Today's natural history museums are true treasure troves, not only for curious visitors, but also for molecular biologists. Many of the samples used for our projects come from museum collections and are associated with a wealth of additional information that was recorded at the time of collection. An invaluable source of information are the museum curators, who like to know the molecular-genetic characteristics of a given specimen. Since many of these are type specimens, which define a given species, it is of great interest to attach the DNA sequence for a given fossil or other specimen in order to facilitate the molecular-genetic classification and analysis of modern samples.
A large number of collections stored in natural history museums are now within reach of molecular genomic analysis. Our proposed analyses of type specimens might therefore open the door to an area we call "museomics" -- the large-scale analysis of the DNA content of museum collections.
Examples of the Scientific Questions to be Addressed
Genetic diversity as related to mammalian extinctions. A major goal is to learn how genetic diversity changes (if at all) as a species approaches extinction, which may well assist with conservation plans for endangered species. One approach would be to sample large percentages of global museum holdings for all recently extinct mammals for which adequate numbers of individuals across a reasonable timeframe (multiple decades at least) are available. (Note that approaching diversity through time with museum collections is especially powerful because samples are usually dated to the nearest year, and commonly to the exact date and month.) Species meeting these criteria include approximately five Australian marsupials, the Caribbean monk seal, Japanese sea lion, perhaps Steller's sea cow, two bat species, possibly the Falkland Islands wolf, and a handful of rodents. Pre-extinction patterns of diversity can be compared across unrelated mammals that have suffered global extinction. For example, is there any overwhelming shared signature of mtDNA diversity that precedes global extinction in a predictable manner across taxa? Or is this different for every species based on the unique conditions of its particular decline?
Documenting the spread of disease from invasive to native species. Dates of local (e.g. insular) or global extinction are known for many mammal species and populations with reasonable accuracy, as are dates of exotic introduction/invasion of certain species into novel landscapes. In some cases it is suspected that extinctions of native species have followed causally from introductions of certain invasive species (especially on islands) and that disease may be involved in some of these cases, but these types of claims generally remain anecdotal. The timing of the global decline of certain endemic insular rodent (and potentially other small mammal) lineages and the global spread of commensal rats offer many iterative, analogous cases for studying the spread of disease from invasive rats (with enormous global population sizes and greater exposure to a vast array of pathogens across time and geography) to comparatively "naive" and isolated endemic rodents with much smaller population sizes and less extensive historical exposure to disease. We predict that comparisons of metagenomes/bacteriomes/viromes sequenced from museum hair samples will be illuminating here.
A systematic study is needed to determine factors affecting the utility of museum specimens for molecular analysis. In our case, did analysis of one Smithsonian sample fail and another prove very successful (see the online supplement for our recent paper) because of differences in exposure to light over a long period? Experiments using comparatively expendable museum specimens with varying documented histories of preservation, storage, etc., are needed to inform museum personnel which sampling risks are more likely to pay off than others, and also how best to preserve both existing and newly acquired specimens for future molecular analysis. One component of such studies will be to determine which associations with microbial species result from particular preservation and/or storage histories, and which reflect the microbiome of the living animal. These studies, together with an inventory of global museum holdings, will set the stage for coordinated and appropriate use of museum specimens to deepen our understanding of evolution and the extinction process.