Matthew T Webster

Matthew T Webster
Uppsala University | UU · Department of Medical Biochemistry and Microbiology

Doctor of Philosophy

About

240
Publications
74,000
Reads
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11,051
Citations
Additional affiliations
January 2007 - present
Uppsala University
Position
  • Professor (Associate)
September 1996 - December 2000
University of Oxford
Position
  • PhD Student

Publications

Publications (240)
Article
Full-text available
Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed popula...
Article
Full-text available
The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptat...
Article
Full-text available
Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speci-ation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepanci...
Article
Full-text available
In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers) by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis), worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nuc...
Article
Full-text available
Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a l...
Article
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant‐pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used mo...
Article
The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that mo...
Article
Full-text available
Evidence is accumulating that gene flow commonly occurs between recently-diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here we compare genetic differentiation across the genomes of bumblebee sp...
Preprint
Full-text available
Populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms, in the last six decades. It is hypothesized that this reflects selection exerted by changes in floral composition under climate change. Here we combine extensive morphometric...
Article
Mountain ranges offer opportunities for understanding how species evolved and diversified across different environmental conditions. Neotropical frogs of the genus Oreobates (Anura: Craugastoridae) are adapted to highland and lowland habitats along the Andes, but many aspects of their evolution remain unknown. We studied their evolutionary history...
Article
Full-text available
The mosaic nature of hybrid genomes is well recognized, but little is known of how they are shaped initially by patterns of breeding, selection, recombination and differential incompatibilities. On the small Galápagos island of Daphne Major, two species of Darwin’s finches, Geospiza fortis and G. scandens, hybridize rarely and back-cross bidirectio...
Article
The Cape honey bee, Apis mellifera capensis, is able to produce female offspring asexually. This phenomenon has now been shown to have a simple genetic basis.
Article
The Cape bee (Apis mellifera capensis) is a subspecies of the honeybee, in which workers commonly lay diploid unfertilized eggs via a process known as thelytoky. A recent study aimed to map the genetic basis of this trait in the progeny of a single capensis queen where workers laid either diploid (thelytokous) or haploid (arrhenotokous) eggs. A non...
Article
Full-text available
Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary c...
Article
Full-text available
Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here we compare the genomic recombination landscape of the highly soci...
Article
Full-text available
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first gene...
Article
Full-text available
Chromosomal inversions can facilitate local adaptation in the presence of gene flow by suppressing recombination between well‐adapted native haplotypes and poorly‐adapted migrant haplotypes. East African mountain populations of the honeybee Apis mellifera are highly divergent from neighbouring lowland populations at two extended regions in the geno...
Article
Full-text available
The availability of powerful high-throughput genomic tools, combined with genome scans, has helped identifying genes and genetic changes responsible for environmental adaptation in many organisms, including the honeybee. Here, we resequenced 87 whole genomes of the honeybee native to Iberia and used conceptually different selection methods (Samβada...
Preprint
Full-text available
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first gene...
Article
Full-text available
The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In Western Europe one such threat is large-scale introductions of commercial strains (C-lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M-lineage a...
Article
Full-text available
A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general...
Article
Full-text available
Homoploid hybrid speciation in animals has been inferred frequently from patterns of variation, but few examples have withstood critical scrutiny. Here we report a directly documented example from its origin to reproductive isolation. An immigrant Darwin’s finch to Daphne Major in the Galápagos archipelago initiated a new genetic lineage by breedin...
Article
Full-text available
Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms d...
Article
Full-text available
Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on...
Data
Quantile-quantile plot of a genome-wide association study between SNPs and highland and lowland habitats. SNP p-values associated with the observed (y-axis) and the expected (x-axis) distribution of allele frequency differences between highland bees (n = 20) and lowland bees (n = 19). Blue line indicates the distribution where observed data equals...
Data
Possible locations of unplaced scaffolds with outlier SNPs. (XLSX)
Data
Divergence and substitutions across genes in highland and lowland haplotypes. (XLSX)
Data
PCA clustering of samples using PLINK multidimensional scaling. (A) Clustering based on all SNPs outside of the r7 and r9 regions. (B) Clustering in the r7 region on chromosome 7. Yellow circle indicates samples that are homozygous for the lowland haplotype. Grey circle indicates samples that are homozygous for the highland haplotype. Pink circle i...
Data
FST distribution produced by coalescent simulations of a population split. 1 million simulated SNPs were binned according to 0.01 intervals. Blue area represents SNP FST distribution (y1-axis). Red line is the cumulate proportion of SNPs (y2-axis). Black dots indicate the proportion (p) of SNPs above an FST threshold (p = 0.05 is the top 50,000 SNP...
Data
Worldwide distribution of highland and lowland haplotypes. (A) Haplotypes detected for the 11 samples sequenced by Fuller et al. Color codes and bottom panels as in Fig 4. Sample order as in S1B Table. (B) A global sample of honey bees from [25]. Symbols as in Fig 4. Sample order as in S1C Table. (C) The r9 region for the African samples and subdiv...
Data
Abdominal pigmentation in monticola forest highland bees and scutellata savannah lowland bees. Stars indicate samples with contrasting haplotypes for r7 (blue) or r9 (green) from the common haplotype in either habitat (see Fig 4). Black bars indicate individuals with back/dark pigmentation across all tergites of the abdomen. (TIF)
Data
Allele frequency differences between population pairs. (A) Genome-wide plot of allele frequency differences (FST) of every nuclear SNP segregating between Mount Kenya highland bees (n = 10) and lowland bees (n = 9). Divergent regions r7 (chromosome 7; blue) and r9 (chromosome 9; green). Black line indicates overall FST across 10 kbp non-overlapping...
Data
Distribution of haplotypes as inferred from divergent SNP genotypes (n) across r7i, r7ii and the unplaced scaffolds. (A) Genotype and haplotype distributions on r7i and r7ii at SNPs that diverge between highland and lowland populations. At every genotype, a sample can be homozygous for the reference allele (0/0), homozygous for the non-reference al...
Data
r7 haplotype breakpoints. (A) Tablet visualization of read mapping across the putative breakpoint at the start of the r7 haplotype using. Reads from bees with r7 lowland haplotypes are yellow. Reads from bees with r7 highland haplotypes are grey. Reads from heterozygous samples are pink. Light blue box indicates spuriously mapped region in highland...
Data
Sample locations and sequence information. (XLSX)
Data
Extended filtering and quality control. (A) Proportion of retained sites across the genome or divergent regions r7 and r9 after stringent filtering for mapping depth and sample coverage (see Results section for filters; r7h = r7 highland haplogroup; r7l = r7 lowland haplogroup; r9h = r9 highland haplogroup; r9l = r9 lowland haplogroup). (B) Average...
Preprint
Full-text available
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Preprint
Full-text available
Whole genome sequencing is opening the door to novel insights into the population structure and evolutionary history of poorly known species. In organisms with large genomes, which includes most amphibians, whole-genome sequencing is excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wi...
Article
Full-text available
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary proc...
Article
Full-text available
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berke...
Article
Full-text available
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berke...
Article
Full-text available
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkel...
Preprint
Full-text available
As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster ) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220...
Data
Low-FST SNPs dominate the dataset and the western subpopulation shows more fixation against other populations. (A) FST was computed for every SNP segregating between the Cape bee (capensis, n = 10) and the scutellata + adansonii (SA; n = 20) background population (n = 6,245,176) and counted for FST bins of 0.05. The distribution is dominated by var...
Data
Extreme haplotype divergence and homozygosity signals centers around outlier SNPs (FST>0.9) and decay after 40–60kbp. (A) Every SNP with FST>0.2 and minimal evidence for extended haplotype homozygosity (XP-EHH) in the Cape bees (XP-EHH>0) was put in FST bins of 0.10. The linked divergence was traced around each SNP by computing FST across 1kbp wind...
Data
The western subpopulation is associated with more extensive selection signals than the eastern subpopulation. (A) SNPs segregating between the Cape bees and the African background population (scutellata + adansonii) were sorted for FST and the top 0.1% (n = 6245) were filtered for minimal evidence for extended haplotype homozygosity in the Cape bee...
Data
Genes with putatively selected variants have elevated selection signals compared to the genomic background. (A) Genetic distance (FST estimator of Reynolds et al. [104]), the population branch statistic (PBS) and cross population extended haplotype heterozygosity (XP-EHH) between the Cape bees and the African background population were estimated fo...
Data
Significantly enriched Gene Ontology terms detected among the Drosophilia orthologs of the candidate accessions. (XLS)
Data
Twelve selective sweeps with high-FST variants detected in the Cape bees. Among the 97 candidate accessions associated with the top 1000 SNPs ranked for the composite selection score (CSS) were 25 accessions that include at least one SNP above the 99.99% FST percentile (FST>0.80). These are located in 12 selective sweeps (labeled from A to L) acros...
Data
Information about the 97 accessions associated with the top 1000 CSS SNPs. (XLS)
Data
Extreme haplotype homozygosity and divergence is more pronounced in Cape bees than the background population and associate with high-FST SNPs. (A) The XP-EHH was estimated for SNPs with MAF>0.02 (n = 6,196,550) using the program selscan ([28]) and binned (units of 0.01; blue distribution). The average XP-EHH for was also computed for 1kbp windows a...
Data
Significantly enriched gene ontology (GO) terms among Drosophila orthologues of the Cape bee candidates. The top 1000 SNPs sorted for their Composite Selection Signal (CSS; FST+XP-EHH) located within 8kbp from the closest gene body were associated with 97 accessions in the honeybee genome (S3 Table), 73 of which had previously been matched to 68 un...
Data
The Cape bees have a larger number of divergent regions across the genome than the other two subspecies. The fixation index (FST) was computed for every SNP segregating between each subspecies and a combined population consisting of the other two African subspecies (further described in Fig 2). (A) A. m. capensis vs adansonii + scutellata. The main...
Data
The gemini deletion is not fixed in the Cape bees and is detected in other African subspecies. Short read data was mapped across the putative 9bp deletion (the thelytoky associated element 1; tae1) in one of the introns of the transcription factor Gemini and visualized using samtools console output. (A) Read data for 10 capensis samples. The deleti...
Data
Fixed SNPs between Cape bees and the African background population. (XLS)
Data
Top 1000 SNPs ranked for the Composite Selection Score (CSS) between Cape bees and the African background population. (XLS)