1
CHAPTER 1
INTRODUCTION
India is well known for its rich heritage of natural diversity, as it intersects
four biodiversity hotspots such as Eastern Himalaya, Western Ghats, Indo-Burma,
and Andaman & Nicobar Islands. It is one among the 17 mega diverse countries
which ranking tenth in the world and fourth in Asia [1]. India harbors nearly 11% of
the world’s floral diversity which documented over 17,500 flowering plants, 6,200
endemic species, 7,500 medicinal plants and 246 globally threatened species in only
2.4% of world’s land area [2]. This is due to varied eco-climatic conditions together
with unique geography and cultural features have contributed to an astounding
diversity of habitats. India’s biogeography is diverse with ten different bio-
geographic zones [3], of which 23.4% of the land area is under forest and tree cover
(Table 1.1).
The Tropical Dry Evergreen Forest (TDEF) is part of the costal bio-
geographic zone in India that is narrowly confined to the East coast province. The
forests are regarded as national treasure that is responsible for India’s rich
biodiversity. “Forest is a unit of vegetation which possesses characteristics in
physiognomy and structure sufficiently pronounced to permit of its differentiation
from other units”. India’s forests were first classified by Sir H.G. Champion in 1936
and later revised by Champion and Seth in 1968 [4]. According to this classification,
there are 6 major types, 16 minor types and about 221 sub-types of forest reported in
India. Tropical Dry Evergreen Forest (TDEF) is one of the minor forest types
classified within the major forest type, Tropical Dry Forest (TDF). The TDEF is
relatively under-studied on aspects of structural and functional ecology, as compared
to the other forests [5].
2
Table 1.1 Biogeographic zones of India
Biogeographic
ZonesBiogeographic Provinces
% of
geographical
area of India
Trans Himalaya
1A: Himalaya - Ladakh Mountains
1B: Himalaya -Tibetan Plateau
1C: Trans - Himalaya Sikkim
3.3
2.2
<0.1
The Himalaya
2A: Himalaya - North West Himalaya
2B: Himalaya - West Himalaya
2C: Himalaya - Central Himalaya
2D: Himalaya - East Himalaya
2.1
1.6
0.2
2.5
The Indian
Desert
3A: Desert – Thar
3B: Desert – Katchchh
5.4
1.1
The Semi Arid4A: Semi - Arid - Punjab Plains
4B: Semi - Arid - Gujarat Rajputana
3.7
12.9
The Western
Ghats
5A: Western Ghats - Malabar Plains
5B: Western Ghats -Western Ghats Mountains
2.0
2.0
The Deccan
Peninsula
6A: Deccan Peninsular - Central Highlands
6B: Deccan Peninsular - Chotta Nagpur
6C: Deccan Peninsular - Eastern Highlands
6D: Deccan Peninsular - Central Plateau
6E: Deccan Peninsular - Deccan South
7.3
5.4
6.3
12.5
10.4
The Gangetic
Plains
7A: Gangetic Plain - Upper Gangetic Plains
7B: Gangetic Plain - Lower Gangetic Plains
6.3
4.5
The Coasts
8A: Coasts - West Coast
8B: Coasts - East Coast
8C: Coasts – Lakshdweep
0.6
1.9
<0.1
Northeast India9A: North - East - Brahamputra Valley
9B: North - East – North East Hills
2.0
3.2
Islands10A: Islands – Andamans
10B: Islands – Nicobars
0.2
0.1
3
1.1 Tropical Dry Evergreen Forest (TDEF)
The TDEF was described as a thin belt of degraded forest occurring on the
south-eastern coastal region of peninsular India [6]. It was first recognized by Sir A.
Wimbush in 1935 the chief conservator of forest of Madras Presidency [7]. He stated
met which is semi- evergreen in character. Many of these species are quite different
from there to the west and although many individual trees are leafless during part of
hot weather much of underground and shrubs retain their leaves with the result that
we never get completely leafless appearance so characteristic of true deciduous
. This vegetation was predominantly composed of trees and
shrubs which have thick dark green foliage throughout the year.
The term TDEF was first officially applied by Sir H.G. Champion in his
classical book on Forest Types of India published in 1936 [4]. The most explicit
analysis of the forest types of India was provided by Champion and Seth in 1968 on
the basis of structure, physiognomy and floristic diversity. These authors were
basically foresters and they had broadly treated all Indian forests under six
categories, viz. Moist tropical forests, Dry tropical forests, Montane sub-tropical
forests, Montane temperate forests, Sub-alpine forests and Alpine scrub [4,8].
Among these the dry tropical forests have three distinct subtypes: tropical dry
deciduous forests, tropical thorn forests and tropical dry evergreen forests (Table
1.1.1).
Most of the world's tropical and subtropical broadleaf forest trees have
tendency to lose their leaves during the dry season to conserve moisture. However,
the TDEF retain their leaves year round hence, named as TDEF. The vegetation of
TDEF occupies different forms of elements includes trees, shrubs, lianas, epiphytes,
herbs, and tuberous species. Blasco and Legris [9] in 1972 reported that, there were
approximately 500 dicotyledonous species, including aquatic, mangrove and
terrestrial species in the whole region. Meher-Homji [10] in 1974 claimed that there
was a total of only 266 species in the TDEF region and contained over 160 woody
species. At present, it is estimated that the TDEF contains about 1,500 species and
4
over half of these species have a medicinal use, timber use and other cultural or
religious uses. Champion and Seth [4] was described TDEF as low forest of trees
with 9–12 m high that forms a complete canopy and they usually grow in lateritic
and sand dune soils. This forest comprised of several evergreen, semi-evergreen and
deciduous species. According to this scheme of classification, TDEF are under type 7
and they include subtypes of ‘typical dry evergreen forest’ (7/C1) and ‘tropical dry
evergreen scrub’ (7/DS1).
Table 1.1.1 Types of forests in India
Major Types Minor TypesArea
(m ha)
% of
forest
area
Moist Tropical Forest
Tropical Wet Evergreen Forest
Tropical Semi-Evergreen Forest
Tropical Moist Deciduous Forest
Littoral and Swamp Forest
4.5
1.9
23.3
0.7
5.8
2.5
30.3
0.9
Dry Tropical Forest
Tropical Dry Deciduous Forest
Tropical Thorn Forest
Tropical Dry Evergreen Forest
29.4
5.2
0.1
38.2
6.7
0.1
Montane Subtropical
Forest
Subtropical Broadleaved Hill Forest
Subtropical Pine Forest
Subtropical Dry Evergreen Forest
0.3
3.7
0.2
0.4
5.0
0.2
Montane Temperate
Forest
Montane Wet Temperate Forest
Himalayan Moist Temperate Forest
Himalayan Dry Temperate Forest
1.6
2.6
0.2
2.0
3.4
0.2
Sub-Alpine Forest Sub-alpine Forest - -
Alpine ScrubMoist Alpine Scrub
Dry Alpine Scrub
3.3
-
4.3
-
5
The ‘typical dry evergreen forest’ was treated under sub-type 7/C1 which are
dominated by trees like Manilkara hexandra, Memecylon umbellatum, Diospyros
ferrea, Chloroxylon sweitenia, Albizzia amara and other evergreen species. Further,
the sub-type 7/DS1 were described as ‘tropical dry evergreen scrub’ which are
dominated by Memecylon edule, Ziziphus xylopyrus, Dichrostachys cinerea, Psydrax
dicoccos, Carissa spinarum, Albizzia amara, Buchanania axillaris, Dodonea viscosa
and other species.
The phyto-sociological classifications of the TDEF vegetation were also
described by several authors as, the Manilkara hexandra series [11], the Manilkara
hexandra – Drypetes sepiaria – Chloroxylon swietenia – Memecylon umbellatum
series [12], the Manilkara hexandra – Memecylon umbellatum – Drypetes sepiaria –
Pterospermum suberifolium – Carmona microphylla facies of the Albizia amara
community [13], the Manilkara hexandra – Chloroxylon swietenia vegetation type
within the Albizia amara zone [14] and the Memecylon edule – Atalantia
monophylla series [15].
However, to distinguish this special forest type of the Coromandel Coast
region from the other forest types, the physiognomic term “dry evergreen” was
retained and officially classified as “Tropical Dry Evergreen Forest” by Champion
and Seth. After a span of 47 years, even today this classification is still followed by
Indian Council of Forestry Research Education (ICFRE) for conservation and
management purposes [8].
1.2 Distribution of TDEF
The TDEF type is considered as rare and unique and as no unified features;
but they are chosen based on local climatic, biotic and edaphic factors [5]. These
factors largely influence the forests physiognomy, stand structure, species
composition, and dynamics. The species of this region were highly variable in terms
of height depending on site location, soil type and the level of human impacts. The
TDEF has restricted global distribution which occurs in some parts of Tropical
America, Africa and Asia.
6
The systematic review made through wide survey of literatures showed the
occurrence of TDEF, either as a vegetation formation or as a forest type in the world.
The distribution of dry evergreen forest is given in Table 1.2.1.
Table 1.2.1 Distribution of TDEF in the world
TROPICS LOCATION REFERENCES
America
Antigua
Bahamas
British Guiana
Jamaica
Trinidad
Tobago
[16]
[17]
[18]
[19]
[20]
[21]
AfricaEthiopia
Tanzania
Zambia
[22]
[23]
[24]
AsiaThailand
Sri Lanka
INDIA
[25]
[26,27]
[4,28,29]
In India, TDEF occurs as a thin patch along the Coromandel Coast of
southern India. Historically, the forest extended from Visakhapatnam in Andhra
Pradesh to Ramanathapuram in Tamil Nadu as a belt of vegetation about a length of
1,800 km and a width of about ca. 60 km and it covers a total area of ca. 1,08,000
km2 [30,31]. It is found in the rain shadow of the Western Ghats and Eastern Ghats.
It is considered as one of the ecoregions in India that is home to number of cities,
including metropolis of Chennai, Pondicherry, Thanjavur, Kanchipuram and Nellore.
The TDEF on the Coromandel Coast of India, which occur as patches, are short-
statured, largely three-layered, tree-dominated evergreen forests with a sparse and
patchy ground flora [32].
7
The TDEF is composed of several indigenous species which are scatteredly
distributed along the Coromandel Coast in three different habitats such as (1) Sacred
groves, (2) Reserve forests, and (3) Isolated hillocks.
1.2.1 Sacred groves
Sacred groves are forest fragments of varying sizes, which are conserved by
local communities based on religious belief, taboos and social sanctions that have
cultural and ecological implications [33,34]. Sacred groves are the home to native
keystone species of plants and animals which represent mini-biosphere reserve,
making them an essential part of the conservation process. There are about 448
scared groves reported in Tamil Nadu and their sizes ranging from less than an acre
to little more than ten acre [35]. Most of the TDEF patches are considered as scared
groves and are still preserved as a result of the religious belief of the local people
[36] (Figure 1.2.1.1). It is believed that one of the prime utilities of sacred grove is
the protection and supply of medicinal plants. It is usually occurs in red lateritic and
clayey soil when intact acts as an effective sponge for the monsoon rains that are
characteristic of the area.
The natural vegetation is dominated by large number of evergreen, and semi-
evergreen tree species such as, Atalantia monophylla, Aegle marmelos, Alangium
salviifolium, Garcinia spicata, Diospyros chloroxylon, Phoenix pusilla, Calophyllum
inophyllum, Strychnos potatorum, Suregaeda angustifolia, Pterospermum canescens,
Pamburus missionis, Mimusops elengi, Lepisanthes tetraphylla, Syzygium cumini,
Diospyros ferrea, Wrightia tinctoria. Considerable areas of TDEF have long been
significantly degraded and fragmented [37] and nearly 80% of the remnants are
conserved as sacred grove [38].
8
9
1.2.2 Reserve forests
Reserve forests are protected on the basis of judicial and various legal
constitution of India. The term reserved forest was used to designate protected forest
areas in India, under the Indian Forest Act, 1927. The vegetation of reserve forests
are usually undisturbed and occur in the clayey, red lateritic and alluvial soil.
Plantation of native tree species and other deciduous species were done by forest
department to enrich the vegetation (Figure 1.2.2.1). It supports evergreen, deciduous
and thorny trees includes Acacia planiformis, Acacia auriculiformis, Acacia
chundra, Butea monosperma, Hardwickia binata, Helicteres isora, Holoptelea
integrifolia, Terminalia bellirica, Pterocarpus santalinus, Dichrostachys cinerea,
Catunaregam spinosarum, Euphorbia antiquarum, Flaucortia indica, Ziziphus
xylopyrus.
1.2.3 Isolated hillocks
A hillock or knoll is a small hill usually similar in their distribution and size
to small mesas or buttes. Several patches of TDEF vegetation found as isolated
hillocks and are scatteredly found along the Coromandel Coast (Figure 1.2.2.1).
Many places it is considered as the megalithic burial sites that indicates the ancient
human colonization and are protected by Archaeological survey of India [31].
Isolated hillocks are usually consists of gravelly and red lateritic soil and the run-off
from the hillocks during the rainy season enriches the soil as well as surrounding
place. The vegetation comprises of dense bushes and scattered stunted trees. Species
such as Buchanania axillaris, Manilkara hexandra, Premna corymbosa, Bauhinia
racemosa, Ziziphus mauritiana, Psydrax dicoccos, Premna mollissima, Catunaregam
spinosa, etc are commonly found in the hillocks. It also supports large number of
animals include mammals and reptiles.
10
11
1.3. Characteristic features of TDEF
The TDEF is floristically distinguished by a fair representation of
characteristic and preferential species, exclusively or mostly confined to this
vegetation type. The preferential tree species such as Atalantia monophylla, Lannea
coromandelica, Lepisanthes tetraphylla, Manilkara hexandra, Memecylon
umbellatum, Psydrax dicoccos, Pamburus missionis, Sapindus emarginatus,
Putranjiva roxburghii, Dolichandrone falcata, Buchanania axillaris, etc signifies
this TDEF vegetation [5,32,38]. Species of climbing habits and liana such as
Combretum albidum, Ventilago maderaspatana, Grewia orientalis, Hugonia mystax,
are also commonly found in this vegetation. Several such species are dominated in
sacred groves that are conserved by local people based on the religious belief.
The key characteristics of TDEF are,
Mostly TDEF occurs in patches and as sacred groves
They extend from the coast to at least 60 km inland
The vegetation is approximately varies between 9-12 m and forming a
complete canopy
Canopy forming trees are coriaceous-leaved, evergreen and posses short
trunks and spreading crown
Undergrowth of the canopy also possess similar features
They occur in climatically dry areas and dry season may extend from three to
six months
It receives an annual rainfall of 900 mm to 1500 mm per year
Little monotypic dominance
Deciduous species, thorny shrubs and climbers are common
Numerous species with climbing habit
Liana is common
Bamboos sparsely represented
Presence of infrequent grass
12
Physiognomically, evergreen species dominates the forest that forms strong
association between the qualitative reproductive traits, pollination and dispersal
spectrum exists among the TDEF species. Ecological niche of the emergent canopy
tree is more suitably filled by deciduous species which can tolerate the drying
atmosphere of the upper canopy better than the evergreen species. It is also contains
mixture of brevi-deciduous and semi-evergreen tree species.
The climate pattern of the TDEF area is significant in determining the
vegetation forms and it is influenced by rainfall of winter season, dry months and
dew that falls between September and April [39,40]. The climate is distinguished by
its inconstancy rainfall pattern that varies in intensity, amount, and distribution both
within and between years. A dissymmetric rainfall regime of rainy season is from
October to January and over 50% of the annual rainfall could fall in these months.
The number of rainy days during October and November vary between 2 and 21
days. The intensity of the rain may also reach 100 mm in a day. Such inconsistency
in the rainfall pattern will inevitably have effects on the vegetation of this region.
The average rainfall varies greatly, but an approximate range could be described as
900- 1500 mm per year [14,40]. It is 2.5 times more that of June to September. The
dry season may extend from January to March or from December to May and is
limited to six months based on the geography.
1.4 Ecological Importance of TDEF
The TDEF are ecologically important because of their unique biotic
communities [25]. The TDEF ecosystems are home to local flora and fauna that
represent a mini-biosphere reserve. It is considered as one of the ecoregions in India
and has evolved as an important reservoir of biological diversity. The TDEF provides
several ecosystem services such as soil conservation, water conservation, seed
preservation, and carbon sequestration [35]. It is an important refuge for rare,
endangered, endemic and threatened medicinal plants (Figure 1.4.1).
The forest with its dense and evergreen characteristic is an excellent
conservator of soil, and when intact acts as an effective sponge for the monsoon rains
13
that are characteristic of the area. In watershed management the forest is very
effective, particularly due to its evergreen nature, maintaining a constant ground
cover that breaks up the rain’s impact. The soil seed banks in TDEF play an
important role in the natural environment of ecosystems. The increase of species
richness in a plant community due to a species-rich and abundant soil seed bank is
known as the storage effect.
The components of TDEF form a complex diverse habitat that is home to a
myriad of animal species such as birds, insects, reptiles and mammals that help to
control the pest population in the agro-ecosystem and promote regeneration of tree
species by dispersing seeds [6,39]. It also facilitate cross pollination of many tree
species that play a significant role in balancing the natural ecosystem. Apparently,
69% of the trees in the coastal forests are dispersed by jackals, civets, bats and
rodents.
Figure 1.4.1 Ecosystem services of TDEF
14
1.5 Economic importance of TDEF
The TDEF biodiversity provides a variety of goods and services to the user
for generating use values. The values are further divided into Timber Forest Product
(TFP) & Non-Timber Forest Product (NTFP) value [41].
1.5.1 Timber Forest Product (TFP)
Several tree species occurring in TDEF area provides wood as source of
timber that are utilized for commercial commodities like building purposes,
agricultural implements, ply wood, packing cases, furniture, musical instruments,
railway sleepers etc. Some of the highly valued timber trees [42] found in the TDEF
is listed in Table 1.5.1.1.
Table 1.5.1.1 High value timbers from TDEF
Botanical Name Family English Name Tamil Name
Albizia lebbeck Fabaceae Lebbek Tree Vagai
Dalbergia sissoo Fabaceae Indian rosewood Sissoo
Eucalyptus tereticornis Myrtaceae Eucalyptus Thailamaram
Gmelina arborea Verbenaceae Gamhar Marakumizh
Holoptelea integrifolia Ulmaceae Indian Elm Aaya
Pterocarpus santalinus Fabaceae Red Sandal Wood Senchandanam
Santalum album Santalaceae Sandalwood Sandhanam
Swietenia macrophylla Meliaceae Mahogany Magogani
Syzygium cumini Myrtaceae Jamon Tree Naaval
Tamarindus indica Fabaceae Tamirind Tree Puliya maram
Tectona grandis Lamiaceae Teak Thekku
Thespesia populnea Malvaceae Portia Tree Poovarasu
15
1.5.2 Non-Timber Forest Product (NTFP)
The NTFP are obtained from the TDEF that does not require harvesting of
trees. These commodities include medicinal plants, foods, fibres, fuel wood, fodder
etc. The TDEF contains several medicinal that are highly traded as raw drugs for
their medicinal value. According to the National Medicinal Plants Board (NMPB) of
India, about 1,289 raw drugs derived from 960 plant species are actively traded in
India to serve domestic as well as international markets [43]. These medicinal plants
raw drugs obtained from plant parts (leaves, stem bark, seeds, roots etc) are widely
used in the preparation natural health products. It is also reported that over 80% of
the medicinal plant raw drugs are collected from the wild with the help of local
farmers or collectors [43]. Some of the highly traded medicinal trees are listed in
Table 1.5.2.1.
Table 1.5.2.1 High trade value medicinal tress from TDEF
Botanical Name Family English Name Tamil Name
Alstonia scholaris Apocynaceae Indian Devil tree Ezhilai palai
Cassia fistula Fabaceae Golden Shower Manja konnai
Ficus religiosa Moraceae Cluster Fig Arasmaram
Helicteres isora Malvaceae Indian screw tree Valampuri
Mimusops elengi Sapotaceae Indian Medaller Mahizhamaram
Pongamia pinnata Fabaceae Indian beech Pungai Maram
Strychnos nux-vomica Loganiaceae Strychnine tree Etti
Terminalia bellirica Combretaceae Belliric Myrobalan Thanrikkai
Wrightia tinctoria Apocynaceae Dyers's Oleander Vetpalai
Zizyphus xylopyrus Rhamnaceae Woody fruite jujube Kottaiilanthai
Butea monosperma Fabaceae Flame of the Forest Kattu Thee
Strychnos potatorum Loganiaceae Clearing Nut Tree Thetthan Kottai
16
Besides, several exotic species are represented in TDEF that are planted
artificially for various purposes such as for horticulture value (Anacardium
occidentale, Manilkara zapota and Psidium guajava), commercial value (fiber/cotton
-Ceiba pentandra), green manure (Delonix elata and Leucaena latisiliqua),
beautification (Delonix regia, Sterculia foetida, Kigelia africana, Nerium oleander,
Tecoma stans), medicinal value (Bixa orellana), or traditional reasons (Cocos
nucifera). These trees are planted either by forest department or by some social
agencies for the benefit of forest to increase the green cover and to enrich the
vegetation. Several introduced species are naturalized and regenerated through seed
dispersal mainly by birds and bats within the TDEF.
1.6 Major threats to TDEF
It is reported that illegal logging is particularly high in tropical countries like
Cameroon 50%, Brazil 80%, Indonesia >90% and Cambodia >90% [44]. The TDEF
is vulnerable in India because of their very narrow geographic boundary, which is
under considerable development pressures. The tree species with timber and
medicinal value are quickly disappearing in TDEF due to overexploitation of forest
resources. Earlier study has reported that the impending threat to the rich native
biodiversity in the TDEF is partly due to its inherent abundance of natural resources
[5,30]. Human activities such as dead wood collection, biomass gathering, lopping of
tender branches and green leaves for cattle’s, creation of footpaths, grazing, mining
of sand and clay, brick-making and collection of wild fruits and vegetables and
indiscriminate collection of plants for medicinal use are greatly affecting the
biodiversity of the TDEF. Increased economic activities along coastal regions have
led to severe fragmentation of these forests and threaten the gene pool of a unique
forest ecosystem.
Moreover, tree species of timber and medicinal value are more concentrated
in Tropical Dry Forest (TDF) and TDEF is one of the minor forest types of TDF
which is greatly affected by commercial harvesting of timber. Illegal logging of
17
timber is become a routine occurrence and considered to be a major problem in the
conservation of TDEF biodiversity. Illegal trade of timber is not only reducing the
economy of the country but also affects the ecological balance of the forest. Besides,
invasion of exotic species has become serious problem in the TDEF. The domination
of the exotic species often threatens and depletes the native tree species.
1.7 Need for conservation strategies in TDEF
Tropical forests are being degraded at a fast pace and it is estimated that over
11,000 tree species may facing a direct risk of extinction [45,46]. Thus, large-scale
biodiversity inventories are critically needed in order to develop informed
conservation strategies for these diverse ecosystems. The TDEF is an endangered
forest type in India, therefore conservation strategies are greatly demanded in order
to conserve this valuable ecosystem [29,47]. Notable scientists have reported that the
impending threat to the rich native biodiversity in TDEF of India is partly due to its
inherent abundance of natural resources [29,32]. The TDEF needs to be given high
priority for natural resource planning strategies that conserve biodiversity as
envisioned in National Environment Policy. Quick and reliable documentation of tree
species is essential in order to conserve the natural resources within TDEF. Plant
taxonomists with botanical field experience are very much limited for the reliable
identification of the tree species in TDEF. Moreover, the tree species are not easy to
identify when the specimen is incomplete, damaged or derived from plant parts such
as leaves, roots, bark, wood and seeds. Currently, it is very much difficult to monitor
the illegal trade of rare, endemic, threatened and medicinal tree species. Species
identification by conventional taxonomy is often challenging in many cases due to
the lack of experienced experts.
Limitations of conventional taxonomy includes,
Species identification often requires reproductive characters (Flowers &
Fruits) that are not easy to obtain from tree species due to seasonal flowering
patterns and many of them are large trees
18
Accurate species level identification requires considerable amount of time
Tree species can be incorrectly identified due to variability in the
morphological characters used for species identification
Morphological keys could be used only by the experts and an inexperienced
person may not correctly identify a species
Seedlings and young plants are mostly difficult to identify
Medicinal plant raw drugs is in incomplete or damaged form and derived
from dried plant parts such as leaves, roots, bark, and wood are also difficult
to identify
Other methods include advanced microscopy, and chemotaxonomy was
showed only limited success in the species identification. Limitations of these
methods are owing to the involvement of complex chemistries, lack of unique
compounds, influence of environmental factors, plant’s age and geographical
variations. Therefore, it is necessary to utilize an alternate method for species
identification.
DNA barcoding is emerging as a valuable tool for quick assessments of
biodiversity that provides high quality data for developing conservation strategies
[48,49]. Large scale DNA barcoding studies are very much limited in bio-diverse
countries like India. In order to speed up the species inventories, DNA barcoding
should be utilized to promote conventional method of species identification.
1.8 DNA barcoding a promising tool for plant species identification
The emerging molecular technology known as DNA barcoding was proposed
by group of scientists lead by Paul Hebert at University of Guelph in Canada in
2003. The team discovered the use of DNA fragment from mitochondrial gene as a
universal ‘identification’ marker for animal species [50,51]. They targeted CO1 gene
(Cytochrome oxidase gene) as a DNA barcode system to identify animal life from
658 base pair fragment of the mitochondrial gene. This region has successfully been
19
implemented in DNA barcoding studies discriminating between species in 95% of
the cases [51,52].
Though the mitochondrial genome has a rapidly changing gene structure,
plant mitochondria has very little variation in most genera [53,54]. It transfer genes
between the nuclear, plastid and mitochondrial genomes in the angiosperms and
estimated over 1,000 previous horizontal transfer events of the CO1 gene. For these
reasons the mitochondria CO1 gene is unsuitable as a source for DNA barcoding in
plants. Therefore, the search for DNA barcodes for plants starts with chloroplast and
nuclear genome.
1.8.1 Characteristics of DNA barcodes
The selection of plant DNA barcoding region involves choosing one or a few
standard loci that can be sequenced routinely and reliably in very large and diverse
sample sets, resulting in easily comparable data which enable species to be
distinguished from one another. It is necessary for DNA barcode should possess
certain characteristics for using them as universal marker [55,56].
The ideal characteristics of DNA barcoding region is listed below,
DNA barcode should be a conserved region
DNA barcode should provide low intra-specific and ample inter-specific
variation
DNA barcodes should be short, universally and easily amplifiable across all
taxa
DNA barcode sequences should align readily and contain a limited number of
INDELS
20
1.9 Plant DNA barcoding
The focus for choosing a universal plant DNA barcode has began on
chloroplast because of high copy number and easy recoverability. Several coding and
non-coding regions were screened for the species identification of plants. The
historical overview of the search for a plant barcode is shown in Figure 1.9.1
(retrieved from Hollingsworth et al. [57]). The colours in figure represent an
informal measure of enthusiasm among DNA barcoding researchers in the
systematics community for CBOL and iBOL adoption of different markers [57]. The
dashed lines indicate the year of three international barcoding conferences in London
(2005), Taipei (2007) and Mexico City (2009). Based on the various studies different
markers were considered as barcodes for plant barcoding [58-66].
The use of DNA barcodes for species identification has led to the
establishment of an international initiative, the Consortium for the Barcode of Life
(CBOL) to develop and promote DNA barcoding. The CBOL established the Plant
Working Group (PWG) which joins researchers from the 50 countries and 6
continents. The main objectives of this group were to establish a suitable gene region
for DNA barcoding based on the multi-national studies, and to address the problems
of DNA barcoding. In 2009, CBOL plant working group officially announced rbcL
and matK marker as core DNA barcode for plant barcoding [54].
21
Figure 1.9.1 Screening of DNA barcodes from chloroplast and nuclear
genome. The symbol represents CBOL recommended marker. Retrieved
from Hollingsworth et al. [57]
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1.9.1 rbcL gene
The rbcL (ribulose-bisphosphate carboxylase) is part of a large subunit of the
RuBisCO protein in land plants. This protein consists of eight small subunits and
eight large subunits which are encoded by a single gene in the chloroplast [67].
RuBisCO is involved in photosynthesis and interacts with its substrates CO2, O2 and
ribulose 1,5 bisphosphate (RuBP) [67].
Figure 1.9.1.1 Schematic representation of rbcL gene (not drawn to scale) [68]Boxes denotes the coding regions, and the connecting lines represent intronregions
The coding region rbcL is situated between the atpB and trnR regions of
chloroplast genome [68] (Figure 1.9.1.1). The rbcL barcode consists of a 600 bp
region at the 59 end of the gene, located at bp 1–600 in the complete Arabidopsis
thaliana plastid genome sequence (gi 7525012:54958–56397). The rbcL sequences
have been used in various systematic studies and phylogenetic tree analysis [67,69].
1.9.2 matK gene
The chloroplast maturase K gene (matK) is situated within an intron of the
trnK gene (Figure 1.9.2.1) [70]. The gene is approximately 1,535 bp long and
encoded for group II intron maturase [71]. The matK barcode region consists of a ca.
841 bp region at the center of the gene, located between bp 205–1046 in the
complete A. thaliana plastid genome sequence (gi 7525012:2056–3570). Only a 600-
800 bp region of the matK gene are utilized for DNA barcoding [72].
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The matK gene evolves three times faster than rbcL [73] and several studies
suggest it can effectively discriminate between species in the angiosperms. It is also
widely used in many systematic studies.
Figure 1.9.2.1 Schematic representation of matK gene (not drawn to scale) [70,71,73] Boxes denotes the coding regions and the connecting lines representintron regions and intergenic spacer
The choice of rbcL and matK as a core DNA barcodes was based on the
straight forward recovery of the rbcL region and the discriminatory power of the
matK region. However, species level identification with rbcL and efficient PCR
success of matK are limited in many plant groups [57].
1.9.3 Multigene tiered approach
There is no single DNA barcode that can perform well for barcoding plants. It
is generally agreed that the multigene tiered approach would perform better than the
single maker in discriminating plant groups [54,64,74,75]. Newmaster et al. [75] and
Purushothaman et al. [76] described this as the multigene tiered approach wherein
barcodes are constructed from two ‘tiered’ gene regions; an easily amplified and
aligned region is used for the first tier (rbcL) that acts as a scaffold on which data
from a more variable second-tier region are interpreted for species identification.
The chloroplast rbcL was proposed as the first tier marker because of its
universality and demonstrated success for differentiating congeneric plant species
[58,63]. The second tier variable marker may be chloroplast trnH-psbA (non-coding)
and matK (coding) or nuclear ITS2. The rbcL+matK combination were reported to
give better discrimination than other marker, and the combination were gave
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appreciably greater species resolution than the other combination [57]. These coding
regions have easy alignable nature of the data that also facilitates character based
analyses and comparative analyses of DNA barcode diversity among taxonomic
groups and geographical regions. Other studies also supported the importance of
using combined analyses which increases the species identification success
[61,64,77].
1.10 DNA barcoding studies on tropical, subtropical and temperate forests
DNA barcoding has been used in many botanical studies ranging from
detailed study on single genus to ecosystem level surveys in tropical, subtropical and
temperate forests. DNA barcoding of 1,073 trees from tropical forest of French
Guiana suggested that it could increase the quality and the speed of biodiversity
surveys [77]. DNA barcoding was found to be useful for detecting errors in
morphological identifications and increased the identification rate of juveniles from
72% to 96%. DNA barcoding of 200 accessions from tropical forest plots in
Northeast Queensland also showed that it could rapidly estimate species richness in
forest communities [78]. Tripathi et al. [79] have studied 300 specimens from
tropical trees of North India, and suggested that DNA barcoding will be useful in
large-scale biodiversity inventories.
Vegetation surveys in four equally sized temperate forest plots in the Italian
pre-alpine region of Lombardy, Valcuvia by morphological identification and DNA
barcoding revealed that the later could save time and resources [80]. Parmentier et al.
[81] have assessed the accuracy of DNA barcoding in assigning a specimen to a
species or genus by studying 920 trees from five lowland evergreen forest plots in
Korup and Gabon, Africa. DNA Barcoding was found to be useful in assigning
unidentified trees to a genus, but assignment to a species was less reliable, especially
in species-rich clades. In a large study that included 2,644 individuals representing
490 vascular plant species, mostly from the Canadian Arctic zone, again showed that
DNA barcoding differentiated the taxa more at the genus level than at the species
level [82].
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In another interesting study of tropical forest, DNA barcoding was applied on
1,035 samples representing all the 296 species of a Forest Dynamics Plot on Barro
Colorado Island in Panama [83]. DNA barcode data from rbcL, matK and trnH-psbA
were found to be sufficient to reconstruct evolutionary relationships among the plant
taxa that were congruent with the broadly accepted phylogeny of flowering plants.
The same research group studied another Forest Dynamics Plot in the
Luquillo Mountains of Northeast Puerto Rico that encompassed a mix of old growth
and secondary forest that has been largely free from human disturbance since the
1940s. This study again reinforced the congruence of the barcode phylogeny with the
phylogeny of flowering plants as per APG III classification [84]. DNA barcoding
was also used to construct community phylogeny in order to understand the patterns
of species occurrence in forest habitats [85].
Community phylogeny which was constructed for the Dinghushan Forest
Dynamics Plot in China by sequencing rbcL, matK, and trnH-psbA loci from 183
species showed that closely related species tend to prefer similar habitats. The
patterns of co-occurrence within habitats are typically non-random with respect to
phylogeny. While phylogenetic clustering was observed in valley and low-slope,
phylogenetic over-dispersion was characteristic of high-slope, ridge-top and high-
gully habitats. However, there is no such large scale DNA barcode study has been
carried out in rich biodiversity country of India.
1.10.1 Tree Barcode of Life (Tree-BOL)
The importance of DNA barcoding of tree species was highlighted by 4th
International DNA barcode Conference in 2012. A global initiative “Tree-BOL,”
a Tree Barcode of Life as created to DNA barcode all tree species in the world. The
primary objective of the Tree-BOL is to DNA barcode 100,000 species of trees. The
main purpose of DNA barcoding is to monitor CITES-listed trees and medicinal
plants from the illegal trade of Africa.
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1.11 Need for reference DNA barcode library
Identification of plant species is of critical importance in conservation and
utilisation of biodiversity, but this may be hindered by a lack of taxonomic expertise
[86]. Therefore, establishment of an appropriate reference DNA barcode library is
essential for reliable species identification. DNA barcode library is primarily depends
on the authentic reference sequence from well identified voucher sample. Global
search engines like GenBank and Barcode of Life Database (BOLD) are commonly
used for the purpose of species identification. However, most of the DNA barcode
sequences in the GenBank database are not linked to voucher specimen for
verification and database curation is largely left in the hands of individual users,
making it difficult to detect and remove mis-identified specimens or contaminated
sequences [57].
In contrast, BOLD database addresses this issue they contains link between
vouchers, sequences, trace files and other metadata but it is poor in species richness,
especially for plants. The database needs to expand with DNA sequences for
successful species identification. Therefore, developing regional reference DNA
barcode library with authentic DNA sequence will be helpful to resolve these issues
and give accurate species identification. At the same time, reference DNA barcode
library will be highly useful in monitoring the rare and threatened species of
particular region. Developing regional reference DNA barcode library could be
effectively used for the floristic assessments that are essential for enforcing
conservation measures.
1.12 Benefits of DNA barcoding
DNA barcoding plays a crucial role in the plant systematics which will
accelerate the discovery of many new species in near future [9]. Specimen
identification involves assigning taxonomic names to unknown specimens using a
DNA reference library of morphologically pre-identified vouchers.
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DNA barcoding is well established method, and has been shown to bring
important benefits to applications such as monitoring illegally sourced wood
products from the forest [87] and medicinal plants identification [59,75,76,88-92].
One of the major problems in wood products identification is it does not possess the
diagnostic features required for plant identification and hence reliable identification
is extremely challenging. In these cases, DNA barcoding will help lawmakers to set
enforcement and to seize the illegal wood products particularly form CITES
appendix plants.
Instead of identifying the whole plants, many cases DNA barcoding is useful
in the identification of medicinal plant parts such as dried leaves, roots, seeds,
rhizomes, fruits, and powders [89-92] although it is difficult or impossible using
traditional morphological taxonomy. DNA barcoding will be helpful to promote the
conventional taxonomy by establishing species identification from any form of the
sample. It is highly desirable for rapid species identification, since it does not rely on
morphology of the plants, not affected by the external factors and identification can
be done from live or dead tissues.
Besides, DNA barcoding can also helps to develop the biological knowledge,
increases the research interest on conservation biology and understanding the
concepts of plant evolution. It helps many professions involve making or using plant
identifications such as taxonomists, ecologists, conservationists, foresters,
agriculturalists, forensic scientists, customs and quarantine officers [93]. DNA
barcoding strategies have been employed for the verification of plant products
ranging from medicinal plants [94] to kitchen spices [95], berries [96], and tea
products [97]. Ecological applications include the identification of invasive species
[98,99], and reconstruction of past vegetation and climate from plant remains in the
soil [100]. DNA barcoding have been used to create phylogenetic trees for use in
phylogenetic community ecology [83,84].
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1.13 Objectives of the study
Major objectives of this study includes,
To assemble a reference DNA barcode library for trees and medicinal plants
occurring in TDEF
To utilize the TDEF reference barcode library for species identification of
wood samples
To utilize the TDEF reference barcode library for species identification of
medicinal plant raw drugs