Publications by authors named "Peter D Fields"
Article Synopsis
- Genomic regions involved in parasite defense, like the MHC, are highly variable, with multiple factors like single nucleotide polymorphisms and copy number variations contributing to this diversity.
- The study focuses on the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, revealing significant genetic variation and non-homologous haplotypes, suggesting the region is under balancing selection and has a long evolutionary history.
- The research highlights the interplay of ancient resistance mechanisms and hyper-divergent genomic environments, offering insights into the evolution of disease resistance not just in Daphnia, but across the broader Cladocera class.
Article Synopsis
- Salinization is a growing global issue that impacts freshwater organisms like Daphnia magna, raising concerns about their adaptability to increasing salinity levels.
- Research showed that Daphnia populations with higher salt tolerance are better adapted to their native habitats, as evidenced by a correlation between local salinity and salt tolerance.
- A crucial gene, TPS, linked to trehalose production was identified as key to managing salinity stress, with experiments confirming that animals lacking functional TPS struggle to tolerate higher salinity.
Two important characteristics of metapopulations are extinction-(re)colonization dynamics and gene flow between subpopulations. These processes can cause strong shifts in genome-wide allele frequencies that are generally not observed in "classical" (large, stable, and panmictic) populations. Subpopulations founded by one or a few individuals, the so-called propagule model, are initially expected to show intermediate allele frequencies at polymorphic sites until natural selection and genetic drift drive allele frequencies toward a mutation-selection-drift equilibrium characterized by a negative exponential-like distribution of the site frequency spectrum.
View Article and Find Full Text PDFBalancing selection is an evolutionary process that maintains genetic polymorphisms at selected loci and strongly reduces the likelihood of allele fixation. When allelic polymorphisms that predate speciation events are maintained independently in the resulting lineages, a pattern of trans-species polymorphisms may occur. Trans-species polymorphisms have been identified for loci related to mating systems and the MHC, but they are generally rare.
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- Researchers sequenced and analyzed the genomes and transcriptomes of two New Zealand snail species, Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, to understand their evolutionary context as relatives of the freshwater snail Potamopyrgus antipodarum.
- Both species share a similar set of genes related to meiosis and sperm functions, indicating obligate sexual reproduction and laying the groundwork for studying P. antipodarum's unique biological traits, including its sexual and asexual lineages.
- Though P. kaitunuparaoa appears to be the closest relative to P. antipodarum, significant gene flow through introgression occurs between the two species; however, the mitochondrial genome acts as a
Article Synopsis
- Researchers have completed a high-quality chromosome-level genome assembly for the angiosperm genus Silene, specifically Silene conica, using advanced genomic technologies.
- The assembly consists of 10 scaffolds representing each chromosome, with a total length of 862 Mb and minimal gap content, confirming a reduced base chromosome number compared to its ancestral state of 12.
- The study also reveals that Silene conica has a large mitochondrial genome with unknown sequences, and the new assembly will aid in future comparative genomic research within the Silene genus, especially regarding sex chromosome evolution.
Unlabelled: The angiosperm genus has been the subject of extensive study in the field of ecology and evolution, but the availability of high-quality reference genome sequences has been limited for this group. Here, we report a chromosome-level assembly for the genome of based on PacBio HiFi, Hi-C and Bionano technologies. The assembly produced 10 scaffolds (one per chromosome) with a total length of 862 Mb and only ~1% gap content.
View Article and Find Full Text PDFMicrosporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis.
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- Understanding the genomic aspects of infectious diseases is crucial for co-evolution theory and has implications in healthcare, agriculture, and epidemiology.
- Traditional models predict that specific host and parasite genotypes are linked in infection and resistance, but there's been limited evidence of this in nature.
- The study found significant genomic associations between host and parasite genomes in Daphnia magna and Pasteuria ramosa, demonstrating evidence of co-evolution supported by lab trials linking phenotype to genotype.
Article Synopsis
- The study explores how specific genetic interactions between the crustacean Daphnia magna and the bacterial parasite Pasteuria ramosa contribute to balancing selection, which is key for maintaining genetic diversity.
- Researchers identified a dominant locus, named the F locus, that correlates with resistance to infection, and localized it within a 28.8-kb region on the host's genome, revealing 13 genes of interest.
- Notably, candidate genes, including a fucosyltransferase, suggest that resistance mechanisms may involve changes in the host's glycan structures, laying the groundwork for future studies on genetic resistance in natural populations.
Article Synopsis
- The study investigates the genomic diversity of the microsporidian parasite Ordospora colligata, emphasizing the role of evolutionary processes like phylogeography and natural selection in shaping this diversity.
- Results reveal a close phylogeographic relationship between O. colligata and its host, Daphnia magna, indicating a long-term relationship and adaptations to colder environments as opposed to other related parasites.
- The research also highlights the identification of regions under selection pressure and provides insights into the evolution of one of the smallest known eukaryotic genomes, illustrating how various factors contribute to the genomic variation of obligate parasites.
Article Synopsis
- Outbred laboratory mice (Mus musculus) are popular in biomedical research due to their high reproduction rates and availability, and high throughput genome sequencing (HTS) helps ensure the genetic quality and reproducibility of studies using these mice.
- A study on a newly established Swiss-derived outbred population (J:ARC) utilized exome sequencing to explore their genetic architecture and found characteristics typical of well-maintained outbred stocks, comparing it to the Diversity Outbred (J:DO) stock.
- The J:DO stock showed greater genetic variation and interindividual variability but had a higher frequency of potentially damaging genetic variants, indicating that diverse genetic backgrounds can help buffer against harmful mutations under varying selective pressures.
Article Synopsis
- - Recent advancements in long-read sequencing, specifically PacBio technology, have enabled researchers to sequence entire mitochondrial genomes, which allows for deeper exploration of their structure and recombination.
- - A study on two New Zealand freshwater snail species revealed a previously undetected ∼1.7 kb noncoding region and a mitochondrial genome structure similar to plant chloroplasts, consisting of a large single-copy region and inverted repeats.
- - The findings show evidence of "flip-flop" recombination and distinct haplotypes in the snails' mitochondrial genomes, prompting new questions about the role of inverted repeats in the evolution of these genomes.
Article Synopsis
- The study investigates how extinction and recolonization in habitat patches affect the evolution of metapopulations, specifically comparing them to larger, stable populations.* -
- Using whole-genome pool-sequencing on 60 subpopulations of Daphnia magna, researchers found that metapopulations show lower genetic diversity and higher differentiation, supporting the propagule model which states that colonization leads to genetic bottlenecks.* -
- The results indicate that younger and more isolated subpopulations experience reduced effective population sizes and genetic drift, revealing that the evolutionary dynamics of metapopulations differ significantly from those of larger, stable populations.*
Article Synopsis
- Researchers found that a large segment of mitochondrial DNA (numt) has integrated into Chromosome 2 of the Arabidopsis thaliana plant, measuring 641 kb—larger than its entire mitochondrial genome.
- * The accurate sequencing of this numt was achieved using advanced long-read sequencing technologies, which revealed it shares 99.933% similarity with the mitochondrial genome and exhibits complex repetitive structures.
- * Findings show high levels of cytosine methylation in the numt, suggesting it is transcriptionally inactive and informing our understanding of numt evolution and its role in the nuclear genome.*
Speciation is a complex and continuous process that makes the delineation of species boundaries a challenging task in particular in species with little morphological differentiation, such as parasites. In this case, the use of genomic data is often necessary, such as for the intracellular Microsporidian parasites. Here, we characterize the genome of a gut parasite of the cladoceran Daphnia longispina (isolate FI-F-10), which we propose as a new species within the genus Ordospora: Ordospora pajunii sp.
View Article and Find Full Text PDFArticle Synopsis
- The study explores how genomic diversity in the microsporidium Hamiltosporidium, a parasite of the crustacean Daphnia magna, can shed light on its ecology and evolutionary history.
- Researchers analyzed genomic samples from 18 populations across Eurasia, focusing on factors like modes of reproduction, transmission, and geography to understand their effect on genetic variation and population structure.
- Findings revealed two main parasite lineages, a lack of alignment with host lineages, and suggested a recent spread of the parasite influenced by changes in reproduction and transmission methods, highlighting broader patterns seen in other parasite species.
Article Synopsis
- Daphnia magna serves as a key model for studying host-parasite coevolution due to its interaction with microparasites, showing unique ecological and evolutionary traits compared to other arthropods like Drosophila.
- The study analyzed the genomes of 36 D. magna clones from Europe to investigate adaptive protein evolution, revealing high genetic diversity that is structured among populations but not as strongly adapted as seen in Drosophila.
- Findings indicate a prevalence of weakly deleterious genetic variants in D. magna, suggesting reduced selection effectiveness and emphasizing local adaptation instead of widespread adaptive fixation across its populations.
Article Synopsis
- Phylogenomic approaches provide innovative methods to understand ancient evolutionary relationships, particularly in branchiopod crustaceans, despite challenges in estimating phylogeny from ancient events.
- The study reconstructs long-debated relationships among Cladocera (waterfleas) by utilizing advanced genetic data and analyses, affirming the monophyletic nature of this group while revealing significant evolutionary differences in body plans.
- Findings suggest that the ancestor of Cladocera originated around 325 million years ago, following a rapid radiation event around the Perm/Triassic boundary, prompting further investigation into the impacts of homoplasy and rapid diversification in evolutionary biology.
Article Synopsis
- Understanding how genetic diversity is maintained in natural populations is crucial for evolutionary biology, especially in the context of coevolving hosts and parasites.
- This study focuses on a bacterial parasite's infection characteristics by examining over 50 isolates and their interactions with 12 genotypes of the host, Daphnia magna, revealing significant variation in parasite phenotypes and multiple infection strategies.
- The findings suggest that infection success does not depend on geographic distance, supporting the Red Queen hypothesis that both hosts and parasites evolve to maintain high genetic diversity in their interactions.
Article Synopsis
- Long-term host-parasite coevolution, especially in the context of the Red Queen hypothesis, helps explain how genetic diversity aids in developing resistance to parasites, particularly in the case of Daphnia magna and Pasteuria ramosa.
- The study demonstrates that host populations of Daphnia magna maintain high levels of genetic diversity for pathogen resistance even across different geographic locations, contrasting with patterns of genetic isolation found in other areas of their genome.
- Genetic analysis reveals that specific resistance loci show signs of balancing selection, indicating that negative-frequency-dependent selection plays a crucial role in sustaining this diversity and the host's ability to combat the virulent bacterium.
Article Synopsis
- * The review highlights three new methods—co-GWAS, population genomics extensions, and temporal correlations—that help identify coevolving genetic loci and reconstruct coevolutionary history.
- * The authors discuss the principles, advantages, and limitations of these approaches across various organisms and note the need for further research to enhance understanding of coevolution through full genome data.
Article Synopsis
- - The study investigates how asexual reproduction affects genome evolution, particularly in the New Zealand freshwater snail, Potamopyrgus antipodarum, which has both asexual and sexual lineages that compete with each other.
- - Using whole-genome sequencing, researchers analyzed the abundance of rDNA (genes for rRNAs) and found unique gene cluster architectures and significant differences between asexual and sexual individuals.
- - The results show that asexual P. antipodarum have many more copies of rDNA and histone genes compared to sexual ones, indicating that the shift to asexuality leads to notable genomic changes that could impact their biological functions.
Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding-involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50% in one generation; however, little is known about the empirical variation on a genome level surrounding this figure and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analysed whole genomes of mothers and selfed offspring, observing the predicted 50% heterozygosity reduction on average.
View Article and Find Full Text PDFStudies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging.
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