Biology subjects

Fields, P.

Publications and source records attributed to Fields, P..

7 recordsLinked to original sources

bioRxiv2026

Genomic evidence for within-species thermal adaptation in collagen genes

Collagen is the most abundant protein in animals. Its thermal stability depends on its specific amino acid composition within the repeated Gly-Xaa-Yaa motifs forming the triple helix structure. Proline increases collagen rigidity, while serine enhances its elasticity--properties that contribute to collagen function and that vary with temperature. Although variation in collagen composition has been linked to temperature adaptation across evolutionary distinct taxa, its role within a species remains unclear. Here, we tested whether collagen genes across populations of the freshwater crustacean, Daphnia magna, show a signature of local adaptation to the ambient temperature. Analysing 39 collagen genes from 215 D. magna populations across three phylogeographic lineages spawning four continents, we found that animals from populations in warmer climates have higher proline and lower serine content in collagen--consistent with enhanced protein stability at higher temperatures. This variation was also associated with experimentally measured upper temperature tolerance. Parallel directional patterns of amino acid change appeared across genetically distinct lineages. Collagen genes also showed strong signatures of positive selection, comparable to that of immune-related genes, supporting a scenario of polygenic molecular role in adaptive responses. Our findings provide evidence of intraspecific molecular evolution in collagen amino acid composition driven by environmental temperature. Additionally, our study bridges macroevolutionary patterns with microevolutionary processes, posing the first intraspecific evidence that collagen genes can contribute to responses to environmental gradients at the molecular level, and thus, advancing our understanding of molecular adaptation of constrained structural proteins in an environmental context.

evolutionary biology↗

bioRxiv2025

Whole-genome sequence of Potamopyrgus antipodarum: a model system for the maintenance of sexual reproduction reveals a recent whole-genome duplication

Key unanswered questions in biology center on the causes, consequences, and maintenance of sexual reproduction ("sex"). Genome-driven processes are central to the evolutionary and genetic mechanisms inherent to sex, making genomic resources a fundamental part of answering these questions. We present the first genome assembly for a species that is uniquely well-suited for the study of (a)sex in nature, Potamopyrgus antipodarum. This New Zealand snail is unusual in featuring multiple separate transitions from obligately sexual to obligately asexual reproduction, leading to the coexistence of phenotypically similar sexual and asexual forms, a feature that is required to directly study the maintenance of sex. These separately derived asexual lineages constitute separate evolutionary experiments, providing a powerful means of characterizing how the absence of sex affects genome evolution. Our genome assembly provides critical steps towards understanding causes and consequences of sex in this system and important resources for the rapidly growing P. antipodarum and molluscan genomics research community. In characterizing this genome, we uncovered unexpected evidence for a recent whole-genome duplication (WGD) in P. antipodarum. This discovery sets the stage for using P. antipodarum to evaluate processes of rediploidization following WGD and assess whether WGD might drive transitions to asexuality.

genomics↗

bioRxiv2023

Genome evolution and introgression in the New Zealand mud snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species P. antipodarum--a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness--and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum--a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of non-introgression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species. Significance StatementNo whole-nuclear genome sequences are currently available for snails of the genus Potamopyrgus, best known for Potamopyrgus antipodarum, an invasive species of rivers and lakes worldwide, and a famous model for the study of the evolution of sex. We have sequenced and analyzed the genome of sexual P. estuarinus and P. kaitunuparaoa, the closest known relatives of P. antipodarum. We show that 1) the genomes are very similar in gene content and size, 2) P. kaitunuparaoa is the closest relative to P. antipodarum, 3) significant introgression has occurred between P. estuarinus and P. kaitunuparaoa; these genomes set the stage for powerful direct analyses of the genomic features, e.g., sex to asexual transitions and invasive success, that make P. antipodarum unique.

evolutionary biology↗

bioRxiv2022

Uncovering the genomic basis of infection through co-genomic sequencing of hosts and parasites

Understanding the genomic basis of infectious disease is fundamental objective in coevolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite coevolution often assume that infection requires specific combinations of host and parasite genotypes. Coevolving host and parasite loci are therefor expected to show associations that reflects an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically-interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic coevolution among wild populations.

genomics↗

bioRxiv2020

Cyto-nuclear linkage disequilibrium resulting from admixture

Previous studies of North American populations of the invasive plant Silene latifolia showed significant cyto-nuclear linkage disequilibrium (CNLD) between SNP variants of a mitochondrial gene (atp1) and the most common allele at nuclear microsatellite loci. Fields et al. (2014) hypothesized that this CNLD arose partially as a consequence of admixture that occurred during the colonization of North American (NA) populations of S latifolia via seed dispersal from genetically differentiated European populations that represent a portion of the native range of this species. In order to evaluate the plausibility of the admixture hypothesis, as opposed to metapopulation processes alone, we estimated CNLD for these same loci using data collected from eastern (EEU) and western (WEU) European populations of S. latifolia known to be genetically differentiated and likely sources of the spread of the study species to North America. We show that the CNLD found previously in NA populations of S. latifolia can be attributed to admixture of the previously isolated European demes coupled with decay since that time. Our applied framework allows the separation of the forces generating and dissolving statistical associations between alleles in cytoplasmic organelles and the nuclear genome and may thus be of utility in the study of plant or animal microbiomes.

evolutionary biology↗

bioRxiv2018

Elevated O-GlcNAcylation Enhances Pro-Inflammatory Th17 Function by Altering the Lipid Microenvironment

Chronic, low-grade inflammation increases the risk of atherosclerosis, cancer, and autoimmunity in diseases like obesity and diabetes. Here, we show that increased levels of the nutrient-responsive, post-translational protein modification, O-GlcNAc (O-linked {beta}-N-acetylglucosamine) are present in naive CD4+ T cells from a diet-induced obesity murine model, and elevation in O-GlcNAc leads to increased pro-inflammatory IL-17A production. Importantly, CD4+ T helper 17 (Th17) cells, which secrete IL-17A, are increased in obesity and contribute to the inflammatory milieu. We found increased binding of the Th17 master transcription factor, ROR{gamma}t, at the IL-17 locus and significant alterations in the lipid microenvironment, leading to increased ligands capable of increasing ROR{gamma}t transcriptional activity. Importantly, the rate-limiting enzyme of fatty acid biosynthesis, acetyl CoA carboxylase 1 (ACC1), is necessary for production of these ROR{gamma}t activating ligands and is O-GlcNAcylated. Thus, we have identified O-GlcNAc as a critical link between excess nutrients and pathological inflammation.

immunology↗

bioRxiv2018

Identification of general patterns of sex-biased expression in Daphnia, a genus with environmental sex determination

Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna. This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia.\n\nShort summaryIn some species with environmental sex determination, gene expression can be compared between genetically identical males and females. Here, we investigated sex-biased expression in one such species, D. magna, and compared it with data from two congeners. We found that all three species have a common set of 675 genes with consistent differential expression and with a strong bias towards overexpression in females rather than males. Moreover, the proportion of sex-biased genes in each of the three Daphnia species was similar to Drosophila species with genetic sex determination, suggesting that sex-biased expression is not necessarily reduced under environmental sex determination.

genomics↗