James I. Cohen’s research while affiliated with Weber State University and other places

During the past 20 yr, the phylogenetics of Boraginaceae has taken shape using plastid DNA regions and the nuclear ribosomal internal transcribed spacer (ITS), but these regions only reflect a limited understanding of the evolutionary history of the family. Using hybridization-enrichment sequencing, 531 nuclear regions from lineage-specific and Angiosperms353 loci were sequenced and aligned for 49 species from across Boraginaceae. Additionally, the Angiosperms353 loci were incorporated with a broader dataset of the same loci from 115 accessions of Boraginales and relatives. Based on multiple phylogenetic approaches and datasets, the resolved phylogenies of Boraginaceae were quite similar to our current understanding, yet multiple taxa were recognized in different positions. These included: 1) Echiochiloideae as sister to Cynoglossoideae instead of to the rest of the entire family, 2) Moritzinae as nested within Boragininae, and 3) Lasiocaryeae and Trichodesmeae not resolved as sisters. These different positions recovered, via different methods, using hundreds of nuclear loci suggest that incomplete lineage sorting, hybridization, and lineage-specific shifts in substitution rates may have occurred during the early origin of the family. In analyses of Boraginales, Namaceae was resolved as non-monophyletic, providing evidence that a broader Hydrophyllaceae may again be appropriate, and Lennoaceae was nested in Ehretiaceae. While both sets of loci allowed for a well-resolved and well-supported phylogeny to be reconstructed, the lineage-specific loci recovered some of the more intriguing phylogenetic relationships in part because these loci appear to be less conserved than those from Angiosperms353. The two sets of loci provide an interesting complement for understanding patterns of evolution within the family and order.

Background Lithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome. Results The phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization. Conclusions This study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae.

Hybridization between rare and widespread species can result in loss of genetic integrity for the rarer species, which can have management and conservation implications. One rare species, Phlox hirsuta , is a serpentine endemic in northern California, and it frequently co‐occurs with a widespread congener, Phlox speciosa . Putative hybrids were recognized based on intermediate morphology, so the possibility of hybridization was explored using floral morphological and molecular data. Ninety‐eight individuals of P. hirsuta and P. speciosa were collected from each of three sites, and floral features were measured and compared. Eleven microsatellite loci were amplified for species and putative hybrids, and inter‐ and intraspecific genetic diversity and relationships were investigated with multiple methods. Variation in morphological and molecular data was recovered. Floral variation was greater for P. hirsuta than P. speciosa . Putative hybrids were genetically allied with P. speciosa , but two individuals of P. hirsuta were resolved to have genetic similarity with P. speciosa . While hybridization is possible between the species, it is uncommon and appears to be primarily unidirectional. The small number of recognized hybrids may be due to ineffective interspecific pollination, hybrids being less fit than parents, and/or small sample sizes. Reinforcement does not appear to play a role in secondary contact between species. Both microsatellite loci and floral morphology varied across the small geographic range of P. hirsuta , suggesting local differentiation and adaptation are possible over short distances.

Plant reproductive ecology explores aspects of the biology and ecology of plants ranging from breeding systems, plant–pollinator interactions, seed germination, floral traits, and much more [...]

Iris lacustris, a northern Great Lakes endemic, is a rare species known from 165 occurrences across Lakes Michigan and Huron in the United States and Canada. Due to multiple factors, including habitat loss, lack of seed dispersal, patterns of reproduction, and forest succession, the species is threatened. Early population genetic studies using isozymes and allozymes recovered no to limited genetic variation within the species. To better explore genetic variation across the geographic range of I. lacustris and to identify units for conservation, we used tunable Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations from Michigan and Wisconsin, and because the species is polyploid, we filtered the single nucleotide polymorphism (SNP) matrices using polyRAD to recognize diploid and tetraploid loci. Based on multiple population genetic approaches, we resolved three to four population clusters that are geographically structured across the range of the species. The species migrated from west to east across its geographic range, and minimal genetic exchange has occurred among populations. Four units for conservation are recognized, but nine adaptive units were identified, providing evidence for local adaptation across the geographic range of the species. Population genetic analyses with all, diploid, and tetraploid loci recovered similar results, which suggests that methods may be robust to variation in ploidy level.

Identifying units for appropriate management and conservation of rare species is an important and challenging process, and population genetics can inform this decision making. Using Phlox hirsuta, a rare species restricted to serpentine soils in Northern California and with a geographic range of less than 15 km, we examined genetic variation within and among populations, using tunable Genotyping-by-Sequencing (tGBS) to generate single nucleotide polymorphisms (SNPs) as well as 11 microsatellite loci, to identify population structure, patterns of migration and selection, and units for conservation. Multiple methods recognized three geographically structured population clusters. The species has undergone a recent genetic bottleneck, and the increase in population size may be influenced by the changing climate. Patterns of gene flow are greater from south to north than in the opposite direction. Some of the genes under selection are putatively involved in adaptation to edaphic conditions, and genes under selection differ among the populations. Four population units were identified as suitable for conservation purposes based on various partitions of the SNPs.

Oreocarya crassipes, an endangered angiosperm native to the Trans-Pecos region in southern Brewster County, Texas, exhibits distyly, a breeding system that includes two floral morphs with reciprocal positioning of the anthers and stigmas. The long-style (LS) morph has stigmas above the anthers, and the short-style (SS) morph produces anthers above the stigmas. In the present study, multiple aspects of distyly were examined across four populations of O. crassipes including morph ratios, variation in floral morphology, and patterns of macroscopic and microscopic floral development of the morphs. Morph ratios vary among populations, but for all of the samples pooled the ratio was 1 LS:1 SS. Distyly was observed to be well established in the species, with stigma height, anther height, and stigma-anther separation significantly different between the two morphs. Floral developmental patterns are similar to those in related species, suggesting a conserved and similarly co-opted developmental pathway for the origin of distyly in the genus and relatives.

Pollen, the microgametophyte of seed plants, has an important role in plant reproduction and, therefore, evolution. Pollen is variable in, for example, size, shape, aperture number; these features are particularly diverse in some plant taxa and can be diagnostic. In one family, Boraginaceae, the range of pollen diversity suggests the potential utility of this family as a model for integrative studies of pollen development, evolution and molecular biology. In the present study, a comprehensive survey of the diversity and evolution of pollen from 538 species belonging to 72 genera was made using data from the literature and additional scanning electron microscopy examination. Shifts in diversification rates and the evolution of various quantitative characters were detected, and the results revealed remarkable differences in size, shape and number of apertures. The pollen of one subfamily, Boraginoideae, is larger than that in Cynoglossoideae. The diversity of pollen shapes and aperture numbers in one tribe, Lithospermeae, is greater than that in the other tribes. Ancestral pollen for the family was resolved as small, prolate grains that bear three apertures and are iso‐aperturate. Of all the tribes, the greatest number of changes in pollen size and aperture number were observed in Lithospermeae and Boragineae, and the number of apertures was found to be stable throughout all tribes of Cynoglossoideae. In addition, the present study showed that diversification of Boraginaceae cannot be assigned to a single factor, such as pollen size, and the increased rate of diversification for species‐rich groups (e.g. Cynoglossum) is not correlated with pollen size or shape evolution. The palynological data and patterns of character evolution presented in the study provide better resolution of the roles of geographical and ecological factors in the diversity and evolution of pollen grains of Boraginaceae, and provide suggestions for future palynological research across the family.

Pathogenic Yersinia bacteria, including Y. pseudotubuclosis Y. enterocolitica, and Y. pestis, contain the mosaic plasmid pYV that encodes for, among other things, a number of proteinaceous virulence factors. While the evolutionary histories of many of the biovars and strains of pathogenic Yersinia species are well documented, the origins of many of the individual virulence factors have not been comprehensively examined. Here, the evolutionary origins of the genes coding for a set of Yersinia outer protein (Yop) virulence factors were investigated through phylogenetic reconstruction and subsequence analysis. It was found that many of these genes had only a few sequenced homologs and none of the resolved phylogenies recovered the same relationships as was resolved from chromosomal analyses. Many of the evolutionary relationships differ greatly among genes on the plasmid, and variation is also found across different domains of the same gene, which provides evidence of the mosaic nature of the plasmid as well as multiple genes on the plasmid. This mosaic aspect also relates to patterns of selection, which vary among the studied domains.