Model Behavior

When the Human Genome Project officially launched in 1990, its supporters believed that by identifying and ordering the genes found in human beings, they could unwrap the essence of our humanity and explain just what it meant to be human. They predicted they would find about 100,000 genes in total, since such a complex creature as man would logically have a complex genome.

They were in for a surprise.

Instead of differences, they found similarity—all humans are about 99.9 percent genetically alike—and instead of 100,000 protein-coding genes, they found just a fraction. In fact, the latest data suggests we may have as few as 19,000, on par with the genome of some nematode worms.

Once they recognized that the human genome could provide limited answers on its own, scientists in the burgeoning field of comparative genomics turned instead to other model systems. Among them is a trio of UTA biologists, who each chose a different model through which to investigate the topic. For Todd Castoe, it was snakes, while colleague Trey Fondon turned to fancy pigeons and Jeff Demuth beetles. Fueled by technological advances, the researchers are exploring the genetic mechanisms and evolutionary processes that make these creatures—and humans—tick.

Beetle Mania

In biology Associate Professor Jeff Demuth’s lab, the action centers on the order Coleoptera, more commonly known as beetles. Dr. Demuth uses the insects (mostly flour beetles) primarily because they’re easy to work with.

“We can just put them in a jar of flour, and they will interbreed with whatever we put together, so we can do some really powerful genetics by making crosses,” he says. “We can create multiple generations in my graduate students’ lifetime. They’re a great genetic model system.”

Another point in beetles’ favor is their sheer number and diversity. They are the most diverse group of animals on Earth, with more than 350,000 described species. (In comparison, mammals have about 5,000.) Beetles are thought to have been around since the time of the dinosaurs, and the extreme breadth of their genetic patterns, which have had millions of years to evolve, makes them a particularly effective tool for comparative genetics and genomics studies.

In 2010, Demuth suggested to Ph.D. student Heath Blackmon that he look at data on beetle karyotypes (a profile of the size and number of an organism’s chromosomes). Blackmon spent the next year going through the published scientific literature, ultimately building a database of 4,797 Coleoptera karyotypes compiled from 227 sources. Although the bulk of the work was finished in that first year, the publicly available database, which is hosted on UT Arlington’s website, continues to grow.

Using information from that database, Demuth and Blackmon co-authored a paper for the June 2014 issue of Genetics that looked at why some beetle lineages tend to lose the Y chromosome, which is what determines sex in many animals. The work was supported by a grant from the National Institutes of Health.

“I’m interested in how biodiversity arises,” Demuth says. “Sex chromosomes are really important to that—they’re associated with speciation rates, or how quickly new species arise. But I’m also fascinated by sex determination, how most of life comes up with two sexes, because there are so many different ways they arrive at that solution. There are XY systems, ZW systems, systems where the chromosomes all look the same but it’s just one gene that says be a male or a female. How does that happen?”

In the past, Y chromosome evolution was mostly studied in small flies (Drosophila) and mammals, but Demuth and Blackmon believed these were poor models since they didn’t provide much sex chromosome diversity. However, there are thousands of beetles that have completely different sex chromosomes from one another.

The Y chromosome is generally poorly understood—it is mostly full of repetitive elements, or “junk DNA,” which makes identifying genes difficult. Scientists believed that the Y chromosome would inevitably decay over time and be lost, as mutations are generally harmful and the Y can’t separate good mutations from bad ones by recombining maternal and paternal chromosomes (X’s can recombine in females, but Y’s are only found in males).

However, in comparing the sex chromosome transitions of 1,126 species from the main beetle suborders Adephaga and Polyphaga, Demuth and Blackmon came up with another hypothesis, one they dubbed the “fragile Y.” Although some members of Polyphaga had highly degenerated Y chromosomes, they were rarely lost, a surprising find. Noting that Polyphaga also use a distance-pairing mechanism to combine sex chromosomes, the duo hypothesized that the loss of the Y chromosome instead had to do with the way a species performs meiosis, the cell division that ultimately allows a sperm or egg to contain the correct number of chromosomes. Demuth and Blackmon successfully tested their theory against data from a parallel example, placental mammals (Eutheria) and marsupials (Metatheria).

Their theory also provides potential insight into the relatively high frequency of the most common sex-chromosome abnormality in humans, Turner syndrome (TS), which occurs in about 3 percent of all conceptions and results in 99 percent prenatal mortality. The disease is caused primarily by meiotic XY pairing mistakes in fathers and leaves potential offspring with only a single X chromosome from the mother. TS is inevitable in humans because we require the close pairing of the XY chromosomes during meiosis and need the Y chromosome to create males, but mutation makes it harder for the two to pair well.

While the “fragile Y” hypothesis won’t immediately help find a cure for TS, it does provide a perspective on similar diseases that can’t be gained just through the study of humans, or even other mammal model systems like mice (which perform meiosis more or less the same way).

Bird’s the Word

About a decade ago, after working in canine genetics, biology Assistant Professor Trey Fondon went looking for a new model system. He wanted something that would be easier to work with in a laboratory setting.

“Dogs’ diversity makes them a great system with which to make genetic discoveries, but to really prove your findings, you have to do classical genetics, which isn’t feasible in dogs,” he explains. “So for years, we tested discoveries from dogs using mice, and that ended up being very difficult, expensive, and time-consuming.”

After exploring a few options, Dr. Fondon settled on fancy pigeons. Descended from the rock pigeon (Columba livia), the birds are a domesticated version made up of hundreds of breeds. Unlike the pigeons often seen in parks—which are the feral descendants of escaped domestic pigeons—fancy pigeons come in a startling range of shapes, sizes, and colors. This is the result of painstaking work by pigeon fanciers, who through centuries of breeding have amplified naturally arising variations and created the dramatic differences we see today. And that makes the birds an excellent model for study.

Although Charles Darwin used them to try to understand genetic inheritance, fancy pigeons for the most part have been neglected in the scientific study of genetics. “But now the molecular tools have matured to the point where taking a non-model system and making it a model system can be done in very short order,” Fondon says. “We can apply them quite readily now to something we know almost nothing about and rapidly learn a great deal.”

Currently, the bulk of Fondon’s work looks at pigmentation variation in pigeons. In addition to being an easily seen trait, color has been well-researched in other model systems, so there’s already ample information about its underlying genetics. Fancy pigeons have about 30 to 40 well-characterized color traits, and geneticists currently know of about 100 to 120 genes that affect color in various other species.

“There’s a good chance that at least half of those traits are caused by genes on our list,” Fondon says. “It just comes down to figuring out which ones go with which. And since very few researchers are studying the species, it’s easy to map them in pigeons because it’s virgin territory.”

More broadly, Fondon is exploring vertebrate mutation processes. Pigmentation—a trait in pigeons that already offers the necessary inherited diversity—simply offers a way to investigate the origins of inherited variations.

“The simple answer is that they come from mutations. But that’s just a word, not an explanation,” he says. “Mutations are very diverse, and in different species, we find different patterns of mutations and different mutation rates. To answer our fundamental research questions, we have to map and identify the mutations that are responsible for expressed variations. Some traits will be relatively easy, some very difficult, and some impossible. So we pick off the easy things first, like pigmentation variation, leveraging what we already know.”

Still, Fondon believes understanding pigmentation is important in and of itself.

“Many pigmentation traits are also accompanied by neurological defects,” he explains. “The cells that produce pigment—in humans, mice, pigeons—are derived from the cells that also produce many neurons.”

As a result, many inherited pigmentary conditions in humans also have neuronal conditions, and physicians can use those pigmentary aspects of the syndrome to diagnose what’s wrong with the patient. (A white forelock, for example, is associated with some forms of Hirschsprung’s disease, caused by missing nerve cells in the colon.)

In the last two years, Fondon and his lab team have linked eight pigmentation traits to their genes and believe they’re close on a few more.

“We can’t study a trait that’s present in every member of a bird species, because to do genetics, we need variation and variation doesn’t hang around much in natural populations,” he says. “But pigeons can tell us where to look. I study them not for their own sake, but for what they can tell us about fundamental processes, which can be applied directly to many other species.”

Snake insights

Despite the many physiological and morphological differences among species, all vertebrates possess a similar number and complement of genes. But searching through the billions of base pairs in vertebrate genomes to identify the DNA differences responsible for outward variations has proved difficult.

“We took a tack early on and said that if we want to understand how changes in the genome encode for really big differences among species—particularly differences in how vertebrates function or look or are shaped—we should look for differences that were incredibly extreme,” Assistant Professor Todd Castoe says. “Our hope was that a huge phenotypic difference would equate to a huge genetic difference, and we could form these links much more easily because they’re more obvious.”

Snakes, with their elongated lungs, scale-covered eyes, highly toxic venoms, and forked tongues, fit the bill.

In the 1990s, Stephen Secor, Dr. Castoe’s collaborator and an evolutionary physiologist at the University of Alabama, was the first to research snakes’ ability to thoroughly remodel their organs upon feeding. More recently, to figure out how this trait might work on a molecular level, Castoe led a 38-person team (which also included UTA biologists Matthew Fujita and Eric Smith) that sequenced the genome of the Burmese python (Python molurus bivittatus), one of the first two snake genomes to be published. They also studied which genes were turned on and off in the python’s heart, liver, kidneys, and small intestine to understand how molecular changes directed physiological changes over a 10-day feeding period. The Proceedings of the National Academy of Sciences published the results.

Native to Southeast Asia but recently introduced into the Florida Everglades, Burmese pythons are known to partially shut down and shrink their organs to conserve energy between feedings, which can occur as rarely as once or twice a year. For 10 days after they eat, their major organs undergo an extensive remodeling—the heart can increase in mass by 50 percent and the liver by 100 percent—before their tissues re-atrophy once digestion is completed.

“Their blood also becomes like whipping cream,” Castoe adds, “filled with 40 times the amount of fat that it would take to kill a human.” This large dose of fat powers the energetically expensive task of rapidly re-growing organ tissue to digest the meal.

“All vertebrates undergo organ development during embryogenesis, and some can even increase organ size slightly upon exercise, for example. But these guys are turning it on and off like a light switch, and the scale at which it’s happening is incredible and unmatched. It’s the most extreme spike seen in any vertebrate,” he says. “So why can snakes do this, but nothing else can? All vertebrates essentially share a similar set of genes, so if we can figure out how this works in snakes, it would probably tell us something important about how we might be able to, say, grow human heart tissue or regenerate damaged kidney tissue.”

While the snake’s metabolism started out working like that of every other vertebrate, strong evolutionary selection has changed it substantially over time due to a small number of tweaks in key molecules. And since metabolic proteins are extremely difficult to work with in a lab setting, snakes provide the perfect way to search for clues.

“By understanding how evolution can modify things, and what the result is, we’re literally learning from evolution’s experiments,” Castoe says. “In some cases, we’re learning things we couldn’t test any other way.”

Moving forward, he plans to continue working on organ remodeling—comparing the python genome to that of other species—and to investigate the genes that make toxic venoms to determine exactly how they are evolutionarily born and regulated.

“In all of this work, we’re trying to pull these various features out of genomes—the features in genomes that change the physiology, morphology, and ecology of species,” Castoe says. “One of the best ways to do that is to look at the variation that’s already there. Comparative genomics takes advantage of evolutionary experiments that are impossible to recreate and learns from them.”

About Top Photo: Beetles are the world's most diverse group of animals, with more than 350,000 species.