single species ID Flashcards
Why are phenotypic ID’s challenging?
because they are susceptible to variation in expertise.
What are the results and impacts of invasive earthworms?
tree seedlings, ferns, wildflowers, and water quality decline given changes in physical and chemical properties of soil
what is a universal species test?
this is a primer set to amp a spectrum of species
what kind of species test is challenging to exclude other species?
species-specific test
what is a mixed species test?
you can amplify a set of species
T/F: universal tests will amplify all species equally.
false
what are the implications of species tests?
- specificity
- sensitivity
- validation
what are the advantages of small DNA segments?
more likely to get viable profiles, and since this is most likely degraded it will still work
what is the disadvantages to small DNA segments?
too small they might not contain genetic variation
what is the problem with too much variation?
primers might not work or stick on properly.
what is often the first and only question for a wildlife forensic or non-human foresnic scientist?
species identification
T/F: universal tests are required prior to running tests for individual identification or population assignments.
false, species specific tests are required
how can you get DNA from an egg?
scrapping the exterior or swabbing the interior of an egg
T/F: in cases such as shark finning DNA can be tracked back to geographic regions where population stocks can be identified.
true
what is a biological species?
group of individuals that can breed together but not with other groups
biological species are ____ from other groups.
reproductively isolated
what is the phylogenetic species concept?
group whose members are descended from a common ancestor and who all possess a combination of certain defining or derived traits
T/F: forensic DNA profiles are determined based on similarity or disimilarity of different markers
true
What are the exceptions to morphological species identifications?
cryptic species and ecotypes.
A species that looks the same but genetically is different is considered what?
a cryptic species.
T/F: ecotypes can be defined as a species that has strong selective pressures amongst the same species and they are reproductively isolated.
false, they are NOT reproductively isolated.
what is a monophyletic group?
an ancestral population and all descendants
what does incomplete lineage mean?
the species that may be monophyletic might have very similar DNA as they haven’t been apart for long enough
what is the ideal DNA barcode?
something that is:
- present in all organisms
- distinguishes all species
- easily amplified and sequenced
what is the ideal DNA barcode for animals?
COI, mtDNA
what is the ideal DNA barcode for plants?
matK + rbcL, cpDNA
what is the ideal DNA barcode for fungi?
ITS, nDNA
why do plants not require mtDNA identification?
it does not have a lot of genetic variation
What does the ITS stand for? what is it used for and why?
nuclear ribosomal internal transcribed spacer used to identify fungi because it is highly repeated, contains variable regions and is flanked by conserved sequences
T/F: you can get a good profile from a yellow/brown leaf.
false, it will be the best for green as they have more chloroplasts.
what are the specific genes that plant species ID can be gained from?
matK and rbcL genes
what kind of specific identification does mtDNA work well with? (inter/intra)
interspecific variation
T/F: mtDNA is paternally inherited.
false, maternally
what enzyme does mtDNA and cpDNA lack?
proofreading enzyme
what are the commonly used genes for mtDNA?
cyt b, COI, 12s and 16s rRNA
T/F: COI works well in bats.
false, not well
what gene has the best in-house database?
cyt b
T/F: cyt b is invariable making primer design not easy across species.
false it is great for primer design
what is the 2% rule?
there is an approximate 2% sequence divergence in COI genes if it is below 2% then it is a different species
what is the barcode of life project?
inventory of biodiversity and under representation of diversity of life from general taxonomy
Why is the NCDI worse than BOLD?
because bold is validated over and over where as the NCDI is just user uploaded and could contain errors
What DNA does hybridization occur with?
mtDNA
what is heteroplasmy? what is a famous example?
having more than one mtDNA profile, the Romanovs had 2
what is reticulate evolution?
two species with the same mtDNA
what is interspecific introgression?
also hybridization where things come back together then diverge then come back together
what is the problem with intraspecific divergent lineages?
its in insects mostly but it can kill gametes leading to species ID issues.
what are nuclear pseudogenes? how do you fix it?
caused by retroviruses which pull out pieces of the genome and put them other places, fixed by dilution
when nuclear pseudogenes are run through gels what does the gel look like?
gel will look like inactive versions of the genome resulting in more than one band.
T/F: hybrids will have the same maternal mtDNA
true
what does hybridization lead to?
speciation along spatial and temporal gradients
what is an example of hybrids that is causing issues in Canada/Alaska?
grizzly bear and polar bears
what does BLAST stand for?
basic local assignment search tool
what do you generally search for in a blast search?
nucleotides
in context of the 2% rule what number in BLAST is very important?
the ident number which will give you percentage
T/F: on BLAST you will always get a full sequence overlap
false, not always
how are species specific markers best accomplished?
via qPCR with TaqMan assay
what do universal primers do?
look for regions of no/less variation adjacent to variation
