Reestablishment of \u3cem\u3eCrataegus\u3c/em\u3e Species Associated With Tennessee Gas Pipeline LLC’s Northeast Upgrade Project Loop 323 in High Point State Park

The Botany Department of the Morris Arboretum of the University of Pennsylvania was contracted by CH2M to provide, in as much as possible, identifications to species level of Crataegus (hawthorn) trees growing in proximity to the expanded natural gas pipeline right-of-way,designated Northeast Upgrade Project Loop 323 (NEUP Loop 323), through High Point State Park in Sussex County, New Jersey. In addition to species identification, seed collection was identified as a task to be completed in the initial phase of this project

Baseline Studies of Aquatic Plants and Water Quality in Selected State Park Lakes

This project was undertaken as a baseline study of aquatic plant species and water quality in a set of six state parks lakes selected by the Pennsylvania Bureau of State Parks. Inventories were conducted at these lakes during the field season of 2014. Water quality parameters were measured in these lakes by staff from Pennsylvania Department of Environmental Protection’s Clean Lakes Program between 2007 and 2015. Specimens of all species observed were collected and deposited in the herbarium at the Morris Arboretum of the University of Pennsylvania. For various reasons cited in this report, the value of conducting detailed aquatic plant species/water quality analyses at these lakes was very limited. Nonetheless, this project accomplished its main goal of serving as a plant diversity baseline against which future studies can be compared

Natural Resources Inventory of Wissahickon Valley Watershed Association Preserves and the Green Ribbon Trail

The purpose of this study is to provide The Wissahickon Valley Watershed Association with baseline information needed to help guide appropriate resource management and education decisions. The area under consideration in this study includes the named preserves of the Wissahickon Valley Watershed Association (WVWA) (approximately 331 acres), and the Green Ribbon Trail and associated WVWA-owned lands from the trailhead at the Upper Gwynedd Township Park in North Wales to the boundary of Fort Washington State Park near Skippack Pike, a distance of about 13.1 kilometers (8.14 miles) not counting the trail interruption at the Cedarbrook Country Club

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution

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

Assessing Herbarium Specimen Image Quality with FineFocus

The Mid-Atlantic Megalopolis Thematic Collections Network, a digitization project funded by the U.S. National Science Foundation, seeks to digitize ca. 800,000 herbarium specimens through imaging, transcription, and georeferencing. The use of autofocus alone in herbarium specimen imaging with a digital single-lens reflex camera does not yield consistently sharp images, even with relatively two-dimensional specimens and a proper selection of focus point. The FineFocus technique provides a way of assessing contrast, as a proxy for focus quality, through analysis of a standard text target using two freeware programs run through a batch script. By calculating a numeric value, this protocol provides an objective way to obtain a high level of focus quality for a specific imaging rig with given conditions before proceeding with imaging. Adjusting focus with FineFocus yields noticeably sharper images, allowing users to see fine details otherwise obscured by poor focus, such as secondary venation. This technique can be easily implemented in herbarium digitization workflows to improve the quality of specimen images

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.This is the peer reviewed version of the following article: Conover, Justin L., Nisa Karimi, Noah Stenz, Cécile Ané, Corrinne E. Grover, C. Skema, Jennifer A. Tate et al. "A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?." Journal of Integrative Plant Biology (2018), which has been published in final form at doi: 10.1111/jipb.12746. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.</p