The research behind a taxonomic monograph: a case study from (Convolvulaceae).

Systematic monographs are an important tool for understanding biodiversity. However, while papers that outline systematic methods for biogeography, phylogenetics and diversification are commonplace, papers that cover methods for monographic and taxonomic research are rare. In this paper, we describe how we conducted a monographic study of , drawing attention to the resources we made use of and the practical steps we took, with a particular focus on how we integrated results from molecular and morphological analyses.

Repeated shifts out of tropical climates preceded by whole genome duplication.

While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene-tree conflict, and life-history changes. Climatic shifts may also have facilitated increases in flowering plant diversification rates.

Leveraging co-production within ecosystem restoration to maximize benefits to coastal birds.

Coastal Louisiana's ecosystems are threatened by anthropogenic factors exacerbated by climate change induced sea-level rise. The 2010 Deepwater Horizon oil spill resulted in injuries and deaths to coastal birds in Louisiana, and the ongoing loss of habitat has limited the potential for successful nesting of resident birds throughout the coast. Habitat loss is being addressed through increased large-scale ecosystem restoration as a result of settlement funds from the Deepwater Horizon oil spill.

Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling.

Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow-contributes significantly to overall diversity within mountain systems, but the origins of alpine plant diversity are poorly understood. Here, we quantify the processes that generate alpine plant diversity and their changing dynamics through time in Saxifraga (Saxifragaceae), an angiosperm genus that occurs predominantly in mountain systems.

Deconstructing age estimates for angiosperms.

Estimates of the age of angiosperms from molecular phylogenies vary considerably. As in all estimates of evolutionary timescales from phylogenies, generating these estimates requires assumptions about the rate that molecular sequences are evolving (using clock models) and the time duration of the branches in a phylogeny (using fossil calibrations and branching processes). Often, it is difficult to demonstrate that these assumptions reflect current knowledge of molecular evolution or the fossil record.

Supporting habitat restoration in the northern Gulf of Mexico through synthesis of data on multiple and interacting benefits and stressors.

Outcomes of landscape scale restoration and conservation can be maximized when planning is based upon quantitative and decision-relevant information. Existing tools to support data-driven planning are hindered by regionally inconsistent information and a need for advanced methods to analyze data of varying spatial resolution and coverage. We present a synthesis methodology for region-wide derived metrics to characterize natural resource value, ecosystem stress, and social vulnerability to inform implementation of conservation and restoration projects.

Heuristics, species, and the analysis of systematic data.

Disagreements over how to define species potentially render them incomparable, yet biologists routinely count and compare species. This 'species problem' persists despite the wealth of data and methods available to contemporary systematists. A heuristic approach to species provides a consistent yet flexible means of selecting, assessing, and integrating different biological data.

exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates.

We present a method of divergence time estimation (exTREEmaTIME) that aims to effectively account for uncertainty in divergence time estimates. The method requires a minimal set of assumptions, and, based on these assumptions, estimates the oldest possible divergence times and youngest possible divergence times that are consistent with the assumptions. We use a series of simulations and empirical analyses to illustrate that exTREEmaTIME is effective at representing uncertainty.

Discovery and characterization of sweetpotato's closest tetraploid relative.

The origin of sweetpotato, a hexaploid species, is poorly understood, partly because the identity of its tetraploid progenitor remains unknown. In this study, we identify, describe and characterize a new species of Ipomoea that is sweetpotato's closest tetraploid relative known to date and probably a direct descendant of its tetraploid progenitor. We integrate morphological, phylogenetic, and genomic analyses of herbarium and germplasm accessions of the hexaploid sweetpotato, its closest known diploid relative Ipomoea trifida, and various tetraploid plants closely related to them from across the American continent.

Species as a Heuristic: Reconciling Theory and Practice.

Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the "species problem" stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited.

3D Printed N-95 Masks During the COVID-19 Pandemic: Lessons Learned.

Early in 2020, the pandemic resulted in an enormous demand for personal protective equipment (PPE), which consists of face masks, face shields, respirators, and gowns. At our institution, at the request of hospital administration, the Lifespan 3D Printing Laboratory spearheaded an initiative to produce reusable N95 masks for use in the hospital setting. Through this article, we seek to detail our experience designing and 3D printing an N95 mask, highlighting the most important lessons learned throughout the process.

Impact of nonlinearity including bleaching in MUTC photodetectors on RF-modulated electro-optic frequency combs.

We use the drift-diffusion equations to calculate the responsivity of a modified uni-traveling carrier (MUTC) photodetector (PD) with a frequency comb input that is generated by a series of short optical pulses. We first use experimental results for the responsivity of the MUTC PD to obtain an empirical model of bleaching in pulsed mode. We incorporate our empirical bleaching model into a drift-diffusion model to calculate the impact of nonlinearity in an MUTC PD on RF-modulated electro-optic frequency combs.

The Implications of Interrelated Assumptions on Estimates of Divergence Times and Rates of Diversification.

Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field-including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling.

Deterministic access of broadband frequency combs in microresonators using cnoidal waves in the soliton crystal limit.

We present a method to deterministically obtain broad bandwidth frequency combs in microresonators. These broadband frequency combs correspond to cnoidal waves in the limit when they can be considered soliton crystals or single solitons. The method relies on moving adiabatically through the (frequency detuning)×(pump amplitude) parameter space, while avoiding the chaotic regime.

Obtaining more energetic modelocked pulses from a SESAM-based fiber laser.

A major design goal for femtosecond fiber lasers is to increase the output power but not at the cost of increasing the noise level or narrowing the bandwidth. Here, we perform a computational study to optimize the cavity design of a femtosecond fiber laser that is passively modelocked with a semiconductor saturable absorbing mirror (SESAM). We use dynamical methods that are more than a thousand times faster than standard evolutionary methods.

The temporal dynamics of evolutionary diversification in Ipomoea.

Molecular phylogenies are used as a basis for making inferences about macroevolutionary history. However, a robust phylogeny does not contain the information that is necessary to make many of these inferences. Complex methodologies that incorporate important assumptions about the nature of evolutionary history are therefore required.

Insights from Empirical Analyses and Simulations on Using Multiple Fossil Calibrations with Relaxed Clocks to Estimate Divergence Times.

Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data do not provide direct information about rates but instead provide direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch.

The Implications of Lineage-Specific Rates for Divergence Time Estimation.

Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates-which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates-defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates-defined as variation in the average rate across all branches at each sampled locus.