Thursday, 7 July 2022

Evolution News - How DNA Analysis is Adding to Our Knowledge of Evolutionary Biology

Source: OIST

Hidden in genetics: The evolutionary relationships of two groups of ancient invertebrates revealed | Okinawa Institute of Science and Technology Graduate University OIST

One of the things a study of modern biology teaches is an appreciation of just how much of an achievement was Darwin's and Wallace's Theory of Evolution by Natural Selection considering the relatively small amount of knowledge they had access to, compared to today. in fact, all they really had to go on was morphology - i.e., the outward appearance of organisms, albeit aided with a hand lens and low-powered light microscopes. They had no knowledge of genetics, nor any inkling of how information was modified in one generation and passed onto the next.

Not surprisingly, then, they got some things wrong, especially where convergent evolution gave some species the appearance of being related when in fact they were both the product of the same environmental selectors pushing their evolution towards similar solutions, but coming from different branches of the evolutionary tree. And some problems they left unresolved, because, although there reasons to suppose two very dissimilar taxons were related based on their positions in the geological column, there was no basis for placing them firmly in the tree of life as either sister groups, distant cousins, or only very distantly related as the descendants of much earlier forms that had diversified considerably over time so they were morphologically very dissimilar.

Just such a case was the relationship between two ancient groups, the Kamptozoa and Bryozoa, small marine invertebrates related to animal like snails, earthworms, leeches, and ribbon worms.

That conundrum has now been resolved using the modern science of genetics and DNA analysis - a source of information detail of which the founding fathers of modern biology could only dream.

The work was carried out by a team of scientists from the Marine Genomics Unit, Okinawa Institute of Science and Technology (OIST) Graduate University, Onna-son, Okinawa, Japan. with colleagues from the Department of Invertebrate Zoology, St. Petersburg State University, Saint-Petersburg, Russia and the Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan, led by Konstantin Khalturin of OIST. Their work is published, open access in Science Advances.

As the Okinawa Institute news release explains:
A scanning electron microscopy image of a Kamptozoa, a small aquatic invertebrate

Credit: Dr. Natalia Shunatova.
Highlights
  • Kamptozoa and Bryozoa are two phyla of small aquatic invertebrates that are related to animals like snails, earthworms, leeches, and ribbon worms.
  • But questions surrounding the precise location of these two phyla on the tree of life and how closely related they are to these other animals have always puzzled evolutionary biologists.
  • To answer these questions, researchers sequenced the transcriptome of four species of Kamptozoa and two species of Bryozoa, but to a far higher quality level than had previously been achieved. While past datasets had completeness of 20-60%, in this study, the transcriptome completeness was over 96%.
  • In doing so, the researchers revealed that the two phyla split from their relatives earlier than previous studies have suggested, and found that they form a distinct group, called Polyzoa.
  • The dataset generated from this study could also be used to answer other fundamental evolutionary questions—such as the more precise evolutionary relationships of the other animals, and how life diversified.

The evolutionary relationships of Kamptozoa and Bryozoa and their place on the tree of life have been revealed in this new study. The study found that they split from mollusks and worms earlier than expected and that they are part of a distinct group, called Polyzoa.

Kamptozoa and Bryozoa are two phyla of small aquatic invertebrates. They are related to snails and clams (collectively called mollusks), bristleworms, earthworms, and leeches (collectively called annelids), and ribbon worms (nemertea). But their precise position on the tree of life, and how closely related they are to these other animals, has always puzzled evolutionary biologists. Previous studies have consistently moved them around. What’s more, while Kamptozoa and Bryozoa were originally considered to form one group, they were separated based on their appearance and anatomy. Now, by using cutting-edge sequencing technology and powerful computational analysis, scientists from the Okinawa Institute of Science and Technology Graduate University (OIST), in collaboration with colleagues from St-Petersburg University and Tsukuba University, have revealed that the two phyla split from mollusks and worms earlier than previous studies have suggested, and thus they indeed form a distinct group.

A genome is the full set of genetic information found in every cell. It is subdivided into genes. These genes are made up of DNA base pairs and each gene contains the instructions needed to create a protein, and thus leads to the proper care and maintenance of a cell. For the instructions to be carried out, the DNA must first be transcribed into RNA. A transcriptome is the result of this, like the reflection of a genome but written in RNA base pairs rather than DNA.

We’ve shown that by using high quality transcriptomic data we can answer a long-standing question to the best of our current techniques

Our main finding is that the two phyla belong together. This result was originally proposed in the 19th century by biologists who were grouping animals based on what they looked like.

Dr. Konstantin Khalturin, lead author
Marine Genomics Unit
Okinawa Institute of Science and Technology Graduate University
Onna-son, Okinawa, Japan.
This genetic information differs among species. Those who are closely related have very similar genetic information, while a greater evolutionary distance results in more genetic differences. By using this data, researchers have improved our knowledge of animal evolution, but some questions still prove difficult to answer.

As Kamptozoa and Bryozoa are closely related to mollusks, annelids, and nemertea, small mistakes in the dataset, or missing data, can result in an incorrect placement on the evolutionary tree. Furthermore, while collecting these tiny animals, it’s easy to pick up other organisms, such as algae, that contaminate the sample. Dr. Khalturin highlighted that they were careful to avoid contamination and later screened their dataset for RNA of algae and small animals to remove any that might have come from them.

In total, the researchers sequenced the transcriptome of four species of Kamptozoa and two species of Bryozoa, but to a far higher quality level than had previously been achieved. While past datasets had completeness of 20-60%, in this study, the transcriptome completeness was over 96%.

Using these transcriptomes, they predicted proteins and compared them to similar data of 31 other species, some of which were closely related to Kamptozoa and Bryozoa, such as clams and bristleworms, and others which were more distant, such as frogs, starfish, insects, and jellyfish. The high-quality datasets meant that they could compare many different genes and proteins simultaneously. Dr. Khalturin credited the powerful computational capabilities that the researchers could access at OIST.
Copyright: © 2022 The authors.
Published by American Association for the Advancement of Science.
Open access (CC BY 4.0)
The team give more technical details in the abstract to their paper in Science Advances:
Abstract

The phylogenomic approach has largely resolved metazoan phylogeny and improved our knowledge of animal evolution based on morphology, paleontology, and embryology. Nevertheless, the placement of two major lophotrochozoan phyla, Entoprocta (Kamptozoa) and Ectoprocta (Bryozoa), remains highly controversial: Originally considered as a single group named Polyzoa (Bryozoa), they were separated on the basis of morphology. So far, each new study of lophotrochozoan evolution has still consistently proposed different phylogenetic positions for these groups. Here, we reinvestigated the placement of Entoprocta and Ectoprocta using highly complete datasets with rigorous contamination removal. Our results from maximum likelihood, Bayesian, and coalescent analyses strongly support the topology in which Entoprocta and Bryozoa form a distinct clade, placed as a sister group to all other lophotrochozoan clades: Annelida, Mollusca, Brachiopoda, Phoronida, and Nemertea. Our study favors the evolutionary scenario where Entoprocta, Cycliophora, and Bryozoa constitute one of the earliest branches among Lophotrochozoa and thus supports the Polyzoa hypothesis.

The modern science of genetics and our ability to extract and analyse the whole genome of species is proving invaluable in determining accurate relationships between species, based entirely on the theory of evolution and the knowledge that all living organisms are the product of a long, slow evolutionary process of diversification from a single common ancestor, just as Darwin and Wallace hypothesised 160 years ago. Despite over a century and a half of scientific discoveries in biology, geology and cosmology, during which almost every branch of science has had to undergo fundamental revision, each major scientific discovery has added to and confirmed the basic principles of evolutionary biology.

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