Genetic Biodiverisity

Question 1

What is DNA coiled into?

Answer 1

Paired chromosomes

Question 2

Define allele

Answer 2

each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome. They code for different phenotypes.

Question 3

What are the three things genetic variation is maintained by?

Answer 3

1) Mutation
2) Recombination
3) Migration/gene flow

Question 4

______ _______ and _______ allow adaptation to new and changing enrivonments

Answer 4

Genetic variation and heterozygosity allow

adaptation to new and changing environments

Question 5

Define genetic drift

Answer 5

variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce

Question 6

Gene frequencies are altered by… (name three)

Answer 6

1) Genetic drift
2) Selection pressures
3) Migration and gene flow

Question 7

Variation or heterozygosity prevents what?

Answer 7

Variation / heterozygosity prevents expression of

deleterious homozygous recessive genes

Question 8

What is the minimum viable population size?

Answer 8

100 animals

Question 9

What do we discover using genetics and how? List four.

Answer 9

1) Species identity (clustering algorithms)
2) Parentage (seeking identical sequences)
3) Phylogeny & biogeography (similarity to other sequences from other regions)
4) Genetic diversity within populations (statistical noise in gene sequence frequencies)

Question 10

Name some genetic tools.

Answer 10

1) Allozymes (protein electrophoresis of variable enzymes - hardly used now)
2) AFLP (Amplified Fragment Length Polymorphisms) - 100s of DNA fragments, coding and non-coding (little used now)
3) Microsatellites (repeated short DNA sequences, non-coding)
4) Sequencing (Nulclear DNA alone or with mitochondrial DNA)
5) Next generation sequencing (High throughput methods)

Question 11

Why is it important for conservationists to keep up with modern genetics?

Answer 11

1) Species boundaries informing conservation investments
2) Conservation breeding programmes
3) De-extinction
4) Forensic work (pathogens/wildlife crime/ reconstructions)
5) High throughput metabarcoding

Question 12

Why is it important to understand species boundaries? Give an example.

Answer 12

So you are able to prioritise resources

There is one species of Asian elephant (Elephas maximus indicus) but
taxonomists agreed that the populations in Sri Lanka (Elephas maximus maximus) and Sumatra (Elephus maximus sumatrense) are validly different subspecies (island endemics!). Hence elephant conservation resources should certainly target these populations.

Question 13

Why should the Sri Lankan elephants not be considered a conservation priority?

Answer 13

In Borneo it is known that mainland elephants were introduced in the 18th century and let go. There are pygmy elephants there now that were isolated for 300,000 years whereas Sri Lankan elephants have shared halplines with E. m. indicus and are not especially worth preserving.

Question 14

DNA sequences tell us that we have at least ____ African elephant species

Answer 14

No, we know from DNA sequences that we have at least 2 African spp, savannah elephants and forest elephants. Further, the forest elephant has 2 clades (West and Central Africa) going back c. 5 MYBP that are as separate as species.

Question 15

How many giraffes are there?

Answer 15

It used to be 1 species with 9 subspp; Fennessy et al (2016) found 4 spp, with 2,1,1 and 4 subspp in each.

Question 16

When and how did the UK gain a new amphibian?

Answer 16

Just in 2014 the UK gained a new amphibian, when DNA data showed that toads on Jersey were not Bufo bufo but Bufo spinosus.

Question 17

Why are genetic tools important for cryptic species?

Answer 17

They identify differences in species that are morphologically similar and share the same habitat.

Question 18

How do you confirm if you really do have cryptic species?

Answer 18

Maybe you really have 2 cryptic species that won’t interbreed, despite looking visually similar to us. Look for linkage with a fast-evolving nuclear sequence, eg “Extension Factor 1α”,

Question 19

Since mitochondrial genes are inherited differently from ______ genes, non-random distributions between their inheritance (linkage disequilibrium) suggest a barrier to __________ exchange; ____________.
By contrast, a random distribution between _______ and mitochondrial pools argues for their ________ in a common genetic pool – hence ___ ________.

Answer 19

Since mitochondrial genes are inherited differently from nuclear genes, non-random distributions between their inheritance (linkage disequilibrium) suggest a barrier to genetic exchange; speciation.
By contrast, a random distribution between nuclear and mitochondrial pools argues for their swapping in a common genetic pool – hence one species.

Question 20

What has indicated that a neotropical butterfly called the two barred flasher has ten cryptic species?

Answer 20

Initial barcoding by Hebert et al (2004) suggested that this clade comprises 10 cryptic species, with host-specific parasitic flies exhibiting cryptic host specificity (Smith et al 2006).

Brower (2006), who reanalysed the COI data and suggested that the DNA data only proved 2 isolated clades, and suggested between 3 and 7.

Question 21

What did the DEFRA waxtongues project bring to light?

Answer 21

Waxcap fungi (Hygrocybe), which are populat conservation icons due to being big and colourful and very habitat specific

But DEFRA discovered multiple cryptic species so there will need to be lots of renaming; the commonest waxcap in the UK (H. conica) turns out to be 11 species, 5 of which occur in the UK (but which one was the type specimen? Only that one can be called H. conica thanks to the law of precedence)

Question 22

What is the default barcode of life? Why is it the default?

Answer 22

The default barcode of life is mt Cytochrome oxidase 1 (=COI). Non-recombining, good resolution, low intra-specific vs high interspecific variance. Is maternally inherited.

COI is not useful for plants because it hardly evolves at all

Question 23

What is wrong with the Florida panther (Puma concolor) in terms of genetics?

Answer 23

1) Small population ( approx. 100-160 animals)
2) Congenital heart disease
3) Single testicle abnormality
4) 85-90% sperm abnormal

Question 24

How can we conserve the Florida panther (Puma concolor)

Answer 24

1) Reserves, habitat enhancement
2) Captive breeding programmes
3) Cross-breeding with closely related subspecies

Question 25

What is the only animal to have been brought back from extinction?

Answer 25

Spanish ibex cloned from a cell from the last survivor in 2009. (It dies after a few hours).

Question 26

De-extinction has been tried by _______ ________; Aurochs came back as ______ _____. The quagga has come back as _____ ______”. These are NOT recreating the original _________.

Answer 26

De-extinction has been tried by selective breeding; Aurochs came back as Heck cattle. The quagga (basically a less stripy subsp of zebra) has come back as “Rau’s quagga”. These are NOT recreating the original genome.

Question 27

Why is recreating mammoths controversial?

Answer 27

1) Each mammoth exhumed will differ from Indian elephants in thousands of key gene sequences, both coding sites and promoters
2) Even if you get most the genome right, the host uterus will be different from ancestral.
3) Is it ethical to create just a few neo-mammoths, given these are intelligent social animals?
4) It would cost a lot of money (perhaps better spent on conserving our extant elephants)

Question 28

What can wildlife crime forensics do?

Answer 28

It can provide evidence of illegal hunting (where did the meat come from?)

e.g. Sturgeons make caviar but EU has strict limits on which spp can be imported, however, eggs look very similar so DNA is used

Question 29

How can forensics prevent wild-caught chicks being used by falconers?

Answer 29

Falconers can breed captive birds, but not use wild-caught chicks. Until recently this was almost unenforceable, but DNA can check parentage.

The first UK prosecution for this was in 1992, of a falconer in Liverpool who claimed 4 goshawk chicks were captive-reared when DNA tests (using hypervariable mini-satellites) showed them unrelated to their “mother”.

Question 30

What is eDNA?

Answer 30

Environmental DNA (eDNA) is nuclear or mitochondrial DNA that is released from an organism into the environment. Sources of eDNA include secreted faeces, mucous, gametes, shed skin, hair and carcasses. Recent research has shown that the DNA of a range of aquatic organisms can be detected in water samples at very low concentrations using qPCR (quantitative Polymerase Chain Reaction) methods.