Using singleton densities to detect recent selection in<i>Bos taurus</i>

Hartfield, Matthew; Poulsen, Nina Aagaard; Guldbrandtsen, Bernt; Bataillon, Thomas

doi:10.1002/evl3.263

Cited by 7 publications

(2 citation statements)

References 107 publications

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“…On the other hand, the ancestral effective population size is estimated to be roughly N e =62,000 (MacLeod et al, 2013). This change in effective population size presents a challenge for demographic inference, selection scans, genome-wide association, and genomic prediction (MacLeod et al,2013, 2014; Hartfield et al, 2022). For these reasons, it was useful to develop a detailed simulation model for cattle to be added to the catalog.…”

Section: Examples Of Added Speciesmentioning

confidence: 99%

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Lauterbur

Cavassim

Gladstein³

et al. 2022

Preprint

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Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

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Section: Examples Of Added Speciesmentioning

confidence: 99%

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Lauterbur

Cavassim

Gladstein³

et al. 2022

Preprint

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“…However, variant calling is challenging. Errors can occur in each step of variant identification, including sequencing errors, incorrect alignment to the reference genome (2), or erroneous variant calling (3).…”

Section: Introductionmentioning

confidence: 99%

Exploring the impact of sequence context on errors in SNP genotype calling with Whole Genome Sequencing data using AI-based autoencoder approach

Kotlarz,

Mielczarek,

Biecek

et al. 2024

Preprint

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A critical step in the analysis of WGS data is variant calling. Despite its importance, variant calling is prone to errors. Our study investigated the association between incorrect SNP and variant quality metrics and nucleotide context. In our study, incorrect SNPs were defined in twenty Holstein-Friesian cows by comparing their SNPs genotypes identified by whole genome sequencing with the IlluminaNovaSeq6000 and the EuroGMD50K genotyping microarray. The data set was divided into the correct set of SNPs (666,333 SNPs) and the incorrect set of SNPs (4,557 SNPs). The training data set consisted of only the correct SNPs, while the test data set contained a balanced mix of all the incorrectly and correctly called SNPs. An autoencoder was constructed to identify systematically incorrect SNPs that were marked as outliers by a one-class support vector machine and isolation forest algorithms. The results showed that 59.53% (±0.39%) of the incorrect SNPs had systematic patterns, with the remainder being random errors. The frequent occurrence of the CGC trimer was due to mislabeling a call for C. Incorrect T instead A call was associated with the presence of T in the neighboring downstream position. These errors may arise due to the fluorescence patterns of nucleotide labelling.

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Lineage-specific genes are clustered with allorecognition loci and respond to G × E factors regulating the switch from asexual to sexual reproduction inNeurospora

Wang

Kasuga

et al. 2022

Preprint

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As de novo elements of the genome, orphan genes have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. However, there is a lack of working hypotheses as to what role they play. Systematic investigation of the evolutionary history, genome structures, expression dynamics and regulation of orphan genes in well-studied models can shed light on their functions in reproductive isolation. The 670 orphan genes that we identified in the genome of the fungal model Neurospora crassa were aggregated adjacent to the telomeres, and over 63% of them formed clusters with 61% of the het-like genes—genes that regulate self-recognition and define vegetative compatibility groups. Nearly all orphan-het clusters are syntenic within closely related species, suggesting relatively recent colocalization. Analysis of transcriptomic data from N. crassa conditions associated with growth and reproduction reveals 342 orphan genes that are dynamically expressed during both asexual and sexual phases. Among these, 37% were expressed in a detectable manner when the fungus was cultured on common carbon resources, but 64% were detectable on unusual carbon sources such as furfural and HMF—wildfire-produced chemicals that are a strong inducer of sexual development in N. crassa. Expression of a significant portion of the orphan genes was sensitive to light and temperature, factors that regulate asexual and sexual reproduction, among other fungal activities. Coordinate expression in orphan-het gene clusters was detected during early hyphal branching. Furthermore, orphan genes and clustered het-like genes respond similarly to mutations in transcription factors adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the orphan genes was affected by a mating locus mutant. Functional interactions between orphan and het-like genes likely consolidate vegetative incompatibility during asexual reproduction, but possibly promote crossings between vegetative compatibility groups during sexual reproduction. Their involvement in the balance between genome homogeneity and heterogeneity in vegetative compatibility likely contribute to Neurospora speciation. Orphan genes are potential targets for the manipulation of fungal growth, a key aspect of both the control of fungal pathogenicity and the iterative improvement of fungal biotechnology.

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Using singleton densities to detect recent selection inBos taurus

Cited by 7 publications

References 107 publications

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations

Exploring the impact of sequence context on errors in SNP genotype calling with Whole Genome Sequencing data using AI-based autoencoder approach

Lineage-specific genes are clustered with allorecognition loci and respond to G × E factors regulating the switch from asexual to sexual reproduction inNeurospora

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