Browsing by Subject "Speciation"

Recombination occurs during meiosis to produce new allelic combinations in natural populations, and thus strongly affects evolutionary processes. The model system Drosophila has been crucial for understanding the mechanics underlying recombination and assessing the association between recombination rate and several evolutionary parameters. Drosophila was the first system in which genetic maps were developed using recombination frequencies between genes. Further, Drosophila has been used to determine genetic and environmental conditions that cause variation in recombination rate. Finally, Drosophila has been instrumental in elucidating associations between local recombination rate and nucleotide diversity, divergence and codon bias, as well as helping determine the causes of these associations.

Here I present a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, I report significant fine-scale heterogeneity of local recombination rates. However, I also observed "recombinational neighborhoods", where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. I further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. I noted strong crossover interference extending 5-7 Mb from the initial crossover event. Further, I observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. I documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, I found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models.

Next, I looked at the role of chromosomal inversions in species maintenance by examining the impact of inversions distinguishing species to disrupt recombination rates within inverted regions, at inversion boundaries and throughout the remainder of the genome. By screening nearly 10,000 offspring from females heterozygous for 3 major inversions, I observed recombination rates within an inverted region in hybrids between Drosophila pseudoobscura and D. persimilis to be ~10-4 (similar to rates of exchange for inversion heterozygotes within species). However, despite the apparent potential for exchange, I do not find empirical evidence of ongoing gene exchange within the largest of 3 major inversions in DNA sequence analyses of strains isolated from natural populations. Finally, I observe a strong 'interchromosomal effect' with up to 9-fold higher (>800% different) recombination rates along collinear segments of chromosome 2 in hybrids, revealing a significantly negative association between interchromosomal effect and recombination rate in homokaryotypes, and I show that interspecies nucleotide divergence is lower in regions with larger changes in recombination rates in hybrids, potentially resulting from greater interspecies exchange. This last result suggests an effect of chromosomal inversions on interspecies gene exchange not considered previously.

Finally, I experimentally tested for a novel male-mediated effect on female recombination rates by crossing males that differed by either induced treatment variation or standing genetic variation to genetically identical females. After assaying recombination frequency in the offspring of these genetic crosses, I fitted these data to a statistical model where I showed no effect of male temperature treatment or male genetic background on offspring recombination rate. However, I did observe a difference of recombination rates of offspring laid 5-8 days post-mating between males treated with Juvenile Hormone relative to control males. Environmental variation in male ability to affect recombination rate in their mates suggests the potential for sexual conflict on optimal proportion of recombinant offspring, perhaps leading to changes in population-level recombination rates with varying levels of sexual selection.

Overall, my map of fine-scale recombination rates allowed me to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation. Furthermore, I have identified several similarities and differences between inversions segregating within vs. between species in their effects on recombination and divergence, and I have identified possible effects of inversions on interspecies gene exchange that had not been considered previously. Finally, I have provided some evidence that males may impact female recombination rates, although future work should attempt to explore the range of male differences that impact this trait and the mechanism through which males impact the outcome of female meiosis.

Not all ferns grow in moist and shaded habitats. One notable example is the ecologically unusual clade of notholaenids. With approximately 40 species, the notholaenids have adapted to and diversified within the deserts of Mexico and the southwestern United States. In my dissertation, I studied the evolution and diversification of notholaenid ferns, using an approach that integrates data from multiple sources: biochemistry, biogeography, cytology, ecological niche modeling, molecular phylogeny, morphology, and physiology.

In Chapter 1, I infer a species phylogeny for notholaenid ferns using both nuclear and plastid DNA sequences, and reconstruct the evolutionary history of “farina” (powdery exudates of lipophilic flavonoid aglycones), a characteristic drought-adapted trait, that occurs on both the gametophytic and sporophytic phases of members of the the clade. Forty-nine notholaenid and twelve outgroup samples were selected for these analyses. Long (ca. 1 kb) low-copy nuclear sequences for four loci were retrieved using a recently developed amplicon sequencing protocol on the PacBio Sequel platform and a bioinformatics pipeline PURC; plastid sequences from three loci were retrieved using Sanger sequencing. Each nuclear/plastid dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Ancestral states were reconstructed using likelihood (re-rooting method) and MCMC (stochastic mapping method) approaches. Ploidy levels were inferred using chromosome counts corroborated by spore diameter measurements. My phylogenetic analyses results are roughly congruent with previous phylogenies inferred using only plastid data; however, several incongruences were observed between them. Hybridization events among recognized species of the notholaenid clade appear to be relatively rare, compared to what is observed in other well-studied fern genera. All characters associated with farina production in the group appear to be homoplastic and have complex evolutionary histories.

In Chapter 2, I focus on the infraspecific diversification of Notholaena standleyi, a species that thrives in the deserts of the southwestern United States and Mexico and has several “chemotypes” that express differences in farina color and chemistry. Forty-eight samples were selected from across the geographic distribution of N. standleyi. Phylogenetic relationships were inferred using four plastid makers and five single/low-copy nuclear markers. Sequences were retrieved using PacBio and the PURC pipeline. Ploidy levels were inferred from relative spore size measurements calibrated with chromosome counts, and farina chemistry was compared using thin-layer chromatography (TLC). My studies of Notholaena standleyi reveal a complex history of infraspecific diversification traceable to a variety of evolutionary drivers including classic allopatry, parapatry with or without changes in geologic substrate, and sympatric divergence through polyploidization. Four divergent clades were recognized within the species. Three roughly correspond to previously recognized chemotypes: gold (G), yellow (Y), and pallid/yellow-green (P/YG). The fourth clade, cryptic (C), is newly reported here. The diploid clades G and Y are found in the Sonoran and Chihuahuan Deserts, respectively; they co-occur (and hybridize) in the Pinaleño Mts. of eastern Arizona. Clades G and Y are estimated to have diverged in the Pleistocene, congruent with the postulated timing of climatological events that divide these two deserts. Clade P/YG is tetraploid and partially overlaps the distribution of clade Y in the eastern parts of the Chihuahuan Desert. However, PY/G is apparently confined to limestone, a geologic substrate rarely occupied by members of the other clades. The newly discovered diploid clade, cryptic (C), is distributed in the southern Mexican states of Oaxaca and Puebla and is highly disjunct from the other three clades.

In Chapter 3, I study the ecological niche differentiation among the three major chemotypes––G, Y, and P/YG. Using both ordination and species distribution modelling techniques, the ecological niches for each chemotype were characterized and compared. The main environmental drivers for their distributions were identified, their suitable habitats in both geographic and environmental spaces were predicted, and their niche equivalencies and similarities were tested. My ecological niche analyses results suggest that all three chemotypes are ecologically diverged. The ecological niches of the two parapatric, sister diploid chemotypes, G and Y, are significantly different from one another. Chemotype G occupies a very extreme niche with higher solar radiation, and lower rainfall and higher temperatures in the wettest quarter. The niche space of tetraploid chemotype P/YG is similar but not equivalent to the other two chemotypes. Its distribution model is highly influenced by the high percentage of Calcids and warmer temperatures in the wet season, reflecting the fact that it is confined to limestone in areas of lower elevation/latitude.

In Chapter 4, I gather together all my other studies related to Notholaena standleyi, including: 1) morphological and anatomical observations of its desiccation-tolerant leaf, with special focus on the farina; 2) two cases of hybridization between the chemotypes, one between the diploid chemotype Y and tetraploid chemotype YG, and another between diploid chemotypes Y and G; and 3) morphological and physiological comparisons between the two diploid chemotypes Y and G. My plan is to finalize these studies and submit them for publication in the near future.

In Chapter 5, I summarize collaborative contributions that I made to other fern studies during my Ph.D.

Meiotic recombination creates genetic diversity by shuffling combinations of alleles across loci, yet alleles at neighboring loci often remain non-randomly associated. This non-random association is known as linkage-disequilibrium (LD), and it has evolutionarily important effects both within and between species. Nucleotide diversity at a given locus may be reduced by directional selection on the locus, or by selection on neighboring linked loci. Recombination rates and nucleotide diversity are positively correlated across loci within many species, which can be explained by linked selection reducing nucleotide variation disproportionately in regions of low recombination. However, the independent contributions of different types of linked selection are difficult to disentangle. Between species, chromosomal inversions have been proposed to suppress recombination in hybrid inversion heterozygotes and thereby maintain LD and species distinction, but many models of how this happens are overly simplistic—they often ignore non-crossover gene conversion, which reduces LD. Little direct empirical data exist on gene conversion with respect to inversions in hybrids, so despite existing models, inversions may be quite ineffective at keeping hybridizing species distinct. Here, I examine the evolutionary consequences of LD at two levels: nucleotide diversity within species, and recombination-suppression in hybrids between species. I present three investigations driven by this overarching goal of understanding how LD plays into fundamental evolutionary mechanisms. First, I examine nucleotide variation in Drosophila pseudoobscura, and I present a novel test for evidence that particular kinds of selection at linked sites (background selection and/or soft sweeps) may reduce nucleotide variation even in the absence of hard selective sweeps. Second, I show that inversions are permeable to non-crossover gene conversion, which occurs throughout inverted regions in intra- and inter-specific hybrids. I provide a genome-wide empirical analysis of gene conversion rates both within species and in species hybrids, and I estimate that gene conversion occurs at a rate of 1 x 10-5 to 2.5 x 10-5 converted sites per bp per generation in experimental crosses within D. pseudoobscura and between D. pseudoobscura and its naturally-hybridizing sister species D. persimilis. Finally, I use extensive whole-genome sequence data to re-examine patterns of introgression and divergence in the D. pseudoobscura / D. persimilis system. I show how failing to consider variation in evolutionary rate can lead and has led to misinterpretations regarding effects of introgression. Through these genomic examinations, I refine our understanding of how recombination and linkage disequilibrium have shaped the divergence and speciation of Drosophila pseudoobscura and D. persimilis.

Speciation has occurred countless times throughout history, and yet the genetic mechanisms that lead to speciation are still missing pieces. Here, we describe the genetics of two processes that can act alone or together to cause speciation: hybrid sterility and meiotic drive. We use the Drosophila pseudoobscura/D, persimilis species as a model system to study these processes. We expanded on a prior study and saw little variation in strength of previously known hybrid sterility alleles between distinct strains of D. persimilis and the Bogota subspecies of D. pseudoobscura. Introgression of an autosomal, noninverted hybrid sterility allele from the USA subspecies of D. pseudoobscura into D. persimilis demonstrated that the D. pseudoobscura copy of a D. persimilis hybrid sterility factor also causes hybrid male sterility in a D. pseudoobscura bogotana background. This allelism suggests that the introgressed allele is ancestral, but was lost in the Bogota lineage, or that gene flow between D. pseudoobscura USA and D. persimilis moved the sterility-conferring allele from D. persimilis into D. pseudoobscura. To further understand the genetic basis of speciation, we asked if meiotic drive in D. persimilis is associated with hybrid sterility seen in D. persimilis/D. pseudoobscura hybrids. QTL mapping of both traits along the right arm of the X chromosome, where both drive and hybrid sterility loci are found, suggest that some of the causal loci overlap and may be allelic.

Speciation is a constantly ongoing process whereby reproductive isolating baririer build up over time until groups of organisms can no longer exchange genes with each other. Adaptation is thought to play a major role in the formation of these barriers, although the genetic mechanisms and geographic mode underlying the spread of barriers due to adaptive evolution is poorly understood. Critically, speciation may occur in stages through the formation of intermediate partially reproductively isolated groups. The idea of such widespread ecotypes has been the subject of great controversy over the last century. Even so, we have relatively little understanding about whether widespread ecotypes exist, wheather they are reproductively isolated, and how adaptive alleles are distributed among partially isolated groups. In this dissertation, I examined these issues in widespread coastal perennial and inland annual ecotypes of the yellow monkeyflower, Mimulus guttatus. First, I determined that coastal and inland populations comprise distinct ecotypic groups. I then determined that these ecotypes are adapted to their respective habitats through genetically based flowering time and salt tolerance differences. I assessed the genetic architecture of these adaptations through quantitative trait loci (QTL) analysis and determined the geographic distribution of the underlying alleles through latitudinally replicated mapping populations. I quantified the contribution of these loci to adaptation in the field through the incorporation of advance generation hybrids in reciprocal transplant experiments. In the process, I discovered a widespread chromosomal inversion to be involved in the adaptive flowering time and annual/perennial life-history shift among the ecotypes. Overall, the results of this study suggest that widespread reproductively isolated ecotypes can form through the spread adaptive standing genetic variation between habitats and that chromosomal rearrangements can integral to this process.

The earth is home to roughly 9 million eukaryotic species. The formation and maintenance of this diversity requires the accumulation of barriers to reproduction. One of the most common post-zygotic barriers in plants is hybrid seed inviability (HSI). Despite its commonality, we know relatively little about the genetic mechanisms and evolutionary forces which are responsible for this barrier, particularly in naturally co-occurring species. Here I tested the role of parental conflict in HSI between co-occurring monkeyflowers in the M. guttatus species complex. I assessed the strength and directionality of HSI within and between phenotypically described perennial variants of the M. guttatus species complex. I find substantial HSI between two morphologically described variants, M. guttatus and M. decorus, amounting to ~30-50% reproductive isolation. Genetically distinct clades of M. decorus vary in their ability to cross with M. guttatus in both magnitude and direction of RI. Intriguingly, northern and southern clades of M. decorus are also incompatible with one another, showing strong, symmetric hybrid seed inviability. In all cases, HSI is accompanied by parent of origin effects on F1 seed size, consistent with a role of resource allocation to hybrid inviability. Parent of origin effects on reciprocal F1s were not limited to final size. I characterize the developmental trajectory of seeds between M. guttatus and both the northern and southern clades of M. decorus. Hybrid seeds show similar developmental trajectories depending on their end fate (i.e. viable vs inviable), despite differing in the maternal and paternal contributors in these crosses. Inviable seeds are characterized by patterns of paternal excess; chaotic and malformed endosperm. Viable hybrid seeds are characterized by maternal excess; limited, and precocious endosperm development. Relatively normal embryo development early on suggests that hybrid seed inviability stems, in part, from malformed endosperm. Lastly, I use a combination of modeling, next generation sequencing, and genotyping approaches to determine the genetic architecture and basis of HSI. I find that the genetic basis of HSI is complex, wherein several maternally and paternally inherited nuclear loci interact to cause HSI. In total, I show the presence of multiple perennial species in the M. guttatus species complex. These species show little phenotypic or obvious ecological differentiation, but are genetically unique and have substantial post-zygotic reproductive isolation, namely through the formation of inviable seeds. Patterns of seed development and final size are indicative of parent of origin effects on resource allocation to endosperm. Despite relatively low genetic differentiation for the group, the genetic basis of HSI is quite complex, involving multiple maternally and paternally interacting alleles. Future work will be needed to determine the identities of these genes, as well as patterns of repeatability across the complex.

One of the major goals of evolutionary biology is understanding the process of species formation. There is particular interest in how selection can favor species formation through the process of reinforcement. When two diverging taxa produce maladaptive hybrids, selection will favor greater reproductive isolation between the taxa. Reinforcement often results in a pattern of reproductive character displacement, which is defined as two species having greater reproductive isolation in sympatry then in allopatry. Floral-color divergence in the native Texas wildflower, Phlox drummondii, constitutes one of the best documented cases of reinforcement in plants. P. drummondii and a closely related species, P. cuspidata produce similar light-blue flowers throughout the allopatric parts of their ranges. However, in the area of sympatry P. drummondii has dark-red flowers, which has been shown to decrease hybridization between the two species. In the following work, I investigate the causes and consequences of the process of reinforcement and the pattern of character displacement in P. drummondii. First, I identify the genetic basis of the flower color variation as regulatory changes in two genes controlling the type and amount of anthocyanin floral pigments. I then evaluate neutral genetic variation across the range of P. drummondii and conclude there is extensive gene flow between allopatric and sympatric areas of the range, which indicates that selection and not genetic drift is responsible for the flower color variation. By investigating genetic variation at the loci underlying flower color variation I find a molecular signature of a selective sweep at one of the two flower color loci, further indicating that selection is responsible for this flower color variation. Finally, I measure selection on flower color in both sympatry and allopatry. I find no evidence that flower color variation is a response to ecological character displacement or local adaptation in the area of sympatry. I find evidence of pollinator preference for the ancestral allopatric flower color in allopatry, which may explain the persistence of the pattern of character displacement. These investigations of reproductive character displacement and reinforcement address important areas of research in evolutionary biology including the genetic basis of adaptation, the formation of species, and pleiotropy and conflicting selection pressures in species.

Biodiversity is generated by the process of speciation. Because biological species are defined as populations that are unable to exchange genes with one another, the study of the evolution of reproductive isolation occupies the center of speciation research. A key to deciphering how reproductive isolation evolves is to understand the genetic changes that underlie these barriers to gene flow. Intrinsic postzygotic barriers, such as hybrid sterility or inviability, are known to impede gene flow and especially lend themselves to genetic analysis because of their ease of study in a laboratory setting. Because hybrid sterility likely evolves before hybrid inviability, it potentially plays an important role in the cessation of gene flow. Yet, while their X-linked counterparts have been precisely localized, we remain ignorant of the numbers of and interactions among dominant autosomal loci that are predicted to contribute to F1 hybrid male sterility.

To address this conceptual void, I examine the genetic architecture of hybrid male sterility between the allopatric sister species Drosophila persimilis and D. pseudoobscura bogotana. First, using a large-scale backcross analysis, I fine-map autosomal QTL from D. persimilis that confer sterility in male hybrids. This fine-mapping shows that loci contributing to hybrid male sterility reside outside chromosomal rearrangements (i.e., regions of reduced recombination) in this allopatric species pairs. In contrast, these QTL do not contribute to hybrid male sterility in the comparable sympatric hybridizing species D. persimilis and D. pseudoobscura, as predicted by models that suggest that hybridizing species persist because of broad regions of reduced recombination. Next, I use a serial backcross design to introgress these sterility-conferring QTL from D. persimilis into a D. p. bogatana genetic background devoid of other alleles from D. persimilis. This introgression study tested a prediction of the dominance theory proposed to explain Haldane's rule: dominant-acting autosomal loci should interact with recessive-acting X-linked loci to produce sterile hybrid males. Surprisingly, the results demonstrated that the "composite" dominance of the autosomal QTL is more important than the dominance of individual QTL for producing Haldane's rule: epistasis among loci elevated their dominant effects on sterility such that individually-recessive-acting autosomal QTL can contribute to F1 male infertility. Finally, using recombination to generate independent lines bearing only small segments of the identified QTL regions, I examine whether single or multiple loci within these regions contribute to the overall effect of hybrid sterility. While the effect of one QTL depends on epistasis between several loci within that small region, the effect of the other QTL appears to derive from a single genetic factor. These results suggest that estimates of the number of genes that contribute to reproductive isolation are at best, likely too low and, at worst, unattainable with the mapping resolution attainable by standard backcross and introgression approaches.

This dissertation addresses both evolutionary and genetic hypotheses of intrinsic postzygotic isolation. Hybrid male sterility between D. persimilis and D. p. bogotana clearly involves highly specific and complex interactions between homoospecific loci. The mapping results presented here also lay the foundation for the identification and cloning of multiple autosomal sterility-conferring "speciation genes."

Adaptation is central to our understanding of the origin of biological diversity. Yet whether adaptive divergence promotes the formation of new lineages remains poorly understood. My dissertation addresses the role of adaptive divergence in diversification and speciation. I also investigate an alternative mechanism: dispersal, which can promote diversification and speciation through its effects on gene flow and allopatry. To address the role of divergent adaptation and dispersal in the process of diversification, I take an integrated approach, combining both comparative methods with quantitative genetics to characterize patterns of diversification and speciation in the tribe Brassiceae and genus Cakile. I start with a comparative study of the role of dispersal and adaptation in diversification, and then focus on the role of climatic and latitudinal divergence in the processes of adaptive divergence and speciation. In general, I find limited evidence for the role of divergent adaptation in the evolution of intrinsic reproductive isolation. Diversification in the tribe Brassiceae appears to be mediated by dispersal ability, while in the genus Cakile, the evolution of intrinsic reproductive isolation is largely independent of ecological divergence. Thus, while divergent adaptation to novel habitats and climate are likely occurring in Brassiceae, mediated in part by the evolution of long-distance dispersal, the evolution of intrinsic genic reproductive barriers appears to not be influenced by adaptation.