Publication Date


Document Type


Committee Members

Volker Bahn (Committee Member), Christopher Barton (Committee Member), Lisle Gibbs (Committee Member), Jeffrey Peters (Advisor), John Stireman Iii (Committee Member)

Degree Name

Doctor of Philosophy (PhD)


Speciation is primarily regarded as an ancestral split that results in two distinct taxonomic units, and proceeds in stages along a continuum from initiation (i.e., population divergence) to completion (i.e., reproductively isolated species). Establishing how and why populations diverge, including the primary mechanisms influencing these events is a major objective for evolutionary scientists. Focusing on incipient forms, researchers attempt to disentangle the antagonistic nature of selection, genetic drift, and gene flow in the speciation process.

In chapter 1, I investigate the phylogenetic relationships of 14 closely related taxa within the mallard complex (Anas spp.) that underwent a radiation within the past one million years. Using mitochondrial DNA (mtDNA) and 20 nuclear loci for one to five individuals per taxon, I further examine how recombination and hybridization affect species tree reconstructions. In general, relationships within major clades were robust to treatment of recombination (i.e., ignoring or filtering) and inclusion or exclusion of hybridizing taxa, but branch lengths and posterior support were sensitive to both treatments. Of the 14 taxa, the most confounded relationships were those within the New World (NW) group comprising the sexually dichromatic mallard (Anas platyrhynchos) and the monochromatic American black duck (A. rubripes; "black duck"), mottled duck (A. fulvigula), and Mexican duck (A. [p.] diazi). Finally, I address discordance between nuclear, morphometric, and mitochondrial trees, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha) and discuss how alternative modes of speciation (i.e., hybrid speciation) may lead to variance in these relationships.

In Chapter 2, I attempt to disentangle the evolutionary relationships of the New World (NW) group using mtDNA and 17 nuclear loci for a larger per taxon sample size (24-25 individuals per taxon). In general, whereas both Florida and Gulf Coast mottled ducks were differentiated from one another and from the other taxa (mean ΦST = 0.024 - 0.064), mallards, American black ducks, and Mexican duck were not significantly differentiated among nuclear markers (mean ΦST < 0.020). Using coalescent methods to estimate rates of gene flow between mallards and each of the monochromatic taxa generally supported hybridization, but I could not reject complete isolation for any pairwise comparison. Furthermore, species tree reconstructions revealed that phylogenetic relationships were sensitive to stochastic sampling of individuals likely due to incomplete lineage sorting or hybridization. I conclude that members of the NW Mallard group appear to be adaptive incipient morphs, and that future work should focus on genomic regions under selection to better understand the stage and process of speciation in this group.

In Chapter 3, I use restriction site associated DNA (RAD) sequencing methods to generate a pseudorandom sampling of 3,563 autosomal and 172 sex-linked (Z chromosome) markers scattered across the genome to more rigorously test the mechanism of speciation between Mexican ducks (N = 105 individuals from six Mexican states and two US states) and mallards (N = 17). Specifically, I aim to determine the stage of speciation and whether speciation has been driven by few loci with large effects versus many loci with small effects, plumage associated differentiation, or genetic drift. Marker comparisons between mallards and Mexican ducks revealed strong discordance among autosomal ΦST = 0.014), sex-linked (mean ΦST = 0.091), and mtDNA (ΦST = 0.12) markers. In general, divergence at autosomal loci followed a stepping stone model, with a gradual transition in genotypic frequencies from North to South.

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Department or Program

Department of Earth and Environmental Sciences

Year Degree Awarded


Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.