Ecological and Genetic Factors in the Distribution and Abundance of Larval Lake Whitefish

237 Pages·2015·8.77 MB·English

Ecological and Genetic Factors in the Distribution and Abundance of
Larval Lake Whitefish (Coregonus clupeaformis)
at Douglas Point, Lake Huron

by

Lauren M. Overdyk

A Thesis
presented to
The University of Guelph

In partial fulfilment of requirements
for the degree of
Doctor in Philosophy
in
Integrative Biology

Guelph, Ontario, Canada

© Lauren Overdyk, July, 2015
ABSTRACT

ECOLOGICAL AND GENETIC FACTORS IN THE DISTRIBUTION AND
ABUNDANCE OF LARVAL LAKE WHITEFISH (COREGONUS
CLUPEAFORMIS) AT DOUGLAS POINT, LAKE HURON

Lauren M. Overdyk Advisors:
University of Guelph, 2015 Professor Stephen S. Crawford
Professor Robert H. Hanner

Lake Whitefish are an ecologically, economically and culturally important fish
species in the Laurentian Great Lakes. Although much research has been conducted on
spawning-phase adult Lake Whitefish, little research has paid attention to the ecology of
larval Lake Whitefish, especially in the source waters of Bruce Nuclear Generating
Station. This PhD thesis incorporates key ecological and methodological uncertainties
into understanding the effects of environmental conditions on the ecology of larval Lake
Whitefish at Douglas Point, Lake Huron. The result is a set of novel ideas and the
development of novel methods to help answer this question. Chapter 2 investigates the
effects of environmental conditions on the distribution and abundance of zooplankton as
a necessary first step in understanding the ecology of larval Lake Whitefish. Chapter 3
evaluates the consistency between DNA barcoding and visual identification methods
using a case study of larval fish caught in plankton tows at Stokes Bay, Lake Huron. This
evaluation strongly supports the use of DNA barcoding in combination with visual
identification to improve the accuracy and precision of species identification. Chapter 4
explores genetic haplotype variation of Lake Whitefish from Lake Huron using DNA
barcodes from spawning-phase Lake Whitefish collected at 28 sites around Lake Huron
during Fall 2012. While this study did not detect any cryptic lineages of Lake Whitefish
in Lake Huron, it did reveal the presence of rare barcode haplotypes that seem to be
unique to specific sampling sites. Chapter 5 develops a novel, real-time PCR assay to
specifically identify Lake Whitefish in larval fish assemblages. This technique can further
increase the speed of identification of Lake Whitefish. Finally, Chapter 6 investigates the
effects of environmental conditions on the distribution and abundance of larval Lake
Whitefish in nearshore embayments at Douglas Point, Lake Huron. Ultimately, the new
knowledge of larval Lake Whitefish ecology generated in this thesis should be seriously
considered by Canada/Ontario, First Nations and Industry as they work together to
evaluate effects of the existing Bruce Nuclear Generating Station, and the Deep Geologic
Repository for Nuclear Waste that has been proposed for construction at Douglas Point,
Lake Huron.
ACKNOWLEDGEMENTS

There are many people to whom I owe a debt of gratitude over the last four years,
some of who were instrumental in the success of this research and some of who were
entrusted with keeping my sanity and spirits high. Firstly, I would like to thank Dr. Steve
Crawford and Dr. Bob Hanner - my two academic ‘dads’ - who shared their very
different areas of expertise with me, took me under their wing and taught me invaluable
skills. Although the last four years have not always been easy, I am grateful for the
experiences and advice you both have provided.

Secondly, I would like to thank the Saugeen Ojibway Nation (Chippewas of
Nawash Unceded First Nation, Saugeen First Nation) in collaboration with Bruce Power
Limited who supported this research. Specifically, I would like to thank Ryan Lauzon,
(Nawash Fisheries Assessment Program) for his assistance in the field. I would also like
to thank the members of my advisory committee, Dr. Neil Rooney and Dr. Dan Gillis, for
being available to discuss research and life, and for always offering support. With this I
would also like to thank my Crawford lab mates Kathleen Ryan, Colleen Parker, Natalie
Schott, Dr. Andrew Binns and Dr. Shoshanah Jacobs for being academic sounding
boards. I would also specifically like to thank Laura Trout for her support and help in
preparation for my qualifying exam.

The two field seasons in this thesis (Chapters 2 and 6) would not have been
possible with out the assistance of many people. I would like to thank Ashley Wincikaby
and Lindsey Boyd for their hard work and dedication to the collection of my field data.
Lindsey, thank you for being my purse and nerding out over fish as much as me. Your
friendship and support of my work has been invaluable. I would like to thank the
expertise of René Lauzon for his work on our boat and Bill McKeag from the Kincardine
Marina. I would also like to thank Steve Wilson from the physics department for creating
custom tow frames for both the 2013 and 2014 field seasons. I also owe a special thanks
to Bill Thorne, Shannon Snyder and the staff of the Inverhuron Provincial Park. Without
your assistance, kindness and hospitality, my field seasons may not have been possible.
A special thanks to the members of the Lake Huron Fishing Club, especially Mike Hahn,
Eugene Lo, Brian Garnet and Norm Dobson. I would like to thank Dr. Beatrix Beisner
and Katherine Velghe (Université du Quebéc à Montréal – UQAM) for processing water
quality samples and offering advice on field sampling design. A special thanks to Dr.
Josef Ackerman and Dr. Karl Cottenie (University of Guelph) for providing advice for
the completion of these two chapters.

Chapters 3, 4 and 5 would not have been possible without the assistance and
guidance of the following people. For Chapter 3 specifically I would like to thank
members of the Hanner Lab, including Natasha Serrao, Danielle Ondrejicka, Jeff Strohm,
Amanda Naaum, Andrew Frewin and Heather Braid. Special thanks to Colette Ward and
Erling Holm for sharing their expertise with Great Lakes ichthyoplankon, to Justin
Angevaare for advice with statistical analyses, to Colleen Parker for assistance with fish
tissue preparation, to Joan Hewer and anonymous reviewers for edits. Special thanks for
AAC Genomics for sequencing and the Royal Ontario Museum. For Chapters 4 and 5

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specifically I would like to thank Nikole Freeman, Kelly Mulligan, Grace Burke,
Rebecca Eberts (University of Regina), Chris Somers (University of Regina), Wendy Lee
Stott (USGS), Tim Drew (White Lake Fish Culture Station, Sharbot Lake), Cadence
Cumpseth and Chris Ho (BOLD for bioinformatics support). For Chapter 5 I would also
like to thank Dr. Cameron Turner and an anonymous reviewer for comments leading to a
substantial improvement of this manuscript.

I would like to thank my family (Adrian, Karen and Lisen) and close friends for
supporting me through my academic career, especially these last four years. The highs
have been high and the lows have been low and I thank you for sticking by my side
through it all. I appreciate you trying to understand what I have been doing and being
excited about fish even when you weren’t. Last but not least, I thank my partner in crime,
James Langdon for your unwavering support and patience in this final year. Not only did
you brave the frigid waters of Lake Huron in late September for me and my research, but
you were a constant in ensuring I was always at my best. Your contagious cheerleading
has helped me cross the finish line, and for this I am more grateful than you will ever
know.

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TABLE OF CONTENTS

Abstract……………………………………………………………………………………ii

Acknowledgements………………………………………………………………………iii

Table of Contents………………………………...………………………………………..v

List of Figures…………………………………………………………………………...viii

List of Tables……………………………………………………………………….……xii

Chapter 1. Prologue………………………………………..…………………………….1

1.2. References………………………………………..…………………………...9

Chapter 2. Effects of environmental conditions on the distribution and abundance
of zooplankton at Douglas Point, Lake Huron………………………………………..18

2.1. Abstract……………………………………………………………………...18
2.2. Introduction………………………………………………………………….19
2.3. Materials and Methods………………………………………………………24
Sample Design…………………………………………………………...24
Environmental Conditions……………………………………………….25
Water Samples…………………………………………………………...26
Laboratory Analyses……………………………………………………..26
Statistical Analyses………………………………………………………28
2.4. Results……………………………………………………………………….29
Effect of Space-Time on Environmental…..…………………………….29
Effect of Space-Time/Environment on Particle Size Frequency………...30
Effect of Space-Time/Environment on Zooplankton Size Frequency…...31
2.5. Discussion…………………………………………………………………...33
Effect of Space-Time on Environment…………………………………..33
Effect of Space-Time/Environment on Particle Size Frequency………...34
Effect of Space-Time/Environment on Zooplankton Size Frequency…...35
Hypotheses and Predictions……………………………………………...36
2.6. References…………………………………………………………………...42
2.7. Appendices
Appendix 2.1. Larval Lake Whitefish (Coregonus clupeaformis) Gape
Size……………………………………………………………………….65
Appendix 2.2. Larval Burbot (Lota lota)……………...…………………67
Appendix 2.3. Environmental Variables and Particle Size/Zooplankton
Frequencies Observed for all Stations and Samples over weeks 1-3 for the
Inverhuron (IH) transect at Douglas Point, Lake Huron in 2013………..68
Appendix 2.4. Historic Sampling of phyto and nonicththyo-zooplankton at
Douglas Point, Lake Huron………………………………………………73

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Appendix 2.5. Larval Lake Whitefish (Coregonus clupeaformis) Diet.…82

Chapter 3. Increased taxonomic resolutions of Laurentian Great Lakes
ichthyoplankton through DNA barcoding: A case study comparison against visual
identification of Stokes Bay, Lake Huron ichthyoplankton………………………….84

3.1. Abstract……………………………………………………………………...84
3.2. Introduction………………………………………………………………….85
3.3. Materials and Methods………………………………………………………88
3.4. Results……………………………………………………………………….90
3.5. Discussion…………………………………………………………………...92
Concluding Remarks……………………………………………………..96
3.6. References…………………………………………………………………...98
3.7. Appendices…………………………………………………………………109
Appendix 3.1. ROM Catalogue Numbers………………………………109

Chapter 4. Extending DNA barcoding coverage for Lake Whitefish (Coregonus
clupeaformis) across the three major basins of Lake Huron……………………….111

4.1. Abstract…………………………………………………………………….111
4.2. Introduction………………………………………………………………...112
4.3. Materials and Methods……………………………………………………..114
Specimen Collection……………………………………………………114
DNA Barcoding………………………………………………………...115
Haplotype Analysis……………………………………………………..116
4.4. Results……………………………………………………………………...117
4.5. Discussion………………………………………………………………….118
4.6. References………………………………………………………………….121

Chapter 5. Real-Time PCR Identification of Lake Whitefish (Coregonus
clupeaformis) in the Laurentian Great Lakes……………………………………….127

5.1. Abstract…………………………………………………………………….127
5.2. Introduction………………………………………………………………...128
5.3. Materials and Methods……………………………………………………..131
Sample Collection and DNA Extraction………………………………..131
DNA Barcoding………………………………………………………...132
Real-time PCR………………………………………………………….133
5.4. Results……………………………………………………………………...137
5.5. Discussion………………………………………………………………….139
5.6. References………………………………………………………………….142

Chapter 6. The effect of environmental conditions on the distribution and
abundance of larval Lake Whitefish (Coregonus clupeaformis) in nearshore
embayments at Douglas Point, Lake Huron…………………………………………156

6.1. Abstract…………………………………………………………………….156

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6.2. Introduction………………………………………………………………...157
6.3. Materials and Methods……………………………………………………..161
Study Design……………………………………………………………161
Species Identification…………………………………………………...165
Statistical Analyses……………………………………………………..167
6.4. Results……………………………………………………………………...168
Species Identification…………………………………………………...168
Larval Distribution and Abundance…………………………………….169
Effect of Space-Time on Environment…………………………………170
Effect of Space-Time/Environment on Ichthyoplankton Standard
Density………………………………………………………….171
Serendipitous Samples of Ichthyoplankton.............................................173
6.5. Discussion………………………………………………………………….173
Species Identification…………………………………………………...173
Larval Distribution and Abundance…………………………………….174
Effect of Space-Time on Environment…………………………………177
Effect of Space-Time/Environment on Ichthyoplankton Standard
Density………………………………………………………….177
Serendipitous Samples of Ichthyoplankton. …………………………...179
Hypotheses and Predictions…………………………………………….181
6.6. References………………………………………………………………….186
6.7 Appendices………………………………………………………………….209
Appendix 6.1. Non-Lake Whitefish ichthyoplankton distribution and
abundance…………………………………………………..…..209

Chapter 7: Epilogue…………………………………………………………………...210

7.2. References……………………………………………………………….…218

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LIST OF FIGURES

CHAPTER 1: Prologue

Figure 1.1. Location of Douglas Point within Lake Huron (black square and inlay). Map
shows location of Bruce Nuclear Generating Station sites A and B along with
intakes (stars) and discharges (arrows) for each station…………………………14

CHAPTER 2: Effects of environmental conditions on the distribution and
abundance of zooplankton at Douglas Point, Lake Huron.

Figure 2.1. Map of Douglas Point, Lake Huron showing the 2013 sampling transect (DP=
Douglas Point, BO=Outflow for BNGS ‘B’, BI=intake for BNGS ‘B’,
IH=Inverhuron Bay, MP=McRae Point). Circles represent sampling stations at
3m, 10m, 20m and 40m for each transect, with the exception of the discharge
(BO) where strong currents prevented effective sampling at the 3m depth. Stars
indicate location of cooling water intake for BNGS ‘A’ and ‘B’ facilities. Grey
arrows indicate discharge outflows of cooling water systems…………………...51

Figure 2.2. Biplot of the Redundancy Analysis after a forward selection of the
relationship between space-time variables on environmental conditions sampled at
Douglas Point, Lake Huron in 2013. Space-time variable and environmental
condition abbreviations correspond to those in Table 2.2….……………………52

Figure 2.3.A-C. Water temperatures (°C) sampled at the 20m station depth for all sample
depths (1,5,15m) over five weeks for transects (A) Inverhuron (IH), (B) Intake B
(BI) and (C) Outflow B (BO) respectively at Douglas Point, Lake Huron sampled
in 2013……………………………………………………………………………53

Figure 2.4. Uniplot of the Redundancy Analysis after a forward selection of the
relationship between space-time and environmental conditions on particle size
sampled at Douglas Point, Lake Huron in 2013. Space-time variable and
environmental condition abbreviations correspond to those in Table 2.2...……..54

Figure 2.5. Uniplot of the Redundancy Analysis after a forward selection of the
relationship between space-time variables and environmental conditions on
zooplankton frequency by size sampled at Douglas Point, Lake Huron in 2013.
Space-time variable and environmental condition abbreviations correspond to
those in Table 2.2………………………………………………………………...55

Figure 2.6.A-C. Zooplankton frequency sampled at the 20m station depth for all sample
depths (1,5,15m) over five weeks for transects (A) Inverhuron (IH), (B) Intake B
(BI) and (C) Outflow B (BO) respectively at Douglas Point, Lake Huron sampled
in 2013……………………………………………………………………………56

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CHAPTER 2: Appendices

Figure A2.1. Ventral view of larval Lake Whitefish (Coregonus clupeaformis) showing
lower maxillary (limiting gape width) with line indicating widest part of gape.
Scale is 1mm. Widths measured using Image J software………………………..66

Figure A2.2. Images of larval Burbot (Lota lota) collected on 05 July 2013 (Week 3) on
the Douglas Point (DP) transect, station depth of 40m, at a sample depth of 15m
in Lake Huron. Scale =1mm. (A – dorsal, B-ventral). Larval fish was identified
as Lota lota by DNA Barcoding…………………………………………………67

Figure A2.3.1 A-D: Temperature (oC) observed for all stations (3, 10, 20, 40m, A-D
respectively) and samples (1, 5, 15m when available) for the Inverhuron (IH)
transect at Douglas Point, Lake Huron in 2013 across weeks 1-3……………….69

Figure A2.3.2 A-D: Dissolved oxygen (mg L-1) observed for all stations (3, 10, 20, 40m,
A-D respectively) and samples (1, 5, 15m when available) for the Inverhuron (IH)
transect at Douglas Point, Lake Huron in 2013 across weeks 1-3……………….70

Figure A2.3.3 A-D: Total particle frequency observed for all stations (3, 10, 20, 40m, A-
D respectively) and samples (1, 5, 15m when available) for the Inverhuron (IH)
transect at Douglas Point, Lake Huron in 2013 across weeks 1-3……………….71

Figure A2.3.4 A-D: Total zooplankton frequency observed for all stations (3, 10, 20,
40m, A-D respectively) and samples (1, 5, 15m when available) for the
Inverhuron (IH) transect at Douglas Point, Lake Huron in 2013 across weeks
1-3………………………………………………………………………………..72

CHAPTER 3: Increased taxonomic resolutions of Laurentian Great Lakes
ichthyoplankton through DNA barcoding: A case study comparison against visual
identification of Stokes Bay, Lake Huron ichthyoplankton.

Figure 3.1 Diagram of a larval Lake Whitefish (Coregonus clupeaformis) indicating
morphological characteristics, especially mensural and meristic features used in a
dichotomous key for ichthyoplankton of the Great Lakes basin. Adapted from
Faber 2006-13 www.fishbabies.ca……………………………………………...102

CHAPTER 4: Extending DNA barcoding coverage for Lake Whitefish (Coregonus
clupeaformis) across the three major basins of Lake Huron.

Figure 4.1. DNA barcode haplotype variation found in Lake Whitefish (Coregonus
clupeaformis) across North American ecoregions. Each colour represents a
different haplotype. Haplotypes were included from Yukon River, Swan Lake, St.
Laurence River, Sharbot Lake, and Lake Huron. The size of each pie chart is
proportional to the sample size from each location; however, the most dominant
haplotype (A) has been excluded from Lake Huron for the purpose of

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visualization of the less prevalent haplotypes, but all haplotypes for Lake Huron
can be seen in Figure 4.2………………………………………………………..124

Figure 4.2. DNA barcode haplotype variation found in Lake Whitefish (Coregonus
clupeaformis); site numbers correspond to Table 4.1 and L1 and L2 are two sites
sampled in BOLD project Stokes Bay, Ontario, Lake Whitefish [SBOLW]. (A)
Haplotype network analysis of DNA barcode sequences from across North
America; the size of the nodes corresponds to the number of individuals that share
each haplotype; the colour of each unique haplotype corresponds to the pie charts
in B; (B) Geographic distribution of haplotypes from Lake Huron at each site
sampled during 2012, the size of each pie chart is proportional to the sample size
from each location. MB=Main Basin, GB=Georgian Bay, NC= North
Channel…………………………………………………………………………125

CHAPTER 5: Real-Time PCR identification of Lake Whitefish (Coregonus
clupeaformis) in the Laurentian Great Lakes.

Figure 5.1. Standard curve generated from 10-fold serial dilutions of Lake Whitefish
(Coregonus clupeaformis ) DNA from 7.1 ng/µl to 0.71 pg/µl. FAM – fluorescent
reporter 6-carboxyfluorescein…………………………………………………..147

Figure 5.2. Melt curve analysis peaks for: (A) no template control; (B) non-target species
Longnose Sucker (Catostomus catostomus); (C) non-target species White Sucker
(Catostomus commersonii); and (D) target species Lake Whitefish (Coregonus
clupeaformis). Only one distinct melt peak is present in panel D for Lake
Whitefish. No secondary peaks indicate no primer dimer formation………148

Figure 5.3. Results of agarose gel electrophoresis of: (A) traditional PCR using universal
fish primers for the DNA barcode region; and (B) amplification with the
Coregonus- specific primers designed in this study. (A) traditional PCR for
identification of Longnose Sucker (LS; Catostomus catostomus) and Lake
Whitefish (LW; Coregonus clupeaformis) using universal fish primers. NTC
=no template control. Bands are present for both Longnose Sucker (lane 5) and
Lake Whitefish (lane 6) at the expected size of 650 bp. No bands are present for
no-template controls. (B) Results of agarose gel electrophoresis of Real time
PCR product using primers designed in this study. NTC=no template control,
non-target in lanes 3-6 include 2 replicates of Longnose Sucker (lanes 3,4) and
White Sucker (lanes 5, 6). Bands observed for Lake Whitefish (LW) in lanes 7-
10 at approximately 120 bps, which is expected length of product amplicon from
Real time PCR reaction. No bands present for the no template control and non-
target species………………..…………………………………………………149

CHAPTER 6: The effect of environmental conditions on the distribution and
abundance of larval Lake Whitefish (Coregonus clupeaformis) in nearshore
embayments at Douglas Point, Lake Huron.

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