3.4 Evolutionary Relationships and Phylogenetic Analysis

Evolutionary relationships in geomicrobiology explore how microbes have adapted and diversified over Earth's history. By studying phylogeny and molecular markers, scientists can reconstruct microbial family trees and track their development through time.

Interpreting these evolutionary trees in geologic contexts reveals insights into ancient ecosystems and how microbes have shaped Earth's environment. This knowledge helps us understand microbial diversity patterns and predict how communities might respond to future changes.

Evolutionary Relationships in Geomicrobiology

Phylogeny and microbial evolution

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• Phylogeny examines evolutionary relationships among organisms based on shared ancestry and common descent
• Evolutionary relationships connect species through time influenced by genetic changes and environmental adaptations
• Microorganism classification divides life into three domains (Bacteria, Archaea, Eukarya) and follows taxonomic hierarchy (domain, phylum, class, order, family, genus, species)
• Molecular clock hypothesis estimates divergence times between species using rate of genetic changes over time

Methods for phylogenetic trees

• Molecular markers for phylogenetic analysis utilize 16S rRNA gene for prokaryotes, 18S rRNA gene for eukaryotes, and protein-coding genes (RecA, GyrB)
• Sequence alignment identifies conserved and variable regions using multiple sequence alignment tools (MUSCLE, CLUSTAL)
• Tree construction methods include:
  1. Distance-based methods (UPGMA, Neighbor-Joining)
  2. Character-based methods (Maximum Parsimony, Maximum Likelihood)
  3. Bayesian inference
• Bootstrap analysis assesses tree reliability by resampling sequence data to generate confidence values

Interpreting Phylogenetic Trees in Geologic Contexts

Interpretation of phylogenetic trees

• Tree topology shows branching patterns and node relationships, identifying monophyletic, paraphyletic, and polyphyletic groups
• Branch lengths represent genetic distance or time since divergence, longer branches indicate more genetic changes
• Rooted trees show direction of evolution, unrooted trees display relationships without specifying common ancestor
• Geologic time scale integration correlates branching events with major geologic periods (Cambrian, Jurassic)
• Microbial diversity patterns identify dominant microbial groups in different geologic settings (hydrothermal vents, deep subsurface)

Implications of phylogenetic analysis

• Evolutionary adaptations identify genes associated with specific geologic niches (thermophiles, halophiles) and horizontal gene transfer events in extreme environments
• Biogeochemical cycling traces evolution of metabolic pathways related to element cycling (carbon, nitrogen, sulfur)
• Microbial paleontology reconstructs ancient microbial ecosystems and infers metabolic capabilities in extinct microorganisms (stromatolites, microfossils)
• Environmental selection pressures correlate phylogenetic clusters with geochemical parameters (pH, temperature, salinity)
• Microbial community structure assesses stability and resilience over geologic time and predicts community responses to environmental changes (climate shifts, tectonic events)