Richard Hodel, a biology doctoral student in the Laboratory of Molecular Systematics & Evolutionary Genetics, explains how a recent Nature Scientific Reports study shows red mangroves in Cape Canaveral, Florida, are more closely related to mangroves on the Gulf Coast, not the Atlantic.
Hodel and his study co-authors discovered these subtle genetic differences by including data that would normally be discarded under current data-filtering standards. The study suggests these standards might be leading researchers to toss out valuable data.
Mangroves are coastal trees that occur on both the coast of Florida and throughout the Caribbean. They provide incredibly valuable ecosystem services like filtering water and providing habitat for fish and other marine invertebrates. And they also act as a barrier to storm surges due to their root structures.
One of their modes of moving around is that they drop off a propagule from the parent tree, and they can float in saltwater for a really long time and then end up in a totally new location.
We’re very interested in using things such as genetic tools to track where we’ve seen different trees move in the past. What sort of journey did they take to arrive in this place throughout history?
In a very recent study, we were able to use thousands of loci. We found that Cape Canaveral actually looks to be more closely related to some other individuals from the Gulf Coast of Florida and not the Atlantic coast.
A locus is just a position somewhere on the genome of any organism — plant, animal, human, anything. So, we use these as kind of forensic tools to figure out how they are related to one another. RAD-Seq is just a way to get lots of genetic information from many different individuals within a species simultaneously.
What we really started with was the largest unfiltered data set, so we had really no filtering on the loci. And so, at this point in a RAD-Seq study, many researchers would need to filter it down in some way. A really good question is “Are researchers just typically throwing out all this valuable data?”
What we found is that, yes, we’re throwing out way too much data unnecessarily. And some loci filtering is good, but the threshold is way lower than it typically is set in most studies.
Mangrove videos courtesy of Richard Hodel
Figures by Hodel et al. in Nature Scientific Reports
Photo of shuttle: NASA, public domain
Image of DNA: NASA, public domain
Music: “Sunny Day” by Audiobinger, licensed under CC BY-NC-SA 4.0
• Learn more about the Soltis Lab at the Florida Museum.
• Learn more about the McDaniel Lab at the University of Florida’s Department of Biology.