URBANA, Ill. – Published today, in the journal GigaScience, is an article that presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon (Solenodon paradoxus). The endangered species is unusual not only because it is one of the very few venomous mammals, it is also one of only two species remaining from a branch of mammals that split from other insectivores during the “Age of Dinosaurs.”
The genome sequencing and analysis of this endangered animal was carried out by an international team lead by Taras K. Oleksyk from the University of Puerto Rico at Mayagüez and including Alfred Roca from the University of Illinois. While the mammalian tree of life has been heavily researched, the genome of the solenodon adds a distantly related branch to the “genome club,” allowing researchers to answer several evolutionary questions.
Solenodons’ venomous saliva flows from modified salivary glands through grooves on their sharp incisors (“solenodon” derives from the Greek for “grooved tooth”). They also have several other primitive and very unusual characteristics for a mammal: very large claws, a flexible snout with a ball-and-socket joint, and oddly positioned mammary glands.
Solenodons are not just genetically but also geographically isolated. At risk of extinction, they survive only in a few remote corners of the Caribbean islands, with one species in Cuba and the other in Hispaniola. Its nocturnal lifestyle makes it even more elusive and therefore less studied. Thus, it was crucial for the researchers to work with local experts at the Instituto Tecnológico de Santo Domingo and Universidad Autónoma de Santo Domingo and with local guides who helped them track and temporarily capture passing solenodons at night.
“Local resources are absolutely necessary for this kind of work since only they truly know their animals’ behavior,” said Juan Carlos Martinez-Cruzado, one of the lead authors from the University of Puerto Rico at Mayagüez. He added, “This project may open doors to many others to come, and we always assumed this to be one of many projects that will help research, education and conservation efforts in the Dominican Republic.”
For this project, there was more than just the challenge of obtaining the organisms for blood samples; the solenodon genome proved particularly difficult to sequence. Carrying out genomics research in remote parts of the Caribbean was not easy, particularly in terms of transporting high-quality DNA to the lab. This poor-quality DNA and a limited research budget led to spotty genetic information for each individual.
Having already ventured into the wilderness, the researchers embraced this new challenge by coming up with novel approaches to assemble the genome. First, the researchers reasoned that because the species has lived for millions of years in isolation it was somewhat inbred and would have low genetic diversity. This led to a potential work-around, because genomic datasets from each of five solenodons could be pooled to increase the coverage.
Despite initial doubts, this worked better than expected, especially when the researchers combined this with a new approach that provided a low-budget alternative for genome assembly for endangered species with low diversity.
The first author of the paper, Kirill Grigorev elaborated that, for him, the most interesting part of the research was the challenge of putting together the genome sequences in a manner “that was suitable for comparative genomics, using an amount of sequencing data much smaller than in other similar projects.”
After carrying out their assembly, the researchers had data of sufficient quality for answering many scientific questions on solenodon evolution. With regard to conservation plans, the data supports that there was a subspecies split within the Hispaniolan solenodon at least 300,000 years ago, meaning the northern and southern subspecies should be treated as two separate conservation units and may therefore require independent conservation strategies.
These data also shed light on the initial speciation event for this branch, and showed that solenodons likely diverged from other living mammals 73.6 million years ago, a remarkably ancient split that occurred while dinosaurs still roamed the earth. Oleksyk indicated that these results are relevant to “the ongoing debate on whether the solenodons have indeed survived the demise of dinosaurs after the asteroid impact in the Caribbean.
“It is difficult to determine whether the ancestors of solenodons were already in the proto-Antilles when the asteroid that killed off the dinosaurs impacted nearby, or whether their ancestors survived on the North American mainland and later dispersed onto the island,” said Alfred Roca of the University of Illinois, a co-author on the study. “Perhaps their Freddy Krueger-like claws allowed them to burrow their way to safety.”
The article, "Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola," is published in GigaScience. The research was supported, in part, by a grant from the National Science Foundation (award #1432092).