A Species Arises: Ancient Reef-Building Coral Duplicates Genome in Response to Changing Environmental Conditions

By: Wafae El-Arar, Brandon Haffner, Grace Pickering, and Andrew Williams (Stonehill College, BIO323: Evolution, Spring 2020)

Due to rising sea water temperatures, a life-sustaining ecosystem in our oceans is under threat. Coral reefs are dying at a daunting rate, and climate change threatens many species that rely on the reefs. The coral species that are the architects of the reefs, such as Astreopora, or star coral, and Acropora, or stony coral, are some of many under threat. Researchers Yafei Mao and Noriyuki Satoh have been studying these species in order to determine their evolutionary history, and how more information on their evolutionary history can help to better understand coral reef biodiversity and support conservation efforts.  

Acropora donei, by K. Osborne <https://commons.wikimedia.org/wiki/File:Acropora_donei,_Masig.jpg>

Stony coral most likely originated from polyploidy, meaning one of their ancestor’s genome contained two sets of the same chromosomes. Polyploidy can be helpful in the diversification of species in a lineage. An evolutionary event that commonly occurs in plants, polyploidy is the result of a whole genome (an organisms complete set of DNA, including its genes) duplication, or WGD. These events can help reduce the risk of extinction in a species. Mao and Noriyuki researched when a WGD event occurred in stony coral, what happened to the genes after the event, how the genes are expressed during development, and how the WGD plays a role in the biodiversity of the species, specifically regarding toxic proteins found in stony coral.

In order to determine information about the WGD and species relationships in Acropora, genomes of 6 species (5 Acropora and 1 Astreopora) were compared to find all instances of genes in different species that evolved from a common ancestor, or orthologs and paralogs. Orthologs occur when a species splits into two, and paralogs occur when a gene duplicates within a species. As organisms evolve farther from each other, difficulties occur when trying to distinguish orthologs. The program OrthoMCL can create groups that span multiple species designations such as families, classes, or species. The product of this program in this paper was 19,760 gene families that had similar patterns in their protein sequences.  

Another program was used to pare down the gene families into 3,461 genes that contained only one copy in each of the six species. Using these selections, a second program was used to create a family tree of the species indicating where the lineages have split and highlighting relationships. In order to determine when a WGD occurred in the species, the same program was used to pare the gene families down into 883 gene families that had paralogs in at least one of the Acropora species. 883 family trees were constructed, using coding sequences based on the amino acid alignments of the coral.

A key finding from the authors’ statistical analyses was that there was a single WGD in Acropora 28 to 36 million years ago, supported by evidence of many paralogs within the genus. An interesting finding was that some of the coral were evolving diversified toxins for unknown reasons as a result of the WGD. More research needs to be done for why these genes for toxin production evolved in the first place, but it provides us with another point that the coral evolved through polyploidy. 

Previous knowledge suggested that WGD may help species escape extinction events, when there is a large turnover in species diversity. One coral species turnover event (Oligocene-Miocene transition) was thought to have occurred around 15.97 to 33.7 million years ago. This timing correlates to that of the WGD in stony coral, which supports the idea that WGD helps organisms avoid extinction when a drastic environmental change occurs..

In the future, scientists should focus on gathering more data, as well as figuring out the molecular mechanisms that would cause a WGD. This paper is only one of the initial steps in understanding these instantaneous speciation events.

Article: Mao, Y., and N. Satoh. 2019. A Likely Ancient Genome Duplication in the Speciose Reef-Building Coral Genus, Acropora. iScience 13: 20–32.

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