Taxonomy and Phylogenetics

Why is taxonomic identification important?

Proper taxonomic identification ensures accurate classification of organisms, which is essential for economy, food security, and health.

How can misidentification be economically costly?

Misidentification can lead to losses in agriculture, fisheries, and trade, as incorrect species identification affects resource management and market value.

How does taxonomic misidentification impact food security?

Incorrect identification can lead to contaminated or mislabeled food products, affecting nutrition and food supply chains.

How does taxonomic misidentification affect health?

Misidentifying disease-causing organisms, allergens, or toxic species can lead to medical misdiagnoses and health risks.

Taxonomy definition

Theory & practice of classification

Phylogenetics definition

The study of the “tree of life”

Evolutionary history of taxonomic groups

Systematics definition

Process to classify organisms according to their phylogeny

What is taxonomy?

•Establishing the identity of organisms (naming organisms).

•Describing organisms - recognition of differences (& similarities).

•Preserving organisms’ collections.

•Classifying organisms.

Classification definition

verb) Making sense of the relatedness of organisms in the world. (noun) A
descriptive group of organisms.

How did indigenous populations contribute to early classification?

Indigenous groups like the Inuit, Aborigines, and Native Americans developed rudimentary classification systemsbased on their environment, often distinguishing organisms by their use, danger, or characteristics.

Why do humans have an innate ability to classify?

Classification has survival value, helping humans distinguish edible vs. poisonous plants and harmless vs. dangerousanimals.

How did Aristotle contribute to early classification?

Aristotle (384–322 BC) created one of the first biological classification systems, categorizing organisms into plants and animals, and further subdividing animals based on characteristics like habitat and movement.

How many species of living organisms are estimated to exist (excluding bacteria)?

Around 10.9 million species.

What does classification involve?

•Arranging populations & species into groups.

•Groups based on shared characteristics/traits.

•Recognition of different groups (= delimitation).

•Ordering (= arranging) them.

•Ranking them (= conferring status).

•The first step involves the delimitation of populations into species.

Who was Carl Von Linné (Carolus Linnaeus) and what was his contribution to biology?

Carl Von Linné (1707-1778), a Swedish naturalist, revolutionized the way life was described by developing a binomial nomenclature system for naming species. Example: “Physalis annua ramosissima, ramis angulosis glabris, foliis dentato-serratis” was later simplified to Physalis angulata.

What is the taxonomic hierarchy?

Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species.

What is the correct formatting for binomial nomenclature?

In binomial nomenclature, genus (capitalised) and species (lowercase) names are always given in italics.

How should family, order, and class names be written in taxonomy?

Family, order, and class names should not be italicised but must be capitalised.

What scientific advances in the 1700s and 1800s contributed to the development of Darwin's theory of evolution?

Advances in geology (fossils, Earth's age), anatomy (homology, vestigial structures), and evolutionary concepts (extinction, inheritance of traits) set the stage for Darwin's theory of evolution by natural selection.

What were some of Jean-Baptiste Lamarck’s ideas on evolution?

Lamarck believed that organs within organisms gained increasing complexity, and that environmental factors influenced evolutionary change. He suggested that changes occurred due to incremental adaptation.

Why were Lamarck's theories considered fundamentally incorrect?

Lamarck’s theory was incorrect because he misunderstood the cause of evolutionary change, attributing it to positive environmental influences, rather than negative selective pressures that remove less-adapted traits over time.

What role did Darwin’s finches play in the development of Darwin’s theory?

Darwin studied finches after his voyage, noting their diverse beak morphology. Helped him think about evolutionary adaptation.

What is the theory of common descent in Darwin’s theory of evolution?

The theory of common descent suggests that all species share a common ancestor and have diverged over time through evolution. This idea underpins Darwin's theory, showing how species evolve and share genetic links.

How does the theory of common descent relate to natural selection?

The theory of common descent is a broader component of Darwin's evolutionary theory, while natural selectionexplains the mechanism through which species adapt and evolve over time, shaping the diversity of life from a common origin.

How does the theory of common descent explain the similarity between species within a genus?

The theory of common descent explains that species within a genus are more similar to each other because they share a common ancestor, reflecting their evolutionary history.

What does the theory of common descent tell us about grouping species?

The theory of common descent encourages us to seek natural groupings of species that reflect their evolutionary history, rather than grouping based on superficial characteristics.

What did Alfred Russel Wallace’s Sarawak Law (1855) propose about species evolution?

Wallace's Sarawak Law proposed that distinct species may have a common ancestor, and these ancestors could give rise to closely allied species, contributing to the understanding of evolution and common descent.

What was John Hunter's contribution to evolutionary theory?

John Hunter (1728-1793) arrived at the idea of common ancestry before Wallace or Darwin, but his ideas were considered too radical for 18th-century scientists, and he couldn't get his work published.

Why does the species concept matter in classification?

The species concept is crucial because correctly defining species is the first step in creating a natural classification system based on evolutionary history. Without accurate species discrimination, we cannot build a comprehensive understanding of evolutionary relationships.

What is the typological species concept?

The typological species concept is based on morphology/phenotype and was influenced by Plato’s "forms". It was used by Linnaeus and involves defining a species from a single specimen (type specimen) as the standard for the species.

What are the problems with the typological species concept?

The typological species concept ignores intraspecific variation, assuming all individuals of a species conform to a single 'type, which overlooks natural variation within a species.

Sexual Dimorphism

Where the two sexes of a species look substantially different in form (e.g.
colouring, size, appendages, physical shape)

What is the biological species concept?

The biological species concept defines species based on interbreeding and reproductive isolation, emphasizing gene pools and the coadaptation of genes. It focuses on intrinsic mechanisms of isolation (not geographic barriers like mountains or rivers).

What are the key criteria for defining species in the biological species concept?

The key criteria for the biological species concept are interbreeding between individuals and reproductive isolation that prevents gene flow between different species.

What triggers the evolution of reproductive isolating mechanisms?

The evolution of reproductive isolating mechanisms is expected when gene pools significantly diverge, and when there's no hybrid vigour (no benefit from interbreeding between different populations of the same species).

What are the two types of reproductive isolation mechanisms?

Reproductive isolation mechanisms are:

1. Pre-zygotic: Barriers that occur before fertilization, such as habitat isolation, morphological differences, behavioral differences, or gametic incompatibility.

2. Post-zygotic: Barriers after fertilization, leading to hybrid inviability (failure of the offspring to develop) or hybrid sterility (offspring are sterile, like mules).

Which taxa is predicted to include the highest number of individual species?

Invertebrates

Advantages of typological species concept

•Morphology can be readily observed and perceived

•Relatively easy to communicate it outside scientific community

Disadvantages of typological species concept

•Intra-specific variation in fossils

•Cryptic species (e.g. Pipistrelle spps.)

•Artificial concept (excludes natural mechanisms)

Advantages of biological species concept

•This is a species concept based on a mechanism

Disadvantages of biological species concept

•Excludes asexually reproducing organisms and Palaeospecies (fossils)

•Evolutionary intermediacy (e.g. ring species)

•Allopatric species can be a challenge

•Many living organisms have never been observed mating.

Biospecies

A species is a group of interbreeding organisms that can produce viable, fertile offspring and are reproductively isolated from other groups.

Morphospecies

A species is defined based on shared physical characteristics (morphology) that distinguish it from other groups.

Are morphospecies valid?

Yes, in most cases, morphologically distinct populations represent isolated gene pools and valid biological species.

Why is morphology a reliable indicator of species?

Morphology is largely controlled by genetics, meaning distinct forms often indicate separate species.

What is a key criterion for recognizing morphospecies?

If two coexisting populations show no intermediate forms, they are likely separate species.

What are cryptic species?

Species that are genetically and behaviorally distinct but morphologically identical.

Example of cryptic species?

Common Pipistrelle bats (split into two species in 1999 due to different echolocation frequencies, despite identical morphology).

What is a limitation of using the Morphospecies Concept?

It may fail to distinguish cryptic species that look identical but are biologically different.

Problems of biological species concept

1.Asexually reproducing organisms

•Do not fulfil the criterion of interbreeding - they are clonal

•e.g. some aphids, all bdelloid rotifers & prokaryotes

2.Evolutionary intermediacy

•Populations in process of becoming separate species

•Ring species

•Anagenesis in paleospecies

•Where does one species end and the other begin???

3. Allopatric populations

   Not actually or potentially interbreeding

What is a ring species?

A connected series of populations that can interbreed with neighboring populations, but the two extremes cannot interbreed.

What is a Paleospecies?

A paleospecies refers to an extinct species known primarily from fossil evidence.

What is a sympatric population?

A sympatric population refers to two or more populations of the same or different species that live in the same geographic area and have the potential to interact. Despite living in the same environment, these populations may avoid interbreeding due to differences in behavior, ecology, or reproductive strategies.

What is an allopatric population?

An allopatric population occurs when populations of the same or different species are geographically separated, preventing them from interbreeding. This geographical isolation can lead to the development of new species through allopatric speciation, as isolated populations may evolve differently due to varying environmental pressures

Can Allopatric Populations Interbreed?

Allopatric populations, once geographically separated, may interbreed if brought into contact due to human movement, the retreat of natural barriers (like glaciers, water bodies, or deserts), or other factors.

Subspecies

•aggregates of local populations of an individual species

•Inhabit different geographic subdivisions of the range of that species

•Differing taxonomically* from other populations of the spp.  (*usually means morphologically)

•They cannot, by definition, be sympatric

What is a Polytypic Species?

A polytypic species is a species that contains multiple subspecies.

What is an Incipient Species?

An incipient species refers to a population or subspecies that is in the early stages of becoming a distinct biological species. This process occurs due to reduced gene flow and evolutionary forces like natural selection or genetic drift, often following isolation by physical barriers.

How are subspecies denoted?

•Each subspecies denoted by a trinomen

•e.g. great tit: Parus major major & P. major excelsus

What are subspecies a result of?

While it is not based on genetic differences, subspecies are often a result of reduced gene flow due to isolation by extrinsic barriers like geographic features (mountains, rivers, deserts). Over time, subspecies may evolve into separate species through processes like natural selection or genetic drift, potentially becoming incipient species.

Recognition species concept

•Allopatric populations not interbreeding

•BUT recognize each other as potential mates = same species

Advantages of recognition species concept

•Removes uncertainty regarding allopatric populations

•Relies completely on the mechanism (more coherent)

Disadvantages of recognition species concept

•Excludes asexually reproducing organisms and Palaeospecies (fossils)

•Evolutionary intermediacy (e.g. ring species)

•Only truly valid for animals (analogies can be made for insect pollinated plants)

•Even harder to assess than the Biospecies.

Phylogenetic species concept

•Species is a “tip” on a phylogeny

•Smallest inclusive monophyletic* grouping

•Relies on common ancestry and shared evolutionary history to define species

Advantages of phylogenetic species concept

•Recognizes the role of history in generating species explicitly and can be reasonably objective.

•Can use nearly any sort(s) of data (morphological, behavioural, genetic).

Disadvantages of phylogenetic species concept

•Subdivision of lineages into species can be rather arbitrary (no distinct definition)

•Ring species are not differentiated & subspecies are not recognized (legal ramifications for wildlife protection law).

Genetic species concept

Defining a species based on its DNA/RNA/Protein sequence similarity

Advantages of genetic species concept

•Can provide independent evidence for morphological and biological species

•For bacteria: can be very useful and save a lot of time

•Can deal with asexually reproducing organisms and Palaeospecies (fossils);

•Can uncover cryptic species that morphological studies would not.

Disadvantages of genetic species concept

•Also relies, to some extent, on human judgment of how much difference is enough to constitute separate species

•Communicating with non-specialists about DNA taxonomy can also be very difficult.

Purposes of classification

•Index of stored information

•Enables predictions & generalisations   to be made concerning the biology of organisms

What are delimitation and ordering in Biological Classification?

• Species Delimitation: Determining which populations should be considered separate species based on genetic, morphological, or behavioral traits.

• Genus, Family, and Higher Taxa Delimitation: Deciding which groups of species should be classified together in broader categories based on their evolutionary relationships (phylogeny).

• Ordering: The hierarchical arrangement of organisms from species to domain, ensuring each level reflects evolutionary connections.

What is a Phylogenetic Tree (Tree of Life)?

A phylogenetic tree, also known as the Tree of Life, is a diagram that represents the evolutionary relationships among different species or groups. It shows how species are related through common ancestry, with branches representing the divergence of species over time.

Danger of the 'Tree' Concept:

•Tips of tree are not ‘more evolved’ or ‘better’

Dendrograms

A branching phylogenetic tree showing clusters of groups of related
organisms. Usually without an indication of how similar they are

What is Ranking in Biological Classification?

Ranking refers to assigning status to supraspecific groups (categories above the species level) in the hierarchical classification system.

Toplogy

The pattern or arrangement of branches and stems in a phylogenetic tree

Main methods of classification

1.Phenetics

2. Cladistics

3. Orthodox approach

What is phenetics?

• Phenetics classifies organisms based on overall phenotypic similarity (observable traits).

• All traits are treated equally (no distinction between primitive/derived or homologous/analogous).

• Evolutionary history and genealogy are ignored.

• Claimed to be highly objective with fixed criteria.

• Results in phenograms, which group species by shared traits, not evolutionary relationships.

Phenetics definition

Grouping based on overall phenotypic similarities. All characteristics are
given equal importance in the analysis.

Problems with phenetics

•Does not control for the confounding effects of the phenotypic similarity that is due to convergent evolution

•Due to similar selection pressures or mimicry

•So cannot be depended on to reflect evolutionary history.

Convergent evolution

Where two similar structures evolve in separate evolutionary lineages in
unrelated species/groups

Limpets and barnacles - convergent evolution

• Limpets (molluscs) and barnacles (crustaceans) have dome-shaped armored coverings.

• Phenetic classification might group them together due to this similarity.

• However, the armored covering in each species has a different origin (not homologous).

• The similarity is due to phenotypic convergence, where natural selection shaped similar traits in response to wave/current action.

Homologous

From the same embryonic origin

Analogous

The same function, but from different genetic origins

Homologous Features of Barnacles and Crabs

• Barnacles share homologous features with crabs (both are arthropods).

• The armored covering in barnacles and crabs has a similar origin.

• Both animals have jointed limbs, a characteristic of arthropods.

Mimicry

Where an organism takes on the form/colour/characteristics of another
organism, either as a defence or a predation mechanism

Example of mimicry

• Convergent evolution can occur when a palatable species evolves to resemble an unpalatable species (e.g., non-venomous species mimicking venomous species).

• This mimicry occurs due to selection pressure for the mimic to avoid predation.

• In this case, the mimicking species undergoes convergence with the harmful species, benefiting from similar traits that deter predators.

Cladistics definition

Grouping based on an inferred genealogy

Cladistics

•Based on inferred genealogy (ancestry / evolutionary history)

•Trees = cladograms

•Based on shared, derived homologous characters.

•Weighting of characters

•Claimed to be highly ‘objective’ & (importantly) to reflect evolutionary history.

•Requires all supraspecific groupings (taxa) to be monophyletic

•Paraphyletic taxa are invalid

•Polyphyletic taxa are invalid.

•(They are grouped on the basis of convergences)

Monophyletic

A 'supraspecific' grouping which contains all of the known decendents of a
common ancestral species (e.g. chimpanzees and bonobos)

Paraphyletic

A 'supraspecfic' grouping which contains some, but not all, of the known
descendents of a common ancestor (e.g. chimpanzees and humans)

Polyphyletic

A 'supraspecific' grouping which contains decendents from fundamentally
different lineages

How are monophyletic taxa recognised?

•Traits provide different kinds of information on genealogy (groups’ history)

•Infer whether a change in a trait occurred early or late in ancestry.

•Groupings should be based only on new traitstates arising in the nearest common ancestor

Why do taxa resemble one another

1.The character arose early on in the ancestry of the taxa, before the occurrence of the nearest common ancestor

•i.e. the character ‘goes back’ more than one branching point

•e.g. jaws in amphibians + reptiles + birds + mammals

•A shared primitive (i.e. ancestral) character

2.The character originated in the nearest common ancestor = shared derived character

•Advanced lungs: lungfish + amphibians + reptiles + birds + mammals

•Jaws: jawed fish + amphibians + reptiles + birds + mammals

•Amniotic egg

3.The character originated independently, by convergence

•e.g. elongated, worm-like body shape in some fishes, some amphibians & some reptiles

•Homoplasy: similarity due to convergence

Homoplasy

Similarity of a characteristic due to convergent evolution or phenotypic
convergence

Derived Characters

Characteristcs that arose from a similar origin, but have since changes in the
later lineages of organisms (e.g. forelimbs in reptiles and birds).

What are Unshared Derived Characters?

• Unshared derived characters are traits that are acquired by, and restricted to, a phyletic line (a lineage) after it branched off from its sister-group.

• These characters are derived because they are new evolutionary traits that appeared after the lineage diverged from a common ancestor.

• They are unshared because they are not present in the sister-group, making them useful for distinguishing between different evolutionary lineages.

Character polarity

Where a characteristic exists in two states, sometimes with intermediates
inbetween.

Methods for assessing character polarity

•Outgroup comparison

•Embryology

•Fossil record 

Outgroup

A group of organisms which is similar, but a fundamentally different lineage.
Used to orientate the analysis as something to compare to, when doing a
phylogenetic analysis