[MARMAM] Dissertation on dolphin genetics available

Sarah Courbis sarahcourbis at gmail.com
Sat Dec 17 15:16:25 PST 2011

My dissertation is now available.  Please feel free to send me a request
for the pdf.

Population Structure of Island-Associated Pantropical Spotted Dolphins
attenuata*) in Hawaiian Waters

Chapter 1:  Introduction to Population Genetics & Spotted Dolphins

Chapter 2:  Evidence of Multiple Populations of Pantropical Spotted
Dolphins (*Stenella attenuata*) within Hawaiian Waters

Chapter 3:  Comparisons to Explore Potential Baselines for Biologically
Significant Genetic Differentiation Levels:  Population Structure of
Pantropical Spotted Dolphins in the North Pacific

Chapter 4:  Are Small Sample Sizes and Use of Slow Evolving DNA Regions
Hindering Resolution of the Phylogenetic Relationships among Delphinids:  *
Stenella* as an Example Genus

Chapter 5:  Conclusions

The citation is:
Courbis, S. 2011. Population Structure of Island-Associated Pantropical
Spotted Dolphins (*Stenella attenuata*) in Hawaiian Waters. Ph.D.
Dissertation. Portland State University. Portland, OR. 164pp.


Understanding gene flow, diversity, and dispersal patterns is important for
predicting effects of natural events and anthropogenic activities on
dolphin populations. With the very recent exceptions of false killer whales
(*Pseudorca crassidens*), spinner dolphins (*Stenella longirostris*), and
common bottlenose dolphins (*Tursiops truncatus*), Hawaiian odontocete
species are managed as single stocks within the U.S. Hawaiian Exclusive
Economic Zone.  These exceptions are a result of recent studies that have
indicated that some species have populations that show fidelity to
individual islands or groups of islands, resulting in genetic
differentiation, often with management implications. The first part of my
study (following the introductory chapter) focused on population structure
of pantropical spotted dolphins (*Stenella attenuata*) near the Hawaiian
Islands.  Because of the level of human interaction, pantropical spotted
dolphin populations need to be defined accurately to be managed in a way
that will avoid local population losses, especially given that the
commercial and recreational troll fisheries near the islands “fish on
dolphins” to catch tuna.  I analyzed genetic samples for mtDNA and
microsatellite loci from four island regions: Hawai‘i, the 4-islands area,
O‘ahu, and Kaua‘i/Ni‘ihau. My results support genetic differentiation among
the regions of Hawai‘i, the 4-islands area, and O‘ahu and suggest that
pantropical spotted dolphins near Kaua‘i/Ni‘ihau are likely transient and
in very low numbers.  There was no strong evidence to support sex-biased
dispersal or group fidelity.  Possibly, differentiation is mediated by
behavior adapted to differing habitat types.  From a management
perspective, spinner and bottlenose dolphin populations near the Hawaiian
Islands have been split into separate stocks for management based on levels
of genetic differentiation similar to those found for pantropical spotted
dolphins.  These precedents suggest that comparable action should be taken
to split pantropical spotted dolphin stocks near the Hawaiian Islands.

Most population studies rely heavily upon fixation indices like *F*ST to
determine whether populations are genetically differentiated.  When
*F*STvalues are low but significantly different from zero, it can be
to interpret the biological significance of these values.  As part of my
study, I suggest that one way to evaluate whether small *F*ST values
indicate significant differentiation is to compare *F*ST values with other
populations considered to be separate based on factors such as extreme
distance or morphological differences.  I examined pantropical spotted
dolphins from the coastal and offshore Eastern Tropical Pacific (ETP),
Hawaiian Islands, and China/Taiwan to examine the utility of comparing
*F*STvalues across separate populations. Among Hawaiian Island
*F*ST values are significantly different from zero but small. The
comparison of these *F*ST values with more distant populations in the ETP
and China/Taiwan indicated that differences among Hawaiian Island regions
were similar in magnitude to those found between the offshore and coastal
ETP sub-species, but smaller than between the Hawaiian Island regions and
the other regions examined. This suggests a level of reproductive isolation
among the Hawaiian Islands regions that is comparable to that of offshore
and coastal ETP populations, and supports the value of fixation index
comparisons in evaluating differentiation among putative populations. My
results suggest that assigning specific numerical baseline *F*ST values may
not always be biologically meaningful but that determining whether related
populations with geographic or other separation show a preponderance of
similar, lower, or higher fixation index values can help evaluate whether
genetic differences among sympatric or parapatric groups warrants
designating them as separate populations for management.

          Lastly, I explore whether the fast evolving mtDNA control region
may be more suited to phylogenetic comparisons among the *Stenella* than
slower evolving gene regions and whether the small number of haplotypes
generally used in phylogenetic analyses is adequate for defining
relationships among dolphins.  Usually, slow evolving regions, such as gene
regions, are used in phylogenetic analyses because species and genera have
been isolated long enough for variation to have accumulated in such regions
but not so long that many reversals (*i.e.* a mutational change in sequence
that later changes back to the original sequence) have occurred.  The mtDNA
control region is typically used for population genetic comparisons rather
than phylogenetic comparisons because it is considered to be a fast
evolving region.  Historically, dolphin phylogeny has been examined using
gene regions, which have resulted in ambiguous and unexpected
relationships.  However, the lack of variation in the mtDNA control region
for pantropical spotted dolphin populations and the fact that recent
studies have found that the mtDNA control region in cetaceans evolves at
about one quarter the rate of other mammals, raises the question as to
whether this region would be better suited to phylogenetic studies for
the *Stenella
*(and potentially other dolphin species).  In comparing 346 haplotypes from
five species of *Stenella* world-wide, I found that the mtDNA control
region is probably not a good region to use for phylogenetic analyses, and
that even faster evolving regions might perform better.  The differences in
the mtDNA control region were not sufficient to distinguish clear
relationships among the *Stenella*.  I also found that when subsets of
haplotypes chosen at random were compared, the results differed among
comparisons, suggesting that there is value in using more than the usual
one or two haplotypes when making phylogenetic comparisons.  Given the
recent increases in sequence availability (*e.g*. GenBank) and computing
power, researchers should strongly consider using many haplotypes from a
variety of populations in their phylogenetic comparisons.


Sarah Courbis
Operations Coordinator
DLNR/Hawaiian Islands Humpback Whale National Marine Sanctuary
sarahcourbis at gmail.com
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