A mutation leading to a segregating site of a sample can be classified by the number of sequences in the sample that inherits the mutant nucleotide; it can also be classified by the frequencies of the two segregating nucleotides at the resulting segregating side. We define the size of a mutation to be the number of sequences in the sample that inherits the mutant nucleotide and the type of mutation (segregating site) to be the smallest value of the frequencies of segregating nucleotides. Each of these two classifications of mutations is analogous to allelic types in a sample of genes. Assuming the neutral Wright-Fisher model, we derived in this paper the mean and variance of the frequency of mutations of each size and type, and the covariance between the numbers of mutations of two different sizes and two different types. Potential applications of these results are discussed.
Evidence-based psychiatric genetics, AKA the false dichotomy between common and rare variant hypotheses
A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
Inferring population mutation rate and sequencing error rate using the SNP frequency spectrum in a sample of DNA sequences
The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta
A new test for detecting recent positive selection that is free from the confounding impacts of demography
Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus
Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platforms
Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error
Variation of estimates of SNP and haplotype diversity and linkage disequilibrium in samples from the same population due to experimental and evolutionary sample size
The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific
Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications
Estimation of population heterozygosity and library construction-induced mutation rate from expressed sequence tag collections
Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster
Demographic inference reveals African and European admixture in the North American Drosophila melanogaster population
Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins
Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome
An efficient estimator of the mutation parameter and analysis of polymorphism from the 1000 genomes project
Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator
The number of candidate variants in exome sequencing for Mendelian disease under no genetic heterogeneity
Single Geographic Origin of a Widespread Autotetraploid Arabidopsis arenosa Lineage Followed by Interploidy Admixture
Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy
Human genetic variation database, a reference database of genetic variations in the Japanese population
A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome
Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces
Unconstrained evolution in short introns? - an analysis of genome-wide polymorphism and divergence data from Drosophila
Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species
Phylogeographical Structure in Mitochondrial DNA of Legume Pod Borer (Maruca vitrata) Population in Tropical Asia and Sub-Saharan Africa
Patterns of nucleotide sequence variation in ICAM1 and TNF genes in twelve ethnic groups of India: roles of demographic history and natural selection
Epistasis and the evolutionary dynamics of measured genotypic values during simulated serial bottlenecks
Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size
Including the genetic values of the possible parents when analyzing pedigrees that contain MULT groups
An analytical framework in the general coalescent tree setting for analyzing polymorphisms created by two mutations
Can the site-frequency spectrum distinguish exponential population growth from multiple-merger coalescents?
Genetic structure at three spatial scales is consistent with limited philopatry in Ricord's Rock Iguanas (Cyclura ricordii )
How relatedness between mates influences reproductive success: An experimental analysis of self-fertilization and biparental inbreeding in a marine bryozoan
Genomic processes underlying rapid adaptation of a natural Chironomus riparius population to unintendedly applied experimental selection pressures
Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection.
Disjunct distribution of highly diverged mitochondrial lineage clade and population subdivision in a marine bivalve with pelagic larval dispersal
A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)
Insights from Fisher's geometric model on the likelihood of speciation under different histories of environmental change.
Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes.
Comparative analyses of population structure in two subspecies of Nigella degenii: evidence for diversifying selection on pollen-color dimorphisms
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations
Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation
Unravelling first-generation pedigrees in wild endangered salmon populations using molecular genetic markers
Intercoalescence time distribution of incomplete gene genealogies in temporally varying populations, and applications in population genetic inference
Considerations for monitoring population trends of colonial waterbirds using the effective number of breeders and census estimates
The opposing effects of genetic drift and Haldane's sieve on floral-morph frequencies in tristylous metapopulations
Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species
Small coastal streams-Critical reservoirs of genetic diversity for trout (Salmo trutta L.) in the face of increasing anthropogenic stressors
The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics
The limit of resistance to salinity in the freshwater cyanobacterium Microcystis aeruginosa is modulated by the rate of salinity increase
Transition Densities and Sample Frequency Spectra of Diffusion Processes with Selection and Variable Population Size
Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population
Pheromone-binding proteins based phylogenetics and phylogeography of Maruca spp. from Asia, Africa, Oceania, and South America
Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects
A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide
Phenotypic variability can promote the evolution of adaptive plasticity by reducing the stringency of natural selection
Interpretations arising from Wrightian and Malthusian fitness under strong frequency dependent selection
Evolution of aging through reduced demographic stochasticity - an extension of the pleiotropy theory to finite populations
Interbreeding between local and translocated populations of a cleaner fish in an experimental mesocosm predicts risk of disrupted local adaptation
Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation
The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients
Population diversity and virulence characteristics of Cryptococcus neoformans/C. gattii species complexes isolated during the pre-HIV-pandemic era
Understanding the classics: the unifying concepts of transgressive segregation, inbreeding depression and heterosis and their central relevance for crop breeding
Unidirectional response to bidirectional selection on body size. I. Phenotypic, life-history, and endocrine responses
The effects of migration load, selfing, inbreeding depression, and the genetics of adaptation on autotetraploid versus diploid establishment in peripheral habitats.
Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant
Incorporating genetic selection into individual-based models of malaria and other infectious diseases
The identification and determination of toxin genes of Vibrio strains causing hemorrhagic disease on red drum (Sciaenops ocellatus) using PCR
Identifying Priority Giant Anteater (Myrmecophaga tridactyla) Populations for Conservation in São Paulo State, Brazil.
A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size
DESCARTES' RULE OF SIGNS AND THE IDENTIFIABILITY OF POPULATION DEMOGRAPHIC MODELS FROM GENOMIC VARIATION DATA
Addressing Darwin's dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load?
How eukaryotic algae can adapt to the Spain's Rio Tinto: a neo-Darwinian proposal for rapid adaptation to an extremely hostile ecosystem.
Estimating the capability of different phytoplankton groups to adapt to contamination: herbicides will affect phytoplankton species differently
The relative importance of factors determining genetic drift: mating system, spatial genetic structure, habitat and census size in Arabidopsis lyrata.
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Alzheimer's Disease: MS4A
Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.
Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.
Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.
Genetic Screens in iPSC-derived Brain Cells
Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.
This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Pharmacology of Proteinopathies
This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.
Alignment-free Sequence Analysis Tools
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.