taxonomy and phylogenetics Flashcards
what is taxonomy?
What is the importance of taxonomy to biology, health, and industry?
Establishing the identity of organisms (naming organisms).
Describing organisms - recognition of differences (& similarities).
Preserving organisms’ collections.
Classifying organisms.
Taxonomy underlies all other disciplines
Misidentification can be very problematic
Economically
Food security-nutrition
Health
Who are the key persons in the development of evolutionary theory and classification?
early classification (Aristotle - 384-322BC):
Indigenous populations – e.g Inuit, Aborigines, Native Americans
* Independently developed rudimentary / artificial classifications
* e.g. Inuit have numerous words for snow
* Humans have an innate ability to classify
* Survival value – e.g. edible vs poisonous, harmless vs dangerous
Classification making sense of the worlds biological diversity
Linnaeus: the father of modern taxonomy
* Carl Von Linné: 1707-1778(Carolus Linnaeus)
* Swedish naturalist
* Revolutionised how life was described
Jean-Baptiste Lamarck (1744-1829)
* Organs within organisms gain increasing complexity
* Environment impacts on evolutionary change
* Conflict between simplicity and complexity
- Fundamentally WRONG
- Had some key concepts along correct lines (incremental change, importance of environment)
- Causation of the change was misunderstood. It’s not a positive change, it’s a lack of selective(negative) pressure
diversity of life and cataloguing it - what that involves
- All kinds of living organism: c. 10.9 million spp. (not counting bacteria) *
- Animals: ca. 9.8 million living spp.
- Plants: ca. 0.3 million living spp.
- Fungi: ca. 0.6 million living spp.
- Prokaryotes: >0.1 million living spp.
- Extinct organisms: ? millions of spp.
cataloguing it:
* 10.9 million spp. Estimated; c. 1.4 million spp. currently catalogued
* Estimates: 360 – 2000yrs. to complete recording all species
* Majority of spp. are probably Insects
* Fungi are the major group of uncatalogued spp.
classifying involves:
* 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.
What is the correct format for taxonomic nomenclature?
Eg. Homo sapiens ~abbreviated to H.sapiens
Genus and species names=always in italics
Family, order, class names= NOT italicised but always capitalised
theory of common descent
- Component of Darwin’s theory of evolution
- The other theory of natural selection
Explains: why members of taxonomic group(eg. Species in a genus)
More similar to one another than to members of apparently equivalent groups
The theory tells us to seek ‘natural’ groupings
Ie. Groups reflect evolutionary history
similar theories:
Alfred Russel Wallace
* Wallace’s ‘Sarawak Law’ (1855):
* “Two or three distinct species may havehad a common antitype [= ancestor], andeach of these may again have becomethe antitypes from which other closelyallied species were created”
John Hunter (1728-1793)
* Arrived at the idea of common ancestry even earlier than Wallace or Darwin
* Couldn’t get published
* Too radical idea for 18thC scientists!
What are the key concepts that are used to define a species?
typological species concept
- Typology based on morphology/phenotype
- Stems from Plato’s “forms” and used by Linnaeus
- Applied in museum research (type method) where a single specimen (type specimen) is the basis for defining the species
Morphospecies: based on overall similarity (nowadays accounting for intra- specific variation, e.g. sexual dimorphism).
Advantages
* Morphology can be readily observed and perceived
* Relatively easy to communicate it outside scientific community
Disadvantages
- ignores intraspecific variation
eg. Sexual dimorphism (difference between male/female)
Eg. Life stages (caterpillars->butterfly)
Eg. geographical/other variants
* Intra-specific variation in fossils
* Cryptic species (e.g. Pipistrelle spps.
* Artificial concept (excludes natural mechanisms)
reproductive isolation
- Evolution of Reproductive Isolating Mechanisms
- Expected when gene pools significantly diverged
- No hybrid vigour (heterosis) - interbreeding between
populations within a species - Pre-zygotic (habitat, morphology, behaviour, gametes)
and post-zygotic (viability or sterility of offspring) - Hybrid inviability (resulting from disharmonious gene
combinations)
What are the key concepts that are used to define a species?
Biological species concept
Population genetics concept
Based on Mendelian + post-Mendelian genetics
- Note criteria: interbreeding and reproductive isolation
- Think about gene pools & ‘coadaptation’ of genes within pools
- Reproductive isolation via intrinsic mechanisms (not geographical barriers such as mountains or rivers - they are extrinsic).
- Biospecies: based on the ability of different individuals to interbreed and produce viable offspring in the wild
Advantages
* This is a species concept based on a mechanism
Disadvantages
* 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.
What other species concepts are there besides Typological and Biological definitions?
- recognition species concept
Allopatric populations not interbreeding
BUT recognise each other as potential mates = same species
advantages:
Removes uncertainty regarding allopatric populations
Relies completely on the mechanism (more coherent)
disadvantages:
Excludes asexually reproducing organisms and Palaeospecies(fossils)
Evolutionary intermediacy(eg. Ring species)
Only true for valid animals(analogies can be made for insect pollinated plants)
- 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:
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:
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
Geneticists equivalent of the morphospecies concept
Measure is genetic similarity or distance
Advantages
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:
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
what is classification/purpose of classification
- Purposes of classification
- Index of stored information
- Enables predictions & generalisations to be made concerning the biology of organisms
- An undescribed bird species (single, dead specimen) - new to science
- Based on morphology: Order Psittaciformes, Family Psittacidae
We can predict: Arboreal, claws used both to manipulate food & to climb. Flight is fast. Nests in a hole. Eggs pure white. Young naked upon hatching
What are the key principles behind classification?
delimitation:
Eg. Indian rhino: more features in common with each other
Form a group distinct from all other animals
Ordering:
Indian rhino + javan rhino
Not identical but so similar can be put into one group
All rhinos
Share certain features so form a larger group
Rhinos, Tapirs, horses
Even these share certain features so form an even larger group
dendograms:
Classifications are often expressed as trees(dendrograms)
ranking:
Involves conferring status of supraspecific groups
topology:
Arrangement of tree branches + stem
What are the processes/concepts behind compiling taxonomies based on these approaches:
Phenetics !!!
Cladistics
Orthodox approach
- Based on overall phenotypic similarity.
- All characters given equal weighting:
- Primitive / Derived
- Homologous / Analogous
- Genealogy (cladogenetic history) ignored.
- Evolutionary history ignored.
- Claimed to be highly ‘objective’, fixed criteria (compared with ‘orthodox’ method).
- “Phenograms”
Problems:
* 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
convergence evolution: selection pressures
Eg. Barnacles
* Based on the dome-shaped armoured covering, limpets & barnacles would be classified together
* But - the armoured covering has a different origin in those 2 animals (i.e. not homologous).
* There has been phenotypic convergence between limpet (mollusc) & barnacle (crustacean) - due to selection pressure of wave/current action
convergence evolution: mimicry
* E.g. a palatable sp. under selection pressure to resemble an unpalatable sp.
* E.g. non-venomous sp. mimics venomous sp.
* Convergence by one of the 2 spp.
What are the processes/concepts behind compiling taxonomies based on these approaches:
Phenetics
Cladistics !!!
Orthodox approach
- 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.
- Willi Hennig 1950
- Requires all supraspecific groupings (taxa) to be monophyletic
- i.e. each must comprise all of the known descendant species of the common ancestral species
- Paraphyletic taxa are invalid
- Polyphyletic taxa are invalid.
- They are grouped on the basis of convergences
cladistics - monophyletic taxa, taxa resemblances, defining taxon, character polarity
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 trait states arising in the nearest common ancestor
Taxa resemble one another for 3 reasons:
1. Character arose early on in the ancestry of the taxa, before occurrence of nearest common ancestor
Ie. The character ‘goes back’ more than one branching point
Eg. Jaws in amphibians + reptiles + birds + mammals
A shared primitive(ancestral) character
2. Character originated in the nearest common ancestor = shared derived character
3. The character originated independently, by convergence
Eg. Elongated, worm like body in fish + reptiles
Homoplasy- similarity due to convergence
defining a taxon: unshared derived character
Characters acquired by, and restricted to, a phyletic line after it branched off from its sister-group are unshared derived character
Eg. Mammary gland in mammals
Eg. Feathers in birds
Unshared, derived characters define each particular taxon(end branch)
character polarity:
* Suppose a character exists in 2 states:
* e.g. viviparous vs oviparous reproduction in Amniotes
* Which is derived state? Which is ancestral state?
* There are several methods for assessing character polarity:
* Outgroup comparison
* Embryology
* Fossil record
What are the processes/concepts behind compiling taxonomies based on these approaches:
Phenetics
Cladistics
Orthodox approach !!!
- Based on both genealogy (cladogenesis) & divergence (anagenesis).
- Weighting of homologous characters.
- Non-DNA/RNA orthodox classifications criticised
- too subjective/inaccurate
- despite attempting to take account of anagenesis (e.g. branch lengths estimated by dating fossils)
- Trees are phylogenies or ‘phylograms’.
why/benefits:
*Classifications based on molecular genetic data (DNA, RNA): are ‘orthodox’
* Provide information on genealogy (cladogenesis) AND rates of evolutionary divergence (anagenesis)
*Recognises clades AND grades
*They are more objective than ones based on other data - they more accurately reflect genetic relationships.
reasons morphology is still used/necessary:
* Key advantage of DNA
* Much DNA unaffected by natural selection (being selectively neutral ‘junk’) = evidence of ancestry
* Freedom from natural selection = ‘junk’ DNA mutation = highly informative traces
* Non-molecular, e.g. morphology-based classifications, have involved far too much subjectivity
* But there is sometimes good agreement with molecular, cladistics, phenetics
* In other cases, a radical change in tree results.
* e.g. cetaceans shown to be offshoot of artiodactyls (ungulates).
diadvantages:
Data could be misinterpreted
Needs to be considered in context
