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.

Creature Feature 23

Greetings, everyone! This week, we're going to talk about a group of freshwater fish that are found in Hell Creek. This group is amiidae, which are more commonly referred to as Bowfins!

Amiid fish models, WIP. Due to lack of adequate fossil reference material, appearance is based on modern relatives.

Currently, there are two species of fish from Hell Creek currently assigned to the family Amiidae - these are Kindleia fragosa, and Melvius thomasi (Pearson et al., 2002). The former appears to have been extremely common, with over 2,600 specimens assigned to the species. Melvius thomasi is less common, with only 67 specimens from the taxon found in Hell Creek (Pearson et al., 2002).

The family Amiidae is a lineage of basal ray-finned fishes, consisting of four subfamilies. All four are known from as far back as the Jurassic (Grande and Bemis, 1998), though the only living member of this family is the modern bowfin, Amia calva. The modern bowfin is commonly found throughout the eastern United States, and in southeastern Canada. Their habitat includes the drainage basins of the Mississippi river, the Great Lakes, and many rivers that flow along the Eastern seaboard and Gulf of Mexico (Fuller, 2006).

Bowfins today prefer vegetated, swampy water, lowland lakes and rivers, and are even occasionally found in brackish water. Their color and pattern allows them to camouflage themselves in slow-moving water where vegetation helps to conceal them from both potential predators and their prey. They will often hide among roots and submerged logs (Rudolph and Robison, 2004; Laerm and Freeman, 2008). They also are able to breathe air as necessary, which allows them to tolerate low-oxygen environments (Rohde, 2009).

Modern bowfins are ambush predators, traveling into shallow water at night to prey on smaller fish and invertebrates such as crawfish, aquatic insects, and mollusks (Indiana Department of Fish and Wildlife). Juveniles tend to preferentially target invertebrate prey, whereas the adults primarily eat other fish - however, they are known to be highly opportunistic, and it is unlikely that they will turn down any easy meal (Rohde, 2009). They are quite agile and quick fish with ferocious appetites (Stewart and Watkinson, 2004; Schultz, 2010).

One thing that readers will note with this Creature Feature is that I mostly talked about modern relatives of the extinct Amiid taxa found in Hell Creek. This is because I have been unable to find any in-depth information on paleoecology/paleobiology of the Hell Creek amiid fish, and as such I have given information on the closest modern relative. Given that they are in the same family, it seems reasonable to assume that their habits would be at least somewhat similar. After all, the habitats where modern Amia are found today were rather abundant in Hell Creek, which would explain their common occurrence.

Well, I hope this has given you a bit more information on the Amiid fish of Hell Creek! Tune in next week for another Creature Feature!

Acknowledgements:

 Pearson, D. A.; Schaefer, T.; Johnson, K. R.; Nichols, D. J.; Hunter, J. P. 2002. Hartman, John H.; Johnson, Kirk R.; Nichols, Douglas J., eds. Vertebrate Biostratigraphy of the Hell Creek Formation in Southwestern North Dakota and Northwester South Dakota. Geological Society of America Special Paper 361 (Boulder, Colorado). The Hell Creek Formation and the Cretaceous-Tertiary boundary in the northern Great Plains: An integrated continental record of the end of the Cretaceous: 145-167.

Grande, L.; Benis, W. E. 1998. A Comprehensive Phylogenetic Study of Amiid Fishes (Amiidae) Based on Comparative Skeletal Anatomy. An Empirical Search for Interconnected Patterns of Natural History. Memoir (Society of Vertebrate Paleontology) 4: 1-679.

Fuller, Pam (April 11, 2006). Amia calva. USGS Nonindigenous Aquatic Species Database. US Geological Survey. Retrieved June 14, 2016.

Rudolph, John Miller; Robison, Henry W. 2004. Fishes of Oklahoma. University of Oklahoma Press. p. 58.

Laerm, Joshua; Freeman, B. J. January 2008. Fishes of the Okefenokee Swamp. University of Georgia Press. p. 37.

Rhode, Fred C. 2009. Freshwater fishes of South Carolina. University of South Carolina Press. p. 80.

Indiana Department of Fish & Wildlife. Bowfin (Amia calva). Indiana Department of Natural Resources. Retrieved June 14, 2016.

Stewart, Kenneth; Watkinson, Douglas. 3 May 2004. Freshwater Fishes of Manitoba. Univ. of Manitoba Press. p. 51.

Schultz, Ken. 15 December 2010. Ken Schultz's Field Guide to Freshwater Fish. John Wiley & Sons. p. 64.

Sci-Day 20: Crash Course in Evolutionary Biology, part 1

Greetings, fans! I've decided to start a new Sci-Day mini-series, that will be based on my Evolutionary Biology class that I took in the Spring semester, in terms of organization (ie subject order) and topics. For this reason, unless otherwise stated, most of this information comes from the relevant lecture slides from the course, though I'm certain any Evolutionary Biology textbook would also contain the same or at least similar information. I will also say that because there will be a lot of stuff related to inheritance, alleles, and genes, you should do some reading up on exactly what those terms mean. You should have a good understanding of Mendelian inheritance, what an allele/locus/gene is, but we will not have to worry about things such as how DNA is replicated or any of the molecular processes. Since I am focusing all of my time on writing this, I do not have the time to give links to specific sources to get that information, but a decent Google search for terms such as "Mendelian inheritance" should give you a good enough start.

A key thing that I think is most interesting is that, while the things we will discuss are not really possible to test or examine in extinct species, once Dinosaur Battlegrounds has been fully released and all features are in place, simulations could let us investigate such questions given certain assumptions. One thing of note: I have covered several topics that would otherwise be included in this mini-series, so I will reference those posts instead of posting the same thing again.

In this post, I will just be introducing you to the topic of evolutionary biology, why it's important, and what it is. I hope you enjoy this, and learn something new!

Before we get started on anything, we need to ask ourselves one key question:

What is evolution?

To put it very simply, evolution is CHANGE. This may be development in an individual, such as in the life cycle of a frog. It can also be ecosystem change; for example, the recession of the Western Interior Seaway towards the very close of the Cretaceous altered the ecosystems surrounding it (as well as the Seaway itself, obviously). There is also cultural evolution - these are changes in how humans communicate with one another, but because humans are boring and we want to get to the good stuff that relates to dinosaurs, we'll just pretend it doesn't count.

However, the type of evolution that you probably first think of when you hear the word is biological evolution. Biological evolution is the change in properties of some population of organisms over generations. These properties must be HERITABLE, which leads us to a more precise and accurate definition: biological evolution is the change in allele frequencies in a population over time. A sort of 'synonym' for biological evolution is 'descent with modification', a term used by Darwin himself in his famous work, "On the Origin of Species".

Evolution is extremely important to understand because it is the central unifying theory of modern biology. As Dobzhansky put it, Seen in the light of evolution, biology is, perhaps, intellectually the most satisfying and inspiring science. Without that light it becomes a pile of sundry facts some of them interesting or curious but making no meaningful picture as a whole" (Dobzhansky, 1973). It allows us to gain an understanding of both how observed features (on a genetic and anatomical basis) developed, and why. Perhaps the best example I can think of would be the evolution/origin of birds. Without any evolutionary context it would be impossible to understand just how birds evolved powered flight, or their origins. Now, because of our great understanding of biological evolution, as well as advances in both methodology and biological theory, we know that birds evolved from a lineage of theropod dinosaurs during the Mesozoic.

That is all for this week - I could go on forever about how cool and important evolution is, but I don't want to end up being redundant and boring! Next week we'll go a bit more into Darwinian evolution, so stay tuned!

Acknowledgements:
Evolutionary Biology, Spring 2016. Lecture Notes. University of Kansas.
Dobzhansky, T. 1973. Nothing in biology makes sense except in the light of evolution. The American Biology Teacher 35: 125-129.

Creature Feature 22

Greetings, fans! Sorry about the lack of posts lately, I have been busy with work in the lab. This week, we're going to take a look at some of the turtles from Hell Creek, namely, the family Baenidae!

Plesiobaena antiqua, one of the species of Baenid turtle from Hell Creek. Work in progress.

Baenidae is an extinct clade of bottom-dwelling riverine turtles that were endemic to North America (Gaffney, 1972). They were an extremely diverse group during the late cretaceous, with between 14 and 17 species recognized from the Campanian through the Maastrichtian (Lyson and Joyce, in press). Interestingly, several species of Baenid turtle from Hell Creek actually survived into the Paleocene, making it by when many species perished (Lyson and Joyce, 2009).

Originally, some of the now-recognized species of Baenid turtle from Hell Creek were assigned to the genus Plesiobaena, but a redescription of several relevant specimens revealed that they were actually separate species (Lyson and Joyce, 2009). These include Peckemys brinkman, and Cedrobaena putorius (formerly Plesiobaena putorius). Other species of Baenid turtle from Hell Creek include Eubaena cephalica, Gamerabaena sonsalia, Palatobaena cohen, Stygiochelys estesi, and Neurankylus eximius (Lyson and Joyce, 2009).

Most baenids appeared to have preferred stream channel habitats, with the possible exception of Neurankylus eximius, which may have preferred floodplains as opposed to active channel margins (Hutchison and Archibald, 1986; Brinkman, 2005). It is likely that the high diversity of Baenid turtles was possible due to specializations in diet/habitat preference, and there is evidence for this based on the cranial morphology of several coexisting Baenid species. For example, the diet of Cedrobaena putorius and Palatobaena cohen likely consisted largely of molluscs and other hard-shelled crustaceans, whereas Peckemys brinkman and Eubaena cephalica appear to have been more generalist (Lyson and Joyce, 2009).

Well, I hope this has given you a bit more info on one of the families of turtles from Hell Creek! Note that the above picture is only representative of a single species, and additional models/textures will be made to represent the different taxa.

Acknowledgements:
Gaffney, E. S. 1972. The systematics of the North American family Baenidae (Reptilia, Cryptodira). Bulletin of the American Museum of Natural History 147: 241–320.
Lyson, T. R.; Joyce, W. G. In Press. A new baenid turtle from the Upper Cretaceous (Maastrichtian) Hell Creek Formation of North Dakota and a preliminary taxonomic review of Cretaceous Baenidae. Journal of Vertebrate Paleontology.
Lyson, T. R.; Joyce, W. G. 2009. A Revision of Plesiobaena (Testudines: Baenidae) and an Assessment of Baenid Ecology Across the K/T Boundary. Journal of Paleontology 83 (6): 833-853.
Hutchison, J. H.; Archibald, J. D. 1986. Diversity of turtles across the Cretaceous/Tertiary Boundary in northeastern Montana. Palaeogeography, Palaeoclimatology, Palaeoecology 55:1–22.
Brinkman, D. B. 2005. Turtles: Diversity, paleoeology, and distribution,. 202–220. In P. J. Currie, E. B. Koppelhus (eds.). Dinosaur Provincial Park: A spectacular ancient ecosystem revealed. Indiana University Press, Bloomingdale. 

Creature Feature 21

Hello, everyone! Sorry about the delay, there were some issues that prevented me from getting something out yesterday.

Today, we're going talk about another crocodylian from Hell Creek - Borealosuchus sternbergii!

Borealosuchus sternbergii model, WIP.

Borealosuchus sternbergii was originally assigned to the genus Leidyosuchus, but a reevaluation of that genus led to the formation of the new genus Borealosuchus, to which B. sternbergii was assigned - it is now the type species for the genus Borealosuchus (Brochu, 1997).

A paper in 2012 placed Borealosuchus as the most basal member of the genus. The exact relationships between Borealosuchus and the rest of crocodylia is not fully resolved - many phylogenic analyses placed the genus closer to Brevirostres (alligators and crocodiles) than to Gavialoidea (gharials) (Brochu et al., 2012), several placed it closer to Gavialoidea than to Brevirostres (Puértolas et al., 2011), and a few placed it outside of Crocodylia entirely (Pol et al., 2009). However, the authors note that all three are equally parsimonious (Brochu et al., 2012), so only further research will be able to resolve this issue.

Unfortunately, there is not much for me to write about Borealosuchus paleobiology or paleoecology, as most of the research that involves the genus is about its relationships to other crocodylians rather than the actual lifestyle of the animal. However, based on my own knowledge of crocodylians and modern ecosystems I have a few ideas about how it may have lived. Keep in mind that this is purely speculative and should be taken with a grain of salt.

While Borealosuchus does not have resolved relationships to other crocodylians, its cranial anatomy appears similar to that of modern crocodiles. This, combined with the fact that the Hell Creek formation was bordered by the shrinking Western Interior Seaway, makes me think that it may have lived similarly to the modern American crocodile (Crocodylius acutus). In the Everglades, American crocodiles and American alligators are separated for the most part by habitat preference - they tend to be closer to the coast, in more salty bodies of water such as brackish lakes, mangroves, lagoons, etc. Alligators, on the other hand, prefer more inland, fresh water. It could be that Borealosuchus shared this preference, with Brachychampsa dominating in the more inland bodies of water. In fact, the original material from which B. sternbergii was described came from the Lance formation (Gilmore, 1910), which was a coastal floodplain environment - this may be supportive of my hypothesis.

Well, I hope this has given you a bit more information about Borealosuchus sternbergii! I know it was a bit short, but I did what I could with what I could find.

Acknowledgements:

Brochu, C. A. 1997. A review of "Leidyosuchus" (Crocodyliformes, Eusuchia) from the Cretaceous through Eocene of North America. Journal of Vertebrate Paleontology 17 (4): 679-697.

Brochu, C. A.; Parris, D. C.; Grandstaff, B. S.; Denton, R. K. Jr.; Gallagher, W. B. 2012. A new species of Borealosuchus (Crocodyliformes, Eusuchia) from the Late Cretaceous-early Paleogene of New Jersey. Journal of Vertebrate Paleontology 32 (1): 105-116.

Puértolas, Eduardo; Canudo, José I.; Cruzado-Caballero, Penélope. 2011. A New Crocodylian from the Late Maastrichtian of Spain: Implications for the Initial Radiation of Crocodyloids. PLoS ONE 6 (6) e20011.

Pol, Diego; Turner, Alan H.; Norell, Mark A. 2009. Morphology of the late Cretaceous crocodylomorph Shamosuchus djadochtaensis and a discussion of neosuchian phylogeny as related to the origin of Eusuchia. Bulletin of the American Museum of Natural History 324: 1-103.

Gilmore, C. W. 1910. Leidyosuchus sternbergii, a new species of crocodile from the Cretaceous Beds of Wyoming. Proceedings of the United States National Museum 38(1762): 485-502.

Sci-Day 19: Color in Dinosaurs

Greetings, fans! This Sci-Day I will be discussing a rather interesting topic that relates to some of my own work - coloration in dinosaurs [though my work currently is focused on modern reptiles].

For obvious reasons, when imagining coloration in long-extinct creatures we mostly have to make educated guesses based on modern animals. However, there are exceptions, such as in the case of the early Cretaceous Microraptor, where scans with an electron microscope revealed preserved melanosomes [pigmentation cells] within the feathers, the orientation/stacking of which was consistent with black, iridescent coloration in modern birds such as the starling - this may have served a similar function as in the modern analogue, for sexual display purposes (Li, 2012). Preserved melanosomes have also been found in Sinornithosaurus, though its coloration was not uniform across the body (Zhang et al., 2010). A follow-up study in 2012 showed that the colors were reddish brown, yellow, black, and gray, which were distributed across the body (Naish, 2012). It is important to note that such exceptions are rare, and for the most part we do not know what color dinosaurs were. For this reason, we must look at modern analogues for inspiration. This requires us to understand the uses of coloration in the natural world, so that we may hypothesize the possible roles colors may have played in the lives of dinosaurs.

In order to hypothesize what roles and importance color might have had in the lives of dinosaurs, we first need to understand a bit more about color vision from both an anatomical and evolutionary standpoint. In vertebrates, there are two specialized types of receptors in the back of the eye - rods and cones. The former of the two are responsible for low-light contrast, whereas the latter are responsible for perceiving color. Cone cells contain one of several proteins called opsins, each of which has a different spectral sensitivity - in other words, each type of pigment is best able to detect a particular set of wavelengths in the spectrum. By having many, many cone cells with several different pigment types, the eye can perceive multiple different colors.

Based on this information, it is somewhat intuitive that the number of different types of cone cell pigment an animal has influences its ability to see colors. Humans and other primates have three different types of pigment - in other words, we have trichromatic color vision. However, the earliest vertebrates actually had tetrachromatic color vision, which was then lost in mammals. Thus, reptiles and birds actually both have tetrachromatic vision (Bowmaker, 1998), meaning that they have a much better ability to see color than we do. Taking this into account, along with the many examples of the importance of color in both lineages, it is rather safe to assume that dinosaurs also used color in many different ways.

Another thing we must understand is the mechanisms responsible for coloration in both reptiles and birds. As many people know, color is generated by specialized cells collectively known as chromatophores. The most widely known of these is the melanophores, which produce melanin (the pigment responsible for black and shades of brown). However, reptiles and other poikilothermic vertebrates have two additional types of chromatophore that produce chemical pigments, known as xanthophores (responsible for yellows) and erythrophores (responsible for reds) - these two contain a mixture of different pteridine and carotenoid pigments (Bechtel, 1978). In addition, they also have structural chromatophores called iridophores - rather than containing chemical pigments, these cells reflect different wavelengths of light based on the structure of the cells themselves. Together, different combinations, densities, and distribution of these chromatophores allows for a diversity of colors. However in birds, the only chemical pigment cells are melanophores - the many colors that we see in bird plumage is due to the structure of the feathers themselves. For example, peacock feathers are actually pigmented brown, but their structure interacts with these melanophores to create the vivid colors we perceive (Ball, 2012).

This makes one wonder - when were these specialized chromatophores we find in reptiles lost? My intuition tells me that it likely coincided with the appearance of feathers - since they have an alternate mechanism for generating diverse colors, there is no need for the chromatophores (plus they are found in the skin which is covered by the feathers). However, this is simply speculation and would require further evidence such as molecular data to investigate.

Back to the topic at hand, given the diversity of coloration within reptiles and birds, it is fair to assume that non-avian dinosaurs also came in many different colors. Many modern reptiles and birds use color as a signaling tool, as an indicator of mate quality/health, to intimidate rivals, and obviously to blend in to the environment. Additionally, many reptile and bird species that make use of conspicuous color signals show significant variation in the color of the relevant appendage/body part across their range. A great example of this would be the dewlaps found in the genus Anolis, where a single species may have vastly differing dewlap color and shape between localities. This might have been the case in some dinosaur species if they too used such a signal. For example, perhaps Triceratops would flood its frill with blood to create bright colors to attract mates and intimidate rivals - if it did so, there may have been vastly differing frill colorations between areas of its natural range. Obviously this is purely hypothetical, but it is not beyond the bounds of sound reasoning.

Well, I hope you have enjoyed this week's Sci-Day! Since my current project is related to pigmentation in reptiles, it is helpful for me to explain the mechanisms behind it as well!
Acknowledgements:
Li, Quanguo. 2012. Reconstruction of Microraptor and the Evolution of Iridescent Plumage. Science 335: 1215-1219.
Zhang, Fucheng; Kearns, Stuart L.; Orr, Patrick J.; Benton, Michael J.; Zhou, Zhonghe; Johnson, Diane; Xu, Xing; Wang, Xiaolin. 2010. Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds. Nature 463 (7284): 1075-1078.
Naish, Darren. 2012. Planet Dinosaur: The Next Generation of Killer Giants. Firefly Books. p. 192.
Bowmaker, J. K. 1998. Evolution of colour vision in vertebrates. Eye 12 (3b): 541-547.

Bechtel, H. Bernard. 1978. Color and Pattern in Snakes (Reptilia: Serpentes). Journal of Herpetology 12 (4): 521-532.

Ball, Philip. 2012. Nature's Color Tricks. Scientific American 306 (5): 74-79