Taxonomy and Systematics

• Phylogeny studies evolutionary relationships, while systematics classifies organisms.

Taxonomy

• It is a formal system for naming and classifying species.
• It aims to illustrate the evolutionary relationships between different organisms.

Taxonomy & Systematics

• Taxonomy is a formal system for naming and classifying species.
• Systematics is a broader science that classifies organisms based on similarity and biogeography.
• Systematic zoologists aim to discover animal species, reconstruct evolutionary relationships, and classify animals based on these relationships.

Taxonomy and Evolution

• The introduction of evolutionary theory redefined the role of taxonomists from classification to systematization.
• Classification involves constructing classes by grouping organisms with a common feature or "essence."

Systematization

• It groups species into units of common evolutionary descent, using character variation to diagnose these systems.
• An essential character is not required to be maintained throughout the system for recognition as a taxon.

Classification Vs Systematization

• Classification asks if a species contains the defining feature of a taxonomic class.
• Systematization asks if a species' characteristics confirm its descent from the most recent common ancestor of a particular taxon.

Linnaean Classification

• Carolus Linnaeus developed our hierarchical classification scheme.
• The scheme includes Kingdom, Phylum, Class, Order, Family, Genus, and Species.

Linnaean System Details

• All animals are placed in Kingdom Animalia.
• Names of animal groups at each rank are called taxa.
• Ranks can be subdivided into additional levels of taxa like superclass and suborder.

Binomial Nomenclature

• This is the system Linnaeus used for naming species.
• It involves genus and species names that are latinized and italicized, with only the genus capitalized, e.g., Sitta carolinensis.

Trinomial Nomenclature

• A trinomial name includes a subspecies epithet, such as Ensatina escholtzii escholtzii, or E. e. klauberi.

Species Definition

• It is difficult to define species precisely.
• Criteria include common descent.
• They are the smallest distinct groupings of organisms sharing a pattern of descent determined using morphological and molecular techniques.
• Members of a species need to form a reproductive community that excludes other species.

Species Distribution

• The geographic range is the species' distribution in space.
• Evolutionary duration is its distribution in time.
• A worldwide species is cosmopolitan.
• A species with a very localized range is called endemic.

Typological Species Concept

• The is concept relies on type specimens presenting the ideal form for the species, used for comparison when naming new specimens.
• Scientists still designate type specimens.

Biological Species Concept

• This concept emerged during the evolutionary synthesis.
• A species is defined as a reproductive community of populations reproductively isolated from others, occupying a specific niche.
• Sibling species fit this category but require molecular techniques for differentiation.
• The biological species concept lacks a temporal dimension, raises questions about the necessary degree of reproductive isolation, and applicability to asexually reproducing species.

Evolutionary Species Concept

• This states a single lineage of ancestor-descendant populations maintains its identity from other lineages, with its distinct evolutionary tendencies and historical fate.
• The definition accommodates both sexual and asexual forms, as well as fossils.

Phylogenetic Species Concept

• It defines a species as an irreducible grouping of organisms diagnosably distinct from other groupings, with a parental ancestry and descent pattern.
• Both asexual and sexual groups are covered.

Evolutionary Vs Phylogenetic Species Concepts

• The main difference is that the latter emphasizes recognizing the smallest groupings of organisms that have undergone independent evolutionary change as separate species.
• This discerns the greatest number of species but may be impractical and disregards details of the evolutionary process.

Systematics

• A major goal of systematics is to infer the evolutionary tree or phylogeny.
• Phylogeny is the evolutionary history of a species or related group.

Inferring Phylogenies

• Phylogenies are inferred by identifying organismal features, known as characters, that vary among species.
• These characters can be morphological, chromosomal, molecular, behavioral, or ecological.

Homologous Characters

• Shared characters from common ancestry are homologous.
• Independent evolution of similar non-homologous characters, as known as homoplasy.
• Homoplasy refers to features shared between species not inherited from a common ancestor.

Homology and Analogy

• Similarity due to convergent evolution, called analogy, can be a problem when making a phylogeny, instead of shared ancestry.
• Wings of birds, bats, and insects are examples of convergent evolution as they developed independently.

Analogous Structures

• Analogous structures or molecular sequences that evolved independently are also called homoplasies. -Wings of bats, birds, and insects.

Shared Primitive Characters

• A shared primitive or ancestral character is a homologous structure that predates the branching of a particular clade from other members.
• This is shared beyond the taxon being defined.
• Mammals all have a backbone, which is also present in other vertebrates.

Shared Derived Characters

• A shared derived character is an evolutionary novelty unique to a particular clade.
• All mammals having hair, which is unique amongst other animals.

Character States

• An ancestral is the form of a character found in the common ancestor, while later-arising, variant forms are called derived character states.
• Determining the polarity of a character means determining which state is ancestral.

Polarity Determination

• Determined by using outgroup comparison which includes an outgroup, closely related, but not part of the group being examined (ingroup).
• If the outgroup and study group share some characteristics its considered ancestral for the study group.
• Character groups found in the study grou but not the outgroups are considered derived.

Clades

• This are organisms or species that share derived character states and form a subset within a larger group.
• A synapomorphy is a derived character shared by the members of a clade.
• They are unit of evolutionary common descent
• Derived states create a formation of nested hierarchy of all characters in a study group.

Plesiomorphic States

• Ancestral character states for a taxon are known as plesiomorphic.
• Sharing these ancestral characters is called symplesiomorphy.
• Unlike synapomorphies, symplesiomorphies do not provide information on nesting of clades, leaving out groups with derived characters.

Cladograms

• A nested hierarchy of clades is represented as a cladogram based on shared synapomorphies.

Phylogenetic Tree

• A phylogenetic tree an alternative way of representing evolutionary relationships.
• The branches represent real lineages that occurred in the evolutionary past.
• It includes evolutionary information about the duration of lineages and amounts of evolutionary change.

Cladograms Characters

• Cladograms are constructed using characteristics found using comparative morphology, comparative biochemistry, and comparative cytology.
• Comparative morphology examines structures and developmental origins.
• Comparative biochemistry examines sequences of amino acids and nucleotides.
• Comparative cytology uses variation in chromosomes.

Taxonomy Theories

• A theory allows us to rank taxonomic groups.
• Two popular theories are evolutionary and phylogenetic systematics.
• Both are based on evolutionary principles, but may sometimes conflict.

Cladistics

• In cladistics, a valid clade is monophyletic.
• It consists of the ancestor species and all its descendants.

Paraphyletic Clades

• A paraphyletic clade consists of an ancestral species and some, but not all, of its descendants.

Polyphyletic Grouping

• A polyphyletic grouping includes types of organisms that lack a common ancestor.

Evolutionary Taxonomy

• Evolutionary taxonomy uses common descent and the amount of adaptive evolutionary change to rank higher taxa.
• This classification type can include paraphyletic groupings and groupings.

Phylogenetic Systematics

• Phylogenetic systematics, or cladistics, emphasizes common descent and uses cladograms.
• All taxa must be monophyletic.
• Cladistic taxonomists have moved chimpanzees, gorillas, and orangutans into the family Hominidae with humans.
• Humans and chimps form a sister group, as do the human/chimp group and gorillas.

Taxonomy Theories Compared

• Both evolutionary and cladistic taxonomy accept monophyletic groups and reject polyphyletic groups.
• They differ on accepting paraphyletic groups, with traditional evolutionary taxonomy doing so, but phylogenetic systematics not doing so.
• This difference has important evolutionary implications.

Animal Taxonomy: Current State

• Modern animal taxonomy was established using evolutionary systematics and recent cladistic revisions.
• PhyloCode is a new taxonomic system being developed as an alternative to Linnaean taxonomy.
• It replaces Linnean ranks with codes denoting the nested hierarchy of monophyletic groups conveyed by cladograms.
• Terms like "primitive," "advanced,” “specialized" and "generalized” are used for specific characteristics and not for groups as a whole.

Systematics

• Systematists can never be sure of finding the single best tree in a large data set.
• They narrow possibilities using maximum parsimony and maximum likelihood principles.

Parsimony

• The most parsimonious tree requires the fewest evolutionary events in shared derived characters.
• Occam's Razor operates this principle.

Maximum Likelihood:

• The principle states that given rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events.

Phylogenetic Tress: The Best Hypothesis

• The best hypotheses for trees are those that align with data: morphological, molecular, and fossil.

Molecular Systematics

• Much of an organism's evolutionary history is documented in its genome.
• Comparing nucleic acids or other molecules is valuable for tracing evolutionary history.

Major Divisions of Life

• Aristotle's two kingdom system included plants and animals, but one-celled organisms posed an issue.
• Haeckel (1866) proposed Protista for single-celled organisms.
• R.H. Whittaker (1969) proposed a five-kingdom system to distinguish prokaryotes and fungi.
• Woese, Kandler, and Wheelis(1990) then proposed the the monophyletic domains Eucarya, Bacteria and Archaea- based on ribosomal RNA sequences.
• Revisions are necessary to clarify taxonomic kingdoms based on monophyly.
• "Protozoa" are neither animals nor a valid monophyletic taxon, while "Protista" is not a monophyletic kingdom composed of seven or more kingdoms.

Animal Kingdom Major Subdivisions

• Traditional groupings are based upon embryological and anatomical characters.
• Branch A (Mesozoa) includes phylum Mesozoa/the mesozoa.
• Branch B (Parazoa) includes phylum Porifera/the sponges and phylum Placozoa.
• Branch C (Eumetazoa) includes all other phyla.
• Grade II (Bilateria) includes all other phyla.
• Division A (Protostomia) is protostome characteristics.
• Acoelomates are phyla Platyhelminthes, Gnathostomulida, and Nemertea.
• Pseudocoelomates are phyla Rotifera, Gastrotricha, Kinorhyncha, Nematoda, Nematomorpha, Acanthocephala, Entoprocta, Priapulida, and Loricifera.
• Eucoelomates are phyla Mollusca, Annelida, Arthropoda, Echiurida, Sipunculida, Tardigrada, and Onychophora.
• Division B (Deuterostomia) is deuterostome characteristics.
• Here is phyla Phoronida, Ectoprocta, Chaetognatha, Brachiopoda, Echinodermata, Hemichordata, as well as Chordata.
• Recent molecular phylogenetic research challenged traditional Bilateria classification.
• Grade II is Bilateria.
• Subdivision A (Protostomia) is Lophotrochozoa which is phyla platyhelminthes, Nemertea, Rotifera, Gastrotricha, Acanthocephala, Mollusca, Annelida, Echiurida, Sipunculida, Phoronida, Ectoprocta, Entoprocta, Gnathostomulida and Chaetognatha, as well as Brachiopoda.
• Ecdysozoa are phyla Kinorhyncha, Nematoda, Nematomorpha, Priapulida, Arthropoda, Tardigrada, Onychophora, and Loricifera.
• Subdivision B (Deuterostomia) is phyla Chordata, Hemichordata, and Echinodermata