Biology subjects

Gardner, J.

Publications and source records attributed to Gardner, J..

23 records · Page 2Linked to original sources

bioRxiv2020

Using GC content to compare recombination patterns on the sex chromosomes and autosomes of the guppy, Poecilia reticulata, and its close outgroup species

Summary/AbstractGenetic and physical mapping of the guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in mammalian sex chromosomes pseudo-autosomal regions (PARs). We here used the intronic GC content to indirectly infer the recombination patterns on guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. Using intron sequences, which are likely to be under weak selection, we show that almost all guppy chromosomes, including the sex chromosome (LG12) have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of guppy chromosomes, which were not determined in the guppy genome assembly.

evolutionary biology↗

bioRxiv2020

Locating the sex determining region of linkage group 12 of guppy (Poecilia reticulata)

We describe new genetic mapping results from 6 full-sib families in the guppy (Poecilia reticulata), two of which included recombinants between the X and Y chromosomes. These recombinants confirm that the guppy sex-determining locus is in the region identified by all previous studies, including a recent report suggesting a candidate sex-determining gene in this fish, close to the pseudo-autosomal region (or PAR) at the chromosome terminus. Our results suggest the presence of some errors in the current assembly of the guppy genome. In males, crossing over occurs at a very high rate in the PAR, and our genetic map of the region allows us to correct the marker order. We also identified two unplaced scaffolds carrying genes that map to the PAR. Genetic mapping cannot be used to order markers in the region where crossing over is infrequent. However, our recombinant male is informative about the order, under the reasonable assumption that crossovers are infrequent. Our mapping families and natural population samples also show that the recently proposed candidate for this species sex-determining gene is not completely sex-linked. We detect an association between individuals sex and an SNP in the sex-determining region, but not with a marker 0.9 Mb away from it, suggesting that variants in this region may be in linkage disequilibrium with the actual sex-determining factor, but that the factor itself has not yet been identified. So far, no consistently male-specific variant has been identified in the guppy sex-determining region.

genetics↗

bioRxiv2020

Environmental Exposures Influence Nasal Microbiome Composition in a Longitudinal Study of Division I Collegiate Athletes

BackgroundThe anterior nares host a complex microbial community that contributes to upper airway health. Although the bacterial composition of the nasal passages have been well characterized in healthy and diseased cohorts, the role of prolonged environmental exposures and exercise in shaping the nasal microbiome in healthy adults is poorly understood. In this study, we longitudinally sampled female collegiate Division I athletes from two teams experiencing a similar athletic season and exercise regimen but vastly different environmental exposures (Swim/Dive and Basketball). Using 16S rRNA gene sequencing, we evaluated the longitudinal dynamics of the nasal microbiome pre-, during-, and at the end of the athletic season. ResultsThe nasal microbiota of the Swim/Dive and Basketball teams were distinct from each other at each time point sampled, driven by either low abundance (Jaccard, PERMANOVA p<0.05) or high-abundance changes in composition (Bray-Curtis, PERMANOVA p<0.05). The rate of change of microbial communities were greater in the Swim/Dive team compared to the Basketball team characterized by an increase in Staphylococcus in Swim/Dive and a decrease in Corynebacterium in both teams over time. ConclusionsThis is the first study that has evaluated the nasal microbiome in athletes. We obtained longitudinal nasal swabs from two gender-matched teams with similar age distributions (18-22 years old) over a 6 month period. Differences in the microbiota between teams and over time indicate that chlorine exposure, and potentially athletic training, induced changes in the nasal microbiome.

microbiology↗

bioRxiv2019

Context-dependent probability estimation and its neurocomputational substrates

Many decisions rely on how we evaluate potential outcomes associated with the options under consideration and estimate their corresponding probabilities of occurrence. Outcome valuation is subjective as it requires consulting internal preferences and is sensitive to context. In contrast, probability estimation requires extracting statistics from the environment and therefore imposes unique challenges to the decision maker. Here we show that probability estimation, like outcome valuation, is subject to context effects that bias probability estimates away from other stimuli present in the same context. However, unlike valuation, these context effects appeared to be scaled by estimated uncertainty, which is largest at intermediate probabilities. BOLD imaging showed that patterns of multivoxel activity in dorsal anterior cingulate cortex (dACC) and ventromedial prefrontal cortex (VMPFC) predicted individual differences in context effects on probability estimate. These results establish VMPFC as the neurocomputational substrate shared between valuation and probability estimation and highlight the additional involvement of dACC that can be uniquely attributed to probability estimation. As probability estimation is a required component of computational accounts from sensory inference to higher cognition, the context effects found here may affect a wide array of cognitive computations.\n\nHighlightsO_LIContext impacts subjective estimates on reward probability - Stimuli carrying greater variance are more strongly affected by other stimuli present in the same context\nC_LIO_LIThis phenomenon can be explained by reference-dependent computations that are gated by reward variance\nC_LIO_LIMultivoxel patterns of dACC and VMPFC activity predicts individual differences in context effect on probability estimate\nC_LI

neuroscience↗

bioRxiv2018

Sexually dimorphic recombination can facilitate the establishment of sexually antagonistic polymorphisms in guppies

Summary/AbstractRecombination suppression between sex chromosomes is often stated to evolve in response to polymorphisms for mutations that affect fitness of males and females in opposite directions (sexually antagonistic, or SA, mutations), but direct empirical support is lacking. The sex chromosomes of the fish Poecilia reticulata (the guppy) carry SA polymorphisms, making them excellent for testing this hypothesis for the evolution of sex linkage. We resequenced genomes of male and female guppies and, unexpectedly, found that variants on the sex chromosome indicate no extensive region with fully sex-linked genotypes, though many variants show strong evidence for partial sex linkage. We present genetic mapping results that help understand the evolution of the guppy sex chromosome pair. We find very different distributions of crossing over in the two sexes, with recombination events in male meiosis detected only at the tips of the chromosomes. The guppy may exemplify a route for sex chromosome evolution in which low recombination in males, likely evolved in a common ancestor, has facilitated the establishment of sexually antagonistic polymorphisms.

evolutionary biology↗