Taxonomy and Classification

Taxonomy

• The science of naming and classifying organisms.
• Aims to establish universally accepted names.
• Organizes life into groups.

Binomial Nomenclature

• Developed by Carolus Linnaeus.
• Assigns each species a unique two-part name: genus and species.
• Uses Latin or Latinized names.
• The genus is capitalized, and the species is in lowercase.
• Both genus and species are italicized or underlined.

Taxonomic Hierarchy

• Ranges from broadest to most specific.
• Includes Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.
• Mnemonic: "Dear King Philip Came Over For Good Spaghetti."

Classification

• Provides a consistent way to organize and study the diversity of life.

Phylogeny

• The study of the evolutionary history and relationships among organisms.
• Phylogenetic trees visually represent these relationships.
• Shows ancestors and descendants.
• Shared ancestry means related species evolved from a common ancestor.
• Evidence comes from morphological, genetic, and biochemical data.

Homologous Structures

• Anatomical features that share a common ancestry.
• May have different functions.
• Example: the pentadactyl limb in vertebrates.

Analogous Structures

• Similar functions but different evolutionary origins.
• Example: wings of insects and birds.

Vestigial Structures

• Remnants of organs/structures that had a function in an ancestor but have lost their use over time.
• Example: the human appendix.

Convergent Evolution

• Unrelated organisms independently evolve similar traits.
• Occurs due to similar environmental pressures.

Systematics

• Uses phylogenetic data to classify organisms.
• Aims to reflect evolutionary relationships.
• Modern classification relies heavily on molecular data; DNA and protein sequences.

Molecular Clocks

• Use mutation rates in DNA to estimate the time of divergence between species.
• Phylogenetic trees are hypotheses and subject to change.

Domains of Life

• Three domains: Bacteria, Archaea, and Eukarya.
• Bacteria and Archaea are prokaryotic, lacking a nucleus and membrane-bound organelles.
• Eukarya includes eukaryotic cells with a nucleus and complex organelles.

Kingdoms

• Protista is a diverse group of eukaryotic microorganisms, and not monophyletic.
• Fungi includes eukaryotic, heterotrophic organisms that obtain nutrients by absorption.
• Plantae consists of eukaryotic, autotrophic organisms capable of photosynthesis.
• Animalia comprises eukaryotic, multicellular, heterotrophic organisms that obtain nutrients by ingestion.

Viruses

• Not included in the classification system because they are not considered living organisms.
• Lack cellular structure and cannot reproduce without a host cell.
• Consist of genetic material (DNA or RNA) enclosed in a protein coat called a capsid, and sometimes a lipid envelope.

Cladistics

• Method of classification that groups organisms based on shared derived characters (synapomorphies).
• A clade is a group of organisms that includes a common ancestor and all of its descendants.

Shared Characters

• Shared ancestral characters were present in a distant ancestor.
• Shared derived characters evolved more recently and are shared only by a subset of the group.

Principle of Parsimony

• The simplest explanation (the tree with the fewest evolutionary changes) is the most likely.
• Constructing a cladogram involves identifying shared derived characters.

Outgroups

• Closely related to the group being studied but not part of it.
• Used to determine which characters are ancestral and which are derived.

Fossil Record

• Provides evidence of past life and can be used to infer evolutionary relationships.
• Fossils are typically found in sedimentary rocks.
• Dated using radiometric dating techniques.
• Incomplete, as fossilization is a rare event and not all organisms fossilize easily.
• Fossils can provide information about the morphology, behavior, and environment of extinct organisms.

Biogeography

• The study of the geographic distribution of organisms.
• Provides insights into how species have evolved and dispersed over time.
• Continental drift and plate tectonics have shaped species distribution.
• Endemic species are found only in a specific geographic area.

Comparative Anatomy

• Involves comparing the anatomical structures of different species.
• Provides evidence of evolutionary relationships and adaptation.
• Homologous, analogous, and vestigial structures are important concepts.

Developmental Biology

• Studies the processes of growth and development in organisms.
• Similarities in embryonic development can indicate evolutionary relationships.
• Homeotic genes, which control the development of body structures, are highly conserved across different species.

Genomics

• The study of entire genomes, including genes and non-coding DNA.
• Comparing genomes can reveal evolutionary relationships and identify adaptive genes.

Proteomics

• The study of the entire set of proteins produced by an organism.
• Provides information about gene expression and protein function.

Bioinformatics

• The use of computational tools to analyze biological data.
• Essential for managing and interpreting large datasets from genomics, proteomics, and other fields.

Molecular Data

• Increasingly used in taxonomy and phylogeny; DNA, RNA, proteins.
• Provides a wealth of information for reconstructing evolutionary relationships.
• Molecular clocks use mutation rates to estimate divergence times.
• The three-domain system (Bacteria, Archaea, Eukarya) is based on molecular data.

Horizontal Gene Transfer

• The transfer of genetic material between organisms that are not parent and offspring.
• Common in bacteria and archaea.
• Can complicate the construction of phylogenetic trees.

Importance of Taxonomy

• Important for identifying, naming, and classifying organisms.
• Provides a standardized system for communication and research.

Importance of Phylogeny

• Important for understanding the evolutionary history and relationships of organisms.
• Provides a framework for studying biodiversity and conservation.

Classifications

• Classification systems are constantly evolving as new data and methods become available.
• Modern classification relies on morphological, molecular, and ecological data.
• The goal is to reflect the true evolutionary relationships among organisms.