Related Experiment Video
Updated: Jul 2, 2025
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.2K
Computationally efficient demographic history inference from allele frequencies with supervised machine learning.
Linh N Tran1,2, Connie K Sun2, Travis J Struck2
1Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA.
Biorxiv : the Preprint Server for Biology
|February 26, 2024
Summary
We developed donni, a new neural network method for inferring population demographic history from genomic data. Donni offers faster and computationally efficient demographic inference with accuracy comparable to existing methods.
Area of Science:
- Population genetics
- Genomic data analysis
- Computational biology
Background:
- Inferring population demographic history from genomic data is crucial across scientific fields.
- The dadi method, based on allele frequency spectrum (AFS) and maximum composite likelihood optimization, is widely used but computationally intensive.
- There is a need for more efficient demographic inference methods.
Conclusions:
- Donni offers a more efficient alternative for demographic history inference.
- Supervised machine learning presents a promising approach for developing sustainable and computationally efficient demographic inference tools.
- This advancement facilitates broader application of genomic data in understanding population dynamics.
Related Concept Videos
01:49Hardy-Weinberg Principle
72.1K
Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
72.1K
01:25What is Population Genetics?
57.9K
A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
57.9K
01:09Mutation, Gene Flow, and Genetic Drift
58.4K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
58.4K
01:29Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
54
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
54
03:33Genetic Drift
39.8K
Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.
39.8K
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K