microbial phylogenetics

Examples of microbial phylogenetics in the following topics:

• Phylogenetic Analysis

  • The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
  • Microbial phylogenetics is the study of the evolutionary relatedness among various groups of microorganisms.
  • The molecular approach to microbial phylogenetic analysis revolutionized our thinking about evolution in the microbial world.
  • There are four steps in general phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA), and (iv) phylogenetic treeing and evaluation.
  • Multilocus sequence analysis (MLSA) represents the novel standard in microbial molecular systematics.

• Environmental Diversity of Microbes

  • The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea, and most lineages of the Eukarya are microorganisms.
  • In turn, the environment and the recent temperature anomalies play a crucial role in driving changes to the microbial communities.
  • For microbiologists, it is critical to study microbial adaptation to different environments and their function in those environments to understand global microbial diversity, ecology, and evolution.
  • Interfering with natural microbial biomass disrupts the balance of nature and the ecosystem and leads to loss of biodiversity.
  • Summarize how microbial diversity contributes to microbial occupation of diverse geographical niches.

• The Origins of Archaea and Bacteria

  • In phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria.
  • A microbial mat is a multi-layered sheet of prokaryotes that includes mostly bacteria, but also archaea .
  • The first microbial mats likely obtained their energy from chemicals found near hydrothermal vents.
  • Fossilized microbial mats represent the earliest record of life on earth.
  • The mat helps retain microbial nutrients.

• Nucleic Acid Sequencing and rRNA Analysis

  • The 16SrRNA gene is used for phylogenetic studies, as it is highly conserved between different species of bacteria and archaea.
  • Unfortunately, while primers can be defined to amplify this gene from single genomes, this method is not accurate enough to estimate the diversity of microbial communities from their environments.
  • Paradoxically, methodological denial is now a rule in published articles that use 16S rRNA gene amplicon surveys to study unknown microbial communities.
  • Describe how the 16SrRNA gene can be used for phylogenetic studies and in medical microbiology for bacterial identification

• Alphaproteobacteria

  • Aerobic anoxygenic phototrophic bacteria are alphaproteobacteria, widely distributed marine plankton that may constitute over 10% of the open ocean microbial community.
  • Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off later than most other phyla and Classes of Bacteria with the exception of Betaproteobacteria and Gammaproteobacteria.

• Shared Features of Bacteria and Archaea

  • In phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of Gram-positive bacteria.

• Limitations of Phylogenetic Trees

  • Limitations of phylogenetic trees include the inability to distinguish evolutionary time and relatedness between distinct species.
  • Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order.
  • Remember, any phylogenetic tree is a part of the greater whole and, as with a real tree, it does not grow in only one direction after a new branch develops.
  • This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column.
  • Identify the limitations of phylogenetic trees as representations of the organization of life

• Web, Network, and Ring of Life Models

  • To more accurately describe the phylogenetic relationships of life, web and ring models have been proposed as updates to tree models.
  • In 1999, a phylogenetic model that resembles a web or a network more than a tree was proposed.
  • A consequence of the new thinking about phylogenetic models is the idea that Darwin's original conception of the phylogenetic tree is too simple, but made sense based on what was known at that time.
  • In the (a) phylogenetic model proposed by W.
  • Describe the web, network, and ring of life models of phylogenetic trees

• Phylogenetic Trees

  • Phylogenetic trees illustrate the hypothetical evolution of organisms and their relationship to other species.
  • Unlike a taxonomic classification diagram, a phylogenetic tree can be read like a map of evolutionary history.
  • Many phylogenetic trees have a single lineage at the base representing a common ancestor.
  • Rooted phylogenetic trees can serve as a pathway to understanding evolutionary history.
  • Describe the various types of phylogenetic trees and how they organize life

• Limitations to the Classic Model of Phylogenetic Trees

  • The concepts of phylogenetic modeling are constantly changing causing limitations to the classic model to arise.
  • The concepts of phylogenetic modeling are constantly changing.
  • Many phylogenetic trees have been shown as models of the evolutionary relationship among species.
  • Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 , which served as a pattern for subsequent studies for more than a century.
  • Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships.