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Population Growth

Population Growth

Population size is dynamic, increasing with birth rates and immigration, and decreasing with death rates and emigration. In ideal conditions with unlimited resources, populations can increase exponentially, which plots as a J-shaped growth rate curve of population size against time. This type of curve is characteristic of newly-introduced invasive species, or populations that have suffered catastrophic declines and are rebounding.However, realistic environmental conditions limit the number of...

What is Population Genetics?

What is Population Genetics?

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.While some alleles of a given gene might be observed commonly, other variants...

Mutation, Gene Flow, and Genetic Drift

Mutation, Gene Flow, and Genetic Drift

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).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...

Genetic Drift

Genetic Drift

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.Life is not fair. A deer grazing contentedly in a field can have her meal cut tragically short by a bolt of lightning. If the doomed doe is one of only three in the population, 1/3 of the population’s gene pool is lost. Random events like this can...

Distributions to Estimate Population Parameter

Distributions to Estimate Population Parameter

The accurate values of population parameters such as population proportion, population mean, and population standard deviation (or variance) are usually unknown. These are fixed values that can only be estimated from the data collected from the samples. The estimates of each of these parameters are sample proportion, the sample mean, and sample standard deviation (or variance). To obtain the values of these sample statistics, data are required that have particular distribution and central...

Genetic Variation

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...

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Updated: Jun 10, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

TreesimJ: a flexible, forward time population genetic simulator.

Brendan O'Fallon¹

¹Department of Genome Sciences, Foege Building S-250, Box 355065 3720 15th Ave NE, Seattle, WA 98195-5065, USA. brendano@u.washington.edu

Bioinformatics (Oxford, England)

|July 31, 2010

Summary

TreesimJ is a novel forward time population genetic simulator that generates genealogies under complex evolutionary scenarios. This tool aids researchers in analyzing gene genealogies and understanding evolutionary forces.

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Area of Science:

Population Genetics
Computational Biology
Evolutionary Biology

Background:

Existing population genetic simulators are limited: backward-time simulators handle simple models but not complex genealogies, while forward-time simulators allow complex scenarios but don't produce genealogies.
A gap exists for tools that can generate genealogies under arbitrarily complex selective and demographic models.

Purpose of the Study:

To introduce TreesimJ, a forward-time population genetic simulator capable of sampling genealogies.
To provide a flexible platform for simulating complex evolutionary scenarios, including fitness and demographic models.

Main Methods:

TreesimJ employs a forward-time simulation approach.
It incorporates a variety of configurable data collectors for sampling population statistics.
The software allows for the development of new fitness and demographic models.

Main Results:

TreesimJ enables the sampling of genealogies, genetic data, and population parameters under complex evolutionary conditions.
It offers diverse output options, including traces, histograms, summary statistics, genetic sequences, and genealogies.

Conclusions:

TreesimJ facilitates the analysis of gene genealogies and related data in populations with varied selective and demographic histories.
The simulator is valuable for researchers investigating the interplay between evolutionary forces, demographic factors, genealogical structure, and genetic variation patterns.