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PhD_00_Thesis.lof
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\contentsline {figure}{\numberline {3.1}{\ignorespaces Modified haplotype network from Phillips \textit {et al.}\nobreakspace {}\cite {phillips2019incomplete}.}}{47}{figure.caption.8}%
\contentsline {figure}{\numberline {3.2}{\ignorespaces Infographic of the inner workings of {\tt HACSim} using {\tt Nstar = Hstar = perms = 5} as a hypothetical example.}}{54}{figure.caption.12}%
\contentsline {figure}{\numberline {3.3}{\ignorespaces {\tt HACSim} algorithm pseudocode.}}{56}{figure.caption.13}%
\contentsline {figure}{\numberline {3.4}{\ignorespaces Visual depiction of {\tt HACSim} sampling model.}}{58}{figure.caption.14}%
\contentsline {figure}{\numberline {3.5}{\ignorespaces Outputted haplotype accumulation curve and haplotype frequency barplot for equal haplotype frequencies.}}{62}{figure.caption.16}%
\contentsline {figure}{\numberline {3.6}{\ignorespaces Initially outputted haplotype accumulation curve and haplotype frequency barplot for unequal haplotype frequencies (three dominant haplotypes).}}{65}{figure.caption.19}%
\contentsline {figure}{\numberline {3.7}{\ignorespaces Final outputted haplotype accumulation curve and haplotype frequency barplot for unequal haplotype frequencies (three dominant haplotypes).}}{65}{figure.caption.20}%
\contentsline {figure}{\numberline {3.8}{\ignorespaces Initially outputted haplotype accumulation curve and haplotype frequency barplot for Lake whitefish (\textit {C. clupeaformis}.}}{69}{figure.caption.22}%
\contentsline {figure}{\numberline {3.9}{\ignorespaces Final outputted haplotype accumulation curve and haplotype frequency barplot for Lake whitefish (\textit {C. clupeaformis}.}}{69}{figure.caption.23}%
\contentsline {figure}{\numberline {3.10}{\ignorespaces Initially outputted haplotype accumulation curve and haplotype frequency barplot for Deer tick (\textit {I. scapularis}).}}{72}{figure.caption.25}%
\contentsline {figure}{\numberline {3.11}{\ignorespaces Final outputted haplotype accumulation curve and haplotype frequency barplot for Deer tick (\textit {I. scapularis}).}}{72}{figure.caption.26}%
\contentsline {figure}{\numberline {3.12}{\ignorespaces Initially outputted haplotype accumulation curve and haplotype frequency barplot for Scalloped hammerhead (\textit {S. lewini}).}}{74}{figure.caption.28}%
\contentsline {figure}{\numberline {3.13}{\ignorespaces Final outputted haplotype accumulation curve and haplotype frequency barplot for Scalloped hammerhead (\textit {S. lewini}).}}{75}{figure.caption.29}%
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\contentsline {figure}{\numberline {4.1}{\ignorespaces Local optima for Scenario II (1 dominant haplotype) for a population size of 10000.\relax }}{103}{figure.caption.33}%
\contentsline {figure}{\numberline {4.2}{\ignorespaces Local optima for Scenario III (2 dominant haplotypes) for a population size of 10000.\relax }}{103}{figure.caption.34}%
\contentsline {figure}{\numberline {4.3}{\ignorespaces Local optima for Scenario IV (3 dominant haplotypes) for a population size of 10000.\relax }}{104}{figure.caption.35}%
\contentsline {figure}{\numberline {4.4}{\ignorespaces Local optima for Pea aphid (\textit {A. pisum}) for a population size of 10000.\relax }}{104}{figure.caption.36}%
\contentsline {figure}{\numberline {4.5}{\ignorespaces Local optima for Lake whitefish (\textit {C. clupeaformis}) for a population size of 10000.\relax }}{105}{figure.caption.37}%
\contentsline {figure}{\numberline {4.6}{\ignorespaces Local optima for Common mosquito (\textit {C. pipiens}) for a population size of 10000.\relax }}{105}{figure.caption.38}%
\contentsline {figure}{\numberline {4.7}{\ignorespaces Local optima for Deer tick (\textit {I. scapularis}) for a population size of 10000.\relax }}{106}{figure.caption.39}%
\contentsline {figure}{\numberline {4.8}{\ignorespaces Local optima for Gypsy moth (\textit {L. dispar}) for a population size of 10000.\relax }}{106}{figure.caption.40}%
\contentsline {figure}{\numberline {4.9}{\ignorespaces Local optima for Scalloped hammerhead shark (\textit {S. lewini}) for a population size of 10000.\relax }}{107}{figure.caption.41}%
\contentsline {figure}{\numberline {4.10}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Scenario II (1 dominant haplotype).}}{108}{figure.caption.42}%
\contentsline {figure}{\numberline {4.11}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Scenario III (2 dominant haplotypes).}}{109}{figure.caption.43}%
\contentsline {figure}{\numberline {4.12}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Scenario IV (3 dominant haplotypes).}}{110}{figure.caption.44}%
\contentsline {figure}{\numberline {4.13}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Pea aphid (\textit {Acyrthosiphon pisum}).}}{111}{figure.caption.45}%
\contentsline {figure}{\numberline {4.14}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Lake whitefish (\textit {Coregonus clupeaformis}).}}{112}{figure.caption.46}%
\contentsline {figure}{\numberline {4.15}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Common mosquito (\textit {Culex pipiens}).}}{113}{figure.caption.47}%
\contentsline {figure}{\numberline {4.16}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Deer tick (\textit {Ixodes scapularis}).}}{114}{figure.caption.48}%
\contentsline {figure}{\numberline {4.17}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Gypsy moth (\textit {Lymantria dispar}).}}{115}{figure.caption.49}%
\contentsline {figure}{\numberline {4.18}{\ignorespaces Frequency plot showing all located local optima and the number of times each was found by {\tt HACSim} for Scalloped hammerhead shark (\textit {Sphyrna lewini}).}}{116}{figure.caption.50}%
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\contentsline {figure}{\numberline {5.1}{\ignorespaces Depiction of the DNA barcode gap as a traditional dotpot for Canadian Pacific fishes assessed by Steinke \textit {et al.}\nobreakspace {} \cite {steinke2009dna}.}}{151}{figure.caption.61}%
\contentsline {figure}{\numberline {5.2}{\ignorespaces Depiction of intraspecific and interspecific genetic distances as a modified dotplot for Canadian Pacific fishes assessed by Steinke \textit {et al.}\nobreakspace {}\cite {steinke2009dna}.}}{153}{figure.caption.62}%
\contentsline {figure}{\numberline {5.3}{\ignorespaces Depiction of species' genetic distances as an altered quadrant plot taken from Hubert and Hanner \cite {hubert2015dna}.}}{155}{figure.caption.63}%
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