A5020301143- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Cytomegalovirus and herpesvirus research
- Animal Behavior and Reproduction
- Herpesvirus Infections and Treatments
- Influenza Virus Research Studies
- Chromosomal and Genetic Variations
- Plant and animal studies
- Primate Behavior and Ecology
- Wildlife Ecology and Conservation
- Mathematical and Theoretical Epidemiology and Ecology Models
- Genetic Associations and Epidemiology
- Plant Virus Research Studies
- Mycobacterium research and diagnosis
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- CRISPR and Genetic Engineering
- Evolution and Paleontology Studies
- HIV Research and Treatment
- Pleistocene-Era Hominins and Archaeology
- Evolutionary Game Theory and Cooperation
- RNA Research and Splicing
Arizona State University
2016-2025
Aarhus University
2025
Northwestern University
2023
University of Washington Bothell
2023
École Polytechnique Fédérale de Lausanne
2011-2018
SIB Swiss Institute of Bioinformatics
2012-2018
Eisenhower Medical Center
2017
Mayo Clinic
2017
University of Fribourg
2015
University of Massachusetts Chan Medical School
2009-2014
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence Neandertal genome composed more than 4 billion nucleotides from three individuals. Comparisons to genomes five humans different world identify number genomic regions that may have been affected by positive selection ancestral modern including genes involved metabolism cognitive skeletal development. show...
The Taming of the Silkworm Silkworms, Bombyx mori , represent one few domesticated insects, having been over 10,000 years ago. Xia et al. (p. 433 published online 27 August) sequenced 29 domestic and 11 wild silkworm lines identified genes that were most likely to be selected during domestication. These those enhance silk production, reproduction, growth. Furthermore, silkworms probably only once from a large progenitor population, rather than on multiple occasions, as has observed for other animals.
The genes of all organisms have been shaped by selective pressures. relationship between gene sequence and fitness has tremendous implications for understanding both evolutionary processes functional constraints on the encoded proteins. Here, we exploited deep sequencing technology to experimentally determine possible individual point mutants under controlled conditions a nine-amino acid region Hsp90. Over past five decades, limited glimpses into function sparked long debate regarding...
African genomics and skin color Skin varies among human populations is thought to be under selection, with light maximizing vitamin D production at higher latitudes dark providing UV protection in equatorial zones. To identify the genes that give rise palette of tones, Crawford et al. applied genome-wide analyses across diverse (see Perspective by Tang Barsh). Genetic variants were identified likely function phenotypes. Comparison model organisms verified a conserved MFSD12 pigmentation. A...
Additive Effects Although specific genes involved in animal coloration have been identified, the underlying selection for genetic variation color-specific adaptation is not well understood. Examining Agouti gene and other loci deer mice of Nebraska, where predation selects light-colored light environments dark-colored dark environments, Linnen et al. (p. 1312 ) find evidence multiple variants under affecting coloration. The color Sand Hills result a single large-effect mutation, but because...
Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some remain brown during the in regions with low snow cover. We show that cis-regulatory variation controlling expression of Agouti gene underlies this adaptive polymorphism. Genetic at clustered coat color across multiple hare and jackrabbit species, revealing history recurrent interspecific flow. Brown coats snowshoe likely originated from an introgressed black-tailed allele has swept high...
In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or networks. Such annotations used assess and/or verify validity genome and statistical methods that have been perform analyses. Furthermore, results frequently considered validate "true-positives" if identified make...
How natural selection affects mouse coat color Evolution, at its core, involves changes in the frequency of alleles subject to selection. But identifying target can be difficult. Barrett et al. investigated how allele frequencies affecting pigmentation change over time (see Perspective by Pelletier). Wild-caught mice ( Peromyscus maniculatus ) were exposed avian predators against naturally occurring dark or light backgrounds. Natural yielded shifts coloration owing genetic variants Agouti...
Recently, there has been increased awareness of the role background selection (BGS) in both data analysis and modelling advances. However, BGS is still difficult to take into account because tractability issues with simulations difficulty nonequilibrium demographic models. Often, simple rescaling adjustments effective population size are used. neither a proper characterization how could bias or shift inference when not properly taken account, nor thorough whether sufficient solution. Here,...
The question of the relative evolutionary roles adaptive and nonadaptive processes has been a central debate in population genetics for nearly century. While advances have made theoretical development underlying models, statistical methods estimating their parameters from large-scale genomic data, framework an appropriate null model remains elusive. A incorporating known to be constant operation, genetic drift (as modulated by demographic history population) purifying selection, is lacking....
Patterns of variation and evolution at a given site in genome can be strongly influenced by the effects selection genetically linked sites. In particular, recombination rates genomic regions correlate with their amount within-population genetic variability, degree to which frequency distributions DNA sequence variants differ from neutral expectations, levels adaptation functional components. We review major population processes that are thought lead these patterns, focusing on patterns...
The field of population genomics has grown rapidly in response to the recent advent affordable, large-scale sequencing technologies. As opposed situation during majority 20th century, which development theoretical and statistical genetic insights outpaced generation data they could be applied, genomic are now being produced at a far greater rate than can meaningfully analyzed interpreted. With this wealth come tendency focus on fitting specific (and often rather idiosyncratic) models data,...
How locally adapted ecotypes are established and maintained within a species is long-standing question in evolutionary biology. Using forest prairie of deer mice (
In 2002 Kim and Stephan proposed a promising composite-likelihood method for localizing estimating the fitness advantage of recently fixed beneficial mutation. Here, we demonstrate that their composite-likelihood-ratio (CLR) test comparing selective neutral hypotheses is not robust to undetected population structure or recent bottleneck, with some parameter combinations resulting in false positive rate nearly 90%. We also propose goodness-of-fit discriminating rejections due directional...
Adapting Coat Color Simple phenotypic changes can often be the target of selection—for example, variations in coat color that provide protection against detection by predators. Linnen et al. (p. 1095 ) explore underlying molecular mechanisms behind production pale deer mice living on light-colored Nebraska Sand Hills. The live sand are significantly lighter than conspecifics nearby darker soils. This was found to due de novo at Agouti locus. Thus, rapid adaptive change does not always rely...
Research has shown that RNA virus populations are highly variable, most likely due to low fidelity replication of genomes. It is generally assumed DNA viruses will be less complex and show reduced variability when compared viruses. Here, we describe the use high throughput sequencing for a genome wide study viral from urine samples neonates with congenital human cytomegalovirus (HCMV) infections. We HCMV intrahost genomic variability, both at nucleotide amino acid level, comparable many...
Abstract A major goal of population genomics is to reconstruct the history natural populations and infer neutral selective scenarios that can explain present-day polymorphism patterns. However, separation between hypotheses has proven hard, mainly because both may predict similar patterns in genome. This study focuses on development methods be used distinguish from equilibrium nonequilibrium populations. These utilize a combination statistics basis site frequency spectrum (SFS) linkage...
Rapid typing of genetic variation at many regions the genome is an efficient way to survey variability in natural populations effort identify segments that have experienced recent selection. Following such a scan, individual may be chosen for further sequencing and more detailed analysis patterns variability, often perform parametric test selection estimate strength selective sweep. We show here not accounting ascertainment loci analyses leads false inference when true model neutrality,...
Populations of human cytomegalovirus (HCMV), a large DNA virus, are highly polymorphic in patient samples, which may allow for rapid evolution within hosts. To understand HCMV evolution, longitudinally sampled genomic populations from the urine and plasma 5 infants with symptomatic congenital infection were analyzed. Temporal compartmental variability viral quantified using high throughput sequencing population genetics approaches. generally stable over time, ∼88% SNPs displaying similar...
The challenge of distinguishing genetic drift from selection remains a central focus population genetics. Time-sampled data may provide powerful tool for these processes, and we here propose approximate Bayesian, maximum likelihood, analytical methods the inference demography time course data. Utilizing novel statistical computational tools, evaluate whole-genome datasets an influenza A H1N1 strain in presence absence oseltamivir (an inhibitor neuraminidase) collected at thirteen points....