This and my next blog post deal with essentially the same refutations of creationist mythology and pseudo-science. The mythology is the Bible’s unambiguous claim that a creator god made everything for its favourite creation, humankind; the pseudo-science is the creationist claim that no new genetic information can arise without the direct intervention of that creator god, because, so they tell us, new genetic information can only be produced by magic, otherwise it would violate the laws of thermodynamics [sic]. Both claims are demonstrable nonsense, of course.Doubtless God could have made a better berry, but doubtless God never did
Dr. William Butler, Physician - (1535–29 January 1618)
Talking of the strawberry.
The first example concerns a fruit now ripening in UK gardens and fields — the strawberry. If strawberries had been specially created for humans, we might expect them to have arrived fully formed, already perfect for our tastes and purposes. Instead, like other cultivated crops, they bear the marks of a long evolutionary history followed by recent human selection, breeding and improvement.
A May 2025 paper published in the journal Horticulture Research by researchers from the U.S. Department of Agriculture and collaborating institutions, describes a new way to reconstruct the deep evolutionary history of the cultivated strawberry, Fragaria × ananassa. Their work helps explain how the modern strawberry acquired its complex octoploid genome — not by magic, but by ordinary, natural processes of genome duplication, hybridisation and subsequent evolutionary divergence.
Cultivated strawberries, like many crop plants, are polyploids. Humans are normally diploid, with two sets of chromosomes; cultivated strawberries are octoploid, with eight sets. In the notation used by geneticists, humans are 2n, while the cultivated strawberry is 2n = 8x = 56. This genomic complexity is the outcome of a series of ancient whole-genome duplication and hybridisation events in which entire chromosome sets from different ancestral lineages were brought together in one organism.
Whole-genome duplication does not require supernatural intervention. It is a well-known natural process, especially common in plant evolution. Initially, it duplicates existing genetic material, but those extra gene copies then provide raw material for mutation, altered regulation, divergence, subfunctionalisation and neofunctionalisation. In other words, duplicated genes can be retained, modified, silenced, repurposed or combined in new ways. Hybridisation adds another layer of novelty by bringing together different genomes, producing new combinations of genes and regulatory networks in a single evolutionary lineage.
The research team disentangled the strawberry’s complex polyploid genome by exploiting the evolutionary signatures left by long terminal repeat retrotransposons, or LTR-RTs. These mobile genetic elements accumulate in genomes over time and can act rather like molecular time stamps. By comparing patterns of similarity between these elements across chromosomes, the researchers were able to reconstruct the strawberry’s subgenome architecture and infer the timing of major genome-merging events.
Using this serial similarity matrix method, the researchers found evidence for three successive allopolyploidisation events in the evolutionary history of the cultivated strawberry genome: first between about 3.1 and 4.2 million years ago, then between about 1.9 and 3.1 million years ago, and finally between about 0.8 and 1.9 million years ago. The result is a genome composed of multiple subgenomes with different ancestry, interacting and evolving together over time.
What is perfectly clear from this research is that new genetic variation and genomic complexity can arise through entirely natural mechanisms. Polyploidy, hybridisation, mutation, transposable elements and selection are not gaps in biology into which a magic creator needs to be inserted; they are part of the normal machinery of evolution. The cultivated strawberry is not evidence of special creation, but of a long, traceable evolutionary history later shaped by human cultivation.
Glossary^ Strawberry Genome Evolution. Genome: The complete set of genetic material in an organism. In plants, genomes can be especially complex because entire chromosome sets may be duplicated or combined through hybridisation.The Horticulture Research paper was later the subject of a January 2026 press release via EurekAlert! from Nanjing Agricultural University (on behalf of whom, Oxford University Press publishes the open access journal Horticulture Research):
Chromosome: A long DNA molecule containing many genes and regulatory sequences. Chromosomes are inherited in sets, one set from each parent in ordinary sexual reproduction.
Diploid (2n): Having two sets of chromosomes, one from each parent. Humans are diploid, with 23 pairs of chromosomes.
Polyploid: Having more than two complete sets of chromosomes. Polyploidy is common in plants and has played a major role in the evolution of many crops.
Octoploid: Having eight sets of chromosomes. Cultivated strawberry, Fragaria × ananassa, is an octoploid species, normally written as 2n = 8x = 56.
Whole-genome duplication (WGD): A natural event in which the entire genome is duplicated. This instantly creates extra copies of genes, some of which may later be modified, silenced, repurposed or retained for new functions.
Hybridisation: The crossing of two different species or genetically distinct lineages. In plants, hybridisation can bring together two different genomes in a single organism.
Autopolyploidy: Polyploidy produced by duplication of chromosome sets within a single species or lineage.
Allopolyploidy: Polyploidy produced when genomes from different species or lineages are brought together, usually through hybridisation followed by whole-genome duplication.
Allooctoploid: An octoploid organism whose eight chromosome sets originated from different ancestral lineages. The cultivated strawberry is an allooctoploid.
Subgenome: One ancestral component within a larger polyploid genome. In cultivated strawberry, the modern genome contains multiple subgenomes inherited from different ancestral lineages.
Progenitor species: An ancestral species that contributed genetic material to a later species. In polyploid evolution, the exact progenitors may be difficult to identify because some may be extinct or may have changed substantially since the genome-merging event.
Transposable element (TE): A mobile piece of DNA capable of copying or moving itself within the genome. These elements are abundant in plant genomes and can leave useful evolutionary signatures.
Retrotransposon: A type of transposable element that copies itself through an RNA intermediate before inserting the copy back into the genome.
Long terminal repeat retrotransposon (LTR-RT): A retrotransposon with repeated DNA sequences at both ends. Because these elements accumulate changes over time, their similarities and differences can help reconstruct evolutionary history.
Serial similarity matrix (SSM): The method used in this study to compare LTR-RT similarity patterns across chromosomes. These patterns help researchers identify which chromosomes belong to the same ancestral subgenome.
Subgenome partitioning: The process of sorting the chromosomes of a polyploid organism into their ancestral genome groups.
Sequence identity: A measure of how similar two DNA sequences are. High identity suggests a more recent common origin; lower identity usually indicates a longer period of divergence.
Clustering: A computational method for grouping chromosomes or sequences according to similarity. In this research, clustering helped reveal the different ancestral components of the strawberry genome.
Genomic divergence: The accumulation of genetic differences between lineages over time. Divergence can be used to estimate when ancestral lineages separated.
Neofunctionalisation: The process by which a duplicated gene copy evolves a new function while the original copy retains its old role.
Subfunctionalisation: The process by which duplicated gene copies divide the original gene’s functions between them.
De novo gene: A new gene that arises from previously non-coding DNA or through substantial modification of existing sequences. This is one way genuinely new genetic information can arise naturally.
Mya: Million years ago. The strawberry study uses this timescale to estimate when major genome-merging events occurred in the evolutionary history of the octoploid strawberry genome.
A genomic time machine traces how the modern strawberry came to be
Polyploid genomes, formed through repeated whole-genome duplication and hybridization, underpin the evolution of many important crops, yet their internal structure often remains unresolved when ancestral species are unknown.
This study presents a new genome-wide strategy to disentangle complex polyploid genomes by exploiting the evolutionary signatures of long terminal repeat retrotransposons. By systematically comparing similarity patterns of these elements across chromosomes, the research reconstructs subgenome architecture and infers the timing of major genome-merging events. Applied to the cultivated octoploid strawberry, the approach reveals a multi-step evolutionary history shaped by successive allopolyploidization events, offering a clearer picture of how complex plant genomes assemble and diversify over millions of years.
Whole-genome duplication has repeatedly reshaped plant genomes and driven evolutionary innovation, ecological adaptation, and crop diversification. In allopolyploid species, chromosomes originate from different ancestral genomes, forming multiple subgenomes that diverge and interact over time. Identifying these subgenomes is essential for understanding genome evolution, yet traditional methods rely heavily on known diploid progenitors, which are often extinct or unknown. Transposable elements, especially long terminal repeat retrotransposons, accumulate in lineage-specific patterns and retain molecular traces of past evolutionary events. However, robust frameworks for translating these patterns into reliable subgenome assignments have broad gaps. Based on these challenges, there is a need to develop new strategies to reconstruct polyploid genome evolution in the absence of known progenitor genomes.
Researchers from the U.S. Department of Agriculture and collaborating institutions reported a new bioinformatic framework in Horticulture Research, published (DOI: 10.1093/hr/uhaf132) on May 21, 2025, that reconstructs the evolutionary history of complex polyploid genomes. Using a serial similarity matrix approach based on long terminal repeat retrotransposons, the team reassessed the genome of cultivated octoploid strawberry (Fragaria × ananassa). Their analysis clarifies subgenome structure and identifies multiple ancient genome-merging events that shaped the modern strawberry, resolving long-standing debates about its evolutionary origin.
The researchers developed a method that tracks genome evolution through three conceptual phases: before progenitor species diverged, during their independent evolution, and after genome merger. Long terminal repeat retrotransposons proliferating during the divergence phase retain subgenome-specific signatures. By calculating similarity matrices of these elements across chromosomes and examining clustering patterns at different similarity thresholds, the team created a “serial similarity matrix” that captures evolutionary signals across time.
The method was first validated in well-characterized allopolyploid crops, including teff and cotton, where it correctly separated known subgenomes and distinguished pre- and post-polyploidization events. It was also tested on artificially constructed polyploid genomes, confirming its sensitivity to divergence time and transposon abundance.
Applied to octoploid strawberry, the approach identified four distinct subgenomes and revealed three sequential allopolyploidization events occurring between approximately 3.1–4.2, 1.9–3.1, and 0.8–1.9 million years ago. The analysis supports close relationships between two strawberry subgenomes and Fragaria vesca and Fragaria iinumae, while challenging earlier models that proposed additional diploid progenitors. The results indicate that extinct or unsampled relatives likely contributed to strawberry genome formation, highlighting the complexity of polyploid evolution.
“This work demonstrates how transposable elements can function as evolutionary time stamps embedded in plant genomes,” said one of the study's senior authors. “By focusing on when and where these elements expanded, we can reconstruct genome history even when direct ancestral references are missing. This method provides a powerful new lens for studying polyploid crops and moves beyond reliance on incomplete progenitor data, offering a more objective and reproducible framework for evolutionary genomics.”
Beyond strawberry, this approach has broad implications for crop genomics and plant breeding. Many agriculturally important species—including wheat, cotton, and sugarcane—are polyploids with complex evolutionary histories. Accurate subgenome resolution can improve gene annotation, trait mapping, and comparative genomics, ultimately supporting precision breeding and crop improvement. By enabling reconstruction of genome evolution without known ancestors, the serial similarity matrix method expands the toolkit for studying biodiversity, speciation, and adaptation. It also provides a transferable framework for investigating other complex polyploid organisms, helping bridge evolutionary biology and applied agricultural science.
Publication:Haomin Lyu, Shujun Ou, Won Cheol Yim, Qingyi Yu
Deciphering octoploid strawberry evolution with serial LTR similarity matrices for subgenome partition
Horticulture Research, 12(8) 2025, uhaf132, https://doi.org/10.1093/hr/uhaf132
Far from supporting the creationist claim that genomes are fixed entities which can only be modified by divine magic, the strawberry shows the opposite. Its genome carries the evidence of duplication, hybridisation, divergence and selection — the ordinary, natural processes by which evolution produces novelty. There is no need to invoke a supernatural genetic engineer when the mechanisms are observable, testable and entirely consistent with known biology.
Nor is there anything here that even remotely violates the laws of thermodynamics, creationist claims notwithstanding. A living organism is not a closed system. It grows, reproduces and evolves by taking in energy and matter from its environment. Duplicating genes, rearranging genomes and preserving useful variation by natural selection are chemical and biological processes, not miracles. The creationist objection is not a scientific argument but a slogan, usually repeated by people who neither understand thermodynamics nor genetics. In other words, it's no more an argument against science than the mindless squawk of a trained parrot.
The cultivated strawberry is especially awkward for creationists because it is familiar, attractive and domesticated. It is not some obscure fossil or remote microbe that can be dismissed as irrelevant. It is a fruit many of us grow, pick, buy and eat, and yet inside every strawberry is a complex evolutionary history written into its chromosomes. Its sweetness and size are the products of recent human selection, but the genomic raw material on which that selection acted was supplied by deep evolutionary history.
In other words, the strawberry is not evidence of a perfect creation made for human benefit. It is evidence of an imperfect, changeable, historically contingent living organism whose genome has been repeatedly remodelled by natural processes and then further altered by human cultivation. Once again, the facts point not to a magic creator, but to evolution doing exactly what creationists insist it cannot do.
Advertisement
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
Amazon
All titles available in paperback, hardcover, ebook for Kindle and audio format.
Prices correct at time of publication. for current prices.
No comments :
Post a Comment
Obscene, threatening or obnoxious messages, preaching, abuse and spam will be removed, as will anything by known Internet trolls and stalkers, by known sock-puppet accounts and anything not connected with the post,
A claim made without evidence can be dismissed without evidence. Remember: your opinion is not an established fact unless corroborated.