In Caenorhabditis nematodes, the androdioecious, self-fertilizing reproductive strategy has evolved relatively recently from gonochoristic, outcrossing ancestors. Transitions in mating system impact how genes are vertically transmitted between generations and horizontally between populations through gene flow. To date, species-wide studies have targeted selfing species, and we have limited understanding about how population genetic processes have shaped the genome structure and evolutionary history of outcrossing species of Caenorhabditis. To fill this gap, I investigate patterns of genetic variation and population genetic processes focusing on two outcrossing species in the genus, C. brenneri and C. remanei, using a survey of nucleotide polymorphisms in a multipopulation, multilocus context. I discover extensive genetic diversity in Caenorhabditis brenneri, termed hyperdiversity, giving this species the highest known levels of nucleotide polymorphism for any multicellular eukaryote. Genetic crosses between populations, extensive intra-locus recombination, and evidence of weak selection on codon usage all suggest that this is due to a large effective population size in the species and not an artifact of cryptic species divergence. I demonstrate that C. remanei also is characterised by high genetic variation globally, albeit not as extreme as in C. brenneri, and within each local population. Despite geographic barriers, considerable gene flow occurs between inter-continental locations. While exploring genetic diversity in C. remanei, I discovered C. sp. 23, a new, gonochoristic species reproductively isolated and highly divergent from it. Subsequently, taking advantage of this newly discovered species pair, I explore the patterns of postzygotic reproductive isolation between C. remanei and C. sp. 23. I find evidence of partial F1 hybrid inviability, strong F1 hybrid male sterility (Haldane’s rule) and strong F2 hybrid breakdown between the two. The findings from this thesis, especially the notion of hyperdiversity, can be taken advantage of to answer key questions on testing limits of natural selection, of evolution of genome complexity as well as identifying and characterising functional, non-coding regulatory elements. Discovery of a new species pair in Caenorhabditis helps establish an emerging age of speciation genetics in the worm.

In Caenorhabditis nematodes, the androdioecious, self-fertilizing reproductive strategy has evolved relatively recently from gonochoristic, outcrossing ancestors. Transitions in mating system impact how genes are vertically transmitted between generations and horizontally between populations through gene flow. To date, species-wide studies have targeted selfing species, and we have limited understanding about how population genetic processes have shaped the genome structure and evolutionary history of outcrossing species of Caenorhabditis. To fill this gap, I investigate patterns of genetic variation and population genetic processes focusing on two outcrossing species in the genus, C. brenneri and C. remanei, using a survey of nucleotide polymorphisms in a multipopulation, multilocus context. I discover extensive genetic diversity in Caenorhabditis brenneri, termed hyperdiversity, giving this species the highest known levels of nucleotide polymorphism for any multicellular eukaryote. Genetic crosses between populations, extensive intra-locus recombination, and evidence of weak selection on codon usage all suggest that this is due to a large effective population size in the species and not an artifact of cryptic species divergence. I demonstrate that C. remanei also is characterised by high genetic variation globally, albeit not as extreme as in C. brenneri, and within each local population. Despite geographic barriers, considerable gene flow occurs between inter-continental locations. While exploring genetic diversity in C. remanei, I discovered C. sp. 23, a new, gonochoristic species reproductively isolated and highly divergent from it. Subsequently, taking advantage of this newly discovered species pair, I explore the patterns of postzygotic reproductive isolation between C. remanei and C. sp. 23. I find evidence of partial F1 hybrid inviability, strong F1 hybrid male sterility (Haldane’s rule) and strong F2 hybrid breakdown between the two. The findings from this thesis, especially the notion of hyperdiversity, can be taken advantage of to answer key questions on testing limits of natural selection, of evolution of genome complexity as well as identifying and characterising functional, non-coding regulatory elements. Discovery of a new species pair in Caenorhabditis helps establish an emerging age of speciation genetics in the worm.

Theory predicts that sexual reproduction confers an advantage over asexual reproduction due to the generation and maintenance of genetic variation afforded by the processes of recombination and segregation. However, this prediction has rarely been empirically tested. Oenothera is a flowering plant genus whose evolutionary history is punctuated with numerous transitions from sexual reproduction to a form of functionally asexual reproduction known as Permanent Translocation Heterozygosity (PTH). In Ch. 2, a greenhouse experiment examined patterns of phenotypic and genetic variation within and between populations across eight Oenothera species, representing four independent transitions to PTH. I found some evidence for a decrease in heritability and an increase in population differentiation in phenotypic traits associated with the loss of sex. Ch. 3 explored the possibility that rare outcrossing events represent a mechanism for the maintenance of variation in a PTH species. Analysis of microsatellite markers showed evidence for extremely low rates of outcrossing in natural populations (< 1%) of O. biennis, a PTH species.

Theory predicts that sexual reproduction confers an advantage over asexual reproduction due to the generation and maintenance of genetic variation afforded by the processes of recombination and segregation. However, this prediction has rarely been empirically tested. Oenothera is a flowering plant genus whose evolutionary history is punctuated with numerous transitions from sexual reproduction to a form of functionally asexual reproduction known as Permanent Translocation Heterozygosity (PTH). In Ch. 2, a greenhouse experiment examined patterns of phenotypic and genetic variation within and between populations across eight Oenothera species, representing four independent transitions to PTH. I found some evidence for a decrease in heritability and an increase in population differentiation in phenotypic traits associated with the loss of sex. Ch. 3 explored the possibility that rare outcrossing events represent a mechanism for the maintenance of variation in a PTH species. Analysis of microsatellite markers showed evidence for extremely low rates of outcrossing in natural populations (< 1%) of O. biennis, a PTH species.

Abalone (Haliotis spp.) are marine broadcast spawners that inhabit temperate and tropical waters across the globe. Their importance as a fisheries resource has resulted in considerable research into key aspects of their biology, particularly around growth and reproduction. In addition, there has been ongoing interest regarding the genetic variation in both wild and hatchery populations. The majority of abalone dispersal probably occurs during a pelagic lecithotrophic larval stage. In general, oceanographic features, life history characteristics, and larval dispersal ability can manipulate dispersal and gene flow patterns of marine fauna. In the case of abalone, considerable research has examined the population genetic structure of a variety of species, and several papers implicate ocean currents and life history characteristics as important factors that define population genetic structure. In comparison to other abalone species, little information regarding the genetic structure of New Zealand's endemic H. iris exists. The goal of this thesis was to elucidate the genetic structure of H. iris using mitochondrial and nuclear markers in regards to two potential barriers to gene flow, the Cook Strait region and the gamete recognition protein, lysin. The genetic structure of H. iris was first examined in regards to a consistent pattern of genetic structure emerging in recent literature of coastal marine invertebrates around New Zealand: specifically, a north-south genetic split that occurs in the Cook Strait region (Chapter 2). Two regions of the mitochondria (totaling 1055 bp) were amplified across 477 individuals from 25 locations around New Zealand. A north-south split around the Cook Strait region was evident among H. iris samples. Unlike the other studies of New Zealand coastal marine invertebrates, the north-south split for H. iris was not located across regions of reported upwelling; instead the split was located across Cook Strait narrows. The north-south split was reflected in increased haplotype diversity for the northern samples. Genetic structure was also examined using microsatellite loci. After unsuccessful attempts at cross-species amplification using 8 loci developed for H. rubra and 11 loci developed for H. midae, 13 polymorphic loci were isolated de novo for H. iris (Chapter 3). Of these, three very polymorphic loci were optimized for population genetic analyses. These three loci were used to genotype 447–459 individuals from the same 25 locations examined with mitochondrial DNA (Chapter 4). Like the mitochondrial DNA, the microsattelites indicated population genetic structure around the Cook Strait region; however the split identified with microsatellites occurred in the greater Cook Strait region with two sample sites from the north of the South Island grouping with the North Island. Extrinsic barriers, like the Cook Strait region, are the primary focus of studies examining differentiation in marine invertebrate fauna. However, dispersal of an individual to a new population does not necessarily mean it can successfully reproduce with individuals of the new population. Potentially, populations may be diverging at genes essential for reproduction, i.e. gamete recognition proteins. The abalone egg recognition protein, lysin, is one of the best characterized gamete recognition proteins in marine broadcast spawners. Despite its well-understood function and structure, studies examining variation in lysin have been limited to small sample sizes (N ≤ 11) and have found very little variation. Here, lysin was screened across 287 individuals from 17 sampling sites around New Zealand to assess intraspecific variation and genetic structure across the Cook Strait region (Chapter 5). The majority of the variation in a 783 bp fragment spanning from exon 4 to 5, was located in the intron. The variability in this fragment detected no genetic structure among samples or across the Cook Strait region. The variation in lysin was considerably lower than the variation in either the mitochondrial DNA or the microsatellite loci. To determine whether this was an artifact of being a nuclear sequence, which, in general, have a lower mutation rates than microsatellite markers and mitochondrial DNA and a larger effective population size then mitochondrial DNA, or was a signature of a recent selective sweep, 857 bp of the Gα1 intron was assessed for genetic variation in 227 H. iris individuals from 14 sampling locations (Chapter 6). The Gα1 intron was considerably more diverse than the lysin fragment examined, suggesting that the relative lack of variation in the lysin fragment has resulted from a recent selective sweep. Additionally, the Gα1 intron was used to examine population genetic structure across the Cook Strait region and detected a weak but significant pattern of structure consistent with that detected using the microsatellite loci. Overall, the a priori tests of genetic structure based on mitochondrial DNA, microsatellite markers, and the across Gα1 intron all identified a north-south genetic split around the Cook Strait region; however, the patterns of this split was slightly inconsistent among molecular markers. When cluster analyses were applied the patterns of genetic structure became more similar: for the mitochondrial, microsatellite, and Gα1 intron data, cluster analyses indicate that only one sample from the north of the South Island groups with the North Island, while a few discrepancies existed in regards the grouping of samples from the east coast of the North Island.

In this study the genetic diversity in Turkish native sheep breeds was investigated based on microsatellite DNA loci. In total, 423 samples from 11 native and crossbreed Turkish sheep breeds (Akkaraman, Morkaraman, Kivircik, ivesi, Dagli&ccedil / , Karayaka, HemSin, Norduz, Kangal, Konya Merinosu, T&uuml / rkgeldi) and one Iraqi breed (Hamdani) were analyzed by sampling from breeding farms and local breeders. After excluding close relatives by Kinship analysis, the genetic variation within breeds was estimated as gene diversities (HE), which ranged between 0.686 and 0.793. The mean number of observed alleles (MNA) ranged between 5.8 and 11.8. The allele frequency distribution across Turkey showed no gradient from east to west expected in accordance with the Neolithic Demic Diffusion model. The differentiation between different samples of Akkaraman, Dagli&ccedil / and Karayaka breeds was tested by FST index. Akkaraman1 sample from the breeding farm was significantly (P&lt / 0.001) different from the other two Akkaraman samples. Deviation from HW expectations observed for Akkaraman1, ivesi, Morkaraman and HemSin breeds. AMOVA analysis revealed that most of the total genetic variation (~90%) was partitioned within the individuals. In parallel to this observation, when factorial correspondence analysis and shared alleles distances were used to analyze the relationship between the individuals of the breeds, there was no clear discrimination between breeds. Moreover, NJ tree constructed based on DA genetic distance, and PC analyses were used to analyze among breed differentiation. Delaunay Network drew 4 genetic boundaries (two of them being parallel to geographic boundaries) between breeds. All the results indicated that Kivircik was the most differentiated breed. Finally, Mantel Test and Bottleneck analysis did not reveal a significant result. Kivircik breed, among all native Turkish breeds, was found to be the genetically closest to the European breeds based on the loci analyzed. The genetic variation in Turkish breeds was not much higher than that of European breeds, which might be a consequence of the recent sharp decrease in sheep number.

Diss. (sammanfattning). Umeå : Sveriges lantbruksuniv., 2003. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2004. / Härtill 4 uppsatser.