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.

AI can help humans find common ground in democratic deliberation.

Finding agreement through a free exchange of views is often difficult. Collective deliberation can be slow, difficult to scale, and unequally attentive to different voices. In this study, we trained an artificial intelligence (AI) to mediate human deliberation.

Environmental DNA Isolation, Validation, and Preservation Methods.

Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.

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.

An individual differences perspective on pragmatic abilities in the preschool years.

Pragmatic abilities are fundamental to successful language use and learning. Individual differences studies contribute to understanding the psychological processes involved in pragmatic reasoning. Small sample sizes, insufficient measurement tools, and a lack of theoretical precision have hindered progress, however.

Modeling Individual Differences in Children's Information Integration During Pragmatic Word Learning.

Pragmatics is foundational to language use and learning. Computational cognitive models have been successfully used to predict pragmatic phenomena in adults and children - on an aggregate level. It is unclear if they can be used to predict behavior on an individual level.

An Environmental DNA Primer for Microbial and Restoration Ecology.

Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly.

Rewilding in Miniature: Suburban Meadows Can Improve Soil Microbial Biodiversity and Soil Health.

Lawns are a ubiquitous, human-made environment created for human enjoyment, leisure, and aesthetics. While net positive for carbon storage, lawns can have negative environmental impacts. Lawns require frequent mowing, which produces high levels of CO pollution and kills off native plants.

Great ape communication as contextual social inference: a computational modelling perspective.

Human communication has been described as a contextual social inference process. Research into great ape communication has been inspired by this view to look for the evolutionary roots of the social, cognitive and interactional processes involved in human communication. This approach has been highly productive, yet it is partly compromised by the widespread focus on how great apes use and understand individual signals.

Predicting pragmatic cue integration in adults' and children's inferences about novel word meanings.

Language is learned in complex social settings where listeners must reconstruct speakers' intended meanings from context. To navigate this challenge, children can use pragmatic reasoning to learn the meaning of unfamiliar words. A critical challenge for pragmatic reasoning is that it requires integrating multiple information sources, which have typically been studied separately.

Warm (for Winter): Inferring Comparison Classes in Communication.

The meanings of natural language utterances depend heavily on context. Yet, what counts as context is often only implicit in conversation. The utterance it's warm outside signals that the temperature outside is relatively high, but the temperature could be high relative to a number of different comparison classes: other days of the year, other weeks, other seasons, etc.

Logic, Probability, and Pragmatics in Syllogistic Reasoning.

Syllogistic reasoning lies at the intriguing intersection of natural and formal reasoning of language and logic. Syllogisms comprise a formal system of reasoning yet make use of natural language quantifiers (e.g.

How young children integrate information sources to infer the meaning of words.

Before formal education begins, children typically acquire a vocabulary of thousands of words. This learning process requires the use of many different information sources in their social environment, including their current state of knowledge and the context in which they hear words used. How is this information integrated? We specify a developmental model according to which children consider information sources in an age-specific way and integrate them via Bayesian inference.

The Origin and Evolution of Antistasin-like Proteins in Leeches (Hirudinida, Clitellata).

Bloodfeeding is employed by many parasitic animals and requires specific innovations for efficient feeding. Some of these innovations are molecular features that are related to the inhibition of hemostasis. For example, bloodfeeding insects, bats, and leeches release proteins with anticoagulatory activity through their salivary secretions.

Multilocus Metabarcoding of Terrestrial Leech Bloodmeal iDNA Increases Species Richness Uncovered in Surveys of Vertebrate Host Biodiversity.

Leech-derived invertebrate DNA (iDNA) has been successfully leveraged to conduct surveys of vertebrate host biodiversity across the Indo Pacific. However, this technique has been limited methodologically, typically only targeting mammalian 16S rDNA, or both 16S and vertebrate 12S rDNA for leech host determination. To improve the taxonomic richness of vertebrate host species in iDNA surveys, we re-analyze datasets from Bangladesh, Cambodia, China, and Madagascar through metabarcoding via next generation sequencing (NGS) of 12S, 16S (2 types, one designed to target mammals and the other, residual eDNA), nicotinamide adenine dinucleotide hydride dehydrogenase 2 (ND2), and cytochrome c oxidase subunit 1 (COI).

Polite Speech Emerges From Competing Social Goals.

Language is a remarkably efficient tool for transmitting information. Yet human speakers make statements that are inefficient, imprecise, or even contrary to their own beliefs, all in the service of being polite. What rational machinery underlies polite language use? Here, we show that polite speech emerges from the competition of three communicative goals: to convey information, to be kind, and to present oneself in a good light.

Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States.

The SARS-CoV-2 coronavirus is wreaking havoc globally, yet, as a novel pathogen, knowledge of its biology is still emerging. Climate and seasonality influence the distributions of many diseases, and studies suggest at least some link between SARS-CoV-2 and weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months.

A putative chordate luciferase from a cosmopolitan tunicate indicates convergent bioluminescence evolution across phyla.

Pyrosomes are tunicates in the phylum Chordata, which also contains vertebrates. Their gigantic blooms play important ecological and biogeochemical roles in oceans. Pyrosoma, meaning "fire-body", derives from their brilliant bioluminescence.

Selection, drift, and constraint in cypridinid luciferases and the diversification of bioluminescent signals in sea fireflies.

Understanding the genetic causes of evolutionary diversification is challenging because differences across species are complex, often involving many genes. However, cases where single or few genetic loci affect a trait that varies dramatically across a radiation of species provide tractable opportunities to understand the genetics of diversification. Here, we begin to explore how diversification of bioluminescent signals across species of cypridinid ostracods ("sea fireflies") was influenced by evolution of a single gene, cypridinid-luciferase.

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).

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat ( spp.) middens preserve plant and animal remains for tens of thousands of years.

Ultra-gentle soft robotic fingers induce minimal transcriptomic response in a fragile marine animal.

Tessler et al. demonstrate that a 'soft' robot causes less stress to a jellyfish while handling compared to a traditional 'hard' robot.

Ideating iDNA: Lessons and limitations from leeches in legacy collections.

Indirect methods for conducting faunal inventories present great promise, and genomic inventories derived from environmental sources (eDNA) are improving. Invertebrate ingested DNA (iDNA) from terrestrial leeches in the family Haemadipsidae has shown potential for surveying vertebrates and biodiversity monitoring in protected areas. Here we present an initial, and critical, evaluation of the limitations and biases of current iDNA protocols for biodiversity monitoring using both standard and NGS barcoding approaches.

The language of generalization.

Language provides simple ways of communicating generalizable knowledge to each other (e.g., "Birds fly," "John hikes," and "Fire makes smoke").

Luciferin production and luciferase transcription in the bioluminescent copepod .

Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling , a common species found in temperate, northern, and southern latitudes.