A5072652921- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Forensic and Genetic Research
- Bioenergy crop production and management
- Yeasts and Rust Fungi Studies
- Forest Ecology and Biodiversity Studies
- Plant and animal studies
- Forest Insect Ecology and Management
- Plant Molecular Biology Research
- Plant Disease Resistance and Genetics
- Forest ecology and management
- Race, Genetics, and Society
- Mycorrhizal Fungi and Plant Interactions
- Ecology and Vegetation Dynamics Studies
- Plant Reproductive Biology
- Insect-Plant Interactions and Control
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Genomics and Chromatin Dynamics
- Botany and Plant Ecology Studies
- Epigenetics and DNA Methylation
- Wheat and Barley Genetics and Pathology
- Forest Management and Policy
Uppsala University
2020-2024
Umeå Plant Science Centre
2011-2023
Umeå University
2007-2023
Swedish University of Agricultural Sciences
2018-2023
Science for Life Laboratory
2022-2023
Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups the Philippines, including 25 diverse self-identified Negrito populations, along high-coverage genomes Australopapuans Ayta Magbukon Negritos. We possess highest level Denisovan ancestry world-∼30%-40%...
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to present, based on 48 new and 249 published ancient genomes genotypes from 16,638 modern individuals. find regional variation in timing magnitude of gene flow three sources: eastern Baltic, British-Irish Isles, southern Europe. ancestry was widespread Viking period, whereas Baltic is more localized Gotland central Sweden. In some regions, drop current levels external suggests that immigrants contributed...
Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess current European aspen (Populus tremula) by using environmental association analyses identify genetic variants associated with two representative variables describing day variation temperature precipitation. We also analysed patterns differentiation between southern northern...
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there strong imperative to dissect the genetics underlying important wood quality traits in species. We performed functional genome-wide association study (GWAS) 17 using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping 517 mother trees. The were defined modelling properties across annual growth rings. applied Least Absolute Shrinkage Selection Operator...
Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This eventually replaced assimilated incoming Neolithic farmers. The Atlantic façade home to some last Mesolithic sites mainland Europe, represented iconic open-air at Hoedic Téviec in southern Brittany, France. These are known for unusually well-preserved rich burials. Genomic studies European hunter-gatherers have been limited single or few individuals per...
Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, range diversity is orders magnitude more narrow than size. This observation has become known as Lewontin's paradox and although aspects this phenomenon have been extensively studied, underlying causes for remain unclear. Norway spruce (Picea abies) widely distributed conifer northern hemisphere, it consequently plays major role...
Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. genome very large (∼20 Gbp) contains high fraction repetitive DNA. The current assembly (v1.0) covers approximately 60% total size but highly fragmented, consisting >10 million scaffolds. annotation 66,632 gene models that are at least partially validated (www.congenie.org), however, fragmented nature means there currently little information...
Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, delta 45 donors from four human populations-African, East Asian, South European-revealed 175 additional variable junctional alleles. Most these contained coding changes were present at widely differing frequencies populations, a...
Abstract Massively parallel sequencing has revolutionized the field of genetics by providing comparatively high-resolution insights into whole genomes for large number species so far. However, whole-genome resequencing many conspecific individuals remains cost-prohibitive most species. This is especially true with very extensive genomic redundancy, such as coniferous trees. The genome assembly conifer Norway spruce ( Picea abies ) was first published draft any gymnosperm. Our goal to develop...
The rate of meiotic recombination is one the central factors determining genome-wide levels linkage disequilibrium which has important consequences for efficiency natural selection and dissection quantitative traits. Here we present a new, high-resolution map Populus tremula that use to anchor approximately two thirds P. draft genome assembly on expected 19 chromosomes, providing us with first chromosome-scale (Table 2). We then this resource estimate variation in rates across compare these...
Abstract Norway spruce ( Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic genetic studies on have been challenging due to large repetitive genome (19.6 Gb more than 70% being repetitive). To accelerate studies, including population genetics, genome‐wide association (GWAS) selection (GS), related species, we here report design performance a 50K single nucleotide polymorphism (SNP) genotyping...
Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting ecology with evolutionary biology. Thus far, research has shown that plant can underlie in associated communities (e.g., insects, lichen endophytes), those therefore be considered as extended phenotypes. This work, however, been conducted primarily at genotype level not identified key underlying genes. To address this gap, we used genome-wide...
Abstract Aspen ( Populus tremula L.) is a keystone species and model system for forest tree genomics. We present an updated resource comprising chromosome‐scale assembly, population genetics genomics data. Using the resource, we explore genetic basis of natural variation in leaf size shape, traits with complex architecture. generated genome assembly using long‐read sequencing, optical high‐density maps. conducted whole‐genome resequencing Umeå (UmAsp) collection. re‐sequencing data from...
The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale Brittany downstream Loire basin increased differentiation between northern southern sides river Loire, associated higher...
Owing to their long life span and ecological dominance in many communities, forest trees are subject attack from a diverse array of herbivores throughout range, have therefore developed large number both constitutive inducible defenses. We used molecular population genetics methods examine the evolution eight genes European aspen, Populus tremula, that all associated with defensive responses against pests and/or pathogens, earlier been shown become strongly up-regulated poplars as response...
With the rapid advancement of high throughput sequencing, large numbers genetic markers can be readily and cheaply acquired, but most current software packages for map construction cannot handle such dense input. Modern computer architectures server farms represent untapped resources that used to enable higher marker densities processed in tractable time. Here we present a pipeline using modified version OneMap parallelizes over bottleneck functions achieves substantial speedups producing...
Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, genetic and molecular mechanisms controlling this process are poorly understood. The objective study was to compare component resistance in Norway spruce Heterobasidion annosum s.s. its sympatric congener parviporum. root- stem-rot is a major disease caused by members species complex. Resistance both pathogens measured using artificial inoculations half-sib families trees...
Abstract Aspen ( Populus tremula L.) is a widely distributed keystone species and model system for forest tree genomics, with extensive resources developed population genetics genomics. Here we present an updated resource comprising chromosome-scale assembly of P. genomics data integrated into the PlantGenIE.org web resource. We demonstrate use diverse types included to explore genetic basis natural variation in leaf size shape as examples traits complex architecture. genome generated using...
When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling are also expected show strong patterns of genetic differentiation because alternative alleles favoured in different geographical locations. Here, we study 71 single nucleotide polymorphisms (SNPs) from seven associated with inducible defence responses sample Populus tremula collected across Sweden. Four these (PPO2, TI2, TI4 TI5) substantial population differentiation,...