single species ID

Question 1

Why are phenotypic ID’s challenging?

Answer 1

because they are susceptible to variation in expertise.

Question 2

What are the results and impacts of invasive earthworms?

Answer 2

tree seedlings, ferns, wildflowers, and water quality decline given changes in physical and chemical properties of soil

Question 3

what is a universal species test?

Answer 3

this is a primer set to amp a spectrum of species

Question 4

what kind of species test is challenging to exclude other species?

Answer 4

species-specific test

Question 5

what is a mixed species test?

Answer 5

you can amplify a set of species

Question 6

T/F: universal tests will amplify all species equally.

Answer 6

false

Question 7

what are the implications of species tests?

Answer 7

• specificity
• sensitivity
• validation

Question 8

what are the advantages of small DNA segments?

Answer 8

more likely to get viable profiles, and since this is most likely degraded it will still work

Question 9

what is the disadvantages to small DNA segments?

Answer 9

too small they might not contain genetic variation

Question 10

what is the problem with too much variation?

Answer 10

primers might not work or stick on properly.

Question 11

what is often the first and only question for a wildlife forensic or non-human foresnic scientist?

Answer 11

species identification

Question 12

T/F: universal tests are required prior to running tests for individual identification or population assignments.

Answer 12

false, species specific tests are required

Question 13

how can you get DNA from an egg?

Answer 13

scrapping the exterior or swabbing the interior of an egg

Question 14

T/F: in cases such as shark finning DNA can be tracked back to geographic regions where population stocks can be identified.

Answer 14

true

Question 15

what is a biological species?

Answer 15

group of individuals that can breed together but not with other groups

Question 16

biological species are ____ from other groups.

Answer 16

reproductively isolated

Question 17

what is the phylogenetic species concept?

Answer 17

group whose members are descended from a common ancestor and who all possess a combination of certain defining or derived traits

Question 18

T/F: forensic DNA profiles are determined based on similarity or disimilarity of different markers

Answer 18

true

Question 19

What are the exceptions to morphological species identifications?

Answer 19

cryptic species and ecotypes.

Question 20

A species that looks the same but genetically is different is considered what?

Answer 20

a cryptic species.

Question 21

T/F: ecotypes can be defined as a species that has strong selective pressures amongst the same species and they are reproductively isolated.

Answer 21

false, they are NOT reproductively isolated.

Question 22

what is a monophyletic group?

Answer 22

an ancestral population and all descendants

Question 23

what does incomplete lineage mean?

Answer 23

the species that may be monophyletic might have very similar DNA as they haven’t been apart for long enough

Question 24

what is the ideal DNA barcode?

Answer 24

something that is:
- present in all organisms
- distinguishes all species
- easily amplified and sequenced

Question 25

what is the ideal DNA barcode for animals?

Answer 25

COI, mtDNA

Question 26

what is the ideal DNA barcode for plants?

Answer 26

matK + rbcL, cpDNA

Question 27

what is the ideal DNA barcode for fungi?

Answer 27

ITS, nDNA

Question 28

why do plants not require mtDNA identification?

Answer 28

it does not have a lot of genetic variation

Question 29

What does the ITS stand for? what is it used for and why?

Answer 29

nuclear ribosomal **internal transcribed spacer** used to identify fungi because it is highly repeated, contains variable regions and is flanked by conserved sequences

Question 30

T/F: you can get a good profile from a yellow/brown leaf.

Answer 30

false, it will be the best for green as they have more chloroplasts.

Question 31

what are the specific genes that plant species ID can be gained from?

Answer 31

matK and rbcL genes

Question 32

what kind of specific identification does mtDNA work well with? (inter/intra)

Answer 32

interspecific variation

Question 33

T/F: mtDNA is paternally inherited.

Answer 33

false, maternally

Question 34

what enzyme does mtDNA and cpDNA lack?

Answer 34

proofreading enzyme

Question 35

what are the commonly used genes for mtDNA?

Answer 35

cyt b, COI, 12s and 16s rRNA

Question 36

T/F: COI works well in bats.

Answer 36

false, not well

Question 37

what gene has the best in-house database?

Answer 37

cyt b

Question 38

T/F: cyt b is invariable making primer design not easy across species.

Answer 38

false it is great for primer design

Question 39

what is the 2% rule?

Answer 39

there is an approximate 2% sequence divergence in COI genes if it is below 2% then it is a different species

Question 40

what is the barcode of life project?

Answer 40

inventory of biodiversity and under representation of diversity of life from general taxonomy

Question 41

Why is the NCDI worse than BOLD?

Answer 41

because bold is validated over and over where as the NCDI is just user uploaded and could contain errors

Question 42

What DNA does hybridization occur with?

Answer 42

mtDNA

Question 43

what is heteroplasmy? what is a famous example?

Answer 43

having more than one mtDNA profile, the Romanovs had 2

Question 44

what is reticulate evolution?

Answer 44

two species with the same mtDNA

Question 45

what is interspecific introgression?

Answer 45

also hybridization where things come back together then diverge then come back together

Question 46

what is the problem with intraspecific divergent lineages?

Answer 46

its in insects mostly but it can kill gametes leading to species ID issues.

Question 47

what are nuclear pseudogenes? how do you fix it?

Answer 47

caused by retroviruses which pull out pieces of the genome and put them other places, fixed by dilution

Question 48

when nuclear pseudogenes are run through gels what does the gel look like?

Answer 48

gel will look like inactive versions of the genome resulting in more than one band.

Question 49

T/F: hybrids will have the same maternal mtDNA

Answer 49

true

Question 50

what does hybridization lead to?

Answer 50

speciation along spatial and temporal gradients

Question 51

what is an example of hybrids that is causing issues in Canada/Alaska?

Answer 51

grizzly bear and polar bears

Question 52

what does BLAST stand for?

Answer 52

basic local assignment search tool

Question 53

what do you generally search for in a blast search?

Answer 53

nucleotides

Question 54

in context of the 2% rule what number in BLAST is very important?

Answer 54

the ident number which will give you percentage

Question 55

T/F: on BLAST you will always get a full sequence overlap

Answer 55

false, not always

Question 56

how are species specific markers best accomplished?

Answer 56

via qPCR with TaqMan assay

Question 57

what do universal primers do?

Answer 57

look for regions of no/less variation adjacent to variation