A5026432033- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Cutaneous lymphoproliferative disorders research
- Animal Behavior and Reproduction
- CAR-T cell therapy research
- Chromosomal and Genetic Variations
- Fish Ecology and Management Studies
- Toxin Mechanisms and Immunotoxins
- Morphological variations and asymmetry
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Bat Biology and Ecology Studies
- Genetics, Bioinformatics, and Biomedical Research
- Legume Nitrogen Fixing Symbiosis
- Reproductive biology and impacts on aquatic species
- RNA Research and Splicing
- Plant Diversity and Evolution
- Evolution and Paleontology Studies
- Paleontology and Evolutionary Biology
- Genomic variations and chromosomal abnormalities
- Genomics and Chromatin Dynamics
- Plant Parasitism and Resistance
University of Helsinki
2019-2024
University of Sheffield
2017-2021
Institut de Biologia Evolutiva
2019
Population genetic theory predicts that selection should be more effective when the population size (Ne) is larger, and efficacy of correlate positively with recombination rate. Here, we analyzed genomes ten great tits zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates finches have a 2.83-fold larger Ne. We obtained clear evidence purifying in The proportion substitutions 0-fold fixed by positive (α) high both species (great tit 48%; finch 64%) significantly higher When...
Abstract High‐density SNP microarrays (“ chips”) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While chips routinely used human genetics animal plant breeding, they less widely evolutionary ecological research. In this article, we describe the development application high‐density Affymetrix Axiom chip with around 500,000 s, designed to perform genomics studies great tit ( Parus major ) populations. We...
Recent progress has been made in identifying genomic regions implicated trait evolution on a microevolutionary scale many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, key evolutionary innovation linked to patterns of resource use, divergence, and speciation, as model trait. We integrate class-wide geometric-morphometric analyses with sequence 10,322 protein-coding genes well...
Small insertions and deletions (INDELs; ≤50 bp) are the most common type of variability after single nucleotide polymorphism (SNP). However, compared with SNPs, we know little about distribution fitness effects (DFE) new INDEL mutations how prevalent adaptive substitutions are. Studying INDELs has been difficult partly because identifying ancestral states at these sites is error-prone misidentification can lead to severely biased estimates strength selection. To solve problems, develop...
Evidence of eukaryote-to-eukaryote lateral gene transfer (LGT) has accumulated in recent years [1Davis C.C. Wurdack K.J. Host-to-parasite flowering plants: phylogenetic evidence from Malpighiales.Science. 2004; 305: 676-678Crossref PubMed Scopus (196) Google Scholar, 2Richards T.A. Soanes D.M. Foster P.G. Leonard G. Thornton C.R. Talbot N.J. Phylogenomic analysis demonstrates a pattern rare and ancient horizontal between plants fungi.Plant Cell. 2009; 21: 1897-1911Crossref (141) 3Moran N.A....
Linking reproductive fitness with adaptive traits at the genomic level can shed light on mechanisms that produce and maintain sex-specific selection. Here, we construct a multigenerational pedigree to investigate selection maturation gene, vgll3, in wild Atlantic salmon population. The vgll3 locus is responsible for ~40% of variation (sea age first reproduction). Genetic parentage analysis was conducted 18,265 juveniles (parr) 685 adults collected same spawning ground over eight consecutive...
Abstract Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether how this occurs is limited. Here, we present an analysis the great tit (Parus major) genome, aiming detect signals faster-Z evolution. We find mixed evidence faster divergence Z chromosome than autosomes, with significantly higher being found in...
It is known that the effective population size (Ne) and mutation rate (u) vary across genome. Here, we show ignoring this heterogeneity may lead to biased estimates of past demography. To solve problem, develop new methods for jointly inferring changes in detecting variation Ne u between loci. These rely on either polymorphism data alone or both divergence data. In addition demography, can use study a variety questions: 1) comparing sex chromosomes with autosomes (for finding evidence...
Insertions and deletions (INDELs) remain understudied, despite being the most common form of genetic variation after single nucleotide polymorphisms. This stems partly from challenge correctly identifying ancestral state an INDEL thus it as insertion or a deletion. Erroneously assigned states can skew site frequency spectrum, leading to artificial signals selection. Consequently, selective pressures acting on INDELs are, at present, poorly resolved. To tackle this issue, we have recently...
The purpose of this RNA sequencing study was to investigate the biological mechanism underlying how transcription factors (TFs) Twist1 and Zeb1 influence prognosis mycosis fungoides (MF). We used laser-captured microdissection dissect malignant T-cells obtained from 40 skin biopsies MF patients with stage I-IV disease. Immunohistochemistry (IHC) determinate protein expression levels Zeb1. Based on sequencing, principal component analysis (PCA), differential (DE) analysis, ingenuity pathway...
Abstract Whole-genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing divergence following events lead to massive redundancy, such WGD, remain largely unknown. We studied of strength natural selection on Atlantic salmon (Salmo salar) genome, which has undergone WGD...
Abstract Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) a key driving force behind content, through preferential incorporation alleles over AT during recombination, them towards fixation. The majority work on gBGC has focussed its role in coding regions, largely address how it confounds estimates selection. Non-coding regions have received less attention, particularly regard interaction and...
Abstract Recent progress has been made in identifying genomic regions implicated trait evolution on a microevolutionary scale many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, key evolutionary innovation linked to patterns of resource use, divergence and speciation, as model trait. We integrate class-wide geometric-morphometric analyses with sequence 10,322 protein coding genes...
Linking reproductive fitness with adaptive traits at the genomic level can shed light on mechanisms that produce and maintain sex-specific selection. Here, we construct a multigenerational pedigree to investigate selection maturation gene, vgll3, in wild Atlantic salmon population. The vgll3 locus is responsible for ~40% of variation (sea age first reproduction). Genetic parentage analysis was conducted 18,265 juveniles (parr) 685 adults collected same spawning ground over eight consecutive...
Abstract Whole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing divergence following events lead to massive redundancy, such WGD, remain largely unknown. We studied of strength natural selection on Atlantic salmon ( Salmo salar ) genome, which has undergone WGD...