.
The study indicates three species of both Griffith and Beccari (D. jenkinsiana, D. manii, and
D. kurziana) in India, and another three species of Renuka et al. (D. wrightmyoensis, D. aurea, and
D. rarispinosa) from Andaman group of islands could be the variabilities of D. manii that is
colonized throughout the archipelago.
Keywords: Daemonorops, Species delimitation, DNA barcodes, Andaman and Nicobar Islands.
______________________________
*Corresponding author
E-mail: gravikanth@gmail.com
2 Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India using DNA barcodes.
INTRODUCTION
Rattans (otherwise called ‘canes’) are spiny, climbing
palms, widely distributed in the evergreen rain forests
of the paleotropics in Africa, Madagascar, India,
Myanmar, Peninsular Malaysia, Sumatra and
occasionally in Papua-New Guinea and Queensland
(Dransfield et al. 2008). The subfamily Calamoideae,
accounts for the greatest diversity of climbing palms in
South and South East Asia (Baker et al. 1998). Of the
different
genera,
the
genus
Calamus
and
Daemonorops are abundant with highest species
richness in the oriental landmass (Baker et al. 2000a).
They have also colonized most of the volcanic islands
of Indian and east Pacific oceans apart from the
continental lands (Baker et al. 1998).
The phylogenetic studies on calamoideaes
indicate that Calamus is not monophyletic and at the
same time Daemonorops is paraphyletic (they will
have common ancestor but they are not monophyletic
to each other and largely mixed at the tips from the
node of origin) within the sub-tribe Calaminae based
on ITS2 and 5S rRNA (Baker et al. 2000a, 2000b).
However, selection of DNA regions and taxon
sampling were limited in these studies, so paraphyletic
relationship was not highly intended (Baker et al.
2000b). The pleisomorphic transition of Plectocomiinae
(considered to be the basal clade for sub-tribe
Calaminae) to both Calamus and Daemonorops was
distinguished by the presence of prophyllar bracts
(Baker et al. 2000b). Moreover, the genus
Daemonorops was further divided into two subgenera
i.e. Piptospatha and Daemonorops based on the
nature of prophyllar bracts (Beccari 1911, Furtado
1953). Daemonorops is distributed over 101 species
throughout South and South East Asia (Dransfield et
al. 2008). In India, out of 6 species, five are present in
Indo-Myanmar (Andaman Islands) and one in IndoChina (Arunachal Pradesh and Nagaland) (Renuka et
al. 2010, Senthilkumar et al. 2014). Among them,
Daemonorops jenkinsianus belongs to the section
Piptospatha and all other species belong to section
Daemonorops (Basu 1992). Particularly, the species
distributed in the Andaman Islands are morphologically
highly variable in their quantitative measures
(Senthilkumar et al. 2014).Though they have colonized
most of islets of Andaman groups, but few species are
highly circumscribed into smaller forests such as
D. kurzianus, D.wrightmyoensis, and D. aurea (Renuka
et al. 2010). However the taxonomic relatedness is
quite uncertain among them.
The morphological uncertainty plays a pivot role
in this particular genus due to the variance at intraspecific level (within populations) and also the less
dissimilarities within genera (inter-specific). So, here,
Communications in Plant Sciences (ISSN 2237-4027)
based on the molecular studies, the congeneric
species of genus Daemonorops were tested based on
phylogenetic and character analysis using nuclear
DNA barcodes.
MATERIAL AND METHODS
Sampling. For the present study, all the six species of
Daemonorops were collected from Arunachal Pradesh
and Andaman group of islands during the survey on
these climbing palms. Comparative analyses of the
morphological characters of the species are given in
Table 1. Herbarium specimens were prepared with
replicates and deposited at School of Ecology and
Conservation, UAS, GKVK, Bangalore (Table 2). The
Genbank accession numbers and voucher data of the
species are presented in Table 2. Out-groups were
included from sub tribe Plectocomiinae, Korthalsiinae
and also a species from Calamus to construct both
ITS2 and RPB2 trees.
DNA barcodes. The ribosomal internal transcribed
spacer 2-ITS2 (ITS3 F and 28R – Hamzeh and
Dayanandan 2004) and RNA polymerase II (RPB2Palm INT23 – Loo et al. 2007) of the nuclear genome
were selected based on their divergence at both inter
and intra-specific level and also based on the earlier
studies in these climbing palms (Baker et al. 2000).
PCR amplification, sequencing. Genomic DNA was
extracted using a modified CTAB method (Doyle and
Doyle 1987). DNA was amplified for both the markers
ITS2 and RPB2. PCR conditions were followed based
on Senthilkumar et al. (2013). The purified PCR
product was sequenced using an ABI310 automated
genetic analyzer.
Sequence editing, character analysis and datasets.
Sequences were edited in Geneious Pro 5.4.6
(Drummond 2011) and aligned using the program
Muscle (Edgar 2004) inbuilt in MEGA 6.0 (Tamura et
al. 2013). The alignment matrix was imported into the
program Mesquite 2.7.4 (Maddison and Maddison
2010) for the manual alignments when required. Based
on the final alignment, the datasets were designed into
two for each barcode as multiple (using multiple
individuals of 6 congeneric species) and consensus
(using only consensus sequence of multiple individuals
from each species) (Table 3). Further, the distance
analysis and character analysis were performed
simultaneously to check the divergence at both inter
and intra-specific level and also the evolutionary
models (Table 3). The aligned matrix was tested for
models using the program jModeltest v. 2.1.4 (Darriba
et al. 2012).
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)
Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India Using DNA barcodes.
Table 1. Details of voucher specimens and nucleotide submissions of Daemonorops and out groups used in this study.
Species Name
Calamus viminalis Wild.
Locality
Voucher ID
KFRI-Peechi [Kerala]
Senthilkumar 216
ITS2
RPB2
KJ532894
KJ501055
KJ532903
KJ532904
KJ532905
KJ532906
KJ532907
KJ532908
KJ532909
KJ532910
KJ532911
KJ532912
KJ532913
KJ532914
KJ532915
KJ501059
KJ501060
KJ501061
D. aurea Renuka & Vijayak.
Chidiyatapu, Tharmughali Island
[South Andaman (SA)]
Senthilkumar 689, 794, 802
D. jenkinsiana (Griff.) Mart.
IBG [West Bengal]; SFRIItanagar [Arunachal Pradesh]
Senthilkumar 318RA, 605, 643
Nayasahar, Carbyn Chowk,
Kalatang RF [SA]
Senthilkumar 702, 714, 721
Indian Botanical GardenHowrah [West Bengal];
Tharmughali Island [SA]
Senthilkumar 604, 800, 803
Krishna Nallah 12KM, Little
Andaman [SA]
Senthilkumar 851, 870, 871
KJ532916
KJ532917
KJ501067
KJ501068
KJ501069
KJ501070
Papeeta Pahad, Wrightmyo, SA
Senthilkumar 847
KJ532918
KJ501071
D. fissa Blume
South East Asia
Baker et al. (2000)
AJ242073, 74, 75
D. didymophylla Becc.
South East Asia
Baker et al. (2000)
AJ242070, 71, 72
Korthalsia laciniosa(Griff.) Mart.
Mannarghat [SA]
Senthilkumar 694
KJ532919
KJ501072
TBGRI-Palod [Kerala]
Senthilkumar 457A
KJ532921
KJ501077
Tippi-Subansiri [Arunachal
Pradesh]
Senthilkumar 631
KJ532926
KJ501080
D. kurziana Hook.f. ex Becc.
D. manii Becc.
D. rarispinosa Renuka &
Vijayak.
D. wrightmyoensis Renuka &
Vijayak.
Korthalsia rogersii Becc.
Plectocomia himalayana Griff.
KJ501062
KJ501063
KJ501064
KJ501065
KJ501066
Table 2. Morphometric analysis of congeneric species of Daemonorops.
Character/
Species
Stem size
(diameter)
Sheath armature
D. aurea
D. jenkinsiana
D. kurziana
D. manii
D. rarispinosa
D.
wrightmyoensis
3.5 cm
3 cm
5 cm
3
2.5 cm
4.5 cm
Sparingly armed
with group of
spines below the
knee
Densely armed
with needle like
spines
Armed with
distinct papery
spines at mouth
Armed with
dimorphic spines
Unarmed or
rarely armed
Armed with
dimorphic spines
Sheath
indementum
Sheath colour
Absent
Reddish brown
Brown scurfy
Brown tomentum
Absent
Dusty tomentum
Yellowish green
Reddish brown
Pale brown
Brownish green
Straw yellow
Pale green
Inflor. Length
35 cm
80 cm
45 cm
30 cm
40 cm
30 cm
Prophyllar bracts
Greenish brown
Reddish brown
Straw yellow
Yellowish brown
Pale brown
Pale brown
Female Rachillae
Distichus
Sinuous
Sinuous
Sinuous
Distichus
Distichus
Fruit shape
Globose
Globose
Spherical
Spherical
Globose
Oblongoid
2 x 1.5 cm
2 x 1.8 cm
Yellow; tightly
imbricated
2 cm across
1.5 cm across
1.5 cm across
1 x 1.5 cm
Orange yellow
Brown
Pale yellow
Brown
Fruit size
Fruit scales
Golden Yellow
Table 3. Datasets and its character analysis.
Dataset
No. of Taxa
Alignment length
(bps)
Pi
Pui
C
Evolutionary
Model*
ITS2_multiple
12 (25 inds)
303
81 (26.7)
144 (47.5)
158 (52.2)
TPM1uf+G
12
303
49 (16.2)
66 (21.9)
236 (77.9)
TPM1uf+G
10 (17 inds)
679
50 (7.4)
74 (10.9)
604 (90)
HKY+G
RPB2_consensus
10
680
45 (6.6)
78 (11.5)
600 (88.2)
HKY
Combined
12
983
95 (9.7)
50 (5)
838 (85.3)
HKY+G
ITS2_consensus
RPB2_multi
Pi-Parsimony informative; Pui- Parsimony uninformative; C-Conserved sites; * Model selected based on BIC values. The percentage is in parentheses.
Phylogenetic analysis. Bayesian analysis was
perfomed for all the four datasets using mixed models
for the posterior analysis in MrBayes v3.1.2. (Ronquist
and Huelsenbeck 2003). MCMC (Markov Chain Monte
Communications in Plant Sciences (ISSN 2237-4027)
Carlo) was run for 1M generations with 4 chains (of hot
and cold). The run was not continued further once it
reached the split frequency of standard deviation
<0.01. The trees were summarized as 50% majority
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)
3
4 Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India using DNA barcodes.
rule consensus tree and viewed in FigTree v1.3.1
(Rambaut 2009). The related attributes of the tree such
as posterior values and substitution changes per sites
were drawn for each tree.
Maximum parsimony analysis was carried out for
only combined dataset to derive the entire
parsimonious information from both the barcodes using
PAUP* v.4.0b10 (Swofford 2002). Bootstrap analysis
was conducted for 1000 replicates using default
settings except for the ‘maxtrees’ option that was left
unchanged.
UPGMA (Unweighted Pair Group Method
with Arithmatic mean) analysis was done in
MEGA 6.0 for RPB2 consenus dataset with Indian
Daemonorops.
high between these two species (0.165) when they are
analyzed separately (Figure 3).
RESULTS AND DISCUSSION
Morphometric analysis. Both discrete and continuous
trait analysis have shown relatively sufficient
information on congeneric species whether they are
distinct or not (Table 2). Moreover, the comparative
character
analysis
distinguishes
the
section
Piptospatha (D. jenkinsiana) and Daemonorops (other
5 species from Andaman Islands). The following
characters such as stem size, sheath armature, size of
the prophyllar bract, fruit shape are considered as
diagnostic keys among these species. Similarly,
D. jenkinsiana is distinguished by its long prophyllar
bract that enfolds the inner bracts within and forms the
beak (Figure 1). D. kurziana and D. manii differ based
on the large sized stem and densely covered brown
scurfy tomentum respectively (Figures 1 and 2). Mouth
of the sheath covered with papery spines is distinct in
D. kurziana (Figure 2). But, the other 3 species of
Daemonorops are more or less similar to each other
and D. wrightmyoensis differs only in fruit shape
(oblongoid) (Figure 1). D. aurea and D. rarispinoa
stand out as distinct species based on their sheath
armature (rarely or sparingly armed) but the other
quantitative traits are variable within populations
(Figures 1 and 2).
Phylogenetic analysis
Distance analysis. The aligned matrix of all the five
datasets for the distance analysis was carried out to
obtain the pairwise distance (p-distance) using
neighbor joining (NJ) method for both the barcodes.
The region ITS2 shows higher inter-generic mean
distance (0.126) than the RPB2 (0.06) (Figure 2).
Similarly, the distance at inter-specific is relatively high
(0.053) when South East Asian species was included
in the analysis (0.0053) (Figure 3). But, when D. fissa
and D. didymophylla were excluded from the matrix,
the distance is none (0). The distance is significantly
Communications in Plant Sciences (ISSN 2237-4027)
Figure 1. Genus Daemonorops Bl. (1) Sheath sparsely
armed-Daemonorops aurea Renuka & Vijayak. [insectGlobose fruits]; (2) Sheath densely armed & covered by
brown indumentum-D. manii Becc.; (3) Sheath armed with
half
whorled
spines-D.
jenkinsiana
(Griff.)
Mart.
[insect=Sheath covered by reddish tomentum]; (4) D.
wrightmyoensis Renuda & Vijayak. [insect=Oblongoid fruits;
copyright to Renuda & Sreekumar, 2012].
Further, both the regions failed to differentiate the
species (the inter-specific of RPB2 was 0.002,
Figure 3). Among them, RPB2 is comparatively better
to distinguish the congeneric species. So, the distance
tree is generated based on the UPGMA method here.
The UPGMA tree shows two separate clades
i.e. Piptospatha and Daemonorops, which are distinctly
clustered here (Figure 4). The clade 1 collapsed
because they are identical to each other at
inter-specific level. The phylogenetic distance is
weighed as 0.025 from tips to the root which indicate
inter-generic distance at substitutions level (Figure 4).
The evolutionary models were tested for all the
datasets based on their substitution schemes of
invariable sites (I) and gamma distribution (G) (Table
3). The models were selected based on the BIC
(Bayesian information Criterion) from computed
likelihood scores.
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)
Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India Using DNA barcodes.
Figure 2. Daemonorops Bl. (1) Sheath armed with papery
spines-D. Kurziana Hook.f. ex Becc. [insect=rachillae with
yellow fruits]; (2) Sheath sparingly armed-D. rarispinosa
Renuka & Vijayak. [insect=Shiny yellow fruits with strongly
grooved scales].
clade, which is due to the contribution of RPB2 intron
23 (Figure 6). So here, the genetic distance is
minimized to 0.02 in ITS2 dataset but again the
distance is solely represented by south East Asian
species (Figure 6).
Daemonorops is one among the largest genus in
calamoideaes (scaly fruited palms) widely distributed in
Asian tropics. It showed paraphyletic relationship with
genus Calamus (Baker et al. 2000b, Baker et al. 2009).
Further, the congeneric species of this genus is highly
variable in their morphology and has been challenged
for several decades (Beccari 1911, Furtado 1953,
Dransfield et al. 2008, Renuka et al. 2010). The
problem of misidentification is due to higher variability
in their visible morphological characters even at the
population level. So the study was carried out to
contribute an information on species delimitation in
these congeneric species based on the measure of
both inter and intraspecific divergence. However, the
three species namely D. jenkinsiana, D. manii, and
D. kurziana being distinct and another three species
that are highly versatile to be designated as distinct
species based on their described characters that are
quantitatively highly variable. Molecular analysis
carried out in the present study indicates a very low
genetic distance (0) in the Indian Daemonorops
compared to the Daemonorops distributed in the South
East Asia (0.165). The phylogenetic analysis based on
both Bayesian and parsimony reveals that there is
relative increase of node support at the deeper nodes
of Daemonorops when multi loci analysis was carried
out using the combined dataset. RPB2 intron region
shows comparatively high mean distance than ITS2 for
Indian Daemonorops. Thus, species delimitation
cannot be derived alone with single gene or marker.
Moreover, for such studies, the marker selection
should be robust and highly informative. Besides, the
sampling of the study system also should be complete
and dense for robust analysis.
CONCLUSION
Figure 3. Distance analysis between the gene trees of ITS2
and RPB2 in MEGA 6.0. The histogram represented the
mean distance with standard error bars.
Character based analysis. Bayesian analysis result
the majority rule consensus tree which shows higher
posterior density values at each node. But the clade
Daemonorops is not resolved in data sets of multiple
individuals of both ITS2 and RPB2 or otherwise it
shows that they are identical (Figure 5). Hence, when
the genetic distance is compared, there is large gap
(0.04-0.009) between the gene trees. Moreover, the
combined dataset shows the relative increase of the
posterior values at deeper nodes in Daemonorops
Communications in Plant Sciences (ISSN 2237-4027)
The study indicates three species (D. jenkinsiana,
D. manii, and D. kurziana) in India, and another three
species (D. wrightmyoensis, D. aurea, and
D. rarispinosa) from Andaman group of islands could
be the variabilities of D. manii that is colonized
throughout the archipelago. The study however has
not been able to resolve the distance between
D. kurziana and D. manii due to the limited markers
that were used. The study suggests a complete
revision of the genus Daemonorops using a number of
DNA regions as well as species to resolve the species
delimitation not only in the Indian subcontinent but also
for other South East Asian species.
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)
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6 Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India using DNA barcodes.
Figure 4. UPGMA tree of congeneric species of genus Daemonorops using RPB2 palm Intron 23; tree shows both clade 1 and 2
of Indo-China and Indo-Myanmarese, respectively.
Figure 5. Bayesian posterior analysis using multiple individuals of congeneric species of Daemonorops using nuclear ribosomal
spacer (ITS2) and intron (RPB2) regions. Asterisk indicates deeper nodes with relatively high posterior values in RPB2 than
ITS2.
Communications in Plant Sciences (ISSN 2237-4027)
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)
Umapathy et al. 2015. Species delimitation in congenerics of Genus Daemonorops from India Using DNA barcodes.
Figure 6. Bayesian posterior tree based on combined analysis (ITS2+RPB2). Tree represented by consensus of multiples of
each congeneric species (RPB2 sequences are not available for South East Asian species). Values at right side of the node
indicate the posterior probabilities in percent and the values above the bootsrap support derived from parsimony analysis.
Acknowledgements
We are thankful to the Principal Chief Conservator of Forests,
Haddo, Port Blair, and Chief Wildlife warden, Haddo, Port Blair, for
permitting to explore the forests throughout the A and N islands. We
thank Dr. C. Murugan, Scientist ‘C’, Ms. Lakra, Botanist of the
Andaman and Nicobar regional centre, BSI, for their helpful guidance
to visit different localities. We also acknowledge the Department of
Biotechnology, Government of India, for its financial support to carry
out this study.
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RESUMO
Delimitação de espécies congêneres do gênero Daemonorops
da Índia, usando código de barras de DNA. Daemonorops é um
dos gêneros mais ricos de palmeiras, amplamente distribuído em
florestas perenifólias do Sul e Sudeste da Ásia, e especialmente
abundante na Malásia peninsular. O gênero compartilha o clado
filogenético com o gênero Calamus, mas distintamente
caracterizado pela presença de brácteas profilares na subtribo
Calaminae da família Areraceae (Palmae). Contudo, as espécies do
gênero Daemonorops apresentam grande variabilidade e
homoplasia em suas características morfológicas. Plantas do gênero
Daemonorops de origem na Índia contemplam seis espécies, das
quais cinco estão distribuídas no grupo de ilhas Andaman e uma
espécie na Indo-China. Os objetos de estudo são as espécies da
Indo-Myanmar (Ilhas Andamar), pois há dúvidas quanto à separação
em espécies distintas. Portanto, o objetivo da pesquisa foi testar a
delimitação de espécies congêneres usando análises filogenéticas e
de caráter dos genes nucleares. O estudo indica a ocorrência de
três espécies (D. jenkinsiana, D. manii, and D. kurziana) na Índia;
enquanto outras três espécies (D. wrightmyoensis, D. aurea, and
D. rarispinosa) que ocorrem no grupo de ilhas Andaman podem ser
variedades de D. manii que colonizaram o arquipélago.
Palavras-chave: Daemonorops, Delimitação de espécies, Código
de barras de DNA, Ilhas Andaman e Nicobar.
Quality of English writing and reference information
are of totally responsibility of authors.
Communications in Plant Sciences (ISSN 2237-4027)
Commun. Plant Sci. 5(1-2): 1-8 (Jan-Jun 2015)