VL 11: Museomics for reconstructing past biodiversity

Question 1

What is museomics?
What DNA library is mostly used?

Answer 1

Sequencing and analyzing DNA from specimens preserved in museum collections for archival purposes
aka archival or historical DNA (< 200 years old).

Single- stranded libraries -> more efficiently with shorter DNA fragents

Question 2

Ancient DNA Facts

Answer 2

= Studying DNA from specimens that died hundreds - thousands of years ago, e.g. fossils or mummies.

Many factors affect the DNA negatively after an organisms death.

Northern hemisphere better for antient DNA sample conditions, because cold, less UV light etc.

Question 3

When and why were Museum collections established?

Answer 3

in the Age of Discovery = Period from 15th - 17th century, during which European seafarers explored, colonized, and conquered regions across the world
➢ Race among European royal families to explore
➢ First biological material from animals and plants of the ”new worlds”
➢ Cultural goods of remote civilizations

1. Wunderkammer= exhibition of a collection of curiosities, rare natural objects and scientific instuments (Baroque times, just for elite). Predecessor of modern-day Natural History Museum
2. Museum national d’histoire naturell Formally established in 1793 by the government, first public museum nad center of research for evolutionary concepts
3. Museum für Naturkunde Berlin first to seperate a display from main collection (for reserach purposes)

Question 4

What are Name-bearing type specimens? Name two types

Answer 4

Name- bearing type specimens: Bilogical type that determines the application of a species name

Holotype: Single physical example of an organism used for the formal description of a species

Syntypes: Two or more types used for the description of a species (no holotype designated)
* Lectotype = Single specimen selected from group of syntypes as single type
* Neotype = Specimen later selected as the type (holotype lost, destroyed)

Question 5

What are pitfalls of morphological classifications? Name two.

Answer 5

Morphological classification comes with some pitfalls:
➢ Modern taxonomy is organizing organisms in the context of evolution

1) Cryptic species = Morphologically similar /nearly identical organisms that are genetically distinct and constitute separate species

2) High morphological difference in closely related species

Question 6

What are the presevation challanges, working with historical DNA?

Answer 6

Dry specimens tend to preserve DNA tolerably well
Wet specimens vary strongly:
* Those fixed in formalin have highly degraded DNA, but better colour preservation. (conformational changes, deamination, abasic sites, strand breaks.)
* Those fixed in ethanol may have good DNA, but loose all heir colour.

Contaminantion

Question 7

What is the significance of mitochondrial DNA in museomics?

Answer 7

Mitochondrial DNA is abundant and structurally stable (circular), making it easier to recover and amplify from degraded samples compared to nuclear DNA.

But: Recent technological advances and methodological improvements made the nuclear genome accessible for museomics as well.

Question 8

What is HyRAD?

Answer 8

HYRAD SEQ
= biotinylated RAD fragments (random fraction of the genome) used as baits to capture homologous fragments from genomic libraries/ shotgun sequencing.

It combines RAD sequencing with hybridization capture to target specific genomic regions, particularly useful for analyzing fragmented DNA in museomics.

• capture genetic diversity around restriction sites e.g. population genetics

Question 9

What is HybSeq?

Answer 9

1. Ortholog identification -> Bait tiling (many small baits cover the sequence of interest)
   2.Genomic DNA is sheered and assembled into size selected library
2. Incubated with baits (24h)
3. RNA bait-DNA hybrids ‘fished’ out of mixture by incubation with streptavidin-labelled magnetic beads & captured on a magnet
4. RNA baits digested after washing steps
5. Amplification + sequencing of target DNA only

• capatures predefined genomic regions to study specific markers e.g. evolutionary research (Barcode fishing)

Question 10

What is a barcode?

Answer 10

Short and standardized regions of the genome
that can be used for species identification.

Question 11

MuseoFrogCap advantage

Answer 11

No high-quality reference data and high quantity DNA needed (huge difference to hyRAD)