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

Abstract

To establish a technique which minimized the effects of fixation on the extraction of DNA from formalin-fixed tissues preserved in scientific collections we extracted DNA samples from fixed tissues using different methods and evaluated the effect of the different procedures on PCR and sequencing analysis. We investigated muscle and liver tissues from museum specimens of five species of fruit-eating (frugivorous) bats of the Neotropical genus Artibeus (Chiroptera, Phyllostomidae): A. fimbriatus, A. lituratus, A. jamaicensis, A. obscurus, and A. planirostris. The results indicated that treatment of tissues in buffered solutions at neutral pH and about 37°C for at least four days improves the quality and quantity of extracted DNA and the quality of the amplification and sequencing products. However, the comparison between the performance of DNA obtained from fixed and fresh tissues showed that, in spite of the fact that both types of tissue generate reliable sequences for use in phylogenetic analyses, DNA samples from fixed tissues presented a larger rate of errors in the different stages of the study. These results suggest that DNA extracted from formalin-fixed tissue can be used in molecular studies of Neotropical Artibeus bats and that our methodology may be applicable to other animal groups.

Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes

“…For museum specimens, the marker length often determines the amplification success (Martinkova & Searle 2006;Lee & Prys-Jones 2008) and that was also true for the evaluated Tephritid collections. The variable amplification success of the Teph658 marker for the relatively recent samples (collected after 2000) illustrates that the DNA quality obtained from museum specimens can vary substantially (Junqueira et al 2002;Mandrioli et al 2006;Scatena & Morielle-Versute 2008;Wandeler et al 2007). An experimental study on Drosophila simulans reports a significant reduction in the amplification success even in 2-year-old specimens, particularly for longer fragments (1332 and 1822 bp) (Dean & Ballard 2001).…”

Unlocking inaccessible historical genomes preserved in formalin

“…Of the few genetic studies of formalin‐fixed museum specimens, most have targeted nuclear (Bibi et al, 2015; Joshi et al,2013; Lutterschmidt et al, 2010; Palmer, 2009; Scatena & Morielle‐Versute, 2008; Shiozaki et al, 2021) and high copy mitochondrial (Appleyard et al, 2021; Boyle et al, 2004; Shedlock et al, 1997) loci via PCR amplification due to the difficulty and unpredictability of nuclear DNA extraction. There are few examples of broader‐scale genomic sequencing of formalin‐fixed museum specimens and none have recovered whole vertebrate genomes.…”

DNA extraction from formalin-fixed tissue: new light from the deep sea

“…In fact, many specimens prized for their morphological novelty have been kept in formalin for years (Thatje et al, 2008). Therefore, it becomes desirable to overcome barriers to molecular analysis caused by the traditional processes of preservation and considerable resources are being invested in obtaining DNA from formalin-fixed museum specimens (Scatena and Morielle-Versute, 2008;Santos et al, 2009).…”