Creature Feature #1

For the first Creature Feature, we will be focusing on one of the largest and most famous predators to ever walk the Earth - Tyrannosaurus rex.

This massive dinosaur is one of the most well-represented giant theropods in the fossil record. There are specimens ranging from juvenile to sexually mature adults, and a few are astonishingly intact - in fact, there have even been specimens with some of their soft tissues still preserved. This relative and extremely fortunate abundance of material has allowed scientists to learn a vast amount about this ancient carnivore.

Tyrannosaurus rex was one of the largest carnivores of all time - the largest specimen known (the famous 'Sue') was 12.29 meters long (~40 feet) and is estimated to have weighed 9500 kilograms, or 10.5 tons (Hutchinson et al., 2011). While there are theropods that were larger than T. rex, it still stands out for its terrifying bite. Its massive and serrated teeth combined with a specially adapted skull to generate the highest bite force of any known land animal - it could slam its jaws down with an estimated 12,800 pounds of force. This allowed it to tear through flesh and bone with equal ease.

The skull of Tyrannosaurus rex was huge (nearly 5 feet in length) had extremely large fenestrae, or openings, to reduce its weight and provide large surfaces for muscle attachment - a characteristic that is observed in all theropods. However, its snout was much narrower in comparison to the back of its head than in other carnivorous dinosaurs such as Allosaurus fragilis; this adaptation results in a large degree of overlap between its eyes and acute binocular vision. The degree of visual overlap in Tyrannosaurus is even higher than that of a modern hawk (Stevens, 2006)!

Tyrannosaurus is in a family positioned in the clade Coelurosauria - due to the fact that at least one member of each of the Coelurosaurian subgroups has been preserved with some trace of feathery integument has led some paleontologists to believe that Tyrannosaurus rex was at least partially covered in primitive feathers (Zanno and Makovicky, 2010). The technique that led to this hypothesis will be the topic in this week's Sci-day post. Not all agree with this hypothesis, as it does not account for the possibility of secondary loss. Until direct evidence of feathers or large preserved remains of scales are found, however, we will be unable to know which of the two is correct. This is why, in Dinosaur Battlegrounds, the player will be given the choice to play either as a feathered or a scaled Tyrannosaurus.

If you prefer, you will have the choice to play as a scaly T. rex in Dinosaur Battlegrounds.

The growth rate of Tyrannosaurus rex was astounding - estimates put the peak rate at 1790kg per year (Hutchinson et al., 2011)! This growth is observed to slow down at approximately 16 years of age, and this was further supported when medullary tissue (only found in ovulating birds) was found in the femur of a 16-20 year old T. rex (Schweitzer et al., 2005).

Interestingly, the survival rate of Tyrannosaurus appears to follow a Type I survival curve, with low mortality among the juveniles, and mortality increasing with age. In fact, most specimens of Tyrannosaurus appear to have died within 6 years of reaching sexual maturity. However, this may not be indicative of reality, as it is also possible that this is due to collecting bias - the larger and more spectacular adult specimens are more appealing for fossil collectors and thus would be harvested in larger numbers even if their relative abundance was lower (Erickson et al., 2006). This may also be due to the fact that adult Tyrannosaurus lived very dangerous lives considering the prey that they hunt, and thus were more likely to be killed by their prey than the juveniles.

Tyrannosaurus had a surprisingly well-developed brain. It had extremely acute senses, with the ability to sense low-frequency sounds and extremely large olfactory bulbs for smell (Witmer and Ridgely, 2009). While these two abilities were extreme on their own, they were also combined with incredible eyesight - its visual acuity was even greater than that of modern eagles (Stevens, 2006)! Its large brain is also believed to have been sophisticated enough for some primitive form of group hunting - while not quite true 'pack hunting', as it lacks the organization of a pack hunt, it is still a step above fully solitary hunting (Witmer, 2011).

Well, I hope this has given you a bit more knowledge about the famous Tyrannosaurus rex!

Acknowledgements:
Hutchinson JR, Bates KT, Molnar J, Allen V, Makovicky PJ. 2011. A Computational Analysis of Limb and Body Dimensions in Tyrannosaurus rex with Implications for Locomotion, Ontogeny, and Growth. PLoS ONE 9(5): e97055.

Stevens, Kent A. 2006. Binocular vision in theropod dinosaurs. Journal of Vertebrate Paleontology 26 (2), 321-330.

Lindsay E. Zanno and Peter J. Makovicky. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution. Proceedings of the National Academy of Sciences, 2010

Schweitzer MH, Wittmeyer JL, Horner JR. June, 2005. Gender-specific reproductive tissue in ratites and Tyrannosaurus rex. Science 308 (5727): 1456-60.

Erickson GM, Currie PJ, Inouye BD, Winn AA. July, 2006. Tyrannosaur life tables: an example of nonavian dinosaur population biology. Science 313 (5784): 213-7.

Witmer, Lawrence M.; Ridgely, Ryan C. September, 2009. New insights into the brain, braincase, and ear region of Tyrannosaurs (Dinosauria, Theropoda), with implications for sensory organization and behavior. The Anatomical Record 292 (9): 1266-1296.

Witmer, Lawrence. July 13, 2011. Dino gangs: solitary, communal, or cooperative hunting in tyrannosaurs. Pick and Scalpel. WitmerLab at Ohio University. Retrieved January 3rd, 2016.

Sci-Day 24: Taphonomy

Hello, fans! As many of you know, I've been extremely busy - not only have I been working in the herpetology lab, but also I've been out in Montana digging up a T. rex, and have been spending time in the vertebrate paleontology lab helping to prepare the fossils that we brought back from the Montana site. However, I figured I'd talk about a rather important aspect of paleontology - namely, taphonomy!

First things first - do NOT confuse TAPHONOMY with TAXONOMY! The two are similar in sound, but VERY different in meaning. Taphonomy is basically the study of what happens between the time an organism dies, and the time it is discovered by the paleontologist. Taphonomy is extremely important because taphonomic factors may have large impacts on results.

Taphonomy involves many different subfields. One such example is Biostratinomy. This specifically involves the changes that occur between the time of death, and the time at which the organism in question is actually buried. There are several different types of changes that may take place, including the following:

Physical: transport (ie body flows down a river), breakage (ie the remains are broken apart), or exhumation (being unearthed prior to fossilization)
Chemical: Things such as oxidation and early changes in minerology, depending on the environment in which the organism is deposited
Biological: Things such as decay, scavenging, reworking of the burial site by burrowing organisms or roots, or boring directly into the bones themselves by certain species of animal/plant

These factors have important effects on the results and interpretations of studies. For example, if you find remains of a dinosaur, that does not mean the animal was specifically living right around where you found it. It may have died miles away, and was simply transported to where you happened to find it. There are ways to determine whether or not a specimen was transported very far before its burial, but that is a subject for another time.

Another subset of taphonomy is the process of diagenesis - this is the study of changes that occur between burial and fossilization (or destruction). This has important implications in paleontology, as the actual shape and features on the fossil itself may not be the same as the original bone - they may be due to things such as crushing, or other factors that come into play during this process. There are ways to test for such biases, but I will not get into them here.

To sum up, taphonomy is an extremely important topic to understand in Paleontology, as taphonomic factors can be significant biases that influence what we see in the fossil record. I hope you enjoyed today's Sci-Day!

Sci-Day 23: Hell Creek environment

Greetings, fans! Today, I figured I'd give a bit of an overview of the Hell Creek environment. Hopefully, reading this will give you some idea of what to expect when you are roaming through the game!

The Hell Creek formation, as many of you know, was deposited in the North-Midwest United States (and some Southern parts of Canada) in the very end of the Cretaceous, as well as the very beginning of the Paleogene (but we're not going to talk about the Paleogene Hell Creek because we're focusing on the dinosaur-filled part!).

Most of the sediments from the formation appear to have been laid down by fluctuating channels and deltas, with rare swamp deposits in the easternmost portion, where it bordered the Western Interior Seaway. To the west were the newly formed Rocky mountains. The environment of Hell Creek, along with the contemporaneous Lance and Scollard formations, has been interpreted to have been subtropical, well-watered environments, with floodplains, swamps, coastal plain, and estuarine environments, with many rivers, streams, and lakes flowing through them (Lofgren, 1997; Breithaupt, 1997; Eberth, 1997). The vegetation was largely dominated by angiosperms such as laurels, magnolias, palms, sycamores, and beech trees, though conifers such as bald cypress and redwoods were present. Much rarer were the cycads (Only a single species - Nilssonia yukonensis) and ginkgos (One species - Ginkgo adiantoides).

As I've said before, the environment we will be using for our demo will be that of the dig site I will be going to in around one week. The T. rex appears to have died around an oxbow lake - a type of lake formed when a meander (a loop) in a meandering river is cut off from the rest of the river. Lakes such as these are often not very far from an active river, which you can see in the early stages of our map. The lake itself would likely have many aquatic plants such as water lettuce, water lillies, and a few others. In between the bodies of water would be woodland, dominated primarily by angiosperms, though things such as bald cypress might thrive in areas where the water level rises frequently due to their ability to survive fluctuating water levels. One thing that we know for sure is that there were horsetails around the lake, as there have been recovered, intact fossils of these found in the deposit.

Based on several factors, it appears that the lake would have been quite murky/muddy, which is not represented in this screenshot, but that is being taken into account. You can see the murkier water in the below screenshot of a floodplain area surrounding a river system. Such environments were common in Hell Creek - many sites were deposited when a river flooded a large area, burying anything living [or dead] within a certain area (these types of deposits are known as Crevasse Splays). Note that we do not have all of the angiosperm vegetation models ready yet, so the plant distributions and densities that you see here are not indicative of what they will be in the final product.

Well, I hope this has given you a bit of a better idea of what Hell Creek was like! I am looking forward to going out to Montana and getting a better idea of what things are like in the field!

Acknowledgements:
Lofgren, D.F. 1997. "Hell Creek Formation". In: Currie, P.J.; Padian, K., editors. 1997. The Encyclopedia of Dinosaurs. San Diego: Academic Press. pp. 302-303.

Breithaupt, B.H. 1997. "Lance Formation". In:  In: Currie, P.J.; Padian, K., editors. 1997. The Encyclopedia of Dinosaurs. San Diego: Academic Press. pp. 394-395.
Eberth, D.A. (1997). "Edmonton Group". In: Currie, P.J.; Padian, K., editors. 1997. The Encyclopedia of Dinosaurs. San Diego: Academic Press. pp. 199-204.

Creature Feature 25

Hello, fans! Sorry for not posting last week, I've been very busy with working in the lab. This week, we will be looking at a special family of lizards from Hell Creek, the Polyglyphanodonts!

Polyglyphanodont template model, early WIP.

Polyglyphanodonts were the dominant group of lizards in both North America (Longrich et al., 2012) and Asia (Gao and Hou, 1996) during the Late Cretaceous, and died out during the KT extinction. Because many species are known only from fragmentary remains of the jaw and teeth, many are classified based on dental characters. However, this is still enough to reveal a significant level of diversity within the group. For example, Chamopsiids such as Chamops had blunt, crushing teeth that are indicative of an omnivorous diet, while species such as Peneteius had multicusped teeth somewhat akin to those of some mammals. This diversity in dentition indicates a diversity in ecology, and it is likely that Polyglyphanodonts had vastly differing diets and habitat preferences among species. Considering there were multiple different species in Hell Creek, it is likely that there was a degree of niche partitioning between them.

Polyglyphanodontians closely resembled modern teiids, and many species previously classified as teiids have been reassigned to this group (Gauthier et al., 2012). While there has been considerable dispute as to the relationships of the group, most recent analyses (Reeder et al., 2015) place them as sister to Iguania.

Well, that's this week's Creature Feature! There isn't really all that much I can say since the remains of the various species from Hell Creek are quite fragmentary, so I gave it everything I could.

Acknowledgements:

Longrich, N. R., A.-B. S. Bhullar, et al. 2012. Mass extinction of lizards and snakes at the Cretaceous-Paleogene boundary. Proceedings of the National Academy of Sciences 109(52): 21396--21401.

Gao, K.; Hou, L. 1996. Systematics and taxonomic diversity of squamates from the Upper Cretaceous Diadochta Formation, Bayan Mandahu, Gobi Desert, People's Republic of China Canadian Journal of Earth Sciences 33 (4): 578-598.

Gauthier, J. A.; Kearney, M.; Maisano, J. A.; Rieppel, O.; Behlke, A. D. B. 2012. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. Bulletin of the Peabody Museum of Natural History 53: 3-308.

Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J. 2015. Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa. PLoS ONE 10 (3): e0118199.

Sci-Day 22: Crash Course in Evolutionary Biology, part 3

Happy Sci-Day, everyone! This week, we are continuing our Crash Course series, and this week's topic will be Hardy-Weinberg equilibrium!

Hardy-Weinberg equilibrium essentially is when the various factors that contribute to biological evolution "balance out". Keep in mind that this equilibrium is only related to the allele of interest - if the allele is in Hardy-Weinberg equilibrium, that simply means that the gene is not undergoing biological evolution (ie allele frequencies not changing significantly in frequency in the population), but it does not mean the SPECIES is not undergoing biological evolution.

Hardy-Weinberg equilibrium is the null hypothesis when investigating population genetics - in other words, it is assumed initially that the population is in HWE with respect to that allele, and the data is collected which may either support or refute that hypothesis. Null hypotheses are critical for any scientific research, as they provide a relatively decent framework for keeping things objective. If the null hypothesis is not supported, then alternative hypotheses are proposed to explain the data.

Anyways, what is important to know about Hardy-Weinberg Equilibrium is that the factors that may cause violations. These include asexual reproduction, non-random mating, small population size, migration (also known as gene flow), mutation, and selection. If any of these are happening to a great enough extent, an allele will not be in Hardy-Weinberg Equilibrium.

The way to test to see if a population is in Hardy-Weinberg equilibrium is relatively straightforward. The first step is to genotype a large sample of animals in the population of interest - for a gene with alleles A and a, you would record how many AA individuals there were, how many Aa individuals there were, and how many aa individuals there were. The next step is to calculate the allele frequencies. To show how this works, let's consider a sample of 500 T. rex, with 300 AA, 75 Aa, and 175aa. To calculate the frequency of A, we add up two times the number of AA homozygotes (600) and the number of heterozygotes (75), and divide that by two times the number of individuals in the entire sample (1000). We multiply the total number by 2 because each individual has two copies of the gene, so the total number of alleles in the population is twice the number of individuals. This is also why we don't multiply the number of heterozygotes by 2 - they only have a single copy of the allele we're looking at. Anyways, the resulting frequency of the A allele is 0.675. Since the frequencies of the two alleles have to add up to 1, we can simply subtract .675 from 1 to get the frequency of a, which is .325.

Now, we have to figure out the EXPECTED genotype frequencies under HWE. This is easy to do. For the expected frequency of AA, simply square the frequency of the A allele. For Aa, it's 2(frequency of A)(frequency of a). For the expected frequency of aa, simply square the frequency of a. Now, we can use this to calculate what the EXPECTED genotype counts would be if the population were in HWE. To do this, we simply multiply the frequency of each genotype by the total number of individuals in the sample. For our example above, the expected counts would be 227.813AA, 219.375Aa, and 52.813aa.

The last step is to test whether these deviations are statistically significant. To do this, we conduct a test called the chi squared test. This, too, is relatively simple math. For each genotype, you do this:
((Observed individuals - expected individuals)^2)/Expected individuals. In our example, doing this with AA would be ((300 - 227.813)^2)/227.813), yielding a value of around 22. In order to get chi squared, you have to do this same calculation for each genotype, and then sum them all up. Once you have a chi squared value, you check it with a table, and see where your chi squared value is mapped according to how likely those results would be based on the expectations. If the probability is less than 0.05, it is considered statistically significant. In our case, the probability is less than 0.001, which is VERY significant!

The important thing about a violation of HWE is that it means there is something that is causing this deviation, which may be selection, migration, etc., which can tell you more about what is happening in the population. While this is not possible to do with prehistoric animals currently, it is possible that Dinosaur Battlegrounds could provide hypothetical simulations to conduct investigations of this sort, that might give some insight into population dynamics in prehistoric creatures.

Well, I hope this has taught you something about Hardy-Weinberg equilibrium! It's a very important concept to understand in evolutionary biology, so make sure you understand it! :)

Creature Feature 24

Hello, everyone! This week, we will be looking at the Xenosaurid lizard, Exostinus lancensis!

Exostinus lancensis model, WIP. Due to extremely fragmentary nature of fossil material, model is based on modern Xenosaurus.

As stated above, Exostinus lancensis belongs to the family Xenosauridae, which currently consists of a single extant genus. Modern Xenosaurus are native to Mexico and Central America, and are distinguished by knob-like scales, and a flattened head and body - this is an adaptation for living in cracks within cliff faces. The genus Exostinus actually includes a second species, E. serratus, which appears to be problematic. This is because a recent phylogenetic reanalysis of the family Xenosauridae recovered E. lancensis as sister to E. serratus and Xenosaurus, which would make the genus paraphyletic (Bhullar, 2011).

Furthermore, it is possible that the specimens assigned to E. lancensis actually represent more than a single species, but only more work and more complete remains will be able to resolve this issue (Bhullar, 2011).

Due to the fragmentary nature of what is known, I cannot say for sure how closely it resembled modern Xenosaurus and thus it is difficult to make any inferences on behavior or ecology. However, its dentition (or at least that of E. serratus) does resemble that of modern Xenosaurus (Bhullar, 2011), which eat mainly invertebrates, though they will eat smaller lizards or other vertebrates when the opportunity arises.

I am sorry that there is not much more I can say, but I do not want to make large leaps and say things that are not true - to admit our ignorance is the first step in the quest for knowledge!

Acknowledgements:

Bhullar, S. 2011. The Power and Utility Of Morphological Characters In Systematics: A Fully Resolved Phylogeny of Xenosaurus and Its Fossil Relatives (Squamata: Anguimorpha). Bulletin of the Museum of Comparative Zoology 160(3): 65-181.

Sci-Day 21: Crash Course in Evolutionary Biology, part 2

Happy Sci-Day, everyone! As we continue progress on the game, we are continuing to provide you with educational posts so that you will have a better understanding of exactly what goes into development, and why it takes so much effort to do what we wish to do. Today, I will be continuing with my Evolutionary Biology Crash Course mini-series - this week, we're going to cover Darwinian evolution!

First thing we need to understand is the difference between the terms "pattern" and "process" as they are used in Evolutionary Biology, and how they relate to one another. Studying patterns is identifying the order in nature - this is the stuff we see with our own eyes (as well as genetic sequence data). Studying patterns is where we infer or determine the actual mechanisms that generate and maintain this order. Patterns are the result of processes. An analogy you might use to remember this would be to think of baking a cake - the cake itself is the 'pattern', and the raw ingredients and instructions for mixing them are the 'processes'.

Now, let's move on to Darwinian evolution. Darwinian evolution is concerned with natural selection, which consists of three main components. Two of these relate to traits - genes, and environment. The third is related to the limits of natural selection, which we will cover later. The result of these three components is a change in the population over time.

There are some important things we need to understand about how natural selection works. Natural selection sorts based on phenotypes (the actual observed characteristic that results from interactions between genes and environment), not genotypes. Genes or genotypes by themselves do not code for specific traits. Rather, genotypes determine traits in the context of some particular set of environmental conditions. Natural selection results in adaptation. An adaptation is any trait that makes an organism more fit in its environment. An example would be the flat, paddle-like tail of Champsosaurus, which would allow it to swim far more efficiently than it would otherwise.

There are some key differences between natural selection and evolution. Natural selection acts on an individual level, whereas evolution occurs within populations. Even though an individual changes over time (development - the study of development within individuals over time is also known as ontogeny), individuals do not experience biological evolution. Furthermore, natural selection is merely one possible mechanism that can result in biological evolution - we will cover additional mechanisms as we get further into this crash course.

As I briefly mentioned further up, natural selection has limits. Some of these are due simply to physics - ie there is a maximum size to individual cells due to surface area/volume ratio which has key implications for nutrient exchange. Others are due to more biological/ecological factors. Natural selection can only act on existing variation - while new alleles/traits arise through things such as mutation, natural selection cannot act upon them until they are introduced. Furthermore, traits are only beneficial in a certain set of environmental conditions - natural selection cannot result in perfection. A great example of the costs of natural selection would be the modern cheetah. They have many traits that allow them to run at incredible speeds, but these result in a far more lightweight and fragile anatomy. This fragility means that they are not able to defend a kill against larger predators, and thus they may end up wasting lots of energy on a hunt only to have their food taken by a lion or hyena.

Another very important thing to understand is that evolution does not show foresight. One of my pet peeves as an evolutionary biologist is when someone uses words like "try", "need", or "want" when they are describing natural selection. Unlike in Disney movies, making a wish will not lead to any increase in fitness, nor will the "power of friendship." For example, if a hypothetical trait required several less-fit intermediates to evolve (again, this is purely hypothetical), it would not evolve because those required intermediates would be removed from the population.

Well, I hope this has helped you understand a bit more about natural selection/Darwinian evolution! Before you tune in next week, make sure to read Sci-Day #1 that reviews cladistics and phylogenetics!

Acknowlegements:
BIOL 412 (Evolutionary Biology). Lecture slides, January 26, 2016.