Hannes Svardal
A5056647680- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- Fish Biology and Ecology Studies
- Fish biology, ecology, and behavior
- Evolutionary Game Theory and Cooperation
- Environmental DNA in Biodiversity Studies
- Fish Ecology and Management Studies
- Amphibian and Reptile Biology
- Bat Biology and Ecology Studies
- Epigenetics and DNA Methylation
- Mathematical and Theoretical Epidemiology and Ecology Models
- Microbial Community Ecology and Physiology
- Genomics and Chromatin Dynamics
- Virology and Viral Diseases
- Physiological and biochemical adaptations
- Genetic and phenotypic traits in livestock
- Molecular Biology Techniques and Applications
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Aquatic Ecosystems and Biodiversity
- Genomics and Rare Diseases
- Adipose Tissue and Metabolism
- Identification and Quantification in Food
University of Antwerp
2019-2025
Naturalis Biodiversity Center
2019-2025
Gregor Mendel Institute of Molecular Plant Biology
2014-2024
Austrian Academy of Sciences
2014-2024
Vienna Biocenter
2015-2024
Wellcome Sanger Institute
2016-2021
Province of Antwerp
2021
University of Cambridge
2017-2019
National University of Singapore
2016
Chinese Academy for Environmental Planning
2016
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate...
Patterson's D, also known as the ABBA-BABA statistic, and related statistics such f
Abstract The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 across all major lineages. average sequence divergence between pairs is only 0.1–0.25%. These values overlap within species, with 82% heterozygosity shared species. Phylogenetic analyses suggest that diversification initially proceeded serial branching from a generalist...
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate genomes representing global biodiversity. These provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses population functional genomics, are expected revolutionize conservation genomics.
The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed hybridization between ancestral lineages can provide genetic raw material fuel such exceptionally high diversification rates, and evidence for this recently presented Victoria region superflock. Here, we report genomes also show two split 3-4 Ma, today represented by cichlids...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such only available a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling most accurate genomes date. Here we summarize these developments, introduce set quality standards, present lessons...
We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member Old World (OWM) superfamily is uniquely valuable for genetic investigations simian immunodeficiency virus (SIV), which it most abundant natural host species, and wide range health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small their ancestors from West Africa during colonial era. use to...
Abstract Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts other can be found in local populations along Mediterranean Sea. Here we provide evidence these ‘relicts’ occupied post-glacial Eurasia first and were later replaced by invading ‘non-relicts’, which expanded through east–west axis Eurasia, leaving traces admixture...
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...
Abstract Patterson’s D , also known as the ABBA-BABA statistic, and related statistics such f 4 -ratio, are commonly used to assess evidence of gene flow between populations or closely species. Currently available implementations require custom file formats impractical evaluate all hypotheses across datasets with many Dsuite is a fast C++ implementation, allowing genome scale calculations -ratio combinations tens hundreds species directly from variant call format (VCF) file. Furthermore,...
Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but genetic bases of their domestication phenotypic diversification largely unknown. We assembled de novo genome a wild Betta splendens whole-genome sequenced 98 individuals across five closely related species. find evidence bidirectional hybridization between domesticated ornamental betta other discover dmrt1 as main sex determination gene in that it has lower penetrance B. . Furthermore, we genes...
Abstract Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large segregating in benthic subradiation that each suppress recombination over more than half a chromosome. Two were transferred from deepwater pelagic Diplotaxodon via admixture, while others established early deep clade. Introgression haplotypes lineages inside and outside radiation coincided with...
Abstract The East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one nature’s most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise within Malawi. These were based on aligning short reads linear reference genome, which ignores the contribution larger...
Salmonids have a remarkable ability to form sympatric morphs after postglacial colonization of freshwater lakes. These often exhibit differences in morphology, feeding, and spawning behaviour. Here we explore the genetics morph differentiation by establishing high-quality, annotated reference genome for Arctic charr use this as resource population genomic analysis from two Norwegian Icelandic The four lakes represent spectrum genetic between one lake with no morphs, implying phenotypic...
Abstract The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status labeled as of least concern by IUCN, it declining in many parts its range where populations are fragmented and isolated. A high-quality reference genome an important resource for genomic researchers who trying to understand interpret signals population decline, inbreeding, accumulation deleterious mutations. Here, we assembled annotated a chromosome-level B....
As the world is hit by sixth mass extinction, it becomes increasingly important to understand factors relevant conservation of species, so that we may protect biodiversity best our abilities. Although genetic diversity known reflect population demography and contribute health adaptability, not explicitly used as a criterion in assessments International Union for Conservation Nature (IUCN). Additionally, studies comparing estimates between species often rely on summarizing results across...
Phenotypic variation within populations has two sources: genetic and environmental variation. Here, we investigate the coevolution of these components under fluctuating selection. Our analysis is based on lottery model in which polymorphism can be maintained by negative frequency-dependent selection, whereas favored due to bet-hedging. In our model, phenotypes are characterized a quantitative trait stabilizing selection with optimal phenotype time. Genotypes their phenotypic offspring...
Abstract Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence is an excellent system study epigenomic adaptation. Here, we present a comparative genome-wide methylome transcriptome study, focussing on liver muscle tissues...