Sunday, 11 December 2022

Creationism in Crisis - How Intensive Agriculture Enabled a Pervasive Weed to Evolve

How intensive agriculture turned a wild plant into a pervasive weed | UBC Science - Faculty of Science at the University of British Columbia
A 155-year-old waterhemp herbarium specimen from the Missouri Botanical Garden Herbarium
One of the easiest ways to refute Creationism, and especially their preposterous claim that the Theory of Evolution (TOE) is about to be overthrown by mainstream science in favour of a primitive Bronze Age superstition involving imaginary supernatural entities and magic, is to show examples of evolution being observed over time.

This is exactly what an international team led by researchers from the University of British Columbia (UBC), Canada, did with regard to the common waterhemp, Amaranthus tuberculatus which has changed over time from being a relatively unimportant North American wild plant which grows near lakes and streams to becoming a pervasive agricultural weed which is almost impossible to eradicate from fields, having evolved even herbicide resistance. This adaptation has also enabled the southwestern variety to spread eastwards, interbreeding with the eastern variety and so spreading the evolved genes. Environmental change has allowed incompletely speciated varieties to come back together, interchange genes and merge back into a single variety again, in a process analogous to Homo sapiens, Denisovans and Neanderthals merging into modern humans.

In order to understand how this transformation occurred, the scientists compared 187 modern waterhemp plants, sampled from fields and neighbouring wetlands with over 100 samples preserved in herbaria since 1820. What they ended up with was a complete evolutionary history showing changes in hundreds of genes across the species genome over time. The surprising thing was that this evolution had occurred so rapidly over such a short period of time.

These had been produced by natural selection which fitted the plant to exploit the new niche produced by intensive human agriculture. A significant environmental change had resulted in a significant evolutionary change in the plant's genome, just as the TOE predicts.
The evolutionary adaptations included an ability to tolerate drought, an ability to grow rapidly and so out-compete crops, and herbicide resistance.

The research is outlined in the UBC news release:
An international team led by researchers at the University of British Columbia (UBC) compared 187 waterhemp samples from modern farms and neighbouring wetlands with more than 100 historical samples dating as far back as 1820 that had been stored in museums across North America. Much like the sequencing of ancient human and neanderthal remains has resolved key mysteries about human history, studying the plant’s genetic makeup over the last two centuries allowed the researchers to watch evolution in action across changing environments.

The genetic variants that help the plant do well in modern agricultural settings have risen to high frequencies remarkably quickly since agricultural intensification in the 1960s. The types of changes we’re imposing in agricultural environments are so strong that they have consequences in neighbouring habitats that we’d usually think were natural.

Modern farms impose a strong filter determining which plant species and mutations can persist through time. Sequencing the plant’s genes, herbicides stood out as one of the strongest agricultural filter determining which plants survive and which die.

In the absence of herbicide applications, being resistant can actually be costly to a plant, so the changes happening on the farms are impacting the fitness of the plant in the wild,

Dr. Julia M. Kreiner, lead author
Postdoctoral researcher
Department of Botany. University of British Columbia, Canada
The researchers discovered hundreds of genes across the weed’s genome that aid its success on farms, with mutations in genes related to drought tolerance, rapid growth and resistance to herbicides appearing frequently.

The findings could inform conservation efforts to preserve natural areas in landscapes dominated by agriculture. Reducing gene flow out of agricultural sites and choosing more isolated natural populations for protection could help limit the evolutionary influence of farms.

Common waterhemp is native to North America and was not always a problematic plant. Yet in recent years, the weed has become nearly impossible to eradicate from farms thanks to genetic adaptations including herbicide resistance.

While waterhemp typically grows near lakes and streams, the genetic shifts that we’re seeing allow the plant to survive on drier land and to grow quickly to outcompete crops. Waterhemp has basically evolved to become more of a weed given how strongly it’s been selected to thrive alongside human agricultural activities.

Professor Sarah Otto, co-author.
Killam University Professor
University of British Columbia, Canada.

These results highlight the enormous potential of studying historical genomes to understand plant adaptation on short timescales. Expanding this research across scales and species will broaden our understanding of how farming and climate change are driving rapid plant evolution.

Professor Stephen Wright, co-author
Professor in Ecology and Evolutionary Biology
University of Toronto, Canada
Notably, five out of seven herbicide-resistant mutations found in current samples were absent from the historical samples. Waterhemp carrying any of the seven herbicide resistant mutations have produced an average of 1.2 times as many surviving offspring per year since 1960 compared to plants that don’t have the mutations.

Understanding the fate of these variants and how they affect plants in non-farm, ‘wild’ populations is an important next step for our work.

Professor John Stinchcombe, co-author
University of Toronto.
Herbicide resistant mutations were also discovered in natural habitats, albeit at a lower frequency, which raises questions about the costs of these adaptations for plant life in non-agricultural settings.

Agricultural practices have also reshaped where particular genetic variants are found across the landscape. Over the last 60 years, a weedy southwestern variety has made an increasing progression eastward across North America, spreading their genes into local populations as a result of their competitive edge in agricultural contexts.
More technical detail is given in the team's published paper in Science:

North America has experienced a massive increase in cropland use since 1800, accompanied more recently by the intensification of agricultural practices. Through genome analysis of present-day and historical samples spanning environments over the past two centuries, we studied the effect of these changes in farming on the extent and tempo of evolution across the native range of the common waterhemp (Amaranthus tuberculatus), a now pervasive agricultural weed. Modern agriculture has imposed strengths of selection rarely observed in the wild, with notable shifts in allele frequency trajectories since agricultural intensification in the 1960s. An evolutionary response to this extreme selection was facilitated by a concurrent human-mediated range shift. By reshaping genome-wide diversity across the landscape, agriculture has driven the success of this weed in the 21st century.

Kreiner, Julia M.; Latorre, Sergio M.; Burbano, Hernán A.; Stinchcombe, John R.; Otto, Sarah P.; Weigel, Detlef; Wright, Stephen I.
Rapid weed adaptation and range expansion in response to agriculture over the past two centuries
Science; 378
(6624); pp 1079-1085; DOI: 10.1126/science.abo7293

Copyright © 2022 The Authors, published by American Association for the Advancement of Science. Reprinted by kind permission under license #5445520926459
What stands out from this work is that with over 100 genes involved in the different adaptations - drought tolerance, rapid growth, herbicide resistance, etc - is the fact that evolutionary changes can and do occur in parallel. Creationist parodies always present them as either happening in a strict sequence, one following another, or as a single event in a single individual - whichever false model gives them the least likelihood of happening by chance. This falsified figure is them presented as evidence of intelligent intervention.

With over 100 genes all free to evolve independently across an entire species of hundreds of thousands, or millions of individuals, and given the filter of natural selection, the 'right' mutations can accumulate very quickly and chance combinations with synergistic results can arise frequently. As we see in this study, most of the evolutionary changes have occurred since about 1960 when intensive agriculture began in the USA, i.e., significant evolution in a little over 60 years, driven by significant environmental changes, exactly as predicted by the Theory of Evolution by Natural Selection.

So, unless they want us to believe their magic invisible god is being deliberately obstructive of agriculture and trying to make it difficult to grow crops, Creationists need to explain why this shouldn't be regarded as evidence of evolution happening as the TOE describes it and so is evidence that the TOE is more than capable of explaining the observations as well as making testable predictions. Certainly, the mainstream scientists who carried out this study were in no doubt about the validity of the TOE and regarded it as the fundamental explanation of biology and observable biological change over time.

Thank you for sharing!

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