Snaking Around Evolution

By: Nia Campbell, Chris Driscoll, Ethan Fultz, and Rachael McCabe (Stonehill College, BIO323 Evolution, Spring 2018)

Regressive evolution is the process where a trait is lost or becomes dysfunctional in a species over generations. This type of evolution is the opposite of constructive evolution, where a species evolves a new or more complex structure. Regressive evolution is a difficult method to use to classify species into evolutionary lineages because it often can only be identified by finding a genetic trace, such as a mutated or deleted gene in the species’s genome. In a paper published by Christopher A. Emerling in 2017, three traits found in relatives of snakes were examined in snakes for evidence of regressive evolution: presence of claw keratin, taste receptors, and light-associated genes.

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In this study, Emerling used genomes from NCBI’s Whole Genome Shotgun contig database. He used eight snake species in the infraorder Alethinophidia to carry out genomic analysis. No genomes were available from the other serpent infraorder, Scolecophidia, so they were not used in this study. This prevented confirmation of gene losses in both infraorders; however, Emerling was able to identify gene losses that took place in the stem serpent lineage. Using the snake genomes and genomes of serpent relatives, Emerling was able to compare the presence and absence of genes in all of the species. When evidence of gene dysfunction was found, the genome was compared against the NCBI database genomes using the BLAST program.

The first genes that were analyzed were those that code for keratin, the material that produces claws, hair, and scales. In this study, claw keratin was analyzed. The state of keratin genes in the snakes were compared to relatives with claws, such as lizards, to look for any differences between the two. The results of the analysis showed that the keratin gene was present in snakes but was a pseudogene in all of the species analyzed. The presence of a pseudogene indicates that the gene was mutated, in this case making the gene nonfunctional. Having the genes for claw keratin production indicates that snakes descended from ancestors that had claws, and therefore limbs, and lost them over time. This is strong evidence for regressive evolution causing limb loss in snakes.

Next, the genomes were analyzed to determine if the genes that produce taste buds were present. Like the keratin gene analysis, the snake genomes were predicted to have genes that had become nonfunctional or deleted by regressive evolution. Emerling predicted that the snakes would have no working taste buds, as many close relatives of snakes do not have taste buds. The results of this analysis showed that many snakes have lost taste buds, but all species retained at least one taste receptor. The presence of taste receptors does not support Emerling’s hypothesis that snakes evolved by regressive evolution from other species that lack taste buds completely, such as crocodiles and turtles. If the genes had been found to be completely deleted or mutated in the snakes, it would have supported the hypothesis that snakes evolved a lack of taste buds through regressive evolution. Complete lack of taste buds is common in marine species, where the salt water makes prey essentially tasteless. Because snakes still retain some of their taste receptors, the hypothesis that snakes evolved from marine species is not fully supported.

Finally, genes encoding for light sensitivity were analyzed for loss of function in the snake species. The results of the analysis showed that three out of five of the light-associated genes were intact. All eight snake species also shared four mutations that led to inactive genes. This pattern of inactive genes was found to be similar to other species such as mammals and crocodilians, supporting the hypothesis that they were lost through regressive evolution. The genes that were lost corresponded to the genes lost in vertebrates living in dim-lit environments. Because snakes have lost the same genes as these vertebrates, the hypothesis that snakes could have evolved from a nocturnal, burrowing, or deep-sea marine species is supported.

In conclusion, genomic analysis is extremely useful when trying to find evidence for regressive evolution. Deleted or mutated genes leave a clue behind as to what the ancestral traits of species could have been. Regressive evolution can also be an important tool when creating phylogenetic trees and analyzing lineages. The regressive evolution that led to loss of  claw keratin and light-associated genes in snakes gives a little more insight into what the ancestors of snakes may have looked like and what environment they may have lived in.

Link to access the article:

Citation: Emerling, C.A. 2017. Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes. Molecular Phylogenetics and Evolution 115: 40–49.

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