! 16!

Introduction

! 17!

Recent assessments of the conservation status of many wildlife species indicate an

alarming rate of population decline on a global scale (Ceballos et al., 2005; Schipper

et al., 2008; Karanth and Chellam, 2009). Due to ongoing natural and anthropogenic

processes such as climate change, land use practices, human persecution, habitat

conversion and overexploitation, many of these species had faced severe decline in

population sizes, range contractions and in some cases extinction (Ceballos et al.,

2005), thereby engendering significant efforts at their recovery. Such efforts require

demographic, behavioural, genetic and life-history information of a species of interest

(Flagstad et al., 2003; Miller and Waits, 2003; Leonard et al., 2005) at ecological time

scales, over which various population processes, for e.g. demographic changes,

migration, local extinction, colonization etc. occur (Martin and Simon, 1990; Carroll

et al., 2007). Acquiring this information in the wild can however be problematic for

most species, and particularly challenging when endangered, rare, cryptic and elusive

species are involved. Given that many biodiversity hotspots are subject to a multitude

of pressures, including habitat degradation, conflict with agriculture, hunting, disease

and commercial trade (Sillero-Zubiri and Laurenson, 2001) globally, it is very

important to integrate ecological, demographic and genetic approaches to study rare,

elusive species for their future survival.

Large carnivores, for example, represent one such group of endangered and

rare species. As top predators, large carnivores play very critical role in maintaining

their structure and diversity and thus actively shape ecological interactions in

biological communities (Terborgh et al., 2001; Steneck, 2005). Generally due to high

trophic level, low population densities, slow life histories and affected by negative

anthropogenic impacts, they are predisposed to high extinction risk (Purvis et al.,

2000; Cardillo et al., 2005). This is clearly evident in current global evaluation of

! 18!

terrestrial mammals, which suggests endangered predatory carnivores within the

families Felidae, Canidae and Ursidae are the most threatened due to severe decline

in population size and range contractions (Ceballos et al., 2005; Schipper et al., 2008).

Currently most of the large carnivore species are considered endangered globally

(Fuller, 1995) and are major targets for conservation efforts (Weber and Rabinowitz,

1996) across global carnivore biodiversity hotspots. This decline scenario is

particularly severe for the family Felidae, where except for the domestic cat (Felis

catus) all other species are either classified as threatened or endangered (Nowell and

Jackson, 1996).

The tiger (Panthera tigris) typifies large feline carnivores severely threatened

by human impacts. Tigers as a species historically occurred across 30 present-day

nations ranging from Eurasia from the Sunda Islands, west through the Indian

subcontinent to the Indus river and north along the Pacific seaboard to 60° north

latitude and a wide swath of central Asia from the Russian Far East to eastern Turkey

(Nowell and Jackson, 1996; Sanderson et al., 2006). This huge range encompassed a

variety of habitats, including taiga and boreal forests, tropical evergreen, moist and

dry deciduous forests, alluvial grasslands and mangroves. However, this wide

distribution was primarily influenced by environmental changes associated with

Pleistocene glaciation events (Kitchener and Dugmore, 2000) and further drastically

depleted by intense human activities in the form of habitat loss, prey decline and

direct hunting (Sanderson et al., 2006). With only five of the eight genetic subspecies

surviving now (Luo et al., 2004), current global estimates of wild tigers range from

3000–3500 individuals restricted to only 7% of their historical range (Sanderson et

al., 2006; Morell, 2007). High adaptability and fecundity in different habitat types,

climatic regimes, landscapes and prey bases have allowed tigers to survive this

! 19!

massive onslaught and habitat loss during last couple of centuries (Schaller, 1967;

Sunquist et al., 1999). Globally most of the remaining tiger populations now persist in

relatively small populations (between 20-100 individuals) that are confined to often

spatially isolated, patchy forests (Sanderson et al., 2006; Ranganathan et al., 2008).

While negative anthropogenic impacts on tigers, their prey, and habitats continue,

impending local extinctions of isolated small populations, if unnoticed, will threaten

long-term survival of the species. However, conservation efforts through studying

distribution, ecology and demography of remaining tiger populations have posed

serious challenges to researchers due to their elusive nature, large home ranges and

low densities. Traditional approaches such as radio tracking, and subsequently non-

invasive photographic capture-recapture methods were used successfully to study

tiger ecology in different parts of their range (Smith et al., 1987; Smith, 1993;

Karanth et al., 2004; Wegge et al., 2004; Kawanishi and Sunquist, 2004; Simchareon

et al., 2007). However, these long-standing approaches require years of intensive

fieldwork and associated technical and logistical concerns, which could limit their

utility while studying such endangered species (Gros et al., 1996; Gese, 2001).

In recent years, non-invasive genetic sampling has emerged as an alternative

option to solve some of the problems associated with the study of rare, endangered or

cryptic species (Taberlet et al., 1999; Waits, 2004). The characterization of non-

invasive materials using molecular markers has allowed biologists to study species at

the population level and below in a myriad of contexts such as species identification

(Symondson, 2002), individual identification (Taberlet and Luikart, 1999),

relatedness and kinship patterns (Oka and Takenaka 2001; Ross 2001), dispersal

patterns and individual movements (Gagneux et al., 2001; Stow et al., 2001),

inferring population structure (Pritchard et al., 2000), population assignment

! 20!

(Blanchong et al., 2002), phylogeography (Avise, 2000), population size estimation

(Schwartz et al., 1999; Mills et al., 2000; McKelvey and Schwartz, 2004a,b; Paetkau,

2004; Lukacs and Burnham, 2005a,b and Miller et al., 2005), sex determination

(Shaw et al., 2003), dietary analysis (Farrell et al., 2000) and wildlife forensics

(Palumbi and Cipriano, 1998). The success of these approaches has been instrumental

in the emergence of conservation genetics as a recognizable sub-discipline of

conservation biology over the last decade. Surprisingly, however, to date relatively

few studies have been carried out using exhaustive population sampling based on only

non-invasive material (Buchan et al., 2003; Goossens et al., 2005; Zhan et al., 2006),

possibly due to concerns about the financial and logistical constraints involved in

collecting and processing very large numbers of samples in this way. However, recent

technological and theoretical advances in non-invasive population genetic and

analytical approaches make DNA-based population studies for rare and cryptic

species economically and logistically feasible (Beja-Pereira et al., 2009; Goossens

and Bruford, 2009). Given these facts, studying tigers through non-invasive genetic

approaches appears to be a potentially attractive tool, along with other standard

approaches to gain a better understanding of the remaining populations at different

scales.

With about 60% of the overall wild population retained in an estimated 8-25%

of remaining global habitat, currently the Indian subcontinent is the most important

stronghold for tigers (Sanderson et al., 2006; Ranganathan et al., 2008; Jhala et al.,

2008). However, like many other species, intense human activities have resulted in

severe population decline of tigers and at times local extinction (for e.g. Sariska,

Panna) during the last couple of centuries (Rangarajan, 2006; Karanth et al., 2010).

Subsequently, conservation efforts have typically focused on maintaining viable

! 21!

number of individuals within populations and increasing local tiger population sizes

in different habitats across the subcontinent through detailed studies on spatial

distribution, habitat diversity, ecology, population dynamics and tiger population

monitoring at local scales (Karanth et al. 2004; Karanth et al. 2006; Karanth et al.,

2008; Karanth et al., 2011). Studies on historical presence/absence models indicate a

much higher population size and high degree of tiger habitat connectivity in historical

compared with modern times in the Indian subcontinent (Karanth et al., 2010).

However, the effect of severe decline in tiger population size and habitats during last

two centuries on current genetic variation and population structure is unknown. It can

be expected that such decline in population size and habitat continuity would result in

loss of genetic variation and increased genetic differentiation, due to decreased gene

flow between tiger populations. Limited phylogeographic studies (Luo et al., 2004;

Sharma et al., 2008) till date revealed only moderate levels of variation in extant

Indian tigers, in spite of more than half of the global population and the most varied

habitat conditions occurring in this region. It is critical to adequately assess the

genetic makeup and diversity of historical and remaining tiger populations, and

understand their relevance from a future conservation perspective in the Indian

subcontinent. Studying genetic variation at the population level is fundamentally

important in the understanding of a species’ ecology and evolution as genetic

diversity retains the history of a species, and is vital for survival and future adaptation

to changes (Steneck, 2005). Low genetic variation can increase extinction risk (for e.g.

Saccheri et al., 1998) for species with small populations (Frankham, 1996), and a

detailed study focusing on current and historical patterns of tiger genetic variation and

population structure will be extremely important to evaluate the evolutionary potential

of the remaining smaller populations across the subcontinent.

! 22!

Given that currently tigers in the subcontinent persist in small populations,

another crucial parameter of interest is within population dynamics such as

distribution, population estimation, genealogical relationships and inbreeding at

different geographical scales. Such information is fundamental to understanding

behavioural and ecological attributes of populations and hence has significant

influence on management decisions. As previously mentioned, these are difficult

parameters to estimate for wild tigers using traditional approaches (for e.g. camera

trapping) at large landscapes due to logistical and technical concerns. Moreover, some

of the important population parameters for e.g. relatedness among individuals,

inbreeding cannot be estimated using standard field techniques. Although field-based

long-term studies at local scales have been instrumental in understanding tiger

distribution patterns, dispersal, social structure and population estimation (Smith,

1987; Smith, 1993; Karanth et al. 2004; Karanth et al. 2006; Karanth et al., 2008;

Karanth et al., 2011), use of genetic approaches to study Indian tigers has been only

limited to individual identification (Bhagavatula and Singh 2006). Further studies

need to include large-scale non-invasive sampling and appropriate genetic approaches

to explore above-mentioned population parameters in Indian tigers. Ideally, such

interdisciplinary approaches including ecological, demographic and genetic

information should be used to prioritize conservation efforts for the future survival of

the species.

Given the above background, the aims of the present study are as follow:

1. To assess phylogeography and demographic history of the Indian tigers.

2. To compare historical tiger genetic variation with the modern ones and to

evaluate historical and contemporary patterns of population structure.

! 23!

3. To estimate relative population abundance of tigers using genetic individual

identification and capture-recapture approach at a local scale.

4. To develop molecular approaches to ascertain distribution and demography of

tigers and leopards over large landscapes.

5. To assess genetic relatedness among individual tigers within and between two

adjacent tiger populations in Mysore-Malenad Tiger Landscape, Western

Ghats.

These aims are specifically described in the thesis chapters that follow. The first and

second question is examined in Chapter 1 and 2, the third question in Chapter 3, while

the fourth and fifth questions are addressed in Chapter 4.

Overall, the findings of this study will link the use of molecular tools and data

to long-term ecological and demographic approaches to help understanding tiger

biology at different ecological scales. Resulting information from demographic,

ecological and genetic considerations should provide deeper insights to factors that

will be critical to site-based tiger conservation in the Indian subcontinent and other

regions. Finally, the genetic approaches and tools developed in this study will have

immense potential for application for many more endangered species across the globe.

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