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Year 2 Semester 1 > origins and classification of life > Flashcards

origins and classification of life Flashcards

1
Q

define taxonomy

A

classification of organisms in an organised system. incoporating the desccription, identificatoin, and niomenclature

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2
Q

define phylogenetics

A

reconstructing the evolutionary history and relationships of organisms

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3
Q

describe some economic benefits to taxonomy

A

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

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4
Q

describe benfit of taxonomy to biosecuirty

A

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

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5
Q

descibe the relevance of taxonomy in maori culture

A

Taonga species are sacred and need looking after - whakapapa

conserve culturally significant species

looking after the environment is important part of their culture

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6
Q

describe an example where incorrect taxonomy caused a large scale problem

A

1.3 tons of opium poppy seeds were ceased by the UK in afghanisatan
they were actually just mung beans

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7
Q

describe the benefit to human health from taxonomy

A

tropical bacteria on the rise due to climate change. need to identify pathogens in order to cure them

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8
Q

what % of species on earth have been classified? why is this an issue?

A

10%

what if we havent classified aan organism of huge ecological importance that is on the verge of extinction

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9
Q

describe a case study where phylogenetic infomation was crucial in tackling a disease

A

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

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10
Q

how many species on earth

A

5 to 30 million

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11
Q

what are the expectations of a classification

A 
easy to use 
aid to memory
preditive 
consise 
stable
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12
Q

give some examples of poor classificaion systems

A

size
colour
use to humans

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13
Q

give examples of when classifcations changed

A

renaissance - clusius, placed species in groups that were useful to humans, started to use more science

darwinian era - when evoloution was being discovered

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14
Q

give a pro and a con for evolution as a classification system when considering ease of use

A

it is universal and relates all organisms together

but we dont know all teh evo relationships

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15
Q

give a pro and a con for evolution as a classification system when considering it as an aid to memory

A

evo relationnships often follow morphology

homoplast and convergent evolution can conter this e.g anteaters and pangolins

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16
Q

give a pro and a con for evolution as a classification system when considering it as predictive

A

name of taxon gives info about evolutionary relationships

but this is always predictive of biologically relevant infomation e.g. jacobea vulgaris and eruifolia

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17
Q

give a pro and a con for evolution as a classification system when considering a classification system to be concise

A

hieracry is compatible with systems of taxonomic classification

but we do get superfluous names such as ginkgo,only one species in a whole phylum

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18
Q

give a pro and a con for evolution as a classification system when considering a classification system to be stable

A

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

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19
Q

why should a classification system be stable?

A

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

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20
Q

how do the expectations of stability and predictivity clash

A

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

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21
Q

give two arguments against the reality of species

A

speciation is a gradual and continuous process - gradual pattern of speciation. rather than a punctuated pattern

some species hybridise

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22
Q

arguments in favour of species

A

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

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23
Q

how many species concepts are there

A

around 25

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24
Q

what are the two types of problem with species concepts

A

operational - difficulty in appling

theoretical - inherit problems of the species definiton

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25
Q

define the biological specis concept and give iperational and theoretical problems with it

A

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
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26
Q

define the morphologicl species concept

give operational and theoretical problems with it

A

defining species by them looking the same

theoreticacl

  • convergent evolution
  • cryptic species

oppertoinal

  • sexual dimorphism
  • objective hard to apply hard and fast rules
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27
Q

define the phylogenetic species concept

A

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

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28
Q

what is another issue with the phylogeneic species conept

A

It can lead to over splitting, get very small groups with no biological significance

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29
Q

describe a case study where the phylogentic species concept was crucial for conservatoin

A

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.

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30
Q

describe why neither the morphological or the phylogenetic species concept works perfecty for bacteria

A

two bacteria cacn be very similar in morphology but very different genetically

two bacteria can be very different morphologically but very closely related genetically

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31
Q

how do we tackle the porblem of species concepts and microorganisms when classifiying them

A 
use a polyphasic approach 
use multiple sources of infomation 
- phylogenetic 
- genotypic 
- phentypic
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32
Q

what two ways are phylogenies formed with bacteria?

A

using the 16s gene sequence

or the whole genome

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33
Q

give ane xample to show the large genetic diveristy in bacteria

A

ecoli shares just 28% of its DNA with other ecoli strains

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34
Q

define a microbial species

A

all memebers of a species should be monophyletic and should be genetically and phenotypically cohesive with their traits being distinct form another species

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35
Q

why is the 16s gene used

A

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

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36
Q

describe the method of DNA hybridisation in classificatoin of microorganisms

A

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

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37
Q

what % similairty must 16s rRNA genes have to be from the same species

A

3%

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38
Q

give examples of phenotypic traits used to classify microorganisms

A 
lpid chemstry 
cell wall chemistry 
temperture, salinity, pH
metabolism 
motility 
morphoogy
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39
Q

how many species are discovered every year

A

18,000

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40
Q

why do we need to describe new species

A

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

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41
Q

describe some of the datat that is important to use in the publication of a new species

A

meta data
location e.g. where it was found
when it was found
enrvironment, altutude gps

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42
Q

why is meta data useful

A

prehaps know the number of species in sample, estimates of total number

increases the scientific value because can test for relaibility

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43
Q

why should a scientific paper include the species concept used

A

allows repetitionn

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44
Q

give some general risks to misidentifying an organism

A

dont spot an invasive speces
loss of money
loss of ability to solve a problem

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45
Q

give the sea star example of a negative consequence of making a taxonomic error

A

sea star thought to be native but was actually invasive, by time this was realsied it was to late to stop the invasion

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46
Q

what is a voucher speciemen

A

permaent record of a species stored in a herbarium

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47
Q

give the napeoleons willow on st helena exmple of vouchers being useful

A

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

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48
Q

define type specimen

A

the name of the type speciemn cant be chaged, it is the example of the species

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49
Q

give an example of a voucher being very important in a study

A

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

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50
Q

describe the problem of the misidentification of the lustianian slug in central europe

A

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

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51
Q

give methods used to identify a species

A 
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
52
Q

describe how a phylogenetic study told us about the origin of the sweet potato

A

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

53
Q

describe how phylogenetics found a doctor guility

A

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

54
Q

describe how phylogenies have been used to work out histroical human knowledge

A

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

55
Q

desribe the data matrix needed to form a phylogeny

A

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

56
Q

define the term homologus

A

similar states shared due to common ancestry

57
Q

define analogy or homoplasy

A

similairty not due to common ancestry

58
Q

define a character in a dna sequnce allignment

A

each position in a dna sequnce so

59
Q

why can you not apply the same cost to all charcter state changes in a dna sequence allignment

A

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

60
Q

define a transition mutation

A

purine to purine or (c to t) pyrimidine to pyrimidine

61
Q

define a transversion mutatoin

A

guarnine to thymine i.e. a purine to a pyrimdine or vice versa

62
Q

what are some `problems with genbank

A

huge number without names e.g. uncultured fungus. 12,000 per year
not curated for accuracy and 20% of sequences are misannotated

63
Q

describe a good gene region

A 
low mutation within a species 
high mutation between species 
conserved flanking region
universally present 
good prior data 
phylogenetically informatoive
64
Q

why is mtDNA used in animal barcoding

A

every cell has 100 mts

each has several genomes

65
Q

what gene region do bacteria barcoding use

A

16s

66
Q

why dont fungi barcodes use the mtDNA CO1 gene

A

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

67
Q

why doesnt its 5.8 work for plants

A

10,000 copies of the genome

not kept all the same

68
Q

what gene is used for plant bacroding

A

trna uaa gene

chloroplast dna

69
Q

what are two problems with chloroplast dna

A

poor resolution

not as universal - omits ferns

70
Q

how would a bar coding gene look like

A

dna region with two conserved parts and a variable region in between

primer attaches to the conserved region and you amplify the variable region

71
Q

why may pcr fail

A 
more than one fungi 
dna degraded 
contaminatoin 
species of fungus with mutation in primer site 
multiple copy locus 
researcher failiure
72
Q

at what percent identity is an OTU formed

A

97%

73
Q

desribe the truffle study in boston

A

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

74
Q

when would you use metabarcoding vs normal barcoding

A

meta - to look at the whole community

normal to identify a species

75
Q

describe illumina sequencing

A

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

76
Q

what differs between ion torrent and illumina metabarcoding and why would you use ion over illumina

A

digital detection caused by H ion charges and pH meter

ion has more errors but it gives 70 million shorter reads in one go

77
Q

why is metabacroding good for reducing animal and plant bias in biodiveristy

A

taxonomic bias to plants and animals

excludes fungi and bacteria

78
Q

define metabarcoding

A

obtain gene regions from multple species at once matching sequences to database to obtain community level infomation

79
Q

give some advantages of metabarcoding

A

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

80
Q

what are some disadvantages to metabarcoding

A

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

81
Q

what was the purpose and predictions of the 1000 springs project

A

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

82
Q

give some facts about the 1000 springs project

A

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

83
Q

describe the distriution of organisms in relation to pH

A

bimodal distribution

no microrganisms detected below 0.5 pH

84
Q

what the most significant factors in chaging the community compoistion of the hot springs

A

pH
then temperture
other had very little impact on OTU richness

85
Q

what is beta diveristy and how was it used in the 1000 springs project

A

the comparison of communities

pH was the major definer of similairty between community composition

86
Q

what was an unusal species found in teh 1000 springs project

A

veneivirbrio
- never barcoded any where else
endemic nz species but likely an endemic species

87
Q

what are two reasons why the 1000 spring project is usefule

A

academic - luca - likely originated in a hot spring

industrial proesses - thermophiles in hot springs will have interesting enzymes

88
Q

the 1000 springs project enabled the cultivation of _______

A

methanotrophs

89
Q

what are the problems with describing a species based only on a photo

A

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

90
Q

describe an argument for specimen free taxonomy

A

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

91
Q

give an example were specimen taxonomy pushed a species back towards extinction

A

slender button daisy thought extinct
doc ranges found a patch
in marlborough
first thing they did was take samples

92
Q

what is the middle ground between the photo and specimen taxonomy debate

A

facebook post in croatia saw a new species of indonesian pygmy devil. teams used the photo and went into the field to identify it

93
Q

what is a great auk species

A

a species where the last individual was killed out of intrest, named so because the last great auk was killed in this fashion

94
Q

what is the counter argument agsinst great auk species

A

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

95
Q

why do we need specimens for fungi

A

dna searches are not great for fungi 43,000 species in genbank without names

96
Q

give an example where morphology failed in fungi

A

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

97
Q

describe how we know very little about some soil fungi

A

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

98
Q

what was the reason for the undereported OTUs in soil clone group 1

A

wrong primer
- used its 2.2 3.5% of sequences
lsu7 gave 95% of sequences

99
Q

describe a case where a sample was based on dna alone

A

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

100
Q

define plesiomorphic and apomorphic chacrter states

A

plesiomorphic states - ancestral state

apomorphic state - derived state

101
Q

synapomorphy -

A

a derived charcter state shared by two or more taxa suggesting common origin from an ancestral taxon, provide evidence for a evolutionary relationship

102
Q

define polytomy and dichotomy

A

polytomy - unresolved branching pattern

dichotomy - resolved branching pattern

103
Q

why do we need an outgroup

A

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

104
Q

define homoplasy

- give three types

A

where two speceis have the same charcter state for reasons other than inheritance

  • convergence
  • reversal - changes back to plesiomorphic
  • parralelism - same ch state
105
Q

give three examples of optimality criteron

A

maximum parsimony
maximum likelihood
bayesian infernce

106
Q

give six practical examlpes of phylogenies

A

kumara
ancestral traits
forensics
account for phylogenetic autocorrelation
reveeal ecologicall patterns in community comoposition
study location of a speceis

107
Q

describe the alder and willow phylogenetic study. an example of phylogenetics in ecology

A

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

108
Q

describe how a phylogeny can reveal ecological patterns in community composition

A

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.

109
Q

describe how phylogenies can account for phylogenetic autocorrelation of traits

A

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

110
Q

what do branch lengths tell us

A

the number of character state changes between an ancestor and a descendent

111
Q

what is the effect of branch length on parsimony

A

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

112
Q

what tackles the problme of max parsimony and branch length

A

models of nucleotide subsitution

113
Q

what three types of paramter are there in nucleotide models

A

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

114
Q

why is more paramter rich model not always the best

A

add up the incertainties caused by each paramter

- gives penalties agsint how accurate the model is

115
Q

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

A

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

116
Q

how does max like work

A

uses a model of nucelotide subsitution

compares the likelihood vlaue of a data set being the result of an evolutionary pattern

117
Q

how does bayseian infernce work

A

it uses prior probabilites and posterior probabilities

118
Q

what two types of trees re to represent trees not signifcantly differenct from one and other

A

strict - only the rleationships present in all trees

50% majority tree - where pesent in 50% or more of trees

119
Q

in a bay calcualted phylogenetic tree what does the percentage mean

A

the number of occurances that that relationship has within all the trees that are statistically significant

120
Q

describe prior probabilites what is a flat prior

A

use data from prior studies and infomation

usually use a flat prior which assumes the probabiity is the same

121
Q

how can a probability distrbution arise from `phylogenetic trees what process analyses this

A

the same tree could have different probabilities dependant on the infered branch length o each tree

analysed by markov chain monte carlo analysis

122
Q

give the key principles of nomenclature

A

each group with a paticular circumscription can only bear one name

the nomenclature is based upon priority of publication

123
Q

a name that breaks the nomenclature rules is

A

illegitamate

124
Q

the original name of a species whose name has been changed is called

A

a basionym

125
Q

if a genus name is changed teh specifc epithet will

A

stay the same unless it breaks the one name rule

Year 2 Semester 1 (6 decks)

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