The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome

One thousand plant transcriptomes and the phylogenomics of green plants

Abstract: Green plants (Viridiplantae) include around 450,000–500,000 species1, 2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life

Botanical Report of Tierra Redonda Mountain BLM Area of Critical Environmental Concern, San Luis Obispo County, California (W120˚59’41”; N35˚45’59”).

The purpose of this document is to report the results of a botanical survey of a portion of the Tierra Redonda Mountain Area of Critical Environmental Concern. The survey was conducted for the Bureau of Land Management, and executed between October 2009 and June 2010. Tierra Redonda Mountain is the type locality for the Tierra Redonda formation, and has weathered to form steep slopes of exposed chaparral and protected woodlands. Four general community types were found; foothill woodland, chaparral, southern coastal scrub and dune scrub. Alliances determined by The Manual of California Vegetation (2nd ed.) were: Quercus douglasii Woodland, Quercus agrifolia Woodland, Pinus sabiniana Woodland, Adenostoma fasciculatum Shrubland, Adenostoma fasciculatum—Salvia mellifera Shrubland, Ceanothus leucodermis Shrubland, Eriogonum fasciculatum Shrubland, Arctostaphylos glauca Shrubland, Heteromeles arbutifolia Shrubland, Ericameria ericoides Shrubland and Achnatherum speciosum Herbaceous Alliances. A total of 242 species were identified in the survey area, most with a respective voucher specimen housed in the Robert F. Hoover Herbarium (OBI) on the Cal Poly, San Luis Obispo campus

Where will they sit? : The life and work of Mennonite central committee in the Philippines

Philippinexii, 250 p.; 22 cm

Spontaneous urban flora of Los Angeles: Transect data

The city of Los Angeles comprises nearly 500 square miles and supports nearly four million people that reside on lands that were once composed of a diverse mosaic of wetland and upland plant community associations. On top of these historic vegetation layers are socioeconomic legacies of a redlining grading system for the city established by the Federal Housing Administration's Home Owners Loan Corporation (HOLC). Throughout neighborhoods in public parkways, the spaces between property bounds and the road, resides an often overlooked spontaneous and self-propagating community of native and introduced taxa. With an interest in documenting this flora at a time of rapid environmental and socioeconomic change in the city, I performed a series of floristic checklists for nearly 400 blocks comprising nearly 50 total miles at sixteen neighborhoods throughout the city between the end of January and middle of March 2021. Transects were walked within specific neighborhood communities chosen to represent all four HOLC codes and a combination of historic wetland and upland vegetative communities. Across all transects and sites, I found a total of 168 spontaneous self-propagating plant taxa, and a significant effect of historical plant community (upland, wetland) on plant species richness and phylogenetic diversity but not HOLC code. I also present and discuss patterns of community similarity and turnover between sites. This dataset of plant species presence by block, and the list of transect locations, is publicly available via dataDryad so that it may serve as a point of reference for future studies of urban ethnobiology.Data was collected by performing a series of walking transect checklists to identify and list each species that occurs on each block surveyed. Data consists of a matrix of each transect and whether each taxon was present (1) or absent (0)

Changes in the Genome: Polyploidy, Hybridization, and Genome Size Evolution Explored Through Selaginella and Vascular Plants

The evolutionary processes responsible for generating and maintaining the remarkable diversity of life on earth are mutation, selection, drift, recombination, and gene flow. The relative magnitude of these processes, and their tempo, can be inferred from studying genomes or samples of the genome from individuals or multiple individuals. My dissertation focuses on three types of change in vascular plant genomes, with a focus on lycophytes in the genus Selaginella (Selaginellaceae). In Appendix A I characterize the extremely small genome sizes of Selaginella, and compare their observed disparity in genome size to other vascular plant clades. In Appendix B I examine the temporal activity of long terminal repeat retrotransposons (LTR-RTs) in vascular plants. I illustrate that across vascular plants LTR-RT activity largely explains the observed diversity in genome size. In Appendix C and D I focus on abrupt changes in the genome via polyploidy and hybridization. In Appendix C I demonstrate the importance of climatic niche divergence in polyploid plant species. In Appendix D I investigate the evidence of hybrid speciation in hybrids formed between Selaginella arizonica and S. eremophila in the Sonoran Desert. Using transcriptome sequencing and complementary morphological and ploidal inference, I suggest that both homoploid hybrid and allopolyploid species were formed from the same parents S. arizonica and S. eremophila. This system is the first known example of two types of stabilized hybrid derivatives from the same parents in natural populations.Release after 08/01/202

Pathogenic Copy Number Variants (pCNVs) in Individuals diagnosed on the Autism Spectrum Disorder (ASD): A Closer look at Candidate Genes

The genetic basis for autism spectrum disorders (ASDs) is well established, and its heterogenetic nature provides us with substantial evidence for the many chromosomal aberrations associated with this complex disorder. However, little is known about the genes that occupy the different chromosomal regions and the gene networks they participate in as they relate to phenotypes associated with ASDs. Here, the author reports candidate genes that may be implicated with the observed clinical phenotypes in 9 patients diagnosed with an ASD identified to have pathogenic copy number variants (pCNVs) through array-comparative genomic hybridization (CGH). Formal clinical assessments, which include a full physical examination, a medical history report, as well as a family history, were administered by a clinical geneticist unaware of the array-CGH results. Candidate genes were then compiled through the genome browser of the Database of Genomic Variants website and subsequently narrowed down utilizing the SUSPECTS database. Additional information on each candidate gene was obtained through the NCBI, iHOP, and metalife databases. The author’s findings suggest a number of genes involved in neurodevelopment as well as craniofacial and systemic features that may account for the observed phenotypes in the 9 affected patients.Science, Faculty ofUnreviewedUndergraduat

Data from: The small nuclear genomes of Selaginella are associated with a low rate of genome size evolution

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella. We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella. Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome