Rosa Rubicondior: Refuting Creationsm - Evolution By Loss of Genes, Horizontal Gene Transfer And Gene Duplication

Refuting Creationsm

Evolution By Loss Of Genes, Horizontal Gene Transfer And Gene Duplication

Nitzschia sp

By Kristian Peters - Own work,
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Nitzschia sing1 lives on the alginate in the cell walls of decaying brown algae.

A borrowed bacterial gene allowed some marine diatoms to live on a seaweed diet | PRESS-NEWS.org

A fundamental axiom of creationism is the claim that any loss of genetic information is invariably detrimental—so much so that any mutation resulting in such a loss would be fatal and could therefore play no role in evolution. A second axiom asserts that new genetic information cannot arise naturally and must instead be supplied by a supernatural intelligent designer.

Both of these assertions are demonstrably false. Nevertheless, they continue to feature in creationist apologetics, relying on the audience's ignorance and incredulity to pass as justification for belief in an intelligent creator.

To add further difficulty for creationist claims, scientists have now identified a marine diatom, Nitzschia sing1, that has not only lost the genes and organelles required for photosynthesis — present in its photosynthetic relatives — but has also adapted successfully without them. It achieved this by acquiring new genetic information through horizontal gene transfer from a marine bacterium. The transferred gene subsequently underwent extensive duplication and diversification into three gene families, each with complementary functions. Together, these 91 versions of the acquired gene enable N. sing1 to metabolise alginate, a carbohydrate found in the cell walls of brown algae such as kelp.

What information do you have on the diatom, Nitzschia sing1?

Nitzschia sing1 is a non-photosynthetic, or apochlorotic, diatom that has adapted to a heterotrophic lifestyle by acquiring the ability to metabolize alginate, a polysaccharide found in the cell walls of brown algae. This adaptation allows N. sing1 to thrive as an epiphyte on seaweeds in intertidal zones.

The key to this metabolic capability is the acquisition of an alginate lyase (ALY) gene through horizontal gene transfer (HGT) from a marine bacterium. This event enabled N. sing1 to break down alginate into simpler compounds. Following this acquisition, the ALY gene underwent extensive duplication and diversification, resulting in 91 distinct genes categorized into three families:

CA Family: Retains the original endolytic function, cleaving alginate polysaccharides into smaller oligosaccharides.
$A^{n - T M D}$ Family: Evolved to include transmembrane domains, potentially facilitating the transport of alginate-derived substrates into the cell.
$A^{n} C^{n}$ Family: Developed an exolytic function, breaking down alginate oligosaccharides into monosaccharides for energy metabolism.
This evolutionary process of gene acquisition, duplication, and functional diversification has allowed N. sing1 to occupy a new ecological niche, relying on alginate as a carbon source instead of photosynthesis.

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How this example of horizontal gene transfer and subsequent multiple duplication was discovered is the subject of an open access paper in PLOS Biology and a press release in Press-News.org:

A borrowed bacterial gene allowed some marine diatoms to live on a seaweed diet
One group of diatoms lost their chlorophyll and stopped photosynthesis to consume carbohydrates from seaweed instead
A group of diatom species belonging to the Nitzschia genus, gave up on photosynthesis and now get their carbon straight from their environment, thanks to a bacterial gene picked up by an ancestor. Gregory Jedd of Temasek Life Sciences Laboratory, Singapore, and colleagues report these findings in a new study published April 1st in the open-access journal PLOS Biology.

Unlike most diatoms, which perform photosynthesis to generate carbon compounds, some members of the genus Nitzschia have no chlorophyll and instead consume carbohydrates from seaweed and decaying plant matter. Previously, it was unclear how exactly they made this major lifestyle transition, so researchers sequenced the genome of one species, Nitzschia sing1, to look for clues.

N. sing1’s genome sequence showed that the diatom carries a gene for an enzyme that breaks down alginate, a carbon polymer in the cell walls of brown algae – a group that includes kelp and other common seaweeds. The gene originally came from a marine bacterium, and an ancestor of N. sing1 took up the gene and incorporated it into its genome. Further analysis showed that, over time, the original gene was duplicated multiple times, with copies acquiring a variety of mutations that resulted in new functions. Those new functions have enabled N. sing1 to take up and break down alginate into carbon building blocks for the cell, so that photosynthesis is no longer necessary. This development also opened up a new ecological niche for this group of diatoms – living on seaweed in the intertidal zones.

While N. sing1 and many of its relatives can break down alginate, other non-photosynthetic Nitzschia species cannot, suggesting that these diatoms likely have other strategies for gaining carbon compounds. The researchers propose that sampling more Nitzschia species from the environment and sequencing their genomes will lead to a better understanding of how these diatoms source their carbon. Additional work in this area could also help us to learn more about how a single species diversifies into a range of new species and how carbon and other nutrients move through coastal habitats.

The authors add,
In this study we show how a non-photosynthetic diatom (diatoms are ancestrally photosynthetic microalgae) evolved the ability to metabolize the abundant brown algal cell wall polysaccharide alginate. This work not only identifies the evolutionary origins of a complex metabolic capability but also reveals the genetic mechanisms underlying the innovations that ultimately permitted these diatoms to occupy a new environmental niche as obligate heterotrophs.

Publication
Lim ZH, Zheng P, Quek C, Nowrousian M, Aachmann FL, Jedd G (2025) Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization.
PLoS Biol 23(3): e3003038. https://doi.org/10.1371/journal.pbio.3003038

First, a note about nomenclature:

Is it usual to include a numeric character in a species name?

No, it is not usual or permissible under the International Code of Nomenclature for algae, fungi, and plants (ICN) or the International Code of Zoological Nomenclature (ICZN) to include numeric characters (e.g., digits like "1") in a scientific species name.

Key points:

Scientific names must be Latinised and follow specific grammatical conventions.
Names must consist of letters only from the Latin alphabet.
Numbers, hyphens, or other symbols are not permitted in formal binomial names.

So, what is Nitzschia sing1?

The inclusion of “sing1” strongly suggests that:

This is not a formally described species.
“sing1” may be a lab designation, strain identifier, or genomic isolate label used in research databases or pre-publication material (e.g., "Nitzschia sing1" in genome sequencing projects).
For example, genome studies often name a strain “sing1” to distinguish it from other samples before formal naming.

Conclusion:

Nitzschia sing1 is not a valid species name under botanical or zoological nomenclature rules. It most likely refers to a particular isolate or strain used in experimental or genomic research.

If you'd like, I can help check whether this strain has been formally named or remains an informal designation.

Yes, please.

Upon further research, it appears that Nitzschia sing1 is not a formally recognized species name in scientific taxonomy. Instead, "sing1" is a strain designation used in research contexts to identify a specific isolate of the genus Nitzschia. This particular strain has been the subject of genomic studies due to its unique non-photosynthetic, heterotrophic lifestyle, which involves metabolizing alginate from brown algae.

In formal taxonomic nomenclature, species names do not include numeric characters or strain identifiers. Therefore, while Nitzschia sing1 is useful for research purposes to denote this specific strain, it does not represent an officially described species within the genus Nitzschia.

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Abstract
A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.

Introduction
How organisms obtain energy is a fundamental determinant of their form, function, and evolutionary trajectory. Photoautotrophs obtain energy from sunlight, while heterotrophs depend on chemical energy derived from these primary producers. Transitions between trophic strategies constitute major evolutionary steps that can lead to adaptive radiation. A prime example is the acquisition of photosynthesis through endosymbiosis between a eukaryotic heterotroph and a photosynthetic cyanobacterium that occurred around 1.5 billion years ago [1]. This key event led to the emergence of land plants, green and red algae, and glaucophytes (Archaeplastida). Subsequent endosymbiosis between a green or red alga and eukaryotic heterotroph led to other algal lineages, which together with members of the Archaeplastida comprise the known eukaryotic photoautotrophs (reviewed in [2–5]).

While multiple endosymbiotic transitions and the diversity of eukaryotic photoautotrophs attest to the advantages of this trophic strategy, loss of photosynthesis leading to secondary heterotrophs has also occurred in each major photosynthetic lineage. In many cases, this involves a transition to parasitism and narrowing of the habitat range. Such transitions have occurred in flowering plants [6,7], green [8] and red [9] algae, and apicomplexans such as Plasmodium and Toxoplasma [10,11]. Loss of photosynthesis has also led to many free-living secondary heterotrophs. This has occurred in the green [12–15] and red [16] algae, cryptophytes [17,18], euglenids [19], dinoflagellates [20,21], colpodellids [22], chrysophytes [23,24], and diatoms [25,26]. Here, mechanisms for nutrient uptake include phagotrophy and osmotrophy. However, in most cases, the genetic and physiological basis for adaptation to obligate heterotrophy is poorly understood.

In the microalgal diatoms [27–29], loss of photosynthesis in the genus Nitzschia led to free-living heterotrophs that occupy the nutrient-rich waters of the intertidal zone. These colorless or apochlorotic diatoms have been isolated from decaying plant material and the surface of green, red, and brown algae [25,26,30–33]. Moreover, they have been shown to grow on sole carbon sources consisting of cellulose [34] and the algal cell wall polysaccharides carrageenan, agarose [31,33,34], and alginate [33]. Genome sequences have also revealed genetic signatures of apochlorotic diatoms: a β-ketoadipate pathway for metabolism of lignin-derived aromatic compounds and rewiring of mitochondrial glycolysis have been implicated in Nitzschia Nitz4 [35], while expansion and diversification of solute transporters, carbohydrate-active enzymes (CAZymes), and a unique secretome have been documented in Nitzschia putrida [36].

Here, we sequence the genome of the apochlorotic diatom N. sing1 and show that its ancestor acquired a Polysaccharide Lyase 7 (PL7) family alginate lyase (ALY) gene by horizontal gene transfer (HGT) from a marine bacterium. This founder gene went on to expand through a combination of tandem gene duplication and transposition. Subsequent diversification of the paralogs gave rise to three major families comprising 91 genes. One N. sing1 ALY family retains the original endolytic function. By contrast, the two others underwent domain duplication, gain, loss, mutation, and rearrangement to encode new functions that can account for alginate oligosaccharide import and conversion into monomers. Thus, a full alginate catabolic pathway appears to have originated through neofunctionalization of paralogs derived from a single gene obtained by HGT. ALY genes are absent from the apochlorotic diatoms N. putrida and N. Nitz4, suggesting a high degree of ecophysiological diversity within the apochlorotic lineage. Together, our data show how HGT, coupled with gene duplication and neofunctionalization, led to the evolution of a complex metabolic capability supporting the transition to obligate heterotrophy.

Fig 2. Phylogeny, evolution and domain rearrangements of N. sing1 ALYs.
(A) Maximum likelihood phylogenetic tree constructed from the nucleotide sequences of all N. sing1 ALY A-domains (bootstrap replicates = 1,000). A-domains from the $A^{n - T M D}$ and $A^{n} C^{n}$ family genes form a monophyletic group (shaded in gray) with 100% bootstrap support. These two families also share a 15 bp insertion, suggesting they derived from a common ancestor. A-domains with mutations in conserved catalytic residues are marked with a black cross. Domains belonging to the CCA or A subfamily ALYs are marked with a red asterisk. Bootstrap support for nodes is summarized in the legend. Related to S3 and S10 Figs. The data underlying this figure can be found in S5 Data. (B) Schematic diagrams illustrating the evolutionary genetic events leading to the different ALY families. Domain representations are described in the legend. Note that the order of events is arbitrary. Specific ALYs are identified for illustrative purposes.

Lim ZH, Zheng P, Quek C, Nowrousian M, Aachmann FL, Jedd G (2025)
Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization.
PLoS Biol 23(4): e3003038. https://doi.org/10.1371/journal.pbio.3003038

Copyright: © 2025 The authors.
Published by PLoS. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Like almost every other scientific discovery, the discovery of Nitzschia sing1, a non-photosynthetic diatom that has lost its photosynthetic machinery yet adapted successfully through gene acquisition, directly challenges creationist ideology. First, creationists often claim that any loss of genetic information is inherently harmful and incompatible with evolutionary progress. However, N. sing1 demonstrates that losing complex systems such as the plastid and the genes required for photosynthesis can be advantageous under certain ecological conditions. Far from being fatal, this loss allowed the diatom to exploit a new niche as a heterotroph, showing that genetic loss can be evolutionarily viable—even beneficial.

Secondly, creationism asserts that new genetic information cannot arise naturally and must therefore be the product of an intelligent designer. Yet N. sing1 acquired a gene for alginate metabolism from a marine bacterium via horizontal gene transfer — a well-documented natural process. This gene was not only retained but duplicated and diversified into multiple gene families with complementary functions. Together, these adaptations enabled the organism to break down alginate, a carbohydrate found in brown algae. This case provides a clear, empirical example of new, functional genetic information emerging and diversifying through natural mechanisms — refuting the idea that complex genetic innovation requires divine intervention.

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