A5012488792- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Lepidoptera: Biology and Taxonomy
- Plant and animal studies
- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic and phenotypic traits in livestock
- Evolution and Genetic Dynamics
- Species Distribution and Climate Change
- Animal Behavior and Reproduction
- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Wildlife Ecology and Conservation
- Genetic and Environmental Crop Studies
- Ecology and Vegetation Dynamics Studies
- Avian ecology and behavior
- Environmental DNA in Biodiversity Studies
- Oil Palm Production and Sustainability
- Animal Vocal Communication and Behavior
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- Fish Ecology and Management Studies
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Insect and Arachnid Ecology and Behavior
Uppsala University
2016-2025
Harvard University
2010-2014
The genome of the zebra finch — a songbird and model for study vertebrate brain, behaviour evolution has been sequenced. Its comparison with chicken genome, only other bird available, shows that genes neural function implicated in cognitive processing song have rapidly evolving lineage. also vocal communication engages much brain transcriptome identifies potential integrator microRNA signals linked to communication. studying Comparison are Moreover, brain. is an important organism several...
Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied are important avian speciation models that show pre- as well postzygotic isolation. We sequenced assembled 1.1-Gb genome, physically mapped assembly chromosomes using a low-density linkage map re-sequenced population samples each species. Here we species differentiation highly heterogeneous with approximately 50 'divergence islands'...
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing population genomic analyses. We used a custom collared flycatcher 50 K SNP array develop high-density map with 37 262 markers assigned 34 groups in 33 autosomes Z chromosome. The best-order contained 4215 markers, total distance 3132 cM mean genetic between 0.12 cM. Facilitated by being designed include from most scaffolds, we obtained second-generation assembly that approaches...
Understanding the causes and consequences of variation in rate recombination is essential since this parameter considered to affect levels genetic variability, efficacy selection, design association linkage mapping studies. However, there limited knowledge about factors governing variation. We genotyped 1920 single nucleotide polymorphisms a multigeneration pedigree more than 1000 zebra finches ( Taeniopygia guttata ) develop map, then we used these map data together with recently available...
Abstract Although there is growing interest to take genomics into the complex realms of natural populations, a general shortage genomic resources and tools available for wild species. This applies not at least birds, which approaches should be helpful questions such as adaptation, speciation population genetics. In this study, we describe genome‐wide reference set conserved avian gene markers, broadly applicable across birds. By aligning protein‐coding sequences from recently assembled...
Abstract Background Obtaining a draft genome sequence of the zebra finch ( Taeniopygia guttata ), second bird to be sequenced, provides necessary resource for whole-genome comparative analysis gene evolution in non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and contrast these with situation mammals, we aligned protein-coding sequences 8,384 1:1 orthologs chicken, finch, lizard three mammalian species. Results We found clear...
Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability complete sequences for two bird species, chicken zebra finch, provides, first time, an ideal opportunity to analyze relationship between (chromosomal CNV) recombination on a genome-wide level. aims this study were therefore threefold: (1) combine...
Characterizing and quantifying genome size variation among organisms understanding if evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate association with transposable elements (TEs) across lepidopteran lineages using novel assembly the common wood-white (Leptidea sinapis) population re-sequencing data from both L. sinapis closely related reali juvernica together 12 previously available assemblies. A...
Migration is typically associated with risk and uncertainty at the population level, but little known about its cost-benefit trade-offs species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks outbreaks. Here, we use genomic data investigate levels of heterozygosity long-term size dynamics migratory insects, as an alternative classical short-term approaches such regional field monitoring. We analyse whole-genome sequences from 97...
Abstract Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated ancestral karyotype gene synteny is often across deep divergence, although examples of extensive genome reshuffling recently been demonstrated. The genus Leptidea has an unusual level variation rearranged sex chromosomes, but extent...
Recombination is a key molecular mechanism that has profound implications on both micro- and macroevolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, particular Lepidoptera (moths butterflies). The wood white butterfly (
A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched...
Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across avian genome, we performed brain transcriptome using Roche 454 10 different non-model species. Contigs from de novo assemblies were aligned two available reference genomes, chicken zebra finch. In total, identified 6499 genes all species, with approximately 1000...
The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype relied almost exclusively on comparative molecular cytogenetics only the largest chromosomes. Here, novel whole information from 21 sequences (most newly assembled) made available an interactive browser (Evolution Highway) was analyzed. Focusing six...
Relatively little is known about the character of gene expression evolution as species diverge. It for instance unclear if generally evolves in a clock-like manner (by stabilizing selection or neutral evolution) there are frequent episodes directional selection. To gain insights into evolutionary divergence expression, we sequenced and compared transcriptomes multiple organs from population samples collared (Ficedula albicollis) pied flycatchers (F. hypoleuca), two which diverged less than...
Reshuffling of genetic variation occurs both by independent assortment chromosomes and homologous recombination. Such reshuffling can generate novel allele combinations break linkage between advantageous deleterious variants which increases the potential efficacy natural selection. Here we used high-density maps to characterize global regional recombination rate in two populations wood white butterfly (Leptidea sinapis) that differ considerably their karyotype as a consequence at least 27...
Data from completely sequenced genomes are likely to open the way for novel studies of genetics nonmodel organisms, in particular when it comes identification and analysis genes responsible traits that under selection natural populations. Here we use draft sequence chicken genome as a starting point linkage mapping wild bird species, collared flycatcher - one most well-studied avian species ecological evolutionary research. A pedigree 365 flycatchers was established genotyped single...
By taking advantage of a recently developed reference marker set for avian genome analysis we have constructed gene-based genetic map the collared flycatcher, an important "ecological model" studies life-history evolution, sexual selection, speciation, and quantitative genetics. A pedigree 322 birds from natural population was genotyped 384 single nucleotide polymorphisms (SNPs) 170 protein-coding genes 71 microsatellites. Altogether, 147 gene markers 64 microsatellites form 33 linkage...
Abstract With the access to draft genome sequence assemblies and whole‐genome resequencing data from population samples, molecular ecology studies will be able take truly genome‐wide approaches. This now applies an avian model system in ecological evolutionary research: Old World flycatchers of genus F icedula , for which we recently obtained a 1.1 Gb collared flycatcher assembly identified 13 million single‐nucleotide polymorphism ( SNP )s this species its sister species, pied flycatcher....
There is increasing evidence that dosage compensation not a ubiquitous feature following sex chromosome evolution, especially in organisms where females are the heterogametic sex, like birds. Even when it occurs, can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may reflect expression at protein level. Here, we used liquid chromatography-tandem mass spectrometry detect quantify expressed...
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map detailed genome annotation painted lady butterfly (Vanessa cardui) - non-diapausing, highly polyphagous species famous its long-distance migratory behavior almost cosmopolitan distribution. Our results reveal complex interplay between regional recombination rate variation, duplications transposable element activity...
Abstract Species frequently differ in the number and structure of chromosomes they harbor, but individuals that are heterozygous for chromosomal rearrangements may suffer from reduced fitness. Chromosomal like fissions fusions can hence serve as a mechanism speciation between incipient lineages, their evolution poses paradox. How get fixed populations if heterozygotes have fitness? One solution is this process predominantly occurs small isolated populations, where genetic drift override...
Abstract A new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process difficult to obtain. Here we report discovery of a European hybrid butterfly lineage, finding that be considered surprising given intense and long-term study butterflies. The lineage describe is mainly inhabiting an island Baltic Sea was previously designated as subspecies (horkei) one parental (Aricia artaxerxes). By...