Rosa Rubicondior: Refuting Creationism - Evolution of Cultivated Cotton

Wild cotton, on left, has short, brown, and coarse fibers, while modern domesticated cotton has white, fine and abundant fibers. A new study led by Iowa State University scientists identified the northwestern Yucatan Peninsula in Mexico as the original source of domesticated cotton.

Photo: Corrinne Grover/Iowa State University.

Cotton’s roots trace to Yucatan Peninsula, where wild gene pool runs deepest - News Service

My last blog post looked at the evolution of the strawberry and how the evidence of multiple whole-genome duplications and speciation by hybridisation refutes several basic creationist, counter-evidential myths and articles of faith.

This post deals with the evolution and cultivation of the cotton plant, which again refutes the childish notion of divine creation, perfectly suited for use by the creator god's favourite creation, humankind, as well as the creationist article of faith that no new genetic information can arise without the direct intervention of a designer god, because this would supposedly violate the laws of thermodynamics.

As a recent paper in Proceedings of the National Academy of Sciences of the USA (PNAS), by a team of researchers including Professor Jonathan Wendel of Iowa State University, has shown, modern upland cotton, Gossypium hirsutum, is the result of thousands of years of human selection acting on naturally occurring genetic variation. The team traced its domestication to the Yucatán Peninsula in Mexico, probably to the north-western Yucatán, where wild populations still retain the deepest gene pool. Cotton was first domesticated there about 5,000 years ago, which, if creationist chronology were taken seriously, places it before the supposed genocidal global flood, which it appears to have survived along with the people who cultivated it.

The researchers found that domestication transformed a wild, perennial shrub with small bolls and short, coarse, brown fibres into the modern crop with abundant, long, fine, white fibres. This was not the result of a single act of magical design, nor of a sudden, miraculous improvement, but of long-term selection acting on many mutations of relatively small effect, accumulated and filtered over many generations.

The team also showed that, while human selection produced fibres more useful to people, it did so at a cost. Useful traits present in wild populations, such as disease resistance and salt tolerance, were left behind as farmers selected repeatedly from a restricted subset of the original wild gene pool. Each generation of selection narrowed the genetic base still further, pushing cultivated cotton through a genetic bottleneck.

The researchers reached these conclusions by comparing the genomes of cultivated cotton with those of specimens collected from wild populations across the plant's native range. Their analyses showed that domesticated cotton is most closely related to wild cotton from north-western Yucatán, where two random wild plants still show, on average, about twice as much genetic difference as two random modern cultivars.

After cultivated upland cotton spread out of the Yucatán, it eventually became the dominant cotton crop worldwide, displacing or overshadowing other cotton species that had been independently domesticated in South America, Africa and India. Today, Gossypium hirsutum, or upland cotton, accounts for about 90% of the world's cotton crop.

Background^ cotton, economics and disease. Cotton is one of the world's most important non-food crops and, by far, the most important natural fibre crop. It is woven not only into clothing and household textiles but also into the economies of many poorer countries, where it provides income, export earnings and employment for millions of small farmers, farm workers, transport workers, processors and textile workers.

Globally, cotton is grown in about 80 countries and supports about 32 million growers, benefiting more than 100 million families. Recent world production is around 26 million tonnes of cotton lint a year, with China, India, Brazil, the United States and Pakistan among the major producers or consumers. Its importance is therefore not just agricultural but industrial, social and political.

Modern upland cotton, Gossypium hirsutum, accounts for about 90% of the world's cotton crop. Yet this highly successful crop is not a perfectly designed plant, handed to humans ready-made. It is the product of thousands of years of human selection from a wild ancestor with shorter, coarser, brownish fibres. The modern crop has been reshaped by artificial selection into a plant with abundant, long, white fibres useful to people.

That selection came at a cost. Domestication and later crop improvement pushed cultivated cotton through a genetic bottleneck, narrowing its gene pool. Useful wild traits, including some forms of disease resistance and salt tolerance, were lost or left behind as farmers and breeders selected mainly for fibre quality, yield, plant form and ease of cultivation.

Cotton is susceptible to several important diseases, many of which are difficult to control once established:

Fusarium wilt - a vascular disease caused by Fusarium oxysporum f. sp. vasinfectum. It can cause stunting, yellowing, wilting and plant death. Some forms, including Race 4, are especially serious because they can attack plants without the help of nematodes and can persist in soil.

Verticillium wilt - another soil-borne vascular disease, caused by Verticillium species. It causes leaf mottling, yellowing, defoliation and loss of young bolls. The fungus can survive for long periods in soil as resistant resting structures.

Bacterial blight, or angular leaf spot - caused by Xanthomonas citri pv. malvacearum. It can infect leaves, stems and bolls, producing angular lesions, blackened stems and boll damage. It can spread through infected seed, crop debris, rain splash, irrigation water and contaminated equipment.

Seedling diseases - caused by several soil fungi and fungus-like organisms, including Pythium, Rhizoctonia and Fusarium. These can cause damping-off, poor emergence and weak crop stands.

Target spot and leaf spot diseases - foliar diseases that can reduce photosynthesis and cause premature defoliation, especially in warm, humid conditions.

Boll rots - infections of the developing cotton boll, often involving opportunistic fungi and bacteria, sometimes following insect damage or wet weather.

Texas root rot - a destructive soil-borne fungal disease in some cotton-growing regions, capable of killing plants rapidly under favourable conditions.

Nematode-associated disease - root-knot and reniform nematodes damage roots and can make plants more vulnerable to wilt diseases, especially Fusarium wilt.

In evolutionary terms, this is exactly what we would expect from domestication: useful traits for humans are exaggerated, while other traits may be reduced, lost or left behind. A crop bred for fibre quality and yield is not necessarily well equipped to resist every pathogen, tolerate every soil condition or cope with every environmental stress.

The wild cotton populations of the Yucatán therefore matter because they preserve genetic variation that modern cultivated cotton has lost. Far from supporting the idea of perfect divine design, cotton shows the familiar evolutionary pattern of descent with modification, artificial selection, trade-offs, bottlenecks and the practical importance of genetic diversity.

The paper in PNAS was accompanied by a news item from Iowa State University:

Cotton’s roots trace to Yucatan Peninsula, where wild gene pool runs deepest

Quick look

A research team led by Iowa State University botanists confirmed cotton was domesticated from a diverse population native to Mexico’s Yucatan Peninsula, a potentially fruitful target for finding genetic traits that could strengthen the world’s most important fiber crop.

There’s nothing like this in nature, Jonathan Wendel said as he showed a visitor in his Bessey Hall office the long white puffs billowing from a cotton boll – the protective flower capsule of the plant cultivated by humans for thousands of years. In the wild, cotton bolls are far smaller and hold darker, coarser and shorter fibers.

How did we get from there to here? Wendel, a distinguished professor of ecology, evolution and organismal biology at Iowa State University, has been asking that question for decades.

This is my 40th year on faculty, and I came here with this project in mind. And it took 40 years to develop the resources, tools and technologies to solve the problem.

Professor Jonathan F. Wendel, Senior author.
Department of Ecology, Evolution, and Organismal Biology
Iowa State University, Ames, IA, USA.

Wendel and a team of 19 co-authors outlined an answer in a paper published last month in the Proceedings of the National Academy of Sciences, showing that newly collected wild plant samples and advanced analysis of genomic sequencing data confirm modern cotton was domesticated from a diverse population native to Mexico’s Yucatan Peninsula.

Tracing the lineage of cotton gives scientists a better understanding of how plants evolve. But given the plant’s significance as a crop – cotton remains the most common source of natural textiles, by far – there are also direct practical benefits. Knowing where cotton came from is a genetic treasure map, pointing where to look for valuable traits such as disease resistance or salt tolerance that were lost along the way as farmers bred for other qualities.

When humans domesticate a plant, you pick from a big population and everything else is left behind. Do that for 1,000 generations, and you have a very narrow genetic base. So we’re very interested in that wild genetic diversity. We want to know what’s still out there.

Professor Jonathan F. Wendel.

Collections years in the making

Pinpointing modern cotton’s home in the Yucatan was not a surprise. Earlier studies by Wendel, a prominent expert in cotton genetics, used less precise methods to suggest the peninsula curling to the north in southeastern Mexico was a likely origin of the plant’s domestication – a process that began about 5,000 years ago.

The advent of quick, affordable genome sequencing put a more definitive determination within reach, if Wendel and his colleagues could gather a wide enough sampling of wild specimens. He’s been collecting wild cotton his whole career, scouring herbarium shelves and Caribbean coastlines for variants.

If everything you're looking at has crazy new variation, you clearly haven't reached saturation. But if the next 10 things look like the last thing you picked and everything’s forming a nice tight cluster, well, why bother to keep doubling up?

Professor Jonathan F. Wendel.

Cotton plants steadily gathered over the years were important contributions to the study, but systematic collection in known wild populations was the linchpin. Corrinne Grover, an Iowa State research scientist and assistant adjunct professor in ecology, evolution and organismal biology, led new specimen sequencing and analysis of the complex data.

Our collaborators did an amazing job sampling across the Yucatan strategically, and once we had that sequencing data it was very clear that’s where it came from.

Corrine E. Grover, co-corresponding author.
Department of Ecology, Evolution, and Organismal Biology
Iowa State University, Ames, IA, USA.

Researchers compared hundreds of cotton genomes in different ways to validate their findings, including quantifying the differences between individual genomes and mapping which are most similar. That analysis linked domestic cotton genomes most closely to the specimens from the northwest corner of Yucatan, Grover said.

Essentially, we're building huge data-powered genealogies of these plants, just like you could with people.

Professor Jonathan F. Wendel.

Mining old plants for new benefits

After cultivated cotton spread out of northwestern Yucatan, it went on to dominate the worldwide population, crowding out other varieties independently domesticated in South America, Africa and India. The species native to Mexico – Gossypium hirsutum, also called upland cotton – accounts for about 90% of cotton plants today, a takeover researchers say was based on gradual improvement as opposed to dramatic mutations.

The diversity left behind in the wild during thousands of years of selective human breeding is most concentrated in cotton’s ancestral home because domestication creates a genetic bottleneck, narrowing the gene pool in successive generations. The genomes of two random wild cotton plants from northwestern Yucatan have on average twice as many genetic differences as two random modern cultivars, researchers found.

As it turns out, cultivated cotton was poured out of a very small genetic bottleneck.

Professor Jonathan F. Wendel.

The benefits of that diversity are obvious when you walk through a greenhouse where both domestic and wild cotton are growing, Grover said. The shorter, more compact domestic plants have fluffier bolls, but their wild brethren are often in better health overall.

We know there are genetic traits in wild populations that could be useful if we can figure out what they are and get them into domesticated cotton. Now we have all this data from the Yucatan, and it’s ready to be mined.

Corrine E. Grover.

Publication:
W. Ning, M.A. Arick, J.A. Udall, C. Hsu, L. Abdala-Roberts, U. Solís-Rodríguez, Y. Briones-May, Z.V. Magbanua, O. Pechanova, C. Bustos-Segura, M.V. Clancy, S. Díaz-Cruz, A. Garnica-Cabrera, M. Mamin, J.Z. Yu, T.C.J. Turlings, G. Hu, D.G. Peterson, C.E. Grover, & J.F. Wendel
Genomic diversity and the domestication history of cotton (Gossypium hirsutum)
Proc. Natl. Acad. Sci. U.S.A. 123(21) e2607107123, https://doi.org/10.1073/pnas.2607107123 (2026).

Significance
Cultivated cotton is the most important source of natural textile fiber globally, yet the geographic origin of the modern gene pool and the amount of diversity within and among natural populations have been unclear. Here, we use extensive sampling of wild populations and comparative genome sequence to quantify the amount and patterning of wild cotton diversity across its native range. We show that the Yucatán Peninsula (México) was the center of original domestication, from which later modern annualized cultivars were derived. Our study quantifies diversity in wild cotton populations and reveals the origin of the cultivated gene pool, the genetic bottlenecks accompanying domestication, and the likely ecological and anthropogenic processes that shaped modern diversity and geographic patterning.

Abstract
Gossypium hirsutum is the leading fiber crop globally, but its origin as a domesticated plant and patterns of diversity in the wild remain to be elucidated. Here, we use extensive sampling of wild populations and comparative genome sequence data to illuminate the scope and patterning of wild cotton diversity across its native range. Analyses confirm the hypothesis that the Yucatán Peninsula (México) is the center of domestication, from which the original perennial forms and later modern annualized cultivars were derived. Population structure and phylogenomic analyses indicate that northwestern Yucatán harbors greater genetic diversity relative to smaller, geographically dispersed populations in northeastern Yucatán and the Caribbean basin. Genetic load and transposable element burden also are the lowest in northwestern Yucatán relative to other regions, consistent with its greater diversity and reflecting the effects of historical genetic bottlenecks in other populations. Populations from Florida and elsewhere in the Caribbean basin maintain unique pockets of diversity. Analyses of selection suggest that cotton domestication entailed long-term accumulation of mutations with relatively minor phenotypic effects, as opposed to a more punctuated process involving major domestication genes. Our study quantifies the scope and scale of genomic diversity in wild cotton, the origin of the cultivated gene pool, and the likely ecological and anthropogenic processes that shaped extant diversity and modern geographic patterning.

Fig. 1.

Morphology and habitat of wild G. hirsutum from the Yucatán Peninsula (México), in comparison to modern cultivars. (A) Natural coastal and inland Yucatán habitats. (B) Close-up view of a leaf (ISC accession 457839). (C) Close-up view of a flower (ISC accession 457839). Pink-to-purple petal coloration is common as flower senesces. (D) Open capsule showing the short, brownish fiber (ISC accession 457836). (E) Closed boll showing subtending bracts (ISC accession 457837). (F) Cultivated cotton field (Begonia, CC BY-SA 3.0, via Wikimedia Commons). (G) Size comparison between wild (Left) and domesticated (Right) cotton capsules. The scale bar represents 1 cm.

Fig. 2.

Field sampling and major genetic groups within wild G. hirsutum. Sample distributions are shown for (A) 158 individuals across four pairs of sites spanning the northern Yucatán (YUC) Peninsula, Mexico, from west (YUC-W) to east (YUC-E), and (B) 166 individuals across 15 sites in south- and north-western Florida (FL), USA. Distributions for Puerto Rico (PR) and Guadeloupe (GD) are Inset in the Upper Right corner of (A) and are as per (28). PCA results of five genetic groups in G. hirsutum (Gh) are shown in (C). Each genetic group is represented by a unique symbol, where colors indicate different sites or groups. PCA including the outgroups G. barbadense (Gb) and G. mustelinum (Gm) is Inset in the Upper Left corner of (C). (D and E) PCA results for Yucatán and Florida cottons, respectively, with each sample represented by a colored shape; samples from the same site share the same color. Outlier samples are connected to the major group by dashed lines (E). A neighbor-joining tree of G. hirsutum (Gh) populations is shown in (F).

W. Ning, M.A. Arick, J.A. Udall, C. Hsu, L. Abdala-Roberts, U. Solís-Rodríguez, Y. Briones-May, Z.V. Magbanua, O. Pechanova, C. Bustos-Segura, M.V. Clancy, S. Díaz-Cruz, A. Garnica-Cabrera, M. Mamin, J.Z. Yu, T.C.J. Turlings, G. Hu, D.G. Peterson, C.E. Grover, & J.F. Wendel
Genomic diversity and the domestication history of cotton (Gossypium hirsutum)
Proc. Natl. Acad. Sci. U.S.A. 123(21) e2607107123, https://doi.org/10.1073/pnas.2607107123 (2026).

Copyright: © 2026 The authors.
Published by the National Academy of Sciences of the USA. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Once again, we have a crop plant that makes perfect sense as the product of evolution, domestication, selection and historical accident, but none at all as the product of intelligent, benevolent design. Cotton was not handed to humans as a perfect, ready-made gift. It was taken from the wild, selected, reshaped and genetically narrowed by human agriculture over thousands of years.

In the process, humans exaggerated the traits they wanted — longer, finer, whiter fibres and a more manageable crop plant — while other useful traits were reduced, lost or left behind. The result was not perfection, but compromise: a productive global crop made more vulnerable by the very process that made it useful. That is not magic. It is biology.

And, inconveniently for creationists, it is biology that unfolded over a timescale that makes a nonsense of their mythology. Cotton was already being domesticated in the Yucatán about 5,000 years ago, at a time when Bible literalists would have us believe the world was either freshly created or about to be wiped clean by a global genocidal flood. Yet there is the evidence: people cultivating cotton, cotton surviving, and its descendants spreading around the world.

What the cotton genome records is not divine foresight, nor a sudden act of creation, but descent with modification, genetic diversity, selection, bottlenecks and trade-offs. In other words, it records evolution — the very thing creationists must deny, misrepresent or explain away because the evidence keeps refusing to fit their favourite origin myth.

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