Martin Stoffel

Martin Stoffel
The University of Edinburgh | UoE · Institute of Evolutionary Biology

PhD

About

40
Publications
139,129
Reads
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1,331
Citations
Additional affiliations
April 2019 - present
The University of Edinburgh
Position
  • Fellow
September 2018 - March 2019
Friedrich Schiller University Jena
Position
  • PostDoc Position
August 2015 - August 2018
Bielefeld University
Position
  • PhD Student
Education
October 2012 - October 2014
Bielefeld University
Field of study
  • Brain&Behaviour
October 2009 - September 2012
Universität Koblenz-Landau
Field of study
  • Psychology

Publications

Publications (40)
Article
Full-text available
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and population viability. In an era of biodiversity loss and climate change, understanding the determinants and consequences of bottlenecks is therefore an important challenge. However, as most studies focus on single species, the multitude of potenti...
Article
Full-text available
The gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups sta...
Article
Full-text available
Runs of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. U...
Article
Full-text available
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs o...
Article
Full-text available
The coefficient of determination R ² quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the fixed-effects complement to the repeatability R (intra-class correlation) for the variance explained by random effects and thus as a tool for variance decomposition. The R ² of a model can be further p...
Article
Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs...
Preprint
In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of in...
Preprint
Full-text available
Runs of homozygosity (ROH) are ubiquitous in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep....
Article
Full-text available
Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publ...
Preprint
Full-text available
The coefficient of determination R ² quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the fixed-effects complement to the repeatability R (intra-class correlation) for the variance explained by random effects and thus as a tool for variance decomposition. The R ² of a model can be further p...
Preprint
Full-text available
Meiotic recombination is a ubiquitous feature of sexual reproduction, ensuring proper disjunction of homologous chromosomes, and creating new combinations of alleles upon which selection can act. By identifying the genetic drivers of recombination rate variation, we can begin to understand its evolution. Here, we revisit an analysis investigating t...
Preprint
Full-text available
Inbreeding depression is a phenomenon of long-standing importance, but we know surprisingly little about its genetic architecture, precise effects and life-history dynamics in wild populations. Here, we combined 417K imputed SNP genotypes for 5952 wild Soay sheep with detailed long-term life-history data to explore inbreeding depression on a key fi...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Replication studies are essential for assessing the validity of previous research findings and for probing their generality. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes...
Article
Full-text available
Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arcto...
Preprint
Full-text available
The gut microbiome is an integral part of a species’ ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups sta...
Article
Full-text available
Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, there is growing interest in the use of gas chromatography (GC) to investigate the chemical basis of eco-evolutionary interactions. Both GC-MS (mass spectrometry) and FID (flame ionization detect...
Data
Details on the bibliographic survey. (DOCX)
Data
Datasets used to generate the results presented in this manuscript. This is a compressed zip archive that includes all the raw data that were used to produce the results shown in the manuscript and in S3 File. (ZIP)
Data
R code and accompanying documentation for all analyses presented in this manuscript. All analysis steps are provided in an Rmarkdown document file. (PDF)
Data
The vignette ‘GCalignR: Step by Step’ gives an more detailed introduction into the usage of the package functionalities to tune parameters for aligning peak data. (HTML)
Data
Summary of published algorithms implemented in publicly available software. (DOCX)
Data
The vignette ‘GCalignR: How does the Algorithms work?’ gives an introduction into the concepts of the algorithm and illustrates how each step of the alignment procedure alters the outcome based on simple datasets consisting of simulated chromatograms. (HTML)
Preprint
Full-text available
A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and negatively impact population viability and adaptive potential. In an era of unprecedented biodiversity loss and climate change, understanding both the determinants and consequences of bottlenecks in wild populations is therefore an increasingly im...
Article
Full-text available
Adult sex ratio (ASR) is a central concept in population biology and a key factor in sexual selection, but why do most demographic models ignore sex biases? Vital rates often vary between the sexes and across life history, but their relative contributions to ASR variation remain poorly understood—an essential step to evaluate sex ratio theories in...
Article
Full-text available
Intra-class correlations (ICC) and repeatabilities (R) are fundamental statistics for quantifying the reproducibility of measurements and for understanding the structure of biological variation. Linear mixed effects models offer a versatile framework for estimating ICC and R. However, while point estimation and significance testing by likelihood ra...
Preprint
Full-text available
Adult sex ratio (ASR) is a central concept in population biology and a key factor in sexual selection, yet why do most demographic models ignore sex-biases? Vital rates often vary between the sexes and across life history, but their relative contributions to ASR variation remain poorly understood--an essential step to evaluate sex ratio theories in...
Article
Full-text available
Chemical signals are arguably the oldest and most fundamental means of animal communication and play a fundamental role in mate choice and kin selection. A key tool for uncovering broad patterns of chemical similarity is gas chromatography (GC). However, downstream analyses rely on the correct alignment of homologous substances, represented by peak...
Article
Full-text available
Heterozygosity-fitness correlations (HFCs) have been widely used to explore the impact of inbreeding on individual fitness. Initially, most studies used small panels of microsatellites, but more recently with the advent of next-generation sequencing, large SNP datasets are becoming increasingly available and these provide greater power and precisio...
Article
Full-text available
Chemical communication underpins virtually all aspects of vertebrate social life, yet remains poorly understood because of its highly complex mechanistic basis. We therefore used chemical fingerprinting of skin swabs and genetic analysis to explore the chemical cues that may underlie mother–offspring recognition in colonially breeding Antarctic fur...
Article
Full-text available
Purpose: The Coping Strategies Questionnaire (CSQ) by Rosenstiel and Keefe (1983) is one of the most widely used measures of coping strategies in pain patients, although its construct and factorial validity is dissatisfying. Verra, Angst, Lehmann, and Aeschlimann (2006) translated the full measure, which assesses eight different coping strategies,...

Questions

Questions (16)
Question
For my project, I want to analyse the bacterial community composition of anal swabs from seals. Thus, I'm searching a reliable service provider for both the library preparation as well as 16s sequencing in Europe.
It would be great if someone has any experiences and could share them!
Question
I'm searching an aesthetic schematic illustration of a population bottleneck, including possible outcomes such as recovery and extinction. Any source is appreciated!
Question
I have a variety of (microsatellite) data sets for different species and want to compare their mean genetic diversity, i.e. their mean number of alleles per locus. This is dependent on the sample size in every data set. Does anyone know a good way to standardize the mean number of alleles to make them comparable across datasets? Preferably already implemented in an R package or possible to implement myself. Thanks!
Question
I´d like to use approximate bayesian computation to compare three different demographic scenarios (bottleneck vs. constant population vs. population decline) for several species with microsatellites. Is there any tutorial or paper that gives an outline over the whole process (from simulation to parameter estimation and model selection) on how to do this in R or with the command line (not in a point-and-klick way)? 
Question
I´m searching an R package or command line program to calculate heterozygosity-excess (similar to BOTTLENECK, Piry et al. 1999) and m-ratio (Garza and Williamson, 2001) tests for population bottlenecks based on microsatellites. 
Would be great if anybody has an idea about that as I have lots of datasets to work on.
Question
I am searching for an organism that is also easy to breed in the aquarium and reproduces relatively quickly (say up to 2 or 3 months is ok). I am open to both salt- and freshwater organisms!
Question
My raw data is simple: One column of SNP IDs followed by two columns for each locus where 1 is allel A and 2 is allel B. A homozogote would thus have 1 1 or 2 2 in the two first columns and a heterozygote 1 2 or 2 1. How can I convert this table into plink binary PED files for the analysis in GCTA? It seems like many of the variables (Family ID, Paternal ID, Maternal ID, Sex etc) are missing in my dataset and I also don´t know whether that could cause any problems.

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