Potential and challenges of DNA analysis in Natural History Collections

Abstract

Natural History Collections (NHC) serve as repositories of a wide range of specimens that are valuable resources for genetic studies. These specimens, housed in natural history museums, herbaria, or research institutes, can be accessed physically or, increasingly, online, due to current digitization efforts. They provide insights into past populations unaffected by recent anthropogenic and climatic changes, as well as those that have become extinct. However, the DNA extracted from NHC specimens is often degraded and susceptible to contamination, posing challenges for genetic analysis. PCR-based approaches can be used to amplify short mitochondrial DNA sequences, allowing for rapid species identification. However, studying nuclear loci using PCR can be costly and time-consuming due to the need for multiple amplifications. The advent of High-throughput sequencing (HTS) has brought a revolution in NHC-DNA research enabling the sequencing of degraded DNA at a more affordable cost. Different methods, such as whole genome sequencing, sequence capture, and restriction digest, have been employed in HTS studies. Whole genome sequencing provides nuclear and mitochondrial sequences but requires a large amount of high-quality DNA. Reduced genome representation methods, such as sequence capture and restriction digest, help reduce sequencing costs but have technical challenges and limitations. Despite the advantages of HTS, NHC-DNA studies face constraints such as incomplete records and the potential for harm to specimens during DNA extraction. NHC specimens should be preserved for future research, and scientists must carefully balance the benefits of genetic analysis with the conservation of these irreplaceable resources.