Biology subjects

Scott, M. F.

Publications and source records attributed to Scott, M. F..

8 recordsLinked to original sources

bioRxiv2023

A High-Fat and Fructose Diet in Dogs Mirrors Insulin Resistance and β-cell Dysfunction Characteristic of Impaired Glucose Tolerance in Humans

This study examined the impact of a hypercaloric high-fat high-fructose diet (HFFD) in dogs as a potential model for human impaired glucose tolerance (IGT) and type 2 diabetes mellitus (T2DM). The HFFD not only led to weight gain but also triggered metabolic alterations akin to the precursors of human T2DM, notably insulin resistance and {beta}-cell dysfunction. Following the HFFD intervention, the dogs exhibited a 50% decrease in insulin sensitivity within the first four weeks, paralleling observations in the progression from normal to IGT in humans. Calculations of the insulinogenic index using both insulin and C-peptide revealed a significant and sustained decrease in early-phase insulin release, with partial compensation in the later phase, predominantly stemming from reduced hepatic insulin clearance. In addition, the Disposition Index, representing the {beta}-cells capacity to compensate for diminished insulin sensitivity, fell dramatically. These results confirm that a HFFD can instigate metabolic changes in dogs akin to the early stages of progression to T2DM in humans. The study underscores the potential of using dogs subjected to a HFFD as a model organism for studying human IGT and T2DM.

physiology↗

bioRxiv2023

Gametic selection and mating systems show mutually dependent evolution

Competition among pollen or sperm (gametic selection) can cause evolution. Mating systems shape the intensity of gametic selection by determining the competitors involved, which can in turn cause mating system evolution. We model the bidirectional relationship between gametic selection and mating systems, focussing on variation in female mating frequency (monandry-polyandry) and self-fertilisation (selfing-outcrossing). First, we find that mating systems affect evolutionary responses to gametic selection, with more effective gametic selection when fertilisation success depends on haploid genotypes, rather than the diploid genotype of the father. Monandry and selfing both reduce the efficacy of gametic selection despite creating intense selection among pollen/sperm from heterozygous males with haploid expression. This effect means selfing can increase mutation load, in contrast to classic predictions where selfing purges deleterious mutations. Second, we show that mating systems can evolve via their effect on gametic selection, with polyandry evolving because it removes deleterious alleles more efficiently and increases offspring fitness. Our population genetic models reveal that this good sperm effect could plausibly give a selective advantage for polyandry over monandry of only around 1%. Selection for polyandry is lessened further if some loci experience balancing selection and is likely to be overwhelmed by any direct fitness effects of mating systems. Similarly, the indirect benefits from manipulating gametic selection have a weak influence on the evolution of selfing, which is dominated by automatic selection and inbreeding depression in our model. Nevertheless, gametic selection can be potentially decisive for selfing evolution because it significantly reduces inbreeding depression, which favours selfing. One test of the predicted interactions between gametic selection and mating system evolution would be to compare evolutionary rates in genes with different expression patterns across different mating systems.

evolutionary biology↗

bioRxiv2022

The establishment of locally adaptive inversions in structured populations

Inversions have been proposed to facilitate local adaptation, by linking together locally coadapted alleles at different loci. Classic prior work addressing this question theoretically has considered the spread of inversions in "continent-island" models in which there is a unidirectional flow of maladapted migrants into the island population. In this setting, inversions are most likely to establish when selection is weak, because stronger local selection more effectively purges maladaptive alleles, thus lessening the advantage of inversions. Here, we show this finding only holds under limited conditions. We study the establishment of inversions in a "two-deme" model, which explicitly considers the dynamics of allele frequencies in both populations linked by bidirectional migration. For symmetric selection and migration, we find that stronger local selection increases the flow of maladaptive alleles and favours inversions, the opposite of the pattern seen in the asymmetric continent-island model. Furthermore, we show that the strength and symmetry of selection also change the likelihood that an inversion captures an adaptive haplotype in the first place. Considering the combined process of invasion and capture shows that inversions are most likely to be found when locally adaptive loci experience strong selection. In addition, inversions that establish in one deme also protect adaptive allele combinations in the other, leading to differentiation between demes. Stronger selection in either deme once again makes differentiation between populations more likely. In contrast, differentiation is less likely when migration rates are high because adaptive haplotypes become less common. Overall, this analysis of evolutionary dynamics across a structured population shows that established inversions are most likely to have captured strongly selected local adaptation alleles.

evolutionary biology↗

bioRxiv2022

Multi-trait ensemble genomic prediction and simulations of recurrent selection highlight importance of complex trait genetic architecture in long-term genetic gains in wheat

Cereal crop breeders have achieved considerable genetic gain in genetically complex traits, such as grain yield, while maintaining genetic diversity. However, focus on selection for yield has negatively impacted other important traits. To better understand selection within a breeding context, and how it might be optimised, we analysed genotypic and phenotypic data from a diverse, 16-founder wheat multi-parent advanced generation inter-cross (MAGIC) population. Compared to single-trait models, multi-trait ensemble genomic prediction models increased prediction accuracy for almost 90% of traits, improving grain yield prediction accuracy by 3-52%. For complex traits, non-parametric models (Random Forest) also outperformed simplified, additive models (LASSO), increasing grain yield prediction accuracy by 10-36%. Simulations of recurrent genomic selection then showed that sustained greater forward prediction accuracy optimised long-term genetic gains. Simulations of selection on grain yield found indirect responses in related traits, which involved optimisation of antagonistic trait relationships. We found multi-trait selection indices could be used to optimise undesirable relationships, such as the trade-off between grain yield and protein content, or combine traits of interest, such as yield and weed competitive ability. Simulations of phenotypic selection found that including Random Forest rather than LASSO genetic models, and multi-trait rather than single-trait models as the true genetic model, accelerated and extended long-term genetic gain whilst maintaining genetic diversity. These results suggest important roles of pleiotropy and epistasis in the wider context of wheat breeding programmes and provide insights into mechanisms for continued genetic gain in a limited genepool and optimisation of multiple traits for crop improvement.

genetics↗

bioRxiv2020

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

BackgroundBreeding has helped improve bread wheat yield significantly over the last century. Understanding the potential for future crop improvement depends on relating segregating genetic variation to agronomic traits. ResultsWe bred NIAB Diverse MAGIC population, comprising over 500 recombinant inbred lines, descended from sixteen bread wheat varieties released between 1935-2004. We sequenced the founders exomes and promotors by capture. Despite being highly representative of North-West European wheat and capturing 73% of global polymorphism, we found 89% of genes contained no more than three haplotypes. We sequenced each line with 0.3x coverage whole-genome sequencing, and imputed 1.1M high-quality SNPs that were over 99% concordant with array genotypes. Imputation accuracy remained high at coverage as low as 0.076x, with or without the use of founder genomes as reference panels. We created a genotype-phenotype map for 47 traits over two years. We found 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Outside of these loci most traits are polygenic, as revealed by multi-locus shrinkage modelling. ConclusionsHistorically, wheat breeding has reshuffled a limited palette of haplotypes; continued improvement will require selection at dozens of loci of diminishing effect, as most of the major loci we mapped are known. Breeding to optimise one trait generates correlated trait changes, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break critical unfavourable trait-trait associations. Finally, low coverage whole genome sequencing of bread wheat populations is an economical and accurate genotyping strategy.

genomics↗

bioRxiv2020

Murine GFP-Mx1 forms phase-separated nuclear condensates and associates with cytoplasmic intermediate filaments: novel antiviral activity against vesicular stomatitis virus

Type I and III interferons (IFNs) induce expression of the "myxovirus resistance proteins" MxA in human cells and its ortholog Mx1 in murine cells. Human MxA forms cytoplasmic structures, some tethered to intermediate filaments. In contrast, murine Mx1 mainly forms nuclear bodies. Both HuMxA and MuMx1 are antiviral towards influenza A virus (FLUAV) (an orthomyxovirus). However, it has long been considered that HuMxA, but not MuMx1, was antiviral towards vesicular stomatitis virus (VSV) (a rhabdovirus). We previously reported that the cytoplasmic human GFP-MxA structures in Huh7 hepatoma cells were phase-separated membraneless organelles (MLOs) ("biomolecular condensates"). In the present study we investigated whether nuclear murine Mx1 structures might also represent phase-separated biomolecular condensates. The transient expression of murine GFP-Mx1 in Huh7 hepatoma and Mich-2H6 melanoma cells led to the appearance of Mx1 nuclear bodies. These GFP-MuMx1 nuclear bodies were rapidly disassembled by exposing cells to 1, 6-hexanediol (5% w/v), or to hypotonic buffer (40-50 mosM), consistent with properties of membraneless phase-separated condensates. FRAP assays revealed that the GFP-MuMx1 nuclear bodies upon photobleaching showed a slow partial recovery (mobile fraction: [~]18%) suggestive of a gel-like consistency. Surprisingly, expression of GFP-MuMx1 in Huh7 cells also led to the appearance of MuMx1 in a novel cytoplasmic giantin-based intermediate filament meshwork and in cytoplasmic structures in 20-30% of transiently transfected Huh7 cells. Remarkably, Huh7 cells with cytoplasmic murine GFP-MuMx1 filaments, but not those with only nuclear bodies, showed antiviral activity towards VSV. Thus, murine GFP-Mx1 nuclear bodies comprised phase-separated condensates. Unexpectedly, GFP-MuMx1 associated with cytoplasmic giantin-based intermediate filaments in a subset of Huh7 cells, and, such cells showed antiviral activity towards VSV.

cell biology↗

bioRxiv2020

X-linked meiotic drive boosts population size and persistence

X-linked meiotic drivers cause X-bearing sperm to be produced in excess by male carriers, leading to female-biased sex ratios. Selection for these selfish sex chromosomes can lead to completely female populations, which cannot produce offspring and go extinct. However, at the population level, moderately female-biased sex ratios are optimal because relatively few males are required to fertilise all the females. We develop eco-evolutionary models for sex-linked meiotic drive alleles to investigate their full range of demographic effects. We find general conditions for the spread and fixation of X-drivers, accounting for transmission bias and other factors associated with the spread of X-drivers such as sperm competition and polyandry. Our results suggest driving X-alleles that do not reach fixation (or do not bias segregation excessively) will boost population sizes and persistence times by increasing population productivity, demonstrating the potential for selfish genetic elements to move sex ratios closer to the population-level optimum. We suggest that researchers should look beyond extinction risk and consider the potential for ecologically beneficial side effects of selfish genetic elements, especially in light of proposals to use meiotic drive for biological control.

evolutionary biology↗

bioRxiv2018

Haploid selection, sex ratio bias, and transitions between sex-determining systems

Sex determination is remarkably dynamic; many taxa display shifts in the location of sex-determining loci or the evolution of entirely new sex-determining systems. Predominant theories for why we observe such transitions generally conclude that novel sex-determining systems are favoured by selection if they equalise the sex ratio or increase linkage with a locus that experiences different selection in males vs. females. We use population genetic models to extend these theories in two ways: (1) We consider the dynamics of loci very tightly linked to the ancestral sex-determining loci, e.g., within the non-recombining region of the ancestral sex chromosomes. Variation at such loci can favour the spread of new sex-determining systems in which the heterogametic sex changes (XY to ZW or ZW to XY) and the new sex-determining region is less closely linked (or even unlinked) to the locus under selection. (2) We consider selection upon haploid genotypes either during gametic competition (e.g., pollen competition) or meiosis (i.e., non-Mendelian segregation), which can cause the zygotic sex ratio to become biased. Haploid selection can drive transitions between sex-determining systems without requiring selection to act differently in diploid males vs. females. With haploid selection, we find that transitions between male and female heterogamety can evolve where linkage with the sex-determining locus is either strengthened or weakened. Furthermore, we find that sex-ratio biases may increase or decrease with the spread of new sex chromosomes, which implies that transitions between sex-determining systems cannot be simply predicted by selection to equalise the sex ratio. In fact, under many conditions, we find that transitions in sex determination are favoured equally strongly in cases where the sex ratio bias increases or decreases. Overall, our models predict that sex determination systems should be highly dynamic, particularly when haploid selection is present, consistent with the evolutionary lability of this trait in many taxa.\n\nAuthor summarySystems of sex determination are strikingly diverse and labile in many clades. This poses the question: what drives transitions between sex-determining systems? Here, we use models to derive conditions under which new sex-determining systems spread. Prevailing views suggest that new sex-determining systems are favoured when they equalize the sex ratio and/or when they are more closely linked to genes that experience differential selection in males and females. Our models include selection upon haploid genotypes (meiotic drive or gametic competition), which biases the sex-ratio and occurs differently in male and female gametes. Surprisingly, we find the two forces (selection to equalize the sex ratio and the benefits of hitchhiking alongside driven alleles that distort the sex ratio) will often be equally strong, and thus neither is sufficient to explain the spread of new sex-determining systems in every case. We also find that new sex-determining alleles can spread despite being less closely linked to selected loci as long as initial linkage is tight or haploid selection is present. Our models therefore predict that loci in previously unexpected genomic locations and/or experiencing various types of selection (including haploid selection) can now be implicated as drivers of transitions between sex-determining systems.

evolutionary biology↗