Monday, 10 May 2021

Evolution News - Refuting More Creationist Dogmas With Real-World Evidence

Illustration of a tree representing the legume family tree with branches representing the six subfamilies. On each branch are flowers or pods of species belonging to the subfamilies.The lines extending from the nutrient bag on the upper left corner indicate the positions of some of the proposed whole-genome duplications.

Credit: Yiyong Zhao, Chien-Hsun Huang, and Hong Ma
Massive molecular study uncovers clues to the evolution and diversification of essential plant family | Eberly College of Science

Every so often a piece of research is published that so devastates yet another Creationist dogma that it's difficult to think it wasn't through a deliberate attempt to refute Creationism.

Yet here we have another one which does that comprehensively without the least effort or intention on the part of the research team. It does it of course by revealing real-world evidence that could not exist if Creationist dogmas were based on real-world evidence.

This time it was a group of researchers from Penn State University Eberly College of science, and the Department of Biology, The Huck Institutes of the Life Sciences, PA, USA, the Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China, and the Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China, who did the work. Their findings were published last February in Molecular Plant sadly behind a paywall. However the article by Sam Sholtis in Penn State Eberly College of Science News has the details:
The most comprehensive study of the family tree for legumes, the plant family that includes beans, soybeans, peanuts, and many other economically important crop plants, reveals a history of whole-genome duplications. The study also helps to uncover the evolution of genes involved in nitrogen fixation—a key trait likely important in the evolutionary spread and diversification of legumes and vital for their use as “green manure” in agriculture. To reconstruct the family tree, researchers compared the DNA sequence of more than 1500 genes from 463 different legume species, including 391 newly sequenced species, that span the diversity of this large plant family.

Legumes make up the third largest family of flowering plants and are incredibly diverse—ranging from tiny herbs to giant trees. They are essential food crops for both humans and livestock, can be used as lumber, and have many other uses. Maybe most importantly, they can ‘fix’ nitrogen—extracting the vital nutrient from the atmosphere and storing it in nodules on their roots in a symbiotic relationship with soil bacteria—making them important as green manure to improve soil health.

This is the largest study of this kind for a single plant family. We went to great lengths to sample as many species as we could to get a broad representation of the legume family, but it is often difficult to get well-preserved specimens that we can extract DNA or RNA from, especially for species found in remote locations. Having this broad representation of species allowed us to build the most detailed nuclear-gene family tree for legumes to date.

Because for most of the species in our study we used transcriptomes and do not have entire genome sequences, we consider these as ‘proposed’ genome duplication events. These kinds of studies are kind of like solving a mystery. If you only have one or a few witnesses it might be difficult to convince a jury of your evidence, but if you have a hundred witnesses who have different perspectives and they all point to the same thing it becomes difficult to dismiss that evidence. In our case, the different species are like our witnesses. The size of our study allowed us to identify events that we might otherwise have dismissed.

Our data support the idea that nodulation and nitrogen fixation originated a single time early in the history of legumes and other related nitrogen-fixing plants and the whole-genome duplication event at the origin of legumes might have been crucial for the evolution of this process,” said Ma. “In addition to this duplication event, we are also able to see gene loss in plants that do not have the ability to nodulate, and evolutionary changes in genes that contributed to their role in nodulation.

Professor Hong Ma, Co-lead author
Huck Distinguished Research Professor of Plant Molecular Biology
Penn State
A paper describing the study, led by Penn State Professor of Biology Hong Ma, appears in the May 2021 issue of the journal Molecular Plant.

There are over 19,000 species in the legume family divided into six subfamilies and then further divided into narrower and narrower groupings based on their evolutionary relationships. There are 765 genera—the grouping one level above species—of which the team sampled members of 333. To build the family tree, the team analyzed gene sequences from the transcriptomes—the portion of the genome that is expressed as genes—of most of the 463 species and a small number of shallowly sequenced whole genomes from across legume diversity.

In addition to helping researchers understand the evolution and diversification of legumes, the new legume family tree helps to clarify the relationship between crop plants and their wild relatives. Although the close relatives of important agricultural crops are often known, studying more distant wild cousins could reveal traits that could be exploited to help plants thrive in changing environments and resist diseases or insect pests.

Across the legume family tree, the research team identified strong evidence for 28 separate whole-genome duplication events. Whole-genome duplications, evolutionary events that result in complete duplication of the entire genome, are fairly common among flowering plants and are thought to allow for functional innovation and evolutionary diversification. One of the duplication events that the team identified appears to have occurred in the ancestor of all members of the legume family.

The two largest subfamilies account for over 17,000 legume species and include all of the species with the ability to fix nitrogen. Nitrogen is an important plant nutrient—most commercial fertilizers contain a mix of nitrogen, phosphorus and potassium—so the symbiotic relationship between some legumes and the microorganisms that allow them to assimilate nitrogen from the atmosphere using root nodules has spurred their success by allowing them to colonize areas with less fertile soil. The research team also identified clues to the evolution of the genes responsible for this important trait.

Although the authors provide evidence of genome duplication and even triplication at different points in the evolution of this huge family, what they don't point out, because they are writing for biologists who understand this well enough, but what Creationists fail to grasp, is that genome duplication results in a set of 'spare' genes that are free to mutate without any loss of function because there is a functional copy of the genes as well. This is exactly how new information can arise as a result of a mutation and why mutations are not always deleterious, or 'devolutionary' (© 2019 Michael J Behe/Discovery Institute Inc) as Creationists now have to refer to it.

As any biologist would understand also, it doesn't need to be duplication of the entire genome; duplication of a chromosome or even of a section of one can also create new information and the potential for repurposing of these 'spare' genes. Genome duplication or polyploidy is a common form of mutation in plants and sometimes in animals. In the case of this large family of flowering plants, it led to diversification and new families arising - again refuting Creationist dogma that evolution can't give rise to new taxons. It both can and does.

Incidentally, did anyone spot any evidence of the impending collapse of the TOE as the best explanation for biodiversity in that article, or in the paper in Molecular Plant? Me neither. I wonder where creationists get the idea from that the TOE is about to be overthrown and replaced by a Bronze Age superstition. Perhaps someone is lying to them about that as well.

Reference:


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