PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.

Speciation with gene-flow in eastern North American red oaks (Quercus section Lobatae)

As foundational species, oaks (Quercus : Fagaceae) support the activities of both humans and wildlife. However, many oaks in North America are declining, a crisis exacerbated by the previous disappearance of other hard mast-producing trees. In addition, the economic demands placed on this drought-tolerant group may intensify if climate change extirpates other, relatively mesophytic species. Genetic tools can help address these management challenges. To this end, we developed a suite of 27 microsatellite markers, of which 22 are derived from expressed sequence tags (ESTs). Many of these markers bear significant homology to known genes and may be able to directly assay functional genetic variation. Markers obtained from enriched microsatellite libraries, on the other hand, are typically located in heterochromatic regions and should reflect demographic processes. Considered jointly, genic and genomic microsatellites can elucidate patterns of gene-flow and natural selection, which are fundamental to both an organism's evolutionary ecology and conservation biology. To this end, we employed the developed markers in an FST-based genome scan to detect the signature of divergent selection among the red oaks (Quercus section Lobatae). Three candidate genes with putative roles in stress responses demonstrated patterns of diversity consistent with adaptation to heterogeneous selective pressures. These genes may be important in both local genetic adaptation within species and divergence among them. Next, we used an isolation-with-migration model to quantify levels of gene-flow among four red oaks species during speciation. Both speciation in allopatry and speciation with gene-flow were found to be major drivers of red oak biodiversity. Loci playing a key role in speciation are also likely to be ecologically important within species