Taxonomy And Phylogenetics Flashcards
(74 cards)
1
Q
Taxonomy – why does it matter?
A
- Taxonomy underlies all other disciplines
- Without it there would be confusion
2
Q
Importance of taxonomic identification?
A
- Misidentification can be costly
o Economically
o Food security – nutrition
o Health
3
Q
What is taxonomy?
A
Taxonomy – theory and practice of classification
4
Q
What is phylogenetics?
A
Phylogenetics – the study of the tree of life – evolutionary history of taxonomic groups
5
Q
What is systematics?
A
Systematics – process to classify organisms according to their phylogeny
6
Q
Why is taxonomy important?
A
- Establishing the identity of organisms (naming organisms)
- Describing organisms – recognition of differences (and similarities)
- Preserving organisms collections
- Classifying organisms
7
Q
How did indeginous population show signs of early classification?
A
Indigenous populations – eg Inuit, Aborgines, Native Americans
- Independently developed rudimentary/artificial classifications
- Eg Inuit have numerous words for snow
- Humans have an innate ability to classify
- Survival value = eg edible vs poisonous, harmless vs dangerous
8
Q
Describe Artistotles classification of living organisms 384-322bc
A
- Red blood vs no red blood
- Hard bodies vs soft bodies
- Shell vs no shell
- Lands, water, air dwellers
Classification = making sense of the worlds biological diversity
9
Q
Estimated numbers of all species?
A
- All kinds of living organisms: c.10.9spp. (Not counting bacteria)
- Animals: ca. 9.8 million spp.
- Plants: ca. 0.3 million living spp.
- Fungi: ca 0.6 million living spp.
- Prokaryotes: >0.1million living spp.
- Extinct organisms: ? Millions of spp.
10
Q
Cataloging life: are we there yet?
A
- 10.9 million spp. Estimated: c 1.4 million spp. Currently cataloged
- Estimates: 360-2000 yrs to complete recording all species
- Majority of spp. Are probably insects
- Fungi are the major group of uncatalogued spp.
- Many are likely to exist in threatened areas
11
Q
What does classification involve?
A
Arranging populations and species into groups
- Groups based on shared characteristics/traits
o Recognition of different groups (=delimitation)
o Ordering (=arranging) them
o Ranking them (=conferring status)
- The first step involved the delimitation of population and species
12
Q
Who was Linnaeus and what system did he develop?
A
Linnaeus : the father of modern taxonomy
- 1707-1778
- Swedish naturalist
- Revolutionised how life was described
Development of taxonomic hierarchy of categories – categories become less inclusive as you move down the hierarchy
- Domain
- Kingdom
- Phylum
- Class
- Order
- Family
- Genus
- Species
13
Q
What is binomial nomenclature?
A
- Scientific names: universal – understood by all scientists worldwide
- Eg Homo sapiens (H. Sapiens)
- Get the format right – genus and species names are always given in italics. Do not italicise the names of families, orders and class – but you must capitalise them
14
Q
What were the 3 main scientific advances towards Darwin’s theories?
A
Scientific advances towards Darwins theories –
- 1700-1800s: numerous new theories in science
Advances in geology
- Fossilisation
- Age of earth
Advances in anatomy
- Homology
- Vestigial structures
Early concepts of evolution and extinction
15
Q
Who was jean-baptise Lamarck and why was he wrong?
A
- Organs within organisms gain complexity
- Environmental impacts on evolutionary change
- Conflict between simiplicity and complexity
Fundamentally wrong - Had some key concepts along the 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
16
Q
What is meant by ‘Darwin’s finches’?
A
- Post voyage: helped by discussions with his ornithologist friend John Gould
- Darwin began to think about their diversity (beak morphology) and relationships
17
Q
What is the theory of common descent?
A
- Component of Darwin’s theory of evolution
o The other theory of natural selection - Explains why members of a taxonomic group (eg species in a genus) are more similar to one another than to a member of apparently equivalent groups (eg species of another genera)
- The theory of common descent tells us to seek ‘natural’ groupings
o Ie groups that reflect evolutionary history
18
Q
What were the 2 other theories that were similar to Darwins?
A
Alrfred Russel Wallace
- Sarawak law: 2 or 3 distinct species may have a common anti-type (ancestor) and each of these may again have become the antitypes from which other allied species were created
John Hunter
- Arrived at the idea of common ancestry even earlier than Wallace or Darwin
- Could’t get published
- Too radical of an idea for C18th scientists
19
Q
Species concept: why does it matter?
A
- The first step of classification involves the delimitation of populations into species
- A natural classification – one based on evolutionary history can be constructed only if the species are correctly discriminated
- But – biologists have not always agreed on what ‘the species’ is
20
Q
What is the typological species concept?
A
- Typology based on morphology/phenotype
- Stems from Platos ‘forms’ and used by Linnaeus
- Applied in museum research (type method) where single specimen (type specimen) is the basis for defining the species
21
Q
What are the problems of typological species?
A
- Ignores intraspecific variation: all individuals of a species are assumed to conform to a type
- Sexual dimorphism – not different species
- Life stages – not different species
- Geographic and other variants – not different species
22
Q
What is the biological species concept?
A
- Population genetics concept
- Based on Mendelian and post-Mendelian genetics
- Note criteria: interbreeding and reproductive isolation
- Think about gene pools and co-adaption of genes within pools
- Reproductive isolation via intrinsic mechanisms (not geographical barriers such as mountains or rivers – they are intrinsic)
23
Q
What is reproductive isolation? Pre/post-zygotic activity?
A
— 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, behavior, gametes)
— Post-zygotic (viability or sterility of offspring)
— Hybrid inviability (resulting from disharmonious genes)
24
Q
Advantages of typological species?
A
- Morphology can be readily reserved and perceived
- Relatively easy to communicate it outside scientific community
25
Disadvantages of typological species?
- Intra-specific variation in fossils
- Cryptic species (eg Pipistrelle)
- Artificial concept (excludes natural mechanisms)
26
Advantages of biological species?
- This is a species concept based on mechanism
27
Disadvantages of biological species?
- Excludes asexually reproducing organisms and palaeospecies (fossils)
- Evolutionary intermediacy (eg ring species)
- Allopathic species can be a challenge
- Many living organisms have never been observed mating
28
Are morphospecies valid?
Morphology is largely under genetic control
- If 2 coexisting populations are morphologically distinct – ie no intermediate forms occur
- They usually can be taken to represent intrinsically isolated gene pools (ie species)
- In general, morphospecies, upon closer inspection are shown to be valid biological species
29
What is the exception to morphospecies?
Exceptions – Common pipestrelle bats
- 1999: split into 2 spp- different echolocation frequencies
- Diverged genetically and behaviourally – not morphologically *cryptic species)
30
What are the 2 problems with biological species concept?
1) Asexually reproducing organisms
a. Do not fulfil the criterion of interbreeding – they are clonal
b. Eg some aphids, all bdelloid rotifers and prokaryotes
2) Evolutionary intermediacy
a. Populations in process of becoming separate species
b. Ring species
c. Anagenesis in paleo species
d. Where does species end and the other begin?
31
What is a ring species?
Ring species: a group of populations where individuals at one end of a geographic distribution are too different to interbreed with individuals at the other end, even though populations along the way can interbreed (for example a desert or a mountain range)
32
What is a paleo species?
Paleo species: only known by fossil record
33
What are Allopatric populations?
3. Allopatric populations (separate non-overlapping geographical regions)
a. Not actually or potentially interbreeding
b. Is this biological or geographical
Sympatric over part of ranges of species a and b
- No intermediate forms in overlap zone.
- Good biological species
Allopatric
- No intermediate forms
- Are they 1 or 2 species
Example Rosella parrots
- Eastern forms sympatric = good biological spp.
- Western forms allopatric = what is their status
- Taxonomists: if morphological difference at last as big as eastern = should be separate species
34
How may allosteric forms interbreeed?
Allopatric forms may interbreed if brought into contact
- Eg human movement, retreat of barrier (glacier, water, desert)
Ruddy and WH ducks – fully interbreed (UK introduction)
- Conservation convention of ‘’introgression’ of 2.spp.
- Culls of Ruddy in Spain and UK
35
What are subspecies?
Ruddy and WH ducks could be classified as subspecies of one species
- Taxonomists could not have known they could interbreed
Subspecies = aggregates of local populations of an individual species
- Inhabit different geographic subdivisions of the range of that species
- Differing taxonomically form other populations of the spp.
- They cannot, by definition, be sympatric
36
What are Polytypic species?
Polytypic species
Subspecies taxonomic concept – not genetic but:
- Evidence of the reduced gene flow (in most cases zero) resulting from isolation due to extrinsic (physical) barriers
- Subspecies are in the process of becoming biological species
- Through natural selection or genetic drift – incipient species
Polytypic species – species with several subspecies
- Each subspecies denoted by a trinomen
- Eg great tit: Parus major and P.Major excelsus
Number of bird species?
- 1909:>19,000 (morphospecies)
- Now: > 8,600 many Polytypic
37
Species or not? Human lice (pediculus)
- Parapatric subspecies or full species
- Are morphologically different – parapatric
- Problem for taxonomists
o Nowadays, the 2 forms of lice are rarely found sharing same individual host
o Body lice – survive up to 1 week, carry typhus and trench fever
o Head lice – die after 24hrs off host, don’t carry disease
38
What is the recognition species concept?
a. Allopatric populations not interbreeding
b. But recognise each other as potential mates (same species)
39
What are the advantages to the recognition species concept?
- Removes uncertainty regarding Allopatric populations
- Relies completely on the mechanism (more coherent)
40
What are the disadvantages to the recognition species concept?
- Excludes asexually reproducing organisms and palaeospecies (fossils)
- Evolutionary intermediacy (eg ring species)
- Only truly valid for animals (analogies can be made for insect pollinated plants
- Even harder to assess than the bio species
41
What is the phylogenetic species concept?
a. Species is a tip on a phylogeny
b. Smallest inclusive mono phyletic grouping
c. Relies on common ancestry and shared evolutionary history to define species
42
What are the advantages to the phylogenetic species concept?
- Recognises the role of history in generating species explicitly and can be reasonably objective
- Can use nearly any sorts of data (morphological, behavioral, genetic)
43
What are the disadvantages of the phylogenetic species concept?
Disadvantages
- Subdivision of lineages into species can be rather arbitrary (no distinct definition)
- Ring species are not differentiated and subspecies are not recognised (legal ramification for wildlife protection law)
44
What is the genetic species concept?
a. Geneticists equivalent of the morphospecies concept
b. Measure is genetic similarities or distance
45
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
46
Disadvantages of the genetic species concept?
- Also relies, to some extent, on human judgement of how much difference is enough to constitute separate species
- Communicating with non-specialists about DNA taxonomy can also be very difficult
47
How many species concepts are there?
Over 20 species concepts have been proposed
48
What are the purposes of classification?
o Index of stored information
o Enables predictions and generalisations mad bee converting the biology of organisms
49
How does classification work?
Delimitation
- Indian rhino: more features in common with each other
o Form a group distinct from all other animals
Ordering
- Indian rhino and Javan rhino
o Not identical but similar so could be put into one group
- All rhinos
o Share certain features so could form a larger group
- Rhinos, tapirs, horses
o Even these share certain features so could form an even larger group
50
What are trees of life?
Post Darwin: trees of life
- Taxonomists /evolutionists became interested in the construction of phylogenetic trees
- Ernst Haeckel (1866) ‘tree of life’
- Danger of tree concept – tips of tree are not more evolved or better
51
What is classification like today?
Today: phylogenetic reconstruction
- Practiced routinely, especially with molecular genetic data
- The hillis tree of life (circular)
52
What are dendrograms? How are they ranked? What is meant by topology?
Dendrograms –
- Classifications are often expressed as trees (dendrogram)
- Each large group of organisms may contain several smaller groups – a pattern of groups within groups
- Pattern of groups can be represented by a branching diagram: a tree
Ranking
- Involves conferring status on supra-specific groups
Topology
- Arrangement of tree branches and stems
53
What are the 3 main methods of classification?
1. Phenetics
2. Cladistics
3. Orthodox approach
54
What is phenetics?
- Based on overall phenotypic similarity
- All characters given equal weighting
o Primitive/derived
o Homologous/analogous
- Genealogy (cladogenetic history) ignored
- Claimed to be highly objective, fixed criteria (compared with orthodox method)
- Phenograms
55
Problems with phenetics?
Problems with phenetics
- Does not control for the confounding effects of the phenotypic similarity that is due to convergent evolution
o Due to similar selection pressures or mimicry
- So cannot be depended on to reflect evolutionary history
56
How is converged evolution a product of selection pressure?
- Based on the dome shaped armoured covering, limpets and barnacles would be classified together
- But-the armoured covering has a different origin in those 2 animals (ie not homologous)
- There has been a phenotypic convergence between limpet (mollusc) and barnacle (crustacean) – due to selection pressure of wave/current action
57
Homologous vs analogous characters
- Barnacles share homologous features with crabs
- The armoured covering has a similar origin and both have jointed limbs (ie both are arthropods)
Which is the biologically correct phylogeny (true or more natural relationship among individuals?) = the one that reflects evolution
58
What is mimicry in convergent evolution?
Convergent evolution: mimicry
- Eg a palatable sp. Under selection pressure to resemble an unpalatable sp.
- Eg non venomous sp. Mimics venomous sp.
- Convergence by one of the 2 spp.
59
What is Cladistics?
- Based on inferred genealogy (ancestry / evolutionary history)
- Trees = cladograms
- Based on shared, derived homologous characters
- Weighting of characters
- Claimed to be highly ‘objective’ and importantly to reflect evolutionary history
60
What did Will Hennig in 1950 contribute to Cladistics?
- Requires all supraspecific groupings (taxa) to be monophyletic
o Ie each must comprise all the known descendants species of the common ancestral species
o Paraphyletic species are invalid
o Polyphyletic species are invalid
They are grouped on the basis of convergences
61
2 examples of invalid classifications?
Endothermic animals: invalid classification = polyphyletic
Reptiles: invalid classification = paraphyletic
62
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 ancestry
- Groupings should be based only on new trait states arising in the nearest common ancestor
63
What are the 3 reasons as to why taxa resemble each other?
1. The character arose early on in the ancestry of the taxa, before the occurrence of the nearest common ancestor
- Ie the character goes back more than one branching point
- EG jaws in amphibians + reptiles + birds + mammals
- A shared primitive (ie ancestral character)
2. The character originated in the nearest common ancestor = shared derived character
a. Advances lungs : lungfish + amphibians + reptiles + birds + mammals
b. Jaws: jawed fish + amphibians + reptiles. + birds + mammals
c. Amniotic egg?
3. The character originated independently by convergence
a. Eg elongated, worm like body shape in some fishes, some amphibians, some reptiles
b. Homoplasmy: similarities due to convergence
64
How can taxons be defined by unshared derived characteristics?
Defining a taxon: unshared derived characters
- Characters acquired by and restricted to a phyletic line after it branched off from its sister group are unshared derived characters
o Mammary glands in mammals
o Feathers in birds? Not considering extinct vertebrates
o Unshared derived characters define each particular taxon (end branch)
65
What is character polarity? What are the methods of assessment?
Suppose a character exists in 2 states:
- Eg viviparous vs oviparous reproduction in aminiotes
- Which is the derived state? Which is the ancestral state
There are several methods for assessing character polarity
- out group comparison
- Embryology
- Fossil record
66
What is Outgroup comparison?
- Use frogs (non-amniote vertebrates)
- Amniotes: Oviparous vs viviparous
- Frogs: oviparous (egg laying)
- Oviparity: ancestral to viviparous because frogs (the outgroup) are oviparous
- Outgroup comparison is the most commonly used method of assessing character polarity
67
What is embryology?
- Although ontogeny does not exactly repeat phylogeny
- Ancestral characters appear earlier in embryological development than derived ones
- Eg cartilage before backbone in vertebrates
68
What are fossil records?
- The character state which appears earliest in a fossil sequence is the ancestral state
69
Problems with Cladistics
- Considers only cladogenesis (genealogy)
- Ignores anagenesis (non-branching lines of descent)
- Sister taxa are therefore given the same rank
o Eg crocodiles + birds
- But crocodiles represent the reptilian ‘grade’ (level of morphological / anatomical / physiogical organisation)
- Birds represent a quite different grade (further from their common ancestor)
70
What is orthodox classification?
- Based on both genealogy (cladogenesis) and divergence (anagenesis)
- Weighting of homologous characters
- Non-DNA/RNA orthodox classifications criticised
o Too subjective/inaccurate
o Despite attempting to take account of anagenesis (eg branching lengths estimated by dating fossils)
- Trees are phylogenies or phylograms
71
Why orthodox?
- Classifications based on molecular genetic data (DNA, RNA) are orthodox
o 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 are more accurately reflect genetic relationships
72
DNA data: no more morphology? 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, eg morphology-based classifications have involved far too much subjectivity
- But there is sometimes good agreement with molecular, Cladistics and phenetics
In other cases, a radical change in tree results
- Eg crustaceans shown to be offshoot of artiodactyls (ungulates)
73
Disadvantages of DNA data?
Disadvantages – could the data be misinterpreted
- Needs to be considered in context
74
What is the future of classification like?
- All classifications are provisional and are perpetually modified because:
o Improvement in methodologies
o New species (and fossils) are discovered
o Organisms continue to evolve
- Molecular techniques rapidly improving
o Most classification will be based on DNA/RNA
o Humans shown to be far closer to chimpanzees than by morphology = 98.4% similar
