Resolving Taxonomic Uncertainty and Clarifying Species Boundaries in the Cymopterus Terebinthinus (Apiaceae) Species Complex
Authors: Taylor Annie 
Published: July 2024

Speciation processes are not well resolved or agreed upon. They are however essential to our general understanding of the evolutionary processes that lead to diversification. Determining the juncture at which a genetically and/or morphologically divergent population becomes a unique species can be challenging, especially with respect to recent divergences and closely related taxa where issues such as incomplete lineage sorting may bring about confounding results. To complicate our theoretical disagreements on species definitions, different models inferring species boundaries may accordingly lump or split species. Using multiple lines of evidence to define species boundaries can greatly improve species inference and preclude erroneous taxonomic groupings. Taxa in the Cymopterus terebinthinus (Apiaceae) species complex have long puzzled botanists owing to their diverse morphologies that are defined as separate varieties. These varieties are often found in generally well-defined geographical subregions of varying habitat types. Additionally, previous phylogenetic studies were interpreted to show that varieties in Cymopterus terebinthinus were not monophyletic. I aim to clarify species boundaries and infer evolutionary relationships in the Cymopterus terebinthinus species complex using phylogenetic inference and species delimitation programs. Additionally, I will compare trends observed in ecological, morphological, and geographical evidence to clade groupings. I apply the genealogical species concept to guide my interpretations of species boundaries in this group. To further explore species boundaries in C. terebinthinus, I sampled from 8-12 populations of the four varieties of C. terebinthinus and 6 populations of C. petraeus. These taxa occur predominantly in the Western United States, ranging from the Rocky Mountains to the Pacific Coast. I then extracted DNA, prepared libraries, and performed target capture with the angiosperms353 bait kit. Libraries were then sent off for next generation sequencing with Illumina. I used HybPiper and HybPhaser to both assemble 353 target genes and filter poorly recovered loci and paralogs. To assemble chloroplast genomes for each sample, I used MITObim as it assembles circular genomes where other assembly methods do not. I used maximum likelihood (RAxML and IQtree) and coalescent based phylogenetic analyses (Astral) in addition to species delimitation analyses (SODA) to infer evolutionary relationships and taxonomic grouping in C. terebinthinus. I also performed analysis of ecological variables including soil and climatic properties to better understand environmental factors related to phylogenetic groupings. I find that in all phylogenetic analyses other than the chloroplast phylogeny, Cymopterus terebinthinus and its varietal infrataxa comprise a monophyletic clade that includes Cymopterus petraeus. The phylogenetic analysis using chloroplast data resulted in a polyphyletic C. terebinthinus and clade assignments that are inconsistent with other biological evidence. I suspect that the nuclear based phylogenies more accurately depict evolutionary relationships in C. terebinthinus. For the majority of samples analyzed, nuclear phylogenies infer clades that largely correspond to previous varietal assignments. Among all four nuclear phylogenetic estimates, six samples did not comprise a clade with their previously assigned taxa. I suspect that various evolutionary factors that often confound phylogenetic analyses, like incomplete lineage sorting and paralogous genes could explain why these six samples did not comprise a clade with their previously identified variety. Additionally, it is possible that these lineages’ recent divergence has resulted in incomplete barriers to gene flow, leading to clade groupings that are not unanimously aligned to previous taxonomic assignment. Overall, clear genetic differentiation is occurring among the currently recognized varieties and might be related to limited seed dispersal in C. terebinthinus. Limited dispersal mechanisms can cause occasional establishment of allopatric populations with restricted gene flow which can lead to diversification. While the phylogenies inferred in this analysis are generally congruent, and genetic structuring among named varieties suggest divergence is occurring, I suspect that speciation is ongoing in this complex.