origins and classification of life Flashcards
define taxonomy
classification of organisms in an organised system. incoporating the desccription, identificatoin, and niomenclature
define phylogenetics
reconstructing the evolutionary history and relationships of organisms
describe some economic benefits to taxonomy
maximise the use of a crop
quality control - have a defined species e.g. manuka honey needs to be xyz
cross breeding - understand the aspects of one species and be able to add these to another
avoid the cost of disease by knowing the microbes involved
describe benfit of taxonomy to biosecuirty
to be able to remove a pest from a country there needs to be sufficient knowledge of the pest to be able to detect it
descibe the relevance of taxonomy in maori culture
Taonga species are sacred and need looking after - whakapapa
conserve culturally significant species
looking after the environment is important part of their culture
describe an example where incorrect taxonomy caused a large scale problem
1.3 tons of opium poppy seeds were ceased by the UK in afghanisatan
they were actually just mung beans
describe the benefit to human health from taxonomy
tropical bacteria on the rise due to climate change. need to identify pathogens in order to cure them
what % of species on earth have been classified? why is this an issue?
10%
what if we havent classified aan organism of huge ecological importance that is on the verge of extinction
describe a case study where phylogenetic infomation was crucial in tackling a disease
malraia in hati after 2010 earthquakes
one source identified through phylogenetic study using barcoding
the barcoding showed close to nepales species
the nepale un soliders had bought it with them
they then knew the exact strain they had to fight
how many species on earth
5 to 30 million
what are the expectations of a classification
easy to use aid to memory preditive consise stable
give some examples of poor classificaion systems
size
colour
use to humans
give examples of when classifcations changed
renaissance - clusius, placed species in groups that were useful to humans, started to use more science
darwinian era - when evoloution was being discovered
give a pro and a con for evolution as a classification system when considering ease of use
it is universal and relates all organisms together
but we dont know all teh evo relationships
give a pro and a con for evolution as a classification system when considering it as an aid to memory
evo relationnships often follow morphology
homoplast and convergent evolution can conter this e.g anteaters and pangolins
give a pro and a con for evolution as a classification system when considering it as predictive
name of taxon gives info about evolutionary relationships
but this is always predictive of biologically relevant infomation e.g. jacobea vulgaris and eruifolia
give a pro and a con for evolution as a classification system when considering a classification system to be concise
hieracry is compatible with systems of taxonomic classification
but we do get superfluous names such as ginkgo,only one species in a whole phylum
give a pro and a con for evolution as a classification system when considering a classification system to be stable
evolutionary histroy can only be one pattern
but our knowledge and understanding of these patterns changes
e.g. hebe genus was changed from figwort family to the plantain family, due to nomencalture they couldnt move all the species names
why should a classification system be stable?
people dont like change, it takes a lot of effort for a field biologist to remeber all the names of the species in their field. for a taxonomist to change this creates a huge amount of work
how do the expectations of stability and predictivity clash
in order to be predictive taxonomy needs to be changed when new infomation comes about but some dont want the names to be changed over and over and hence prefer stability
give two arguments against the reality of species
speciation is a gradual and continuous process - gradual pattern of speciation. rather than a punctuated pattern
some species hybridise
arguments in favour of species
just makes sense
agreement between folk and scientific species - 70% overlap between taxonimists and indigenous people
statistical identification - discrete morpholigical genetic clusters of individuals, patterns coincide with species
how many species concepts are there
around 25
what are the two types of problem with species concepts
operational - difficulty in appling
theoretical - inherit problems of the species definiton
define the biological specis concept and give iperational and theoretical problems with it
can they mate and produce viable offspirng
operational
- data on repoductive isolation is missing for most species
- cannot be appied to fossils or allopatric populatoins
- what if only one individual of a species is found
theoretical
- it isnt universal because of asexual organisms
- dosent accommodate interspecific hybridisation
- ring species make it inconsistnent
define the morphologicl species concept
give operational and theoretical problems with it
defining species by them looking the same
theoreticacl
- convergent evolution
- cryptic species
oppertoinal
- sexual dimorphism
- objective hard to apply hard and fast rules
define the phylogenetic species concept
the smallest monophyletic grouop that are diagnosably distinct from other groups
operational
- dont know all phylo info
theoretical
- species may longer be distinct in the future
what is another issue with the phylogeneic species conept
It can lead to over splitting, get very small groups with no biological significance
describe a case study where the phylogentic species concept was crucial for conservatoin
found a large amoutn of disparity between some dna sequences of organisms from what were believed to be the same species
e.g. african leopoard, field notes form loing time ago stated different sizes, colours coat texture and dsitribution
molecuar data found onevery isolated population who were a subspecies, they were very rare, in a small pocket of the congo.
need gen diveristy in a population to ensure survival, losing this subspecies would reduced the gen diversity of the specie.
describe why neither the morphological or the phylogenetic species concept works perfecty for bacteria
two bacteria cacn be very similar in morphology but very different genetically
two bacteria can be very different morphologically but very closely related genetically
how do we tackle the porblem of species concepts and microorganisms when classifiying them
use a polyphasic approach use multiple sources of infomation - phylogenetic - genotypic - phentypic
what two ways are phylogenies formed with bacteria?
using the 16s gene sequence
or the whole genome
give ane xample to show the large genetic diveristy in bacteria
ecoli shares just 28% of its DNA with other ecoli strains
define a microbial species
all memebers of a species should be monophyletic and should be genetically and phenotypically cohesive with their traits being distinct form another species
why is the 16s gene used
ribosomal rna
makes the strutucre of the ribosome
if it has large mutations then it wont work
very conserved
has a 1% mutation evevry 50 million years
describe the method of DNA hybridisation in classificatoin of microorganisms
seperate dna strands
try and get two strands from two organisms to match
if they match more than 70% then same species, 20-70% and in teh same genus
what % similairty must 16s rRNA genes have to be from the same species
3%
give examples of phenotypic traits used to classify microorganisms
lpid chemstry cell wall chemistry temperture, salinity, pH metabolism motility morphoogy
how many species are discovered every year
18,000
why do we need to describe new species
intreested in evolutionary relationships - need to fill in the gaps
more species we know the better we understand ecoloy
cant conserve a species we havent identified
discover new crops or medical e.g. sponge family, because they are stationary have to use chemicals to kill pathogens
describe some of the datat that is important to use in the publication of a new species
meta data
location e.g. where it was found
when it was found
enrvironment, altutude gps
why is meta data useful
prehaps know the number of species in sample, estimates of total number
increases the scientific value because can test for relaibility
why should a scientific paper include the species concept used
allows repetitionn
give some general risks to misidentifying an organism
dont spot an invasive speces
loss of money
loss of ability to solve a problem
give the sea star example of a negative consequence of making a taxonomic error
sea star thought to be native but was actually invasive, by time this was realsied it was to late to stop the invasion
what is a voucher speciemen
permaent record of a species stored in a herbarium
give the napeoleons willow on st helena exmple of vouchers being useful
lots of willow trees grown all over the world, suggested to be from the willow napeleon sat under when in excile, extract DNA evidence from a voucher speiement to test if they were from original
define type specimen
the name of the type speciemn cant be chaged, it is the example of the species
give an example of a voucher being very important in a study
ancistrocladus abbreviatus was found to have alkaloids with anti HIV properties
repeated tests failed to get the same result
the plant had been misidentifed when they checked with the voucher
reidentified as ancistrocladus korupensis, did have the anti hiv porperties
describe the problem of the misidentification of the lustianian slug in central europe
spansih slug thoght to be invading in central europe and eating all the crops
actually cryptic species that just looked like the spanish slug
hard to tackle a problem if you dont know the cause
give methods used to identify a species
prior knowledge context info i.e. meta data identification keys and google learn terminology photographic comparisos herbarium species peer networks such as inaturalist verificatoin through any of these means
describe how a phylogenetic study told us about the origin of the sweet potato
phylogeny of kumara
NZ species are part of southern gene pool closely releated to those from peru
all other kumara are part of the northern gene pool coming from european settlers
suggests polynesins vistied
describe how phylogenetics found a doctor guility
lots of his patients were getting Hepatitus c
phylogentic analysis of Hepatitus c strains used
hepatitius c is fast evolving
looked at victims and constructed a phylogeency
the common ancestor of all the species was that found in the doctor himself
describe how phylogenies have been used to work out histroical human knowledge
knowledge of medicinal plants tested with phyligenies of the plants used by tradiontal peoples
if traditional is placeno then there would be no pattern between the trees
but the species were very closely releated between very distant geogrpahical areas
similar compunds in similar famileies
desribe the data matrix needed to form a phylogeny
x axis is the characters with the character state changes
the y axis is the speices, phyla or a gene sequence
the chacters must be genetically based
define the term homologus
similar states shared due to common ancestry
define analogy or homoplasy
similairty not due to common ancestry
define a character in a dna sequnce allignment
each position in a dna sequnce so
why can you not apply the same cost to all charcter state changes in a dna sequence allignment
because different mutations have differnt costs
i.e. transitions are more common than transversions
so you apply a cost to each type of mutation, i.e. if a trasversion is 3 times less likely than a transitions mutation then 2 transitions is more parsimonius than 1 transversion
define a transition mutation
purine to purine or (c to t) pyrimidine to pyrimidine
define a transversion mutatoin
guarnine to thymine i.e. a purine to a pyrimdine or vice versa
what are some `problems with genbank
huge number without names e.g. uncultured fungus. 12,000 per year
not curated for accuracy and 20% of sequences are misannotated
describe a good gene region
low mutation within a species high mutation between species conserved flanking region universally present good prior data phylogenetically informatoive
why is mtDNA used in animal barcoding
every cell has 100 mts
each has several genomes
what gene region do bacteria barcoding use
16s
why dont fungi barcodes use the mtDNA CO1 gene
lacks introns
lacks var within species
no universal primers
no mt inn some fungi
its has been used for a long time, 172,000 sequences
why doesnt its 5.8 work for plants
10,000 copies of the genome
not kept all the same
what gene is used for plant bacroding
trna uaa gene
chloroplast dna
what are two problems with chloroplast dna
poor resolution
not as universal - omits ferns
how would a bar coding gene look like
dna region with two conserved parts and a variable region in between
primer attaches to the conserved region and you amplify the variable region
why may pcr fail
more than one fungi dna degraded contaminatoin species of fungus with mutation in primer site multiple copy locus researcher failiure
at what percent identity is an OTU formed
97%
desribe the truffle study in boston
found white truffles in arnold arboretum
very rare truffle
introduced with introduced trees
used to look at root tips from morphology before with 150 charcteristics
dna made it pointless
then used barcoding found 85% of the trees supported truffles and there were new species not known to science
when would you use metabarcoding vs normal barcoding
meta - to look at the whole community
normal to identify a species
describe illumina sequencing
adapters to end of fragments - tags and provides binding sites
amplification
sequencing using optical detection of paticular dyes and number of cycles gives sequence length
analyse by forming contigs
what differs between ion torrent and illumina metabarcoding and why would you use ion over illumina
digital detection caused by H ion charges and pH meter
ion has more errors but it gives 70 million shorter reads in one go
why is metabacroding good for reducing animal and plant bias in biodiveristy
taxonomic bias to plants and animals
excludes fungi and bacteria
define metabarcoding
obtain gene regions from multple species at once matching sequences to database to obtain community level infomation
give some advantages of metabarcoding
greater coverage provided by metabarcoding allows better coverage of community structture
includes crucial but non visable species
good for maori whakapapa- entire understanding of ecosystem meta barcoding can conserve the ecossytem health - ahua
improve producitvity of crops
pest knowledge improved
what are some disadvantages to metabarcoding
assumes all pcr samples are consistent - all species represented
assumes sequences can be linked to names
have to assemble into otus
need quality reference data otherwise they are useless
arbuscular mycorrhizal fungi badly amplified
bias to conditons e.g. cold prevents dna degredation
what was the purpose and predictions of the 1000 springs project
develop a databse of the endemic microbial communities in NZ geothermal ecosystems
predict more archea
higher diversithy in lower tempertures
neutral pH at higher diveristy
give some facts about the 1000 springs project
ranged from 13.9 degrees to 100.6 degrees
used ion torrent metabarcoding
38.1 million reads
and a total of 28,500 otus with an average of 386 per pool
describe the distriution of organisms in relation to pH
bimodal distribution
no microrganisms detected below 0.5 pH
what the most significant factors in chaging the community compoistion of the hot springs
pH
then temperture
other had very little impact on OTU richness
what is beta diveristy and how was it used in the 1000 springs project
the comparison of communities
pH was the major definer of similairty between community composition
what was an unusal species found in teh 1000 springs project
veneivirbrio
- never barcoded any where else
endemic nz species but likely an endemic species
what are two reasons why the 1000 spring project is usefule
academic - luca - likely originated in a hot spring
industrial proesses - thermophiles in hot springs will have interesting enzymes
the 1000 springs project enabled the cultivation of _______
methanotrophs
what are the problems with describing a species based only on a photo
photos are incomplete, we only know morphology, nothing about life histroy or ecology
species are hypothesise, they hence need to be replicable and flasefiable
a photo cant be flasifiable
describe an argument for specimen free taxonomy
taxonomy involves killing need a speciemen
species that havent been found are likely to be rare, taking a speciemen pushes further towrds extinction
also rare thing sbeccome collectable, may not realise the damage until it is to late
give an example were specimen taxonomy pushed a species back towards extinction
slender button daisy thought extinct
doc ranges found a patch
in marlborough
first thing they did was take samples
what is the middle ground between the photo and specimen taxonomy debate
facebook post in croatia saw a new species of indonesian pygmy devil. teams used the photo and went into the field to identify it
what is a great auk species
a species where the last individual was killed out of intrest, named so because the last great auk was killed in this fashion
what is the counter argument agsinst great auk species
102 great auk species exist today in science collections, most after extinction
but millions have been harvested for food oil and feathers
scientists have come a long way
modern collecting adheres to strict permiting regulations and gudidelines
- cant collect individuals when it effects the population
why do we need specimens for fungi
dna searches are not great for fungi 43,000 species in genbank without names
give an example where morphology failed in fungi
candida krusei is drug resistant and used in cholcate production
is asexual
pichia kudriazevii is a sexual yeast
- ethanol production
99.6% similar genomes
one is the anamorph (asexual mold) and the other is the telemorph (sexual stage, typical fruiting body) of the same species
describe how we know very little about some soil fungi
soil clone group 1- no real taxonomy
- a group found in alpine soils and degrade organic molecules
anne rosling found it to be the most ubiquitous fngus only known from its dna sequence in th eworld
- used meta data to find it was birch or pine associated and that there were over 100 OTUs in the group
new taxonomy up to family level created - the archaeorhizomyces
what was the reason for the undereported OTUs in soil clone group 1
wrong primer
- used its 2.2 3.5% of sequences
lsu7 gave 95% of sequences
describe a case where a sample was based on dna alone
sporohrix fungi phylogeny saw a seperate genus within a genus - cant be true
basal species - sporohrix lignivoris, 5 specimens
took a bunch of uncultured unnamed samples with high matches and made 3 distinct species they could find samples for.
new genus hawksworthiomyces
one species without a sample so named sequencia eNAS (environmental nucleotide acid sequence) caused a large debate
the type specimen for this species is a gen bank entry
define plesiomorphic and apomorphic chacrter states
plesiomorphic states - ancestral state
apomorphic state - derived state
synapomorphy -
a derived charcter state shared by two or more taxa suggesting common origin from an ancestral taxon, provide evidence for a evolutionary relationship
define polytomy and dichotomy
polytomy - unresolved branching pattern
dichotomy - resolved branching pattern
why do we need an outgroup
apopmorhic and plesimorphic states are relative terms
hence we need the bottom of the tree to be deifned as plesimorphic
so we have a closely related speceis that is not in the ingroup to base the tree
define homoplasy
- give three types
where two speceis have the same charcter state for reasons other than inheritance
- convergence
- reversal - changes back to plesiomorphic
- parralelism - same ch state
give three examples of optimality criteron
maximum parsimony
maximum likelihood
bayesian infernce
give six practical examlpes of phylogenies
kumara
ancestral traits
forensics
account for phylogenetic autocorrelation
reveeal ecologicall patterns in community comoposition
study location of a speceis
describe the alder and willow phylogenetic study. an example of phylogenetics in ecology
both alder and willow are invasive and use ectomycorrhiza
- isolated the dna of the fungi and the plant
asked the q do invasive trees invade with invasive fungi
took samples from north and south
alder had similar fungi on both island but willow had very different fungi on different islands
large amounts of tomentella and thelephora - very boring fungi, basic and undistinctive and therefore are understudied
took samples from europe
every nz sample with alder or willow
every nz sample with native trees
constructed a phylogeny and the samples on alder and willow were far more related to european samples than they were nz samples
suggests co invasion
describe how a phylogeny can reveal ecological patterns in community composition
frans joesph glacier
- glacial retreat has left lots of different soil ages
range from 2 years old with some basic plant communities
to 500 years old with a rich podocarp forest to being 120,000 years where the forest is starting to break up again
Nitrogen peaks in the middle because there are more nitrogen fixing plants
phosphorus declines throughout
took fungal samples and shows there are differnces in fungal community between the sites. the plants drive soil change and teh soil change drives fungal change
the different species occur across a gradient
a phylogeny was constructed and the groups were releated in refernce to whicih part of the glacial area they existed in.
describe how phylogenies can account for phylogenetic autocorrelation of traits
statistics assume that all data is independant of one and other however evolution means this isnt true
a study looked at comparing wether ectomicorrhial or arbuscular micorhiza had any effect on the amount of nitrogen, phosphorus and leaf mass area
statistics alone suggest that there is a significant difference for phosphorus and leaf mass area
however the groups with arbuscular mycirhiza are going to be more related to one and other and hence are more likley to share traits anyway
used a phylogentic independant contrast uses the branch lengths to test indepedance of traits which accounts for phylogeny
then a monte carlo simulation where you assume everything is random
neither found anything significant
leaf traits do not evolve with root traits
what do branch lengths tell us
the number of character state changes between an ancestor and a descendent
what is the effect of branch length on parsimony
maxinmum parsimony would assume the lowest number of charcter state changes
so would assume one even if multiple had occured e.g. c to g g to a a to t
max pars would assume c to t
this reduces the branch length and therefore the numver of chacter state changes and could end up gettig a less parsimnoious tree
what tackles the problme of max parsimony and branch length
models of nucleotide subsitution
what three types of paramter are there in nucleotide models
subsitution type e.g. jc says all likely gtr says each is different
rates of mutation differ at differing points acros the genome e.g. conserved vs mutating regions
frequency of nucleotides
jc predicts equal proportions
why is more paramter rich model not always the best
add up the incertainties caused by each paramter
- gives penalties agsint how accurate the model is
compare maximum parsimony maximum likelyhood and bayseian inference with the following measures
optimiality criteron
computation demands
models of nucleotide sub
ability to estimate branch length
statistical probabilities for trees and clades
focuses on finding
opimality criterion
max par - fewest numer of ch state changes
max like - highest likelyhood value
bay - highest prosterior probability
computation demands
- all high
nucleotides sub model
- used in max like and bay
abiity to estimate branch length
- poor in max par and is ok in both max like and bay
statisitcal probs
- only bay
focus on finding
- best tree and those not signifcantly wose for bay others find a single tree
how does max like work
uses a model of nucelotide subsitution
compares the likelihood vlaue of a data set being the result of an evolutionary pattern
how does bayseian infernce work
it uses prior probabilites and posterior probabilities
what two types of trees re to represent trees not signifcantly differenct from one and other
strict - only the rleationships present in all trees
50% majority tree - where pesent in 50% or more of trees
in a bay calcualted phylogenetic tree what does the percentage mean
the number of occurances that that relationship has within all the trees that are statistically significant
describe prior probabilites what is a flat prior
use data from prior studies and infomation
usually use a flat prior which assumes the probabiity is the same
how can a probability distrbution arise from `phylogenetic trees what process analyses this
the same tree could have different probabilities dependant on the infered branch length o each tree
analysed by markov chain monte carlo analysis
give the key principles of nomenclature
each group with a paticular circumscription can only bear one name
the nomenclature is based upon priority of publication
a name that breaks the nomenclature rules is
illegitamate
the original name of a species whose name has been changed is called
a basionym
if a genus name is changed teh specifc epithet will
stay the same unless it breaks the one name rule
