Paleoecology and Poop, a Perfect Pair

By Shaena Montanari
Posted: February 11, 2013

It’s time to stop feeling sheepish and discuss poop. That’s right. You may not know this, but both modern and fossil poop can tell us so much information about biology, ecology, and environments that I think we need to talk about it. Instead of saying poop one million times in this entry, I will use the more official terms us scientists use: fossil poop is called a coprolite, while modern (fresh) samples are typically called scats. Feel a little less embarrassed now?

You may be wondering how interesting a coprolite can be. After all, fossilized excrement may look funny but it surely cannot be useful, right? Well just two weeks ago in PLOS ONE we saw that a 270 million year old shark coprolite contains remains of tapeworm egg casings, which is the earliest example of vertebrate intestinal parasites (Dentzien-Dias et al. 2013). Also, fossil freshwater bivalve shells were discovered in vertebrate coprolites from the Karoo Basin in South Africa, making them the first record of any freshwater bivalve in the Early Triassic (Yates et al. 2012).

Tapeworm eggs in a shark coprolite. From Dentzien-Dias et al. 2013

More traditionally though, coprolites are used to glean ecological information relating to the animal it came from and the environment it lived in. Knowledge about the diets of extinct animals can give us an indication of past vegetation structures and help us understand how climate change can alter landscapes and food webs. Researchers out of New Zealand were able to use extinct moa coprolites for radiocarbon dating and ancient DNA analysis (Wood et al. 2012). Moa were giant herbivorous birds (up to 250 kg) that went extinct shortly after the arrival of humans on the island. Moa coprolites can give us direct evidence of moa diet, and therefore the vegetation structure of their habitat, before the arrival of humans.

Moa coprolites sampled from Wood et al. 2012

Pollen, along with DNA of both the moa and the plant remains in the coprolites were examined. 67 species of plants were identified in the coprolites, indicating the moa was a generalist browser ~6,500 BP.

In addition to diets, coprolites can also be used to obtain ancient genomes from extinct species, such as cave hyenas (Bon et al. 2012) and the first Americans (Jenkins et al. 2012). Under the right conditions, DNA will be preserved in coprolites and provide previously unknown information about genetic diversity of extinct populations and species.

Perhaps most importantly, coprolites can have a very important place in conservation paleobiology. Animal-plant (or any prey) interactions are often not preserved in the fossil record, and things like coprolites are the only record of these interactions. Conservation scientists want to know what these relationships were like before human colonization in many areas, and this is a useful proxy to determine the “natural state” of animal-environment interactions. Wood et al. 2012 describes a pollen analysis of a coprolite from a kakapo- a rare flightless parrot endemic to New Zealand. Evidence from the coprolite shows they used to feed on a cryptic root parasite, but now the ranges of these two species do not overlap, which can indicate a shifting position of the kakapo in the larger food web. Evidence from coprolites will not only help us understand biology of animals that was previously unknown, but also will allow us to see a snapshot in time of ancient environments, and this helps us learn more about what we should try and conserve. Looks like poop science might be more useful than you thought!

 

References:

Bon C, Berthonaud V, Maksud F, Labadie K, Poulain J, Artiguenave F, Wincker P, Aury JM, Elalouf JM. (2012) Coprolites as a source of information on the genome and diet of the cave hyena. Proceedings of the Royal Society B: Biological Sciences 279, (1739) 2825-2830.

Dentzien-Dias PC, Poinar G Jr, de Figueiredo AEQ, Pacheco ACL, Horn BLD, et al. (2013) Tapeworm Eggs in a 270 Million-Year-Old Shark Coprolite. PLoS ONE 8(1): e55007. doi:10.1371/journal.pone.0055007

Jenkins JL, et al. (2012) Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves. Science 337 (6091), 223-228.

Wood, J. R., Wilmshurst, J. M., Worthy, T. H., Holzapfel, A. S. and Cooper, A. (2012), A Lost Link between a Flightless Parrot and a Parasitic Plant and the Potential Role of Coprolites in Conservation Paleobiology. Conservation Biology, 26: 1091–1099. doi: 10.1111/j.1523-1739.2012.01931.x

Wood JR, Wilmshurst JM, Wagstaff SJ, Worthy TH, Rawlence NJ, et al. (2012) High-Resolution Coproecology: Using Coprolites to Reconstruct the Habits and Habitats of New Zealand’s Extinct Upland Moa (Megalapteryx didinus). PLoS ONE 7(6): e40025. doi:10.1371/journal.pone.0040025

Yates AM, Neumann FH, Hancox PJ (2012) The Earliest Post-Paleozoic Freshwater Bivalves Preserved in Coprolites from the Karoo Basin, South Africa. PLoS ONE 7(2): e30228. doi:10.1371/journal.pone.0030228

 

Category: Paleontology | Tagged | 1 Comment

Known From Fossils First

By Sarah Werning
Posted: January 29, 2013

While writing your dissertation, you come across many fascinating tidbits written as passing remarks. They are so interesting that you happily spend time chasing down the original references and learning more, only later to find them frustratingly difficult to work into your dissertation. Such is the case with this story, the tale of living animal species previously known only from fossils.

The Mountain Pygmy-possum, Burramys parvus, was first described by Robert Bloom in 1896, based on a handful of jaws he collected from Pleistocene cave deposits (~15,000 years old) in New South Wales, Australia. In 1896, scientists only recognized three families of marsupials: Phalangeridae (Australian/Papuan arboreal possums and their allies), Macropodidae (kangaroos and their allies – basically anything that lived in Australia that wasn’t a phalangerid), and Didelphidae (all North and South American marsupials). Today, living marsupials are divided into seven orders comprised a total of ~22 families. Clearly, a lot of research on marsupial diversity and relationships has been done in the last 115 years.

Burramys parvus fossil jaws

A plate from Broom’s (1896) description of the fossil marsupial, Burramys parvus.

At the time, Broom noted that the teeth and jaw anatomy of Burramys was distinct from all other marsupials (fossil or living) known at the time. Even just using partial upper and lower jaws, he could tell it wasn’t a great fit with either the Phalangeridae or the Macropodidae. Broom tentatively called it a phalanger, but based on its odd combination of anatomical features, he also proposed it could be a missing link binding the two families together.

Over the next 50 years, a few more Burramys fossils were discovered, but only fragmentary skull and jaw elements. A big part of the problem was that the rock they were preserved in was very hard, and the bone was very soft. Also, the premolar (the large blade-like tooth in the image above) sat at an angle in the jaw such that, as Broom lamented, it was “almost impossible to split the stone without breaking either the bone or the teeth”.

It wasn’t until the 1950s that a new fossil preparation technique helped free the Burramys fossils from the rock and allow their true affinities to be known. Though the limestone was tough to chip or break away with tools, it could easily be dissolved away using acetic acid, better known as vinegar. W.D.L. Ride went back to the original fossils collected by Broom, coated them with a protective layer of methyl methacrylate, poured some vinegar on them, and dissolved the rock away. He could do this because Broom had deposited the fossils in a natural history museum collection (hey, add this to your list of examples of how museum collections enable scientific research decades after specimens are originally collected).

vinegar

Acetic acid: the choice of fossil preparators and french fry enthusiasts the world over.
Image from amazon.com.

In 1956, scientists were still debating whether Burramys was some sort of weird primitive kangaroo or some sort of weird phalanger. Ride (1956) described the newly-prepared Burramys specimens in great detail and showed that while it did have some macropod-like characteristics, it was definitely much closer to the possums. Burramys shared many odd features in common with the pygmy possums, Cercartetus, a living genus then known only from Tasmania, but with fossils known from the same mainland fossil localities. Now that scientists knew which features to look for, more Burramys fossils were recognized over the next ten years, and everyone was pretty content that the great Burramys mystery had finally been solved.

In August 1966, a live Burramys parvus was discovered hanging out in a ski lodge on Mount Hotham in Victoria.

This was a spectacular find, to say the least. Ride (1970) described the event best: “The dream dreamed by every paleontologist had come true. The dry bones of the fossil had come together and were covered with sinews, flesh, and skin.”

“Sorry, brah, but I’ve just been here chilling with snow bunnies for the last eight decades.”
Image (c) Fredy Mercay, accessed from Museum Victoria

For a while, it seemed like that ski-lodge Burramys could even have been the last Burramys; it took four more years before another living animal was discovered. Since then, hundreds more have been trapped, but they’re pretty rare; possibly only 2000 or so Burramys exist in the wild and they are listed as Critically Endangered. With the whole anatomy available, subsequent studies (including DNA studies) confirmed a close relationship with Cercartetus; eventually the two genera were deemed unique enough to qualify for their own family, the Burramyidae.

Not wanting to be outdone by its sister-genus Burramys, in the 1970s, two more species of Cercartetus were discovered on the mainland. Where they were previously just known from fossils.

All I do is be cute and much easier to find in the fossil record.
Image (c) Jamie Harris and borrowed from Warra

How does this keep happening? Why are burramyids easier to find in the fossil record than in the living record? Part of this is location, location, location: Burramys is the only Australian marsupial known exclusively from alpine regions. Before its ski-lodge discovery, nobody knew to look for marsupials so high in the mountains. They also have a very specific habitat, so their distribution is restricted to just three geographically-distant populations. Another reason is that both Burramys and Cercartetus are small and nocturnal. Tiny animals (C. nanus is only ~10 grams) running around in the dead of night are hard to observe.

Another factor likely contributing to the delayed discovery of living burramyids is that they hibernate for insanely long times. What I mean by “insanely long times” is that burramyids have the longest reported hibernation of any mammal.Lots of marsupials experience daily torpor, but only seven species hibernate, including the five living burramyids (Geiser 1994). So hibernation in marsupials is weird just on its own.

To get an idea of how weird burramyid hibernation is, I’ll let the original research (Geiser 2007) on Cercartetus nanus speak for itself: “Pygmy-possums exhibited a prolonged hibernation season lasting on average for 310 days. The longest hibernation season in one individual lasted for 367 days.” So if Cercartetus wanted to check out for all of 2013, it could. Burramys is also a champion hibernator, but only checks out for 5-6 months.

Now, I have no idea what the evolutionary or ecological advantage is to waking up at the exact time of the year you started hibernating last year. But I can tell you that if you’re going to look for living burramyids, your field season is shortened by 6-10 months (maybe a year) right off the bat, just from hibernation.  I think there’s a good case to be made here that the ecology of the living burramyids helps predict why they might easier to find in the fossil record, where your field season is essentially 15,000 years long (and counting).

References:
Broom, R. 1896. On a small fossil marsupial with large grooved premolars. Proceedings of the Linnean Society of New South Wales 10: 563-567.

Geiser F. 1994. Hibernation and daily torpor in marsupials: A review. Australian Journal of Zoology 42: 1-16.

Geiser F. 2007. Yearlong hibernation in a marsupial mammal. Naturwissenschaften 94: 941-944.

Ride, WDL. 1956. The affinities of Burramys parvus Broom, a fossil phalangeroid marsupial. Proceedings of the Zoological Society of London 127: 413-429.

Ride, WDL. 1970. A Guide to the Native Mammals of Australia. Oxford University Press Australia and New Zealand. Melbourne: 249pp.

Category: Paleontology, Zoology | Tagged , , , | 4 Comments

And This is Why We Should Always Provide Our Data. . .

By Andrew Farke
Posted: January 25, 2013

For a long time now, I’ve been beating the drum of “provide your data.” If you’re willing to take take a whole mess of measurements and do a whole bunch of analyses for a published paper, why not share the raw data? New techniques and research questions continually arise, so it can be invaluable for other workers to be able to draw upon previously published databases. Although the situation is improving, it’s still far from perfect. Even today, I’m somewhat embarrassed to point out that some articles in PLOS ONE (a journal whose mission I support as advocate and volunteer academic editor) don’t provide relevant supporting data (recent examples here and here). But rather than dwell on the negatives, I want to point out a recent case study (also in PLOS ONE!) where data reuse benefited authors, journals, and science as a whole.

Derek Larson (now a graduate student at University of Toronto) and Phil Currie (a paleontologist at University of Alberta) published a massive paper in PLOS ONE concerning the identity of carnivorous dinosaur teeth. Paleontologists have a love/hate relationship with these teeth. On the one hand, they’re cool and pointy and fierce-looking. There’s nothing more thrilling than finding a tyrannosaur tooth! On the other hand, teeth kinda stink when it comes to species identification. A dromaeosaurid (“raptor”) tooth is a dromaeosaurid tooth, and you’ll never be able to get down to species level in most cases. So, museums have drawers and drawers of teeth identified as “Tyrannosauridae” or “Troodontidae” or “Dromaeosauridae”. To make matters worse, the delicate skulls and skeletons of many of these carnivores (which are useful for identifying species) are pretty stinkin’ rare.

A selection of carnivorous dinosaur teeth. These are representatives of eight tooth types that occur in rocks spanning 15 million years of evolutionary history–but the general forms surely represent more than eight biological species over this time! Figure 2 from Larson & Currie 2013.. CC-BY.

These vague tooth identifications are problematic for issues of paleoecology and evolutionary interpretations. Let’s say you have three different rock formations with dromaeosaurid teeth, spanning 10 million years of geological time. They all look pretty much the same, but it’s almost certain they represent multiple species (evidence from skeletons shows that dinosaur species just didn’t stick around for very long–a million years or so at most). This is a problem!

Skulls and skeletons of Saurornitholestes come from rocks around 76 million years old, but nearly identical teeth are found in rocks up to 10 million years younger. Odds are decent that they aren’t all the same species, though. Image by Emily Willoughby, CC-BY.

So the big question here is: can we actually find evidence that a dromaeosaurid tooth from the Hell Creek Formation (~66 million years old) is (or isn’t) the same species as a superficially similar tooth from the Dinosaur Park Formation (~76 million years old)? Or are teeth just totally useless? Fortunately, Derek and Phil found a clever work-around. By compiling measurements from over 1,200 different dinosaur teeth, they developed an analysis to look at the overall shapes of teeth from each formation. There is strength in numbers! It turns out that even though the teeth are superficially rather similar, there are subtle discrepancies in measurements between the teeth from rocks of different ages. This is thus consistent with different species at different time intervals. In other words, that dromaeosaurid tooth from 66 million years ago is probably not the same species as that tooth from 76 million years ago.

Here’s the really cool part: Derek and Phil were able to do their analysis so thoroughly and with such a large sample because other authors published measurements for theropod teeth! Although many measurements were original to the PLOS ONE paper, the great majority were from previous studies. Folks like Julia Sankey have released countless data tables of tooth measurements, mainly as a way to describe characteristics of particular specimens. Previous authors may not necessarily have been thinking of the type of analysis implemented by Derek and Phil, but nonetheless released data for others to see and use.

This is a win-win situation for everyone. Researchers Larson and Currie were able to merge the previously-published data with their own new data into a monster analysis (1,200+ data points, remember) that significantly advances science as a whole. These generous previous authors saved Larson and Currie perhaps months of work and thousands of dollars in museum travel! The previous authors also win, through increased utilization of their hard work as well as another citation for their papers. And at the basest level, the journals that allowed and encouraged massive data tables (either as supplementary information or in-text tables) win through an extra citation (which helps the almighty impact factor).

Derek and Phil are also paying it forward–all of their supporting data are accessible. If you want to re-run the analysis tonight, or add your own data, or whatever, you can do it! Here’s a big thank you to all of the folks who advance science by improving data sharing.

Citation
Larson DW, Currie PJ (2013) Multivariate analyses of small theropod dinosaur teeth and implications for paleoecological turnover through time. PLOS ONE 8(1): e54329. doi:10.1371/journal.pone.0054329 [open access]

Category: Open Access, Open Data, Paleontology, PLOS ONE | 5 Comments

So You Wanna Be a Paleoecologist? Part II

By Shaena Montanari
Posted: January 21, 2013

Paleoecology, Paleodiets, and Paleobiology

In my last entry, I explained the basics of stable isotope geochemistry for paleoecology. Now that we have covered what isotopes are and how they work, you may be wondering: what can we use them for in vertebrate paleontology? Luckily, there are loads of interesting questions that can and have been answered using stable isotope geochemistry and vertebrate fossils. I’m going to talk about a few recent papers that exemplify how great stable isotopes are for paleoecologists who are interested in vertebrates, but remember there is an enormous body of work out there for you to check out!

Ancient Food Webs

In modern ecosystems, we frequently examine food webs and dietary habits of apex predators to learn more about how animal communities interact. We also need to know this information for conservation purposes. But how have food webs and dietary niches changed over millions of years? Stable isotopes help us tease apart this complex question. In Domingo et al. (2013), an abundant fossil mammal assemblage from the Late Miocene of Spain was examined to better understand the resource partioning and habitat of extinct carnivorous mammals.

The carbon isotope values from the enamel of all taxa sampled. Carbon isotope values below -10 per mil generally reflect C3 dominated ecosystem. (Click for larger image) From Domingo et al. 2013

The δ13C values of the herbivores indicated this environment was mostly a pure C3 environment, dominated by wooded areas. There were statistically significant dietary differences between two of the sabre-toothed cats when compared with the amphicyonid, indicating dietary niche partioning between top predators. Examining a rich diversity of fossils in one ecosystem has allowed for a food web to be established in this region for the Late Miocene, which would not be possible without stable isotope geochemistry.

Paleodiets and Paleobiology

Stable isotopes are useful when we have enigmatic fossil taxa that have ambiguous morphologies. We often want to know: what did these animals eat? Sometimes, dental morphology cannot tell us everything we want to know about the paleodiets of a mysterious fossil taxon.

Paranthropus boisei is an ancient hominin that lived around 2 million years ago in East Africa. It possessed dental characteristics, such as low-cusped molars, which lead to the popular opinion that P. boisei ate mostly hard nuts and seeds. But, as Cerling et al. (2011) showed, carbon isotopes illustrated P. boisei actually ate mostly C4 grasses and shrubs, more than any other hominin ever studied using this method.

Carbon and oxygen isotope values for P. boisei and other vertebrates in East Africa. P. boisei has a similar to diet to hippos and equids in the area. (Click for larger image) From Cerling et al. 2011.

Stables isotopes can also elucidate the paleodiets of dinosaurs. Spinosaurs were a type of theropod dinosaur with very odd dentition that was quite crocodilian. Their conical teeth have often been thought to be a specialization for piscivory, but this is difficult to prove. By utilizing oxygen isotopes, Amiot et al. (2010) used specimens of spinosaurs from all around the world and showed their oxygen isotope composition is closer to co-occuring crocodiles and turtles than terrestrial theropods. This leads them to conclude spinosaurs may indeed have spent a large portion of their life foraging for food in aquatic environments.

These are just a few examples of how stable isotopes can be used in vertebrate paleontology to tell us more about ecology, biology, and diets of long extinct animals. Although there is a large body of work on this subject, there are still many regions of the world that remain relatively unsampled in this manner. If you want to use stable isotopes at your own field site or on a specimen you have, contact a stable isotope geochemist near you, they are always willing to help!

References 

Amiot R., et al. 2010. Oxygen isotope evidence for semi-aquatic habits among spinosaurid theropods. Geology 38, 139–142.

Cerling,T., et al. 2011. Diet of Paranthropus boisei in the early Pleistocene of East Africa. PNAS 108, (23) 9337-9341.

Domingo, M.S. 2013. Resource partioning among top predators in a Miocene food web. Proc. R. Soc. B. 280, (1750).

 

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Fishing Without a Fossil (Part 1)

By Andrew Farke
Posted: January 18, 2013

Fossils are divided into two broad categories: body fossils and trace fossils. As I tell students in my intro to paleontology class, a body fossil is (unsurprisingly) part of the body of an organism. It can be a bone, a tooth, a shell, a chunk of wood or leaf (all parts of the “body” of the plant), or any other number of miscellaneous parts and pieces. A trace fossil, on the other hand, is something left behind by the behavior of the organism. It might be a footprint, or burrow, or egg, or coprolite (fossil poo).

A steaming pile of trace fossil. . .in this case, fecal leavings attributed to an ancient mammal called an anthracothere. Photo by FunkMonk, CC BY-SA 3.0.

When people think of paleontology, they usually think of body fossils–dinosaur skeletons, fossil insects in amber, or trilobites on a slab of rock. Body fossils usually are the most useful for figuring out which plants and animals lived at a particular site, because these remains are often easily identifiable to species. Trace fossils, on the other hand, can be quite enigmatic. They are usually assigned to ichnogenera and ichnospecies, the trace fossil parallels to genera and species. Along with ichnofamilies and ichnoorders and ichno-everything-else, this whole classification system of ichnotaxa is called ichnotaxonomy. Unfortunately, ichnotaxonomy isn’t as clear-cut as classifications for body fossils. For the latter, one species gets one name. A Tyrannosaurus is always a big, toothy dinosaur. By contrast, one ichnotaxon can be made by a number of different, distantly related organisms. For example, the ichnogenus Thalassinoides is a trace that can be made by sea anemones, acorn worms, fish, or even crustaceans! As a result, many paleontologists tend to poo-poo trace fossils as so ambiguous as to be useless for most purposes.

It’s an anemone! It’s an acorn worm! It’s a crustacean! No, it’s Thalassinoides! Images in the public domain, by Mark Wilson, Parent Géry, Philcha, and USGS.

Thankfully (and perhaps unsurprisingly), trace fossils often provide unique information about the resident animals in long-gone environments, as well as the nature of these environments. Some tracks and burrows are so distinct that they can come from only one type of critter doing one type of behavior–and every once in awhile, it’s something pretty cool!

The Maevarano Formation of northwestern Madagascar has yielded a huge sample of animals from the end of the Age of Dinosaurs, at least 66 million years old. Lots of nifty dinosaurs are represented, including the toothy carnivore Majungasaurus and the long-necked sauropod Rapetosaurus. There are also giant frogs (the appropriately-named Beelzebufo) and bizarre plant-eating crocodiles (Simosuchus), among others. Combined with careful geological investigations, it’s clear that prehistoric Madagascar was a fairly nasty place. Harsh dry seasons gave way to heavy rains that rolled thick and muddy debris flows across the coastal plain, burying the bones of recent victims of the inhospitable climate. This was an adequate place to be a dinosaur or land-savvy crocodile, but not a good place for most kinds of fish. In fact, fish fossils are fairly rare compared to those of other animals (particularly in the well-studied region around the village of Berivotra). During my walkabouts as a member of field crews working in Berivotra, I found lots of turtles and dinosaurs, frequent crocodiles, and scarce frogs, but few fish.

Exposures of rocks from the Maevarano Formation pop up between dry grassy areas outside of Berivotra, Madagascar. The highly seasonal climate is not greatly different from how it was during the end of the Mesozoic. Photo by Andy Farke, CC BY 3.0.

One particular type of fish was conspicuously absent from Late Cretaceous Madagascar–the lungfish. These close relatives of tetrapods (the four-limbed vertebrates including amphibians, lizards, dinosaurs, and mammals) are well-adapted for harsh environments. Lungfish can eke out an existence in shallow, dirty, and oxygen-poor waters (a rudimentary air-breathing lung is a handy trait in this case!), and thus fearlessly tread where other fish simply cannot. Furthermore, lungfish have extremely hard and durable tooth-plates that are a common find in many places. In fact, one site in northwestern Madagascar (perhaps 20 million years older than the rocks of the Maevarano Formation that we’ve just been talking about) was termed “Lungfish Hill” for obvious reasons. As a young graduate student, I remember being slightly thrilled at having found lungfish teeth there, and then being annoyed by not finding much else. In any case, the ~85 million year old occurrence of lungfish, combined with prime lungfish habitat around Berivotra 66 million years ago, made the lack of lungfish in the Maevarano Formation pretty puzzling. Had something happened during that 20 million year stretch to make the lungfish run away?

The modern African lungfish Protopterus, probably even less tasty than it sounds. Image in the public domain, modified from Ray 1908.

Trace fossils to the rescue! It turns out that paleontologists (me included) had just been looking in the wrong place for the wrong type of fossil. Barely 14 kilometers away from the fossil-rich rocks of Berivotra, a new discovery expanded our vision of Madagascar’s Mesozoic.

All will be revealed in Part 2.

Category: Paleontology | Tagged , , , | 3 Comments

So You Wanna Be a Paleoecologist? Part 1

By Shaena Montanari
Posted: December 31, 2012

For the better part of the past three decades, stable isotope geochemistry has become an increasingly common tool vertebrate paleontologists use to find out more about the biology and ecology of extinct organisms. The diet and ecology of an animal can often remain elusive when fossils are merely examined morphologically. Luckily, stable isotopes can tell us specific characteristics about what an animal is eating and the environments it lives in during its lifetime. Despite the fact this method is commonly used these days, there is a lot of background and jargon associated with it that many paleontologists have not been exposed to. In my two part series I am going to describe the foundations of these methods as they apply to paleontology, and then in part two I will highlight some recent work that illustrates how geochemical methods should be seen as an indispensible tool for paleontologists. Hopefully this brief description will help the method of stable isotope ecology become more accessible to all types of paleontologists!

What is an isotope?

Some elements have multiple stable forms with a different number of neutrons in the nucleus, known as isotopes. For example, a normal carbon atom has 6 protons and 6 neutrons in its nucleus, for an atomic weight of 12, but there is also a less abundant form of carbon that exists with an atomic weight of 13, meaning there are 6 protons and 7 neutrons in its nucleus. Heavier stable isotopes tend to be more rare on earth. The differing physical properties of isotopes of the same element lead to a predictable and often times systematic variation in the ratio of heavy to light isotopes in organic materials.

The two stable isotopes of carbon. Credit: S. Montanari (2012).

 

How are they measured?

Stable isotope ratios are measured using a isotope ratio mass spectrometer (IRMS). The basic mass spectrometer design has not been greatly modified since its invention by Alfred Nier in the 1940s while working on the Manhattan Project, hence the design is still called “Nier-type” today. A Nier-type IRMS is constructed of a source, flight tube, magnet, and collector cups. At the source, the sample gas is ionized and then accelerated into the flight tube. A giant magnet deflects the sample based on mass into collection cups, known as Faraday collectors. This collection creates an electrical current that is measured by a connected computer and converted into an isotope ratio. Samples are measured relative to a standard in “per mil” notation. Unknown samples are measured against known standards, which in the case of carbonates is Vienna Pee Dee Belemnite or V-PBD.

A simple schematic of an isotope ratio mass spectrometer. From Wikimedia Commons/USGS

Isotopes in the environment

As bones, teeth, and eggshells mineralize, stable isotopic signatures from the water and food an organism is consuming will be locked in and recorded. Once mineralized, this signature will not change over the life of an animal. When we find a fossil, it is possible to measure these ratios using an IRMS, as previously mentioned, but what do they tell us about the environment specifically?

Perhaps on of the most useful stable isotope systems to understand for paleoecologists is the pattern of carbon isotopic fractionation in plants.  Due to a physical isotope fractionation, C3 type plants preferentially fix 12C bearing Co2 during photosynthesis, resulting in δ13C values that are strongly discriminated from the δ13C of the atmosphere (currently ~-7‰), ranging between -35 and -25‰ depending on climate and ecology. In contrast, C4 plants have δ13C values worldwide between -15 and -11‰. C3 and C4 plants tend to grow under different climate regimes, and this clear delineation in δ13C values of these plants provides a way to track changes in ecosystems and understand dynamics of environments in deep time.

Similar predictable fractionations occur with water in the environment and water in the body of an organism, which allows oxygen isotope ratios, δ18O, to be useful for reconstructing the type of water the organism was drinking in their environment, for example, if it was highly evaporated or not. Oxygen isotope ratios recorded in tooth enamel are related to the drinking water of the organism, which is obtained from the environment. The δ18O of environmental water is determined by the δ18O of precipitation, which in turn is determined by temperature, evaporation, and the source of the precipitation air mass (Dansgaard 1964). Lighter isotopes of oxygen evaporate while heavier ones condense, meaning the greater the distance between the ocean and the air mass, rain will be lighter because heavy isotopes rainout preferentially earlier in travel of the air mass. Enrichment of δ18O is greatest under arid, hot conditions. These systematic variations in the enrichment and fractionation of oxygen isotopes allows us to glean environmental information from the δ18O contained in fossil tooth enamel.

As you can see, there is a lot that can be described surrounding stable isotope ratios in fossils. I have only touched on carbon and oxygen, which are the two most commonly used in vertebrate paleontology isotopic studies, but I will be sure to highlight others in part two of this series where I will dive more into the applications of this method in recent case studies.

Additional reading:

Dansgaard, Willi. 1964. Stable isotopes in precipitation. Tellus 16 (4): 436-468.

Koch, Paul. 2007. Isotopic study of the biology of modern and fossil vertebrates. In Stable Isotopes in Ecology and Environmental Science. 2nd ed. Boston: Blackwell Publishing.

Sulzman, E W. 2007. Stable isotope chemistry and measurement: A primer. Stable Isotopes in Ecology and Environmental Science 1-21.

Category: Background, Paleontology | Tagged , , , , | 2 Comments

Book Review: All Yesterdays

By Andrew Farke
Posted: December 28, 2012

Breathing life back into lost worlds is not an easy task–how do you paint, draw, or sculpt an animal that no human has ever seen? Perhaps as a result of this, paleontological art is full of some well-worn tropes. Tyrannosaurus running at full-tilt in perfect side view. Svelte stegosaurs with not an extra ounce of body fat or fold of skin. Brachiosaurus crossing an empty, dusty plain. Many artists are doing fantastic work, but the field really needs a wake-up, shake-up, and fresh look.

All Yesterdays, by John Conway, C. M. Kosemen, and Darren Naish (along with skeletal reconstructions from Scott Hartman), sets a new standard for how we envision dinosaurs and their prehistoric cohort. These are not “shrink-wrapped” sauropods or battling beasts. They’re living animals much weirder than the bare bones can ever tell.

All Yesterdays Cover

Thumbing my way through the 100-page softcover edition, I continually had my assumptions challenged. One second I’d be thinking “What? There’s not evidence for that!” The next I’d be thinking, “Hmm. . .it’s not in the fossil record, but it’s certainly plausible.” Both of these thoughts on the same illustration, of course! I haven’t had this much fun reading a paleontology book in years.

The authors of All Yesterdays create their magic by turning every convention of paleontological art on its head. Instead of fretting about showing only what is warranted by the fossil record and character optimization (a.k.a., the extant phylogenetic bracket), the authors show much that isn’t excluded by the fossil record. This step away from paint-by-number realism creates something truly phenomenal. Other artists, elsewhere, have made some breathtaking reconstructions of the past. But none have done it like this! Camarasaurus lolls happily in the mud. Protoceratops perch in the trees. A plesiosaur camouflages itself in the muck. These are animals happily being animals, not some 19th century taxidermy mount, or battling monsters “red in tooth and claw.” Brief and informative text accompanying each illustration highlights the knowns and unknowns, with quirky tidbits of trivia about modern animals. Even if the reconstructions are outside the norm, they are not unmoored from reality. All are scientifically rigorous in proportions, posture, environment, and known anatomy. Skeletal drawings help to underscore this point.

The illustrations are not photo-realistic, but this is a welcome relief. In many ways, they are livelier than more detailed work elsewhere. The fluffy outline of therizinosaurs feasting on leaves is only suggested by broad brush strokes, but in my mind I could fill in every extra filament and smell the cool decay of the vegetation on the forest floor. The most stylized are some of my favorites–a particularly memorable example is an amorous encounter between Stegosaurus and Camarasaurus, rendered in a black-and-orange mode reminiscent of a Greek urn.

The last half of the book jostles convention in a different way, by depicting today’s animals as if restored by paleontologists in some far-distant future. Unrecognizable rabbits and iguanas show that so much is never preserved in the fossil record! When artists stay in the shallow end of portraying only that which is absolutely known and tested, we only see the shadows of the living animals.

From the nuts-and-bolts end, the paperback edition (purchased from Lulu) was nicely bound, with an attractive glossy cover. Images were brilliantly and clearly reproduced, which is truly important for a book that relies so heavily on artwork! My only minor complaint was that a final round of copy-editing would have done some good. Many scientific names were not italicized where they should have been (almost one instance per page of text), and a few other minor typos detracted from what was otherwise a thoroughly enjoyable read. My hope is that this will get fixed in future printings. The printed book is also a tad on the expensive side ($35 through Amazon), but this is worth every penny. If you lean towards the electronic end, I would wager that the color ebook versions are just as gorgeous. But, this truly is one you’re going to want in dead-tree format. After I received this book as a Christmas gift from my wife, pretty much everyone in the household for the holidays thumbed their way through!

Congratulations to the authors on creating a truly exciting and innovative book! May it inspire others as it has inspired me.

Conway, J., C.M. Kosemen, & D. Naish. 2012. All Yesterdays: Unique and Speculative Views of Dinosaurs and Other Prehistoric Animals. Irregular Books. ISBN 978-1-291-17712-1. Softback, 100 pages. Further information at Irregular Books.

Image Credit: Protoceratops image and book cover copyright John Conway and co-authors

Category: books, Review | Leave a comment

The Field Museum faces a real threat

By Sarah Werning
Posted: December 21, 2012

I mostly want to use this forum to discuss new, exciting, and integrative paleontological research, but today I need to discuss something that is threatening new, exciting, and integrative paleontological research. Actually, the threat goes much further beyond that, because it threatens research in other types of zoology, botany, anthropology, and geology as well.

The Field Museum in Chicago, IL, is one of the world’s largest natural history museums. By “largest”, I don’t mean “square footage devoted to exhibits”, although it has a lot of that. I’m talking about its collections of natural history specimens, which for the whole museum currently totals over 25 million specimens. But even if we just stick to paleontology, the Field Museum really is a treasure: over 376,700 fossil plants, mammals, birds, reptiles, and invertebrates. It’s an important paleo collection, too, with many rare species and many holotype specimens (the specimens scientists designate as an exemplar when they name a new species). The specimens in the Field Museum collections are researched and augmented by museum curators and their students, but because it is so large and important, the collections really are of global importance. Field Museum specimens are very often studied by other scientists all over the world, who also add new specimens to the collections. This heavy use and constant increase requires specimens to be maintained by a skilled staff of collections managers, preparators, and conservators.

Chicago's natural history treasure chest

A museum of scientific, educational, and cultural importance. CC-BY-SA 3.0 (c) 2011 Joe Ravi, accessed through Wikimedia Commons

Beyond cataloging the diversity of past and present life, Field Museum scientists do a lot of other types of research, which include sorting out the evolutionary and ecological relationships of organisms, exploring the history of the solar system, understanding the effects of climate change, preserving the cultural heritage of many indigenous peoples, and conserving the planet. The scientific mission includes training undergraduate and graduate student researchers, with curators sponsoring students and teaching at three local universities (Northwestern, U of Chicago, and my alma mater, the University of Illinois-Chicago). The scientific and collections staff also does a lot of outreach and education, both in the museum and in Chicago-area schools. This includes a special collection of museum specimens that schools can borrow, to give students hands-on experience with the scientific method.

In short, the Field Museum is an outstanding and important scientific, educational, and cultural institution. You should definitely visit it if you ever travel to Chicago, and you should visit regularly if you live in Chicago.

Tyrannosaurus rex

FMNH PR2081, the Tyrannosaurus rex better known by its nickname, “Sue”. (c) 2005 Shoffman11, via Wikimedia Commons

Earlier this week, the Chicago Tribune, Scientific American, and others reported some highly disturbing news, namely that their forthcoming budget cuts will primarily affect their research and curatorial staff. The Field Museum has a lot of debt, and have already reached the limits of their credit. They have already made a lot of cuts to support staff (janitorial, administrative, etc.), and increased revenue through admissions price changes a few years ago. The current museum president and CEO, Richard Lariviere, and the board of trustees don’t see any way to reduce costs besides narrowing the research scope of the museum, “monetizing” its collections (building new exhibits based on what they have in house already), and eliminating blockbuster travelling exhibits.

Make no mistake, this will have a huge impact on the museum’s ability to do basic science. By cutting  scientists or, equally important, the people who maintain the collections, there will of course be a big and immediate hit to the scientific and educational missions of the museum. This impact is already felt; the Field Museum is under a hiring freeze that has left some collections without a curator in charge of them. And it will be felt further:  Early reports indicate that the museum is looking into whether tenured curators might be let go. Dr. James Hanken, director of Harvard’s Museum of Comparative Zoology, summarized it well in the above Scientific American article: “There’s no way the Field Museum will be able to maintain its position of prominence under those circumstances.”

But even if the economy bounces back quickly and no curators are lost, what happens in the interim is bound to have lasting negative effects. Nontenured staff are likely to get hit harder in the short term. Curators and students preserve the collections through research, but the collections staff are the people who preserve the collections physically and facilitate research, at the Field and elsewhere. If the museum “refocuses” its scientific mission to include just a few areas of research, some collections will suffer harder than others: loans not sent out or returned, broken specimens left unrepaired, specimens misplaced or misidentified, delicate specimens left to degrade at improper temperatures or low alcohol concentrations. Research collections cannot be maintained as a research tool by people who do not know what they are doing.

Dessicated frog specimen

Can you fix this frog? I suspect you cannot.               Image (c) 2012 Claire Smith, accessed on her flickr site.

If curators and other collections staff are axed, the specimens face a slow and sad scientific death. Collections can die from lack of physical maintenance (where they become functionally unusable), or they can die from a lack of research maintenance (where they become functionally irrelevant). Both are a danger here.  This is one of the world’s great natural history collections; its scientific importance cannot be overstated. Its collections preserve the cultural heritage of many indigenous peoples, as well as the natural history heritage of all people. It would be a scientific and cultural tragedy to lose it in either the short or the long term.

Finally, on a personal note:

There is no part of my journey to becoming a professional scientist that has not been touched by the Field Museum. As a child, trips to the Field Museum inspired my love of science and sparked my curiosity about life, the Earth, and how they got this way. Part of the reason I am a biologist today is because my parents, grandparents, and teachers brought me to the Field Museum when I was young. As an undergraduate, I took classes from Field curators at UIC and I volunteered in the Geology Department preparing fossils. The hands-on experience working with fossil specimens and with museum scientists made me sure I wanted to pursue scientific research as a career. At that time, friendships and collaborations were formed that still thrive over a decade later. My MS, PhD, and current research include specimens from the Geology and Herpetology collections, and some of my earliest field experience was gained working with Field Museum paleontologists in Montana. I would not be where I am today without the Field Museum; the exhibits inspired me to love science, the curatorial staff encouraged me to do science, and the collections themselves continue to motivate me in both goals.

Science at the Field Museum is facing a real threat. If you have not signed this petition, please take a minute to do so. Please also take a few more minutes to write to the President and CEO of the Field Museum, Richard Lariviere, who can be reached at:

The Field Museum
1400 South Lake Shore Drive
Chicago, IL 60605

Category: Miscellaneous, Paleontology | Tagged , | 12 Comments

Fossil frogs / The fossil record is not as bad as you think it is

By Sarah Werning
Posted: December 18, 2012

Conventional wisdom holds that the fossil record is data-poor compared to the modern record. Introductory biology textbooks always start their explanation of the fossil record by stating that it is imperfect. They point out that there are lots of holes in the fossil dataset: soft parts aren’t preserved, we can’t get DNA out of them, we don’t have that many examples per species, most species don’t leave a fossil record at all, etc. Obviously, to some extent this is true – if you want to study heart valve structure in extinct rhinos or look at genetic variation in Archaeopteryx, your dissertation will probably be pretty short.

Berlin Specimen of Archaeopteryx

Unsuitable for popgen studies
Image (c) 2009 H. Raab

But ask any paleontologist directly, and she will tell you that “exceptional” preservation (soft and/or delicate body parts preserved in good detail) is actually pretty common; that some species have hundreds or even thousands of fossil representatives (especially invertebrates, animals without backbones); and that we actually have a pretty good idea of which types of organisms were on the scene and where for the last 3.4 billion years. Although we don’t have dinosaur DNA yet, we do have it from mastodons, Columbian and woolly mammoths, and neanderthals (to name just four extinct species).

The fossil record is not just “good, considering all the things that prevent an organism from being preserved”; it’s actually good. We can acknowledge its limitations, but we don’t need to apologize for them at the expense of highlighting the wealth of very good data the fossil record bring to the table, or the types of questions it is uniquely suited to answer. If my posts accomplish anything, I hope it is to show that the fossil record offers a lot more than a basic catalog of the weird things that once lived on our planet.

Among my favorite exceptionally-preserved fossils are the many examples of fossil amphibians (especially frogs and salamanders) at various stages of development. I was excited to see this paper (“Post-metamorphic development of Early Cretaceous frogs as a tool for taxonomic comparisons”) by Zbynĕk Roček and colleagues in the most recent issue of Journal of Vertebrate Paleontology. In it, the authors report new specimens of the frog genus Liaobatrachus from the Cretaceous of China.

In living amphibians, limb bones (and some skull bones) start out as cartilage templates that convert to bone as the animal develops. Some parts of the skeleton will convert to bone early, some will convert late in development, and some will remain as cartilage permanently. Evolutionary relationships determine (in part) which elements of the skeleton convert, which don’t, and the timing and order of these conversions. Sorting out the species, genus, and/or family can be difficult for fossil amphibians if you’re not sure what developmental stage you’re looking at. If a particular element isn’t fully converted to bone (a process called ossification), is it because they are a species that converts late or never, or because the animal is too young to have converted yet? Not knowing could mean you misidentify the fossil, or misinterpret its relationships with other species. This is especially a problem for amphibians, because environment influences their body size greatly – a small animal could be young or an adult with stunted growth.

Salamander (Eurycea sosorum) skeleton stained to show bone (red) and cartilage (blue). Image from: City of Austin, TX website

Roček and his colleagues studied several frogs of the same species (Liaobatrachus), found in close proximity to each other at the same field site. All of the specimens had metamorphosed from tadpoles to frogs, but they were of various sizes and showed different stages of ossification. By looking at which bones were partially or fully ossified in different specimens, the authors were able to determine the order of conversion (= the sequence of ossification) for some of the bones. This meant they could order the specimens by age, even though late juveniles and young adults were very similar in body length.

Liaobatrachus from the Early Cretaceous of China

Image modified from Roček et al (2012), Figures 1B (left) and 1G (right). The juvenile (left) has not ossified its wrists, hands, or the ends of its arm and leg bones, unlike the adult (right). Images not to scale.

It also meant that Roček and his colleagues could confirm which features of the skeleton (the bumps, holes, and grooves found on particular bones) didn’t vary at all through development. This means we can identify future Liaobatrachus specimens using those characteristics, without having to worry that we’re looking at a feature that will change as the animal gets older. Features that change as animals get older are particularly problematic for sorting out evolutionary relationships; some closely-related species only start to look different late in development. Also, species that delay their development may resemble the juveniles of other species. To determine relationships among species, it’s best to look at unique features that remain the same throughout development.

So why care about the developmental stages of fossil frogs, beyond better IDs for future fossils? Well, from studying living amphibians, we know that there is a lot of variation in development across the group. For example, some families of salamanders are characterized by the retention of juvenile features (such as small eyes or gills) into adulthood. The evolution of these changes in developmental timing strongly shaped the diversity of living amphibians. Tracking the patterns of development and the evolutionary relationships of amphibians through their fossil record allows us to form hypotheses about when and why those transitions start happening in the first place.

axolotl, Ambystoma mexicanum

Some salamander species (like these axolotls) retain juvenile features such as gills and small eyes into adulthood). Image (c) 2010 ZeWrestler

 

Reference:
Z Roček, Y Wang, and L Dong. 2012. Post-metamorphic development of Early Cretaceous frogs as a tool for taxonomic comparisons. Journal of Vertebrate Paleontology 32: 1285-1292. doi:10.1080/02724634.2012.700666

Category: Development, Paleontology | Tagged , , , | 10 Comments

Bird brains: what they can tell us about ecology and evolution

By Shaena Montanari
Posted: December 10, 2012

For my inaugural post here at The Integrative Paleontologists, I am going to discuss a recent paper in PLOS ONE that highlights some of the aspects I love most about being a comparative biologist.

Paleoecology is the area of paleontology I am most interested in–and now, many paleontologists are spending a significant portion of their time examining extant species in order to understand more about the features and signals found in the fossil record.  Fossils are often fascinating morphologically but information such as behavior and ecology can be difficult to access in long-dead specimens with no soft tissue preservation and of course, no live observations. We as paleontologists need to think of creative comparative methods that can breathe some life back into old bones.

In their recent paper, Adam Smith and Julia Clarke use high resolution CT scanning to look at a variety of structures in the endocranial region of a group of birds called Charadriiformes (plovers, sandpipers, gulls, terns, and their allies). Within charadriiforms, a wide variety of locomotor and feeding ecologies are represented­–ranging from auks, which are wing-propelled divers, to marsh sandpipers, which are terrestrial ground-foragers.

Razorbill, a type of auk. CC-BY.

Morphology preserved in the brain case of vertebrates can correspond to certain unique ecologies and life histories. Charadriiformes are a good group to test this on because of their diverse ecologies and well-known evolutionary relationships. I will highlight a few of their findings here:

  •  The “wulst”, also known as the sagittal eminence, is a structure in the brain of birds linked to sensory and visual perception. This structure can be reconstructed using a digital endocast. Interestingly, the only two terrestrially foraging species sampled possess a uniquely positioned wulst when compared to the other charadriiforms. On the other hand, both flightless and volant species possess similarly shaped wulsts so it may not be useful in predicting flight styles of birds.
  • The inner ear is comprised of a bony tube, known as a labyrinth. The characteristics of this labyrinth have been known to accurately predict how acrobatically an animal can move.  Although in this group of birds, it appears that labyrinth shape and structure is conserved, even between divers and non-divers.

    Cranial endocasts of four species in this study illustrating differences in endocranial morphology. Smith and Clarke 2012 (CC-BY)

  • Overall, it was shown that flightless wing-propelled divers have relatively smaller brains for their body masses and also smaller optic lobes than volant members of the same group. There was one species, the Black Skimmer (Rynchops niger) that was strikingly different from all of the others that were sampled. The Black Skimmer has, among other unique endocranial characteristics, an unusually large wulst. This seems to be related to the Black Skimmer’s unique tactile feeding ecology– it feeds at the surface of the water by skimming the surface with its lower jaw (video from YouTube here).

Learning the details of these endocranial morphological correlates to behavior and ecology is invaluable to understanding the endocranial characters we see in fossils. Charadriiforms have a robust fossil record; so fossil specimens from this group can be CT scanned in order to enlighten us as to potential feeding and behavioral traits now that the significance of these morphological features are known. I think increasingly paleontologists will turn to studying extant species with new advanced technologies that we can also apply to our fossil specimens, allowing us to better grasp ecology in deep time. Expect to hear more on this topic from me in the future!

Citation:

Smith NA, Clarke JA (2012). Endocranial Anatomy of the Charadriiformes: Sensory System Variation and the Evolution of Wing-Propelled Diving. PLoS ONE 7(11): e49584. doi:10.1371/journal.pone.0049584

Category: Paleontology, PLOS ONE | Tagged , , , , | 1 Comment