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.

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.