A5063702666- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Fish biology, ecology, and behavior
- Fish Ecology and Management Studies
- Fish Biology and Ecology Studies
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Aquatic Ecosystems and Biodiversity
- Evolution and Genetic Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Wildlife Ecology and Conservation
- Identification and Quantification in Food
- Bat Biology and Ecology Studies
- Animal Behavior and Reproduction
- Genetics, Bioinformatics, and Biomedical Research
- Animal Ecology and Behavior Studies
- Physiological and biochemical adaptations
- Isotope Analysis in Ecology
- Insect symbiosis and bacterial influences
- Optical Imaging and Spectroscopy Techniques
- Anatomy and Medical Technology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Aquaculture Nutrition and Growth
- Marine Bivalve and Aquaculture Studies
University of Bern
2021-2025
University of Basel
2016-2024
Swiss Federal Institute of Aquatic Science and Technology
2023-2024
Wellcome Sanger Institute
2015-2022
Zoological Institute
2020
The Gurdon Institute
2014-2016
University of Cambridge
2015-2016
University of Birmingham
2010
Brno University of Technology
2010
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...
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand molecular mechanisms underlying cichlid phenotypic diversity, we sequenced genomes transcriptomes five lineages African cichlids: Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; four members lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent Malawi), Pundamilia nyererei (very recent...
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...
The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery detailed characterization early-stage adaptive divergence two cichlid fish ecomorphs in a small (700 meters diameter) isolated crater lake Tanzania. differ depth preference, male breeding color, body shape, diet, trophic morphology. With whole-genome sequences 146 fish, identified 98 clearly demarcated "islands" high differentiation demonstrated...
Powerful approaches to inferring recent or current population structure based on nearest neighbor haplotype "coancestry" have so far been inaccessible users without high quality genome-wide data. With a boom in nonmodel organism genomics, there is pressing need bring these methods communities access such Here, we present RADpainter, new program designed infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) We combine this together with previously published MCMC...
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...
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 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,...
Abstract Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during early stages speciation. Specifically, focus on extent functional relevance DNA methylome in very young radiation Astatotilapia calliptera crater Lake Masoko, southern Tanzania. Our study focuses two lake ecomorphs that diverged approximately 1,000 years ago a population nearby...
Behavior is critical for animal survival and reproduction, possibly diversification evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental widespread behavioral trait, exploratory behavior, one of largest radiations on Earth, cichlid fishes Lake Tanganyika. By integrating quantitative data from 57 species (702 wild-caught individuals) with high-resolution ecomorphological genomic information, show...
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...
Little is known about when and how planktonic species arise persist in the open ocean without apparent dispersal barriers. Pteropods are snails with thin shells susceptible to dissolution that used as bio-indicators of acidification. However, distinct evolutionary units respond acidification differently, defining boundaries therefore crucial for predicting impact changing conditions. In this global population genomic study shelled pteropod Limacina bulimoides, we combined genetic (759,000...
Summary Recombination is central to genetics and evolution of sexually reproducing organisms. However, obtaining accurate estimates recombination rates, how they vary along chromosomes, continues be challenging. To advance our ability estimate we present Hi-reComb , a new method software for estimation maps from bulk gamete chromosome conformation capture sequencing (Hi-C). Simulations show that produces robust, landscapes. With empirical data sperm five fish species the advantages this...
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources genetic variation responsible phenotypic variation. One their most variable phenotypes is visual sensitivity, with some largest spectral shifts among vertebrates. These arise primarily from differential expression seven cone opsin genes. By mapping quantitative trait loci (eQTL) in intergeneric crosses Lake...
Abstract The role of interspecific hybridization has recently seen increasing attention, especially in the context diversification dynamics. Genomic research now made it abundantly clear that both and introgression—the exchange genetic material through backcrossing—are far more common than previously thought. Besides cases ongoing or recent between taxa, an number studies report “ancient introgression”— referring to results took place distant past. However, is not whether commonly used...
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...
Abstract The role of interspecific hybridization has recently seen increasing attention, especially in the context diversification dynamics. Genomic research now made it abundantly clear that both and introgression – exchange genetic material through backcrossing are far more common than previously thought. Besides cases ongoing or recent between taxa, an number studies report “ancient introgression” referring to results took place distant past. However, is not whether commonly used methods...
Abstract Meiotic recombination is fundamental to evolution of sexually reproducing organisms and differences in rates are important during rapid adaptation organismal diversification. Many unknowns remain regarding how why landscapes evolve nature. Here, we reconstruct maps based on linkage disequilibrium use subsampling simulations show that fine-scale differ substantially between two cichlid fish ecotypes Astatotilapia calliptera diverged only ∼2,500 generations ago. The observed results...
Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on comparison high-quality genome assemblies 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that genomes contain range genes, from as few five fugu many 43 salmon, with latter being...
Cichlid fish of the genus Oreochromis form basis global tilapia aquaculture and fisheries industries. Broodstocks for are often collected from wild populations, which in Africa may be locations containing multiple species. However, many species difficult to distinguish morphologically, hampering efforts maintain good quality farmed strains. Additionally, non-native populations known widely distributed across hybridize with native species, themselves important capture fisheries. The...