Rosa Rubicondior: Creationism Refuted - A Speciation Event 9 Million Years Ago Gave Us Potatoes.

Hybridization and radiation.

Potato evolved from tomato 9 million years ago | EurekaAlert

his story could almost have been tailor-made to embarrass creationists – though, in truth, most scientific papers do that. It concerns the evolution of potatoes by a process that creationists insist never happens: speciation. Adding to their discomfort, this event took place around 9 million years before ‘Creation Week’, during that vast expanse of ‘pre-Creation’ history in which 99.9975% of Earth’s history – and life’s – unfolded.

Speciation is usually a slow, gradual process, occurring over thousands or millions of years as populations diverge under environmental pressures. But in some cases – particularly in plants – a new species can arise almost instantaneously through hybridisation, when a fertile offspring results from the cross between two different species, genetically isolated from both parents.

This latter form of speciation has now been shown to account for the evolution of the potato. Some 9 million years ago, a natural hybridisation event between a tomato-like plant and a species of Etuberosum gave rise to a new lineage. Today, there are around 107 recognised potato species in South America. While closely related to both tomatoes and Etuberosum (a genus with three species that look remarkably like potatoes), neither of those relatives produce tubers. The hybrid did – and that made all the difference.

Researchers from the Chinese Academy of Agricultural Sciences have demonstrated that this ancient hybridisation created the genetic mechanism for tuber formation. This allowed the new species to survive harsher environments by overwintering underground as stem tubers. From this key innovation sprang a radiation of new potato species, each adapting to a range of ecological niches.

And, as an added discomfort for creationists, the scientists show no signs of thinking that the known mechanisms of biological evolution were inadequate to explain how this speciation event occurred and required a special magical act of divine intervention to make it happen by creating new information in the genome.

The genetic control of tuber formation in potatoes. The genetic control of tuber formation in potatoes has been the subject of extensive research, particularly because of its agricultural importance and evolutionary significance. The newly published study in Cell (2025) offers a major advance, pinpointing the evolutionary origin and genetic mechanism behind this trait. Here's a summary of what’s currently known, drawing from both the recent paper and prior research:

Key Genes Involved in Tuber Formation

SP6A – The tuberigen gene

Function: SP6A is a mobile signal that promotes tuber initiation. It is a homologue of the FT (FLOWERING LOCUS T) gene family, which controls flowering in other plants.
Role: It acts as a systemic signalling molecule, moving from leaves (in response to environmental cues such as day length) to the stolons, where tubers form.
Induction: Under short-day conditions, SP6A is upregulated, initiating tuber formation.

IT1 – Identity of Tuber 1

Newly Identified in 2025: This gene is derived from the Etuberosum lineage.
Function: It acts synergistically with SP6A to trigger stem swelling and identity transition from stolon to tuber.
Significance: The study suggests that IT1 provides the structural developmental control, while SP6A provides the environmental trigger.

Regulatory Network and Environmental Cues

Tuber formation is influenced by both genetic factors and environmental signals, particularly:

Photoperiod (day length) – Short days promote tuberisation via SP6A.
Temperature – Cool soil temperatures favour tuber development.
Hormonal signals – Particularly gibberellins, which inhibit tuberisation, and cytokinins, which promote it.

SP6A interacts with hormonal pathways and transcription factors to form a regulatory cascade that initiates tuber growth.

Evolutionary Perspective (New Study Highlights)

The 2025 Cell study shows that tuber formation evolved via hybridisation between a tomato-like ancestor and Etuberosum ~9 million years ago.
Neither parent species could form tubers, but the hybrid combined SP6A (from tomato lineage) and IT1 (from Etuberosum), enabling tuber development for the first time.
This event gave rise to a new, tuber-forming lineage that could survive harsher climates by overwintering underground.

Practical Applications

Understanding this mechanism helps improve tuber yield and adaptation under changing climate conditions.
It also offers tools for genetic engineering in potato breeding, such as:

Manipulating SP6A for better day-length adaptability.
Targeting IT1 for tuber enhancement in non-tuberous Solanaceae.

Key Reference

Zhang, Z. et al. (2025).
Hybridisation between tomato and Etuberosum gave rise to the tuber-forming lineage of potatoes.
Cell, 188(16), 3486–3500. https://www.cell.com/cell/fulltext/S0092-8674(25)00736-6

The research has just been published in Cell. The findings are also summarised in a Cell Press news release via EurekAlert.

Potato evolved from tomato 9 million years ago
An international research team has uncovered that natural interbreeding in the wild between tomato plants and potato-like species from South America about 9 million years ago gave rise to the modern-day potato.
In a study publishing in the Cell Press journal Cell, researchers suggest this ancient evolutionary event triggered the formation of the tuber, the enlarged underground structure that stores nutrients found in plants like potatoes, yams, and taros.

Our findings show how a hybridization event between species can spark the evolution of new traits, allowing even more species to emerge. We’ve finally solved the mystery of where potatoes came from.

Sanwen Huang, corresponding author
Chinese Academy of Agricultural Sciences, China.
As one of the world’s most important crops, the potato’s origin had long puzzled scientists. In appearance, modern potato plants are almost identical to three potato-like species from Chile called Etuberosum. But these plants do not carry tubers. Based on phylogenetic analysis, potato plants are more closely related to tomatoes.

To solve this contradiction, the research team analyzed 450 genomes from cultivated potatoes and 56 of the wild potato species.

Wild potatoes are very difficult to sample, so this dataset represents the most comprehensive collection of wild potato genomic data ever analyzed.

Zhiyang Zhang, first author
Agricultural Genomics Institute, Shenzhen
Chinese Academy of Agricultural Sciences.

They found that every potato species contained a stable, balanced mix of genetic material from both Etuberosum and tomato plants, suggesting that potatoes originated from an ancient hybridization between the two.

While Etuberosum and tomatoes are distinct species, they shared a common ancestor about 14 million years ago. Even after diverging for about 5 million years, they were able to interbreed and gave rise to the earliest potato plants with tubers around 9 million years ago.

The team also traced the origins of the potato’s key tuber-forming genes, which are a combination of genetic material from each parent. They found the SP6A gene, which acts like a master switch that tells the plant when to start making tubers, came from the tomato side of the family. Another important gene called IT1, which helps control growth of the underground stems that form tubers, came from the Etuberosum side. Without either piece, the hybrid offspring would be incapable of producing tubers.

This evolutionary innovation coincided with the rapid uplift of the Andes mountains, a period when new ecological environments were emerging. With a tuber to store nutrients underground, early potatoes were able to quickly adapt to the changing environment, surviving harsh weather in the mountains.

Tubers also allow potato plants to reproduce without seeds or pollination. They grow new plants by simply sprouting from buds on the tuber. This trait allowed them to rapidly expand and fill diverse ecological niches from mild grasslands to high and cold alpine meadows in Central and South America.

Evolving a tuber gave potatoes a huge advantage in harsh environments, fueling an explosion of new species and contributing to the rich diversity of potatoes we see and rely on today.

Sanwen Huang.

Publication:
Zhang et al.
Ancient hybridization underlies tuberization and radiation of the potato lineage.
Cell (2025) doi: 10.1016/j.cell.2025.06.034.

Highlights

The potato lineage is of ancient homoploid hybrid origin
Alternate inheritance of highly divergent parental genes contributed to tuberization
Hybridization and tuberization triggered species radiation and niche expansion

Summary
Interspecific hybridization may trigger species radiation by creating allele combinations and traits. Cultivated potato and its 107 wild relatives from the Petota lineage all share the distinctive trait of underground tubers, but the underlying mechanisms for tuberization and its relationship to extensive species diversification remain unclear. Through analyses of 128 genomes, including 88 haplotype-resolved genomes, we revealed that Petota is of ancient hybrid origin, with all members exhibiting stable mixed genomic ancestry, derived from the Etuberosum and Tomato lineages ca. 8–9 million years ago. Our functional experiments further validated the crucial roles of parental genes in tuberization, indicating that interspecific hybridization is a key driver of this innovative trait. This trait, along with the sorting and recombination of hybridization-derived polymorphisms, likely triggered the explosive species diversification of Petota by enabling occupation of broader ecological niches. These findings highlight how ancient hybridization fosters key innovation and drives subsequent species radiation.

Introduction
Hybrid speciation, the recombination of different alleles and genes from distinct species, is a significant evolutionary force.1,2,3,4,5,6 Since standing genetic variation can be reassembled into combinations, via hybridization, it generates phenotypes that enable adaptation to environments and may further lead to the accelerated origin of many additional species.7,8,9,10 An evolutionary radiation in one lineage is likely to occur when ancient hybrid speciation had taken place.11,12 While ancient hybrid speciation has been detected previously,13,14,15 adaptive species radiation triggered by it, especially through the key innovation, remains unexplored. Here, we not only show that the cultivated potato and its 107 wild relatives are derived from an ancient hybrid speciation event, but also that tuber formation itself, a key innovative trait, has a hybrid ancestry.

The cultivated potato (Solanum tuberosum L.) is currently the world’s third most important staple crop, and with wheat, rice, and maize, is responsible for 80% of human caloric intake.16 Within the genus Solanum, the cultivated potato and its closely related 107 wild species comprise the monophyletic Petota lineage (hereafter referred to as Petota), which is ecologically and morphologically distinct from the closely related Etuberosum and Tomato lineages (hereafter referred to as Etuberosum and Tomato, respectively), the former being a small monophyletic lineage of three species from southern South America, and the similarly monophyletic latter consisting of 17 cultivated and wild tomato species.17,18,19,20,21,22,23 In contrast with Tomato, both Petota and Etuberosum are geophyte species (plants with underground re-sprouting organs), which enable vegetative propagation through underground stems, termed stolons in Petota and rhizomes in Etuberosum (Figure 1A).24 Additionally, Petota has specialized tuber organs, the swollen portions of stolons, which store water and carbohydrates and serve as important nutritional and reproductive organs.

Figure 1 Geographical distribution and phylogenetic conflicts

(A) The geographic distribution of Petota (golden dots), Tomato (red dots), and Etuberosum (blue dots) (excluding cultivated species) is shown based on verified georeferenced collection records.
(B) The phylogeny is depicted using 500 trees randomly sampled from the 1-Mb windows with 200-kb step size (gray lines), and a coalescent-based species tree (black lines) with all nodes resolved.
(C) A rooted concatenated tree based on four-fold degenerate sites with site concordance factor (sCF) and site discordance factor (sDF) values shown by the pie chart on each node. In the pie charts: red represents sCF proportions averaged over 100 sites, blue indicates the sDF proportions for the first alternative topology, and gray represents sDF proportions for the remaining alternative topologies. The suffixes H1 and H2 denote haplotype 1 and haplotype 2 of the haplotype-resolved genomes, respectively.

Although somatic hybridizations between Petota and Etuberosum, and between Petota and Tomato, with the same chromosome number, have been successfully produced,25,26 strong postzygotic reproductive isolations (RIs) exist between the three lineages, with artificial inter-lineage crosses producing only small aborted seeds.27 All species of Etuberosum and 35% of Tomato species are self-compatible, in contrast to mostly self-incompatible Petota species.28,29 Tomato and Etuberosum species are mainly diploids, whereas Petota species include both diploids and polyploids. Diploids in all three lineages have the same chromosome number (2n = 24) and similar chromosome morphology with extensive synteny.27,30,31 Recent studies have placed Etuberosum or Tomato as sister to Petota and have shown widespread phylogenetic conflict among the three lineages, possibly due to hybridization and/or incomplete lineage sorting (ILS).32,33 However, it is still unclear how the underlying genetic mechanisms behind morphological divergence and phylogenetic incongruence, particularly the evolutionary origin of the tuber as a pivotal human food source, are linked to this controversial relationship.

Here, we resolve this discordance by showing that Petota originated through an ancient hybridization between Tomato and Etuberosum. The consistent genomic admixture, derived from parental lineages, was observed across 101 high-quality de novo genomes and 349 re-sequenced diploid potato genomes from 57 species within Petota. In addition, we show that this ancient hybrid speciation drove both tuberization and subsequent explosive adaptive species diversification of Petota, via complementary alleles and genes from its two parental lineages. The ability to form tubers appears to represent a key innovation, enabling the Petota ancestor to reproduce asexually and expand into seasonal high-elevation habitats. Collectively, we provide a deep revolutionary understanding of the potato genomes, the origins of the tubers, and the radiation of wild potato species.

Zhang et al.
Ancient hybridization underlies tuberization and radiation of the potato lineage.
Cell (2025) doi: 10.1016/j.cell.2025.06.034.

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

The discovery of how potatoes evolved to form tubers is not just a triumph of modern genetics — it’s also a direct challenge to the core tenets of creationism. Scientists have now traced the origin of tuber formation in potatoes to a single, ancient hybridisation event between two wild plant species: a tomato-like ancestor and a member of the Etuberosum genus. Neither parent species could produce tubers, but the hybrid offspring, around 9 million years ago, combined two key genes — SP6A and IT1 — that together enabled this new lineage to survive by storing energy underground.

This is a textbook example of a natural speciation event, something creationists claim never happens. Here we see a new, fertile, and ecologically successful species arising from hybridisation — demonstrating that evolutionary innovation can be sudden as well as gradual. From that one event, over 100 potato species later evolved, adapting to diverse environments in South America.

Even more inconvenient for young-Earth creationists is the timing of this event. It occurred some 9 million years before the supposed ‘Creation Week’, during a time when, according to their beliefs, nothing existed at all. In reality, this was a period teeming with biological change — precisely the kind of evolutionary history that creationism insists cannot exist.

And perhaps even more embarrassingly, creationists claim their putative creator god created all plants and animals for its favourite creation - humans - which begs the question, why created them in South America when, according to the Bible creation myth, all the humans lived in a small part of the Middle East?

One can only imagine the intellectual contortions required to dismiss this clear, testable, and evidence-rich example of evolution in action. But then, denial of observable reality has always been a hallmark of pseudoscience. What this discovery demands is not spin or evasion, but the intellectual courage to admit when the evidence speaks for itself.

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