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Related Concept Videos

Speciation Rates01:07

Speciation Rates

Speciation can proceed at markedly different rates, and evolutionary biologists commonly describe these differences through the models of gradualism and punctuated equilibrium. Both patterns explain how new species arise, but they differ in the tempo and continuity of evolutionary change. In both cases, evolutionary change arises from heritable variation within populations, with natural selection often shaping traits that improve survival and reproduction under specific environmental conditions.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Frequency-dependent Selection01:21

Frequency-dependent Selection

When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.Positive Frequency-Dependent SelectionIn positive...
Genetics of Speciation02:16

Genetics of Speciation

Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.The genetics of speciation involves the different traits or isolating mechanisms preventing gene exchange, leading to reproductive isolation. Reproductive isolation can be due to reproductive barriers that have effects either before or after the formation of a zygote. Pre-zygotic mechanisms prevent fertilization from occurring, and post-zygotic mechanisms...

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Published on: August 14, 2018

Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate

Guy Baele1, Yves Van de Peer, Stijn Vansteelandt

  • 1Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium.

BMC Evolutionary Biology
|August 12, 2010
PubMed
Summary

We improved evolutionary modeling by using Markov chains for root sequences and context-dependent models. This approach accurately estimates parameters and models substitution rates, outperforming previous methods.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Computational Biology
  • Evolutionary Genetics
  • Bioinformatics

Background:

  • Context-dependent evolutionary models traditionally assume site evolution depends on ancestors and flanking sites.
  • Modeling dependence at the root sequence is challenging due to the lack of an ancestor.
  • Coupled root distributions and context-dependent models offer more realistic evolutionary simulations.

Purpose of the Study:

  • To investigate the use of different orders of Markov chains for modeling dependence at the ancestral root sequence.
  • To evaluate the impact of coupled versus decoupled root distributions on evolutionary models.
  • To improve the accuracy of context-dependent evolutionary models.

Main Methods:

  • Applied varying orders of Markov chains (first-order and second-order) at the ancestral root sequence.
  • Utilized context-dependent models across the phylogenetic tree.
  • Compared coupled and decoupled root distribution models.
  • Analyzed ancestral repeats and pseudogene datasets.
  • Evaluated model fit using Bayes Factors.

Main Results:

  • A second-order Markov chain at the root with a context-dependent model showed strong support for ancestral repeats data.
  • A first-order Markov chain at the root was supported for pseudogene data.
  • Relaxing context-independent assumptions significantly improved model fit.
  • Context-dependent models accurately capture CpG-methylation-deamination substitution rates.
  • The decoupled approach outperformed a coupled approach (Arndt et al.).

Conclusions:

  • Combining root sequence dependency with context-dependent models enables accurate parameter estimation.
  • Designing accurate context-dependent models is complex and requires validating multiple assumptions.
  • Model assumptions vary across datasets, necessitating careful model selection for specific data.