The topic of this video module is how to classify animals based on how closely related they are. The main learning objective is that students will learn how to make phylogenetic trees based on both physical characteristics and on DNA sequence. Students will also learn why the objective and quantitative nature of DNA sequencing is preferable when it come to classifying animals based on how closely related they are. Knowledge prerequisites to this lesson include that students have some understanding of what DNA is and that they have a familiarity with the base-pairing rules and with writing a DNA sequence.

This video demonstrates some of the features of PhyloTree. It then shows the early explosive discovery of mammal species (most major mammal groups were discovered early on), and then shows the slow and steady discovery of cnidarians (many cnidarians remain to be described). The tool can also be used to quickly find the first species that was described in a group. The first siphonophore to be described, for example, was Physalia physalis (the Portuguese man o’ war).

Investigating a Deep Sea Mystery is based on Deep-sea mystery solved: astonishing larval transformation and extreme sexual dimorphism unite three fish families by Johnson, et al. (2009)* published in Biology Letters, Royal Society. The deep sea fishes at the heart of the investigation and this activity were historically classified into three families or clades based on the obvious morphological differences between the members of each group. Over time, as new data was accumulated, a new hypothesis was generated; the three fish clades were really one. Johnson, et al. found patterns in collection data that supported an alternative relationship; that they are the males, females, and larvae of a single family or clade, and that the morphological differences are the result of extreme ontogenetic (developmental) metamorphosis and sexual dimorphism. In this activity students follow the steps of the science team to unravel the mystery of the fishes' classification by analyzing some of the same morphological and phylogenetic data as the science team.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Uncovering the links between microbiome profiles and host conditions is critical to understanding the roles microbes play in human health. However, analysis of microbiome profiles with traditional testing frameworks is made difficult by the high-dimensionality and sparsity of the data. Often this is addressed by incorporating information from closely related microbes. This phylogenetic information is added under the assumption that operational taxonomic units (OTUs) from related taxa will tend to behave similarly, but the complexity of microbe interactions can make this assumption invalid. The recently developed tool, Phylogeny-guided microbiome OTU-Specific association Test (POST), addresses this issue. POST determines how much, if any, information to borrow from neighboring OTUs based on phylogenetic distance and outcome-OTU association. This tool is a local collapsing test built under the kernel machine framework to accommodate complex OTU effects..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Crocodiles, and birds, and dinosaurs—oh my! While classifying organisms is nothing new, phylogeny— or, grouping organisms by their evolutionary relationships—is helping us see life in a whole new light. In this episode of Crash Course Biology, we’ll learn why this kingdom-phylum stuff is going out of style and why phylogenetic trees are in.

Chapters:
The Platypus & Phylogeny
Taxonomy
Systematics
Phylogeny & Genetics
Dr. Motoo Kimura
Phylogenetic Trees
The Complexities of Evolution
Review and Credits

Statistical Physics in Biology is a survey of problems at the interface of statistical physics and modern biology. Topics include: bioinformatic methods for extracting information content of DNA; gene finding, sequence comparison, and phylogenetic trees; physical interactions responsible for structure of biopolymers; DNA double helix, secondary structure of RNA, and elements of protein folding; considerations of force, motion, and packaging; protein motors, membranes. We also look at collective behavior of biological elements, cellular networks, neural networks, and evolution.

This outline was created to be used by my online Fundamentals of Biology students at West Hills College, Lemoore. It is intended to be used with Concepts of Biology by Open Stax.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Termites are one of the few animal lineages able to digest the most abundant biomolecule on earth, lignocellulose. Of the nine families of termites, all but one of them eat wood, with the last feeding on soil. While termites produce enzymes that break down lignocellulose, their gut microbes are still a critical part of the digestion process. But most termite gut microbiome research to date is based on research from wood-feeding or pest species of termites. So, a recent study examined the prokaryotic gut microbes from a sample of termite species that better represent the diversity of termites. The gut microbes possessed a similar set of carbohydrate and nitrogen metabolism genes across the termite phylogenetic tree. The proportions of these genes varied with the hosts’ diet and position on the phylogenetic tree. Surprisingly, the soil-feeding termites didn't even have unique microbial metabolic genes or pathways compared to wood-feeding species..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.