Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops . Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount resultsmore »
Understanding “Alexandrian” extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders
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 more »
- Award ID(s):
- 1655737
- Publication Date:
- NSF-PAR ID:
- 10293916
- Journal Name:
- Conservation genetics
- ISSN:
- 1566-0621
- Sponsoring Org:
- National Science Foundation
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Natalie Cooper (Ed.)1. Historical datasets can establish a critical baseline of plant–animal interactions for understanding contemporary interactions in the context of global change. Pollen is often incidentally preserved on animals in natural history collections. Techniques for removing pollen from insects have largely been developed for fresh insect specimens or historical specimens with large amounts of pollen on specialized structures. However, many key pollinating insects do not have these specialized structures and thus, there is a need for a method to extract pollen from these small and fragile insects. 2. Here, we propose a precision glycerine jelly swab tool to allow for the precise removal of pollen from old, small and fragile insect specimens. We use this tool to remove pollen from five families of insects collected in the late 1970s. Additionally, we compare our method with four previously published techniques for removing pollen from pinned contemporary specimens. 3. We show the functionality of the precision glycerine jelly swab for removing small quantities of pollen across insect families. We found that across the five methods, all removed pollen; yet, it was clear that some are better suited for fragile specimens. In particular, the traditional glycerine jelly swab and the precision glycerine jelly swabsmore »
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Abstract Ancient DNA is transforming our ability to reconstruct historical patterns and mechanisms shaping modern diversity and distributions. In particular, molecular data from extinct Holocene island faunas have revealed surprising biogeographic scenarios. Here, we recovered partial mitochondrial (mt) genomes for 1300–1400 year old specimens ( n = 2) of the extinct “horned” crocodile, Voay robustus , collected from Holocene deposits in southwestern Madagascar. Phylogenetic analyses of partial mt genomes and tip-dated timetrees based on molecular, fossil, and stratigraphic data favor a sister group relationship between Voay and Crocodylus (true crocodiles). These well supported trees conflict with recent morphological systematic work that has consistently placed Voay within Osteolaeminae (dwarf crocodiles and kin) and provide evidence for likely homoplasy in crocodylian cranial anatomy and snout shape. The close relationship between Voay and Crocodylus lends additional context for understanding the biogeographic origins of these genera and refines competing hypotheses for the recent extinction of Voay from Madagascar.
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Accepted Manuscript1.0
- Publisher's Version of Record
- https://doi.org/10.21203/rs.3.rs-769753/v1
