Suitability of DNA extracted from archival specimens of fruit-eating bats of the genus Artibeus (Chiroptera, Phyllostomidae) for polymerase chain reaction and sequencing analysis

Unlocking inaccessible historical genomes preserved in formalin

Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.

Detection of two morphologically cryptic species from the cursor complex (Akodon spp; Rodentia, Cricetidae) through the use of RAPD markers

The cursor complex is a group within the Akodon genus of South American rodents, formed by Akodon cursor and A. montensis. Correct distinction between these two species is of great importance since they can harbor different Hantavirus strains. These species are only distinguishable by means of karyotypic or internal anatomic features, requiring dissection; recently, some other genetic methods have become available. We developed RAPD markers capable of distinguishing between A. cursor and A. montensis. Samples included 42 individuals of A. cursor from four localities and 16 individuals of A. montensis from two localities. Fifty-five bands, 41 of which were polymorphic, were analyzed. A principal component analysis showed that this set of markers could successfully distinguish between the two species, mainly based on three RAPD bands. The number of bands in each population was compared within a 95% confidence interval as a measure of intraspecific variability. The A. cursor populations were found to have marked genetic structure across the study area (AMOVA; F(ST )= 0.21), which in part might be because of the relatively limited dispersal capabilities of this species. Species-specific bands, with potential for species identification, were identified.