Thelytokous Reproduction of Onion Thrips, Thrips tabaci Lindeman 1889, Infesting Welsh Onion and Genetic Variation among Their Subpopulations

Parthenogenesis is not uncommon in thrips. This asexual reproduction produces males (arrhenotokous) or female (thelytokous). Only females are found in the onion thrips (Thrips tabaci Lindeman 1889) infesting Welsh onion (Allium fistulosum) in several areas of Korea. To determine the reproduction mode of T. tabaci, thrips infesting Welsh onion were collected from different localities in Korea. Cytochrome oxidase I (COI) sequences were then assessed. Results showed that all test local populations had signature motif specific to a thelytokous type. These COI sequences were clustered with other thelytokous populations separated from arrhenotokous T. tabaci populations. In a laboratory test, individual rearing produced female progeny without any males. These results support that Korean onion thrips infesting Welsh onion have the thelytokous type of parthenogenesis. Local thrips populations exhibited significant variations in susceptibility to chemical and biological insecticides. Random amplified polymorphic DNA (RAPD) analysis indicated genetic variations of local populations. However, the genetic distance estimated from RAPD was independent of the actual distance among different local populations. These results suggest that genetic variations of T. tabaci are arisen from population subdivision due to asexual thelytokous reproductive mode.

SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes

Background The gene-specific sweep is a selection process where an advantageous mutation along with the nearby neutral sites in a gene region increases the frequency in the population. It has been demonstrated to play important roles in ecological differentiation or phenotypic divergence in microbial populations. Therefore, identifying gene-specific sweeps in microorganisms will not only provide insights into the evolutionary mechanisms, but also unravel potential genetic markers associated with biological phenotypes. However, current methods were mainly developed for detecting selective sweeps in eukaryotic data of sparse genotypes and are not readily applicable to prokaryotic data. Furthermore, some challenges have not been sufficiently addressed by the methods, such as the low spatial resolution of sweep regions and lack of consideration of the spatial distribution of mutations. Results We proposed a novel gene-centric and spatial-aware approach for identifying gene-specific sweeps in prokaryotes and implemented it in a python tool SweepCluster. Our method searches for gene regions with a high level of spatial clustering of pre-selected polymorphisms in genotype datasets assuming a null distribution model of neutral selection. The pre-selection of polymorphisms is based on their genetic signatures, such as elevated population subdivision, excessive linkage disequilibrium, or significant phenotype association. Performance evaluation using simulation data showed that the sensitivity and specificity of the clustering algorithm in SweepCluster is above 90%. The application of SweepCluster in two real datasets from the bacteria Streptococcus pyogenes and Streptococcus suis showed that the impact of pre-selection was dramatic and significantly reduced the uninformative signals. We validated our method using the genotype data from Vibrio cyclitrophicus, the only available dataset of gene-specific sweeps in bacteria, and obtained a concordance rate of 78%. We noted that the concordance rate could be underestimated due to distinct reference genomes and clustering strategies. The application to the human genotype datasets showed that SweepCluster is also applicable to eukaryotic data and is able to recover 80% of a catalog of known sweep regions. Conclusion SweepCluster is applicable to a broad category of datasets. It will be valuable for detecting gene-specific sweeps in diverse genotypic data and provide novel insights on adaptive evolution.

COEVOLUTION WITH SPATIALLY STRUCTURED RICE LANDRACES MAINTAINS MULTIPLE GENERALIST LINEAGES IN THE RICE BLAST PATHOGEN

Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the eco-evolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Magnaporthe oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life histories. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.

Balancing selection and the crossing of fitness valleys in structured populations: diversification in the gametophytic self-incompatibility system

The self-incompatibility locus (S-locus) of flowering plants displays a striking allelic diversity. How such a diversity has emerged remains unclear. In this paper, we performed numerical simulations in a finite island population genetics model to investigate how population subdivision affects the diversification process at a S-locus, given that the two-genes architecture typical of S-loci involves the crossing of a fitness valley. We show that population structure increases the number of self-incompatibility haplotypes (S-haplotypes) maintained in the whole metapopulation, but at the same time also slightly reduces the parameter range allowing for their diversification. This increase is partly due to a reinforcement of the diversification and replacement dynamics of S-haplotypes within and among demes. We also show that the two-genes architecture leads to a higher diversity compared with a simpler genetic architecture where new S-haplotypes appear in a single mutation step. We conclude that population structure helps explain the large allelic diversity at the self-incompatibility locus. Overall, our results suggest that population subdivision can act in two opposite directions: it makes easier S-haplotypes diversification but increases the risk that the SI system is lost.

Molecular Ecology and Systematics of Blue Mussels (Genus Mytilus) (Mytilidae; Bivalvia; Mollusca) in the Southern Hemisphere

<p>The Mytilus edulis species complex, comprised of M. edulis, M. galloprovincialis and M. trossulus, is antitropically distributed in temperate coastal regions of all oceans and main seas of the world. This genus has been heavily studied in the Northern hemisphere but Southern hemisphere populations have received much less attention. This thesis aims to place Southern hemisphere blue mussels into global evolutionary relationships among Mytilus species and investigate aspects of their molecular ecology, including, effects of non-native Northern hemisphere species introductions, biogeography across the Southern hemisphere, regional phylogeographic patterns and population genetics within New Zealand. Southern hemisphere blue mussel phylogenetic reconstruction resulted in the detection of a monophyletic M. galloprovincialis lineage. Two new molecular markers developed with specificity for this lineage and congruence among phylogenetic investigations indicates a panhemispheric distribution of this M. galloprovincialis lineage with implications for naming a new sibling species of the M. edulis complex. This proposed new species, M. meridianus, is distributed in South America, the Kerguelen Islands, New Zealand and Australia at latitudes between ~ 30°S and ~ 55°S. Non-native M. galloprovincialis introduced from the Northern hemisphere have been present in NZ, Australia and Chile for at least ten years and hybridise with native blue mussels. Introgression is observed in New Zealand and Australian but not Chilean hybrid regions. The limited number of introduced mussels in Australia induces hybrid swamping of non-native alleles but an interlineage gender bias towards non-native maternal parents may result in eventual loss of the unique genomic content of native blue mussels in NZ. Southern hemisphere blue mussels form a monophyletic sister clade to a haplogroup shared by Northern hemisphere M. edulis and M. galloprovincialis. Although single gene histories are not congruent with respect to evolutionary relationships within the Northern hemisphere due to introgressive hybridisation after speciation, it is clear that Southern hemisphere blue mussels arose from a species native to the northeast Atlantic Ocean after speciation of the three ‘M. edulis complex’ members. Within the Southern hemisphere monophyletic clade lies three reciprocally monophyletic clades restricted to the geographic regions South America/Kerguelen Islands, New Zealand and Australia. Phylogeographic analysis indicates past gene flow between South American/Kerguelen Islands and New Zealand populations that has ceased at present day and ongoing gene flow between South America and the Kerguelen Islands likely via the West Wind Drift. Within NZ, population subdivision inferred from mtDNA indicates genetic variation is distributed within an east-west phylogeographic split on the North Island. These populations experienced gene flow in the past that has ceased at present day. Microsatellite allele frequencies indicate a different population subdivision within the northwest North Island that has been narrowed down to a 15 km stretch of coastline in a sheltered bay. The abrupt discontinuity within a small geographic area does not conform to classic population subdivision in this broad-cast spawning species, therefore, further investigation into the genomic content of northwest North Island mussels with respect to introgressed non-native genes is warranted. Resolving complex phylogenetic patterns from interspecific introgression is key to understanding the evolutionary history of Southern hemisphere M. galloprovincialis. Further characterisation of hybrid introgression would increase accuracy of (1) inferences of processes contributing to hybridisation dynamics and (2) population subdivision in NZ. Probing the basis for variation of hybridisation dynamics would help to predict the outcomes of Northern hemisphere M. galloprovincialis introductions in other areas of the world.</p>

Molecular Ecology and Systematics of Blue Mussels (Genus Mytilus) (Mytilidae; Bivalvia; Mollusca) in the Southern Hemisphere

<p>The Mytilus edulis species complex, comprised of M. edulis, M. galloprovincialis and M. trossulus, is antitropically distributed in temperate coastal regions of all oceans and main seas of the world. This genus has been heavily studied in the Northern hemisphere but Southern hemisphere populations have received much less attention. This thesis aims to place Southern hemisphere blue mussels into global evolutionary relationships among Mytilus species and investigate aspects of their molecular ecology, including, effects of non-native Northern hemisphere species introductions, biogeography across the Southern hemisphere, regional phylogeographic patterns and population genetics within New Zealand. Southern hemisphere blue mussel phylogenetic reconstruction resulted in the detection of a monophyletic M. galloprovincialis lineage. Two new molecular markers developed with specificity for this lineage and congruence among phylogenetic investigations indicates a panhemispheric distribution of this M. galloprovincialis lineage with implications for naming a new sibling species of the M. edulis complex. This proposed new species, M. meridianus, is distributed in South America, the Kerguelen Islands, New Zealand and Australia at latitudes between ~ 30°S and ~ 55°S. Non-native M. galloprovincialis introduced from the Northern hemisphere have been present in NZ, Australia and Chile for at least ten years and hybridise with native blue mussels. Introgression is observed in New Zealand and Australian but not Chilean hybrid regions. The limited number of introduced mussels in Australia induces hybrid swamping of non-native alleles but an interlineage gender bias towards non-native maternal parents may result in eventual loss of the unique genomic content of native blue mussels in NZ. Southern hemisphere blue mussels form a monophyletic sister clade to a haplogroup shared by Northern hemisphere M. edulis and M. galloprovincialis. Although single gene histories are not congruent with respect to evolutionary relationships within the Northern hemisphere due to introgressive hybridisation after speciation, it is clear that Southern hemisphere blue mussels arose from a species native to the northeast Atlantic Ocean after speciation of the three ‘M. edulis complex’ members. Within the Southern hemisphere monophyletic clade lies three reciprocally monophyletic clades restricted to the geographic regions South America/Kerguelen Islands, New Zealand and Australia. Phylogeographic analysis indicates past gene flow between South American/Kerguelen Islands and New Zealand populations that has ceased at present day and ongoing gene flow between South America and the Kerguelen Islands likely via the West Wind Drift. Within NZ, population subdivision inferred from mtDNA indicates genetic variation is distributed within an east-west phylogeographic split on the North Island. These populations experienced gene flow in the past that has ceased at present day. Microsatellite allele frequencies indicate a different population subdivision within the northwest North Island that has been narrowed down to a 15 km stretch of coastline in a sheltered bay. The abrupt discontinuity within a small geographic area does not conform to classic population subdivision in this broad-cast spawning species, therefore, further investigation into the genomic content of northwest North Island mussels with respect to introgressed non-native genes is warranted. Resolving complex phylogenetic patterns from interspecific introgression is key to understanding the evolutionary history of Southern hemisphere M. galloprovincialis. Further characterisation of hybrid introgression would increase accuracy of (1) inferences of processes contributing to hybridisation dynamics and (2) population subdivision in NZ. Probing the basis for variation of hybridisation dynamics would help to predict the outcomes of Northern hemisphere M. galloprovincialis introductions in other areas of the world.</p>

MULTIMODAL HUMAN BRAIN LONGITUDINAL PARCELLATION ACROSS LIFESPAN

Subdividing the human brain into several functionally distinct and spatially contiguous areas is important to understand the amazingly complex human cerebral cortex. However, adult aging is related to differences in the structure, function, and connectivity of brain areas, so that the single population subdivision does not apply to multiple age groups. Moreover, different modalities could provide affirmative and complementary information for the human brain subdivision. To obtain a more reasonable subdivision of the cerebral cortex, we make use of multimodal information to subdivide the human cerebral cortex across lifespan. Specifically, we first construct a population average functional connectivity matrix for each modality of each age group. Second, we separately calculate the population average similarity matrix for the cortical thickness and myelin modality of each age group. Finally, we fuse these population average matrixes to obtain the multimodal similarity matrix and feed it into the spectral clustering algorithm to generate the brain parcellation for each age group.

Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

Early blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association $$\left( {\overline{r}_{d} } \right)$$ r ¯ d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.