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«A Thesis Submitted for the Degree of PhD at the University of St. Andrews 2012 Full metadata for this item is available in ...»

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CONSERVATION ECOLOGY AND PHYLOGENETICS OF THE

INDUS RIVER DOLPHIN (PLATANISTA GANGETICA MINOR)

Gillian T. Braulik

A Thesis Submitted for the Degree of PhD

at the

University of St. Andrews

2012

Full metadata for this item is available in

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http://hdl.handle.net/10023/3036 This item is protected by original copyright This item is licensed under a Creative Commons License Conservation Ecology and Phylogenetics of the Indus River dolphin (Platanista gangetica minor) Gillian T. Braulik This thesis is submitted in partial fulfilment for the degree of Doctor of Philosophy at the University of St Andrews March 2012 Thesis Declaration

1. Candidate’s declarations:

I, Gillian T. Braulik, hereby certify that this thesis, which is approximately 75,000 words in length, has been written by me, that it is the record of work carried out by me and that it has not been submitted in any previous application for a higher degree.

I was admitted as a research student in October, 2006 and as a candidate for the degree of PhD in October, 2007. The higher study for which this is a record was carried out in the University of St Andrews between 2006 and 2011.

Date:

Signature of Candidate:

2. Supervisor’s declaration:

I hereby certify that the candidate has fulfilled the conditions of the Resolution and Regulations appropriate for the degree of PhD in the University of St Andrews and that the candidate is qualified to submit this thesis in application for that degree.

Date: Date:

Signature of Supervisor: Signature of Supervisor:

3. Permission for electronic publication:

In submitting this thesis to the University of St Andrews I understand that I am giving permission for it to be made available for use in accordance with the regulations of the University Library for the time being in force, subject to any copyright vested in the work not being affected thereby. I also understand that the title and the

Abstract

will be published, and that a copy of the work may be made and supplied to any bona fide library or research worker, that my thesis will be electronically accessible for personal or research use unless exempt by award of an embargo as requested below, and that the library has the right to migrate my thesis into new electronic forms as required to ensure continued access to the thesis. I have obtained any third-party copyright permissions that may be required in order to allow such access and migration, or have requested the appropriate embargo below.

Access to printed copy and electronic publication of thesis through the University of St Andrews.

–  –  –

ABSTRACT

ACKNOWLEDGEMENTS

CHAPTER 1 - GENERAL INTRODUCTION

1.1 SOUTH ASIAN RIVER DOLPHINS

1.1.1 Other River Dolphin Species and Populations

1.2 THE INDUS RIVER

1.2.1 Indus River Mega-fauna

1.3 PREVIOUS DOLPHIN RESEARCH

1.4 HISTORICAL INFORMATION ON INDUS RIVER DOLPHINS

1.4.1 Historical Distribution

1.4.2 Historical Abundance

1.5 DEVELOPMENT OF THE INDUS BASIN IRRIGATION SYSTEM

1.5.1 Barrage Construction

1.5.2 Water Diversion

1.6 CURRENT STATUS OF THE INDUS RIVER DOLPHIN

1.6.1 Present Distribution

1.6.2 Present Abundance

1.6.3 Encounter Rate

1.6.4 IUCN Red List Assessment

1.7 HABITAT USE

1.8 BEHAVIOUR

1.9 LIFE HISTORY

1.9.1 Growth

1.9.2 Sexual Dimorphism

1.9.3 Sexual Maturity

1.9.4 Calving

1.10 ECHOLOCATION

1.11 DIET

1.12 THREATS AND MANAGEMENT

1.12.1 Dolphin Hunting

1.12.2 Pollution

1.12.3 Fisheries Interactions

1.12.4 Canal Entrapment

1.12.5 Downstream Migratory Attrition

1.12.6 Freshwater

1.13 OBJECTIVES OF THIS STUDY

1.14 REFERENCES

CHAPTER 2 - ABUNDANCE OF INDUS RIVER DOLPHINS ESTIMATED USING

MARK-RECAPTURE FROM TANDEM VESSEL SURVEYS IN 2006

2.1 INTRODUCTION

2.1.1 Challenges to Survey Design on the Indus River

2.1.2 Indus River Dolphin Surveys

2.2 METHODS

2.2.1 Study Site

2.2.2 Field Survey Methods

2.2.3 Meeting Model Assumptions

2.2.4 Identification of Matched Groups

2.2.5 Abundance Estimation

2.2.6 Availability Bias

2.2.7 Bias in Group Size Estimates

2.2.8 Trends in Abundance

2.3 RESULTS

2.3.1 Survey Summary

2.3.2 Identification of Matched and Missed Dolphin Groups............. 81 2.3.3 Estimation of Abundance

2.3.4 Availability Bias

2.3.5 Group Size Bias

2.3.6 Trends in Abundance

2.4 DISCUSSION

2.4.1 Survey Design

2.4.2 Potential for Bias in Abundance Estimate





2.4.3 Abundance and Encounter Rate

2.4.4 Trends in Abundance

2.5 REFERENCES

5CHAPTER 3 - CAUSES AND DYNAMICS OF INDUS RIVER DOLPHIN RANGECOLLAPSE

3.1 INTRODUCTION

3.2 METHODS

3.2.1 Last Dolphin Sighting Date

3.2.2 Identifying the Causes of Range Decline

3.3 RESULTS

3.3.1 Interview Surveys

3.3.2 Last Dolphin Sighting Date

3.3.3 Dynamics of Range Decline

3.3.4 Causes of Range Decline

3.4 DISCUSSION

3.4.1 Dynamics of Range Decline

3.4.2 Causes of Range Decline

3.4.3 Implications for the Future

3.5 REFERENCES

CHAPTER 4 - HABITAT USE BY INDUS RIVER DOLPHINS IN THE LOW WATERSEASON

4.1 INTRODUCTION

4.2 METHODS

4.2.1 Data Sets

4.2.2 Habitat Models

4.2.3 Habitat Preference

4.3 RESULTS

4.3.1 Data Summary

4.3.2 Available Habitat

4.3.3 Dolphin Presence

4.3.4 Habitat Models

4.3.5 Habitat Preference

4.4 DISCUSSION

4.4.1 Available Habitat

4.4.2 Habitat Selection

4.4.3 Model Performance

–  –  –

CHAPTER 5 - HIGH LINEAGE DIVERGENCE AND LOW GENETIC DIVERSITY IN

GEOGRAPHICALLY ISOLATED POPULATIONS OF SOUTH ASIAN RIVER

DOLPHIN

5.1 INTRODUCTION

5.1.1 Platanista Nomenclature and Taxonomic Studies................. 184 5.1.2 Formation of the Indus and Ganges River Systems.............. 185 5.1.3 Phylogenetic Study and Conservation

5.2 METHODS

5.2.1 Sample Origin

5.2.2 Sample Collection

5.2.3 Genetic Diversity

5.2.4 Population Differentiation

5.2.5 Phylogeographic Patterns

5.2.6 Divergence Time Estimation

5.3 RESULTS

5.3.1 Molecular Diversity

5.3.2 Population Differentiation

5.3.3 Divergence Time

5.4 DISCUSSION

5.4.1 Lack of Variability

5.4.2 Divergence and Speciation

5.4.3 Conclusions

5.5 REFERENCES

CHAPTER 6 – GENERAL DISCUSSION

6.1 THESIS SYNTHESIS

6.2 ABUNDANCE ESTIMATION

6.3 PLATANISTA SPECIATION

6.4 INDUS DOLPHIN HABITAT AND ENVIRONMENTAL FLOWS

7 6.4.1 Dams

6.5 CLIMATE CHANGE

6.6 PROTECTED AREAS

6.7 MORTALITY MONITORING

6.8 MOVEMENT OF DOLPHINS THROUGH BARRAGES

6.9 DOLPHIN TRANSLOCATION

6.10 CONCLUDING REMARKS

6.11 REFERENCES

APPENDIX I – INTERVIEW QUESTIONNAIRE

APPENDIX II – LOCAL EVENTS CALENDAR USED TO REFINE DATES OF

HISTORICAL DOLPHIN SIGHTINGS

APPENDIX III – DETAILS OF CURRENT AND FORMER FRAGMENTS OF INDUS

DOLPHIN HABITAT

APPENDIX IV – CITES IMPORT AND EXPORT PERMITS

APPENDIX V - PLATANISTA ANCIENT DNA EXTRACTION LABORATORY

PROTOCOLS

–  –  –

List of Figures Figure 1.1 The geography and river systems of South Asia.

Figure 1.2 View of the Indus River looking downstream from Kotri barrage.

Figure 1.3 The Indus River system, and the location of irrigation barrages and dams.

Figure 1.4 Distribution of the Indus (above left) and Ganges (above right) River dolphins in the 1870’s.

Replicated from Anderson (1879).

Figure 1.5 Upstream view of Sukkur Barrage.

Figure 1.6 Aerial photo of the Indus River (flowing from right to left) at Sukkur barrage, illustrating the canals, barrage and change in flow above and below a barrage.

Figure 1.7 Timing of Indus dolphin habitat subdivision, and the decline in size of the longest portion of unfragmented Indus dolphin habitat.

Figure 1.8 Dry season (October to March) river discharge above each barrage (cubic feet per second) on the Indus River system in Pakistan.

Figure 1.9 Abundance and encounter rate of Indus River dolphins in each subpopulation in 2006.

Figure 1.10 Twenty kilometres moving average encounter rate of Indus River dolphins between Jinnah and Kotri Barrages.

Figure 2.1 Map of the Indus River system illustrating the barrages that form the boundaries between the five subpopulations.

Figure 2.2 Frequency of dolphin radial sighting distances.

Figure 2.3 Distance between the exact geographic positions of potentially matched dolphin groups.

Figure 2.4 Frequency of missed and matched sightings by a) group size and b) river state between Chashma and Taunsa barrages.

Figure 2.5 Frequency of missed and matched sightings by a) group size and b) river state between Guddu and Sukkur barrages.

Figure 2.6 Difference in group size estimates for matched sightings.

Figure 2.7 The time taken to estimate the number of dolphins in a group according to group size.

Figure 2.8 Natural logarithm of Indus River dolphin (Platanista gangetica minor) direct counts recorded between Guddu and Sukkur barrages between 1974 and 2008.

Figure 3.1 Map of the lower Indus River system, with rivers and barrages named, and each extant or extirpated Indus dolphin subpopulation numbered.

Figure 3.2 Proportion of respondents that had seen Indus dolphins according to age group.

Figure 3.3 Spatial and temporal dynamics of the Indus dolphin range decline.

Figure 3.4 Characteristics of river sections where river dolphins are present and where they have been extirpated.

Figure 3.5 Probability that an Indus dolphin subpopulation is extant according to proximity to the edge of the former range and the median dry season discharge (cubic feet per second).

Figure 3.6 Relationship between the number of years since a dolphin was sighted and a) subpopulation distance from historical range edge, and b) median dry season discharge, the two significant explanatory variables retained in quasi-Poisson GLM models of the temporal pattern of Indus dolphin range decline.

Figure 3.7 Probability that an Indus dolphin subpopulation is extant with increasing time of isolation Figure 4.

1 Illustration of a typical river cross-section and summary data calculated.

Figure 4.2 Illustration of two 5km segments of the Indus River and the river hydrogeomorphic features recorded.

Figure 4.3 Boxplots of channel geometry and river geomorphology characteristics in different sections of the Indus River.

Figure 4.4 Probability of Indus dolphin presence in relation to total channel crosssectional area (m2).

–  –  –

Figure 5.1 The Indus, Ganges, Brahmaputra and Karnaphuli River systems Figure 5.

2 Median-joining network based on complete MtDNA control region haplotypes for the cetacean Family Platanista.

Figure 5.3 Median-joining network based on partial cytochrome b sequence haplotypes for the cetacean Family Platanista.

Figure 5.4 Maximum likelihood bootstrap consensus tree representing the evolutionary history of Platanista.

Figure 5.5 Elevation of the Indus-Ganges River system drainage divide and of rivers near the divide List of Tables

–  –  –

11 Table 2.1 Summary of direct counts recorded in the Indus dolphin range-wide abundance survey in 2006.

Table 2.2 Comparison of difference distance thresholds used to identify matched and missed sightings.

Table 2.3 Summary of Indus dolphin subpopulation abundance estimation.

Table 2.4 Sighting availability of Indus dolphin groups.

Table 2.5 Comparison of direct counts of Indus River dolphin subpopulations recorded in 2001 and 2006 using identical survey methods.

Table 2.6 Comparison of dolphin encounter rates on the Indus River with those recorded for other river dolphins.

Table 3.1 Indus dolphin sighting records in the Punjab rivers since the 1920s.

Table 3.2 Details of extant and extirpated Indus dolphin subpopulations.

Table 3.3 Summary of spatial range decline model outputs.

Table 3.4 Summary of temporal range decline model outputs.



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