whole genome assembly of the orange jewelweed, Meerb. (Balsaminaceae) using nanopore long-read sequencing.

The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, , has one solitary species, . The two genera also differ in geographic distribution and habitat type ( species are widely distributed in much of the Old World and N.

 (Balsaminaceae), a new species from Yunnan, China.

S.X. Yu, Chang Y.

PhyloM: A Computer Program for Phylogenetic Inference from Measurement or Binary Data, with Bootstrapping.

Quantitative and binary results are ubiquitous in biology. Inasmuch as an underlying genetic basis for the observed variation in these observations can be assumed, it is pertinent to infer the evolutionary relationships among the entities being measured. I present a computer program, PhyloM, that takes measurement data or binary data as input, using which, it directly generates a pairwise distance matrix that can then be subjected to the popular neighbor-joining (NJ) algorithm to produce a phylogenetic tree.

Insights into plant biodiversity conservation in large river valleys in China: A spatial analysis of species and phylogenetic diversity.

Large river valleys (LRVs) are heterogeneous in habitat and rich in biodiversity, but they are largely overlooked in policies that prioritize conservation. Here, we aimed to identify plant diversity hotspots along LRVs based on species richness and spatial phylogenetics, evaluate current conservation effectiveness, determine gaps in the conservation networks, and offer suggestions for prioritizing conservation. We divided the study region into 50 km × 50 km grid cells and determined the distribution patterns of seed plants by studying 124,927 occurrence points belonging to 14,481 species, using different algorithms.

Computational tools for fitting the Hill equation to dose-response curves.

Introduction: Many biological response curves commonly assume a sigmoidal shape that can be approximated well by means of the 4-parameter nonlinear logistic equation, also called the Hill equation. However, estimation of the Hill equation parameters requires access to commercial software or the ability to write computer code. Here we present two user-friendly and freely available computer programs to fit the Hill equation - a Solver-based Microsoft Excel template and a stand-alone GUI-based "point and click" program, called HEPB.

An airtight approach to the inebriometer: from construction to application with volatile anesthetics.

The mechanism by which inhaled anesthetics work is not fully understood, although they have been extensively used. Much research has been done showing the likelihood that there is more than one pathway or mechanism of action. A long-term goal of our laboratory is to decipher these mechanisms using Drosophila melanogaster, an excellent model organism for this purpose.

Chromobacterium vaccinii sp. nov., isolated from native and cultivated cranberry (Vaccinium macrocarpon Ait.) bogs and irrigation ponds.

A large number of Gram-negative, motile, mesophilic, violacein-producing bacteria were isolated from the soils and roots of Vaccinium macrocarpon Ait. and Kalmia angustifolia L. plants and from irrigation ponds associated with wild and cultivated cranberry bogs in Massachusetts, USA.

Tubulin evolution in insects: gene duplication and subfunctionalization provide specialized isoforms in a functionally constrained gene family.

Background: The completion of 19 insect genome sequencing projects spanning six insect orders provides the opportunity to investigate the evolution of important gene families, here tubulins. Tubulins are a family of eukaryotic structural genes that form microtubules, fundamental components of the cytoskeleton that mediate cell division, shape, motility, and intracellular trafficking. Previous in vivo studies in Drosophila find a stringent relationship between tubulin structure and function; small, biochemically similar changes in the major alpha 1 or testis-specific beta 2 tubulin protein render each unable to generate a motile spermtail axoneme.

Phylogenetic inference under varying proportions of indel-induced alignment gaps.

Background: The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods.

Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous.

Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in different species. In a recent study, the influence of heterotachy on the performance of different phylogenetic methods was examined using computer simulation for a four-species phylogeny.

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree.