ZOOL222

Synapomorphy

Shared derived character

Symplesiomorphy

Shared primitive character

Autapomorphy

Derived character unique to one species

Derived character

Trait that appears in recent parts of a lineage, but not in its older members

Primitive character

Character is common to both ancestor and descendent

Monophyly

All descendants of common ancestor

Paraphyly

Some but not all descendants of common ancestor

Polyphyly

Does not include the common ancestor of all descendants

How did life on earth evolve

Began with a single, primitive species more than 3.5 billion years ago - new and diverse species arose over time, mechanism for most evolutionary change is natural selection

Darwin's Theory of Evolution

1. Evolution happens, ie populations change over time

2. Evolution usually happens gradually ie millions of years

3. Speciation occurs ie species split into two or more species

4. All species share a common ancestry

5. Much of the evolutionary change was caused by natural selection, which is the sole process producing adaptation (ie the appearance of design)

6. Processes other than natural selection (ie genetic drift etc) are capable of producing evolutionary change

Proving evolution: increasing complexity

Should see increasing complexity through the fossil record (to prove that populations change gradually over time) ie see organisms starting simply and then increasing in complexity (so shouldn't see complex life forms arriving in fossil records)

Note: is not necessarily progressive, can become complex but then evolve to lose some of that complexity if it isn't useful

Note: increasing complexity is observed

-> Stromatolites, 3.5bya are the first fossil evidence of life, a stone created by bacteria

Increasing complexity of life

Cyanobacteria -> Eukaryotes -> Multicellular -> Cambrian -> Dinosaurs -> Humans

First fossil evidence of life

Stromatolites, 3.5 bya

Rock structures formed by bacteria

Proving evolution: Evidence of speciation

If evolution occurs within lineages, and lineages split, then we should see evidence of gradual change of one species into two over time

Example: Rhizolenia

• Can drill into ocean floor to observe change over time

• Originally one species, but leading to two species being present within the same substrate

• Note, fossil record is hard to capture speciation which some people use as a refute against evolution

Proving evolution: Transitional forms

If all species share common ancestry we should find fossil evidence of transitional forms that connect modern groups to their common ancestors

Creationists use this as a refute eg common ancestor between crocodiles and birds - however there are between reptiles/birds; the transitional form needs to be functional

Hippo and whale: idea that hippos looked like whales, made predictions before evidence - ie hypothesised before fossils

Retrodictions

Things that make sense later - after applying the lens of evolution to it

Facts and data that aren't necessarily predicted by the Theory of Evolution but make sense only in light of the Theory of Evolution

eg vestiges

Remnants: vestiges, embryos, and bad design

Embryos:

• limb buds in dolphin embryos (for legs) evidence that deep in the genetic code of dolphins there is coding for legs

Humans can't make vitamin c:

• metabolic pathway is broken in humans ie broken gene, can't turn other things into fit c

• Evidence that this was lost in humans

Bad design:

• Tarsier

• Nocturnal, need to see at night, adaptations to amplify light

• Eyes slowly got bigger

• Can occur when don't share a common ancestor that may have a solution

• Risky eye sockets (easily damaged) but function outweighs form ie benefit of seeing in the dark outweighs the risk

Proving evolution: natural selection

If evolution results largely from natural selection we should be able to see it happening in nature

• Darwin's finches

Non-selective mechanisms ie evolutionary change without adaptation

• Genetic drift/gene pools

• Founder population disrupted, left with a gene lottery (chance)

• ie there is no selective benefit that results in an adaptive advantage, is just chance

Not all evolutionary change has to be adaptive - look at whether survival of the event was down to advantage

When does a scientific theory become accepted as true?

When it's assertions and predictions and tested over and over again and confirmed repeatedly - ie confirmed to such a degree that it would be reverse to withhold provisional assent

Scientific theory = explanation of observable facts

3 domains of life

Bacteria, Archaea, Eukarya

The "best competing multiple ancestry hypothesis"

One species giving rise to bacteria and one giving rise to Archaea and eukaryotes

Darwin's 4 postulates of natural selection

variation, inheritance, differential survival, and extinction (= individuals succeed because of the traits they have inherited and pass on)

Alternative framework of natural selection

One Long Argument by Ernst Mayr

Facts:

• Super fecundity

• Steady populations

• Limited resources

• Individuals are unique

• Heritability of differences

Inferences:

• Competition

• Differential survival

• Evolution over time

Darwin's Challenges - evolution in the 19th century

Variation - unaware of mutation

Poor fossil record

Inheritance - blending

Time - Earth's age

Evidence life from single form

DNA - language common to all life, based on four-letter code A-C-T-G (Darwin did not know this so had guessed, ie no evidence)

Darwin (adaptive radiation)

Observing finches, idea that the different forms of finch came from one original species

• Beak diversity

Adaptive radiation

The divergence of a clade into populations adapted to many different ecological niches

Natural selection in Galapagos finches. Grant and Grant 2002

• Long term study on the Galapagos

• Natural experiment occurred, drought

• Strong predictive correlation between parents and offspring beak size

• Drought affects survivability, high competition for resources and availability of only certain seeds

• Some finches had a beak size that could open the certain type of seeds

• Lead to a difference in beak size between the generations, which occurred very quickly

What was the cause of the quick change/flexibility in beak size?

• Gene BMP4

• Bone Morphogenic Protein 4; influences beak shape/size

• More expression of BMP4 gives a thicker, deeper beak

BMP4 and beak diversity

Affects the massive amount of population level variation in finches, which gives a flexibility and ability to adaptively radiate in feeding style pretty quickly; predisposed by this genetic architecture

CaM = beak length BMP4 = beak depth/width

Cichlids as examples of adaptive radiation and convergent evolution

• Fish in 2 lakes

• Cichlid variation in the two lakes (only related within the lake, not between)

• Adaptive radiation in the two isolated lakes - original fish which arrives in a lake and adaptively radiates out to fill niches (feeding diversity)

• Strategy used to feed has shaped morphology (phenotypic similarities between the lakes due to similar niches)

Jaw development

• Same gene as the finches

• Shapes mandible formation, huge impact on how an organism feeds

BMP4 gene

The gene that regulates the development of cartilage and muscular cell development in the jaws of a cichlid fish, and in the beaks of finches.

Bone Morphogenic Protein 4

Evidence for commonality of species, as the same gene is doing the same job in birds and fish continents apart

ie is a really good example of natural selection in real time, causing a change that we can observe and confirm and ALSO is an example for commonality

Forkhead box P2 (FOXP2) gene

• Expression and mutation of FOXP2 affects neural circuitry involved in processing sensory-motor information and learned coordinated movements

• Has implication for language development (incorrect speech development in humans)

• In other vertebrates eg birds, can manipulate in song birds: if gene is knocked out it can affect the baby birds ability to learn the song

• Affects problem solving and ritual activity

• In rats it affects their ability to solve a maze (as language can affect fine motor control movements, as involved in speaking)

Evolutionary intermediates

Wrists, ankles, and digits distinguish tetrapod limbs from fish fins

The difference in gene expression is only that the gene is switched on for a shorter time in fish. The discovery over-turned long held notion that limb acquisition was a radical evolutionary event

Tetrapod evolution and developmental Hoxd13 gene expression

• Fin to walking limb not as complex as thought

• Changes in expression of genes, genes mutate

• The limbs have expression of certain genes that ends up changing the bones (eg fusing together) to get better for walking

ie the genetic machinery needed to make limbs was already present in fins, it did not involve the origin of new genes and developmental processes. It involved the redeployment of old genetic recipes in new ways

Evolution and development - vertebrate necks

Mouse and giraffe have the same number of genes, they also have the same 'neck growing' genes, but left on longer in the giraffe

ie it is about gene regulation; small mutations and a regulation for turning those genes on

ie the primary fuel for the evolution of anatomy turns out not to be gene changes but changes in the regulation of genes that control development

Four conditions for natural selection

1. Individuals within species are variable (mutation/recombination)

2. Traits are heritable

3. The overproduction of offspring (more produced than survive)

4. Reproduction and survival are not random (some traits are advantageous or increase fitness) -> an element of randomness is involved eg recombination - the actual selection is what is not random

Theory of Evolution vs Natural Selection

Evolution is an observable process, it is change over time. Evolution is not natural selection, natural selection is a mechanism of evolution (that produces adaptive evolution)

• Selection changes trait distribution within a generation

• Evolution is change in trait distribution between generations; population level thinking (look at population level not individual level); evolution happens when the parent population is different to the offspring population ie generational change

Adaptive evolution is a RESPONSE to selection

Nature of Natural Selection

1. Acts on individuals, but consequences occur in populations

2. Acts on phenotypes, but evolution = changes in allele freq.

3. Not forward looking

4. Acts on existing traits, but new traits can evolve

5. Non-random but not progressive

6. Fitness is not circular

7. Acts on individuals, not for the 'good of the species'

8. Does not lead to perfection

Natural selection in Galapagos finches example

Increase in beak depth after the drought; drought wiped out resources, leaving one type of seed that a bigger beak was suited to. Increase between 176 (year before the drought) to 1978 (year after the drought)

Darwin's finches and selective regime:

• Between first and second drought there was a migrant bird

• Return to smaller beak sizes as a different species of big bird migrated and was better at eating the big seeds

Natural selection is not forward thinking

No planning/ideas and the selective regime can change; selection is something that happens in the current environment (ie if the environment changes)

Natural selection is not perfecting

It's not solving problems or providing tools, but is also not random. Variation is random, selection depends on that variation interacting with it's environment.

ie Trait is beneficial in some way but may be disadvantageous in another (constraints/trade-offs). Also context dependent, suits the organism to the environment so if environment changes then no longer suited

ie evolution just occurs, selection is a result of the environment and the organisms interactions with it

Has flaws and constraints

Selection acts on existing traits...

Over time new traits can evolve

Example: Artificial selection in Corn

• Tested 163 plants

• Oil ranged 4-6%

• Selected 24 ears with highest oil content as parents

• Repeated each generation

• No overlap between the current and original population

ie artificial selection

Problems with the phrase 'survival of the fittest'

• Reliance on reproduction in natural selection (not referred to in survival of the fittest)

• Infers individual change, not population

• Fitness infers eg physical fitness (however, being big and strong might not be suited in every environment, and can then be very expensive to maintain)

• Survival of the fittest in a certain environment

• Fecund: need to have reproductive ability and ability to find a mate

• Always need to look through a contextual lens

• Random chance is involved in survivability, may have better genes but then eg run over by a bus

• Gradual change: is not who survives, but who is trimmed off ie fitness is not circular

Survival of the fittest: Lion pride

• Male is in control of pride, has access to all the breeding females of the pride

• New male will come into the pride and kill all the babies

• Killing the cubs will put the females into heat earlier so that he can then breed with them and he can raise his cubs

• Nothing to do with the good of the pride (eg if resources were low or something), is purely about continuation of that lion's genes

Survival of the fittest: Ground squirrels

• Within their groups the females stick together with their relatives and males wander

• When there was a terrestrial predator arrive, some of these individuals of this group would make alarm calls (individual in danger, more likely they won't live to reproduce) - so some people have argued that this behaviour is for the good of the species, however this kind of altruism can't evolve so can't be explained by natural selection (as trait arisal is genetic, individual's fitness needs to be increased)

Is now known that they are nepotistic not altruistic

• Will alarm call to help their sisters

• They recognise their relatives through phenotypic similarities (their nest sisters, then assume squirrels that look like them are related to them)

• Promoting continuation of their own genes by continuation of their sisters genes

Adaptation

A trait, or integrated suite of traits, that increases the fitness of its possessor is called an adaptation and is said to be adaptive

ie a character modified as a result of a selective advantage through improved function

• Variation of an earlier form

• Heritable

• Enhance fitness (survival + reproduction)

Traits are not always adaptive

Adaptive evolution

A process in which traits that enhance survival or reproduction tend to increase in frequency in a population over time

Adaptions are produced or maintained by natural selection and may be recognised by their:

• Complexity, precision, efficiency (appearance of 'design')

• Broad taxonomic distribution

Examples of complexity and precision

• Mimicry

• Adaptation that arose via natural selection

eg stick insects, orchids (look like they have a bee on it)

Examples of broad taxonomic distribution

Fusiform shape in animals across broad taxonomic groups

• Tuna

• Penguin

• Seal

Adaptive evolution - Feathers for flight?

When looking at adaptation you need to take in the function and the benefit, what benefit does the phenotypic trait provide (look at the context in which the trait first arose)

-> It is heritable -> It is functional -> It increases fitness -> But how did it first evolve: feathers would have first evolved as a covering (like scales) to provide insulation - arising long before flight

Identifying adaptations

• Traits have arisen only once in a common ancestor

• Traits of character may be different than what was selected for eg feathers

• May be learned or cultural (which is not heritable, so is it an adaptation?)

• May simply be correlates of other traits

Not everything is n adaptation. A trait that appears complex and 'designed' is not automatically an adaptation. Need to apply the scientific method.

Example: Why are red blood cells red?

• Simply because of the structures that are in the compounds of the cell that allow them to transport oxygen effectively via haemoglobin - colour comes with it as a side effect

If it's not an adaptation - what is it?

• Chance artifact of history (GGC = glycine)

• Byproduct of another characteristic (red blood)

• Outdated adaptation (calabash fruit and gomphotheres)

• An exaptation (feathers for flight vs heat)

• Result of genetic drift

Calabash fruits and gomphotheres:

• Extremely large fruit

• Gomphotheres were large enough to eat them and distribute the seeds, now there is no animal large enough to do this

• So no longer well adapted to being consumed, so size is not an adaptation anymore ie the things that made it functional have gone away

Exaptation

The process by which features acquire functions for which they were not originally adapted or selected for (so not adapted)

Limits on adaptive evolution

• Trade offs

• Constraints

• Lack of variation

Evolutionary constraints

Restrictions or limitations on the course or outcome of evolution eg phylogeny, physics, genetics

Note: a trade off is different to a constraint, as constraints actually block off a path

Phylogenetic constraints

Limits on current behavior or traits due to patterns and trends in an organism's evolutionary past

eg Animal with feather needs more insulation, but is not going to suddenly sprout hair. Work with the feathers/structures they already have and changes come from these

ie work with variation that is already there

Evolutionary constraints (physical)

There are constraints on size or shape

eg limits to how large you can get (if an ant got too large it would crush it's own legs); when large you also need to be able to spread metabolic heat

Pandas thumb as an example of exaptation and phylogenetic constraints imposed by history

• Pandas have made use of another bone present in their hand

• Situation where common ancestors of bears and the panda would have had the full functioning five joints

• But had a radial sesamoid bone, and in this common ancestor the bone extended a little bit and was attached to muscles on either side

• So this abnormally long bone existed as an exaptation, was there already - was a constraint in that they didn't have a thumb and a situation arose where it would be useful to have a thumb or similar; as easier to feed, strip leaves off bamboo

• So in the panda, the large radial sesamoid bone has evolved to be used as a thumb (so not an adaptation, was already there)

Example of Evolutionary Trade-offs

Longer gonopodium in mosquito fish

In mosquito fish a longer gonopodium is attractive to females, but increases the risk of predation (as increases drag, making them swim slower). This leads to a trade-off between the females selecting for longer gnopodiums while predation is selecting for smaller (to escape predation).

Also an example of sexual selection - where the advantage is not about survival, just reproductive access

Trade-offs vs constraints: Penguins

Fusiform body shape is efficient for movement in water, but slower and more vulnerable on land = Trade-off

Must lay eggs on land because of evolutionary origins (a bird with an egg-laying ancestor) = Evolutionary constraint

ie the phylogenetic constraint of egg laying is the cause of the trade-off/balance between sea and land occupation -> this leads into the idea of evolution not being perfecting, can't just evolve the ability to lay eggs in the water and thus just live in the water

Need to balance between constraints and trade-offs

Phylogeny

The evolutionary development or history of a species or of a taxonomic group of organisms

Studying the adaptive significance of traits

All hypotheses must be tested; is easy to come up with a story to explain the traits

Example: Oxpecker and Impala

• Video that says purpose of oxpecker is to reduce tickload (assuming mutualism)

• Must test hypothesis

• Did an exclusion experiment: used cattle instead of impala

• Chased oxpeckers away in one experiment, and left them in another

• Found no evidence that they provide a reduced tick load) , no consistent results over the trials - very variable

Methods of testing hypotheses about traits that may appear adaptive

1. Experiments

2. Observations

3. Comparative methods

-> make observations more powerful by using comparative methods

Example of studying adaptations: Experiments (Jumping spider and fly)

The spider is a natural predator of the fly; fly dances and has wing markings like a jumping spider

Example of mimicry? Needs to be proven

Several treatments to test for no mimicry, mimicking the jumping spiders to deter non-spider predators, mimicking jumping spider to deter jumping spiders (done through cutting/gluing wings between the tephritid and the house fly and separating between the dancing and markings)

The jumping spiders wouldn't attack when the dance is combined with markings (something is similar enough for spider to not attack, instead retreating)

Conclusions: Jumping spider predation is specifically deterred by the intact display (but not by the controls). Other predators are not deterred. The display therefore is supported as an adaptation to reduce predation by jumping spiders.

Hypothesis and prediction not the same thing

• Hypothesis description about what we know or think we know about the world, has a mechanism and what we think is going on

• Prediction is what would happen if the hypothesis is true (illustrating the advantage), has specific predictions that go with it

Studying adaptations: Observational studies

• Occasionally direct experimentation is impractical or impossible

• Observational studies ideally resemble a 'natural experiment'

• Require meticulous selection, careful and extensive measurement, time, etc

Do have limitations (don't understand all factors and variables that are at play)

eg finches

Example: Garter snakes

• How snakes regulated their body temperature

• Adaptations in which rock they chose to sleep under?

• Were they choosing rocks that would maintain a temperature that was suited to their bodies

• This was observational in the wild. Needed to statistically get a sketch of rock distribution, and to get an idea of if the snakes were distributing randomly

Studying adaptations: Comparative method

Consider evolutionary patterns of traits among related species, must take into account the relationships sample size may be artificially inflated

Complexity (appearance of design) and broad taxonomic distribution -> the two characteristics of adaptation

Can use the spread of traits to test the trait that is present in many taxa; eg things that chase faster prey will be more fusiform (can look at this over broad taxonomic range)

Example: Bats

• Teste size/Group size

• Sometimes live in big social groups and also can have big testes (related?)

• Idea of sperm competition (female may mate lots of times with multiple males, more sperm may mean that they are more likely to be the father)

• As cannot manipulate sperm production ability of these bats, needs to be a comparative method

• Found that as groups size gets large, so do the testes

• Question of sample size

• What if big testes evolved once, and happened to evolve at the same time as group living ie not advantage it just happened - then spreading out into different taxa as all descended from a common ancestor that had both

• Need to tease this out with taxonomy

• Often rely on observational studies, the comparative method involves looking for situations where we have natural experiments (not as controlled, so is useful to do observational experiments across wide taxonomic groups, taking phylogenetic relationships into account)

• ie group size can be smaller than we expect (can look like we are sampling more than we are due to phylogenetic relationships and where the traits arose) - control for this by setting up phylogenetic contrasts (look across different taxa at mating displays); increasing the sample size through phylogenetically independent contrasts

This leads to building up phylogenetically independent contrasts

• Compare traits with taxa

• All different at divergence

• Every time the group size got bigger, so did testes

Compare the taxa that are related directly and compare the traits and look at the differences - and can graph those differences (more power this way)

ie: PHYLOGENY needs to be taken into ACCOUNT

Parthenogenesis

Offspring from unfertilised eggs

Alternatives to sexual reproduction

Asexual, parthenogenesis, fragmentation, binary fission

eg strawberries: seeds are sexual, but the runners are asexual (clones of themselves)

Costs of sexual reproduction

1. Finding a mate uses time and energy

2. Mates may demand additional resources

3. May be exposed to sexually transmitted diseases (risks/costs/dangers)

4. Mating may prove to be infertile (eg birds that mate for life, try to reproduce every year but eggs don't hatch)

Reproductive disadvantage of sexual reproduction

Produces fewer offspring

Sexual vs asexual reproduction

Asexual reproduction generates offspring that are genetically identical to a single parent. In sexual reproduction, two parents contribute genetic information to produce unique offspring.

Asexual reproduction significantly more efficient (less trouble, risk, and cost); however, most organisms reproduce sexually

eg if chickens were parthenogenic, would require no males and lead to exponential growth

The problem of the evolution of sex: John Maynard Smith (1978)

Developed a null model with two assumptions:

1. Female's reproductive mode does not affect number of offspring

2. Female's reproductive mode does not affect probability of offspring survival

Null = what if sex had no benefits ie no trend or relationship

When both modes are happening, often use the number of males in the population as a measure of how much sexual reproduction is happening (as there are no males in asexual)

Under this model asexuals should out-compete sexuals. However, this is generally not observed in nature - so one or both assumptions must be incorrect.

Assumption 1: No effect on number of offspring

• May favour sex when there is male parental care

• But, male parental care is rare and sex is widespread

Assumption 2: No effect on survival of offspring

• Does sex offer a selective advantage for offspring?

Lab studies - the evolution of sex

Nematode (can reproduce asexually and sexually ie self fertilisation and outcrossing)

Exposed to a mutagen, a toxin that creates a difficult environment to survive in. Outcrossing increased rapidly when exposed to the mutagen (so offered more of a fitness benefit in the stressful environment)

Paradox of sex

Sex appears to serve the species at the expense of the individual. Individuals could abandon sex and rapidly out compete sexual rivals in passing on genes, but they do not.

Is sex adaptive?

Creates variety which natural selection acts on - good for the species. But can't work like that, needs to be adaptive ie good for the individual. So can the evolution of sex be explained by 'Group Selection' when natural selection acts on the individual? How many copies of genes get passed on in sexual vs asexual?

Theories to explain the adaptive values of sex

Muller's Ratchet hypothesis Red Queen hypothesis

Muller's Ratchet Hypothesis

Genetic drift with mutation makes sex beneficial, ie sex gets rid of the bad genes or deleterious mutations

Metaphor for how genetic drift can, over time, create an increase in the number of mutations in a population and sex deals with this by getting rid of them/clearing them up

Red Queen Hypothesis

Selection in a changing environment makes sex beneficial, ie selection for good genes and the need to continually improve

Talks about competition, always needing to stay ahead of your enemies; always improving

Biotic interactions drives evolution ie top down biological processes

Muller's Ratchet and Genetic Drift

Only looks at deleterious mutation:

• In asexual reproduction, as deleterious mutations arise, they don't go away - instead getting passed down to all offspring (as like a photocopy)

• Sex mixes up chromosomes of genes, and can have recombinations without any deleterious stretches of genes on it (allows a remix and recombination of 'fresh' mutations, so they can be cleared out)

Can look at how this happens in populations by looking at the rates of errors in DNA; ratio of nonsynonymous to synonymous substitutions

Synonymous = no change or effect in the phenotype of the animal, protein is the same, produces no deleterious effect (ie errors in DNA that don't affect the fitness)

Nonsynonymous = creates a change in the DNA that might be deleterious

Example: Timema walking stick

• The rate of deleterious mutations in the three genes accumlated in the asexually reproducing animals but not in the sexually reproducing

So therefore going to favour sexually reproduction when in an environment where there is a lot of mutation - so if something causes an increase in reproduction rates, then the animal is going to favour sexual reproduction due to this (sexual reproduction can clear them)

Pathogens can select for sex... in a model organism (C. elegans)

Higher outcrossing = more sexual reproduction

Evolution = increase in outcrossing rate, then drops down again once adapted: creation of challenging environment, something has been added that makes the animals adapt.

Coevolution = sexual reproduction maintained at high levels ie benefit is not shortlived. Challenge that isn't an environmental change, but is something that is also alive and evolving and having adaptive change (ie you can evolve to be better, but so can the other thing, so you evolve again)

Red Queen Hypothesis and coevolution

If everyone is moving at the same pace, then have to continuously keep evolving or else fall behind (sexual reproduction is beneficial here, will continuously change the combinations of alleles with new mutations arising and clearing deleterious mutations, increasing the chances of beneficial ones) ie evolutionary arms race

Predicts adaptive value of sex increases when parasitism is high (and disease, and predator-prey interactions)

Example: Infection rates in snail populations (Curtis Lively)

• Relationship between parasitism rate and frequency of males in a population (more males = more sexual reproduction is occurring, as males are not required for asexual reproduction)

Linnean binomial system

Came up with a binomial and hierarchical classification system

Binomial = Genus species Hierarchical = Reflects evolution (Species, genus, family, order, class, phylum, kingdom, domain)

Systematics

A scientific discipline focused on classifying organisms and determining their evolutionary relationships. ie classification of biodiversity

eg Yellow eyed penguins assumed to be native in NZ, turned out they were from a completely different species

Why classify and name species?

• Single unambiguous system

• Global communication

• To reflect evolutionary relationships

• Basis for biological research (medical, biosecurity, conservation)

Binomial system - reflects evolutionary relationships

Taxonomy is a lynchpin of biology

Medical - identify eg specific strains of viruses Biosecurity - identification of specific eg insects that we don't want Conservation - species level and relationships (phylogenetic diversity)

How many species are there?

1.8 million names, 5-150 million estimated

What features make species distinct?

• Ecology (geography, habitat, diet)

• Behaviour

• Morphology

• Chromosomes

• Proteins

• Genes

• Breeding compatibility

• Evolutionary lineages

Can use these differences to establish the different genera (eg moa)

Biological Species Concept (BSC)

Species are groups of interbreeding natural populations that are reproductively isolated from other such groups

Most classic concept

Like should cluster with like (monophyletic clade)

Strict rule: if you can interbreed and produce fertile offspring, you are the same species

Monophyletic

ALL descendants came from one common ancestor

Single origin, like clusters with like

Clade

A group of species that includes an ancestral species and all its descendants.

ie monophyletic group

A group of related animal - can be small or large

Problems with the Biological Species Concept

1. sexual forms only

2. no temporal dimension

3. not a single unit of evolution

4. often not practically testable

ie can have paraphyly (multiple origins), hybridisation can lead to fertile hybrids, and there is incomplete lineage sorting ie morphology differs to DNA

Is bad - can only apply to two species living in the same habitat at the same time - not to allopatric populations (or modern vs prehistoric)

Phylogenetic Species Concept (PSC)

Species are a group whose members are descended from a common ancestor and who all possess a combination of certain derived traits ie defined on the basis of their phylogenetic relationships

Can have primitive or derived traits

Problems with the Phylogenetic Species Concept

• Over-estimates taxonomic diversity as every clade instantly, by definition, become species (each clade has members that are descended from a common ancestor

• Minimum value of absolute mtDNA divergence is used to distinguish species (distinct species can get lumped together) ie DNA barcoding.

eg Haast's eagle biggest in the world, if mated with a little eagle the Haast would probably kill it - so definitely not the same species, but are lumped together

Dealing with ancient DNA

More copies of mitochondrial DNA in cells than nuclear DNA; they degrade at the same rate, but the number difference means mitochondrial is better - it must be well preserved to get nuclear DNA too

-> So incomplete phylogenies for some species

Diagnostic (Integrative) Species Concept (DSC)

• Derivative of the PSC designed to avoid taxonomic over-inflation

• Must be able to identify the species in the field

• Total evidence approach

• Requires congruent datasets

Species concepts

The different ways in which a species is defined

Biological Species Concept (BSC) Phylogenetic Species Concept (PSC) Diagnostic Species Concept (DSC)

Outgroups

Establish polarity and evolutionary trajectory

Require an outgroup (primitive) to establish direction

ie primitive to derived

Needs to be distinguishable from the ingroups (ie establishing some sort of polarity)

Ingroup

What we are trying to find all the evolutionary relationships about