Taxonomy and Systematics Introduction

Taxonomy and Systematics

• Scientists categorize/organize living things.
• Scientists write scientific names correctly.
• Homology is an important concept.
• Cladistics help compose cladograms (phylogenetic trees).
• Likelihood of cladograms is compared using parsimony.
• Molecular clocks date evolutionary events.

Taxonomy

• It describes, names, and classifies living/extinct organisms and viruses.

Systematics

• It studies biological diversity and evolutionary relationships among organisms (extinct and modern).
• Taxonomic groups base on evolutionary relationships derived from systematics.

Taxonomic Organization

• A hierarchical system involves successive levels.
• Each group at any level is a taxon.
• Domain is the highest level.
• All life is within 3 domains: Bacteria, Archaea, and Eukarya.

Taxonomic Groups

• Eukarya includes supergroups Excavata, Land plants and algal relatives, Alveolata, Stramenopila, Rhizaria, Amoebozoa, and Opisthokonta.
• Large eukaryotic kingdoms are: Plantae, Fungi, and Animalia.
• Eukarya includes ~4-10 million species.
• Opisthokonta includes >1 million species.
• Animalia includes >1 million species.
• Chordata includes ~50,000 species.
• Mammalia includes ~5,000 species.
• Carnivora includes ~270 species.
• Canidae includes 34 species.
• Canis includes 7 species.
• lupus includes 1 species.

Binomial Nomenclature

• It includes the genus name and species epithet.
• Genus name is always capitalized.
• Species epithet is never capitalized.
• Both names are italicized or underlined.
• International associations establish and regulate naming rules.

Cladistics

• Cladistics is the study and classification of species based on evolutionary relationships.
• It discriminates among possible phylogenetic trees by considering evolutionary change pathways.
• It chooses the tree requiring the least complex explanation for all available data.
• Phylogenetic trees are also called cladograms.

Cladistic Approach

• It compares homologous traits, called characters in two or more character states.
• Shared primitive character/symplesiomorphy shared by two or more taxa, inherited from ancestors older than their last common ancestor.
• Shared derived character/synapomorphy is shared by two or more species/taxa, originating in their most recent common ancestor.
• A branch point includes 2 species differing in shared derived characters.
• Two taxa that share a common ancestor are sister groups.
• Ingroup is the group of interest.
• Outgroup is a species or group assumed to have diverged before the ingroup.
• Outgroup lacks one or more shared derived characters found in the ingroup.

Constructing Cladograms

• Choose the species.
• Choose characters.
• Determine polarity of character states as either primitive or derived.
• Analyze based on these rules:
  • All species/higher taxa placed on tips, not branch points.
  • Each branch point should have a list of shared derived characters common to all species above, unless later modified.
  • Shared derived characters appear together only once, unless arising independently.
• Choose the most likely/simplest cladogram among options.
• Choose a noncontroversial outgroup as a root for the tree.

Principle of Parsimony

• The preferred hypothesis is simplest for all characters/states, with the fewest changes.
• A cladistic challenge is determining the correct polarity of events.
• Determining which traits are primitive vs. derived, may not always be obvious.
• Fossils can be analyzed.

4 Taxa Example Using Parsimony

• 4 taxa: A-D are being compared
• A is the outgroup, with all the primitive states.
• A comparison of 3 potential phylogenetic trees of organisms, Tree 3, requires the fewest mutations (5) and is the most parsimonious.

Analysing Phylogenies Based on New Data

• Phylogeny shows a species or group's evolutionary history.
• Phylogeny is proposed using tools of systematics, especially cladistics.
• Trees based on morphological or genetic data.

Phylogenetic Trees

• They are diagrams describing phylogeny, showing a hypothesis of evolutionary relationships among various species. They are based on available information.
• Anagenesis means a single species evolves into a different one through lineage change.
• Cladogenesis means a species diverges into 2+ species, emerging multiple lineages from one ancestor.
• Monophyletic group/clade: group of species/taxon, consisting of most common ancestor and all descendants.
• Smaller and more recent clades are nested within larger clades with older common ancestors.
• Paraphyletic group contains a common ancestor and some, but not all, of its descendants.
• Polyphyletic group contains multiple lineages without their common ancestor.
• Over time, taxonomic groups reorganize so that only monophyletic groups are recognized.
• Reptiles were a paraphyletic group because birds were excluded, but are now classified as monophyletic.

Homology

• Homology refers to similarities among various species because they are derived from a common ancestor.
• Bat wings, human arms, and cat front legs share this trait.
• Genes may also be homologous if they're derived from the same ancestral gene.

Morphological Analysis

• First systematic studies focused on morphological features of extinct and modern species.
• Convergent evolution, where traits arise independently due to adaptation, can be problematic.
• Traits from convergent evolution are called analogous traits.

Molecular Systematics

• Genetic data, such as DNA and amino acid sequences, is analyzed to identify and study genetic homologies and propose phylogenetic trees.
• DNA and amino acid sequences from closely related species are more similar than those from distantly related ones.

Molecular Clocks

• Favorable mutations are rare and detrimental ones are eliminated.
• Most mutations are neutral.
• A constant rate of neutral mutations can measure evolutionary time.
• Longer periods since divergence allow more mutation accumulation.
• Molecular clocks not perfectly linear over long periods, because:
  • Not all organisms evolve at the same rate.
  • There are differences in generation times.

Primate Evolution Example

• A study compares DNA sequences on the cyctochrome oxidase subunit II in primates to determine evolutionary patterns:
• The gene mutates fairly rapidly
• Three relevant ancestors were found

Specific Primate Ancestors in the Study

• Ancestor A diverged into siamangs and the modern genera. It took 23 millions years for subsequent change.
• Ancestor D diverged into humans and chimpanzees
• Ancestor E ultimately diverged into modern chimpanzees

Ancient DNA Analysis

• Ancient DNA analysis/molecular paleontology can be used to study flightless bird phylogenies.
• DNA samples stable as long as 50,000-100,000 years under certain conditions.
• Studies gather the data to propose a hypothesis.
• Sequences are very similar.
• New Zealand colonized twice by flightless birds, first by moa, then kiwi ancestor.

Horizontal Gene Transfer

• Horizontal gene transfer refers to processes where an organism incorporates genetic material from another organism without being its offspring.
• Vertical evolution is when there are changes due to descent from a common ancestor or parent.
• Horizontal gene transfer can lead to a "web of life" rather than a tree, by moving genetic material between organisms.
• This is less common in eukaryotes than prokaryotes
• The universial ancestor may have been more of a collective community of cell lineages