DNA analysis

Routinely used laboratory protocols

DNA extractions of museum specimens from vertebrates (dried soft tissues, feathers, bones, teeth) and invertebrates (complete specimens using  commercial kits (spin-columns in individual or 96-well plate formats, salting-out) or phénol-chloroform methods.

PCR, gradient PCR, primer designing and PCR optimisation procedures for degraded DNA or diluted DNA solutions or DNA extracts containing inhibitors.

Quantitative and qualitative DNA evaluation by micro-volume spectrophotometry and electrophoresis on agarose gels.

Sequencing with an ABI 3130xl Genetic Analyser.

Tissue and DNA storage in dry conditions and at -80 °C.

Lab guidelines

Molecular data analysis

• Sequence edition
• DNA sequence alignment
• Distance analysis
• Species identification by DNA barcoding (distance, clustering and phylogenetic methods). Discover here the R package adhoc to calculate ad hoc distance thresholds for DNA barcoding identification.
• Phylogenetic analysis with parsimony, maximum likelihood and Bayesian posterior probabilities
• Haplotype network
• Databasing: Genbank, Barcode of Life Data Systems (BOLD), DaRWIN

Species identification (example of applications)

• Species identification of bird from bird strikes - collision with airplanes (aviation safety)
• Species identification of insect larvae (pest identification, forensic science)
• Species identification of smoked meat (“viande boucanée”) confiscated on markets (food and custom controls)
• Species identification of archived specimens (collection quality control)

DNA analysis of archival DNA

DNA sequences were successfully obtained from a wide range of archived biologic material. Here is a selection:

Type material

• Ansorge’s cusimanse, Crossarchus ansorgei nigricolor (Herpestidae), holotype, RMCA: 88.014-M-0001, coll. Date 1984, genetic markers cytochrome b (376 bp), 16S rRNA (469 bp)
• Prigogine’s nightjar, Caprimulgus prigoginei (Strigiformes), holotype, RMCA 78975, coll. Date: 1955, genetic marker Cytochrome oxidase subunit I (297 bp)
• Phodilus prigoginei (Strigiformes), holotype, RMCA 55987, genetic marker Cytochrome oxidase subunit I
• Ploceus ruweti (Passeriformes), holotype, RMCA 113379, genetic marker Cytochrome oxidase subunit I
• Ploceus feminina (Passeriformes), syntype, RMCA 1675, genetic marker Cytochrome oxidase subunit I
• Ploceus weynsi (Passeriformes), syntype, RMCA 419, genetic marker Cytochrome oxidase subunit I
• Zoothera guttata lippensi (Passeriformes), holotype, RMCA 74-41-A-1, genetic marker Cytochrome oxidase subunit I
• Andropadus hallae (Passeriformes), holotype, RMCA 124702, genetic marker Cytochrome oxidase subunit I
• Apalis schoutedeni (Passeriformes), holotype, RMCA 12406, genetic marker Cytochrome oxidase subunit I
• Francolinus camerunensis ruandae (Galliformes), holotype, RMCA 37745, genetic marker Cytochrome oxidase subunit I
• Melignomon zenkeri (Piciformes), holotype, RMCA 95179, genetic marker Cytochrome oxidase subunit I
• Madagascar water snake, Liopholidophis dimorphus (Serpentes), holotype, ZSM 252/2004, genetic marker Cytochrome oxidase subunit I (664 bp)
• Liophidium maintikibo (Serpentes), holotype, ZSM 2052/2007, genetic marker Cytochrome oxidase subunit I (664 bp)
• Liophidium pattoni (Serpentes), holotype, ZSM 186/2009, genetic marker Cytochrome oxidase subunit I (664 bp)
• Thamnosophis mavotenda (Serpentes), holotype, ZSM 127/2006, genetic marker Cytochrome oxidase subunit I (664 bp)
• Furcifer timoni (Chamaeleonidae), holotype, ZSM 2103/2007, genetic marker Cytochrome oxidase subunit I (664 bp)
• Typhlops rajeryi (Serpentes), holotype, ZSM1589/2008, genetic marker Cytochrome oxidase subunit I (664 bp)
• Typhlops andasibensis (Serpentes), paratype, ZFMK 59787, genetic marker Cytochrome oxidase subunit I (664 bp)
• Lygodactylus sp. (Gekkonidae), ZSM F2324, species under description, genetic marker Cytochrome oxidase subunit I (664 bp)
• Bora’s day-gecko, Phelsuma borai (Gekkonidae), holotype, ZSM 103/2006, genetic marker Cytochrome oxidase subunit I (664 bp)
• Day-gecko, Phelsuma sp. (Gekkonidae), ZSM F1667, species under description, genetic marker Cytochrome oxidase subunit I (664 bp)
• Paracontias kankana (Scincidae), holotype, ZSM 1810/2008, genetic marker Cytochrome oxidase subunit I (664 bp)

Old material

• Shikra, Accipiter badius badius (Falconiformes), RBINS 2659, Coll. Date: 1845, genetic marker Cytochrome oxidase subunit I (100 bp)
• African Goshawk, Accipiter tachiro tachiro (Falconiformes), RBINS4948, Coll. Date: 1852, genetic marker Cytochrome oxidase subunit I (298 bp)

Tooth material

• Blue Duiker, Cephalophus monticola (Cephalophidae), genetic marker cytochrome b gene (470 bp)

Feather material

• Congo peafowl, Afropavo congensis (Phasianidae), RBINS MPLMFLKPC1, genetic marker 16S rRNA (570 bp)

Non destructive DNA extraction of small specimens (<1mm)

• Solenopsis sp. (Formicidae), RBINS : ML : 33688, genetic marker Cytochrome oxidase subunit I (658 bp)