Biology subjects

Mulley, J. F.

Publications and source records attributed to Mulley, J. F..

8 recordsLinked to original sources

bioRxiv2024

A reliance on human habitats is key to the success of an introduced predatory reptile

Understanding the success of animals in novel environments is increasingly important as human-mediated introductions continue to move species far beyond their natural ranges. Alongside these introductions, inhabited and agricultural areas are spreading, and correspondingly most animal introductions occur in populated areas. Commensal species which can live alongside humans by making use of specific conditions, structures, or prey, have a significant advantage. Introduced mammal species often use anthropogenic features in their environment and demonstrate a higher tolerance of human disturbance, but their importance remains understudied in ectotherms. The Aesculapian snake (Zamenis longissimus) is an ectotherm which has been introduced beyond the northern extremities of its natural range. To understand their persistence, we radio-tracked snakes daily over two active seasons, including high-frequency tracking of a subset of males. We investigated snake home range size using Autocorrelated Kernel Density Estimators (AKDE). Using AKDE-weighted Habitat Selection Functions we identified preferences for habitat features in a mosaic of habitats, and we used Integrated Step Selection Functions to further explore how these features influence movement. We revealed a particular preference for buildings in male snakes, while females preferred woodland. We demonstrate that the success of this ectothermic predator is likely tied to a willingness to use human features of the landscape.

animal behavior and cognition↗

bioRxiv2022

Sequence features do not drive karyotypic evolution: what are the missing correlates of genome evolution?

Genome rearrangements are prevalent across the tree of life and even within species. After two decades of research, various suggestions have been proposed to explain which features of the genome are associated with rearrangements and the breakpoints between rearranged regions. These include: recombination rate, GC content, repetitive DNA content, gene density, and markers of chromatin conformation. Here, we use a set of six aligned rodent genomes to identify regions that have not been rearranged and characterize the breakpoint regions where rearrangements have occurred. We found no strong support for any of the expected correlations between breakpoint regions and a variety of genomic features previously identified. These results call into question the utility and repeatability of identifying chromatin characteristics associated with rearranged regions of the genome and suggest that perhaps a different explanation is in order. We analyzed rates of karyotypic evolution in each of the six lineages and found that the Mongolian gerbil genome has had the most rearrangements. That gerbils exhibit very rapid sequence evolution at a number of key DNA repair genes suggests an alternative hypothesis for patterns of genome rearrangement: karyotypic evolution may be driven by variation at a few genes that control the repair pathway used to fix double-stranded DNA breaks. Such variation may explain the heterogeneity in the rates of karyotypic evolution across species. While currently only supported by circumstantial evidence, a systematic survey of this hypothesis is now warranted.

genomics↗

bioRxiv2019

A high-density genetic map and molecular sex-typing assay for gerbils

We constructed a high-density genetic map in Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a high-quality framework map of 1,239cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5,449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1,140 genomic scaffolds (containing [~]20% of annotated genes) into a chromosome-level framework. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is not possible using current visual methods.

genetics↗

bioRxiv2018

Quantifying miscarriage sex bias in England and Wales, 1993-2017

Given an equal sex ratio at conception, we can only explain the excess of human males at birth by greater loss of females during pregnancy. I propose that the bias against females during human development is the result of a greater degree of genetic and metabolic \"differentness\" between female embryos and maternal tissues than for similarly aged males, and that successful implantation and placentation represents a threshold dichotomy, where the acceptance threshold shifts depending on maternal condition, especially stress. Right and left ovaries are not equal, and neither are the eggs and follicular fluid that they produce, and I further hypothesise that during times of stress, the implantation threshold is shifted sufficiently to favour survival of females, most likely those originating from the right ovary, and that this, rather than simply a greater loss of males, explains at least some of the variability in the human sex ratio at birth.

epidemiology↗

bioRxiv2018

When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Understanding the relationship between genome, phenotypic variation, and the ecological pressures that act to maintain that variation, represents a fundamental challenge in evolutionary biology. Functional polymorphisms typically segregate in spatially isolated populations [1, 2] and/or discrete ecological conditions [3-5], whereas dissecting the evolutionary processes involved in adaptive geographic variation across a continuous spatial distribution is much more challenging [6]. Additionally, pleiotropic interactions between genes and phenotype often complicate the identification of specific genotype-phenotype links [7-8], and thus of the selective pressures acting on them. Animal venoms are ideal systems to overcome these constraints: they are complex and variable, yet easily quantifiable molecular phenotypes with a clear function and a direct link to both genome and fitness [9]. Here, we use dense and widespread population-level sampling of the Mohave rattlesnake, Crotalus scutulatus, and show that genomic structural variation at multiple loci underlies extreme geographic variation in venom composition, which is maintained despite extensive gene flow. Unexpectedly, selection for diet does not explain venom variation, contrary to the dominant paradigm of venom evolution, and neither does neutral population structure caused by past vicariance. Instead, different toxin genes correlate with distinct environmental factors, suggesting that divergent selective pressures can act on individual loci independently of their genomic proximity or co-expression patterns. Local-scale spatial heterogeneity thus appears to maintain a remarkably ancient complex of molecular phenotypes, which have been retained in populations that diverged more than 1.5-2 MYA, representing an exceptional case of long-term structural polymorphism. These results emphasize how the interplay between genomic architecture and spatial heterogeneity in selective pressures may facilitate the retention of functional polymorphisms of an adaptive phenotype.

evolutionary biology↗

bioRxiv2017

Inbred or Outbred? Genetic diversity in laboratory rodent colonies

Non-model rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift and so may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly outbred colonies of non-model rodents (gerbils, hamsters, house mice, and deer mice) varies considerably from nearly no segregating diversity, to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the replication crisis. In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other, genetically distinct individuals to explore the genetic basis of a trait.

genetics↗

bioRxiv2017

Intrauterine position probabilities in mice, rats and gerbils

The position of a developing embryo or foetus relative to members of the same or opposite sex can have profound effects on its resulting anatomy, physiology and behavior. Here we treat intrauterine position as a combinatorial problem and determine the theoretical probability of having 0, 1 or 2 adjacent foetuses of the opposite sex for species with random and biased distribution of genders in uterine horns (mice and gerbils), and where the influence of an \"upstream\" male has been proposed to be a factor (rats). As overall litter size increases the probabilities of having 0, 1, or 2 adjacent foetuses of the opposite sex approaches and eventually settles at 0.25, 0.5, 0.25 respectively. However, at biologically-relevant litter sizes probabilities are more variable and the general effect of an increase in litter size is to increase the probability that any particular foetus will be flanked by two members of the opposite sex. When gender ratios within a uterine horn are no longer balanced, the probability that there are 0 adjacent foetuses of the opposite sex increases.

developmental biology↗

bioRxiv2016

Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster

The sand rat Psammomys obesus is a gerbil native to deserts of North Africa and the Middle East1. Sand rats survive with low caloric intake and when given high carbohydrate diets can become obese and develop type II diabetes2 which, in extreme cases, leads to pancreatic failure and death3,4. Previous studies have reported inability to detect the Pdx1 gene or protein in gerbils5-7, suggesting that absence of this key insulin-regulating homeobox gene might underlie diabetes susceptibility. Here we report sequencing of the sand rat genome and discovery of an extensive, mutationally-biased GC-rich genomic domain encompassing many essential genes, including the elusive Pdx1. The sequence of Pdx1 has been grossly affected by GC-biased mutation leading to the highest divergence observed in the animal kingdom. In addition to molecular insights into restricted caloric intake in a desert species, the discovery that specific chromosomal regions can be subject to elevated mutation rate has widespread significance to evolution.

evolutionary biology↗