Klaus‐Peter Koepfli
A5010134908- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Wildlife Ecology and Conservation
- Evolution and Paleontology Studies
- Chromosomal and Genetic Variations
- Genetic and phenotypic traits in livestock
- Identification and Quantification in Food
- Genomics and Chromatin Dynamics
- Human-Animal Interaction Studies
- Species Distribution and Climate Change
- Yersinia bacterium, plague, ectoparasites research
- Animal Genetics and Reproduction
- Genetic Mapping and Diversity in Plants and Animals
- RNA and protein synthesis mechanisms
- Bat Biology and Ecology Studies
- Animal Ecology and Behavior Studies
- Molecular Biology Techniques and Applications
- Animal Diversity and Health Studies
- Pleistocene-Era Hominins and Archaeology
- Marine animal studies overview
- Genetics, Bioinformatics, and Biomedical Research
- SARS-CoV-2 and COVID-19 Research
- Gut microbiota and health
- Gene expression and cancer classification
- Rabies epidemiology and control
National Zoological Park
2016-2025
Conservation Biology Institute
2022-2025
Smithsonian Conservation Biology Institute
2016-2025
George Mason University
2021-2025
ITMO University
2020-2023
Washington Center
2023
St Petersburg University
2013-2021
Siberian Branch of the Russian Academy of Sciences
2019
Smith Institute
2019
National Cancer Institute
2012-2015
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis 48 species representing all orders Neoaves using phylogenomic methods created to handle data. We recovered highly resolved tree that confirms previously controversial sister or close relationships. identified first divergence in Neoaves, two groups named Passerea and Columbea, independent lineages diverse convergently evolved land water bird species. Among Passerea, infer common ancestor core...
Significance The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19, a major pandemic that threatens millions human lives and global economy. We identified large number mammals can potentially be infected by SARS-CoV-2 via their ACE2 proteins. This assist identification intermediate hosts for hence reduce opportunity future outbreak COVID-19. Among species we found with highest risk infection are wildlife endangered species. These represent an...
The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas oldest doglike fossils are found Europe Siberia date to >30,000 ago. We analyzed mitochondrial genomes 18 prehistoric canids from Eurasia New World, along with comprehensive panel modern dogs wolves. all phylogenetically most closely related either ancient or Europe. Molecular dating suggests an onset there 18,800...
Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is central concept in evolutionary biology characterizes histories many groups organisms. One such group Mustelidae, most species-rich family within mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved an array adaptive zones, fossorial badgers to semi-aquatic otters....
Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report de novo assembly an Amur tiger whole-genome sequence as well genomic sequences a white Bengal tiger, African lion, lion snow leopard. Through comparative genetic analyses these genomes, find signatures that may reflect molecular adaptations consistent with big cats' hypercarnivorous diet muscle strength. We leopard-specific determinant in EGLN1 (Met39>Lys39), which is likely to be...
Patterns of genetic and genomic variance are informative in inferring population history for human, model species endangered populations. Here the genome sequence wild-born African cheetahs reveals extreme depletion SNV incidence, density, SNVs coding genes, MHC class I II mitochondrial DNA SNVs. Cheetah genomes on average 95 % homozygous compared to outbred domestic cat (24.08 homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian (62.63 Tasmanian devil, dog other mammalian...
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes 240 species, we identify bases that, when mutated, are likely affect fitness and alter disease risk. At least 332 million (~10.7%) in human genome unusually conserved across species (evolutionarily constrained) relative neutrally evolving repeats, 4552 ultraconserved elements nearly perfectly conserved. Of 101 significantly constrained single bases, 80% outside protein-coding exons half...
Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales...
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis genetic variation across an alignment 241 mammal genome assemblies, addressing prior concerns regarding limited genomic sampling species. compared neutral genome-wide phylogenomic signals using concatenation coalescent-based approaches, interrogated chromosomes, analyzed extensive catalogs structural variants. Interordinal...
Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability discern which positions functionally important. Evolutionary constraint is a powerful predictor function, agnostic cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% the genome as significantly constrained and likely functional. We compared annotation, association studies, copy-number variation,...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. found that although mammals resemble one another total and diversity, they show substantial differences with regard recent accumulation. This includes multiple expansion quiescence events across mammalian tree. Young TEs, particularly long interspersed elements, drive increases size, whereas DNA transposons are associated smaller genomes....
Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between...
Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (
Understanding the regulatory landscape of human genome is a long-standing objective modern biology. Using reference-free alignment across 241 mammalian genomes produced by Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million candidate cis-regulatory elements (cCREs) and 15.6 transcription factor binding sites (TFBSs). We identified 439,461 cCREs 2,024,062 TFBSs under constraint. Genes near constrained perform fundamental cellular processes, whereas genes...
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent functionally conserved despite low sequence conservation. We developed Tissue-Aware Conservation Inference Toolkit (TACIT) associate candidate with species' using predictions from machine learning...
Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) are enriched for brain functions across genetic, epigenomic, transcriptomic datasets. Using massively parallel reporter assays six cell types, we discovered 800 hCONDELs conferring significant differences regulatory activity, half of which enhance rather than disrupt function....
Despite numerous systematic studies, the relationships among many species within dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are origins taxonomically rich canidae fauna South America and development in three trenchant heel, a unique meat-cutting blade on lower first molar. The problem is interest because fossil record provides little evidence for divergent American such as maned wolf bush dog. second issue problematic although complex form, may...
A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly absence topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered represent a single species classified into multiple subspecies. However, geographic variation traits such as pelage pattern clearly evident across range sub-Saharan Africa and abrupt transition zones between different...