Week16-1_Phylogeny

Introduction to Genetics and Evolution

Presentation Title:

B1324 Genetics and Evolution by John McCormack

Key Hashtags and Mentions:

• @LAevolving

• #Evolution

Online Resources

Platform:

MOODLE

Labster Simulations:

• Week 15 - Population Genetics:

  • Focuses on intricate concepts related to population genetics, including in-depth Hardy-Weinberg Equilibrium (HWE) calculations which serve as a foundation for understanding genetic variation in populations.

• Week 16 - Phylogeny:

  • Engages students in a virtual simulation that emphasizes the identification of deep-sea creatures, providing practical relevance to the week’s theoretical content on evolutionary relationships.

Overview of Phylogenetics

Core Topics:

• What is a phylogeny?

  • A comprehensive framework that illustrates the evolutionary history and relationships among species.

• Taxonomy:

  • A systematic classification and nomenclature of organisms based on shared characteristics, crucial for understanding biological diversity.

• Phylogenetic Trees:

  • Graphical representations that depict the evolutionary pathways and relationships among diverse species, illustrating common ancestors.

• Cladistics:

  • A methodological approach for classifying organisms based on shared traits, emphasizing shared ancestry through clades.

• Tree Construction Methods:

  • Techniques such as Maximum Parsimony (the simplest explanation for observed data) and Maximum Likelihood (the most probable tree given specific data) are employed to derive accurate phylogenetic trees.

• Molecular Clocks:

  • Biological tools that estimate the time of divergence between species using the mutation rates of genes, enhancing our understanding of evolutionary timelines.

• Importance of phylogenetic trees in understanding evolution:

  • Essential for deciphering biological relationships, predicting characteristics of organisms, and recognizing evolutionary processes.

Importance of Phylogenies

Disease Spread Monitoring:

• Phylogenetic analysis plays a vital role in epidemiology by tracing the transmission pathways of diseases, such as SARS-CoV-2, utilizing tools like Nextstrain.org to visualize and understand the dynamics of viral spread.

SARS-CoV-2 Phylogenetic Monitoring

Study Data:

• The COG-UK study meticulously tracks the evolution of SARS-CoV-2 in the UK, providing invaluable insights into how viral variants emerge and spread.

Visual Tools:

• Implementation of maps and charts that comprehensively depict genomic variations and their geographical distributions within the UK, allowing for real-time monitoring of the virus's evolution.

Phylogenies in Food Control

Study on Minke Whales:

• Conducted a rigorous analysis of mtDNA samples from Minke whale meat sold in markets, aimed at identifying illegal sales practices, with findings revealing that only 8 out of 14 samples were legally classified as Minke from the Southern Hemisphere.

Importance of phylogenetics in regulatory enforcement:

• This application underscores the necessity of phylogenetic methods in ensuring adherence to conservation laws and preventing illegal wildlife trading.

Evolution of Cancer Tumors

Phylogenetic Analysis:

• Analyzing clone relationships within tumors offers insights into the evolutionary dynamics of cancer, aiding in understanding how tumors adapt and evolve over time.

Clonal Sequences Visualization:

• Diagrams are employed to illustrate different clonal populations originating from a single tumor, providing clarity on the evolutionary history of cancer progression.

Definition of Phylogeny

Quote from Darwin:

• Phylogeny is metaphorically described as the ‘Tree of Life’ phenomenon, encapsulating the diversity of life through shared ancestry.

Description:

• Represents a pattern of evolutionary connections derived from common ancestors, showcasing the intricate relationships among species.

Taxonomy Overview

Definition:

• Taxonomy entails the meticulous classification of living organisms, comprising key processes such as:

  • Species Description: Detailing the distinctive attributes of species.

  • Identification: Methods for recognizing species in various taxa.

  • Nomenclature: Formulating standardized names for organisms.

  • Classification: Sorting species into hierarchical categories based on their relationships.

Importance of Nomenclature

Nomenclature Comparison:

• Akin to name recognition in everyday life, proper nomenclature in biology avoids confusion and enhances communication among scientists.

Example:

• Instances of confusion in identifying actors illustrate the necessity for precise naming conventions in scientific discourse.

Limitations of Common Names

Issues with Common Names:

• Common names lack regulatory standards, resulting in diverse names across languages and cultures without universal understanding.

Examples:

• The Spanish 'Gato' vs. the English 'Cat', highlighting discrepancies and potential misunderstandings in biodiversity communication.

The Linnaeus System

Introduction of Binomial Nomenclature:

• Developed by Carl von Linné (Linnaeus) in 1753, this system provides a standardized method of naming organisms using two parts, namely the genus and species (e.g., Felis catus for domestic cats).

Taxonomic Hierarchy

Taxonomic Groups:

• The hierarchical structure within taxonomy ranks categories from broad to narrow as follows:

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

Taxon:

• A term referring to any unit within this classification hierarchy, crucial for systematic biology.

Example of Hierarchical Classification

Species Identification:

• Panthera pardus (Leopard) is classified within the following taxonomic levels:

  • Domain: Eukarya

  • Kingdom: Animalia

  • Phylum: Chordata

  • Class: Mammalia

  • Order: Carnivora

  • Family: Felidae

Scientific Classification of Domestic Cat

Example:

• Felis catus classification follows the hierarchy defined above, reinforcing the understanding of evolutionary relationships.

Examples of Taxonomic Classification

Common Taxa:

• Lists various species within the Carnivora order, linking their classification directly to phylogenetic relations.

Linking Classification and Phylogeny

Differences:

• The Linnaean classification system may not always align with phylogenetic relationships, necessitating a reevaluation of taxonomic structures based on evolutionary insights.

Ideal Classification:

• Classification should ideally represent groups that include both a common ancestor and its descendant species, offering clarity on evolutionary links.

Phylogenetic Tree Representation

Concept:

• Phylogenetic trees visually encapsulate hypotheses regarding the evolutionary relationships among species, increasing understanding of certain characteristics.

Branch Points:

• Each point on the tree indicates divergences from common ancestors, progressively revealing evolutionary paths.

Interpreting Phylogenetic Trees

Components:

• Important elements of phylogenetic trees include:

  • Common ancestor

  • Sister taxa

  • Evolutionary lineages

Detailed Tree Interpretation

Types of Branches:

• Internal branches (or nodes) symbolize ancestral species, while outgroups are utilized to establish relationships between the primary lineages studied.

Tree Orientation Variability

Tree Flexibility:

• Phylogenetic trees may be drawn in various orientations without altering the inherent relationships depicted within the data.

Tree Branch Rotation

Branch Point Rotation:

• This allows for alternative representations of trees, maintaining the same underlying topology while offering different visual perspectives.

Close vs. Distant Relatives

Understanding Relationships:

• Examination of evolutionary relationships involves understanding the most recent common ancestors in the context of phylogenies.

Limitations of Phylogenetic Trees

Common Misunderstandings:

• Misinterpretation of trees as representing physiological similarities or direct lines of descent, rather than true evolutionary pathways.

Descent Patterns

Key Concept:

• It is essential not to presume that taxa evolve solely from immediately adjacent taxa within phylogenetic trees, as this could lead to misconceptions regarding evolutionary processes.

Tree Thinking Challenge

Activity:

• Engage in identifying the tree with a differing topology among several options, enhancing critical thinking skills in interpreting evolutionary data.

Tree Thinking Challenge Continued

Instructions:

• Conduct an in-depth examination of tree topologies and relationships to reinforce understanding of cladistics concepts.

Introduction to Cladistics

Definition:

• Cladistics operates as a methodological approach for grouping organisms based on shared ancestry, yielding more accurate classifications of organisms.

Monophyletic Definition

Validity Criteria:

• A clade must be monophyletic, meaning it encompasses an ancestor and all of its descendants, ensuring clarity in classification.

Paraphyletic Grouping

Description:

• Defined as a classification that includes an ancestral species and some, but not all, of its descendants, leading to unequal representation in taxonomic groups.

Polyphyletic Grouping

Description:

• This grouping consists of distantly related species but excludes their most recent common ancestor, presenting challenges for accurate phylogenetic interpretation.

Example of Polyphyletic Group

Even-toed Ungulates Study:

• This study reveals intricate relationships among species without recognizing the existence of the last common ancestors, complicating classification efforts.

Building Phylogenetic Trees

Data Gathering:

• Crucial data includes morphological characteristics, genetic sequences, and biochemical data, collectively informing the construction of phylogenetic models.

Traits Definition:

• Traits are defined as characteristics that can vary among organisms and are vital in the phylogenetic tree construction process.

Distinguishing Homology from Analogy

Definitions:

• Homology: Characteristics derived from a common ancestor, showcasing evolutionary lineage.

• Analogy: Similar traits developed independently across different evolutionary paths, emphasizing the divergence in species evolution.

Morphological Character Examples

Homologous vs. Analogous Structures:

• Example: The pentadactyl limb found across species such as sharks, penguins, and dolphins, demonstrating evolutionary variations.

Homological Relationships

Emphasis:

• Highlighting the significance of understanding evolutionary relationships across different species to refine classification systems and enhance biological knowledge.

Evidence for Homology vs. Analogy

Comparison Techniques:

• Employing methods such as analyzing historical fossil records and investigating structural complexities allows for more profound insights into homological versus analogical traits.

Types of Homology

Synapomorphy:

• Shared derived characteristics pivotal for identifying monophyletic groups, critical in clarifying modern phylogenetic trends.

Symplesiomorphy

Definition:

• Characters shared among organisms that identify paraphyletic groups, illustrating shared ancestry but limiting utility in cladistic analyses.

Homoplasy

Definition:

• Characteristics shared by different lineages that arise not from common ancestry but through convergent evolution, challenging traditional views of relatedness and classification.

Visual Representation of Types of Homology

Illustration:

• Demonstrating Synapomorphy, Symplesiomorphy, and Homoplasy across various species, thus contributing to a clearer understanding of their distinctive evolutionary paths.