Speciation is a process by which 1 population splits into 2 distinct populations that in time acquire reproductive isolation (RI). Interestingly, the speed at which RI is attained can be influenced by several factors. My thesis work focuses on how protein-protein interactions affect this process, either by impeding or expediting the acquisition of RI. Here, I present an analysis of cascading positive selection in a group of centromere associated proteins in the Drosophila melanogaster subgroup. Within this group, there are proteins known to interact with rapidly evolving DNA elements located at the centromere, as well as other proteins. While previous work has shown that proteins binding rapidly evolving DNA elements are prone to rapid evolution, I provide evidence that this cascade of positive selection can further extend to other interacting partners. This group of rapidly evolving proteins provides a prime example of protein-protein interactions driving speciation. I also present evidence of protein-protein interactions impeding the process of speciation. Specifically, this work focuses on the sister species D. yakuba and D. santomea. This species pair is of particular interest because previous work has demonstrated that he mitochondrial genome completely introgressed from D. yakuba to D. santomea replacing the native form. By assessing nuclear genes encoding proteins that interact with mitochondrial proteins in the Oxidative Phosphorylation (OXPHOS) pathway, I have identified specific cases of co-introgression in which nuclear encoded mitochondrial partners have introgressed with the mitochondrial genome to allow for the maintenance of physical function, thus maintaining similarities between species, ultimately impeding the process of speciation.

The family Brassicaceae includes a number of important species used as vegetables, oilseeds and medicine. The Brassica B-genome is significantly diverged from the A- and C-genomes, and species containing the B-genome possess many valuable agronomic and disease resistance traits. In this thesis, two populations of interspecific crosses between Brassica napus (AACC) and Brassica carinata (BBCC) were studied, and microsatellite (SSR) markers and genomic in situ hybridization (GISH) techniques were applied to characterize the B-genome chromosome introgressions in the advanced backcross populations and their effect on disease resistance, morphological and seed quality traits. A BC2S3 derived doubled haploid (DH) population was genotyped with 184 SSR markers and DH lines carrying stable B-genome chromosomal segments were identified. The GISH assay demonstrated that three of the 60 DHs were substitution lines in which the B-genome chromosome J13 was common to all. The lines with B-genome chromosomes, B+, were significantly different (P <0.01) from the lines without B-genome chromosomes, B- for some morphological and seed quality traits, such as days to flowering, days to maturity and erucic acid content. Further study revealed that resistance to Sclerotinia stem rot (caused by Sclerotinia sclerotiorum) has been inherited from the B or C genomes of B. carinata in some of the DH lines. Several BC3S1 families of another cross, derived from well-characterized BC3 plants containing introgressed B-genome chromosomes, were analyzed using SSR markers and the GISH assay to study the inheritance of the B-genome chromosome(s) and their association with morphological traits. This study revealed that the B-genome chromosomes tend to transfer through generations, either as whole chromosome(s) or as chromosomes without small terminal segments, as evidenced by low recombination frequencies (~ 0%) between the B and A/C-genome chromosomes. These results were supported by the GISH assay and chromosomes counts, and revealed that many of the BC3S1 lines were addition lines carrying extra B-genome chromosomes. / Plant Science

Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the species. Interspecific hybridization can greatly increase the amount of genetic variation available to plant breeders for improvement. Interspecific hybrids between sorghum and the 19 species in the tertiary gene pool have, until recently, not been successful. The Australian species, S. macrospermum, was recently successfully hybridized with sorghum by using germplasm homozygous for the iap allele, which eliminated reproductive isolation barriers. The objectives of this research were to evaluate the potential for use of S. macrospermum in an introgression breeding program, determine the map position of the Iap locus, and backcross the iap allele into elite Texas A&M germplasm. Interspecific hybrids between S. bicolor and S. macrospermum revealed moderate levels (2.6 II per PMC) of allosyndetic recombination, indicating that introgression through genetic recombination is possible. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ, Y and Z remain unknown. In backcrosses to S. bicolor using the female interspecific hybrid gamete and embryo rescue, BC1F1 plants were recovered. They had high chromosome numbers (2n = 35-70) and were male-sterile but three plants set backcross seed. Ninety-five percent of BC2F1 plants were 2n = 20 chromosomes and 75% of them contained S. macrospermum introgression. BC2F1 plants carried between 0-18.5% S. macrospermum introgression; in total 26% of the S. macrospermum genome was detected in the BC2 generation. Three types of introgression germplasm were created: alien addition lines; alien substitution lines; and introgression lines. Recombinant chromosomes, containing S. macrospermum introgression sites, were identified in multiple introgression lines. The Iap locus was genetically mapped to sorghum chromosome 2 (SBI-02), flanking AFLP markers were 2.1 and 2.7cM away, one AFLP marker shared the same map position (0.0cM). A genetic stock, Tx3361, was created which has iap iap genotype and improved agronomic qualities such as short plant height, white seed color, non-pigmented testa, no awns, reduced lodging, early maturity, and backcross segregation of male-sterility (ms3). This research shows that S. macrospermum is now available to plant breeders for sorghum improvement.

Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the species. Interspecific hybridization can greatly increase the amount of genetic variation available to plant breeders for improvement. Interspecific hybrids between sorghum and the 19 species in the tertiary gene pool have, until recently, not been successful. The Australian species, S. macrospermum, was recently successfully hybridized with sorghum by using germplasm homozygous for the iap allele, which eliminated reproductive isolation barriers. The objectives of this research were to evaluate the potential for use of S. macrospermum in an introgression breeding program, determine the map position of the Iap locus, and backcross the iap allele into elite Texas A&M germplasm. Interspecific hybrids between S. bicolor and S. macrospermum revealed moderate levels (2.6 II per PMC) of allosyndetic recombination, indicating that introgression through genetic recombination is possible. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ, Y and Z remain unknown. In backcrosses to S. bicolor using the female interspecific hybrid gamete and embryo rescue, BC1F1 plants were recovered. They had high chromosome numbers (2n = 35-70) and were male-sterile but three plants set backcross seed. Ninety-five percent of BC2F1 plants were 2n = 20 chromosomes and 75% of them contained S. macrospermum introgression. BC2F1 plants carried between 0-18.5% S. macrospermum introgression; in total 26% of the S. macrospermum genome was detected in the BC2 generation. Three types of introgression germplasm were created: alien addition lines; alien substitution lines; and introgression lines. Recombinant chromosomes, containing S. macrospermum introgression sites, were identified in multiple introgression lines. The Iap locus was genetically mapped to sorghum chromosome 2 (SBI-02), flanking AFLP markers were 2.1 and 2.7cM away, one AFLP marker shared the same map position (0.0cM). A genetic stock, Tx3361, was created which has iap iap genotype and improved agronomic qualities such as short plant height, white seed color, non-pigmented testa, no awns, reduced lodging, early maturity, and backcross segregation of male-sterility (ms3). This research shows that S. macrospermum is now available to plant breeders for sorghum improvement.

No description available.

The study of DNA sequence variation is a powerful approach to study genome evolution, and to reconstruct evolutionary histories of species. In this thesis, I have studied genetic variation in the fungus Neurospora tetrasperma and other closely related Neurospora species. I have focused on N. tetrasperma in my research because it has large regions of suppressed recombination on its mating-type chromosomes, had undergone a recent change in reproductive mode and is composed of multiple reproductively isolated lineages. Using DNA sequence data from a large sample set representing multiple species of Neurospora I estimated that N. tetrasperma evolved ~1 million years ago and that it is composed of at least 10 lineages. My analysis of the type of asexual spores produced using newly described N. tetrasperma populations in Britain revealed that lineages differ considerably in life history characteristics that may have consequences for their evolution. A comparative genomic analysis using three genomes of N. tetrasperma and the genome of N. crassa revealed that the mat a chromosomes in the lineages examine have been introgressed from other Neurospora species and that this introgression has reduced levels of molecular degeneration on the mating-type chromosomes. Finally, I generated a population genomic dataset composed of 92 N. tetrasperma genomes and two genomes of other Neurospora species. Analysis of these genomes revealed that all strains of N. tetrasperma have large regions of suppressed recombination on their mating-type chromosomes ranging from 69-84% of the chromosome and that the extent of divergence between mating-type chromosomes within lineages varies greatly (from 1.3 to 3.2%). I concluded that the source of this great divergence mating-type chromosome is large-scale introgression from other Neurospora species, and that these introgressed tracts have become fixed within N. tetrasperma lineages. I also discovered that genes within non-recombining introgressed regions of the mating-type chromosome have severely reduced levels of genetic variation as compared to the autosomes, and exhibit signatures of reduced molecular degeneration. My analysis of variation in coding regions revealed that positive selection on the introgressed regions has resulted in the removal of deleterious mutations and is responsible for the reductions in molecular degeneration observed.

No description available.

No description available.

Carthamus (Asteraceae) contains both crop species (C. tinctorius, safflower) and weedy species, increasing the need for a better understanding of the genus. Despite previous studies, many outstanding questions remain regarding the phylogenetic relationships of safflower, especially with regards to the weedy species. Investigation of the relationships in Carthamus was done using sequence data. The closest relative to C. tinctorius was studied using microsatellite data. Microsatellite data was also utilized to track the introgression of C. oxyacanthus DNA into the C. tinctorius genome in an interspecific cross. Sequence data supports the division of the genus into two sections, Carthamus and Atractylis. Both sequence and microsatellite data reveal that most traditionally recognized species are not monophyletic. Microsatellite data indicates that C. palaestinus is the closest relative of cultivated safflower. Microsatellites also indicate that C. oxyacanthus DNA is able to move into the C. tinctorius genome, showing potential for breeding programs and raising concerns for potential transgenic crops. / Plant Biology

Die Frage nach der Entstehung und Beibehaltung von sexueller Reproduktion nimmt in der Biologie eine zentrale Stellung ein. Dazu werden seit langem die Vor- und Nachteile asexueller Fortpflanzung diskutiert, da man sich von einer vergleichenden Betrachtungsweise wichtige Aufschlüsse erwartet. Dem kurzfristigen Vorteil der schnelleren Vermehrung stehen langfristige Nachteile entgegen: Aufgrund fehlender genetischer Rekombinationsprozesse können sich schädliche Mutationen im Laufe der Generationen anhäufen ("Muller’s ratchet"), und schnelle Anpassung an eine veränderte Umwelt oder neue Abwehrstrategien gegen Parasiten werden erschwert. Der Amazonenkärpfling, Poecilia formosa, stellt einen Organismus dar, dessen Fortpflanzung in Folge eines interspezifischen Hybridisierungsereignisses vom üblichen bisexuellen Muster abweicht: Es treten normalerweise nur Weibchen auf, die sich gynogenetisch vermehren. Hierbei werden die unreduzierten diploiden Eizellen durch Spermien sympatrisch vorkommender sexueller Wirtsmännchen nahe verwandter Arten (P. latipinna oder P. mexicana) stimuliert, um eine parthenogenetische Entwicklung der Embryonen zu initiieren. Es findet keine Karyogamie statt, so daß die Nachkommen in der Regel untereinander und mit ihren Müttern genetisch identisch (klonal) sind. Molekularbiologische Untersuchungen ergaben jedoch, daß P. formosa wesentlich älter ist, als dies auf der Basis von "Muller’s ratchet" zu erwarten war. Eine mögliche Erklärung dafür wäre, daß in seltenen Fällen väterliches Erbmaterial an die Nachkommen weitergegeben werden kann (paternale Introgression). Sowohl in natürlichen Lebensräumen als auch unter Laborbedingungen konnten nur zwei Formen paternaler Introgression identifiziert werden: Kommt es aufgrund von Karyogamie zu einer tatsächlichen Befruchtung der diploiden Oozyte durch das haploide Spermium entstehen triploide Individuen. In anderen Fällen verbleiben nach der Aktivierung durch das artfremde Spermium nur geringe DNA-Mengen in der Oozyte, die in den Kern aufgenommen werden und im Karyotyp als überzählige Chromosomen, sog. Mikrochromosomen, zu identifizieren sind. Die beiden Formen paternaler Introgression können jedoch auch kombiniert vorliegen. In diesen Fällen entwickelten sich die Individuen überraschenderweise zu phänotypischen Männchen. Die vorliegenden Ergebnisse über paternale Introgression können zur Aufklärung der Frage beitragen, warum P. formosa und andere asexuelle Organismen offenbar länger überlebten, als vorhergesagt. Im Gegensatz zu den bisherigen Annahmen könnte es sich bei spermienabhängiger Parthenogenese nicht etwa nur um eine unvollkommene Parthenogenese handeln, sondern um einen gut angepaßten Fortpflanzungsmodus, der die Vorteile von asexueller mit denen sexueller Fortpflanzung kombiniert. / One of the greatest challenges in evolutionary biology is explaining the widespread occurrence of sexual reproduction and the associated process of genetic recombination. Comparing the advantages and disadvantages of sexual and asexual reproduction is expected to give major insights to that "queen of questions". Whereas asexual females have the short term advantage of producing twice as many daughters as sexual females, they are also expected to suffer from long-term constraints: Due to the absence of genetic recombination, asexuals are prone to accumulate deleterious mutations (Muller´s ratchet), and adaptation to changing environments or the escape from parasite load will be aggravated. The Amazon molly, P. formosa, resembles an organism which shows an alternative reproductive mode to the ubiquitous bisexual reproduction. Being an all-female species due to interspecific hybridization, it reproduces gynogenetically: Unreduced diploid eggs are only activated by sperm of males of closely related sympatric species. Without karyogamy the oocytes develop parthenogenetically leading to genetically identical (clonal) offspring. Molecular phylogenetic data suggest that P. formosa might have survived longer than predicted by Muller´s ratchet. To explain this paradox, two phenomena which have been observed in natural populations as well as in laboratory broods are taken into consideration: Triploidy and occurrence of microchromosomes as a consequence of paternal introgression. Triploidy results from the successful insemination of the unreduced diploid eggs with haploid host sperm and subsequent karyogamy, whereas microchromosomes are small supernumerary chromosomes that seem to be the left over of the enzymatic machinery which normally clears the egg from the sperm nucleus after activation has occurred. Both forms of paternal introgression may also occur in combination. Surprisingly, these individuals developed spontaneously into males. The results on paternal introgression obtained here can contribute to answer the question why P. formosa as well as other unisexual vertebrates survived longer than predicted. Contradictory to common knowledge, gynogenesis might not be an imperfect parthenogenesis but a well adapted reproductive mode combining the advantages of asexual and sexual reproduction.