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This exercise is intended to provide students with a real-world example of how museum specimens can provide additional context to challenges and considerations in the broader field of applied conservation genomics. After a brief introduction to the study system—the conservation status of Iberian lynx (Lynx pardinus)—students will be asked to review an open-access, peer-reviewed publication that features samples from varied museum, archaeological, and paleontological contexts. Through reading the guide and discussion questions, students will reflect upon study design, concepts, and challenges presented at the intersection between the fields of conservation genomics and museum-based studies. The exercise ends with students breaking down the research into the main components (e.g., research question, independent and dependent variables, hypotheses, predictions) to set a structure for critically reading other scientific studies or designing their own research question.
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Applications of Museum Collections and Genomics to Biodiversity Conservation
To address the challenges of sampling endangered or extinct species in the field, many studies have turned to historically underutilized sources of genetic material: natural history museums. Despite the fact that DNA from specimens collected decades or even hundreds of years ago is often fragmented and degraded, research has shown that historical DNA can still be used effectively to infer phylogenetic relationships and intra-specific patterns of population genetic structure. This synthesis aims to provide students and conservation practitioners with a solid understanding of the methodological strategies needed to apply genetic tools to natural history museum specimens. Specifically, we offer clear definitions and essential considerations for designing a conservation genomics project that includes both modern and historical samples. We recommend that instructors use this synthesis to introduce the foundational knowledge required for two companion exercises: “The Application of Conservation Museomics Approaches to the Protection of the Iberian Lynx (Lynx pardinus)” and “Designing a Conservation Genetics Project Incorporating DNA from Museum Specimens.”
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- PAR ID:
- 10648722
- Publisher / Repository:
- American Museum of Natural History
- Date Published:
- Journal Name:
- Lessons in Conservation
- Volume:
- 14
- ISSN:
- 1938-7024
- Page Range / eLocation ID:
- 108 to 148
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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This exercise is intended to provide students with a real-world example of how museum specimens can provide additional context to challenges and considerations in the broader field of applied conservation genomics. After a brief introduction to the study system—the conservation status of Iberian lynx (Lynx pardinus)—students will be asked to review an open-access, peer-reviewed publication that features samples from varied museum, archaeological, and paleontological contexts. Through reading the guide and discussion questions, students will reflect upon study design, concepts, and challenges presented at the intersection between the fields of conservation genomics and museum-based studies. The exercise ends with students breaking down the research into the main components (e.g., research question, independent and dependent variables, hypotheses, predictions) to set a structure for critically reading other scientific studies or designing their own research question.more » « less
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null (Ed.)Species that went extinct prior to the genomic era are typically out-of-reach for modern phylogenetic studies. We refer to these as “Alexandrian” extinctions, after the lost library of the ancient world. This is particularly limiting for conservation studies, as genetic data for such taxa may be key to understand extinction threats and risks, the causes of declines, and inform management of related, extant populations. Fortunately, continual advances in biochemistry and DNA sequencing offer increasing ability to recover DNA from historical museum specimens, including fluid-preserved natural history collections. Here, we report on success in recovering nuclear and mitochondrial data from the apparently-extinct subspecies Desmognathus fuscus carri Neill, 1951, a plethodontid salamander from spring runs in central Florida. The two specimens are 50 years old and were likely preserved in unbuffered formalin, but application of a recently derived extraction procedure yielded usable DNA and partially successful Anchored Hybrid Enrichment sequencing. These data suggest that the populations of D. f. carri from peninsular Florida are conspecific with the D. auriculatus A lineage as suggested by previous authors, but likely represented an ecogeographically distinct genetic segment that has now been lost. Genetic data from this Alexandrian extinction thus confirm the geographic extent of population declines and extirpations as well as their ecological context, suggesting a possibly disproportionate loss from sandy-bottom clearwater streams compared to blackwater swamps. Success of these methods bodes well for large-scale application to fluid-preserved natural history specimens from relevant historical populations, but the possibility of significant DNA damage and related sequencing errors in additional hurdle to overcome.more » « less
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ABSTRACT Biodiversity is facing global change at an unprecedented rate. Understanding how populations have responded to accelerated change over the last century is key to informing effective conservation policies. Serially collected specimens from natural history repositories can provide a window into how populations change over time and highlight further vulnerabilities in remaining populations. Changes in observed population abundance during field surveys suggest that somePlethodonsalamander populations experienced declines since the 1960s, but the potential population genetic consequences of these declines remain unstudied. Thanks to decades of sustained collection‐based efforts,Plethodonsalamanders serve as a model to test the utility of historical DNA to identify shifts in genetic diversity at recent time scales. Here, we investigate demographic change in sixPlethodonspecies through time using DNA from formalin‐fixed museum specimens (1960s–1970s), historic frozen blood (1980s–1990s), and contemporary sampling. We generated several reduced representation SNP datasets using a target‐capture approach to investigate two sites in the Appalachian Range: one with documented declines (Indian Grave Gap) and one without (Skull's Gap). We quantify the impact of bioinformatic choices on estimates of genetic diversity, quantify demographic shifts, and trace changes in allele frequencies in immune‐related loci to explore the potential impact of pathogens on putative declines. We found consistent patterns of genetic diversity change across datasets and filtering regimes. At Skull's Gap, our results suggest that populations were stable or expanding, while at Indian Grave Gap, our results suggest contraction in one species and mixed signals of contraction and expansion in the others. Analyses of immune loci suggest that balancing selection is maintaining shared polymorphism through time in all but one species. Our study outlines important considerations for leveraging historical DNA in time series collections to quantify the genomic effects of localized population declines.more » « less
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NA (Ed.)We used isotopic and genomic data to explore the ecological and social context of cultural practices associated with the mummification of crocodiles in ancient Egypt. Ancient DNA was recovered from four mummified crocodile hatchlings held in the collections of the Peabody Museum of Natural History, Yale University. Previous genetic analyses of crocodile mummies have indicated that most mummies represent the newly resurrected taxon, Crocodylus suchus Geoffroy Saint-Hilaire, 1807. However, mitogenomic data for the Yale Peabody Museum mum- mies indicates that these specimens represent the first genomically authenticated represen- tatives of the Nile crocodile (Crocodylus niloticus Laurenti, 1768) in museum collections. We explore these findings within the broader context of modern and historical distributions of both crocodile species and the potential implications for our understanding of funerary practices involving crocodiles in ancient Egypt.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript
- Journal Article:
- https://doi.org/10.5531/cbc.linc.14.1.7
