BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more.

Premise: Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.

Methods And Results: BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data.

Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.

The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled.

Whole mitochondrial genome phylogeny of Drosophilidae.

A total of 241 mitochondrial genomes were assembled and annotated from the SRA database to reconstruct a mtDNA genome phylogeny for the genus , the family Drosophilidae, and close relatives. The resulting mtDNA genome phylogeny is largely congruent with previous higher-level analyses of species with the exception of the relationships between the melanogaster, montium, anannassae, saltans and obscura groups. Although relationships within these species groups are congruent between nuclear and mtDNA studies, the mtDNA genome phylogeny of the groups is different when compared to earlier studies.

The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification.

Tens of millions of dried seahorses (genus Hippocampus) are traded annually, and the pressure from this trade along with their life history traits (involved parental care and small migration distances and home ranges) has led to near global population declines. This and other forms of overexploitation have led to all seahorse species being listed in Appendix II under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). The signatory nations of CITES recommended a 10-cm size limit of seahorses to ensure harvested individuals have reached reproductive maturity, and have thus had the chance to produce offspring, to maintain a more sustainable global seahorse fishery.

Multiple outgroups can cause random rooting in phylogenomics.

Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods.

The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability.

Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate.

A natural history museum visitor survey of perception, attitude and knowledge (PAK) of microbes and antibiotics.

A kiosk-based survey at the American Museum of Natural History in New York City in 2016-2018 allowed us to assess public knowledge of antibiotics and public attitudes toward microbes in museum goers. Over 22,000 visitors from 172 countries and territories answered several carefully designed questions about microbes and antibiotics. These visitors also entered age, gender, and country demographic data that allowed for stratification along these demographic and geographic divisions.

Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses.

Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differences in tissue tropism and carcinogenicity. The evolutionary features associated with the divergence of are not well understood.

The enigmatic Placozoa part 2: Exploring evolutionary controversies and promising questions on earth and in space.

The placozoan Trichoplax adhaerens has been bridging gaps between research disciplines like no other animal. As outlined in part 1, placozoans have been subject of hot evolutionary debates and placozoans have challenged some fundamental evolutionary concepts. Here in part 2 we discuss the exceptional genetics of the phylum Placozoa and point out some challenging model system applications for the best known species, Trichoplax adhaerens.

The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge.

The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E.

A kiosk survey of perception, attitudes and knowledge (PAK) of Australians concerning microbes, antibiotics, probiotics and hygiene.

Issues Addressed: To obtain a baseline of public perception, attitudes and knowledge (PAK) of Australians about microbes, antibiotics and hygiene like hand washing and use of probiotics.

Methods: Using a kiosk-based survey method at the American Museum of Natural History (AMNH), we remotely assayed PAK of Australians through their interaction with the kiosk. The surveys we used had five and seven multiple answer questions and were analysed using standard comparative approaches.

Correction: Can public online databases serve as a source of phenotypic information for Cannabis genetic association studies?

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

Can public online databases serve as a source of phenotypic information for Cannabis genetic association studies?

The use of Cannabis is gaining greater social acceptance for its beneficial medicinal and recreational uses. With this acceptance has come new opportunities for crop management, selective breeding, and the potential for targeted genetic manipulation. However, as an agricultural product Cannabis lags far behind other domesticated plants in knowledge of the genes and genetic variation that influence plant traits of interest such as growth form and chemical composition.

An Investigation of How Environmental Science Textbooks Link Human Environmental Impact to Ecology and Daily Life.

Making direct connections between humanity and the environment is of ever-increasing importance in the context of today's environmental crisis. We used qualitative content analysis of precollege- and college-level introductory environmental science textbook case studies to study how they portray humanity's link to the environment. We assessed case studies for how specific and data rich they are and for how they link together daily life, human impact, and ecological interactions.

Should Networks Supplant Tree Building?

Recent studies suggested that network methods should supplant tree building as the basis of genealogical analysis. This proposition is based upon two arguments. First is the observation that bacterial and archaeal lineages experience processes oppositional to bifurcation and hence the representation of the evolutionary process in a tree like structure is illogical.

Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets.

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters).

Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata.

The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A.

Distinguishing Extinction and Natural Selection in the Anthropocene: Preventing the Panda Paradox through Practical Education Measures: We Must Rethink Evolution Teaching to Prevent Misuse of Natural Selection to Biologically Justify Today's Human Caused Mass Extinction Crisis.

In the midst of only the 6th mass extinction in the Earth's history, we must rethink how we teach evolution to prevent natural selection from being incorrectly used as a biological justification for inaction in the face of today's human-caused mass extinction crisis. Pundits, policy makers, and the general public regularly identify the extinction of endangered species as natural selection at work, rather than attributing modern-day extinction to the sudden catastrophic bad luck of human caused environmental change, a phenomenon distinct from natural selection. In this natural selection framing, the inability of species to survive in human altered environments is the normal progression of "survival of the fittest" and conservation measures designed to protect species is human interference with natural selection.

Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits.

Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level.

Mitochondrial lipid droplet formation as a detoxification mechanism to sequester and degrade excessive urothelial membranes.

The apical surface of the terminally differentiated mammalian urothelial umbrella cell is mechanically stable and highly impermeable, in part due to its coverage by urothelial plaques consisting of 2D crystals of uroplakin particles. The mechanism for regulating the uroplakin/plaque level is unclear. We found that genetic ablation of the highly tissue-specific sorting nexin Snx31, which localizes to plaques lining the multivesicular bodies (MVBs) in urothelial umbrella cells, abolishes MVBs suggesting that Snx31 plays a role in stabilizing the MVB-associated plaques by allowing them to achieve a greater curvature.