Linnaean System and Taxonomy

• Taxonomy identifies, names, and classifies species.
• Carolus Linnaeus created the basis for modern taxonomy in the 18th-century.

Linnaean System

• Common names for species can be ambiguous, so biologists use a scientific method for naming species.
• The Linnaean system assigns a two-part scientific name (binomial) to each species, consisting of the genus and specific epithet.
• The genus groups closely related species, while the specific epithet distinguishes species within the genus.
• Panthera pardus (leopard) and Panthera leo (lion) share the same genus.
• The genus name is capitalized, and the binomial is italicized.
• After the first use, the genus name can be abbreviated (e.g., P. pardus).
• Linnaeus also introduced a hierarchical system for classifying species: genus, family, order, class, phylum, kingdom, and domain.
• Each classification level (e.g., Felidae, Mammalia) is a taxon (plural, taxa).

Taxonomic Classification Example: Leopard (Panthera pardus)

• Genus: Panthera (lions, tigers, jaguars)
• Family: Felidae (includes Lynx)
• Order: Carnivora (includes Canidae)
• Class: Mammalia
• Phylum: Chordata
• Kingdom: Animalia
• Domain: Eukarya

Classifying an Organism

• Species: a member within a genus.
• Genus: the specific type of carnivore/herbivore, e.g., what type of feline?
• Family: is it a feline or canine?
• Order: a carnivore/herbivore (or other diet), e.g., felines belong to Carnivora.
• Class: a mammal/reptile/bird, e.g, felines belong to Mammalia.
• Phylum: backbone or not?
• Kingdom: animal, bacteria, or archaea?
• Domain: eukaryotic or prokaryotic cells?
• Mnemonic: "Dear King Philip Came Over For Good Soup" assists in remembering the classification order.

Limitations of Hierarchical Classification

• Classifying species into hierarchical groups may seem logical but is arbitrary.
• Inclusive taxa are based on morphological traits chosen by taxonomists, not standardized measurements.

Phylogenies

• Phylogeny is the evolutionary history of a species or group of species.
• Systematics classifies organisms and determines their evolutionary relationships.

Phylogenetic Trees

• Phylogenetic trees are branching diagrams showing evolutionary relationships and patterns of descent, but not timelines.
• Systematists construct phylogenetic trees using morphological and molecular data, as well as fossil evidence.
• Homologies, features resulting from common ancestry, are crucial for understanding evolutionary relationships.
• Distinguishing between homology and analogy is a challenge in constructing phylogenies.

Convergent Evolution

• Convergent evolution occurs when unrelated organisms develop similar traits (analogies) due to similar environments.
• Australian marsupial moles and North American eutherian moles share mole-like features independently.
• Complex structures suggest homology; for example, human and chimpanzee skulls are homologous due to their complexity.

Shared Characters Build Phylogenetic Trees

• Constructing a group’s evolutionary history involves distinguishing homologous from analogous features.

Cladistics

• Cladistics groups organisms by common descent.
• A clade consists of an ancestral species and all its descendants, forming a distinct branch on the tree of life (monophyletic group).
• A monophyletic group includes an ancestor and all its descendants, representing a single branch on the tree of life.

Ancestral vs Derived Characters

• Shared ancestral characters originated in ancestors outside the clade (e.g., backbones in mammals).
• Shared derived characters are evolutionary innovations unique to a clade.
• Shared derived traits identify clades and mark evolutionary branch points.
• Comparing an outgroup to the ingroup helps identify shared derived traits and infer evolutionary relationships.
• Gestation is absent in frogs, iguanas, and the duck-billed platypus, suggesting the platypus is an early branch in the mammalian clade.

Parsimony

• The principle of parsimony suggests the simplest explanation is the most likely.
• Parsimony helps construct phylogenetic trees with the fewest evolutionary changes.
• Computer programs are often used to develop parsimonious phylogenetic trees.

Phylogenetic Trees as Hypotheses

• Phylogenetic trees are hypotheses based on current evidence and can be updated with new data.
• Birds are closely related to certain reptiles, like crocodiles, more than other reptiles.
• Based on this reasoning, biologists hypothesize that traits like nest-building and brooding were also present in dinosaurs.
• Fossil evidence supports the hypothesis that dinosaurs built nests and exhibited brooding.

Analogy

• Analogy is the similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait.

Binomial System

• The binomial system is the two-part format for naming a species, consisting of a genus and specific epithet; for example, Homo sapiens.

Class

• A class is a rank in the hierarchical system of taxonomy. It groups together related organisms that share certain characteristics and is positioned below the "phylum" level but above the "order" level.

Domain

• A domain is a taxonomic category above the kingdom level (Archaea, Bacteria, and Eukarya).

Genus

• In Linnaean classification, the taxonomic category above species; the first part of a species′ binomial; for example, Homo.

Kingdom

• A kingdom is one of the broadest taxonomic ranks, situated below the domain level and above the phylum level.

Molecular Systematics

• Molecular systematics is a scientific discipline that uses nucleic acids or other molecules in different species to infer evolutionary relationships.

Order

• An order is a taxonomic rank that organizes families with shared characteristics. It sits below the class level and above the family level in the hierarchy.

Phylogenetic Tree

• A phylogenetic tree is a branching diagram that represents a hypothesis about the evolutionary history of a group of organisms.

Phylogeny

• Phylogeny is the evolutionary history of a species or group of related species.

Phylum

• A phylum (plural: phyla) is a major taxonomic rank in the classification of organisms. It sits below the kingdom level and above the class level.

Species

• A species is the most specific rank in the biological classification hierarchy.

Taxon

• A taxon is a named taxonomic unit at any level of classification.

Taxonomy

• Taxonomy is the scientific discipline concerned with identifying, naming, and classifying the diverse forms of life.

Molecular Systematics and Genome Evolution

• The more recently two species have branched from a common ancestor, the more similar their DNA sequences are.
• The longer two species are separated, the more their DNA is expected to have diverged.
• Molecular systematics uses DNA and other molecules to determine relatedness.
• Molecular systematics has clarified evolutionary relationships and revolutionized the study of phylogeny.
• Molecular methods led to the introduction of the domain as a higher taxonomic category.
• Molecular studies of ribosomal RNA (rRNA) revealed that many prokaryotes previously classified as bacteria are more closely related to eukaryotes.
• There are three domains: Bacteria, Archaea (both prokaryotic), and Eukarya (including eukaryotes like fungi, plants, animals, and protists).
• Varying rates at which genes evolve enables scientists to use molecular systematics for constructing phylogenetic trees that span both long and short evolutionary timescales.
• Ribosomal RNA (rRNA) genes evolve slowly and are valuable for studying relationships among taxa that diverged hundreds of millions of years ago.
• rRNA studies revealed that fungi are more closely related to animals than to green plants.
• Mitochondrial DNA (mtDNA) evolves quickly, which makes it useful for studying recent evolutionary events.
• mtDNA analysis has been used to construct a phylogenetic hypothesis for bears, including a timeline based on fossil evidence and molecular data.
• mtDNA has been utilized to study human populations, including relationships among Native American groups.
• The Pima of Arizona, the Maya of Mexico, and the Yanomami of Venezuela are closely related and likely descend from migrants that crossed the Bering Land Bridge from Asia to the Americas about 15,000 years ago.
• Polar bears and brown bears can interbreed but genetic evidence confirmed they are distinct species.
• Polar bears and brown bears diverged between 343,000 and 479,000 years ago.
• Human and chimpanzee genomes are remarkably similar.
• Homologous genes are shared due to common ancestry and are widespread across vast evolutionary distances.
• 99% of human and mouse genes are homologous, as are 50% of human and yeast genes.
• Gene duplication has been crucial in evolution, as it increases the number of genes in a genome, creating more opportunities for evolutionary changes.
• The number of genes does not correlate directly with an organism's complexity.
• Humans have only about four times as many genes as yeast.
• rRNA changes very slowly, useful for studying relationships of organisms that diverged long ago.

Molecular Clocks

• The longer two groups have been evolutionarily separated, the more their genetic makeup diverges.
• Dolphins and bats share more similarity in their homologous genes than sharks and tunas do.
• Molecular changes, rather than morphological ones, provide a more accurate measure of time.
• Molecular clock work by estimating the time needed for a specific amount of evolutionary change by tracking genetic mutations.
• A molecular clock with a consistent average rate of change can be calibrated using known evolutionary branch points from the fossil record.
• Molecular clocks have been used to date significant evolutionary events.
• Humans started wearing clothing between 83,000 and 170,000 years ago.
• The data for molecular clocks can come from one gene or many genes.
• Molecular changes happen at variable rates across genes, organisms, and time periods.
• Molecular clocks can date divergences beyond the 550-million-year fossil record, but these estimates assume constant rates over time, making them uncertain.
• A molecular clock estimates the actual time of evolutionary events based on the number of DNA changes.
• Molecular clock is based on the assumption that some regions of genomes evolve at constant rates.
• All of life has a common ancestor and molecular systematics is helping to link all living organisms into a comprehensive tree of life.

Tree of Life

• Phylogenetic trees serve as hypotheses about evolutionary history and are subject to revision or rejection based on new evidence.
• Protists are not monophyletic and thus cannot form a single kingdom.
• Mitochondria and chloroplasts are shown as lineages in the domain Bacteria due to the origin of eukaryotic cells from simpler prokaryotes.
• The first major split was the divergence of Bacteria from the other two domains, followed by the divergence of Archaea and Eukarya.
• Significant gene exchanges have occurred between organisms from different domains during early life due to horizontal gene transfer.
• Horizontal gene transfer is facilitated by plasmid exchange, viral infection, and organismal fusion.
• Gene transfer occurred between a mitochondrial ancestor and early eukaryotes, and between a chloroplast ancestor and early green plants.
• Mitochondria and chloroplasts in eukaryotic cells retain DNA from bacterial lineages.
• Domain Eukarya originated from a prokaryotic lineage that diverged from the archaeal lineage about 2.8 billion years ago.
• The eukaryotic ancestor may have been an archaean.
• Amoebas are the protists most closely related to animals.