Feathery Fossil Makeovers

Photo credit to Wikimedia Commons
Photo credit to Wikimedia Commons

By Karen Zusi
BU News Service

I vividly remember learning in elementary school that scientists didn’t actually know what color the dinosaurs were. Suddenly, I could fill in the dinosaur coloring pages with pink-and-purple polka dots or rainbow stripes and nobody could tell me I was wrong. With my art teacher lamenting our lack of realism in every class project, it was like coming up for a breath of fresh air.

I was a junior in high school by the time anyone got around to telling me that dinosaurs had feathers, too. At sixteen years old, I was the youngest member of my local bird club, and Richard Prum from Yale University came to a chapter meeting to discuss whether Tyrannosaurus rex were actually covered in downy plumage. (His answer at the time was “well, sort of”). The revelation felt like a betrayal, as I’d been drawing dinosaurs with scales my whole life—but I’d just gotten into birdwatching, and I also thought it was the coolest thing ever. Over the nine years since, scientists have actually been using fossils to determine the color of these dinosaur feathers, shedding light on six-year-olds’ drawings worldwide.

We already know how the plumage of modern birds gets its color—from pigments in the feather barbs and from the microstructure of the feather itself.  Scientists suspect that dinosaur feathers functioned similarly. The pigments fall into three groups: melanins, the most common, create colors ranging from black to brown to pale yellow; porphyrins produce pinks, reds, browns, and greens; and carotenoids, acquired from eating plants, produce reds, oranges, yellows, and olive-greens. The microscopic layout of a feather also affects its appearance, depending on how the feather reflects light. Blue and iridescent feather colorings are from this structure.

Of all these pigments, melanins best survive the process of fossilization. Pockets of melanin in feather cells, called melanosomes, show up in fossils as microscopic imprints. When looked at under a powerful microscope, the size, shape, and orientation of the imprints give clues about what the feathers may have looked like. So far, fossils can’t tell us about the carotenoids or the porphyrins, but melanin can show the pattern of darker colors.

The first inkling that fossils might contain information about ancient feather color came in 2008. Scientists knew that some bird-feather fossils had microscopic imprints, but thought the imprints came from bacteria. However, Yale PhD student Jakob Vinther published a paper suggesting that the imprints were actually melanosomes. The research group at Yale confirmed this discovery with another study in 2010, opening the door for predicting color in dinosaur feathers—which is what two groups of researchers in China did the same year.

A team led by Fucheng Zhang analyzed fossil remains of Sinosauropteryx from the Chinese Academy of Sciences in Beijing. They discovered a pattern of melanosomes suggesting rufous-colored tail stripes (the brownish-orange color on robins and bluebirds). A separate team led by Quanguo Li, working with Vinther and Prum, analyzed remains of Anchiornis huxleyi and saw that the dinosaur’s body might have been black or grey with a rufous crest and white-patterned wings.

Further breakthroughs came in the following years. In 2012, PhD candidate Ryan Carney at Brown University published a paper in Nature Communications with evidence that some of Archaeopteryx’s feathers may have been black, and Li published another 2012 paper about the Microraptor, a feathered dinosaur that may have been entirely glossy-black as well.

Scientists continue to research this topic, with groups starting to investigate how the process of fossilization affects what melanosomes look like.  In 2013, researchers noted that fossilization can alter the shape and placement of melanosomes, casting some doubt on the accuracy of previous color analyses. Ornithologists also continue to research the feathers of living birds to better understand their color patterns, which facilitates easier comparisons to fossilized remains.

Without a time machine and a camera, it’s impossible to truly verify theories of dinosaur appearance. But researchers are certainly approaching a clearer understanding than my six-year-old self with her pink-and-purple polka-dotted dinosaurs—and that’s pretty cool.

Replanting the Tree of Life

Illustration by Judith Lavelle
Illustration by Judith Lavelle

By Karen Zusi
BU News Service

Charles Darwin first represented his theory of evolution with an image of the tree of life in 1859: “Of the many twigs which flourished when the tree was a great bush,” he wrote in The Origin of Species, “only two or three, now grown into great branches, yet survive and bear the other branches.” From a single root at the base of the animal kingdom, species have split and changed—some with more success than others—in new patterns represented by these branches. Closely-related species such as humans and chimpanzees share a branch until it splits into twigs at the top of the tree. Distant relatives separate much earlier; the branch for insects divides lower on the trunk than the branches joining primates and canines.

The study of these evolutionary relationships is called phylogeny, and the field involves more than answering fun questions about our relatives in the animal kingdom. By understanding evolutionary relationships, scientists can test drugs on mice, use worms to study theories about nervous system development, and breed fruit flies to investigate changes in certain genes. These models only work if scientists know how closely related these organisms are.

The placement of different branches on the tree used to be based on what animals looked and acted like, with simple animals like sponges and jellyfish rooted at the base of the tree and complex ones emerging as new growth near the crown. Humans have always occupied the branches at the top. However, the technology that sequences and compares genes has sprouted a new tree of life that, rather than being firmly rooted, tends to shift and sway—and gives rise to the idea that our ancestors may not have been so simple after all.

One of the first major shifts to the animal tree came in 1997, when James Lake at the University of California, Los Angeles, and his colleagues published an evolutionary tree that contradicted a fundamental organizing principle of evolution. Scientists had previously classified species based in part on the body cavity between the digestive organs and the outer body wall. They divided animals into one of three groups depending on whether they had a body cavity, a partial cavity, or lacked one altogether. Animals like jellyfish, sea anemones, and tapeworms don’t have one; internally, they are organized by layers of compressed tissue. Nematodes, the roundworms like hookworm and pinworm, have a partial body cavity, and complex animals like humans have a well-organized space for their organs.

Lake showed that this organization scheme using internal structures didn’t hold up when examined with DNA. The nematode branch in particular had been difficult to place on the tree because these creatures can change rapidly over generations, faster than other animals. Accumulating many genetic differences over a short period of time makes them look unrelated to groups that they’re actually close to. Lake specifically used a slowly-evolving nematode species to show that they should be grouped with arthropods—animals including fruit flies, scorpions, and lobsters. Arthropods have a fully-developed body cavity, and nematodes don’t, which tossed that organizing principle out the window. Instead, the data suggested that nematodes came from an ancestor with a body cavity and then lost it through evolution, a “regression” from complex to simple.

Lake still had to answer the question of what other features could connect nematodes and arthropods. Arthropods were previously grouped with the annelids—worms like leeches and earthworms—because both types of animals are segmented in addition to having developed body cavities. According to Lake, it was an office-chair epiphany that cemented the change for him: “I still remember sitting here at the desk going, ‘Why could they be related? What do they have?’” he says of the 1997 study. “And then I said, ‘Oh my god, they molt.’ It was like a magic moment. I sat back in my chair, and I laughed, maybe like a child, and I said ‘That’s it!’” Both arthropods and nematodes molt an outer layer of hard skin while growing. Lake’s change rearranged the tree of life’s branches, creating a new one based on this shared trait.

Gonzalo Giribet at Harvard University headed a research team at the same time that Lake published his work, and reached the same conclusion independently. Instead of using one slowly-evolving nematode species, Giribet increased the overall number of nematode species in his analysis to six. With the larger dataset, his data still showed the same results. Over the next twelve years, as genetic technology improved, other research groups across the country were able to replicate Lake’s results and create a growing body of evidence for the rearrangement. After a slow start, by 2009 the scientific community had overall accepted the change. During the 150th anniversary year of Darwin’s Origin of Species, the Royal Society of London, the world’s oldest scientific academy, held an international biology conference where every speaker endorsed Lake’s results. “By that time I knew everything was done,” he says. “It was really gratifying—it had been a big fight.” Lake was awarded the Darwin-Wallace Medal by the Linnean Society of London in 2011 for the new animal grouping.


Just as Lake’s results were gaining widespread acceptance, another study was rocking the base of the evolutionary tree. Down at the roots, sponges have traditionally been considered the most primitive animals, lacking organs, nerves, and muscles. They live underwater, stuck to rocks, and feed by drawing in water to catch food particles. Sponges are so different from any other type of animal, and so simple, that until recently it seemed almost impossible that anything could have come before them. Surely, these creatures were basic relics of a distant past.

In 2008, Casey Dunn at Brown University led a research group upending that perspective. Dunn’s team provided the first genetic information from a group of animals called ctenophores. These are the “comb jellies”—marine predators that look like blobs of jelly and swim using hair-like projections on their bodies. Until 2008, ctenophores were the only major animal group that scientists had never genetically examined. “We needed a sequence to address this void in such a critical part of the tree,” comments Andy Baxevanis, head of the Computational Genomics Unit at the National Institute of Health who was involved in later research. When Dunn’s team finally sequenced the ctenophore genes and compared them to the rest of the animal kingdom, they found that the ctenophores were so different from everything else that they had to put them at the base of the tree—in place of the sponges.

Ctenophores look more complicated than sponges: they have a nervous system and muscles, and they can move. You’d think they would occupy a higher branch than the sponges, but the story is more complicated. Scientist who have done the genetic analyses think the sponges may have had the precursors to those structures but lost them in an evolutionary “regression”—or never used the building blocks at all. “We find that somewhere way back in their distant evolutionary path, the sponges lost their ability to develop a nervous system,” says Baxevanis. Perhaps sponges simply evolved on their own to be the best filter-feeders in the world, discarding physiology they didn’t need.

Since 2008, more data has been published—including whole genomes—that continue to support the ctenophores’ early split from the rest of the animal kingdom. Researchers have discovered, among other things, that ctenophore muscles are genetically different from every other member of the animal kingdom. However, these conclusions are still hotly debated among the scientific community, especially by sponge researchers. “As soon as ctenophores became the sister group to everything else, everyone went crazy,” says James Ryan, first author of a 2013 paper expanding on Dunn’s research. The only resolution will lie in analyzing more information from different species.

Regardless of where the ctenophores end up on the tree, genetic sequencing has shown that the philosophy of evolution as a ladder of complexity is anthrocentric and outdated. Species gain and lose traits based on what helps them survive and reproduce in their environments, and sometimes that includes losing features that their ancestors had. It’s not really fair to call these changes de-evolutions—animals simply adapt as-needed so they can devote their energy to activities that matter. The shape of the animal tree of life just may be more complex than scientists ever imagined.

Fishing For Conservation: Sharks As Collateral Damage In Commercial Operations

Photo Credit: SEFSC
Photo Credit: SEFSC










By Karen Zusi
BU News Service

The prospect of casting a fishing line and snagging a shark might sound exciting to some young anglers, but for the sharks, getting accidentally caught could be a death sentence.

A study published online this summer in Global Ecology and Conservation investigated the survival rates of twelve different North Atlantic shark species in commercial longline fishing and the potential impacts on their populations. Researchers from the University of Miami found significant differences between each species; their work can be used to inform future conservation targets for sharks in the region.

Unintentional hooking of animals is a major issue in commercial fisheries management. Longlining, a method in which fishing lines with multiple baited hooks per line are released from a boat for later retrieval, often doesn’t include modifications to prevent other species from taking the bait. These longlines can catch unwanted or endangered animals like birds, sea turtles, and sharks (called “bycatch”) as well as commercially-valuable swordfish and tuna.

The shark researchers looked at seventeen years’ worth of longline fishing bycatch data to determine when each species was caught and whether an individual was dead when the line was retrieved. They then investigated factors such as water temperature and hook depth to determine which specific variables might affect each species.

One species may have 80% survival, but if it has 60% survival when you fish in much deeper water, that’s important to consider,” explained Austin Gallagher, a PhD candidate at the University of Miami and the study’s lead author. “That can be used to shed light on mechanisms that lead to mortality.”

The researchers also collated published details of shark physiology to get a picture of each species’ overall reproductive potential. By combining these datasets, the team was able to assign vulnerability scores to different types of sharks. They based the scores on how likely the sharks were to be caught in the first place, how likely they were to die when they were hooked on the line, and how well their populations could bounce back from longline mortality.

The study found that some shark species are more resilient to longlining than others. Tiger and blue sharks had over an 80% survival rate regardless of other factors, while populations of scalloped hammerhead, dusky, longfin mako, and bigeye thresher sharks were highly vulnerable under certain conditions.

Gallagher commented, “This is a huge global problem for the species that aren’t surviving. It’s a really critical thing that we have to start getting our fingers on and developing policies for.” He added that sharks serve a critical function in the environment by “eat[ing] the dead, dying, and diseased fish. They essentially clean the environment out.”

Conservation in longline fisheries is a high-stakes balancing act between protecting the animals and protecting the livelihoods of the fishers. Jordan Watson, a PhD candidate at the University of Alaska working with the National Oceanic and Atmospheric Administration to investigate new mitigation strategies, commented on Gallagher’s study and the importance of tailoring these methods: “It’s good that there are people still collecting the traditional ecological data and figuring out the biology so that we can use the mitigation measures.”

(Des Colhoun/ geograph.org.uk)
(Des Colhoun/ geograph.org.uk)

Watson’s recent work has focused on fishing gear modifications that reduce bycatch without severely lowering the catch of desired species. He continued, “I think bycatch reduction is going to be a story of small victories, and hopefully we can continue to make enough small victories that it will make an impact on the battle.”