Friday 1 December 2023

Creationism in Crisis - Evolution of a Carnivorous Pitcher Plant by Gene Duplication - New Genetic Information Created Naturally

Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo
East Asian pitcher plants capture insects using their highly specialized pitcher-shaped leaves, which may have resulted from duplicated genomes.

Photo: Pierre-Louis Stenger.
Genomic study sheds light on how carnivorous Asian pitcher plants acquired signature insect trap - University at Buffalo

Unlike so many biology, geology and palaeontology papers published recently, this paper doesn't refute creationism by showing how much of Earth's history occurred before creationism's mythical 'Creation Week', although the genetic changes almost certainly did occur in the long period of 'pre-Creation' history.

Instead, it refutes two more of creationism's favourite fallacies:
  1. Genetic information can't be created without the magical assistance of a creator god. This is a fundamental axiom, taught to creationists by cult leaders such as William Dembski, who fooled them by equating 'information' with energy and citing the Third Law of Thermodynamics. It's a belief clung to despite the repeated evidence of gene duplication and repurposing of resulting redundancy.
  2. The fallacy of irreducible complexity which wrongly assumes that a complex system must have arisen as a single event and was so highly unlikely that a magic god must have created it. This is taught to them by another cult leader, Michael J. Behe, despite the evidence that 'irreducibly complex' systems can and do arise by exaptation of pre-existing, redundant structures or steps in a metabolic pathway that arise in parallel in the species gene pool, not all at once in a single event in one individual or cell.
The paper, by a large team of researchers that included Victor Albert, PhD, Empire Innovation Professor in the University at Buffalo Department of Biological Sciences, within the College of Arts and Sciences, concerns the evolution of the carnivorous East Asian pitcher plant, Nepenthes gracilis, in particular the 'pitcher' traps and the condition of dioecy, which is unique in this genus of plants.

And, just in case creationists declare that mere gene duplication wouldn't create enough new genetic information, this species doesn't have just one or a few genes duplicated and repurposed; they don't even stick with a whole genome duplication, They actually have five whole genome duplications making them decaploid, an extreme example of polyploidy!

Do you have anything on the organisation of polyploid genomes into sub-genomes? The complex genome of Nepenthes gracilis is organised into sub-genomes: The organization of polyploid genomes into sub-genomes is a complex and dynamic process that can vary across different species. Polyploidy refers to the condition where an organism has multiple sets of chromosomes. There are two main types of polyploidy: autopolyploidy and allopolyploidy.
  1. Autopolyploidy:
    • In autopolyploidy, an individual has multiple sets of chromosomes derived from the same species. This can happen through the duplication of the entire genome.
  2. Allopolyploidy:
    • Allopolyploidy involves the combination of chromosome sets from different species. This can occur through hybridization between two distinct species followed by genome duplication.
The organization of sub-genomes in polyploids can be characterized by several processes:
  • Homeologous Chromosomes:
    • In both autopolyploids and allopolyploids, duplicated chromosomes are called homeologous chromosomes. These chromosomes are similar but may have small differences due to evolutionary divergence.
  • Genomic Rearrangements:
    • After polyploidization events, genomic rearrangements may occur. These can involve changes in the order and orientation of genes, as well as other structural modifications.
  • Sub-genome Dominance:
    • In some polyploid species, one of the sub-genomes may become dominant in terms of gene expression and function. This phenomenon is known as sub-genome dominance.
  • Gene Loss and Retention:
    • Over time, polyploid genomes may undergo gene loss or retention. Some duplicated genes may be retained for functional redundancy or neofunctionalization, while others may be lost.
  • Epigenetic Modifications:
    • Epigenetic modifications, such as DNA methylation and histone modifications, can play a role in the regulation of gene expression in polyploid genomes.
Understanding the organization of polyploid genomes often involves advanced molecular biology techniques, including next-generation sequencing and bioinformatics analyses. Researchers study the evolutionary and functional implications of polyploidy to gain insights into how these complex genomes are structured and regulated.

For specific information on the organization of polyploid genomes into sub-genomes in a particular species, it's recommended to refer to recent scientific literature and research articles related to that species or contact experts in the field of plant or animal genomics.
The team's research is explained in a press release from the University of Buffalo by Tom Dinki:
Plants’ duplicated genomes may have paved the way for specialized carnivory, separate-sexed plants

Possessing more than two complete sets of chromosomes can be a hindrance to long-term survival of a plant lineage, yet scientists are also finding evidence it’s likely behind some evolutionary innovation.

Sudden inheritance of whole suites of extra gene copies can add redundancy to an organism's regular sets of functions, actually permitting some of those copies to evolve and express in entirely new ways.

In the case of the East Asian pitcher plant, this mutational freedom may have even fine-turned its ability to capture prey and satisfy its appetite for “meat.”

That’s just one of the findings in a new study that sequences the genome of Nepenthes gracilis, a species of carnivorous plant related to Venus flytraps, as well as sundews, beets and spinach.

Our findings not only provide key insights into the adaptive landscape of the Nepenthes genome, but also broaden our understanding of how polyploidy — having multiple sets of chromosomes — can stimulate the evolution of new functions

Professor Victor A. Albert, PhD, co-senior author
Empire Innovation Professor
College of Arts and Sciences
Department of Biological Sciences
University at Buffalo, Buffalo, NY, USA.
Albert is the co-senior author of the study, which was published Thursday (Nov. 23) in Nature Plants, along with Kenji Fukushima, PhD, of the University of Würzburg in Germany. Other contributors from UB include Charlotte Lindqvist, PhD, professor of biological sciences, and PhD students Emily Caroll and Michaela Richter.

Albert’s work was supported in part by the National Science Foundation.

Recessive subgenomes are more free to change function

The idea of “man-eating plants” has long captured our macabre imaginations. Pitcher plants, however, require a much smaller meal.

They capture insects using their highly specialized pitcher-shaped leaves. The bottom of their pitchers are filled with digestive fluids that drown and eventually break down prey. This process releases nutrients, such as nitrogen and phosphate, that allow pitcher plants to thrive in nutrient-poor habitats.

“Plant carnivory is something of a hunt for fertilizer,” Albert says.

In a 1992 study, Albert and colleagues discovered that the Asian, Australian and American pitcher plants possess similar features despite having evolved independently. Later research published in 2017 showed that each of these species co-opted many of the same ancient proteins.

In this new study, Albert and Fukushima’s teams discovered that the specialized pitcher trap of the Asian pitcher plant, or Nepenthes, may have been promoted by polyploidy. Nepenthes’ lineage had already evolved carnivory, so the duplicated genomes may have simply tweaked its mode of capture.

The team discovered that Nepenthes has a decaploid genome in its diploid state, a complex structure almost unprecedented in flowering plants that reflects possession of five whole-genome multiples, or “subgenomes.”

The team found that the fifth subgenome is “dominant,” retaining more gene copies and expressing them at higher levels than the other four older, “recessive” subgenomes. Yet it’s the recessive subgenomes — not the dominant one — that may carry more of the key genes for Nepenthes’ specialized carnivory.

“The dominant subgenome exhibits greater influence of natural selection pressure to maintain gene functions,” Fukushima says. “Whereas the recessive subgenomes, impacted less by functional preservation, have become more free to vary over evolutionary time.”

Some of Nepenthes’ duplicate carnivory genes may have originally evolved for defending against what eventually became their prey. The enzymes that help Nepenthes break down insects’ hard exoskeletons, for example, were repurposed from those that originally shielded plants from being eaten by these animals.

This lineage of Nepenthes didn't evolve new genes to become carnivorous — they grabbed collections, or toolkits, of genes that were already there.

Professor Victor A. Albert, PhD.
One hypothesis suggests that polyploidy has a negligible effect on long-term evolution, as species with multiplicated genomes may undergo extinction at rates higher than those like humans, which have just two sets of chromosomes. Yet the study’s findings add to the evidence that ancient polyploidy events can sometimes underlie evolutionary jumps still visible among plants today.

Evidence found for the evolution of separate male and female plants

Nepenthes is part of the just 6% of flowering plant species that are dioecious, meaning each individual plant produces either male or female flowers. In fact, Nepenthes is the only dioecious carnivorous plant.

Albert and Fukushima’s team also identified a male-specific region of the genome containing three genes potentially responsible for controlling these sex differences. One of these, called LEAFY, is a key gene expressed early in flower development that acts as a master regulator.

LEAFY seems to have had a duplicate form and moved into the Y chromosome region of Nepenthes, thereafter diverging in its function. This use of LEAFY is unprecedented so far in flowering plants. The LEAFY gene is such a central regulator across flowering plants that, when artificially added or deleted through genetic engineering, it will change a plant’s flowering time.

Although we now have bioinformatic evidence pointing toward LEAFY being one of the key genes involved in the sex determination mechanism of Nepenthes, actually proving this is going to require further studies in living plants.

Professor Victor A. Albert, PhD.
The main body of the paper in Nature Plants is behind a paywall, but the abstract is freely available:

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.

What we have here for creationists to lie about is:
  1. New genetic information arising naturally by gene duplication and mutation, with no hint of magic or supernatural entities being involved.
  2. Evolution of 'irreducibly complex' mechanisms by cooption of redundant structures for new functions.
Both of which creationists claim can't happen because their cult leaders fool them into believing so.

Thank you for sharing!

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