Taxonomy/Phylogenetics

Question 1

areas of study with molecular methods?

Answer 1

DNA variation:
-within species
-between species

Question 2

what properties of DNA are studied in molecular methods?

Answer 2

Relatively stable (ancient DNA, crime scene DNA…) allows it to be isolated

can be reliably cut into pieces w restriction enzymes
lengths of these restriction fragments can be measured

DNA strands - can be denatured and reannealed
used in PCR to amplify DNA sample

2 above allow studying inter and intraspecific variation

epigenetic features
e.g. methylation - tend to be attached to cytosines
important functional roles
promoter regions - hig methylation - low activatory protein binding - low expression
and other way around
-also - as individuals get older - DNA methylation increases - can estimate age
methylation also differs between species and individuals - can tell between them

mRNA sequencing (with reverse transcriptase)
Harvest RNA
make cDNA
can see which genes are being expressed in individual/tissue at certain times
(e.g. what genes are an insect expressing in high temps to cope w heat)
can study variation in gene expression among individuals

Question 2

reasons for studying intraspecific genetic variation?

Answer 2

What are the relationships between populations of that species
(are populations genetically isolated, if so why?)

relatedness of two same species individuals (e.g. parentage)

blurring of lines - when comparing 2 individuals- are they the same species or not?

Question 3

detecting DNA methylation?

Answer 3

DNA treated with bisulfite
methylated cytosines protected
inmethylated cytosines converted to Uracil

can sequence the treated DNA to detect these conversions and see which cytosines were ans weren’t methylated

Question 4

properties of relationships between populations of a species?

Answer 4

reflects history, mobility, coevolution with other species
impacts management and conservation

Question 5

mitochondrial DNA sequence study of population structure?

Answer 5

Mitochondrial DNA:
inherited maternally
strongly reflects FEMALE pop structure
Is Haploid, so no heterozygotes
does not recombine so makes interpretation of sequences easier

Question 6

killer whale pop structure study example?

Answer 6

combining DNA with morphological and geographic data

photo ID work - shown they exist in tight social groups
in any one area orcas exist as different ecotypes-
resident or transient
inshore or offshore
specialise in different food (seals, salmon…)

photo ID - associated appearance/phenotype with certain behaviour (populaitons of orcas across world have slight phenotypic differences)

made phylogeny of mtDNA for 66 orca unique haplotypes
showed the physical variation means something and groups close in morphology were closely related

though morphological variation doesn’t always link so closely with relatedness - flat periwinkles have large colour variation but close colour doesnt link directly with close relatedness

Question 7

Phylogeography?

Answer 7

combining DNA with geographic data
-identifying historical refugia (e.g.. during ice ages)
-know where things originated from

Question 8

european hedgehog population phylogeography example?

Answer 8

hedgehog populations refuged in southern europe during glaciation
spread out further north after glaciation receded

used mtDNA of populations - compared ones from different populations throughout europe
variation in hedgehogs in more northern pops due to which refuge they came from
could all be traced back to one of three refugia
colonised N, europe from 3 different refugia

W (spain/iberia - to france, UK)
C (italy to germany, scandinavia)
E (north of greece - to eastern europe, russia)

Question 9

european grasshoppers phylogeography example?

Answer 9

similar situation as hedhehogs
different pops in different southern refugia during glaciation
spread north after receding throughout all europe
populations from each refuge spread to some same places

variation between these now mixed populations not due to adapting differently in same environment over Myrs
but due to coming from different refugia (where they spent more time adapting)

figured out by comparing grasshopper intraspecific genetic similarities and differences - allowing to trace different grasshopper populations back to which unique refuge they spread from

migration from these ice age refugia follows patterns of glacial retreat

Question 10

Phylogeography - tracing ebola outbreak example

Answer 10

handheld genome sequencers used to trace ebola virus genomes in different places at different times

if the same virus sequence is found in different places at different times
correlate them and can infer where and when infected people have moved

MOVEMENT inferred from SEQUENCE SIMILARITY
can learn where infections are originating from (patient zero?)

Question 11

calculating biological age

Answer 11

uses DNA methylation measure
use DNA methylation measure (bisulfate treatment + sequencing)

CpG islands in gene promoter sites become more methylated with age
gene expression goes awry
(age related changes in CpG methylation major factor in cancer and other age related mortality/morbidity)

BUT can also be used to etimate an organism’s age :)
can plot DNA methylation state (estimated age) against known chronological age to see if populations are ageing more rapidly:
-Bechsteins Bats
-works well in whales - correlates tight to chronological age
-seabirds - relationship not as toght
-wild mice - can tell age to about 1.8 days

Question 12

uses for estimating biological or chronological age in wild?

Answer 12

Understanding age structure of poulation - key to animal ecology and conservation - are populations mostly younger, older…

age estimates can help determine:
-animal mortality (how old are members of a population living to?)
-parasite susceptibility
-reproductive life
-impact of anthropogenic activities

Question 13

DNA metabarcoding?

Answer 13

what’s present in a sample?

-collect environmental sample (e.g. seawater sample)
-extract and isolate all the DNA
-amplify sequences with PCR
-sequence the amplified DNA
-can separate out the different sequences (by similarity ig?)
-can identify all the species that inhabit the area

Question 14

DNA barcoding?

Answer 14

uses similarity in 650bp sequence of mitochondrial Cytochrome Oxidase 1 gene (COX1) to see if individuals are part of the same species or not

congeneric pairs (2 individuals from same genus, different species) differ from congeneric partner by 2%
difference of >2% = different species
(doesn’t 100% work, but still high confidence for simple-ish test, ~98% of species show this)
only ~2% of species showed <2% divergence in COX1 sequence
on average different species show 11% divergence
so if >2% divergence = 98% confidence tha they are different species

Amplify DNA sample with PCR
200-few 100 bp long sample
can amplify tiny sample (e.g. body part of insect) to an amount suitable for sequencing

uses mitochondrial DNA so has same benefits/pitfalls mentioned earlier

Question 15

Linnean system?

Answer 15

first done by Linnaeus in 1700s
Hierarchical classification of organisms
nested hierarchy with tiers of classification
gets more and more specific as you go down
-Kingdoms
-Phyla
-classes
-orders
-families
-genera
-species (scientific name = Genus species)

more similar organisms share more of these categories

species can be split into subsets - varieties
classes and orders also split into subsets - sub-X

Question 16

how are organisms classified?

Answer 16

using their phylogeny
i.e. the organism’s evolutionary history - where has it diverged from other species/groups

Question 17

dichotomous key

Answer 17

used for taxonomical identification/classification

key has different questions
each with two answers - two distinct choices at each step

each answer to a question leads to a different question
until answer finally specifies down to what classification it is
questions can get very specific as they get to separating closer and closer relations

Question 18

two modern approaches to classification?

Answer 18

DNA barcodes
Imaging technology (e.g. smartphones)

though these still rely on matching DNA sequence or what’s seen in image to opinion of taxonomic expert

these methids rely on taxonomic identification still to work
(e.g. barcoding needed to know what were different species in the first place to establish “2% rule”)

Question 19

DNA barcoding example

Answer 19

identifying cryptic species
species that look identical but are actually different species
morphological differences tricky to spot

parasitoid fly Patelloa xanthura
thought to have weird range of host caterpillars (4 different)
parasitoids usually stick to very tight host range

DNA barcoding between individuals that were thought to be part of this species
found it was actually 4 different parasitoid species
just very similar morphologically
but different hosts
(DNA barcode differences lined up with host species differences)

Neotropical skipper butterfly Astraptes fuglerator
thought to be 1 species that had lots of intraspecific variation and wide range

caterpillars reared - had far too wide a food plant range for 1 species
subtle variation in colour pattern on caterpillars, and wing pattern differences in adults also correlated with differences in caterpillar food plant
genitalia dissection usually used to distinguish species but too similar here
would take far too long to segregate species by just matching up thses other differences

barcoding was able to easily distinguish them

Question 20

DNA barcoding uses?

Answer 20

speed up biodiversity studies
usually need taxonomic experts to separate species
can allow non-taxonomically trained people to do it

linking adult and juvenile life stages
many species with larval stages - big differences in juvenile and adult
can get species mixed up (similar looking larvae, different adults e.g.)
can DNA barcode - correlate larva to adult by sequence similarity

tracking life cycles - e.g. parasites with complex life cycles, many stages w morphological differences
free living vs parasitic stages - can correlate them as same species despite differences

link make and female morphology - many dipteran and hymenopteran species identity based on male genitals - so harder to distinguish females - barcoding allows this easier

allows easier identification of CONSPECIFICITY

Question 21

DNA barcode databases?

Answer 21

DNA sequences uploaded to databases
can access them and compare sequences from sample to identify species from similarity to known database sequences

difficulties:
newly arisen species - no precedent in database to compare to

Question 21

image analysis identification

Answer 21

typically on smartphones
e.g. iNaturalist app

photograph organism
can suggest own identification but algorithmic image anlysis by app can suggest one

displayed to wider community with identification

identification still relies on prior taxonomic experts knowledge (need to train identification algorithm known data e.g.)

also does not train users to identify things/become taxonomists themselves
but may draw them into becoming one?

CITIZEN SCIENCE

Question 22

Citizen science - adv and disadv

Answer 22

strengths:
-gives wide range of spatial, temporal coverage of species occurrence - and over long term monitoring
-gives huge workforce - relatively low financial investment - cost effective
-detection of rare events or very recent species distribution changes (climate change effects) - from wide range
-large scale monitoring - can detect unexpected biodiversity threats
-increases engagement in taxonomy - can educate to some degree - may inspire some to train

challenges:
-can’t fully ensure data accutacy from untrained identification
-biases in data - geographical/temporal variation in sampling - not even as more users in denser population areas, people also go out at certain times - less out at night, in cold…
-not always great for hypothesis driven research - not as directed - can benefit from scientist direction?

Question 23

molecular phylogenetics basic principles?

Answer 23

use of molecular data to construct phylogenies (genomic data)
phylogenies depicts ancestral relartionships among characters or genetoc sequences

looks for homology as evidence for common ancestry
homology- similarity among organisms due to inheritance from a shared common ancestor

data used to form a phylogenetic tree

Question 24

why make phylogenetic trees?

Answer 24

represents evolutionary relationships (important in biological questions)

provides framework to asks questions about

can ask about:
-morphological evolution
-speciation
-co-evolution (see if divergences in phylogenies of two species line up)
-rates of evolution

Question 25

tree structure

Answer 25

nodes/vertices
branches

tips = external nodes at end of branches
correspond to (usually) extant taxa

internal nodes
correspond to ancestral common ancestors of branches they connect

root
hypothetical last common ancestor of all taxa in tree

branches
correspond to evolutionary lineages
can rotate around nodes (mobile metaphor)

x-axis - corresponds to increasing genetic change/divergence or passing time
if in time then need to calibrate tree - see how much genetic change usually occurs over X number of years

y-axis meaningless

Question 26

common ancestors:

Answer 26

MRCA -internal node representing the Most recent common ancestor between two taxa
aka LCA - Last commmon ancestor (before the species diverged)

other common ancestors nodes futher back but not most recent

can reconstruct morphology of MRCA by looking at the organisms who share it and what conserved traits they share?

Question 27

radial tree

Answer 27

hard to distinguish where root is
used when root is unknown and want to keep tree unrooted

Question 28

paleontologist’s tree

Answer 28

like to put root at bottom
can align taxa with era its from/layer of rock fossil found in

Question 29

horseshoe tree

Answer 29

taxa spread out in curve
useful when there is a lot of info needed to be labelled - so spread it out radially in horseshoe shape

good for display - easy to label tips and looks good
though hard to gain info about relationships - hard to see what nodes are at same time on the concentric circles - might be on different sides of horseshoe would have to trace circle around

Question 30

rooting a tree

Answer 30

Outgroup - one or more taxa that are known to have diverged prior to the group being studied (the ingroup)

rearrange tree so outgroup diverges first
root represents MRCA between in- and outgroup taxa

Question 31

reconstructing evolution on a tree

Answer 31

2 close species have same trait
easiest conclusion - one event where trait arose

however other diagram:
shows group further out on tree also has trait
either:
trait evolved individually twice
or trait evolved once further back in tree - then was lost once
equally parsimonious

MAXIMUM PARSIMONY - reconstruction of trait evolution requiring the fewest state changes

most probable outcome i guess

Question 32

finding the best tree

Answer 32

if looking at sequence changes -
best tree = maximum parsimony = outcome with least nucleotide changes

can rearrange tree to maximise parsimony

Question 33

monophyly and paraphyly

Answer 33

monophyletic-
group of taxa that share a MORE recent common ancestor than to any other taxa
shares traits through COMMON ANCESTRY

paraphyletic-
MRCA of mammals and reptiles also described as reptile so paraphyly of group even more complicated
(greyed?)
DOES NOT CONTAIN ALL OF THE DESCENDENTS

e.g. reptiles are monophyletic ONLY if birds are included
e.g. are tetrapods fish?

Question 34

polyphyly:

Answer 34

artificial grouping based on morphological traits - traits that are not through common ancestrt
(convergently evolved traits)
polyphyletic group has multiple different origins

e.g. mammals and aves in grouping Homeothermia (endotherms??)

Question 35

evolutionary progress on tree?

Answer 35

shared branch length between taxa = shared evolutionary time
after branch has diverged - independent evolutionary time

Basal group - group that diverged earliest from the rest
have longer branch lengths
more basal =/= more “simple” group