Biological Sciences

Permanent URI for this collection

https://hdl.handle.net/10323/11883

Browse

Browsing Biological Sciences by Author "Oleksyk, Taras K"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Assessment of Taxon Sampling on Phylogenetic Reconstructions and Timetrees: A New Methodology And Application
    (2023-01-01) Powell, Christopher Lowell Edward; Battistuzzi, Fabia Ursula; Oleksyk, Taras K; Blumer-Schuette, Sara E
    Over the past three decades, computational capabilities have grown at such a rapid rate that they have given rise to many computationally heavy science fields such as phylogenomics. As increasingly more genomes are sequenced in the three domains of life, larger and more species-complete phylogenetic tree reconstructions are leading to a better understanding of the Tree of Life and the evolutionary histories in deep times. However, these large datasets pose unique challenges from a modeling and computational perspective: accurately describing the evolutionary process of thousands of species is still beyond the capability of current evolutionary models while the computational burden limits our ability to exhaustively explore and test multiple hypotheses. These limitations become even more problematic when attempting to estimate the absolute times within these phylogenetic reconstructions (timetrees). These time estimations are not only constrained computationally by run times and resource requirements but also bound by the availability of fossil data to estimate divergence times for the evolution of species (primary calibrations). All of these issues are particularly severe in prokaryotes, because of the high number of species available in databases, their large evolutionary variability, and the few primary calibrations available. Yet, they represent two out of the three domains of life and are therefore key to reconstructing the Tree of Life. This combination of computational and data constraints is forcing researchers to make choices on the datasets being analyzed without a clear understanding of the consequences of these choices on the accuracy of the results obtained. This work presents an in-depth analysis of the effects of dataset choices on the reconstruction of phylogenetic histories using a newly developed tool (Phylogenetic Assessment of Taxon Sampling) that will enable fast, simple, and reproducible testing of taxon sampling. The PATS pipeline is available on GitHub: https://github.com/BlabOaklandU/PATS
  • Thumbnail Image
    Item
    Leveraging Big Data for Bioinformatic Analysis in Modern Population Genomics
    (2023-01-01) Wolfsberger, Walter; Oleksyk, Taras K; Battistuzzi, Fabia; Westrick, Randal
    The technological advancements and the cost reduction of genomic sequencing provide novel capabilities to pose and answer biological questions on a grand scale. The initial efforts of establishing genomic references for many species of the globe serve as a foundation for the projects that aim to analyze the populations of said species. This expansion of the number of samples involved in individual studies is often connected with increased infrastructural costs for data storage and analysis. Population genomics methods are expanding on the existing genetic approaches, leveraging our ability to automate big data processing and introducing comparative methods to our collection of scientific instruments. It has extensive applications in animal and wildlife research, conservation, and human population analyses. These unique opportunities are associated with emerging challenges related to the nature of the approaches and their relative novelty in the field. Analysis of a multitude of individuals often increases requirements in terms of bioinformatics expertise and resources. An increase in complexity and data volume means researchers often need access to high-performance computing facilities and specific training to utilize them. The field still grows, with new instruments or tests frequently introduced and outdated approaches depreciating. This work reviews population genomics methods and their application related to wildlife research, conservation, and human populations research, employs them to provide answers in multiple studies, and presents a newly developed analysis suite. The suite is aimed to facilitate reproducible, accessible population genomic testing across various fields of application, seeking to address the growing expertise challenges in the field.
  • Thumbnail Image
    Item
    Medically Relevant Genome Diversity in Ukraine
    (2023-01-01) Shchubelka, Khrystyna; Oleksyk, Taras K; Battistuzzi, Fabia; Raffel, Thomas
    Ukraine, the second-largest country in Europe, has a rich history characterized by migrations, epidemics, famines, wars, and occupations, all of which have contributed to the formation of the modern Ukrainian population. However, the genetic composition of Ukraine remains understudied. Previous population genetic studies have largely overlooked the unique genetic makeup of Ukraine due to lack of publicly available genomic data. Yet, recent global assessments of genome diversity have highlighted the presence of numerous endemic variants, underscoring the significance of investigating genetic variation in underrepresented regions like Eastern Europe and, specifically, Ukraine. Such research is vital in the context of worldwide clinical trials and the development of personalized medicine. Local populations, shaped by their distinct histories, harbor a wealth of unexplored genomic variation, which may impact drug response, influence the risk of common and rare diseases, and shape lifestyle adaptations.Comprehensively understanding the genetic makeup of specific populations facilitates more effective identification of genetic markers for disease gene mapping, including family linkage and genome-wide association studies. These investigations aim to uncover susceptibility genes or loci for both Mendelian and complex diseases. Therefore, in this discovery-based study, our objective is to characterize the extensive genetic variation of medically relevant alleles in contemporary Ukraine across various levels of population structure: within major regions of Ukraine, and among the multiethnic population of Transcarpathia. Additionally, we will explore the relationship between lactose persistence genotypes and phenotypes, as well as the genetic factors underlying global developmental delay and intellectual disability in Ukraine.