A History Lesson, or “Phylogenetic Revelations Inspired by Molecular & Morphological Data”

Last week I spent most of my time…

…learning how to extract DNA from tissue samples …




…pipetting liquid A into liquid B to amplify segments of DNA through Polymerase Chain Reaction (PCR)




…and running gels to make sure all of that worked!


These skills are crucial for molecular biology work.

On Friday, I met with Professor Near and learned more about the project, particularly how my molecular work relates to his phylogenetic theories for E. Kennicotti. But first: what is phylogenetics?
Phylogeneticists study the evolutionary history and relationships among individuals or groups of organisms. (Thanks, Google.) We construct trees that show the links between species based on their most recent common ancestor.


This phylogenetic tree shows that A and B share a more recent common ancestor (signified by the nodes) than either does with C. Thus lineages A and B diverged more recently than lineage C.


Professor Near believes that the group known as E. Kennicotti actually contains multiple different species (Rich Harrington, E. France, M. Thomas, & T. Near unpublished). We examine this theory through phylogeography, the examination of geographic distributions of individuals in relation to their genetic lineages; morphological variation, the similarities and differences between the physical structures of individuals; and molecular variation, the similarities and differences between the genetic material of individuals.

Much work has been done already, and more lies ahead.


The Stripetail Darter, or “Etheostoma Kennicotti”

I’ll be working on a new species description of the stripetail darter, also known as Ethiostoma Kennicotti1.jpg6c946c10-9523-4951-a851-b260f86445dcOriginal.jpg

Here’s a shot of my new friend. Ken insisted that I get his good side.


Screen Shot 2016-06-27 at 11.21.34 AM


E. kennicotti is found in small rivers in the eastern US – Tennessee, Ohio, Kentucky, etc.


To do this, I’ll be analyzing the microsatellites of individuals. If you’d like the long explanation of microsatellite genotyping, click away! Here’s the short story: microsatellites are nucleotide repeats found in an individual’s genome (all of its genetic material). The repeats don’t code for anything – some DNA sequences make proteins, while other sequences like microsatellites are more of a mystery. That being said, the number of repeats differs between individuals. We will use the differences between repeat number to gauge the amount of genetic diversity between populations.


My Summer Experience with Fish, or “The Phylogenomics and the Evolution of North American Freshwater Fishes”

Are you interested in genetics? What about fish? (Think swimming in water, not fried on a plate.) When picking a trendy outfit, do you gravitate towards lab coats and safety goggles? Most importantly, how do you feel about identifying and amplifying fish genes while wearing the aforementioned trendy outfit?

Well, you’ve come to the right place. A bit about me: I’m Claire, an undergraduate student studying at Yale University. I’m originally from Texas, listen to R&B, and practice yoga. And I study Ecology & Evolutionary Biology! Because you learn the mechanics of how life works. A few months ago I learned about biology research opportunities organized and funded by the Yale Peabody Museum of Natural History. Check it out if you’re ever in the area; you can never outgrow dinosaur fossils.

So here I am, doing summer research in the Near Lab at Yale thanks to the Peabody. I don’t know too much about the evolutionary history of North American freshwater fish – yet – but I know someone who does. That would be Professor Thomas Near, the driving force behind the lab.

In his own words: “North America is home to the most species rich non-tropical fauna of freshwater fishes on Earth. Investigating the mechanisms responsible for this incredible diversity can add light to some of the oldest questions in evolutionary biology. This research involves the generation of phylogenetic trees using molecular data. A natural byproduct of this work is the discovery and description of new species.”

Translation: a lot of freshwater fish are swimming around North America, and we have yet to discover them all. If you didn’t understand all of the words in Professor Near’s research description, don’t worry. I’m writing about the things that I learn over the summer to make phylogenetics research more accessible to those of us who aren’t science encyclopedias.

Please enjoy the lovely photograph below. I’ll be in lab.