A Comprehensive Investigation of in American Sāmoa

Foreword. Preface. Contributors. Part I Concepts and Methods in Bacterial Population Genetics. 1 The Coalescent of Bacterial Populations. 1.1 Background and Motivation. 1.2 Population Reproduction Models. 1.3 Time and the Effective Population Size. 1.4 The Genealogy of a Sample of Size n. 1.5 From Coalescent Time to Real Time. 1.6 Mutations. 1.7 Demography. 1.8 Recombination and Gene Conversion. 1.9 Summary. 2 Linkage, Selection, and the Clonal Complex. 2.1 Introduction Historical Overview. 2.2 Recombination, Linkage, and Substructure. 2.3 Neutrality versus Selection. 2.4 Clustering Techniques. 3 Sequence-Based Analysis of Bacterial Population Structures. 3.1 Introduction. 3.2 Alignments. 3.3 Phylogenetic Methods. 3.4 Measures of Uncertainty. 3.5 Beyond the Tree Model. 4 Genetic Recombination and Bacterial Population Structure. 4.1 Introduction. 4.2 Constraints on LGT. 4.3 Infl uences of LGT on Sequence Analyses. 4.4 The Detection of Individual LGT Events. 4.5 The Estimation of Homologous Recombination Rates. 4.6 Properly Accounting for LGT During Sequence Analyses. 4.7 Questions Relating Directly to LGT. 5 Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations. 5.1 Introduction. 5.2 Natural Selection. 5.3 Statistical Methods for Detecting the Presence of Natural Selection. 5.4 Statistical Methods for Bacterial Populations. 5.5 An Example. 5.6 Discussion and Perspective. 6 Demographic Infl uences on Bacterial Population Structure. 6.1 Bacterial Population Size. 6.2 Measures of Genetic Diversity. 6.3 The Concept of Effective Population Size. 6.4 Inferring Past Demography from Genetic Sequence Data. 6.5 Population Subdivision. 6.6 What is a Bacterial Population? 6.7 Conclusion. 7 Population Genomics of Bacteria. 7.1 Introduction. 7.2 Classical Bacterial Population Genetics. 7.3 The Genomics Era. 7.4 Bacterial Population Genomics. 7.5 Next-Gen Bacterial Population Genomics. 7.6 Next-Gen Genomics Technology. 7.7 Next-Gen Genomic Data Analysis. 7.8 Conclusions/Future Prospects. 8 The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria. 8.1 Introduction. 8.2 MLVA and Other DNA Fragment-Based Methods. 8.3 SNP and DNA Sequence-Based Methods. 8.4 Conclusion. Part II Population Genetics of Select Bacterial Pathogens. 9 Population Genetics of Bacillus: Phylogeography of Anthrax in North America. 9.1 Introduction. 9.2 History of Anthrax in North America. 9.3 The Anthrax Districts after 1944. 9.4 Molecular Genotyping of B. anthracis. 9.5 Genotypes within the Anthrax Districts in North America. 9.6 Phylogenetic Resolution within the WNA Lineage. 9.7 Phylogeographic Resolution within the Ames Lineage. 9.8 Additional B. anthracis Genotypes in North America. 9.9 Conclusions. 10 Population Genetics of Campylobacter. 10.1 Introduction. 10.2 Human Infection. 10.3 Genetic Structure. 10.4 Models of Campylobacter Evolution. 10.5 Clades and Species. 10.6 Conclusion. 11 Population Genetics of Enterococcus. 11.1 Introduction. 11.2 Antibiotic Resistance. 11.3 Vancomycin Resistance. 11.4 VRE: A Zoonosis or Not? 11.5 Population Structure and Genetic Evolution: Similarities and Differences Between E. faecium and E. faecalis. 11.6 What Is Driving GD in E. faecium and E. faecalis? 11.7 The Accessory Genome of E. faecium and E. faecalis. 11.8 Summary, Conclusions, and Future Perspectives. 12 Population Biology of Lyme Borreliosis Spirochetes. 12.1 Introduction. 12.2 Genome Organization of LB Spirochetes. 12.3 Genotyping of LB Spirochetes and Phylogenetic Tools. 12.4 Population Biology and Evolution of LB Spirochetes. 12.5 Do LB Species Exist? 12.6 Future Research Avenues. 13 Population Genetics of Neisseria meningitidis. 13.1 Introduction. 13.2 A Brief History of Typing of Meningococci. 13.3 Species Separation. 13.4 Sampling Strategies. 13.5 The Clonal Complexes of Meningococci. 13.6 Forces Shaping the Meningococcal Metalineage. 13.7 Virulence, a Mysterious Trait. 13.8 Population Effect of Meningococcal Vaccines. 13.9 Antibiotic Resistance and Meningococcal Lineages. 13.10 Concluding Remarks. 14 Population Genetics of Pathogenic Escherichia coli. 14.1 Introduction. 14.2 E. coli Population Genetics: Clonal or not Clonal? 14.3 The E. coli Phylogenetic Structure. 14.4 The Evolutionary History of a Host-Specifi c Obligate Pathogen: The Shigella and EIEC Case Study. 14.5 What Makes You an Opportunistic Pathogen? 14.6 The Virulence Resistance Trade-off. 14.7 Concluding Remarks. 15 Population Genetics of Salmonella: Selection for Antigenic Diversity. 15.1 Introduction. 15.2 Generation Timescale Diversifi cation. 15.3 Antigenic Diversity in Salmonella. 15.4 Why Are Diverse H and O Antigens Maintained in Salmonella? 15.5 Conclusions. 16 Population Genetics of Staphylococcus. 16.1 Introduction. 16.2 Overview of The Staphylococcal Population Structure. 16.3 Staphylococcal Population Structure in Specific Disease Contexts. 16.4 Origin and Maintenance of Staphylococcal Genetic Variation. 16.5 Macroevolutionary Considerations and Concluding Remarks. Appendix 1 Diversity and Differentiation. 17 Population Genetics of Streptococcus. 17.1 Habitats, Transmission, and Disease. 17.2 Classical Strain Typing. 17.3 Multilocus Sequence Typing (MLST) Based on Housekeeping Genes. 17.4 Species Boundaries and Gene Flow. 17.5 Niche-driving Genes. 17.6 Bacterial Population Dynamics and Selection. 17.7 Machinery of Genetic Change, Revisited. 18 Population Genetics of Vibrios. 18.1 Introduction. 18.2 V. cholerae. 18.3 V. parahaemolyticus . 18.4 V. vulnificus. 18.5 Conclusions. References. Index.

During my Ph.D., I used the next generation sequencing technology to investigate patterns of recombination and the genetic consequences of different reproductive modes of Daphnia magna. More precisely, I have used Restriction site Associated (RAD) sequencing to construct a high-density genetic map that can be coupled with the draft genome assembly of D. magna, thus, providing an essential tool for genome investigations in this widely used model organism (Chapter I). Such a map has enabled characterization of variation in the meiotic recombination rates across the genome of D. magna for the first time. Since recombination rates are an important parameter in almost any type of genetic research, this newly gained insight into the recombination landscape of D. magna offers a fundamental information for future studies of genome evolution, identification of genes underlying phenotypic traits and population genetic analyses. 
\nIn addition to sexual reproduction, D. magna can also reproduce asexually to generate clutches of clonal offspring (ameiotic parthenogenesis). This feature of Daphnia biology is extremely useful for scientific experimentation where the genetic variation among tested individuals has to be minimized. However, over the last decade, reports of genome homogenization (loss of heterozygosity - LOH) in asexual lineages of D. pulex have indicated that asexual genomes are not static as it was previously assumed and that some levels of ameiotic recombination, in addition to mutation, may induce genetic variation among putative clones. However, comparing parthenogenetic offspring with their mothers at several thousand genetic markers generated by RAD-sequencing, I was not able to detect any LOH events in D. magna (Chapter II). I cannot exclude the possibility that ameiotic recombination indeed occurs in D. magna, however, my results indicate that such phenomenon is extremely rare or restricted to the very short genomic regions that I was unable to investigate, despite a high-density of markers used in this study. 
\nNevertheless, the implementation of RAD-sequencing protocol for the genome studies of D. magna still enables interrogation of the transmission of genetic information from parents to offspring at unprecedented resolution. For an example, a RAD-sequencing based analysis of reduction in parental heterozygosity among rare ephippial hatchlings (typically produced by sexual reproduction) found in non-male producing populations of D. magna, has enabled differentiation between self-fertilization and automixis (meiotic parthenogenesis), by uncovering the subtle differences in genetic consequences of these reproductive strategies (Chapter III). Harnessing the ability of high-resolution genetic analysis it was demonstrated that, in the absence of males, D. magna can produce diapause eggs by automixis, and an additional type of asexual reproduction that was not previously reported for this species.
\nFinally, RAD-sequencing European populations of D. magna revealed an association of genetic variation with the geographic location of individual samples (Chapter IV), a task which was not previously amenable using mitochondrial or microsatellite markers. This study provided a better insight into population genetic structure of D. magna and suggested that genetic differentiation is mainly driven by geographic distance. These results set a foundation for forthcoming studies aiming to disentangle past and future evolutionary processes shaping populations of this intriguing model organism.
\nTaken together, research presented in my thesis illustrates the practicality of reduced representation genome sequencing for tackling diverse topics in evolutionary biology. By increasing awareness of non-randomness of meiotic recombination across the genome of D. magna, the diversity of reproductive mechanisms it can employ, and its large-scale population structure, I hope this work will contribute to further understanding of the remarkable adaptive capacity this crustacean is famous for.
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Climate change is predicted to increase forest fires in boreal forests, which can threaten the sustainability of forest genetic resources. Wildfires can potentially impact genetic diversity and population structure in forest trees by creating population bottlenecks, and influencing demography, effective population size (Ne) and various evolutionary processes. We have investigated this critical issue in a widely-distributed, transcontinental, ecologically and economically important and fire-intolerant boreal conifer, white spruce (Picea glauca (Moench) Voss). We tested the hypothesis that in a predominantly outcrossing species with long distance gene flow, such as white spruce, located in primary undisturbed forests, normal forest fires do not adversely affect genetic diversity and population structure. We used 10 nuclear genic and genomic microsatellite loci to examine genetic diversity and population structure of post-fire pristine old-growth (PF-OG) and adjacent post-fire naturally regenerated young (PF-YR) stands. The genetic diversity, inbreeding and genetic differentiation levels, Bayesian population structure, Ne and latent genetic potential were statistically similar between the PF-OG and PF-YR populations. None of the microsatellites showed any signature of selection. Our study demonstrates that normal wild forest fires do not adversely affect genetic diversity, differentiation, and population genetic structure in white spruce. The results should have wide significance for sustainable forest management.

Previous genetic studies of eastern coyotes ( Canis latrans ) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

Trypanosoma lewisi belongs to the so-called atypical trypanosomes that occasionally affect humans. It shares the same hosts and flea vector of other medically relevant pathogenic agents as Yersinia pestis, the agent of plague. Increasing knowledge on the population structure (reproductive mode, population size, dispersal) of this parasite thus represents a challenging but important issue. The use of polymorphic genetic markers, together with suitable population genetics tools, is a convenient way to achieve such objectives. To date, the population biology of T. lewisi is poorly known and, to our knowledge, no population genetics studies have ever been conducted. Here, we present the development of nine microsatellite markers of this species. We investigated their polymorphism in different countries from Africa and South-East Asia from DNAs extracted from the spleen of their rodent reservoirs (essentially rat species). Several amplification problems arose, especially with South-East Asian individuals. This led to retain only those individuals with complete genotypes (most of them originating from West Africa, notably Cotonou, Benin) to ensure an optimal estimate of heterozygosity. Our results pointed towards a mainly (at least 95-99%) clonal mode of propagation, a strong subdivision at the smallest scale available (i.e., urban neighborhoods, i.e. 0.250 km²), and a generation time most probably shorter than 4 months. In future studies, more extensive sampling at smaller geographic scales (i.e., households), within a one- or two-months window and with improved amplification conditions, should lead to a more precise picture of the fine population structure of this parasite.

Humpback whales undertake long-distance seasonal migrations between low latitude winter breeding grounds and high latitude summer feeding grounds. Although arguably one of the best studied of all baleen whales, there remain some critical gaps in our understanding of their population structure, migratory movement and the mixing of putative populations on the feeding grounds. Addressing these uncertainties is important in the development of demographic models that reconstruct the historical trajectory of population decline and recovery following the cessation of commercial whaling. Utilising both mitochondrial and nuclear genetic markers, this thesis examines the population structure and distribution of humpback whales that migrate to separate winter breeding grounds along the north-western and north-eastern coasts of Australia, and their interaction with the endangered populations of the South Pacific. The project investigated three important gaps in knowledge: population structure among putative breeding populations, the mixing of breeding populations on high latitude Antarctic feeding grounds and evidence for sex-specific migration along the eastern Australian migratory corridor. The thesis also reports the discovery and utility of novel nuclear genetic markers (single nucleotide polymorphisms, SNPs). These markers hold promise for facilitating more effective multi-laboratory collaboration. Among the Australian putative populations, weak but significant differentiation was detected across ten microsatellite loci and mitochondrial control region sequences. This pattern of low level differentiation is emerging as a characteristic of Southern Hemisphere humpback whale populations indicating extensive movement at least historically, if not presently. As the first step towards assessing the mixing of Australian and endangered South Pacific humpback whale breeding populations on the Antarctic feeding grounds, a series of simulations were conducted to estimate the statistical power of both mitochondrial and nuclear microsatellite data from these populations for a mixed-stock analysis (MSA). The results of these simulations confirmed that we can draw robust conclusions from our MSA of Antarctic feeding ground samples collected south of eastern Australia and New Zealand in 2010. Using combined mtDNA and microsatellite datasets revealed substantial contributions from both eastern Australia and New Caledonia, but not western Australia; strengthening emerging evidence that these Antarctic waters are utilized by humpback whales from both eastern Australia and the more vulnerable breeding population of New Caledonia, representing Oceania. There was no compelling evidence for sex-specific migration within the eastern Australian breeding population as indicated by the lack of significant differences detected in the patterns of haplotype sharing, haplotype frequency or haplotype differentiation between males and females. Instead, the significant differentiation revealed between the sexes at the nucleotide level for one sampling location and between sampling locations at the haplotype level suggests that humpback whale migration along eastern Australia may be more complex than previously thought. Increasing the statistical power of our genetic datasets through the addition of new informative markers, including the SNPs discovered in this project, and incorporating non-genetic data, will assist in future studies of the population genetic structure and dynamics of Southern Hemisphere humpback whales.

This paper summarises the key findings from recent research on the population genetics and epidemiology of Fusarium pathogens causing head blight and crown rot of wheat in Australia and how this information has enabled the screening and selection of wheat germplasm with improved resistance to Fusarium. By relating new findings to the current state of knowledge, the paper serves as a timely and critical review of the international literature. In Australia, both Fusarium pseudograminearum and F. graminearum can cause both crown rot and Fusarium head blight under artificial inoculation. However, the former species is more widespread and is predominantly associated with crown rot whereas F. graminearum is mainly associated with Fusarium head blight, with limited geographical distribution in and around the Liverpool Plains in northern New South Wales. Studies of population structure and genetics have revealed that both species are genotypically diverse with similar levels of genetic recombination despite Gibberella zeae, the teleomorph of F. graminearum, being homothallic and G. coronicola, the teleomorph of F. pseudograminearum, being heterothallic. A high-throughput and reliable crown rot bioassay has been developed and used to screen over 1500 wheat germplasms to select 17 lines with putative crown rot resistance. Key differences in pathogen biology and epidemiology between Australia and the USA have emerged from other recent collaborative studies, which show that macroconidia constitute the bulk of aerial Fusarium head blight inoculum in Australia, whereas ascospores are the dominant primary inoculum for Fusarium head blight worldwide. The limited spread of splash-dispersed macroconidia of F. graminearum probably explains the restricted geographical distribution of this species in Australia. Other research collaboration has compared the aggressiveness, mycotoxin production and genotypic polymorphisms of the pathogen population from Australia and the USA. These and other differences in pathogen adaptation emphasise that research outcomes from elsewhere must be tested for relevance before applying them to Australian farming systems.

Genetic markers of the Y chromosome are powerful tools for investigating paternal ancestry and are widely used in population and forensic genetics. However, in order to obtain statistics with a higher degree of certainty using these markers, it is necessary to obtain haplotypic frequencies from a representative database, as well as knowing the diversity and structure of the population. The aim of this study was to investigate the genetic diversity of a sample of 1114 unrelated men from three states in the Northeast of Brazil: Paraíba, Pernambuco and Ceará, through the analysis of 23 Y-STRs and to contribute to the expansion of the Brazilian database on these markers. The PPY23 panel had a high discriminatory power, and the population structure was consistent with the historical aspects of the colonization of the Northeast of Brazil. Population comparisons based on paired genetic differentiation values (Fst) revealed no statistically significant differences between the three populations in this study. However, it was observed that Pernambuco and Paraíba were genetically closer to states outside the Northeast region. Y-STR-based haplogroup prediction, carried out using the NevGen software, revealed that the paternal lineage of the populations in this study is essentially European, with little African or Native American influence, just like the rest of the Brazilian population. Additionally, this work contributes to a more representative database for use in forensic and population genetics.

ABSTRACTThe franciscana dolphin, Pontoporia blainvillei, is endemic to the coastal waters of the southwestern Atlantic Ocean and the most endangered dolphin in the area. Four Franciscana Management Areas (FMAs) are currently recognised; however, results of genetic studies suggest the requirement for additional FMAs and highlight the need for more detailed studies in the southern extreme of the species distribution. With this aim, we studied the genetic diversity and population structure of the species analysing an mtDNA control region fragment (434 bp) in 44 individuals collected in four sampling sites located in Southern Buenos Aires. Haplotype diversity (H = 0.75 ± 0.05) was mostly higher than the observed in endangered or near threatened odontocetes. Population structure analyses suggest that three different genetic populations should be recognised within FMA IV: Northern, Eastern and Southern Buenos Aires. Altogether, these results should be taken into account in future conservation plans for the species.

IntroductionMalayemys khoratensis is a freshwater turtle species endemic to northeastern Thailand and Lao PDR. While M. khoratensis is relatively common and widespread in Thailand, its population size and demographic trends remain largely unknown, as direct population estimates are lacking. This species faces significant threats from consumption, exploitation, and trade. Therefore, this study aims to investigate the genetic diversity, population structure, and demographic trends of M. khoratensis in northeastern Thailand, using two mitochondrial DNA genes, Cyt b and ND4.MethodWe grouped the turtles based on three major river basins in northeastern Thailand: Mun, Chi, and Northeast Mekong to assess population structure and test the isolation-by-basin hypothesis. The Cyt b and ND4 genes of 49 M. khoratensis individuals across 15 provinces in Thailand were sequenced, and 15 sequences from a previous study of Ihlow et al. (2016) were included into the analyses. We constructed a haplotype network from the concatenated sequences and analyzed the population structure with the analysis of molecular variance (AMOVA). Additionally, we used a Bayesian Skyline plot (BSP) analysis to estimate the effective female population size and explore the demographic history of this species.ResultsOur analysis identified 13 unique haplotypes defined by 26 polymorphic sites from 64 samples. The total haplotype diversity for M. khoratensis was 0.819, while nucleotide diversity was 0.0031. The haplotype network and AMOVA revealed no distinct population structure among the river basins, suggesting gene flow across these regions. The BSP estimated a stable effective female population size of approximately 130,000 individuals since around 100,000 years ago (late Pleistocene).ConclusionOur findings indicated no significant population structure by river basin, which may be due to natural movement between basins or potential human-mediated translocations linked to the turtle trade. The demographic trend of M. khoratensis appears to have been stable over time. However, given the ongoing exploitation of this species, we recommend regular monitoring of population trends to support its long-term survival.

Effects of fifty years of shelterwood harvesting on genetic diversity and population structure of Oriental beech (Fagus orientalis L.) in the relict Hyrcanian forest

Assessing genetic diversity and population structure is prerequisite to the systematic utilization and conservation of germplasm resources of crop plants. The genetic diversity and population structure in a combined panel of 557 Gossypium hirsutum L. accessions including 375 cultivars and 182 race stocks using 114 pairs of simple sequence repeat primers were evaluated in the current study. Six G. barbadense L. accessions were included as an out-group. Genotyping the diversity panel of 563 accessions with the markers identified a total of 819 alleles and 662 alleles within G. hirsutum. Population structure analysis identified one G. barbadense group and five G. hirsutum groups corresponding to southwestern cultivars, Mexican collections, western cultivars, southeastern and mid-south cultivars, and Guatemalan collections. Average genetic distance of 0.253 indicated a moderate level of genetic diversity in this panel. Analysis of molecular variance revealed a low level of differentiation among cultivated cotton groups compared to landrace accessions. Genetic diversity and population structure analyses suggest landraces of Guatemala could be a potential source of novel genetic variability for U.S. cotton. Further, multiple core sets with different levels of allele richness were identified. The diversity panel and the core sets identified could be a good resource for broadening the genetic base of U.S. cotton and for genetic analysis of agronomic traits.

Genetic structure of the pine needle pathogen <i>Lecanosticta acicola</i> in Lithuania and northern Poland

Chapter 2 - Biological Distances and Population Genetics in Bioarchaeology

Eggplant (Solanum melongena L.) is an important solanaceous crop with high phenotypic diversity and moderate genotypic diversity. Ninety-nine genotypes of eggplant germplasm (species (S. melongena, S. incanum, S. linnaeanum and S. gilo), landraces and heirloom cultivars) from 32 countries and five continents were evaluated for genetic diversity, population structure, fruit shape, and disease resistance to Phytophthora fruit rot. Fruits from each line were measured for fruit shape and evaluated for resistance to two Phytophthora capsici isolates seven days post inoculation. Only one accession (PI 413784) was completely resistant to both isolates evaluated. Partial resistance to Phytophthora fruit rot was found in accessions from all four eggplant species evaluated in this study. Genetic diversity and population structure were assessed using 22 polymorphic simple sequence repeats (SSRs). The polymorphism information content (PIC) for the population was moderate (0.49) in the population. Genetic analyses using the program STRUCTURE indicated the existence of four genetic clusters within the eggplant collection. Population structure was detected when eggplant lines were grouped by species, continent of origin, country of origin, fruit shape and disease resistance.