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The Maximum Genetic Diversity Theory: A Comprehensive Framework for Understanding Evolutionary Processes Cover

The Maximum Genetic Diversity Theory: A Comprehensive Framework for Understanding Evolutionary Processes

BioCosmos
Volume 5 (2025): Issue 1 (January 2025)
By: Shi Huang  
Open Access
|Apr 2025

Figures & Tables

Figure 1.

Illustration of the genetic equidistance result and its interpretation known as the molecular clock. Comparison for tetrapod species (T1–T3; human, bird, frog), which are known to have a most recent common ancestor (T), and another species (X; fish). Time flows from the past (left) to the present (right). Species X is the outgroup species and is equally distant to species T1–T3, the ingroup species, both in terms of time of separation and sequence difference, as measured by the identity matrix. This is illustrated by the lines linking X to T1, T2, and T3 being of equal length, indicating the same level of divergence in both time and sequence. The GEP refers to the fact that X is equally different in protein sequence to T1, T2, and T3. Evolutionary lineages leading to species T1–T3 separated from the lineage leading to X at the same point, V. Furthermore, species T1–T3 are products of an evolutionary process that has been ongoing for the same duration since their common ancestor, V. Therefore, if a given protein exhibits equal divergence when comparing the same fish protein with proteins from different tetrapods, it suggests that the rate at which differences accumulate is similar among tetrapods (T1–T3). The implicit assumption here is that the molecular distance among the species has not yet reached its maximum level, allowing us to infer the rate at which sequence differences accumulate. If, however, the distance has reached an upper limit, it would no longer be related to time or mutation rate, rendering the inference of the rate invalid. GEP, genetic equidistance phenomenon.
Illustration of the genetic equidistance result and its interpretation known as the molecular clock. Comparison for tetrapod species (T1–T3; human, bird, frog), which are known to have a most recent common ancestor (T), and another species (X; fish). Time flows from the past (left) to the present (right). Species X is the outgroup species and is equally distant to species T1–T3, the ingroup species, both in terms of time of separation and sequence difference, as measured by the identity matrix. This is illustrated by the lines linking X to T1, T2, and T3 being of equal length, indicating the same level of divergence in both time and sequence. The GEP refers to the fact that X is equally different in protein sequence to T1, T2, and T3. Evolutionary lineages leading to species T1–T3 separated from the lineage leading to X at the same point, V. Furthermore, species T1–T3 are products of an evolutionary process that has been ongoing for the same duration since their common ancestor, V. Therefore, if a given protein exhibits equal divergence when comparing the same fish protein with proteins from different tetrapods, it suggests that the rate at which differences accumulate is similar among tetrapods (T1–T3). The implicit assumption here is that the molecular distance among the species has not yet reached its maximum level, allowing us to infer the rate at which sequence differences accumulate. If, however, the distance has reached an upper limit, it would no longer be related to time or mutation rate, rendering the inference of the rate invalid. GEP, genetic equidistance phenomenon.

Figure 2.

Schematic representation of the MGD theory of evolution. (A) Macroevolution. As species evolves from simple to complex (taxon A to taxon E), the maximum level of genetic diversity that a taxon can tolerate gets reduced. (B) Microevolution. Accumulation of random mutations within the tolerated range of genetic diversity leads to speciation (from taxon A to taxon B) without much changes in epigenetic complexity or the level of MGD that a taxon can tolerate. MGD, maximum genetic diversity
Schematic representation of the MGD theory of evolution. (A) Macroevolution. As species evolves from simple to complex (taxon A to taxon E), the maximum level of genetic diversity that a taxon can tolerate gets reduced. (B) Microevolution. Accumulation of random mutations within the tolerated range of genetic diversity leads to speciation (from taxon A to taxon B) without much changes in epigenetic complexity or the level of MGD that a taxon can tolerate. MGD, maximum genetic diversity

Figure 3.

The genetic equidistance result and the MGD theory. (A) Maximum genetic equidistance. A 10 amino acid peptide is used to illustrate the evolution process. When the protein is fast evolving, the observed equidistance today would be maximum distance with a HOR. The figure shows 4 overlap positions with an overlap ratio 1. The distance of C–A is 60%, the same as that of that of B–A. This is a schematic representation of the original Margoliash genetic equidistance result. (B) An example of maximum genetic equidistance. Alignment of human, drosophila, and yeast cytochrome C proteins. Human differs from drosophila in 22 amino acid positions. Human and drosophila are equidistant to yeast with 36 amino acid differences. There are 12 overlap positions (in red color) and the overlap ratio is 12/22 = 55%. Other mutant positions are colored in green, blue and orange. (C) Linear genetic equidistance. When the protein is slowly evolving, assuming molecular clock holds, the observed equidistance today would be linear distance with a low overlap ratio. Here every substitution in any species would mean an increase in distance. The figure shows 0 overlap position with an overlap ratio 0. The distance of C–A is 50% and equals that of B–A. (D) An example of linear equidistance. Human, orangutan, and mouse TXND9 gene alignment. There are two amino acid difference between human and orangutan, which are equidistant to mouse with six amino acid differences. The overlap ratio is 0/2 = 0. HOR, high overlap ratio; MGD, maximum genetic diversity.
The genetic equidistance result and the MGD theory. (A) Maximum genetic equidistance. A 10 amino acid peptide is used to illustrate the evolution process. When the protein is fast evolving, the observed equidistance today would be maximum distance with a HOR. The figure shows 4 overlap positions with an overlap ratio 1. The distance of C–A is 60%, the same as that of that of B–A. This is a schematic representation of the original Margoliash genetic equidistance result. (B) An example of maximum genetic equidistance. Alignment of human, drosophila, and yeast cytochrome C proteins. Human differs from drosophila in 22 amino acid positions. Human and drosophila are equidistant to yeast with 36 amino acid differences. There are 12 overlap positions (in red color) and the overlap ratio is 12/22 = 55%. Other mutant positions are colored in green, blue and orange. (C) Linear genetic equidistance. When the protein is slowly evolving, assuming molecular clock holds, the observed equidistance today would be linear distance with a low overlap ratio. Here every substitution in any species would mean an increase in distance. The figure shows 0 overlap position with an overlap ratio 0. The distance of C–A is 50% and equals that of B–A. (D) An example of linear equidistance. Human, orangutan, and mouse TXND9 gene alignment. There are two amino acid difference between human and orangutan, which are equidistant to mouse with six amino acid differences. The overlap ratio is 0/2 = 0. HOR, high overlap ratio; MGD, maximum genetic diversity.

Figure 4.

Time line regarding the GEP. GEP, genetic equidistance phenomenon.
Time line regarding the GEP. GEP, genetic equidistance phenomenon.

Percentage non-identity among species in Dot1_

SpeciesPercentage non-identity
YEASACAEELSTRPUDANTEXENTRTAEGUMYOLU
CAEEL71
STRPU7369
DANTE706629
XENTR7168319
TAEGU72673285
MYOLU726731632
HUMAN7267317321

The MGD theory versus the NT_

FeaturesMGD theoryNT
Micro-evo linear stageNT and natural selectionNT and natural selection
Micro- and Macro-evoDifferent mechanismsSame
Role of epigeneticsYesNo
Noises suppressedYesNo
Neutral regionsComplexity dependentComplexity independent
Time framesAnyRelevant to short times
Mutation ratesAnyTrue for slow rates
Genetic equidistanceMaximum and linearLinear only
MGDYesNo
Genetic variantsMostly non-neutralMostly neutral
Recurrent mutationsCommonRare
Quasi-neutralityCommonRare
Turnover of allelesFast and commonSlow and rare
Non-conservationAdaptive functionNo function
Physiological selectionYesNo
Independent testsConfirmedRejected
Axiom basedYesNo
DOI: https://doi.org/10.2478/biocosmos-2025-0009 | Journal eISSN: 2719-8634
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Language: English
Page range: 41 - 61
Published on: Apr 24, 2025
Published by: The Israel Biocomplexity Center
In partnership with: Paradigm Publishing Services
Keywords:
genetic diversity,
genetic equidistance phenomenon (GEP),
molecular clock,
neutral theory,
maximum genetic diversity (MGD) theory
Related subjects:
Chemistry,
Biochemistry,
Life sciences,
Evolutionary biology,
Philosophy,
History of philosophy,
History of philosophy, other,
Physics,
Astronomy and astrophysics

© 2025 Shi Huang, published by The Israel Biocomplexity Center
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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