By Eli Woodard
Involved group of researchers: James Smith, Annie Taylor, and other members of the research team at Boise State University.
Researcher Annie Taylor explained, “Studying species boundaries and how they relate to biotic and abiotic factors is essential to our general understanding of the evolutionary processes that lead to diversification. We are looking at a highly polymorphic group that is currently considered one species but includes four subspecific (varietal) rankings. Some suspect that speciation has occurred in this group,”.
Taylor, under the supervision of PI James Smith, is working on clarifying species boundaries and inferring evolutionary relationships in the Turpentine Cymopterus (Cymopterus terebinthine) species complex using phylogenetic inference paired with other lines of evidence such as ecology, morphology, and biogeography. This research impacts our understanding of diversification processes in this plant family.
The DNA from 53 samples of Turpentine Cymopterus, collected from various populations throughout the species range, was extracted, prepared, and sequenced by the team. The initial step involved using HybPiper to assemble the target regions of the DNA. Subsequently, a combination of HybPiper and HybPhaser was employed to filter out paralogs which could lead to reads with poor recovery. Alignment of the DNA was accomplished with MAFFT, followed by trimming of misalignments using BMGE.
To infer evolutionary relationships and species boundaries in this group, they utilized a variety of phylogenetic analysis methods. Those designed for concatenated datasets, such as RAxML or IQtree, were used alongside coalescent-based analysis methods, including Astral, SODA, and BEAST. The R2 computing cluster played a crucial role in facilitating all pipelines and analyses.
Taylor explained, “There are many computational challenges involved in this research. We are working with very large sequence files that take up most of the hard drive on a standard computer. Then we use several computationally intensive pipelines that assemble targeted regions for each sequence. These target gene regions are necessary to ensure we analyze orthologous loci that are informative to evolutionary relationships in our samples. Then we use computationally intensive phylogenetic analyses and species delimitation programs to infer evolutionary relationships and species boundaries. Our analyses would not have been possible without access to the R2 computing cluster at Boise State”.
The research has revealed that Cymopterus terebinthinus and its varietal infrataxa comprise a monophyletic clade that includes another species; Cymopterus petraeus. They also found that geographical location was a good predictor of phylogenetic placement, meaning that for the majority of samples analyzed, defined clades largely correspond to previous varietal assignments. Their findings argue that species differentiation processes are likely actively producing divergence within biogeographical regions occupied by this group, but are not yet complete.
Taylor is currently engaged in several related research projects, including studying the entire clade that this species complex belongs to (the PENA clade), while Daniel Botello is studying another species complex in the PENA clade.
Taylor concluded, “This research impacts our understanding of evolutionary processes that lead to diversification. Species diversification is especially complex in plants because hybridization and genome duplication events are common. This study provides insights into evolutionary processes driving diversification in this group, which is poorly understood and understudied”.
To find out how Research Computing can help with a project, email researchcomputing@boisestate.edu.