ANNEX 5: Contents of the handbook on aquatic biotelemetry

INTRODUCTION		1
I.	FISH USE OF TIME AND SPACE	2
1.1	Migration and “migration”: definition and relationship	3
1.2	Genetic fitness: comprehensive approach	4
1.3	Fitness: implications for migration	6
1.4	Methods of study of migration	7
	References	8
II.	METHODS OF STUDY OF FISH BEHAVIOUR	10
2.1	Methods of study independent of the catch	10
2.1.1	Visual observation	10
2.1.2	Resistivity fish counter	10
2.1.3	Hydroacoustics	11
2.2	Methods of study dependent of the catch	15
2.2.1	Variations in density and catch per unit of fishing effort	15
2.3	Tagging and types of marks and tags	17
2.3.1	Introduction	17
2.3.2	Types of marks and tags	18
2.4	Intrinsic biological marks	19
2.4.1	Morphometric and meristic variables and truss network	19
2.4.2	Pigmentation pattern	20
2.4.3	Genetic marks	20
2.4.3.1	Enzymatic polymorphism	20
2.4.3.2	Mitochondrial and nuclear DNA	21
2.4.3.3	Genetic fingerprinting	21
2.4.3.4	Main techniques used in genetic tagging	22
2.4.3.5	Choice of genetic marks	26
2.5	Extrinsic biological marks	27
2.5.1	Parasites	27
2.5.2	Chemometry	28
2.5.2.1	Fatty acids	28
2.5.2.2	Other extrinsic elements	29
2.6	Extrinsic tagging	30
2.6.1	Marking by mutilation	31
2.6.2	Extrinsic chemical marks	34
2.6.3	Marking with dyes	35
2.6.4	Marking by cold branding	36
2.7	Physical marks (“tags”)	37
2.7.1	Physical external tags	37
2.7.1.1	Intra-muscular insertion tags	37
2.7.1.2	Dangling and trans-structural tags	39
2.7.2	Physical internal tags	40
2.7.2.1	EVI (Elastomer Visible Implant) tag	40
2.7.2.2	VI tags.	41
2.7.2.3	Coded wire tags (CWTs)	42
2.7.2.4	Passive Integrated Transponders (PIT tags)	46
2.8	Active physical tags	48
	Biotelemetry transmitters, data storage tags	48
2.9	Choice of methos of study	48
	Bibliographic references	52
ANAESTHESIA, FISH TAGGING, BIASES RELATED TO TAGGING
III.	ANAESTHESIA	58
3.1	Types of anaesthetics, legal aspects	58
3.1.1	Chemical anaesthetics	58
3.1.2	Alternative methods	60
3.2	Stages of anaesthesia	62
3.3	Choice of an anaesthetic	62
3.4	Factors influencing anaesthesia, choice of concentration and duration	64
3.5	Physiological and fish behaviour changes due to anaesthesia	65
3.6	Suggestions to improve anaesthesia protocol and recovery	68
3.7	Instruction sheets for the main anaesthetics	69
IV.	ATTACHING TELEMETRIC TAGS	72
4.1	Introduction	72
4.2	External attachment	73
4.3	Intragastric insertion	74
4.4	Intraperitoneal implantation	75
4.4.1	Incision	76
4.4.2	Positioning the transmitter	77
4.4.3	Closing the wound: stitching	78
	How to stitch	78
	Types of suture	79
	Choice of suture material	80
4.4.4	Alternative methods to close the wound	81
4.4.5	Healing dynamics	83
4.4.6	Prophylaxy, post-operative measures	83
4.5	Weight, dimensions and shape of transmitters: biological restrictions	85
V.	BIASES RELATED TO TAGGING	86
5.1	Survival	86
5.2	Infections and injuries	87
5.3	Consequences on growth and feeding	88
5.4	Effects of tagging on behaviour and physiology	90
5.4.1	Buoyancy and balance	90
5.4.2	Swimming performances and energy consumption	90
5.4.3	Effects on social interactions	91
5.4.4	Activity and habitat selection	91
5.4.5	Other behavioural disturbances	92
5.5.	Rejection and loss of transmitters	92
5.5.1	Shedding of external tags	92
5.5.2	Regurgitation of intra-gastric tags	93
5.5.3	Expulsion of intraperitoneal implants	93
	Mechanism of implant exit	93
	Factors influencing implant exit	95
	CONCLUSIONS	96
	References	97
	Tracking and biotelemetry
	Signals properties, study strategies, use of results
VI.	BASIC PRINCIPLES, SIGNAL PROPAGATION	102
6.1	Specifics and common points of radio and acoustic biotelemetry	103
6.2	Acoustic signal propagation	104
6.2.1	Propagation speed, reflection, refraction	104
6.2.2	Losses related to propagation	105
6.2.3	Noise and decrease of signal/noise ratio	106
6.2.4	Calculation of the maximum reception range	107
6.3	Radio signal propagation	108
6.3.1	Attenuation of radio signals in the water	108
6.3.2	Attenuation in the air and at the air-water interface	109
6.3.3	Losses related to the receiving station	110
6.3.4	Losses and gains related to receiving and transmitting antennae	110
6.3.5	Power of transmitters, sensitivity of receptors	111
6.3.6	Calculation of the maximum reception range	112
6.4	Choice of radio type and transmission frequency according to the environment	113
VII.	POSITIONING THE TRANSMITTING SOURCE	115
7.1	Homing in	115
7.2	Distance positioning by triangulation	115
7.2.1	Basic principle	115
7.2.2	Calculation of cartesian coordinates	116
7.2.3	Triangulation by directional receiving stations	117
7.2.4	Accuracy of positioning by triangulation	117
7.2.5	Reception diagrams and optimisation of the use of directional antennae	118
	Use of a loop antenna	119
	Use of a Yagi antenna	119
7.3	Positioning of combined acoustic /radio transmitters by a single operator	120
7.4	Positioning of acoustic transmitters by hyperbolic navigation	121
7.5	Software for pre-analysis of radio-tracking data “X-Y PGM track”	121
7.5.1	Working principle	121
	General remarks	122
7.5.2	Complementary explanation	122
	Part A	122
	Part B	122
	Part C	123
	Part D	124
	Part E	124
7.5.3	Program list	125
VIII.	STUDY STRATEGY	129
8.1	Data collection frequency	129
8.1.1	Continuous collection	129
8.1.2	Periodic collection (daily or more than daily)	129
8.1.3	Periodic collection (less than daily)	131
	Manual monitoring	131
	Automatic detection	131
8.2	Technical limitation of the number of fish that can be detected	132
8.3	Improvement in detection performance	134
8.3.1	Multi-antenna stations	134
8.3.2	Coded transmitters	136
8.4	Transmitter search, progression speed	136
IX.	CALCULATION OF THE HOME RANGE AND THE ACTIVITY AREA	138
9.1	The convex polygon method	138
9.1.1	Principle	138
9.1.2	Limitations	138
9.2	Bivariate normal models and circular statistics	138
9.2.1	Principle	138
9.2.2	Limitations	139
9.3	Grid methods and probability of use by the species	140
9.3.1	Principle	140
9.3.2	Limitations	140
9.4	Comparison of the different methods	142
9.5	Calculation of a convex polygon surface area	142
X.	BIOTELEMETRY, PROGRAMMABLE TAGS AND SPECIAL APPLICATIONS	144
10.1	Introduction	144
10.2	Measurement of biotelemetry signals	144
10.3	Drawbacks specific to biotelemetry transmitters	147
10.4	Programmable transmitters	148
10.5	Examples	150
10.5.1	Telemetry application in aquaculture	150
10.5.2	Repeated reproductive homing in Barbus barbus	152
10.5.3	Activity of and habitat selection by eel (Anguilla anguilla)	153
10.5.4	Use of cardiac rhythm as a metabolic indicator	155
XI.	SYNTHESIS, CONCLUSION, PRACTICAL ASPECTS	157
11.1	Structure a study or a project	157
	Study objective	157
	Fish	157
	Environment	157
	Calculation of the total study cost, determination of financial feasibility	157
11.2	Information, reward	158
11.3	Risks inherent to biotelemetry methods	158
	References	159