Michelle Jonika

Genetics and Genomics Ph.D. Student · Blackmon Lab · Department of Biology · Texas A&M University
michellemjonika@gmail.com

Current CV | Current Resume

As an evolutionary biologist, I enjoy the puzzle-like nature of coding genetics and genomics problems, specifically bringig this approach to the evolution of genomic content and sex chromosome. Detail-orieted planning, project management, experimental design, annd clear communication are important to my critical thinking and problem solving strategies for research. I am pursuing a Ph.D. in Genetics and Genomics at Texas A&M University with an expected graduation date of Spring 2023, and I am interested in career paths in industry intersecting genetics, genomics, data science, and molecular biology. Check out some of my research projects below!


Education & Experience

Ph.D. in Genetics and Genomics

Graduate Certificate in Business

 Texas A&M University, College Station, TX

The content of genomes can be categorized into different sequence classes, into autosomes and sex chromosomes, coding and noncoding, repetitive and non-repetitive, to name but a few. Each of these classes of the genome have unique mechanisms that govern their evolution. In my dissertation work, I am studying the evolution of the genome on these three scales.
Advised by: Heath Blackmon

August 2018 - Present

PetDx

Bioinformatics Intern | Bioinformatics and Data Science Team

 San Diego, California (Virtual)
  • Leveraged high-complexity data set to predict canine cancer types
  • Used machine learning (Random Forest) approaches to train and evaluate different models
  • Performed extensive data evaluation to curate sample metrics, obtain balanced training and testing sets, and identify meaningful model parameters
June 2022 - August 2022

Bayer Crop Science

Bioinformatics Intern | Genomics Discovery and Application Team

 St.Louis, Missouri (Virtual)
  • Identifying historic data to test for epistasis
  • Developing a statistical testing framework to identify interactions between introgressed loci
  • Three-month, full-time position exposure inn an industry setting
  • Establishig multi-disciplinary connections with teams with expertise in data science, genommics, and precision breeding
May 2021 - August 2021

Bachelor of Science in Forensic and Investigative Science

Minor: Genetics

 Texas A&M University, College Station, TX

Undergraduate Thesis: Genes as Markers of Sex for Forensic Entomology — Identifying genes that can be used for a transcriptional approach to sex identification in blow fly species of forensic importance: Lucilia sericata (Diptera: Calliphoridae) (Meigen), Cochliomyia macellaria (Diptera: Calliphoridae) (Fabricius), and Chrysomya rufifacies (Diptera: Calliphoridae) (Macquart).
Advised by: Aaron M. Tarone

August 2014-May 2018

Gastrointestinal Laboratory (GI Lab) at Texas A&M

Undergraduate Research Technician

 Texas A&M University, College Station, TX

Investigated the effects of antibiotics on the gut health and miicrobioita of companion animals

January 2016-August 2018

Research

Mode and Tempo of Microsatellite Evolution in Hexapods

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.

The Impact of Centromere Type in Chromosome Number Evolution

Despite the fundamental role of centromeres two different types are observed across plants and animals. Monocentric chromosomes possess a single region that function as the centromere while in holocentric chromosomes centromere activity is spread across the entire chromosome. Proper segregation may fail in species with monocentric chromosomes after a fusion or fission, which may lead to chromosomes with no centromere or multiple centromeres. In contrast, species with holocentric chromosomes should still be able to safely segregate chromosomes after fusion or fission. This along with the observation of high chromosome number in some holocentric clades has led to the hypothesis that holocentricity leads to higher rates of chromosome number evolution. To test for differences in rates of chromosome number evolution between these systems, we analyzed data from 4,393 species of insects in a phylogenetic framework. We found that insect orders exhibit striking differences in rates of fissions, fusions, and polyploidy. However, across all insects we found no evidence that holocentric clades have higher rates of fissions, fusions, or polyploidy than monocentric clades. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes. Instead, we suggest that other co-evolving traits must explain striking differences between clades.

Why Not Y Naught: The Paucity of Univalent Sex Chromosome Systems

Genetic sex determination systems have evolved and continue to evolve in a wide diversity of eukaryotes. Synthesizing data from a series of recent papers, we find sex chromosome systems documented in 12,207 plants and animals. However, among all the species with information, only a single species—the New Zealand frog, Leiopelma hochstetteri—appears to have a univalent sex-specific chromosome acting as a dominant sex-determining chromosome. We ask why YO and WO systems are so uncommon. We first evaluate evidence for the existence of YO and WO systems and their potential to arise by reviewing the literature. We then discuss challenges YO and WO systems may face over evolutionary time and the impact of sexually antagonistic (SA) variation on their fates. We conclude that YO and WO systems are unlikely to remain stable, and their transitory nature can explain why they are rare.

Mammalian Pseudoautosomal Region (PAR) Evolution

The classic model of sex chromosome evolution begins with a pair of homomorphic sex chromosomes and leads to eventual decay of the Y chromosome in regions of suppressed recombination. Despite degradation of the Y chromosome, a pseudo-autosomal region (PAR) persists in most species. The PAR is a region of homology between sex chromosomes that maintains recombination and is essential for segregation of sex chromosomes during meiosis. What happens to sex chromosomes once the PAR becomes very small? The fragile Y hypothesis predicts that as PAR sizes become smaller, the risk of aneuploidy increases, increasing the probability of Y chromosome loss, achiasmatic meiosis, or rejuvenation through translocation or fusion of autosomal material. While these outcomes are perceived as rare due to their absence in most mammals, each of them is quite common across the tree of life and all have occurred in mammals. The unique nature of sex chromosomes has made them a focus of evolutionary biology since their discovery more than a century ago, but PAR size has been estimated in just 9 species of mammals. For this reason, many questions have remained unanswered due to limitations of available data and analysis tools.

Current methods to estimate PAR sizes are time consuming and costly. For this reason, I developed an approach to train and deploy a convolutional neural network (CNN) to accurately predict PAR size. I am currently using my developed pipeline to generate training datasets and hope to train and deploy the CNN in the next few months. The trained CNN will allow for estimation of PAR size for hundreds of species both with publicly available genomic sequences and through de-novo sequencing of DNA available from collaborators. Additionally, this tool will be made broadly available to the community as a publicly available genome annotation tool to improve all future genome assemblies. With vastly increased numbers of PAR size estimates, we can for the first time begin to understand the dynamics of this genomic trait and determine whether achiasmatic meiosis, fusions of autosomes to sex chromosomes, and Y loss are associated with small PAR sizes.


Publications

Check out my Google Scholar page

2022

M. Pitonak, M. Aceves, P.A. Kumar, G. Dampf, P. Green, A. Tucker, V. Dietz, D. Miranda, S. Letchuman, M.M. Jonika, D. Bautista, H. Blackmon, J.N. Dulin. 2022. Effects of Biological Sex Mismatch on Neural ProgenitorCell Transplantation for Spinal Cord Injury in Mice. Nature Communications. In Print.

M.M. Jonika, J.M. Alfieri, T. Sylvester, A.R. Buhrow, H. Blackmon. 2022. Why Not Y Naught. Heredity 1-4 [PDF]

J.M. Alfieri, G. Wang, M.M. Jonika, C.A. Gill, G.N. Athrey, H. Blackmon. 2022. A Primer for Single-Cell Sequencing in Non-Model Organisms. Genes 13(2):380 [PDF]

2021

M.L. Pimsler, C.E. Hjelmen, M.M. Jonika, A. Sharma, S. Fu, M. Bala, S.H. Sze, J.K. Tomberlin, A.M. Tarone. 2021. Sexual Dimorphism in Growth Rate and Gene Expression Throughout Immature Development in Wild Type Chrysomya rufifacies (Diptera: Calliphoridae). Frontiers in Ecology and Evolution 9:368 [PDF]

2020

S. Ruckman* (Co-first author), M.M. Jonika* (Co-first author), C. Casola, H. Blackmon. 2020. Chromosome Number Evolves at Equal Rates in Holocentric and Monocentric Clades. PLOS Genetics 16(10):e1009076 [PDF]

M.M Jonika, J. Lo, H. Blackmon. 2020. Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution. Genes 11, 945 [PDF]

M.M. Jonika, C.E. Hjelmen, A.M. Faris, A.M. Tarone. 2020. An Evaluation of Differentially Spliced Genes As Markers of Sex for Forensic Entomology. Journal of Forensic Science. 65:1579-1587 [PDF]

2019

J. Lo, M.M. Jonika, H. Blackmon. 2019. micRocounter: Microsatellite Characterization in Genome Assemblies. G3: Genes | Genomes | Genetics 9(10):3101-3104 [PDF]

R.D. Perkins, J.R. Gamboa, M.M. Jonika, J. Lo, A. Shum, R.H Adams, H. Blackmon. 2019. A Database of Amphibian Karyotypes. Chromosome Research 27:313-319 [PDF]

2018

A.B. Blake, B.C. Guard, J.B. Honneffer, M.M. Jonika, J. Chaitman, J.A. Lidbury, J.M. Steiner and J.S. Suchodolski. 2018. Altered Fecal Fatty Acid, Sterol and Bile Acid Metabolism in Dogs with Acute Diarrhea. Journal of Veterinary Internal Medicine 32:2248.[PDF]


GitHub Repository Coding Contributions


Skills

  • Genomics: SRA, Trimmomatic, bwa, samtools, bamtools, GATK, PLINK, BUSCO, rrBLUP, GEMMA
  • Genetics: Genome structure evolution, Sex Chromosome evolution, Morphometrics, Genomics analysis, Genome Assembly
  • Molecular Biology: Primer optimization, gDNA/DNA extraction, RNA extraction, PCR, qPCR, Gel visualization/imaging
  • Programming: R, Unix/Linux, Git, tidyverse, conda, SQL, Python, LaTeX, HTML/CSS
  • Data Science: Large dataset management (>20 Gb), Bayesian statistics, Phylogenetics, Simulations, Data Visualization (ggplot2)
  • Soft Skills: Project management, Public Speaking, Leadership, Multi-disciplinary collaboration, Adaptive problem solving

Teaching

Teaching Assistant

Anatomy and Physiology I | Spring 2022 (Texas A&M)

Critical Writing in Biology | Spring 2021 (Texas A&M)

Critical Writing in Biology | Fall 2020 (Texas A&M)

Introduction to Genetics Laboratory | Spring 2019 (Texas A&M)

Guest Lecturer

Bioinformatics | Topic: Genetic Privacy | November 2021 (Utah Valley University)

Bioinformatics | Topic: Genetic Privacy | October 2019 (Texas A&M)


Awards & Certifications