Dr. Cassandra Extavour

Developmental Biology, Harvard University

About Cassandra Extavour’s work One of the topics that Cassandra Extavour researches is germ cell development. During a process called embryogenesis, where an animal embryo develops from a fertilized egg cell, only a small percentage of the millions of genetically identical cells created will become germ cells. Germ cells are the cells created in an embryo that contribute their specific genomes to the reproduction of new creatures. The rest of the embryo’s cells become soma cells, which form different parts of the body such as organs, muscle, skin, and bones. These cells reproduce via mitosis, but cannot contribute their specific genomes to the reproduction of new creatures, ending the line of germ cells. A problem in the study of the development of multicellular organisms is then: why do cells that start out with identical genomes do different things in different environments? Cassandra Extavour tries to answer this question by dissecting embryos and ovaries of spiders, crickets, and milkweed bugs, using molecular biology and microscopy tools to map the germline of the cells. The way that a cell is assigned to the germline is caused by a few different ways. In some organisms, before there is an embryo, the molecular content of some cells predetermines them to develop as either germ or soma cells. In other organisms, a cell in the embryo receives chemical signals from neighboring cells that activate or repress genes that turn the cell into a germ cell. Cassandra Extavour is also interested in biological cooperation and the division of labor between germ and soma cells. Biological cooperation is when two or more cells group together to form a new entity, where the cells work together to maximize the reproductive potential of the entity. In the case of multicellular organisms with germ and soma cells, soma cells are called cooperative cells, where they improve the ability of germ cells to transmit their genomes by doing things like producing or preserving energy, at the expense of minimizing their genetic contribution to the next generation. Germs cells, or non-cooperative cells, on the other hand, will use the resources of the soma cells, without contributing its own, in order to preserve its own genome for the next generation. This type of behavior actually benefits the entire organism, and multicellular organisms capitalize on this in order to maximize their reproduction.

Publications: Extavour, CG, M Akam "Mechanisms of germ cell specification across the metazoans: epigenesis and preformation" ''Development'' 2004 Dec125, 130 (24) 589-840 Ewen-Campen, Evelyn E Schwager, and Cassandra GM Extavour, ''The molecular machinery of germ line specification'' Molecular and Cellular Reproduction. Volume 77, Issue 1, pages 3–18, January 2010. Dr. Sebastian Groh

The Evolution of Crocodylomorpha

University College London (UCL) Q&A with Dr. Sebastian Groh:

Q. What is your starting point when reconstructing the history and evolution of something like *Crocodylomorpha, and how do you build from there? A. The starting point is to think about what evolutionary history entails, including how the different species in the animal group are related, when different subgroups within the animal group evolved, and where they evolved. Then, peruse previous research and find the best method for your own. Collect data and, lastly, analyze it. One research method he particularly relies on is collecting data by visiting museums with crocodile fossils and writing down every single detail he observes about their anatomy, which usually takes an entire day! Q. Who is a team comprised of and how do you recruit those people? A. The positions usually included in a research team are: ● Principle Investigator (PI)–They supervise the projects going on within the research team and request funding ● Researchers–Usually people with PhDs, they work on their own research projects, teach undergraduate – PhD students, and help the PI with their tasks ● PhD students ● Master’s and Undergraduate students working on their thesis Recruitment is done through advertisements on job sites or within a department. Q. What have you researched/discovered that might add to our understanding of evolution, and do you have any tips for creating a timeline of life on Earth? A. Dr. Groh has researched animals including: ● Harvestmen–closely related to spiders ● Osteostracans–extinct, fish-like creatures that have a very heavy bony headshield and used to live in the oceans and freshwater systems 400 million years ago. He found out that their “variation in head shape isn’t really linked to where they live, but rather to how old they are!” (I.e. the ones that are 430 million years old have a different set of head shields than those that are 350 million years old). ● Crocodiles–He found out that the three main lineages (the ones leading to alligators, crocodiles, and gharials) have existed and been distinct since approximately 100 million years ago (when dinosaurs still roamed the Earth). They used to be much more diverse than what we currently have—there were plant-eating crocodiles, miniature crocodiles, and more! Dr. Groh highlights the importance of knowing about the evolution of all different kinds of animals in order to create the fullest picture possible of Earth’s timeline. For constructing a timeline of life on Earth, Dr. Groh suggests having a diagram that shows the different relationships between different animal groups in order to keep a better overview.

*Crocodylomorpha is the scientific name for the group consisting of crocodilians (crocodiles, alligators, etc.) and their extinct relatives. Publications:

Groh, S., Upchurch, P., Barrett, P., & Day, J. J. (2020). The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition. Zoological Journal of the Linnean Society, 188 (2), 473-506. doi:10.1093/zoolinnean/zlz117

Groh, S. (2019). A multi-disciplinary approach to the analysis of crocodylian phylogeny, diversity and biogeographic history in Deep Time (Doctoral dissertation). UCL (University College London).

Groh, S., & Giribet, G. (2015). Polyphyly of Caddoidea, reinstatement of the family Acropsopilionidae in Dyspnoi, and a revised classification system of Palpatores (Arachnida, Opiliones). CLADISTICS, 31 (3), 277-290. doi:10.1111/cla.12087

Dr. Mairin Balisi

Ecology and Evolutionary Biology

La Brea Tar Pits and Museum, Los Angeles, and at the University of California, Merced.

About Her Work Dr. Balisi uses the fossil record from the last million years to understand the causes of modern biodiversity, using three main areas of research.

1. The diet and movement of living and extinct animals. Methods: ● Used statistical graphing techniques to show that a Pliocene dog the size of a small wolf and known as the last of the bone-cracking dogs, hunted socially, and that the extinction of the genus could have impacted decomposition and nutrient cycling in North American ecosystems.

2. How ecology and morphology control biodiversity in deep time. Methods: ● Showed that the specialization in both more or less carnivorous traits of primitive canids could have negatively impacted their diversification after the relatively undisturbed first 40 million years of dog evolution. ● Her team estimated body mass using fossil parts, compiled occurrence data, calculated species durations, and formed many statistical tests to look into the relationship of these traits. ● By proving that some of these extinct canids filled niches no longer present or occupied in modern ecosystems, this may be the underlying reason for today’s diminished variety in dog species.

3. Looking for interactions among ecology, the environment, and extinction. Methods: ● Used radiocarbon dating, and studied both the movement and ecomorphological representations of her fossils to see how environmental disturbance shaped the diversity of other small to medium-sized canids to the present. ● Compared patterns of traumatic injury between the saber-tooth cat and dire wolf and helped diagnose the oldest known case of hip dysplasia in a cat, helping us understand causes of more primitive bone injuries in carnivores.

Publications:

Balisi, MA, AK Sharma, CM Howard, CA Shaw, R Klapper, EL Lindsey. Computed tomography reveals hip dysplasia in Smilodon: Implications for social behavior in an extinct Pleistocene predator. bioRxiv 2020.01.07.897348.

Balisi, MA, X Wang, J Sankey, J Biewer, and D Garber. Fossil canids from the Mehrten Formation, late Cenozoic of northern California. Journal of Vertebrate Paleontology 37(6).

Wang, X, SC White, MA Balisi, J Biewer, J Sankey, D Garber, and ZJ Tseng. First bone-cracking dog coprolites provide new insight into bone consumption in Borophagus and their unique ecological niche. eLife 7:e34773. Elizabeth Petsios

Paleontologist

Baylor Department of Geosciences Q&A with Elizabeth Petsios

What can fossils tell us about the K-Pg extinction?

Fossils are the main way we know that a mass extinction happened. By definition, when a lot of different species go extinct in a relatively short amount of time, that’s called a mass extinction. So if we find a bunch of different fossil species from Cretaceous rocks, and then suddenly those =fossil species are gone in Paleogene rocks, we know a mass extinction happened in between. The K-Pg is famous for wiping out whole groups of animals like non-bird dinosaurs, marine reptiles (like mosasaurs), pterodactyls, and ammonites.

How do you analyze fossils?

When we collect fossils, we also make observations that can tell us about when, where, and how that animal lived when it was alive. The first observation we make is: How old are the rocks that this fossil was found in? If the rocks are from the Cretaceous Period (meaning they formed in the Cretaceous), then we know that the fossils found in them were alive in the Cretaceous Period (approx. 150 to 65 million years ago). The second observation we make is: In what environment did these rocks form? From looking at the rocks, we can tell if they formed, for example, in the ocean or if they formed on land. We can also tell some more specific things about these rocks (for example - these rocks formed from sediments at the bottom of a lake). If we can determine what environment the rocks formed in, then we can guess at what environment the fossils that are found in those rocks lived in when they were alive. For example, if I find a rock that formed from sediments near the ocean coastline, I can assume that the fossils I find in those rocks probably lived in the ocean near the coast. By combining all of this information, we can figure out the ecology of things that we can’t study directly because they’re no longer alive today.

How do we study evolutionary trends in fossils?

We can also gather a lot of information from the fossils themselves. When you collect a fossil, you can study its anatomy and morphology (aka, it’s shape). If you collect fossils from the same group through time, you can observe how their anatomy and morphology change through time. For example, if I collected mammal fossils from the Cretaceous, Paleogene and Neogene (the time period after the Paleogene), I can observe a gradual increasePublications: in the body size of mammals over this time span. We can also make observation about how diverse a group is. For example, in the Echinoids from the Tesero Member (Werfen Formation) of the Dolomites (Italy): implications for extinction and survival of echinoids in the aftermath of the end-Permian Cretaceous,mass extinction. there were only a few different species of mammals, but in the Paleogene and Neogene, we see a gradual increase in the number of mammalPaleogenomics species, of echinoids meaning reveals an ancient that originmammals for the double-negative as a group specification were of micromeres becoming in sea urchins.more and more diverse over this time span. These are two examples of very broad A new evolutionary stem group echinoid trends, from the Triassic but ofit’s China also leads possibleto a revised macroevolutionary to study very history specificof echinoids during the end-Permian mass extinction. evolutionary trends as long as we can study the details of the anatomy of these fossils through time. Dr. Mairin Balisi

Ecology, Evolution. Paleobiology

La Brea Tar Pits Museum Q&A with Dr. Mairin Balisi

Q: Have you done any work in specific with humans diverging from chimps? > Has not done any work in specific to this split between humans and chimps but Dr. Mairin Balisi studies modern mammal communities and her research methods give us an insight on how observing this split might be studied.

Q: How can we reconstruct the behavior of extinct animals? > Measurements and equations of the fossils are used to figure out what their prey was and from this we can study and observe the animal to see how and when they evolved and what their environments were like

Q: What kind of tools do you use in your research? > Fossil imaging and scanning

Ecomorphological Controls > Geographic range size does not always impact the duration of a species but observing their carnivory can help scientist observe patterns between their diet in relation to a species duration

Publications:

Balisi, MA, C Casey, and B Van Valkenburgh. Dietary specialization is linked to reduced species durations in North American fossil canids. Royal Society Open Science 5:171861. (doi:10.1098/rsos.171861)

https://www.nature.com/articles/s42003-020-01193-9 Guillem Ylla

Image of Gene Regulatory Networks scientist Extavour Lab At Harvard

Q&A with Guillem Ylla

Q: What have you discovered in studying insect reproduction that can tell us about evolution in general?

A: insects are amazing models to study evolution. They represent near the 90% of the known animal species! In addition, they are extremely diverse and adapted in any possible environment.

Q:As well as what steps have you or people in your field of expertise taken to expand your research if any?

A: There are basically 2 main ways to study evolution in the Extavour Lab where I work. One, is to take multiple genomic information from multiple species and compare them, trying to identify similarities and differences between species. The other way is through experiments. Using molecular biology techniques we can change the genes of an insect, and see what happens when we suppress it or over-expressed it in a given stage. This allows us to test hypothesis regarding the functions of genes. Dr. Carlie Pietsch

Image of Paleontology

scientist San Jose State University

Q&A with Carlie Pietsch Q: How do you use fossils to understand climate events?

A: To understand climate events more broadly is to examine how the fossil community changed. We can look back in the fossil record at the types of plants and animals and if we see major changes, it might be because the environment changed.

Q: How do you decide where to find the fossils?

A: I look for clams and snails that lived 252 million years ago and 66 million years ago. I look at geologic maps to find rocks that were formed in the ocean (limestones) from those times.

Q: Why is understanding these climate events important to understanding the evolution of life on earth?

A: After the big climate shifts we have seen in Earth's history, we often see a change in the types of organisms that make up life on Earth. One way we think evolution happens is through natural selection. As the Earth's climate changes, natural selection changes. The environmental conditions (temperature, rainfall, food sources) that allowed some animals to thrive and have a lot of offspring could change to be more favorable for another animal and lead to a new shift in the average genetic material of that population.

Q:What made you want to become a paleontologist?

A: I have always wanted to be a paleontologist from when I was a little kid. When I was in high school I liked my biology, physics, math, history, music and art classes. I decided to go to college to study biology. I made sure to do more than take my classes- I got small jobs working with fossils at the local museum and then got to start some of my own research.

Publications: Pietsch, C., Ritterbush, K.A., Thompson, J.R., Petsios, E., and Bottjer, D.J., 2019, Evolutionary models in the Early Triassic marine realm: Paleogeography, Paleoclimatology, Paleoecology. 513: 65-85.

Ivany, L., Pietsch, C., Handley, J., Lockwood, R., Allmon, W., and Sessa, J., 2018. Little lasting impact of the Paleocene-Eocene Thermal Maximum on shallow marine faunas. Science Advances 4(9) eaat5528.

Pietsch, C., Harrison, H.C., and Allmon, W.D., 2016, Whence the Gosport Sand (upper Middle Eocene, Alabama)? The Origin of Glauconitic Shell Beds in the Paleogene of the U.S. Gulf Coastal Plain: Journal of Sedimentary Research, v. 86(11), p. 1249-1268. Carrie Whittle

Genetics

Extavour Lab

Q&A with Carrie Whittle Q: How does you research help us understand how and when different organism evolved? A: My research focuses on how (and sometimes when) genes and codons and amino acids from genes have evolved in organisms. Specifically I am focused on why male and female differences in gene expression have evolved in organisms, and how their encoded codons and amino acids have evolved in different organisms. Q: I also read your paper Rapid Evolution of Ovarian -Biased Genes in the Yellow Fever Mosquito (Aedes Aegypti), what do the optimal codons you mentioned tell us about evolution? A: Optimal codons are those that have been optimized over time to be used to for very efficient translation. This means that it cost the organisms less, biochemically, to produce the gene product (protein). About evolution, this tells us that evolution in genes has favored changes that help an organism produce proteins in a less costly manner, and those that are more costly are pushed out of the species’ gene pool. Q: What is the process of identifying these optimal codons? A; The way optimal codons are typically identified is by comparing what codons are used in highly expressed genes in an organism to those that are used in lowly expressed genes. Highly expressed means produced more, and lowly expressed means produced less. For example, in the amino acid Alanine, the codon GCT may be used more often in highly expressed genes than the codon GCC. This suggests that the codon GCT is less costly to produce. Because of this, evolution may cause GCT to be used for a majority of the time in highly expressed genes. Q: Are the genes expressed in yellow fever mosquitos at all reflective of other eukaryotic organisms? A: Yes. The Yellow Fever Mosquito has some housekeeping genes, which are genes that are expressed in a wide range of organisms and often perform similar functions. However, yellow fever mosquitoes also have gene expression patterns that serve roles that are unique to them and their needs. One example of this is genes involved in blood feeding, which the females undertake in order to reproduce. In the study on yellow fever mosquitoes, we identified different expression levels in males and females and studied how fast those genes changes over evolutionary time. It was a surprise to find that highly expressed genes in females evolved rapidly because this is the opposite of what is found in most other animals, including insects. Most other animals including insects have genes with male-biased expressions that usually change faster over evolutionary time. This finding was not reflective of other eukaryotic organisms. Q: Why did you choose to enter this line of genetics or what struck you interest in it? A: I entered this line of genetics because I became interested in how and why genes change over time, and found it very interesting how ce could study gene and genome evolution using computation based approaches (rather than only using lab-based approaches). This topic has implication for all fields of biology, from plant biology, to cell biology, to medicine. For this reason I feel it is very important for all biologists to have some familiarity with molecular evolution.

Publications:

Molecular evolution of testis- and ovary-biased genes in the yellow-fever mosquito

Causes and evolutionary consequences of primordial germ cell specification mode in metazoans