Juraj Bergman
A5027998146- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Primate Behavior and Ecology
- CRISPR and Genetic Engineering
- Pleistocene-Era Hominins and Archaeology
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Species Distribution and Climate Change
- Genetic and phenotypic traits in livestock
- RNA Research and Splicing
- Wheat and Barley Genetics and Pathology
- Animal Ecology and Behavior Studies
- Genomics and Rare Diseases
- Fungal and yeast genetics research
- Genetics and Neurodevelopmental Disorders
- Soil Moisture and Remote Sensing
- Environmental Philosophy and Ethics
- Wildlife Ecology and Conservation
- Fungal Plant Pathogen Control
Aarhus University
2020-2024
Pädagogische Hochschule Wien
2017-2018
University of Veterinary Medicine Vienna
2015-2018
Rudjer Boskovic Institute
2015
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact genomic on fundamental biological processes. Analysis that insight into long-standing questions evolutionary conservation biology is urgent given severe threats these are facing. Here, we present high-coverage whole-genome data from 233 representing 86% genera all 16 families. This dataset was used, together with fossil calibration, create a nuclear DNA...
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding their clinical relevance remains largely incomplete. To systematically decipher the effects human variants, we obtained whole-genome data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these can be inferred to have nondeleterious humans based on presence at high allele...
Large mammalian herbivores (megafauna) have experienced extinctions and declines since prehistory. Introduced megafauna partly counteracted these losses yet are thought to unusually negative effects on plants compared with native megafauna. Using a meta-analysis of 3995 plot-scale plant abundance diversity responses from 221 studies, we found no evidence that impacts were shaped by nativeness, "invasiveness," "feralness," coevolutionary history, or functional phylogenetic novelty. Nor was...
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%...
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for surviving this time period - they could have declined due to similar pressures, increased in population size reductions competition other biotic pressures. We therefore infer histories 139 extant species using genomic data which reveal declines 91%...
Abstract Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , measuring the evolutionary sequence constraint can establish functional relevance putative regulatory elements in genome 3–9 . Identifying genomic that have become constrained specifically primates has been hampered by faster evolution noncoding compared protein-coding 10 relatively short timescales separating primate species 11 previously limited availability whole-genome sequences 12...
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics interspecies gene flow. Our analyses provide an expanded picture evolutionary reticulation among species reveal patterns structure within species, including...
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding their clinical relevance remains largely incomplete. To systematically decipher the effects human variants, we obtained whole data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these can be inferred to have non-deleterious based on presence at high allele frequencies other...
A long-standing question in evolutionary biology is the relative contribution of large and small effect mutations to adaptive process. We have investigated this proteins by estimating rate evolution between all pairs amino acids separated one mutational step using a McDonald–Kreitman type approach genome-wide data from several Drosophila species. find that highest among are more similar. This partly due fact proportion higher similar acids. also neutral Overall our results suggest both...
Abstract The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact genomic on fundamental biological processes. Analysis that insight into long-standing questions evolutionary conservation biology, is urgent given severe threats these are facing. Here, we present high coverage whole-genome data from 233 representing 86% genera all 16 families. This dataset was used, together with fossil calibration, create a...
Abstract Background Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and expression varying along chromosomes. Evolutionary, biological, biomedical analyses aim to quantify this variation, account for it during inference procedures, ultimately determine the causal processes behind it. Since sequential observations chromosomes not independent, is unsurprising that autocorrelation patterns have been observed e.g., in human composition....
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites within intron sequences. Here, we use expression data as well a whole-genome set of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find positive correlation between skew gene expression, comparable strength similar correlations levels genome-wide sequence features. This is relatively stronger for germline,...
The nucleotide composition of the genome is a balance between origin and fixation rates different mutations. For example, it well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences their genomic distributions efficiency mismatch repair mechanisms. Given...
Abstract Background The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric of human sex chromosomes. PAR1 has crucial role in ensuring proper segregation chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate evolution using population genomic datasets extant humans, eight populations great apes, two archaic genome sequences. Results find that fast evolving closer evolutionary nucleotide equilibrium than autosomal telomeres. detect...
In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, consists of two long strands nucleotides or sites that pair via the complementary bases cytosine guanine (C G), on one hand, adenine thymine (A T), other. With whole genome sequencing, most genomic stored in has become available for multiple individuals more populations, at least humans model species, such as fruit flies genus...
ABSTRACT Haeckel’s biogenetic law, or the recapitulation theory remains a controversial subject to this day. Currently, modern version of law is hourglass model with its phylotypic period. Importantly, nothing more than development, and it does not provide any evidence that ontogeny recapitulates phylogeny. However, are mutually exclusive, there several examples recapitulation-like processes observable after period ontogeny. At level transcriptomics, all attempts demonstrate failed. Using...
Abstract Survival and reproduction strategies in mammals are determined by trade-offs between life history traits. In turn, the unique configuration of traits that characterizes mammalian species gives rise to species-specific population dynamics. The dependence dynamics on has been primarily studied as relationship density size-related With recent accumulation genomic data, effective size (number breeding individuals; N e ) over last 100-800 kya become quantifiable for a large proportion...
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics inter-species gene flow. Our analyses provide an expanded picture evolutionary reticulation among species reveal novel patterns structure within species,...
Abstract A longstanding question in evolutionary biology is the relative contribution of large and small effect mutations to adaptive process. We have investigated this proteins by estimating rate evolution between all pairs amino acids separated one mutational step using a McDonald-Kreitman type approach genome-wide data from several Drosophila species. find that higher amongst are more similar. This partly due fact proportion similar acids. also neutral Overall our results suggest both...
Abstract A substitution represents the emergence and fixation of an allele in a population or species is fundamental event from which phylogenetic models sequence evolution are devised. Because increasing availability genomic sequences, we now able to take advantage intraspecific variability when reconstructing tree life. As result, substitutions can be more realistically modeled as product mutation, selection, genetic drift. However, it still unclear whether this increased complexity...