Specht Lab Research Projects, 2019-2020
The following pages contain research projects to start Fall 2019 in the Specht Lab. They are proposals from graduate students and postdoctoral researchers who are leading these research projects as part of their larger research goals within the lab. Each page contains one project. For more information about these research projects or the lead researchers, please check out the Specht Lab website: blogs.cornell.edu/specht.
Please reach out and contact the Lead researcher of any projects you are interested in. You can set up a time to discuss the project as an interview. I’d recommend sending them some information about who you are and why you are especially interested in their project, given your current interests and your future goals.
An Enigmatic Catalyst of Biodiversity: Homoploid Hybrid Speciation in Arisaema (Araceae).
Lead: Justin Scholten (PhD Student, Plant Biology)
Project Description: Homoploid hybrid speciation, a concept that has intrigued evolutionary biologists for decades, stands as a compelling mechanism of generating biodiversity. In contrast to polyploid hybrid speciation, where genome duplication plays a pivotal role in preventing introgression, homoploid hybrid speciation leads to the emergence of a novel species without a change in chromosome number. Through the recombination and assortment of genetic material from two distinct parental species, hybrids may exhibit unique phenotypes that rapidly evolve reproductive isolation from both parental populations in sympatry. This process challenges conventional species concepts and provides invaluable insights into the complex interplay between hybridization, adaptation, and speciation, shedding light on the nuanced mechanisms that drive the remarkable diversity of plant life on Earth.
The goal of this research project is to comprehensively investigate signatures of homoploid hybrid speciation within a species triad of Japanese Arisaema species. To achieve this, the study will be structured around three main aims:
- Morphological and Genomic Evidence of Hybridization: The first aim involves an in-depth examination of morphological and genomic data from the three closely related Arisaema species where homoploid hybrid speciation is hypothesized to occur. By utilizing cutting-edge genetic sequencing techniques and detailed morphological analyses, the project aims to identify and quantify the genetic and phenotypic signatures of hybridization, uncovering evidence of homoploid hybrid speciation. This will help us understand the genetic basis of species formation and evolution within the triad.
- Mechanisms of Reproductive Isolation: The second aim seeks to unravel the intricate mechanisms that facilitate reproductive isolation of the hybrid species from both parental lineages. This investigation will delve into the genetic, ecological, and behavioral factors that contributed to the divergence of the hybrid species, shedding light on the evolutionary dynamics that maintain the integrity of these three distinct lineages.
- Ecological Implications: The third aim focuses on exploring the ecological implications of homoploid hybrid speciation within the Arisaema species triad. Similar to above, this entails a comprehensive analysis of the ecological niches occupied by each species, including habitat preferences, interactions with pollinators and competitors, and potential advantages of hybridization in various ecological contexts. Understanding the ecological consequences of hybrid speciation is vital for assessing the broader impact of this phenomenon on biodiversity and ecosystem dynamics.
Undergraduate’s Role: The undergraduate will assist in data collection and analysis during a 2-4 week field expedition to Shikoku Island (Japan) in May 2024. The student will learn how to collect morphological, genetic, and ecological data in the field in addition to making living and herbarium collections to serve for future study. Upon return, the student will be encouraged to assist in preparing and analyzing the materials they collected for co-authorship opportunities on resulting publications.
Undergraduate’s Qualifications: No prior coursework is required, however students with a strong interest in botany, speciation, and conducting biological fieldwork will find the experience the most rewarding. The student should be physically capable to participate in outdoor fieldwork for the duration of the expedition (2-4 weeks). Individuals with a background in botany, ecology, and field biology are especially encouraged to apply. Preference will be given to students that are fluent or proficient speakers of Japanese. Student must have a valid passport for international travel.
Association of floral traits and biogeography in the genus Calochortus
Lead: Adriana Hernandez (PhD Student, Plant Biology)
Project Description
Many factors influence the evolution of floral traits, such as pollinators, herbivores, and climate. This project will explore the relationship between floral traits and ecological niche space in the context of evolution and adaptation in the genus Calochortus. Calochortus is comprised of 75 species, and it exhibits four floral syndromes with multiple independent derivations of each syndrome across the phylogeny. The genus is distributed throughout North America with a center of diversity in California and a few cases of extremely narrow endemism. The ecological niche of each species will be modeled and niche overlap between species pairs will be calculated in order to associate abiotic variables with floral phenotypes and begin to address the question: how do floral syndromes affect ecological distributions?
Undergraduate’s Role
Undergraduate researcher will work independently to download occurrence data and ecological data from online databases, organize and format data, model ecological niches for each species under a MAXENT model, and calculate niche overlap in ENMTools in R.
Undergraduate’s Qualifications
Although not required, experience working in R is preferred. Attention to detail is essential. Students who are enthusiastic about ecology and floral trait evolution may benefit the most.
Inferring evolutionary history and population dynamics in the hyper-variable Calochortus venustus
Lead: Adriana Hernandez (PhD Student, Plant Biology)
Project Description
This research proposes to address first principles of evolutionary biology– linking phenotype to genotype– in a hyper-variable system, Calochortus venustus (Liliaceae). A genotyping-by-sequencing approach (RAD-Sequencing) will be used to identify thousands of variable genetic sites (SNPs) between individuals. Samples from across a wide phenotypic and geographic distribution have been collected. We aim to reveal if different phenotypes represent different biodiversity entities, to identify genetic variants, and to assess population structure. Phylogenetic tree inference methods will also be used to infer historical range expansion to provide insight into how hyper-variable floral traits evolved across the California landscape. In combination with ecological niche modeling techniques, findings will ultimately be used to reveal if unique phenotypes are delimited by genetic factors such as fixed population structure, abiotic ecological variables such as rainfall, or a combination of both.
Undergraduate’s Role
Undergraduate researcher will work semi-independently to prepare silica-dried floral tissue samples for sequencing. This includes DNA extraction, quality check via nanodrop, Qubit, and gel assays, library preparation, and minimal data entry.
Undergraduate’s Qualifications
No prior lab experience or coursework is required, but students interested in botany, population genetics, evolution, and learning basic DNA techniques will find this experience most rewarding. Attention to detail is essential.
Evolution of Plant Architecture: the inflorescence
Lead: Jesús Martinez-Gómez (PhD Student, Plant Biology)
Project Description:
The arrangement of flowers along a stem, is an important feature of the sessile life of a plant. Plant architecture dictates many aspects of flower development, flower senescence and the formation of fruits. These inturn influences how pollinators interact with a plant which ultimately result in plant reproduction. Despite their importance, we lack an understanding of the evolutionary patterns and processes that shape the diversity of plant architecture. The aim of this project is to synthesize existing plant morphological data and analyze them with contemporary evolutionary/bioinformatics methods and test existing hypothesis of plant architecture evolution. Through this we will gain a deeper understanding of how plant architecture evolved in Monocots.
Undergraduate’s Role:
The undergradaute(s) will score trait data from a variety of online resources, including literature and images of herbarium specimen, under the supervision of a graduate student. The undergradaute(s) will learn how to analyze the data they collected using statistical and phylogenetic approaches. Students will learn how to manipulate data in the language R and analyze this using phylogenetic programs. In addition to research student are required to attend a 1.5-2hr lab meeting once a week (exception can be made for schedule conflicts). Towards the end of the project undergradaute(s) will be highly encouraged to present their research, in the form of a poster or a talk, at a conference such as SACNAS, ABRCMS, Botany and/or Evolution. Students may also be occasionally asked to water plants.
Undergraduate’s Qualifications:
No prior coursework is required, however students with a strong interest in botany, evolution or computational biology will find the experience most rewarding. Student should feel comfortable working on a computer during the duration of their project. Independent individuals with strong attention to detail, who have good record keeping skills and like to learn about plants are encouraged to apply.
The geography of a Neotropical plant radiation: Distribution modelling of the spiral gingers
Lead: Eugenio Valderrama (Postdoctoral Researcher)
Project Description: One of the most widely recognized patterns in ecology and evolutionary biogeography is that lineages tend toward species-richness in tropical regions; however, the mechanisms that originate such patterns of diversity are still poorly understood. In addition, richness is not uniform across the tropical regions – with ca.32,000 species of flowering plants in tropical Africa, ca.50,000 in Southeast Asia and ca.90,000 in the Neotropics. Hypotheses addressing higher species richness in the Neotropics include opportunities for allopatric speciation, the availability of new habitats through uplift of the Andes, and major habitat and climate shifts prompted by shifts in the Amazon river drainage and closure of the Panama isthmus. Possibilities for prezygotic reproductive isolation driven by shifts in pollination syndromes, adaptation to local conditions leading to ecological speciation, or the effects of polyploidization on diversification rates of Neotropical lineages are additional mechanisms proposed to explain the relatively higher diversity of Neotropical plant lineages compared to their Paleotropical congeners.
The family of pantropical Spiral Gingers (Costaceae Nakai; ca.125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher taxonomic diversity in South and Central America (ca.65 Neotropical species, ca.31 African, ca.23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus Costus L (ca.50spp.). The Neotropical species of Costus show multiple shifts in pollination syndromes, with closely related species that are associated with either insects or birds demonstrating rapid ecological isolation. Furthermore, the distributions of Neotropical Costus species show higher overlap (higher degree of sympatry) and diversification rates are higher in the bird pollinated lineages suggesting diversity could not be completely attributed to allopatric speciation. Estimating the distributions of all known Neotropical Costaceae would allow to study the signature of the speciation mechanisms in the geographic range and to compare the role of geography in the speciation of insect vs. bird pollinated and slow vs. fast diversifying lineages.
The undergraduate(s) working on this project will estimate distributions of all Neotropical Costaceae species with Ecological Niche Modelling methods, as well as geographic overlap, niche overlap and niche breadth indexes. A comprehensive dataset of expert curated herbarium specimens as well as climatic and remote sensors data are available. This work will be part of a broader project of the Specht lab aiming at a revision of the taxonomy and a robust species level phylogeny of the Neotropical lineages of the family that will be used to study the distribution and ENM results with phylogenetic comparative methods in collaboration with the student.
Undergraduate’s Role: The student will be involved in data organization, georeferencing and analysis with Geographic Information Systems (GIS) and ENM methods now mostly used within R (e.g. ENMtools, Maxent). Participation in fieldwork will depend on enthusiasm for plant collecting in the tropics and funding applications.
Undergraduate’s Qualifications: Students interested in evolutionary ecology, tropical plants, computational biology and developing analytical skills in R and GIS, are highly encouraged to participate. Enthusiasm for tropical biology and R programming, good record keeping, attention to details and data base handling are crucial. Some familiarity with Spanish (helps with georeferencing) is desirable but not required.
Tissue Culture of Zingiberales Species
Lead: Heather Phillips (PhD Student, Plant Biology)
Project Description: The genetic regulatory network (GRN) for bilateral, otherwise known as zygomorphic, development was originally discovered in the common snapdragon (Antirrhinum majus) and includes several transcription factors belonging to the MYB-like transcription factor family. Through expression and gene evolution analyses, we have confirmed that this same GRN has been co-opted independently within the Zingiberales in order to direct zygomorphic floral development. Using a candidate gene approach, we are developing knockout lines for the transcription factors involved in zygomorphic development of several Zingiberales species, including Costus spicatus, Musa basjoo and Canna indica. A loss of zygomorphic development in these lines will confirm the role of these genes in zygomorphic development.
The undergraduate(s) working on this project will work in collaboration with the Plant Transformation Facility (PTF) to establish stable tissue culture for these species of interest, as well as within the Specht lab to develop cloning vectors for these knockout lines. This project will involve a variety of wet lab benchwork, including media preparation, tissue culture work and molecular cloning.
Undergraduate’s Role:
The undergraduate researchers will be in involved in media preparation, tissue culture, and molecular cloning work related to developing targeted CRISPR/Cas9 knockout lines. The students may also have the opportunity to assist with the development of stable transformation protocols for the species of interest. The student will also be encouraged to participate in weekly Specht lab meetings.
Undergraduate’s Qualifications:
Students with an interest in plant morphology, evolution and development will find this experience the most rewarding. The student should also have some prior experience with wet lab work, however some training can be provided. Attention to detail and good note-taking skills, especially in a laboratory environment, are essential. The student should be comfortable and enthusiastic about working in a wet laboratory environment and repeating experiments as necessary. They will be expected to enroll in several online safety courses and follow all guidelines related to safe laboratory procedures.
Fusion in flowers: Evolution of the CUC Gene Family
Lead: Heather Phillips (PhD Student, Plant Biology)
Project Description: Fusion of various floral organs, including the sepals, petals and stamens, has driven increased phenotypic variation within specific angiosperm families and allowed for the development of specialized plant-pollinator relationships. The degree of floral fusion varies widely within angiosperms, however the condition of fused petals, or sympetaly, is ancestral to the Asterids. This trait likely evolved in the most recent common ancestor of the order Ericales and Asterids, and within the Ericales, has been lost and regained multiple times.
Fusion is driven by the NAC-domain boundary genes, including Arabidopsis CUP-SHAPED COTYLEDON (CUC) and Petunia NO APICAL MERISTEM (NAM). Increased expression of these boundary genes at the boundaries of organ primordia promotes organ separation, while a loss of function often leads to fused phenotypes. Based on this model of fusion, the student will investigate the CUC family of genes within the Ericaceae family. This will include gene isolation via PCR, sequencing, and phylogenetic analysis.
Undergraduate’s Role:
The student will perform DNA extractions for species of interest within the family Ericaceae, and isolate CUC gene sequences using PCR. Given the time available, they may also be involved in morphology scoring of these species for the degree of floral fusion and related floral traits. The student will also be encouraged to participate in weekly Specht lab meetings.
Undergraduate’s Qualifications:
Students with an interest in plant morphology, evolution and development will find this experience the most rewarding. The student should also have some prior experience with wet lab work, however training can be provided. Attention to detail and good note-taking skills, especially in a laboratory environment, are essential. The student should be comfortable and enthusiastic about working in a wet laboratory environment and repeating experiments as necessary. They will be expected to enroll in several online safety courses and follow all guidelines related to safe laboratory procedures.
Angiosperm wide investigation of floral organ size and fusion
Lead: Jacob Landis (NSF Postdoctoral Fellow)
Project Description: In angiosperms (flowering plants) flowers play an important part in reproduction by attracting the appropriate pollinators. The overall size of flowers and their shape (which can change based on which floral organs are fused and how) help govern which visitors to the flowers get access to the pollen or the nectar. Across the flowering plants flowers range in size from microscopic flowers in Wolffia to flowers 3 feet in diameter in Rafflesia. Several studies have looked at the genetics of flower size and floral fusion, with many candidate genes having been identified. However, most of these genes have only been characterized in model plant species such as Arabidopsis thaliana. The expression patterns and whether these genes play a role in floral organs in nonmodel species is yet unknown. This project will start to address these unknowns by using a data set of 165 transcriptomes spanning the angiosperm tree of life. Known candidate genes will be identified, aligned, and analyzed. The goal is to determine if candidate genes are found in all angiosperms, or if certain clades retain a subset of genes. Signatures of selection will also be calculated to look at the evolution of these genes across all of angiosperms.
The undergraduates working on this project will help with the identification and analyses of candidate genes, as well as relating the genetic information back to phenotypic information widely available. This project does have a strong bioinformatic aspect, with future wet lab work possible in the near future. Previous computational experience is not necessary but a desire to learn computational methods is ideal.
Undergraduate’s Role:
The undergraduate researchers will be involved in data analysis using a suite of phylogenetic programs including candidate gene identification, alignment, gene tree building, and tests for sings of selection. Additionally, searching through available databases will need to be done to identify flower phenotypes to associate with genes.
Undergraduate’s Qualifications:
Interests in bioinformatics is a must, but previous experience is not required. Attention to detail and following a protocol are essential skills. Interest in evolution and how traits change between closely related species will make the project more fulfilling.