Graduate Thesis Or Dissertation

Phylogenetics and genomic patterns of speciation in Pinus with an empahsis on subgenus Strobus

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  • Data from nuclear ribosomal internal transcribed spacer regions (nrITS) and chloroplast DNA (cpDNA) have failed to resolve phylogenetic relationships in Pinus. To provide greater interspecific resolution, five low-copy nuclear genes were developed from mapped conifer anchor loci. Four genes were sequenced from species representing all Pinus subsections. Individual loci do not uniformly support the nrITS or cpDNA hypotheses. Combined analysis of low-copy nuclear loci produces a well-supported subsectional topology. The phylogenetic positions of P. nelsonii and P. krempfii are of systematic interest. Results strongly support P. nelsonii as sister to sect. Parrya, and suggest a moderately well-supported position of P. krempfii as sister to the remaining sect. Quinquefoliae. The most informative locus, a Late Embryogenesis Abundant-like gene, was used to explore phylogenetic relationships among closely related species in subg. Strobus. Thirty-nine species were sequenced, with two or more alleles representing 33 species. Nineteen of 33 species exhibited allelic nonmonophyly in the strict consensus tree. Nucleotide diversity was strongly associated (P<0.0001) with the degree of species monophyly. While species nonmonophyly complicates phylogenetic interpretations, this locus offers greater topological support than cpDNA or nrITS. Lacking evidence for hybridization, recombination, or imperfect taxonomy, incomplete lineage sorting remains the best explanation for trans-species polymorphisms. The absence of allelic coalescence is a severe constraint in the application of phylogenetic methods in Pinus, and taxa sharing similar life history traits may show analogous patterns. While lack of coalescence may limit their utility in traditional phylogenetics, nuclear genes remain highly informative in describing speciation events. Pinus chiapensis is a threatened species originally described as a variety of P. strobus. Prior morphological work suggests P. chiapensis is a distinct species, but that taxonomy is not universally accepted. Multiple accessions of three probable progenitors were sequenced at three nuclear loci. No interspecific allele sharing occurs with P. chiapensis, and its alleles are monophyletic at two loci. Results demonstrate that P. chiapensis is a distinct species. However, determination of the sister species is complicated by lack of species monophyly and interlocus variability. Pinus ayacahuite is the least likely progenitor, but the relationship of P. chiapensis to P. monticola or P. strobus is unclear.
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