7 Phylogenetic Marker
This is part of the UHH MSc Biology Course EvoSys 2023 (6/11)
7.1 Nuclear Single-Copy-Marker
Fine, but …
- Small amount is not easy to amplify
- Problem of introns
- diploid inheritance: cloning might be necessary
- recombination
7.2 Ribosomal DNA
- abundant
- highly conserved, universal primer is possible
- alighment is much more difficult since no reading frame is applied
- 18S is more conserved than 28S
7.3 Mitochondrial DNA
Ring DNA
- 15-20 kb, 22 tRNAs, 2 rRNAs, 13 proteins, control region
- abundant (5-10 DNA in one Mitochondrium, ca. 1000 Mitochondria/cell
- almost homoplastic (maternal inheritance as bottle neck)
- no intron
- rapid lineage sorting
- no recombination
- no pseudogene (but possible in nuclear mitochondrial DNA segment)
- no repare system, thus higher substitution rate
7.4 DNA Barcoding, DNA Fingerprinting (profiling)
DNA Marker, e.g., COI, etc.
7.4.1 Microsatellite
- 10-100 repeats of a 1-6 bp DNA fragment
7.4.2 AFLP (Amplified fragment length polymorphism)
- selective amplification of a subset of digested DNA fragment to generate and compare unique fingerprints for genome of interest
- do not require prior information regarding the targeted genome
- for assessing intragenetic, population-level phylogenies and biogeographic patterns
7.4.3 RAD (Restriction site associated DNA sequencing), ddRAD
- SNPs: single nucleotide polymorphisms
- Codominant Marker