Creationism in Crisis - No Doubt That Lycophytes Evolved, The Question is How?

Spikemoss, Selaginella arbuscula, Hawaiʻi.

Credit: DutraElliott (CC BY-NC-SA 4.0)

Marsh Clubmoss, Lycopodiella inundata, with sundew, Drosera rotundifolia.

Credit: Christian Fischer via Wikipedia (CC BY-SA 3.0)

A Window into Plant Evolution: The Unusual Genetic Journey of Lycophytes - Boyce Thompson Institute

Creationists who are desperate to believe they are winning the argument against evolution in the science community and converting biologists to believing in magic and a supernatural magician or two, will not want to read about the discovery by an international team of researchers concerning the evolution of a small group of plants known as lycophytes.

First, a brief introduction to lycophytes, courtesy of ChatGPT 3.5:

Tell me all about lycophytes, their life cycle and evolutionary history, please. Lycophytes are a group of vascular plants that belong to the division Lycophyta. They are among the oldest living lineages of vascular plants and have a rich evolutionary history. Lycophytes include plants like clubmosses, quillworts, and spikemosses. Here's an overview of their life cycle and evolutionary history:

Life Cycle of Lycophytes:

The life cycle of lycophytes, like other vascular plants, involves alternation of generations, with distinct haploid (gametophyte) and diploid (sporophyte) phases.

1. Spore Formation (Sporophyte Generation):
   • The dominant and visible phase is the sporophyte, which begins with the germination of a spore.
   • The spore develops into a small, independent gametophyte, often referred to as a prothallus.
2. Gamete Production (Gametophyte Generation):
   • The gametophyte produces male and female gametes (sperm and eggs).
   • Typically, the male gametes (sperm) are produced in structures called antheridia, while the female gametes (eggs) are produced in archegonia.
3. Fertilization:
   • Water is often required for the sperm to swim to the egg, facilitating fertilization.
   • After fertilization, a zygote is formed.
4. Sporophyte Development:
   • The zygote develops into a new sporophyte, which becomes the mature, visible plant.
   • The sporophyte produces spores through meiosis in specialized structures called sporangia.
5. Spore Release and Dispersal:
   • Spores are released from the sporangia and dispersed to new locations.
   • Upon landing in a suitable environment, the spore germinates, and the cycle begins anew.

Evolutionary History:

Lycophytes have a long evolutionary history, dating back to the Devonian period (approximately 419-358 million years ago). Some key points in their evolutionary history include:

1. Early Diversification:
   • Lycophytes were part of the early vascular plant radiation during the Devonian, coexisting with other early plant groups like ferns and seed plants.
2. Ancient Giants:
   • During the Carboniferous period (358-298 million years ago), some lycophytes, such as Lepidodendron and Sigillaria, grew into large tree-like forms in swampy environments.
3. Decline and Modern Forms:
   • While the giant lycophytes declined and became extinct by the end of the Carboniferous, smaller forms persisted.
   • Modern lycophytes, like clubmosses and quillworts, are much smaller and are found in a variety of habitats, ranging from moist forests to arid environments.
4. Living Representatives:
   • Today, lycophytes are represented by three main groups: clubmosses (Lycopodiaceae), spikemosses (Selaginellaceae), and quillworts (Isoetaceae).
5. Phylogenetic Position:
   • Lycophytes are part of an ancient lineage that diverged early in the evolution of vascular plants. They are not as diverse as some other plant groups, but they provide important insights into the early stages of plant evolution and the development of vascular tissues.

In summary, lycophytes have a fascinating evolutionary history, and their life cycle involves alternation of generations with distinct sporophyte and gametophyte phases. They have adapted to various environmental conditions and continue to play a role in our understanding of plant evolution.

An international team of researchers led by Dr. Fay-Wei Li of the Boyce Thomson Research Institute, Ithaca, NY, USA, have discovered that lycophytes have maintained a remarkably consistent genetic structure for over 350 million years, as explained in their published paper in PNAS.

The team sequenced the genomes of two species, Huperzia asiatica and Diphasiastrum complanatum, which diverged from a common ancestor about 350 million years ago (approximately when amphibians started to crawl onto land). Surprisingly, it was discovered that about 30% of their genes have remained in the same arrangement since their divergence, exhibiting an unusual evolutionary pattern known as synteny.

The exceptionally slow pace of genomic evolution sets these plants apart. Understanding why these plants have changed so little could reveal important aspects of plant evolution and genetics.

Professor Dr. Fay-Wei Li, co-senior senior author
Boyce Thompson Institute, Ithaca, NY, USA

This study opens a window into the past, showing us how remarkably stable the genetic makeup of these plants has been. It’s like finding a living fossil at the genetic level.

Dr. Li Wang, co-author
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture
Agricultural Genomics Institute at Shenzhen
Chinese Academy of Agricultural Sciences, Shenzhen, China

The scientists also observed a notable retention of duplicated gene copies following whole genome duplication events, which is unusual.

While a handful of duplicate genes may evolve new roles, the vast majority are lost relatively quickly through a process known as diploidization.

Dr. David Wickell, co-first author
Boyce Thompson Institute, Ithaca, NY, USA

However, the researchers found that these homosporous lycophytes often retained both sets of genes with relatively few alterations, even after hundreds of millions of years of evolution.

That homosporous lycophytes have retained so many duplicate genes and so much synteny is fascinating, a little bit surprising, and doesn’t necessarily fit with our traditional ideas of how genomes reorganize themselves after a large-scale duplication. While it’s still unclear precisely what is driving this difference, we believe that further study of homosporous plants has the potential to provide novel insights into plant genetics and evolution across all land plants. It also underscores the importance of preserving biodiversity, as these amazing plants hold vital clues to the history of life on Earth.

Dr. David Wickell.

Sadly, the full paper in PNAS is behind an expensive paywall, but the authors' statement of significance and the abstract to their paper is publicly available:

Significance

Lycophytes occupy a critical phylogenetic position sister to all other vascular plants. Unlike seed plants, they comprise heterosporous (Selaginellaceae and Isoetaceae) and homosporous (Lycopodiaceae) lineages. Homosporous plants have long been known to possess large genomes with considerably more chromosomes than heterosporous counterparts. However, limited genomic resources for homosporous lycophytes have hindered efforts to identify precise differences underlying this fundamental distinction. Here, we assembled chromosome-level genomes of homosporous lycophytes, Huperzia asiatica and Diphasiastrum complanatum. Despite 350 Mya of divergence and independent whole genome duplications, synteny is remarkably well preserved between these genomes. This, combined with significantly reduced nucleotide substitution rates, suggests a contrasting mode of genome evolution between heterosporous and homosporous lycophytes.

Abstract

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Creationists will need to ignore the fact that, even though this team of scientists discovered something unusual about the evolution of these two lycophytes, there is never any suggestion that magic and not evolution was involved in the process. The entire question is how these genomes remained so stable despite 350 million years of evolution, not whether they evolved according to the fundamentals of evolution theory.

The principle of evolution is so firmly embedded withing biological science that to anyone who understands it, it is inconceivable that anything else might account for the facts. If something unusual is discovered, the question is always, "How did this evolve”? not "What magic caused this"?

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