Among-Locus Heterogeneity in Genetic Diversity and Divergence in Two Pairs of Duck Species (Genus: Anas)

Genetic diversity and divergence at a locus are the result of interactions among the fundamental evolutionary forces of mutation, genetic drift, gene flow and natural selection. Variation in the strength of these forces can cause high heterogeneity in diversity and divergence across the genome. The overall objective of this thesis was to examine the role of population history vs. selection in generating heterogeneity in genetic diversity and differentiation. In Chapter 1, I examine the role of dispersal behavior in causing genetic differentiation and population structure within and between two morphologically distinct Australian duck species that differ in ecology and life history characteristics. A five-locus nuclear dataset revealed nearly no divergence and similar values of genetic diversity between species. However, as predicted, I found significant population structure in the sedentary chestnut teal (Anas castanea) but no structure within the vagile grey teal (A. gracilis). In Chapter 2, a more rigorous examination of differentiation among nineteen autosomal loci also failed to uncover a genetic distinction between these two species. However, DNA sequences from seven loci sampled from the Z-chromosome revealed strong differentiation between chestnut and grey teal. Furthermore, the most divergent loci are clustered on the shorter p-arm of the chromosome, close to the centromere, suggesting this region as an island of differentiation that may have been important in the speciation process. These two species of Australian teal are perhaps the most recently diverged taxa examined to date that reveal a large Z-effect. In Chapter 3, I quantitatively tested the contribution of gene flow and introgression to the heterogeneity of genetic diversity and differentiation in two deeply divergent taxa, the falcated duck (A. falcata) and the gadwall (A. strepera). Consistent with previously published mitochondrial DNA analyses, 19 nuclear loci revealed the introgression of nuclear DNA from the falcated duck into the allopatric population of gadwall in North America, but not into the sympatric population in Eurasia. Furthermore, gene flow was insufficient to explain the high heterogeneity in genetic diversity in both species and differentiation between the taxa. Indeed, this heterogeneity failed to fit neutral models of population history, suggesting that selection may be having a pervasive effect throughout the genome. Overall, this research reveals heterogeneous patterns of diversity and differentiation among nuclear loci in both early and later stages of divergence. Gene flow alone could not explain this heterogeneity, suggesting a prominent role of selection. Substantial divergence at some loci suggests that the strength of divergent selection overrides the homogenizing effects of gene flow and maintains species integrity

Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals

Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z-chromosome (females are heterogametic, ZW). We tested for elevated Z-differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal Anas gracilis and the dichromatic chestnut teal A. castanea. Despite prominent morphological differences, these two species are genetically indistinguishable at both mitochondrial DNA (mean ΦST < 0.0001) and 17 autosomal loci (mean ΦST = 0.0056). However, we detected elevated Z-differentiation (mean ΦST = 0.281) and tentative evidence of an island of differentiation on the Z-chromosome. This elevated differentiation was explained by a high frequency of derived alleles in chestnut teal that were absent in grey teal, which parallels independent evidence for a gain in dichromatism from a monochromatic ancestor. Coalescent estimates of demographic history and simulations indicated that the elevated Z-differentiation was unlikely to be explained by neutral processes, but instead supported a role of divergent selection. We discuss evidence for models of speciation with gene flow versus adaptive divergence in the absence of gene flow and find that both hypotheses are plausible explanations of the data. Overall, these teal have the weakest background differentiation documented to date for a species showing a large Z-effect, and they are an excellent model species for studying speciation genomics and the evolution of sexual dichromatism

IMa2 input files

IMa2 input files for 7 Z-chromosome loci and 17 autosomal loci. Sequences are partitioned into two populations "CT" for chestnut teal and "GT" for grey teal. Sequences have been filtered to be consistent with no recombination

Phased FASTA files

FASTA files for phased alleles from 7 Z-chromosome introns and 17 autosomal introns sequenced from chestnut teal and grey teal

Specimen data for Australian Teal

Specimen information for 23 Chestnut teal (Anas castanea) and 48 grey teal (Anas gracilis), including specimen number, DNA number, sex, and collection locality

Concatenated NEXUS files

NEXUS files of concatenated DNA sequences for 7 Z-chromosome loci (69 individuals; 2637 bp) and 17 autosomal loci (71 individuals; 5351 bp). Each individual is represented by a single consensus sequence with polymorphic positions coded by IUPAC ambiguity codes. Missing data are coded as "?"

Expanding the Scope of Replicable Unnatural DNA: Stepwise Optimization of a Predominantly Hydrophobic Base Pair

As part of an ongoing effort to expand the genetic alphabet for <i>in vitro</i> and eventually <i>in vivo</i> applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs exemplified by d<b>5SICS</b>-d<b>MMO2</b> and d<b>5SICS</b>-d<b>NaM</b>. When incorporated into DNA, the latter is replicated and transcribed with greater efficiency and fidelity than the former; however, previous optimization efforts identified the <i>para</i> and methoxy-distal <i>meta</i> positions of d<b>MMO2</b> as particularly promising for further optimization. Here, we report the stepwise optimization of d<b>MMO2</b> via the synthesis and evaluation of 18 novel <i>para</i>-derivatized analogs of d<b>MMO2</b>, followed by further derivatization and evaluation of the most promising analogs with <i>meta</i> substituents. Subject to size constraints, we find that <i>para</i> substituents can optimize replication via both steric and electronic effects and that <i>meta</i> methoxy groups are unfavorable, while fluoro substituents can be beneficial or deleterious depending on the <i>para</i> substituent. In addition, we find that improvements in the efficiency of unnatural triphosphate insertion translate most directly into higher fidelity replication. Importantly, we identify multiple, unique base pair derivatives that when incorporated into DNA are well replicated. The most promising, d<b>5SICS</b>-d<b>FEMO</b>, is replicated under some conditions with greater efficiency and fidelity than d<b>5SICS</b>-d<b>NaM</b>. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new SAR data, and importantly identify multiple new candidates for eventual <i>in vivo</i> evaluation