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Florida Plants on the Tree of Life

Komal Handoo, Anika Hedrich, Jose Santana, Ethan Stolen, and Griffin Willman

Authors:  Komal Handoo*, Anika Hedrich*, Jose Santana*, Ethan Stolen*, Griffin Willman*, Douglas Soltis, Pamela Soltis, Johanna Jantzen

Faculty Mentor:  Johanna Jantzen

College:  College of Liberal Arts and Sciences

Abstract

Plant phylogenies are useful in several key applications, including analysis of geographical distributions, biodiversity, and evolutionary history. In particular, phylogenetic trees have the potential to show many of the ways different species and traits associated with them are related. There are still many gaps in the tree of life, including many plant species that have yet to be sequenced. We created unique trees of Florida plants within certain clades to show how species within these groups are related. In an effort to resolve phylogenies for Florida plants, genetic information for these species was found by performing PCR on extracted DNA samples and obtaining sequences from GenBank for comparison. We created optimal phylogenies of five plant clades using RAxML software and plotted observed traits, including ploidy, geographical distribution, petal morphology, and medicinal properties, on these trees. Each clade was used to answer a specific question. For these clades, we either reconstructed ancestral states of morphological traits, estimated the number of origins of chemical compounds, evaluated the geographic distribution, or calculated the phylodiversity within Florida. We demonstrate the utility of phylogenies to answer a wide range of questions about the evolutionary history of the flora of Florida.

Poster Pitch

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Poster

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44 Responses
  1. Johanna Jantzen

    Welcome to our poster! The undergrad researchers are here from 2-3 today to answer your questions.

  2. Griffin Willman

    Hi! My name is Griffin Willman. I studied how geographical distance affects the genetic relatedness of species within the family Poaceae (grasses). My section is highlighted in green on the poster. Feel free to ask questions you have about my research or our general methods. My peers will also be here to answer any questions. Thanks!

  3. Douglas Soltis

    nice job folks. Griffin, you found that in a geographic area there were groups of closely related species. Are some of those close relatives largely endemic to that area or that general portion of Florida? That is in some cases are we looking at clusters of related endemics to a region….or are these all widespread? thanks

    1. Griffin Willman

      Yes! Many of my species were endemic to certain areas. For example, a few of the species only appeared along Florida’s coast, and others only occurred in the South. I tried to include as many of these types of species as possible, but since I was analyzing grasses, they were somewhat limited and many were also widespread throughout the state.

      1. Douglas Soltis

        okay that so that is kind of cool–maybe looking at areas of species divergence and endemism. So many cool things you learn from a phylogeny!

  4. Maria Cortez

    Here are two questions to all the students involved in this project, Komal, Anika, Jose, Ethan and Griffin.
    1 – What was the most important lesson you learned by doing this research?
    2 – Have you thought about how to communicate your research to the general public?

    1. Anika Hedrich

      The most important lesson I learned by doing this research was the basic necessities of conducting research and documenting all of our findings. We had a wonderful balance between hands on research experience in the Soltis lab, where we were taught how to follow proper procedure, as well as detailed lessons online of how to best analyze the data we collected. One aspect that I will carry on with me from this project in particular is how to keep an organized lab notebook. Regarding your question about communicating my research to the general public, I have no plans right now on how to best convey my findings, but that is a great idea of something that can be done in the future. Thank you so much for your questions.

    2. Ethan Stolen

      Thank you for the question. The most important lesson that I learned from completing this research project was understanding the biodiversity of plants in Florida and the importance of phylogenetic research. For example, we studied plant phylogenies in an effort to better understand the species distribution within Florida. This research showed us how important the biodiversity of Florida is and the effect that climate change will have on our state.

    3. Ethan Stolen

      Thank you for you question about how to communicate our findings with the public. I think that it is important that we communicate the results of our study, not just to our peers at this symposium, but also to the public so that they can gain an appreciation for the diverse flora of Florida. I think that sharing this information at public outreach events would be the way to go.

    4. Griffin Willman

      I really learned the importance of documenting everything done in the lab. This was imperative to helping me keep track of all the steps and procedures of the molecular methods we used. I think this research could be really beneficial to the general public. If for nothing else, it can be used to show the diversity and range of Florida’s ecosystems. Showing these phylogenetic relationships and presence of differing species in different ecoregions could help illustrate to people the complexity of the environments around them. That said, I haven’t thought of specific ways to share this with the public yet, but I will consider it for the future. Thank you!

    5. Komal Handoo

      Hi Maria, thanks for your question! This being my first research experience, was a completely new environment and I learned a lot, from different lab procedures, to working with new people, to what it really means to do research. I think the most important thing I learned was that research is not super cut and dry, and you don’t always get the answer you want or the one you’re expecting. However, it is still an extremely rewarding experience and I learned so much that I will carry forward with me.

      In terms of communicating my research with the general public, I think there is more to be expanded on in my research before I try to convey it to the general public – for one, I want to use additional loci to help eliminate some of the polytomies in my phylogenetic tree. Further research could be done on species closest to those with known phytochemicals, such as Crataegus pentagyna and Crataegus marshallii to see whether they also contain phytochemicals with medicinal properties. I definitely think this research is a work in progress, but in the future I hope to share at more symposiums.

    6. Jose Santana

      Thank you for your question! The most important thing that I learned through this research is that research challenges you to strengthen your focus, organization, and discipline. In regards to focus, it was required every time I entered the Soltis Lab and had to use the tools at my disposal effectively and accurately. Organization was also a key part of this experience, as keeping all of my data organized across different formats was a challenge that I was only able to tackle as my organizational skills got better through the research. Discipline was needed in order to truly appreciate the research process, and realize that the work that myself and fellow peers are doing is important for our collective knowledge. It gave me a deeper appreciation for the process and all of the people who carry it out, as it became kind of noble in my head. As for your other question, no I have not thought of this, but that you’ve asked and put the idea into my head, I am going to look into resources on how this could happen.

      1. Maria Cortez

        Jose, I just saw your reply now, sorry. Yep, you do have to be disciplined when doing research. 100% agreed with this!

        I am happy you will think of a way on how to reach the pubic with your research!

    7. Maria Cortez

      Hi everyone, thanks for the answers! In the rush to write down my questions I forgot to congratulate you, Johanna, Doug and Pam on this amazing job! Well done.
      I agree that documenting your work in very important and very problematic if overlooked, so I am happy to hear you learned this lesson.
      I also, think phyogenies are very important and can be used to answer so many questions, like explaining the complexity of an environment!
      Outreach is one of the best tools to engage with the public, and you can start by explaining what you did to the “lay” people surrounding you.
      Not getting the answer you expect is totally normal, and in my humble opinion should be looked at with as much excitement as if you had gotten the expected answer. Any answers is valid, as long as you followed the proper methodology, The important thing is how to interpret it ; )

  5. Lauren Whitehurst

    Hi all! It is great to see the final poster, it looks fantastic!
    Komal, I am very interested in the medicinal properties of plants I love the approach you took. Do you know if there is a history of any native people of Florida who used Crataegus for its medicinal properties?
    Great job to all!

    1. Komal Handoo

      Hey Lauren, thank you for your question! So there are only 10 known Crataegus species in Florida, none of which have known medicinal properties. The species with known medical qualities have been found mostly in China and Europe, specifically the UK. One of the reasons I explored this research was to see if any of the Floridian Crataegus species would be closely related enough those species in China and Europe to potentially also have medicinal properties. One species in Florida that seemed likely is Crataegus marshallii, I know the tree is hard to see on the poster, but Crataegus marshallii is a sister to Crataegus monogyna, which has been used in Traditional Herbalism as well as Evidence Based Medicine to treat cardiac problems. This could potentially mean that Crataegus marshallii might also share some of the same phytochemicals that contribute the medical efficacy of Crataegus monogyna.

      1. Douglas Soltis

        cool –this relates to my similar hotspot question. So has the chemistry of Crataegus marshallii been examined? For most plants no one has looked closely at chemical composition

        1. Komal Handoo

          I hadn’t seen any literature on any Florida Crataegus species being known for their medicinal properties, but the tree indicated that Crataegus marshallii likely does, and when I looked it up, someone at UF has done research on it being used by Native Americans to strengthen the heart and lower blood pressure! However, apart from that one website, I was unable to find anything else on it, and nothing in medical journals, so I guess the assumption is that it must have a similar chemistry, but has not yet been tested.

  6. Prabha Amarasinghe

    This is a great collection of multiple studies. Congratulations, all!

    I have a question related to medicinal properties associated with phytochemicals in Crataegus: Did you use any program to map/link phylotochemicals in the Crataegus phylogeny? If so, what is the program? Good job, Komal!

    1. Komal Handoo

      Hi Prabha, thank you for your question! So, the records of Crataegus species with associated medicinal properties/high concentration of phytochemicals were drawn from literature on their historic use as well as modern day research on their use in alternative medicine. From these I recorded the species used, but I didn’t test their phytochemical levels myself. I then used rbCl and matK loci to create a phylogenetic tree of as many Crataegus species as I could, including those known medical plants, as well as all Floridian species of Crataegus. The program I used to create this tree was Mesquite, and I mapped the trait using maximum parsimony. I highlighted the known species in blue on the tree separately. I hoped this properly answered your question!

  7. Ginny Greenway

    Interesting research questions everyone!
    Komal- do you think using a phylogenetic approach could help us to predict/ identify plant species which may have useful medicinal properties we don’t yet know of?

    1. Komal Handoo

      Hey Ginny, that’s exactly what I was hoping! After developing the tree, we can now see at least a couple species, such as Crataegus pentagyna, marshallii, and hupehensis, that have closely related evolutionary patterns to species with known medicinal properties, and while they have so far not been proven to also have these medicinal properties, they can be tested and potentially be used in medicines. Thank you so much for your question!

  8. Pam Soltis

    Awesome work, everyone!!! You are amazing!
    Could each of you please answer the following question?
    To what extent do you think the character or variable that you examined has phylogenetic signal? I know you’re still gathering and analyzing data to some extent, but what do your preliminary data say about this? In general, is everything phylogenetically based, or are some characters random with respect to their evolutionary history?

    1. Griffin Willman

      From my preliminary data, I can see that in some of the ecoregions I analyzed, only certain species that are closely related are present. However, in others, nearly all of the species are present or only a few, unrelated species are. This leads me to believe that there are very specific factors that determine the success of individual species within the family I looked at (Poaceae). In some of the ecoregions, all of the factors necessary are present for many species, and in others, only those for a select few. So, I would say that sometimes, success in an ecoregion is phylogenetically based and other times it is more random. You bring up a really interesting distinction here, and I would like to continue to investigate that. Thank you!

    2. Ethan Stolen

      The trait that I examined, polyploidy, does seem to have a phylogenetic signal based on the preliminary data. This is illustrated by a number of clades within my phylogeny having a uniform number of chromosomes, indicating that the chromosome number is phylogenetically based. However, the chromosome numbers can still vary within clades, as I saw one species with 98 chromosomes. So I think that while the trait is phylogenetically based, there is also the possibility of genomic duplication occurring randomly.

  9. Derek Pena

    I applaud your for your highly detailed research that covered a wide variety of topics regarding the flora here. I was wondering what sorts of future implications the tracking of the evolution of the medicinal properties in the genus Crataegus could potentially have? Do you have any ideas as to how that may help explain some historical uses of this genus in medicine or benefit the development of medicine in the future?

  11. Lauren Whitehurst

    Hi again!
    Griffin, what made you chose those two ecoregions to analyze and did you expect major differences between these two regions?
    Anika, this is a very interesting idea! I would be very interested to see the results of the PD analyses. Do you have any preliminary guesses as to which county might have the highest Phylogenetic Diversity?
    Great work!

    1. Griffin Willman

      Hi!
      I plotted a character matrix for all of the ecoregions present in Florida as designated by the EPA, but I chose those two to include on the poster because they show a clear relationship between region and genetic relatedness. It might be a little difficult to see, but the branches that are “bolded” on the tree indicate that species is present within that ecoregion. There are groups of bolded species that are close together on these two trees, indicating that some relationship is present. There are other ecoregions where this also occurred, but I thought these two did a good job of illustrating this relationship.

    2. Anika Hedrich

      Hi! At this moment, I am still in the process of analyzing my results, and it seems that both Alachua and Dade county have high levels of phylogenetic diversity.

  12. Douglas Soltis

    Hi Ethan.

    Good job–I wonder if there might be a difference between diploids and related polyploids in habitat/niche rather than range size?
    thanks

    1. Ethan Stolen

      Thank you for the suggestion! I think that this is definitely the next question to be asking in this research. I found that there is a negative correlation between the chromosome number and range size, and I thought that this could possibly be due to the polyploid species being more adapted to a single niche and therefore having a smaller range size, contrary to my prediction. I am thinking that this might reveal some information about how species evolve and the effect of polyploidy on the evolution.

  13. Marta L. Wayne

    Great teamwork. Really enjoyed your presentation and learning more about your research. I will definitely be looking into historical uses of hawthorne.

  14. Douglas Soltis

    Hi Anika

    It will be cool to see those PD estimates by county! Alachua county actually has a high PD overall but these family analyses are interesting. Are all of the Plantaginaceae in your study natives? There are a number of nonnative weedy introduced species

    1. Anika Hedrich

      Alachua county did have one of the higher PD levels! I am not sure if all of the Plantaginaceae in my study are natives, and you bring up an interesting point. I will have to do more research into the possibility of nonnatives that may be present and if they impacted my results.

  15. Ellen Humbel

    Awesome and diverse work!
    Jose – do you have any thoughts on why we see these patterns in flower morphology across clades? Could this be related to the types of pollinators visiting these taxa?

  16. Douglas Soltis

    Hi Jose

    Might be good to look at seed characters too–these are often tied to dispersal mechanisms so that would be neat to look at now as well

  17. Douglas Soltis

    Hi Komal

    So it looks like there is one small clade (hotspot) in particular where these compounds occur–is that in two species? So in their closest relatives in that clade were the compounds lost? Or has no one really looked?

    this reminded me of the hotspot in TreeTender!

    1. Komal Handoo

      The assumption is that no one has looked, since there was no available literature on their uses as medicine. The research project was aimed to find these species that were phylogenetically related enough that they might also possess high concentrations of phytochemicals that can be used for medicine, especially in Florida. Hopefully in the future I can test their levels of the specific phytochemicals known to aid in high blood pressure and other heart problems, which can then potentially be used in medicines!

  18. Shan

    Hi Jose,

    Very cool study!

    I have a question about the relationship between flower morphology and pollinators. Does the species with only disc flower (which I guess is non-showy) have less/fewer pollinators?

    Shan

  19. Dr. Donnelly

    I like this poster – a really nice presentation of an interesting collection of projects. Nice work!