Assembly and analysis of the genome of Notholithocarpus densiflorus.

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes, and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.

The magmatic origin of the Columbia River Gorge, USA.

Along subduction zones, high-relief topography is associated with sustained volcanism parallel to the plate margin. However, the relationship between magmatism and mountain building in arcs is poorly understood. Here, we study patterns of surface deformation and correlated fluvial knickpoints in the Columbia River Gorge to link long-term magmatism to the uplift and ensuing topographic development of the Cascade Range.

Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences.

In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e.

Ancient trees: irreplaceable conservation resource for ecosystem restoration.

Ancient trees contribute multifaceted ecosystem benefits to old-growth forests, rewilding, and human cultural landscapes. As such, we call for international efforts to preserve these hubs of diversity and resilience. A global coalition utilizing advanced technologies and community scientists to discover, protect, and propagate ancient trees is needed before they disappear.

Old and ancient trees are life history lottery winners and vital evolutionary resources for long-term adaptive capacity.

Trees can live for many centuries with sustained fecundity and death is largely stochastic. We use a neutral stochastic model to examine tree demographic patterns that emerge over time, across a range of population sizes and empirically observed mortality rates. A small proportion of trees (~1% at 1.

"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19.

The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them.

Is speciation an unrelenting march to reproductive isolation?

Speciation is often portrayed as an "incomplete" or "incipient" process if two groups of organisms, technically distinguishable either by morphology or genetics, can exchange genes. The ultimate outcome of diversification, given this perspective, is complete reproductive isolation. But an increasing amount of evidence suggests that speciation is rarely complete and inter-fertility between different taxonomically accepted species is consistently maintained.

Discovering and Applying the Urban Rules of Life to Design Sustainable and Healthy Cities.

The city and its urban biome provides an extreme laboratory for studying fundamental biological questions and developing best practices for sustaining biodiverse and well-functioning ecological communities within anthropogenic built environments. We propose by studying urban organisms, urban biotic communities, the urban biome, and the interactions between the urban biome and peri-urban built and natural environments, we can (1) discover new "rules of life" for the structure, function, interaction, and evolution of organisms; (2) use these discoveries to understand how novel emerging biotic communities affect and are affected by anthropogenic environmental changes in climate and other environmental factors; and (3) apply what we have learned to engage residents of the urban biome, and design cities that are more biologically diverse, are provided with more and better ecosystem services, and are more equitable and healthier places to live. The built environment of the urban biome is a place that reflects history, economics, technology, governance, culture, and values of the human residents; research on and applications of the rules of life in the urban biome can be used by all residents in making choices about the design of the cities where they live.

Application of remote sensing technology to estimate productivity and assess phylogenetic heritability.

Premise: Measuring plant productivity is critical to understanding complex community interactions. Many traditional methods for estimating productivity, such as direct measurements of biomass and cover, are resource intensive, and remote sensing techniques are emerging as viable alternatives.

Methods: We explore drone-based remote sensing tools to estimate productivity in a tallgrass prairie restoration experiment and evaluate their ability to predict direct measures of productivity.

Fruit development of Lithocarpus (Fagaceae) and the role of heterochrony in their evolution.

Stone oaks, or Lithocarpus species of Fagaceae are ecologically important canopy trees in the tropical and subtropical forests over East Asia, and the fruits of which are important food sources for insects and vertebrates there. The great fruit morphological variation of this genus represents two fruit types, acorn and enclosed receptacle fruit types. However, the evolutionary mechanisms of differentiation into these two fruit types with contrasting morphology remain a puzzle.

The oak syngameon: more than the sum of its parts.

One of Anthropocene's most daunting challenges for conservation biology is habitat extinction, caused by rapid global change. Tree diversity has persisted through previous episodes of rapid change, even global extinctions. Given the pace of current change, our management of extant diversity needs to facilitate and even enhance the natural ability of trees to adapt and diversify.

Botanic gardens should lead the way to create a "Garden Earth" in the Anthropocene.

The strength and expertise that botanic gardens bring to conservation are based on their detailed knowledge and understanding of the care, management, and biology of a diversity of plant species. This emphasis on the organism has led to many and conservation programs aimed at protecting endangered species, restoring threatened populations, and establishing living plant and seed collections of endangered species. In China, the scale and pace of change in land and resource use, often leading to environmental degradation, has created a strong emphasis on improving environmental conditions.

Correction: Associated morphometric and geospatial differentiation among 98 species of stone oaks (Lithocarpus).

[This corrects the article DOI: 10.1371/journal.pone.

Associated morphometric and geospatial differentiation among 98 species of stone oaks (Lithocarpus).

Two fruit types can be distinguished among stone oaks (Lithocarpus) species: the 'acorn' (AC) and the 'enclosed receptacle' (ER) types. Our morphometric analysis of 595 nuts from 98 species (one third of all Lithocarpus spp.) found substantial transition in mechanical protection of the seed between two woody fruit tissues (exocarp and receptacle) of two fruit types.

Exploring the potential of gametic reconstruction of parental genotypes by F hybrids as a bridge for rapid introgression.

Interspecific hybridization and genetic introgression are commonly observed in natural populations of many species, especially trees. Among oaks, gene flow between closely related species has been well documented. And yet, hybridization does not lead to a "melting pot", i.

Patterns of genomic diversification reflect differences in life history and reproductive biology between figs (Ficus) and the stone oaks (Lithocarpus).

One of the remarkable aspects of the tremendous biodiversity found in tropical forests is the wide range of evolutionary strategies that have produced this diversity, indicating many paths to diversification. We compare two diverse groups of trees with profoundly different biologies to discover whether these differences are reflected in their genomes. Ficus (Moraceae), with its complex co-evolutionary relationship with obligate pollinating wasps, produces copious tiny seeds that are widely dispersed.

Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa.

Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp.

An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data.

Background: Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult because de novo assembly for non-model genomes and multi-genome alignment are challenging.

Results: To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method ( https://sourceforge.

Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics.

Motivation: Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.

Variable mating behaviors and the maintenance of tropical biodiversity.

Current theoretical studies on mechanisms promoting species co-existence in diverse communities assume that species are fixed in their mating behavior. Each species is a discrete evolutionary unit, even though most empirical evidence indicates that inter-specific gene flow occurs in plant and animal groups. Here, in a data-driven meta-community model of species co-existence, we allow mating behavior to respond to local species composition and abundance.