William Amos

William Amos
University of Cambridge | Cam · Department of Zoology

PhD

About

260
Publications
62,069
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12,522
Citations
Introduction
Most important (in my view) is my idea that mutation rate is influenced by genetic heterozygosity. If true, sections of classical population genetic theory would need revisiting. One finding is that African humans have diverged more from our common ancestor than non-Africans. I also study tuberculosis susceptibility in British cattle, microsatellite evolution, the role of heterozygosity in animal fitness, human population history and marine mammal breeding behaviour and population structure.
Additional affiliations
October 1996 - present
University of Cambridge
Position
  • Professor of Evolutionary Genetics

Publications

Publications (260)
Article
Full-text available
Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance fro...
Article
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During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSP), which reconstruct population fluctuations based on genetic data, and Species Distribution Models, which allow us to back‐cast th...
Preprint
Full-text available
It is widely accepted that non-African humans carry a few percent of Neanderthal DNA due to historical inter-breeding. However, methods used to infer a legacy all assume that mutation rate is constant and that back-mutations can be ignored. Here I decompose the widely used admixture statistic, D, in a way that allows the overall signal to be apport...
Preprint
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A large and rapidly expanding literature has grown out of the observation that humans carry a genetic legacy reflecting ancient inter-breeding with archaic hominins such as Neanderthals and Denisovans. However, a recent study suggests that a commonly used statistic used to assess legacy size, D, is driven mainly by heterozygous sites in Africa acti...
Article
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The detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA BABA test or D statistic, which identifies excess allele sharing between non-sister taxa. Part of the appeal of D is its simplicity, but this...
Preprint
Full-text available
ABSTRCT The detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA BABA test or D statistic, which identifies excess allele sharing between non-sister taxa. Part of the appeal of D is its simplicity, b...
Article
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Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans wh...
Article
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Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 d...
Article
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In a handful of mammals, females show an extended postreproductive lifespan (PRLS), leading to questions over why they spend a substantial portion of their lifespan nonreproductive. Theoretical and empirical studies suggest that PRLS may evolve when 1) demographic patterns lead to increasing local relatedness as females age, and 2) females come int...
Preprint
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During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally. Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in struc...
Article
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Understanding when, where and which mutations are mostly likely to occur impacts many areas of evolutionary biology, from genetic diseases to phylogenetic reconstruction. Africans and non-African humans differ in the mutability of different triplet base combinations. Africans and non-Africans also differ in mutation rate, possibly because heterozyg...
Preprint
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The idea that humans interbred with other Hominins, most notably Neanderthals, is now accepted as fact. The finding of hybrid skeletons shows that fertile matings did occur. However, inferences about the size of the resulting legacy assume that back-mutations are rare enough to be ignored and that mutation rate does not vary. In reality, back-mutat...
Data
Supplementary Figure 3. Neighbour-joining tree based on the similarity of EBSP profiles.
Data
Supplementary Figure 4. Global position of sampling sites with all profiles from each major region overlaid.
Data
Supplementary Figure 1. EBSPs of populations with the largest sample sizes from each of the four major regions.
Article
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The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from th...
Article
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Few now dispute that a few percent of the DNA of non-African humans is a legacy of interbreeding with Neanderthals. However, heterozygosity and mutation rate appear to be linked such that the loss of diversity associated with humans migrating out of Africa caused a mutational slowdown, allowing Africans to diverge more from both our common ancestor...
Article
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To enhance their conservation value, several hundred islands worldwide have been cleared of invasive alien rats, Rattus spp. One of the largest projects yet undertaken was on 43 km2 Henderson Island in the Pitcairn group, South Pacific, in August 2011. Following massive immediate mortality, a single R. exulans was observed in March 2012 and, subseq...
Article
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Whole genome sequencing of families of Arabidopsis has recently lent strong support to the heterozygote instability (HI) hypothesis that heterozygosity locally increases mutation rate. However, there is an important theoretical difference between the impact on base substitutions, where mutation rate increases in regions surrounding a heterozygous s...
Article
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Microsatellite mutations identified in pedigrees confirm that most changes involve the gain or loss of single repeats. However, an unexpected pattern is revealed when the resulting data are plotted on standardized scales that range from the shortest to longest allele at a locus. Both mutation rate and mutation bias reveal a strong dependency on all...
Article
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Sir, We write as senior scientists about a problem vital to the scientific enterprise and prosperity. Nowadays, funding is a lengthy and complex business. First, universities themselves must approve all proposals for submission. Funding agencies then subject those that survive to peer review, a process by which a few researchers, usually acting ano...
Article
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Substitution rate is often found to correlate with life history traits such as body mass, a predictor of population size and longevity, and body temperature. The underlying mechanism is unclear but most models invoke either natural selection or factors such as generation length that change the number of mutation opportunities per unit time. Here we...
Article
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Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We th...
Article
In racing Thoroughbred horses, blood cell counts and key biochemistry parameters are used to monitor horse health during training. The most common measure is total white blood cell (WBC) count, usually coupled with estimates of the relative abundance of the five main types of WBC. However, WBC can go down and up when challenged, making interpretati...
Article
Maternal investment in reproduction and parental care is an important determinant of both offspring and maternal fitness. However, optimal investment strategies may differ depending on offspring sex, potentially resulting in a sex-biased distribution of maternal resources or adaptive variation in offspring sex ratio. We used morphometric and geneti...
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The social structure of a population is a crucial element of an individual's environment, fundamentally influencing the transfer of genes, information and diseases. A central question in social network analysis is how different traits affect associations within populations. However, previous studies of animal social networks have typically focused...
Article
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Many efforts have been made to detect signatures of positive selection in the human genome, especially those associated with expansion from Africa and subsequent colonization of all other continents. However, most approaches have not directly probed the relationship between the environment and patterns of variation among humans. We have designed a...
Article
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Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard,...
Article
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The "heterozygote instability" (HI) hypothesis suggests that gene conversion events focused on heterozygous sites during meiosis locally increase the mutation rate, but this hypothesis remains largely untested. As humans left Africa they lost variability, which, if HI operates, should have reduced the mutation rate in non-Africans. Relative substit...
Article
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Bovine tuberculosis (bTB) imposes an important financial burden on the British cattle industry, yet despite intense efforts to control its spread, incidence is currently rising. Surveillance for bTB is based on a skin test that measures an immunological response to tuberculin. Cattle that fail the test are classified as "reactors" and slaughtered....
Data
Data set used for fitting models. Columns are: # = sample number; Age = age at slaughter in days; Breed, given as the breed code, see Table 1; a1, a2, b1 and b2 are the four swelling size measurements given as first (1) and second (2) for the avian (a) and bovine (b) injection sites; da and db are the swelling size differences, given as the second...
Data
Average skin thickness recorded in VeBus for breeds within study population. For breed codes see Table 1. (DOCX)
Data
Prediction of avian skin thickness measurement (a2) by ‘22’ genotype. Summary of a Poisson error structure regression model exploring the association between having the ‘22’ genotype and size of the second avian skin thickness measurement (a2). Coefficients are reported to 2 significant figures, with 95% confidence intervals. Significant associatio...
Data
Prediction of bovine skin thickness measurement (b2) by ‘22’ genotype. Summary of a Poisson error structure regression model exploring the association between having the ‘22’ genotype and size of the second bovine skin thickness measurement (b2). Coefficients are reported to 2 significant figures, with 95% confidence intervals. Significant associat...
Article
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The Major Histocompatability Complex (MHC) is one of the best known and best characterised components of the immune system, yet its functions remain somewhat enigmatic, including both anti-pathogen activity and kin recognition. To explore the importance of the MHC relative to literally hundreds of other components of the immune system, we compared...
Article
In cooperatively breeding vertebrate societies, contributions to offspring care can vary greatly between group members. Kin selection theory predicts that cooperation will be favoured when directed towards relatives and when the cost to benefit ratio is low. The fitness costs of helping in turn depend on the impact of energetic investments in care...
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Although recent years have witnessed a rapid growth in the number of genetic studies of Antarctic organisms, relatively few studies have so far used nuclear markers, possibly due to the perceived cost and difficulty of isolating markers such as microsatellites. However, an often overlooked alternative is to use amplified fragment length polymorphis...
Article
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The mating system of the Mediterranean monk seal was studied combining the use of diverse technologies. Sexual dimorphism in size was limited. Sexual activity was only observed to occur in the water. The different segments of the population segregated spatially: females, pups, and juveniles aggregated inside two main caves, whose entrances were con...
Article
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McLaughlin and Chadwick describe an X-linked tandem repeat that is transcribed, conserved and defies X inactivation. Is it selfish, functional or just an oddity? See research article: http://genomebiology.com/2011/12/4/R37
Article
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Associations between specific host genes and susceptibility to Mycobacterial infections such as tuberculosis have been reported in several species. Bovine tuberculosis (bTB) impacts greatly the UK cattle industry, yet genetic predispositions have yet to be identified. We therefore used a candidate gene approach to study 384 cattle of which 160 had...
Article
Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater geneti...
Article
Genetic heterozygosity in wild, unmanaged animal populations is often associated with protection against infectious disease. However, little is known about the relationship between heterozygosity and disease susceptibility in domesticated livestock, where disease resistance has the potential to improve animal welfare and productivity. We have inves...
Article
Microsatellites form an abundant class of DNA sequences used widely as genetic markers. Surprisingly, the length of human microsatellites varies highly predictably with distance from Africa, apparently following the linear decline in variability that arose as we colonised the world. Such patterns have been used to argue that heterozygosity modulate...
Article
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Detecting regions of the human genome that are, or have been, influenced by natural selection remains an important goal for geneticists. Many methods are used to infer selection, but there is a general reliance on an accurate understanding of how mutation and recombination events are distributed, and the well-known link between these processes and...
Article
Of key importance for understanding cooperative societies is the way in which reproductive opportunities are distributed among group members. Traditionally, skew has been thought of as a product of intrasexual competition. However, cooperatively breeding species often live in mixed-sex groups, so the behaviour of one sex has the potential to influe...
Article
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Technological developments allow increasing numbers of markers to be deployed in case-control studies searching for genetic factors that influence disease susceptibility. However, with vast numbers of markers, true 'hits' may become lost in a sea of false positives. This problem may be particularly acute for infectious diseases, where the control g...
Article
I have studied mutation patterns around very short microsatellites, focusing mainly on sequences carrying only two repeat units. By using human-chimpanzee-orangutan alignments, inferences can be made about both the relative rates of mutations and which bases have mutated. I find remarkable non-randomness, with mutation rate depending on a base's po...
Article
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Freshwater mussels (Unionoida) show high intraspecific morphological variability, and some shell morphological traits are believed to be associated with habitat conditions. It is not known whether and which of these ecophenotypic differences reflect underlying genetic differentiation or are the result of phenotypic plasticity. Using 103 amplified f...
Article
1.Genetic analysis is increasingly recognized as a key tool for understanding demography, and is particularly useful for describing patterns of gene flow between putative populations. Most effort has been directed towards vertebrate systems, where any one study often benefits from marker development in related species. The greater diversity of inve...
Article
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Single nucleotide polymorphisms (SNPs) are distributed highly non-randomly in the human genome through a variety of processes from ascertainment biases (i.e. the preferential development of SNPs around interesting genes) to the action of mutation hotspots and natural selection. However, with more systematic SNP development, one might expect an incr...
Article
The Grey Fantail Rhipidura albiscapa is a socially monogamous passerine endemic to Australia. Behavioural and morphological clues point to opposing conclusions as to its breeding system; sexual monomorphism and monochrome colorations suggest monogamy, whereas relatively large testes and a prominent cloacal protruberance are more indicative of multi...
Article
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The study of genetic differentiation between allopatric island populations should ideally account for regional palaeogeography, as this can often help to explain current distribution patterns. Here we present a study of two subspecies of the lizard Laudakia stellio in the Greek Cyclades, an excellent model for studying vicariant speciation over a r...
Article
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Species that pass repeatedly through narrow population bottlenecks (<100 individuals) are likely to have lost a large proportion of their genetic variation. Having genotyped 92 Raso larks Alauda razae, a Critically Endangered single-island endemic whose world population in the Cape Verdes over the last 100 years has fluctuated between about 15 and...
Article
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Why do males and females often differ in their ability to cope with infection? Beyond physiological mechanisms, it has recently been proposed that life-history theory could explain immune differences from an adaptive point of view in relation to sex-specific reproductive strategies. However, a point often overlooked is that the benefits of immunity...
Article
Understanding the forces that govern the distribution of single nucleotide polymorphisms is vital for many of their applications. Here we conducted a systematic search to quantify how both SNP density and human-chimpanzee divergence vary around different repetitive sequences. We uncovered a highly complicated picture in which these quantities often...
Article
If natural selection chose where new mutations occur it might well favour placing them near existing polymorphisms, thereby avoiding disruption of areas that work while adding novelty to regions where variation is tolerated or even beneficial. Such a system could operate if heterozygous sites are recognised and 'repaired' during the initial stages...