Abstract
Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillus gerbillus, Gerbillus andersoni, Gerbillus nanus, Gerbillus amoenus, Gerbillus perpallidus and Gerbillus pyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillus nanus (Asian origin) and Gerbillus amoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillus perpallidus and Gerbillus pyramidum, specimens considered as belonging to one Gerbillus pyramidum subspecies (Gerbillus pyramidum floweri) appeared closer to Gerbillus perpallidus suggesting that they (Gerbillus pyramidum floweri and Gerbillus perpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillus floweri. Furthermore, the three other Gerbillus pyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest.
Highlights
DNA sequences have proven useful in taxonomic studies, and they represent a primary source of information when it comes to the delimitation of species (Wiens 2007)
A comparison of the results obtained using amplified PCR products from two DNA concentrations showed that the obtained sequences were identical in all but seven individuals, making us suspect the presence of nuclear copies of mitochondrial DNA (Numt)
The phylogenetic tree (Fig. 1) obtained using NJ presented here shows a similar topology to the Bayesian inference (BI) tree with our museum specimens distributed in four main clades
Summary
DNA sequences have proven useful in taxonomic studies, and they represent a primary source of information when it comes to the delimitation of species (Wiens 2007). For more than 25 years the recovery of DNA from ancient paleontological, archaeological and historic study specimens is routinely conducted (Pääbo 1989, Cooper 1994) The analysis of such DNA sequences has been instrumental in clarifying the systematics of extinct taxa, but it can be of help in modern taxa that are difficult to sample today. The primary concern is that the sequences obtained are usually of relatively small size, due to the degraded state of the DNA of museum specimens Given this limitation, the choice of the gene that will be targeted is of special concern: it has to be sufficiently variable to contain enough information, even in a small fragment, to allow distinguishing a particular species from its sister and other closely allied ones. Sequences as short as one hundred base pairs long have been shown to meet these requirements, for genes like cytochrome oxdydase 1 (CO1) in insects, or cytochrome b (cytb) in rodents (Hajibabaei et al 2006, Galan et al 2012)
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