Organizing Life

Chapter 19: Organizing Life

19.1 Systematic Biology

  • Definition of Taxonomy: Taxonomy is the branch of biology that identifies, names, and organizes biodiversity into related categories.

    • A natural system of classification reflects the evolutionary history of organisms.

    • The practice of naming and identifying organisms began with ancient civilizations such as the Greeks and Romans.

  • Historical Classification:

    • Aristotle classified living things into groups, such as horses, birds, and oaks.

    • During the Middle Ages, Latin was commonly used for the description of organisms.

Linnaean Taxonomy

  • Developed by Carolus Linnaeus in the mid-eighteenth century.

    • Binomial nomenclature is the system for naming organisms consisting of two parts:

    1. Genus name (first word, capitalized)

    2. Specific epithet (second word, lowercase)

    • Example: Lilium bulbiferum (a species of lily) and Lilium canadense (another species) are different species within the genus Lilium.

    • A species is referred to by its complete binomial name (Genus species); the genus name can be used alone to refer to a group of closely related species.

Classification Hierarchy

  • Modern taxonomists use the following levels of classification:

    • Species: the most basic unit, consisting of a single type of organism.

    • Genus: one or more species.

    • Family: one or more genera.

    • Order: one or more families.

    • Class: one or more orders.

    • Phylum: one or more classes.

    • Kingdom: one or more phyla.

    • Domain: one or more kingdoms.

Example Classification System

  • DOMAIN: Eukarya

  • KINGDOM: Animalia

  • PHYLUM: Chordata

  • CLASS: Mammalia

  • ORDER: Rodentia

  • FAMILY: Muridae

  • GENUS: Mus

  • SPECIES: Mus musculus (house mouse)

  • Second Example Classification:

  • SPECIES: Rana catesbeiana (North American bullfrog)

    • DOMAIN: Eukarya

    • SUPERGROUP: Opisthokonts

    • PHYLUM: Chordata

    • CLASS: Amphibia

    • GENUS: Rana

    • ORDER: Anura

    • FAMILY: Ranidae

Classification of Groups

  • The higher the category, the more inclusive it becomes:

    • The species is the most exclusive category.

    • Organisms grouped in the same domain share general characteristics in common.

    • The higher categories have become standardized due to advances in molecular biology, such as DNA barcoding, which allows for comparisons of DNA sequences to identify organisms.

19.2 The Three-Domain System

  • Research by Carl Woese compared nucleotide sequences of rRNA in prokaryotes and eukaryotes, leading to the conclusion that all organisms evolved along three distinct lineages:

    • Domain Bacteria:

    • Comprises unicellular prokaryotic organisms that reproduce asexually.

    • Two main types:

      1. Cyanobacteria: large, photosynthetic bacteria, hypothesized to be among the first organisms to contribute oxygen to Earth's atmosphere.

      2. Heterotrophic bacteria: non-photosynthetic; crucial for ecosystem functioning and chemical cycling; some are parasitic and cause diseases.

    • Domain Archaea:

    • Prokaryotic unicellular organisms that reproduce asexually.

    • Thrive in extreme environments resembling early Earth conditions.

    • Their plasma membranes and cell walls differ from those of bacteria, and they vary in rRNA sequences.

    • Domain Eukarya:

    • Organisms can be unicellular or multicellular.

    • Have cells with a membrane-bounded nucleus.

    • Sexual reproduction is common.

    • Diversity includes protists, plants, fungi, and animals.

      • Protists present classification challenges, leading to the establishment of the supergroup category, situated below domain and above kingdom.

      • Fungi: mostly multicellular, saprotrophic organisms forming spores, lacking flagella, with cell walls made of chitin.

      • Plants: photosynthetic, multicellular organisms adapted primarily to land, evolving from aquatic photosynthetic protists.

      • Animals: motile, multicellular, heterotrophic organisms descended from heterotrophic protists.

Major Distinctions Among the Three Domains of Life

  • Bacteria:

    • Single-celled

    • Membrane lipids: Phospholipids, unbranched

    • Cell wall: Yes (contains peptidoglycan)

    • Nuclear envelope: No

    • Membrane-bounded organelles: No

    • Ribosomes: Yes

    • Introns: Some

  • Archaea:

    • Single-celled

    • Membrane lipids: Varied branched lipids

    • Cell wall: Yes (no peptidoglycan)

    • Nuclear envelope: No

    • Membrane-bounded organelles: No

    • Ribosomes: Yes

    • Introns: Some

  • Eukarya:

    • Some unicellular, many multicellular

    • Membrane lipids: Phospholipids, unbranched

    • Cell wall: Some yes, some no

    • Nuclear envelope: Yes

    • Membrane-bounded organelles: Yes

    • Ribosomes: Yes

    • Introns: Yes

19.3 Phylogeny

  • Systematic biology: A quantitative science that compares traits of living and fossil organisms to infer evolutionary relationships.

    • Data sources include:

    • Fossil records

    • Comparative anatomy and development

    • Sequence, structure, and function of RNA and DNA molecules

    • Phylogeny: The evolutionary history of a group, often depicted as a phylogenetic tree indicating lines of descent.

    • Branching points represent divergences from a common ancestor, giving rise to two or more new groups.

Ancestral and Derived Traits

  • Ancestral Traits:

    • Present in all members of a group

    • Present in the common ancestor

    • Not useful for clarifying evolutionary relationships.

  • Derived Traits:

    • Present in some members of a group, absent in the common ancestor.

    • Critical for understanding evolutionary relationships.

    • Example: An opposable thumb is a derived trait present in primates, not present in the common ancestor of all mammals.

Cladistics

  • Cladistics: A method that utilizes shared derived traits to hypothesize evolutionary history.

    • The resulting phylogenetic depiction is termed a cladogram.

    • A clade is defined as an evolutionary branch that includes:

    • A common ancestor

    • All its descendant species

    • A cladogram is subject to change as new traits are discovered and incorporated.

    • Cladistics operates as a hypothesis-based, quantitative science which is subject to testing.

Parsimony

  • Cladistics is guided by the principle of parsimony, which proposes that the minimum number of assumptions leads to the most logical explanations.

    • The optimal cladogram minimizes the number of unexplained shared derived characters and assumed evolutionary changes.

    • Reliability hinges on the skill and knowledge of the investigator.

Constructing a Cladogram

  • Utilizes data sets of traits across various species to establish evolutionary relationships.

Tracing Phylogeny: Challenges & Concepts

  • Fossil Records: Often incomplete, making phylogenetic determinations challenging.

  • Homology: Refers to structures derived from a common ancestor; homologous structures relate through common descent (e.g., forelimbs of vertebrates).

    • Convergent Evolution: Distantly related species may evolve similar structures due to adaptation to analogous environments.

    • Analogy: Similarities arise due to adaptive convergence, rather than common ancestry (e.g., wings of insects and bats).

Behavioral and Molecular Traits

  • Behavioral Traits: Include parental care, mating calls, etc.

  • Molecular Traits:

    • Assumed close relation when two species share similar base-pair sequences.

    • Dissimilar sequences suggest distant relationships.

DNA Sequence Alignment Example

Given a sequence of nucleotides compared across various species, differences may indicate evolutionary relationships.

Protein Comparisons and Molecular Clocks

  • Immunological Techniques: Assess cross-reaction levels to determine relationships.

  • Amino Acid Sequencing: Similar protein sequences indicate close relations.

  • Molecular Clock: Employs neutral nucleotide sequences, assuming a constant mutation rate over time.

    • Comparative analysis of mtDNA sequencing correlates a 5.1% nucleic acid difference with a timeline of 2.5 million years ago (MYA) among songbird species.

Phylogeny from Molecular Data

Illustrates evolutionary timelines and relationships based on molecular comparisons.