Dinosaur color patterns reconstructed!

Excellent fossil finds in China over the last two decades have added a lot to our understanding of dinosaur diversity and the origin of feathers and birds. Two recent reports have given us a glimpse of the coloration and patterning of feathered dinosaurs, feeding the imagination of all dinosaur aficionados.

Birds themselves actually ARE dinosaurs; however, when most people say dinosaurs, they really mean "all dinosaurs except birds."

An international collaboration reported in January that specialized microscopy reveals sub-cellular, repetitive structures in the dermal layer of what’s thought to be fossilized feathers. They make a very convincing argument that the tiny structures are pigment-creating cellular subunits called melanosomes. The shape of these fossilized melanosomes is reported to be identical to the shape of  melanosomes in modern birds. This data not only strengthens the argument that these bird-like dinos really did have feathers, but also allows researchers to interpret their color pattern.

Animals today typically have two kinds of melaonosomes: oblong melanosomes produce black pigment and more spherical melanosomes produce colors ranging from reddish brown to yellow. Researchers can tell from the distribution of melanosomes that dinos known as Confuciusornis had variation of color within individual feathers. A specimen of a Sinosauropteryx dinosaur suggests that these fellas had stripes of “chestnut to reddish-brown tones” on their tails. Check out an artist’s rendition here.

Birds are thought to have descended from Theropod dinosaurs: a bipedal, primarily carnivorous group of dinos that includes the giant T. rex.

A second report in February uses similar techniques to reconstruct the appearance of Anchiornis huxleyi, the oldest known feathered dinosaur, which lived in the Late Jurassic (about 155 million years ago). The spectacular fossil described in this study allowed researchers to reconstruct the plumage pattern of the entire animal.  A. huxleyi is thought to have had dark, probably gray feathers on its body with specks of reddish-brown color on its face.  The feathers on its limbs were white and black and to top it all off, this guy had a crown of reddish-brown feathers on top of its head.  You must check out this down-right snuggly 3D projection of A. huxleyi on National Geographic’s website.

A. huxleyi’s feathered forelimbs weren’t suited for flying.  The fact that these feathers had such a variety of pattern indicates they may have been used for communication– perhaps to attract a mate of to startle an enemy.

Original reports:

Zhang et al, Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 2010.

Li et al, Plumage Color Patterns of an Extinct Dinosaur. Science 2010.

Apologies for the delay!

I’ve been busy working on applications for a couple writing programs. Please check back soon for more animal science!

Some things got shelved during application season.

Horse genome sequenced

A thoroughbred warming up before a race

The beautiful and powerful horse, critical to human exploration and farming, is the latest animal to join the genome party. The genome of a female Thoroughbred was sequenced by the Broad Institute and was reported in last week’s issue of Science.

Horses were first domesticated ~5000 years ago in Central Asia in the region now known as Khazakhstan. Evidence from the horse genome bolsters the idea that the founding gene pool of the domestic horse consisted of many, many mares and just a few busy stallions.  Researchers can tell this, in part, by looking at the sequence variation in the horse’s Y chromosome.

The genome of the horse, like the genomes of all of our animal cousins, can teach us about human disease.  Horses and humans both suffer from muscle disorders and inflammatory diseases and these diseases may have similar genetic causes.  About 15,000 of the 20,000 genes in the horse genome have a close counterpart in the human genome.

There are also many extended stretches of genes in the horse genome that are in the same chromosomal order as found in humans. This property of shared order, called synteny, can tell us many interesting things about the history of a genome. For example, the number of places in which the order of genes differs between species can tell you how closely related they are– genomes that share more syntenic regions are typically more closely related to one another than genomes that do not share as much synteny.

A leopard-spotted Appaloosa

In order to explore the genetic basis of the differences in shape, strength and speed of the world’s many horse breeds, The Horse Genome Project partially sequenced the genomes of several other breeds and identified which places in the genome differ from breed to breed.  Because certain breeds are more prone to certain diseases, this research will aid in the identification of the genetic basis of some of these maladies. The enchanting spots of the Appaloosa, for example, are likely caused by an alteration of a gene that produces a protein found in both skin cells as well as eyes called melastatin 1.  If a horse has two copies of the spotty version of melastatin 1, it will suffer from a form of night blindness.  The study’s authors have narrowed down the source of this genetic alteration to just two candidate single-letter (i.e. A, T, G, or C) changes in the melastatin 1 gene.

Monarch GPS uses circadian clock to adjust direction

Monarch butterfly in East Texas.

Every Fall, monarch butterflies begin their long-distance migration from the northern United States and southern Canada to central Mexico.  Monarchs navigate this 2000 mile journey using a combination of inputs from the sun and from their own biological clocks.  Every good Boy Scout knows that in order to navigate by the sun, you must account for the time of day because the cardinal directions’ relation to the sun changes as the sun moves across the sky. But without a wristwatch, the monarchs depend on their own internal sense of time and surprisingly, this sense of time doesn’t come from the brain, but instead comes from their antennae.

To determine which way is south (or south-west), monarch butterflies use an internal circadian clock to calibrate the information they get from the position of the sun.  Circadian clocks regulate circadian rhythms, the natural ~24-hour cycle of many organisms.  These biological clocks are composed of a molecular network of genes whose expression levels cycle up and down over the 24-hour day. Circadian clocks can be reset by external light and researchers can use artificial lighting to make changes in the internal clocks of butterflies kept indoors. A monarch that has been kept indoors with an artificial light-day cycle that is delayed from the natural light cycle will fly in the wrong direction when put outside. Their circadian clock is off-kilter and so their sun compass will be calibrated incorrectly.

It was always assumed that the circadian clock that modulates the navigation of the monarch was in the brain, since other circadian clocks are found there. However, a recent paper in Science showed that the circadian clock that helps the monarch

A pitstop on the way to Mexico.

navigate is actually found in the antennae. The study’s authors tested groups of monarchs whose antennae had removed as well as monarchs with their antennae painted black.  Both groups were able to fly as vigorously as normal butterflies, but they flew in the wrong direction, illustrating that monarchs need their antennae to properly calibrate their sun compass.

As you might expect, the authors also found that circadian-clock genes were cycling up and down in the antennae as they do in the brain. Removing the antennae did not effect the rhythm of circadian clock genes in the brain. Furthermore, input from the brain was not necessary for the oscillations of the circadian clocks of the antennae– the circadian clock genes cycled even in detached antennae cultured in a petri dish and the cycling of clock genes in the cultured antennae could be reset by artificial light conditions.

The monarch’s sun compass is found in the central brain, so it was surprising to see that the circadian clock that calibrates it is in a structure outside of the brain.  It is interesting that a neural circuit that regulates a complex behavior like migration has a major component outside of the brain.

Bees get a grip

A report from Cambridge University earlier this year shows how the cells of a certain shape on the surface of flowers can act as footholds for visiting bees and earn them some repeat customers. These footholds allow the bees to get a better grip on a flower so they can relax a bit as they sup upon the plant’s nectar.

Bee gripping a yellow snapdragon. Image credit: www.flickr.com/
photos/montaleast13/

Although most cells in a plant have smooth surfaces, the cells on the surface of petals of most flowering plants have a conical shape that make for a rough surface on the petal. The advantage of having conical cells on the surface of petals had been somewhat of a mystery until behavioral tests on bees showed that they encourage insect visitors to stop by often.

To test the idea that conical cells on petals provide a better grip for pollinators like bees, Dr. Beverly Glover and colleagues created fake flowers that were either slightly rough, replicating the fine, textured surface of flowers possessing conical cells, or that were perfectly smooth. They then tested bees’ preference to land on textured vs. smooth flowers (the bees were convinced to perform this assay by the sugary reward found in the center of all of the fake flowers). If the fake flowers were presented to the bees at a horizontal angle, the test bees exhibited no preference for either textured or smooth (about 50% of the time, the bees would land on the textured flower surface). However, if the fake flowers were presented vertically to the bees, making landing and gripping more of a challenge, the bees would land on the textured flower about 60% of the time

Using high-speed video photography, the researchers were able to watch several bees attempt to land on the fake flowers– the bees on smooth, vertical surfaces continuously scrambled their feet and were unable to stop moving their wings. In contrast, bees on the textured, vertical surface could find footholds and were able to stop beating their wings and come to a resting position– a much more efficient way to load up on energy.

The researchers were also able to test this idea on natural flowers with two strains of snapdragons– one that has the texture-causing conical cells and another that has a mutation that prevents the conical cells from forming and therefore has smooth flowers. When the researchers presented flowers at a horizontal angle to the bees, the bees visited the textured flowers about 50% of the time. However, if the flowers were presented vertically to the bees, the bees would land on wild-type, textured flowers more often than on mutant, smooth flowers– about 75% of the time. One thing to note is that the lack of conical cells on the petals of the mutant strain of snapdragons makes the flowers of the mutant to look lighter in color. This is because more white light is reflected off of the flower’s surface. The bees can detect this color difference and thus learn that the darker flowers make better landing pads.

mmm delicious nectar. Image credit: www.flickr.com/photos/audreyjm529

The authors suggest that having a good foothold and being able to rest its wings makes nectar collection easier for a bee. Bees on grippy flowers expend less energy while eating (because they’re not beating their wings and struggling to stay put) and thus the net energy gain of a nectar meal is higher on textured flowers.

Since the main job of a flower’s petals is to attract pollinators, plants with flowers that are easier to rest upon and more efficient food sources are more likely to be visited by a bee. While stopping by for some nectar, the bee picks up some pollen and can then do the plant a favor by bringing it to another plant for cross-fertilzation. This sounds like a potential example of adaptive evolution by the plant– altering the shape of its petal surface cells could give them a reproductive advantage.

Half-pint pups pack an extra copy of a signaling gene

http://www.flickr.com/
photos/sindykids

Many popular dog breeds, including daschunds, corgis, and basset hounds, exhibit traits of chondrodysplasia, a form of dwarfism that causes the dogs’ limbs to be reduced in length and often slightly curved in shape. In order to explore the genetic basis of canine chondrodysplasia, authors of a study recently published in Science used a genetic test known as association analysis to see if they could find any genetic features, or genotypes, that were associated only with short-limbed breeds and not with longer-limbed breeds. Interestingly, they found that all of the short-statured breeds had an extra copy of one of their genes, a gene that produces a molecule used in cellular signaling.

The researchers examined 76 different dog breeds, from tall to tiny, to look for genetic features specific to the short-limbed group. Using high-throughput DNA detection and sequencing technologies, the authors were able to focus in on 5 kilobases (kb) of DNA found only in the short dogs’ genomes. Within that 5 kb region, they identified an extra-copy of the gene that encodes the ligand FGF4, a signaling molecule involved in a type of cell-to-cell communication known as receptor tyrosine kinase signaling.

This second copy they found is a retrogene– a copy of a gene that arises by the reverse-transcription of the original gene’s transcript ( a messenger RNA) back into DNA.

Who ya callin' tiny?

Because it is derived from a messenger RNA (a temporary copy of a gene that directs protein production), the retrogene does not have the same regulatory regions as the original gene and therefore can be expressed at inappropriate times or places. The authors hypothesize that atypical expression of the FGF4 transcript in cartilage could lead to over-activation of its signaling pathway, which may lead to the chondrodyplastic phenotype. Indeed, many instances of dwarfism in humans are caused by over-activation of the very same specific pathway to which FGF4 belongs. This illustrates how genetic studies in our canine friends are much more than fodder for conversations amongst animal-lovers. Because humans and dogs share many genes in common, we can learn about the processes of our own development through studies in dogs.

To read in detail about this study, check out:

An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs. Science 2009.

This post originally appeared on the class blog for Advanced Genetics at UT Austin.