Four researchers working at the University of Arkansas have found a natural mechanism by which new genes can arise, which gives the lie to creationist claims that this is impossible.
Before moving on to the details of their discovery which has just been published, open access, in the Oxford University Press journal Molecular Biology And Evolution, I'll first discuss the current state of understanding of how new genetic information arises naturally, without the need for magic.
Tell me all about how new genes can arise naturally, with specific examples, please. New genes can arise naturally through several mechanisms, including gene duplication, de novo gene origination, exon shuffling, retroposition, and horizontal gene transfer. Here’s a breakdown of these processes with specific examples:The AI panel on the right is a dialogue with ChatGPT4o, about how new genetic information can arise naturally (current as of May 2023) and the relevance of Information Theory to genetics. Creationists might find it distressing as it refutes some of their sacred dogmas
- Gene Duplication
One of the most common ways new genes arise is through gene duplication, where an existing gene is copied in the genome. The duplicated gene can accumulate mutations over time without affecting the original gene’s function. If these mutations lead to a novel function, the duplicated gene becomes a new gene.
Example:
- Globin genes (hemoglobin and myoglobin): The globin gene family arose through multiple rounds of gene duplication and divergence. Hemoglobin (which carries oxygen in the blood) and myoglobin (which stores oxygen in muscles) both originated from an ancestral globin gene that duplicated and evolved to serve slightly different roles in oxygen transport.
- De Novo Gene Origination
New genes can also arise from previously non-coding regions of the genome. Mutations in these regions can create new open reading frames (ORFs) that result in the production of functional proteins.
Example:
- BSC4 gene in yeast: In Saccharomyces cerevisiae, the BSC4 gene emerged de novo from a previously non-coding region of the genome. This gene plays a role in DNA damage repair, an important function that evolved from non-coding DNA.
- Exon Shuffling
Exon shuffling occurs when exons (the coding sequences of genes) are rearranged, duplicated, or moved between genes through recombination events. This can create new combinations of protein domains, giving rise to new genes.
Example:
- Tissue plasminogen activator (TPA): This protein involved in breaking down blood clots arose from exon shuffling. Its exons encode different protein domains, which originally came from other proteins, but were rearranged to form a new gene with a unique function.
- Retroposition (Retrotransposition)
In retroposition, a messenger RNA (mRNA) transcript of a gene is reverse-transcribed into DNA and inserted back into the genome. This can result in the creation of a new gene if the inserted sequence gains new regulatory elements and becomes functional.
Example:
- PGK2 gene in mammals: This gene, involved in spermatogenesis, arose through retroposition. It originated from a copy of the phosphoglycerate kinase 1 (PGK1) gene, which is important for glycolysis. The duplicated copy gained specific regulation in the testes, giving it a specialized role in reproduction.
- Horizontal Gene Transfer
This process involves the movement of genetic material between different species, often mediated by viruses or plasmids. It’s common in bacteria and other single-celled organisms, allowing them to acquire new genes rapidly.
Example:
- Antibiotic resistance genes in bacteria: Many bacteria acquire antibiotic resistance genes via horizontal gene transfer. For instance, genes that code for beta-lactamases (enzymes that break down beta-lactam antibiotics like penicillin) are frequently transferred between bacterial species, allowing for the spread of resistance.
- Gene Fusion/Fission
Gene fusion occurs when two separate genes combine to form a single, novel gene, whereas gene fission happens when a single gene splits into two distinct genes. These processes can give rise to new genes with modified or combined functions.
Example:
- YEATS gene family: These genes arose from gene fusions between two unrelated gene families. YEATS domain-containing proteins play roles in chromatin modification and gene expression regulation.
- Mutation and Evolutionary Selection
Once new genes are created by any of the mechanisms above, they can undergo mutations that either make them more useful (positive selection) or neutral. Through evolutionary processes, beneficial mutations may lead to the retention and spread of the gene in a population.
Example:
- Antifreeze proteins in Antarctic fish: Some species of Antarctic fish evolved genes for antifreeze glycoproteins through mutations in genes related to digestive enzymes. These proteins prevent the formation of ice crystals in their blood, enabling survival in freezing waters.
- Mobile Genetic Elements
Transposons, also called "jumping genes," can carry genetic material from one location to another within a genome, leading to new gene formations.
Example:
- RAG1 and RAG2 in the immune system: These genes, critical for the adaptive immune system in vertebrates, may have originated from transposable elements that were co-opted for their role in recognizing and cutting DNA during immune cell development.
Summary
New genes arise naturally through diverse mechanisms, including gene duplication, de novo origination, exon shuffling, retroposition, horizontal gene transfer, and mutation. These processes allow genomes to evolve and adapt to new challenges by creating novel proteins with unique functions.
Creationists claim the Second Law of Thermodynamics prevents new genetic information arising naturally, so intelligent intervention must be involved. Is there any merit to that claim?
The creationist claim that the Second Law of Thermodynamics prevents new genetic information from arising naturally is a misunderstanding of both the law and how biological systems work. Here's why:
What the Second Law of Thermodynamics Actually States
The Second Law of Thermodynamics deals with entropy, often described as the measure of disorder in a system. It states that in a closed system, the total entropy (or disorder) tends to increase over time. In other words, without input from outside, closed systems naturally progress toward states of greater entropy or less organization.
Biological Systems Are Not Closed Systems
One of the key reasons this claim is flawed is that living organisms are not closed systems. Biological systems constantly exchange energy and matter with their environment, primarily through sunlight (for plants) or food (for animals). Organisms use this energy to maintain and even increase their internal order.
- Example: Plants take in sunlight and use it to drive photosynthesis, a process that produces highly ordered molecules like glucose from simpler substances like carbon dioxide and water.
- Similarly, evolutionary processes that produce new genetic information—such as mutations, natural selection, and genetic recombination—are fueled by the energy and matter organisms gain from their environment.
In short, because living organisms are open systems that continuously receive energy from their surroundings, they can decrease their internal entropy and build complex structures, including DNA.
Entropy and Information in Genetics
Creationists often equate the Second Law with the idea that "disorder always increases," leading to the assumption that genetic mutations must result in a loss of information. However, this analogy is overly simplistic and doesn’t reflect how genetic information works.
- Mutations can increase genetic information: Mutations are changes in DNA sequences, and while some mutations may be harmful or neutral, others can increase genetic diversity and lead to the development of new traits or functions. For example, a gene duplication event provides extra genetic material that can evolve new functions through mutation and natural selection, resulting in an increase in information over time.
- Evolution creates order: Evolution by natural selection tends to favor organisms that are better adapted to their environments, which can result in increased complexity and order over generations. For instance, the evolution of the vertebrate eye shows a clear increase in complexity and functionality over time.
Thermodynamics and Evolution Are Not in Conflict
Thermodynamics and evolution operate at different levels of organization and on different scales. The Second Law of Thermodynamics is focused on physical processes and energy distribution, not on how biological systems evolve or accumulate information. The process of evolution, driven by genetic variation and natural selection, fits well within the framework of the Second Law, because living systems are open and constantly interacting with their environments.
Expert Rebuttals
Many biologists, physicists, and chemists have addressed this misconception. For example:
- Isaac Asimov, a biochemist and prolific science writer, noted that while the Second Law does apply universally, it does not imply that order cannot arise in localized systems. He explained that localized decreases in entropy are not only possible but common, provided there is a source of energy—like the sun for life on Earth.
- Douglas Futuyma, an evolutionary biologist, emphasized that the increase in complexity and adaptation in biological systems is driven by natural selection, which sorts genetic variation into patterns that are more complex, functional, and adaptive.
Conclusion
The claim that the Second Law of Thermodynamics prevents the natural increase of genetic information and requires intelligent intervention has no scientific merit. It is based on a misunderstanding of both thermodynamics and evolutionary biology. In reality, life is an open system, and evolution, powered by external energy, is fully consistent with the laws of thermodynamics. Natural processes like mutation, gene duplication, and selection are more than sufficient to explain the rise of new genetic information.
Does the Second Law of Thermodynamic (2LOT) have any relevance to information theory and does information theory have any relevance to genetic information?
Yes, the Second Law of Thermodynamics (2LOT) is relevant to information theory, and information theory is highly relevant to genetic information. However, the way these concepts interrelate is often misunderstood, particularly in the context of biological evolution. Let’s break down these connections:
Conclusion
- Relevance of the Second Law of Thermodynamics to Information Theory
The connection between the 2LOT and information theory arises from the work of Claude Shannon, the founder of information theory, who explored how information and entropy are related.
- Shannon Entropy: Shannon introduced a concept of entropy in information theory, which measures the amount of uncertainty or disorder in a set of data or a communication signal. This is mathematically analogous to thermodynamic entropy, which measures disorder in a physical system.
- Information as a Reduction in Uncertainty: When information is transmitted or stored, it reduces uncertainty about the state of a system. Just as the 2LOT states that the total entropy (disorder) in a closed system increases over time, Shannon’s concept of entropy describes the amount of uncertainty in information. However, there is no inherent conflict with increasing complexity or order in information, especially when an external energy source is involved, as is the case in biological systems.
In summary, while there is a mathematical similarity between thermodynamic entropy and Shannon entropy, their physical interpretations differ. In thermodynamics, entropy represents physical disorder, while in information theory, entropy represents uncertainty or lack of information. The Second Law of Thermodynamics doesn’t prohibit the creation or increase of information, provided there is external energy to counterbalance increases in entropy.
- Relevance of Information Theory to Genetic Information
Information theory is highly relevant to genetics because DNA is essentially a coded system of information. Genes encode instructions for building proteins, and this genetic information can be understood in terms of data storage, transmission, and processing—which are central concepts in information theory.Examples of Information Theory in Genetics
- DNA as a Code: The sequence of nucleotides (A, T, C, and G) in DNA can be viewed as a digital code, much like the 1s and 0s in computer code. Information theory provides tools for understanding how this information is encoded, transmitted, and potentially altered through processes like mutation, recombination, and gene expression.
- Mutations and Genetic Information: In genetics, mutations can be seen as changes to the "code" of DNA. While some mutations might introduce errors or noise, others can add new functional information. From an information-theoretic perspective, the mutability of DNA means that genetic information is not static; it can change, increase, or adapt over time through natural processes.
- Gene Duplication and New Information: One key concept from information theory is that copying data doesn’t necessarily increase uncertainty but may provide the basis for increased information through divergence. This is analogous to gene duplication, where an extra copy of a gene can mutate and evolve a new function, adding new functional information to the genome.
- Shannon Entropy and DNA Sequences: Shannon's formula for entropy has been applied to DNA sequences to measure the level of order or randomness in genetic material. A highly ordered sequence has low entropy, while a random sequence has high entropy. This approach helps scientists study the evolution and variability of genetic material.
- Mutations and Noise: In information theory, "noise" refers to random alterations of a signal during transmission. In genetics, mutations can be thought of as "noise" in the transmission of genetic information. However, not all mutations are harmful. Some can lead to new functions and thus increased information, especially when guided by natural selection.
- Compressibility and Genetic Complexity: Information theory is also used to explore the compressibility of genetic sequences. Highly ordered sequences are more compressible, while random sequences are not. This concept is used to understand the complexity of genomes and how they evolve over time.
- Does the Second Law of Thermodynamics Apply to Genetic Information?
While thermodynamic entropy and Shannon entropy are conceptually similar, the Second Law of Thermodynamics does not directly apply to genetic information in the way creationists often argue. Biological systems are not closed systems—they are open systems that exchange energy and matter with their environment. As long as there is an input of energy (e.g., from the sun in ecosystems), local decreases in entropy (increases in order) are not only possible but expected.
In fact, biological systems often increase in complexity and order over time due to evolutionary processes like mutation, gene duplication, and natural selection. These processes operate within the framework of the 2LOT because energy is being continually added to the system, allowing living organisms to maintain and build complexity, including the generation of new genetic information.
- The Second Law of Thermodynamics does not prevent the increase or evolution of genetic information because living organisms are not closed systems; they draw energy from their environment to maintain order and evolve.
- Information theory provides valuable tools for understanding genetic information, including how DNA codes, stores, and transmits biological instructions, and how mutations can lead to new information.
In sum, information theory is highly relevant to genetics, but the Second Law of Thermodynamics, when properly understood, does not pose any barrier to the natural processes that generate new genetic information [my emphasis].
Creationists dogma states that no new genetic information can arise without the help of their magic creator god. They try to give this claim a gloss of science by claiming it would contravene the Second Law of Thermodynamics (2LOT). This has been corrected so many times, especially when repeated by their ci=ult leaders, that repeating it can only be regarded as a deliberate attempt to mislead their audience.
Creationists confuse the meaning of genetic information with the amount of information, taking that to mean the number of coding triplets in DNA where one triplet is the template for one amino acid. What matters is not the number of triplets or the number of amino acids in the protein a gene codes for, but what that protein does; in other words, what it means in terms of its utility to the organism, in that organism's environment.
Take, as an example, a gene which stopped humans at about the age of 18 months from making the digestive enzyme, lactase, which is needed to digest the lactose sugar in milk. In a society which doesn't have cattle, that gene means the baby would stop breast feeding. Breast feeding acts as a natural contraceptive by producing a hormone that suppresses ovulation, so stopping breast feeding means the mother begins to ovulate again and can have another baby. This is beneficial to the human species, so the gene which stops the baby producing lactase is beneficial, so became dominant in the gene pool.
However, in a culture which has cattle, milk tends to be in plentiful supply, so having a gene which prevents adults from digesting milk and milk products denies them access to this potential valuable source of nutrition, so a mutation which breaks the gene that stops lactase production is now beneficial. The condition known as lactase persistence counters lactose intolerance. It also means babies can be switched to cows’ milk so breast feeding can be discontinued along with the contraception it provided. More babies and more nutrition into adulthood. The mutation may have reduced the amount of genetic information, or it may have increased it, but either way, it changed the meaning of the information in the context of a culture with cattle.
But take cattle out of the equation, and lactose intolerance would be beneficial again, and is the norm in cultures which do not have cattle such as parts of Africa where the tsetse fly, which carries the sleeping sickness parasite that makes keeping healthy cattle impossible is common.
The evidence, as usual, is against counter-factual creationism in that several ways in which new genes can arise are known. One of the best known is gene or whole genome duplication in which a new copy of a gene arises by chance mutation due to a mistake in replication involving cells in the germ line - cells than make eggs and sperm. The original gene is still available to continue its function, while the new copy can mutate without any detriment to the organism. This way a duplicate gene can be repurposed for a new function.
Venomous snakes provide a very good example of new information arising by gene duplication.
There is a natural evolutionary arms race between a venomous snake and it preys species (of which there are usually several), so when a prey species becomes immune to the snake venom it normally does so by small changes in receptor sites on cells such as nerves to which the venom binds and disrupts the cell's functions. If the snake's gene that coded for that toxin mutated in a way that overcame the resistance it might no longer be effective against other prey species. However, if the snake has a spare copy of the gene the spare can mutate and eventually hit on a modified venom that overcomes the prey's resistance, while the snake's venom is still effective against other prey species. This is the mechanism by which most snake's venom is now a cocktail of lots of different toxins that are effective against different prey species.
King cobra, Ophiophagus hannah
The archetypal venomous snake
The archetypal venomous snake
Gene duplication and repurposing is also responsible for the 'clotting cascade' in vertebrates in which one enzyme catalyzes the production of the next in a sequence, resulting in the production of fibrin to form a blood clot. Over time, genes have duplicated and been repurposed to refine this mechanism that creationists like to claim is 'irreducibly complex'. It is, in fact, the product of a well-understood evolutionary process, as are all other examples of 'irreducible complexity'.
That long preamble was by way of introduction to a new discovery of an alternative mechanism by which new genes can arise without the assistance of a magic invisible man in the sky:
Researchers Publish Breakthrough Study on How New Genes Evolve
Where do new genes come from? That’s the question a team of biological sciences researchers from the U of A set out to answer in a new study.
They did so by examining the evolution of antifreeze proteins in fish — an essential adaptation that allows fish to survive in freezing waters by preventing ice formation through the binding of their antifreeze proteins to ice crystals.
SculpinPhoto by Eric Heupel
The team investigated these proteins in three unrelated fish lineages and uncovered surprising results. While the proteins in each lineage are functionally and structurally similar, they evolved independently from different genetic sources. This phenomenon, known as convergent evolution, represents a rare case of protein sequence convergence. It demonstrates how the same adaptive traits — and even nearly identical protein sequences — can be produced through entirely different evolutionary trajectories.
From left: Nathan Rives, Xuan Zhuang and Vinita Lamba.
The study provides concrete examples of different evolutionary mechanisms that can lead to the birth of new genes. Findings suggest that new genes can form by repurposing fragments of ancestral genes while incorporating entirely new coding regions (the protein-coding parts of the DNA). This innovative concept bridges the gap between entirely new gene formation from noncoding regions and the more traditional model in which new functions can arise from duplicated genes.
The study, "Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence," was published in Molecular Biology and Evolution. Co-authors included Nathan Rives, Vinita Lamba, C-H Christina Cheng and Xuan Zhuang. The co-first authors, Rives and Lamba, are Ph.D. students in the Zhuang Lab at the U of A, which is led by assistant professor of biological sciences Xuan Zhuang, who oversaw the study. Cheng is a professor in the School of Integrative Biology at the University of Illinois Urbana Champaign.
The group’s work also introduces a new model that advances understanding of the mechanisms behind new gene evolution: Duplication-Degeneration-Divergence. This model explains how new gene functions can arise from degenerated pseudogenes — formerly functional genes that lost their original role. This model also highlights how genes that appear to be nonfunctional or "junk" can evolve into something entirely new, a concept that holds significant implications for understanding adaptation under extreme environmental stress.
In the context of molecular evolution, this work represents a significant step forward in understanding how new genes are born and evolve, offering fresh perspectives on functional innovation — or gene recycling and adaptation.
It will be apparent to anyone with the courage to read research such as this, (which will exclude most creationists) that people who should know better but pretend not to have been systematically misleading and misinforming creationist dupes about the relevance of Information Theory and the Second Law of Thermodynamics to genetic information and in particular the question of how genetic information arises.Abstract
Determining the origins of novel genes and the mechanisms driving the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. Recently evolved fish antifreeze proteins (AFPs) offer a unique opportunity to explore these processes, particularly the near-identical type I AFP (AFPI) found in four phylogenetically divergent fish taxa. This study tested the hypothesis of protein sequence convergence beyond functional convergence in three unrelated AFPI-bearing fish lineages. Through comprehensive comparative analyses of newly sequenced genomes of winter flounder and grubby sculpin, along with available high-quality genomes of cunner and 14 other related species, the study revealed that near-identical AFPI proteins originated from distinct genetic precursors in each lineage. Each lineage independently evolved a de novo coding region for the novel ice-binding protein while repurposing fragments from their respective ancestors into potential regulatory regions, representing partial de novo origination—a process that bridges de novo gene formation and the neofunctionalization of duplicated genes. The study supports existing models of new gene origination and introduces new ones: the innovation–amplification–divergence model, where novel changes precede gene duplication; the newly proposed duplication–degeneration–divergence model, which describes new functions arising from degenerated pseudogenes; and the duplication–degeneration–divergence gene fission model, where each new sibling gene differentially degenerates and renovates distinct functional domains from their parental gene. These findings highlight the diverse evolutionary pathways through which a novel functional gene with convergent sequences at the protein level can evolve across divergent species, advancing our understanding of the mechanistic intricacies in new gene formation.
Introduction
Evolutionary adaptation is fundamentally a genetic process, heavily dependent on the emergence of novel genetic components essential for the development of new adaptive traits. New genes, harboring unique functions, stand as a significant wellspring of genetic innovation (Long et al. 2003, 2013; Santos et al. 2017), underscoring the need to comprehend the mechanisms governing their origination—a crucial yet comparatively overlooked source of evolutionary innovation. The inaugural paper investigating the origin of new genes, authored by Long and Langley (1993), marked the beginning of a growing body of research on the evolution of novel genes in the three decades that followed. Initially, gene duplication was proposed as the exclusive method of gene origination (Ohno 1970; Jacob 1977), where the duplicated copy could accumulate mutations and evolve new functions through neofunctionalization or subfunctionalization if the parental gene had multiple functions (Lynch and Conery 2000; Lynch and Force 2000.1). In recent years, advancements in genomics have increasingly supported alternative routes of novel gene origination, particularly de novo birth from genetic material that was previously noncoding for proteins (Tautz 2014; McLysaght and Guerzoni 2015; Schlötterer 2015.1; McLysaght and Hurst 2016; Schmitz and Bornberg-Bauer 2017.1; Van Oss and Carvunis 2019). The grand challenge that persists lies in elucidating the molecular mechanisms of new gene origination, deciphering the functions of the proteins they encode, and the fitness the proteins confer (Moyers and Zhang 2015.2; Guerzoni and McLysaght 2016.1). In the absence of an ecological context, inquiries related to adaptation are especially challenging to address in model species.
The diverse fish antifreeze proteins are remarkable evolutionary innovations that emerged under strong selective pressures from sea-level glaciation in Polar regions. This makes them ideal systems for exploring the origination and evolution of new genes endowing a crucial adaptive function driven by natural selection. These proteins serve as a quintessential adaptation in marine bony fishes inhabiting frigid polar or subpolar waters, countering the threat of freezing death in icy, sub-zero temperatures. The strong environmental selective pressure of potential freezing death has led to the adaptive evolution in multiple polar and subpolar fish taxa, independently driving the evolution of multiple, structurally distinct types of antifreeze proteins, including antifreeze protein (AFP) types I, II, and III, and antifreeze glycoprotein (AFGP) across various fish lineages. Regardless of structural differences, all AF(G)Ps share the crucial function of protecting the fish from freezing by binding to internalized ice crystals and halting their growths in their blood and body fluids, thus preventing organismal freezing (Devries 1971). Therefore, these proteins definitively represent convergent evolution of a novel function. With well-studied freeze-preventing function, they also exemplify a rare case of a monogenic trait that alone confers a clear life-saving benefit to the organism. The structural variations in AF(G)Ps stem from their distinct genetic ancestry (Cheng and Zhuang 2020). With these unique attributes, fish antifreeze proteins offer excellent avenues into discovering the diversity of possible genetic sources and mechanisms that natural selection has harnessed in evolutionary adaptation.
Over the past two decades, investigations into the evolutionary mechanisms of fish antifreeze protein have significantly advanced the field of evolutionary biology, exemplifying conceptual models and theories related to the emergence of novel genes and functions (Cheng and Zhuang 2020). Our prior work has contributed to the discovery of a clear example of the de novo birth of the AFGP gene in northern codfishes (gadids) (Zhuang et al. 2019.1). These studies illustrate the formation of essential components for the new gene from noncoding DNA, providing concrete evidence for the “proto-ORF” model (McLysaght and Guerzoni 2015), wherein a nonfunctional ORF (open reading frame) was present before regulatory signals for expression were acquired. We further elucidated the evolutionary process leading to functional innovation of the de novo cod AFGP gene and the evolutionary dynamics of the genotype under different strengths of natural selection (Zhuang and Cheng 2021). Other studies on fish AF(G)P evolution have revealed diverse mechanisms underlying new gene origination. These include a rare case of protein sequence convergence between the AFGP gene of the Antarctic notothenioids and the unrelated northern codfishes (Chen et al. 1997a). The first example of partial de novo evolution was observed in the AFGP gene of Antarctic notothenioids, where untranslated sequences and a secretory signal were recruited from a functionally unrelated trypsinogen gene, while a novel coding sequence partially de novo evolved from an intron within the ancestral gene (Chen et al. 1997.1b; Cheng and Chen 1999). Also, the neofunctionalization of a cytoplasmic enzyme (sialic acid synthase) into the secreted type III AFP of the zoarcid fishes supported the “Escape from Adaptive Conflict (EAC)” model (Deng et al. 2010). Additionally, the evolution of type II AFP from a preexisting ancestor C-type lectin (Ewart and Fletcher 1993.1) provided evidence for transmission to distant species through horizontal gene transfer (Graham and Davies 2021.1). Lastly, type I AFP (AFPI) in the starry flounder arose from GIG2 (grass carp reovirus-induced gene 2), with an unrelated function of viral resistance (Graham et al. 2022). Despite these advancements, among the known fish AF(G)Ps, the evolutionary mechanisms of AFPI are less understood, leaving a notable knowledge gap in the field.
The AFPI is a newly-emerged protein family found in four phylogenetically distant northern marine teleost fish groups—flounders (Duman and DeVries 1976; Graham et al. 2022), the cunner (Hobbs et al. 2011), sculpins (Hew et al. 1980), and snailfishes (Evans and Fletcher 2001). These groups belong to three divergent orders—Pleuronectiformes (flounders), Labriformes (cunner), and Perciformes (sculpins and snailfishes), which diverged from each other approximately 100 million years ago (Hughes et al. 2018; Near and Thacker 2024). Multiple isoforms of AFPI have been identified in these fishes, expressing in different tissues and varying in protein size and in the presence/absence of a signal peptide (Gourlie et al. 1984; Gong et al. 1996; Baardsnes et al. 2001.1; Evans and Fletcher 2001; Marshall et al. 2004; Hobbs et al. 2011). Despite these differences, the protein structures and amino acid sequences of AFPI are remarkably similar across these different fish lineages. Most of them are amphipathic alpha helices comprising 11-amino acid (aa) repeats rich in alanine (Ala) with evenly spaced threonine (Thr) residues. Although structurally analogous, suggesting a common ancestry, AFPI genes from different species exhibit distinct intronic sequences and variable utilization of the Ala codon, suggesting a polyphyletic origin instead (Graham et al. 2013.1). The emergence of AFPI is thus hypothesized to result from convergent evolution, encompassing both functional and, in some instances, rare protein sequence convergence. This unique characteristic positions AFPI as an exceptional model for investigating diverse evolutionary pathways in the development of a new protein with a novel function, shedding light on the molecular mechanisms underpinning their formation.
In this study, we explored the genomic origins and evolutionary mechanisms of AFPI in three of the four AFPI-bearing (AFPI+) taxa. Leveraging the power of cutting-edge long-read sequencing technology, we performed de novo whole-genome assembly for two species, namely Pseudopleuronectes americanus (winter flounder) and Myoxocephalus aenaeus (grubby sculpin). Additionally, we included a third AFPI+ lineage, Tautogolabrus adspersus (cunner), and 14 other related species from the three taxonomic groups (Table 1). All of these species have chromosome-level genome assemblies, except for the ballan wrasse, which has a scaffold-level assembly available in GenBank. The evolutionary relationships among these species were constructed and visualized with Timetree (supplementary fig. S1, Supplementary Material online). We annotated and characterized the complete AFPI family and the homologous genomic regions across all 17 genomes. By conducting in-depth comparative analyses, we successfully pinpointed the distinct genetic precursor in each taxon. Furthermore, we deciphered the different evolutionary processes that led to the convergence of protein sequences for this novel gene family in these divergent taxa.
[…]
Discussion
The study of new gene origination is an emerging field in molecular evolution, pivotal for understanding evolutionary mechanisms underlying new traits and adaptive functions. This study investigates the origination of a new gene with known adaptive function in three divergent fish lineages, elucidating the underlying evolutionary mechanisms behind a rare instance of molecular convergence at the protein sequence level. New genes can arise through various mechanisms, including modifying preexisting genes, sequence rearrangements such as gene fusion or fission, and de novo generation of a new ORF (Long et al. 2013). The evolutionary pathways of AFPI revealed in this study serve as exemplary illustrations of these fundamental mechanisms. The AFPI in the three lineages demonstrates a partial de novo evolution, where the new genes repurpose noncoding regions from a preexisting gene while generating an entirely novel ORF. This unique evolutionary process provides a valuable opportunity to investigate both functional innovations from preexisting genes and the de novo origination of functional domains.
This raises the question of why they need people to be misinformed about science, but any reading of the Discovery Institute’s 'Wedge Strategy', which was originally intended to remain secret until they could sustain the denial of authorship no longer, that there is a far-right political agenda that requires people to be misled and misinformed about all aspects of scientific rationalism, because that undermines the fundamentalist religion they plan to use to control people with if ever they gain the power to do so.
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