A5066629691- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Identification and Quantification in Food
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Fish Ecology and Management Studies
- Chromosomal and Genetic Variations
- Machine Learning in Bioinformatics
- Ichthyology and Marine Biology
- Coral and Marine Ecosystems Studies
- Parasite Biology and Host Interactions
- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Historical Studies and Socio-cultural Analysis
- Literature and Culture Studies
- Pancreatic function and diabetes
- Marine Ecology and Invasive Species
- French Historical and Cultural Studies
University of Copenhagen
2020-2024
The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself1. However, little known about what its evolution, as most studies rates have focused on single species with different methodologies2. Here we quantify across vertebrates by sequencing comparing high-coverage genomes 151 parent-offspring trios from 68 mammals, fishes, birds reptiles. We show that per-generation varies among a factor 40, being higher for males than females in mammals birds,...
In the past decade, several studies have estimated human per-generation germline mutation rate using large pedigrees. More recently, estimates for various nonhuman species been published. However, methodological differences among in detecting mutations and estimating rates make direct comparisons difficult. Here, we describe many different steps involved pedigree-based rates, including sampling, sequencing, mapping, variant calling, filtering, appropriately accounting false-positive...
Abstract The accurate and complete assembly of both haplotype sequences a diploid organism is essential to understanding the role variation in genome functions, phenotypes diseases 1 . Here, using trio-binning approach, we present high-quality, reference genome, with haplotypes assembled independently at chromosome level, for common marmoset ( Callithrix jacchus ), an primate model system that widely used biomedical research 2,3 full spectrum heterozygosity between two involves 1.36%...
Abstract Background Understanding the rate and pattern of germline mutations is fundamental importance for understanding evolutionary processes. Results Here we analyzed 19 parent-offspring trios rhesus macaques (Macaca mulatta) at high sequencing coverage ∼76× per individual estimated a mean 0.77 × 10−8de novo site generation (95% CI: 0.69 10−8 to 0.85 10−8). By phasing 50% parental origins, found that mutation positively correlated with paternal age. The lineage contributed 81% de...
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or limited number of makers have presented sometimes conflicting evidence the genetic structure S. pilchardus populations. Here, we show that whole genome data from 108 individuals 16 areas across 5000 km species’ distribution range (from Eastern Mediterranean to archipelago Azores) support at least three clusters. One includes Azores and Madeira,...
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, influences new mutations on relative to extrinsic processes such as fluctuations unknown. Here, we provide first germline mutation rate (μ) estimate a invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf....
Abstract Background The Nile rat ( Avicanthis niloticus ) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity humans in these aspects, compared the widely used Mus musculus Rattus norvegicus models, holds promise better translation research findings clinic. Results We report 2.5 Gb, chromosome-level reference genome assembly with fully resolved...
Abstract Lewontin’s paradox, the observation that levels of genetic diversity (π) among animals do not scale linearly with variation in census population sizes ( N c ), is an evolutionary conundrum, where most extreme mismatches between π and are found for highly abundant marine invertebrates. Yet, whether new mutations influence relative to extrinsic processes remains unknown taxa. Here, we provide first direct germline mutation rate μ ) estimate a invertebrate, using high-coverage (60x)...
Abstract In the past decade, several studies have estimated human per-generation germline mutation rate using large pedigrees. More recently, estimates for various non-human species been published. However, methodological differences among in detecting mutations and estimating rates make direct comparisons difficult. Here, we describe many different steps involved pedigree-based rates, including sampling, sequencing, mapping, variant calling, filtering, how to appropriately account...
Abstract Understanding the rate and pattern of germline mutations is fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios rhesus macaques ( Macaca mulatta ) at high sequencing coverage ca. 76X per individual, estimated an average 0.77 × 10 −8 de novo site generation (95 % CI: 0.69 - 0.85 ). By phasing 50 to parental origins, found that mutation positively correlated with paternal age. The lineage contributed 81 mutations, a trend...
The European sardine ( Sardina pilchardus , Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or limited number of makers have presented sometimes conflicting evidence for the genetic structure S. populations. Here we show that whole genome data from 108 individuals 16 areas across 5,000 Km species’ distribution range (from Eastern Mediterranean to archipelago Azores) supports at least three clusters. One includes Azores and Madeira, with...
Whole genome sequence data is an ideal tool for characterizing processes in ecology and evolution. Despite the lowering sequencing costs, it can be challenging to produce a high-coverage resequencing non-model species. New population genomics analysis pipelines based on genotype likelihoods allow significant reduction cost by efficiently extracting information from low coverage data. We demonstrate robustness of such approaches with genomic set consisting two draft genomes European sardine (...
Whole genome sequence data is an ideal tool for characterizing processes in ecology and evolution. New population genomics analysis pipelines based on genotype likelihoods allow a significant reduction cost by efficiently extracting information from low coverage data. We demonstrate the robustness of such approaches with genomic set consisting two draft genomes European sardine ( Sardina pilchardus , Walbaum 1792), resequencing 103 individuals 16 sampling areas across 5,000 Km species’...
Abstract The lack of consensus methods to estimate germline mutation rates from pedigrees has led substantial differences in computational pipelines the published literature. Here, we answer Susanne Pfeifer's opinion piece discussing pipeline choices our recent article estimating rate rhesus macaques (Macaca mulatta). We acknowledge between method that applied and one preferred by Pfeifer. Yet, advocate for full transparency justification as long rigorous comparison remains absent because it...
Abstract The Nile rat ( Avicanthis niloticus ) is an important animal model for biomedical research, including the study of diurnal rhythms and type 2 diabetes. Here, we report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated Vertebrate Genomes Project (VGP). highly contiguous, contig N50 11.1 Mb, scaffold 83 95.2% sequence assigned to chromosomes. We used novel workflow identify 3,613 segmental duplications quantify duplicated genes....