scholarly journals Understanding “Alexandrian” extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders

2021 ◽  
Author(s):  
Alex Pyron ◽  
David A. Beamer ◽  
Chace R. Holzheuser ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Population Declines ◽  
Sandy Bottom ◽  
Sequencing Errors ◽  
Plethodontid Salamander ◽  
Anchored Hybrid Enrichment

Abstract 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.

scholarly journals Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

2018 ◽  
Author(s):  
Jimmy A McGuire ◽  
Darko D Cotoras ◽  
Brendan O'Connell ◽  
Shobi Z S Lawalata ◽  
Cynthia Y Wang-Claypool ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Base Pairs ◽  
Holotype Specimen ◽  
The Status ◽  
Taxonomic Problem ◽  
Low Coverage

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

scholarly journals Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4470 ◽  
Author(s):  
Jimmy A. McGuire ◽  
Darko D. Cotoras ◽  
Brendan O’Connell ◽  
Shobi Z.S. Lawalata ◽  
Cynthia Y. Wang-Claypool ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Base Pairs ◽  
Holotype Specimen ◽  
The Status ◽  
Taxonomic Problem ◽  
Low Coverage

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

scholarly journals Squeezing water from a stone: High-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

2018 ◽  
Author(s):  
Jimmy A McGuire ◽  
Darko D Cotoras ◽  
Brendan O'Connell ◽  
Shobi Z S Lawalata ◽  
Cynthia Y Wang-Claypool ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Extraction Procedure ◽  
Genetic Data ◽  
Museum Specimens ◽  
Base Pairs ◽  
Holotype Specimen ◽  
The Status ◽  
Taxonomic Problem ◽  
Low Coverage

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

scholarly journals Sex biases in bird and mammal natural history collections

2019 ◽  
Vol 286 (1913) ◽  
pp. 20192025 ◽  
Author(s):  
Natalie Cooper ◽  
Alexander L. Bond ◽  
Joshua L. Davis ◽  
Roberto Portela Miguez ◽  
Louise Tomsett ◽  
...  
Keyword(s):  
Body Size ◽  
Natural History ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Sex Ratios ◽  
Museum Specimens ◽  
Male Bias ◽  
Biological Sex ◽  
Natural History Collections ◽  
Sex Biases

Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.

scholarly journals Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

2019 ◽  
Vol 7 ◽  
Author(s):  
Brian Stucky ◽  
James Balhoff ◽  
Narayani Barve ◽  
Vijay Barve ◽  
Laura Brenskelle ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Use Cases ◽  
Data Systems ◽  
Multiple Sources ◽  
History Data ◽  
Insect Ecology ◽  
Many Sources ◽  
Multicellular Organisms ◽  
Initial Results

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

First description of the male of the linyphiid spider Disembolus  corneliae (Chamberlin & Ivie, 1944) (Araneae, Linyphiidae)

Zootaxa ◽  
2018 ◽  
Vol 4526 (3) ◽  
pp. 393
Author(s):  
MARC A. MILNE
Keyword(s):  
New Species ◽  
Natural History ◽  
Museum Specimens ◽  
American Museum ◽  
First Time

The erigonine linyphiid genus Disembolus currently contains 24 described species (World Spider Catalog 2018). Disembolus was erected by Chamberlin and Ivie (1933) to accommodate their new species D. stridulans Chamberlin and Ivie from Utah. Since then, 23 species have been added to the genus. Chamberlin (1949) described D. zygethus Chamberlin, but the majority of species were added to the genus by Millidge (1981). Millidge (1981) described 16 species from museum specimens at the American Museum of Natural History and transferred five species from the genera Tapinocyba and Soudinus (D. alpha (Chamberlin 1949), D. kesimbus (Chamberlin 1949), D. phanus (Chamberlin 1949), D. sacerdotalis (Crosby & Bishop 1933), and D. corneliae (Chamberlin & Ivie 1944)). The last species added to the genus was D. bairdi Edwards described by Edwards in 1999. Disembolus corneliae Chamberlin and Ivie was described from the female only by Chamberlin and Ivie (1944) as Soudinus corneliae. The species was then transferred to Disembolus by Millidge (1981). Herein, I describe the male of the species for the first time. 

scholarly journals Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data

2018 ◽  
Vol 12 (S5) ◽  
Author(s):  
María Gabriela Valdés ◽  
Iván Galván-Femenía ◽  
Vicent Ribas Ripoll ◽  
Xavier Duran ◽  
Jun Yokota ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Large Scale ◽  
Genetic Data ◽  
Chemotherapy Response ◽  
Lung Cancer Patients ◽  
Key Features ◽  
Pipeline Design

scholarly journals A 21st Century Vision for Neotropical Snake Systematics

2018 ◽  
Vol 1 (1) ◽  
pp. 58
Author(s):  
Robert Alexander Pyron
Keyword(s):  
Species Richness ◽  
Natural History ◽  
Global Change ◽  
South America ◽  
Ecosystem Function ◽  
Museum Specimens ◽  
Fine Grained ◽  
The Past ◽  
The Caribbean ◽  
Recent Synthesis

We live in an unprecedented age for systematics and biodiversity studies. Ongoing global change is leading to a future with reduced species richness and ecosystem function (Pereira, Navarro, & Martins, 2012). Yet, we know more about biodiversity now than at any time in the past. For squamates in particular, we have range maps for all species (Roll et al., 2017), phylogenies containing estimates for all species (Tonini, Beard, Ferreira, Jetz, & Pyron, 2016), and myriad ecological and natural-history datasets for a large percentage of species (Meiri et al., 2013; Mesquita et al., 2016). For neotropical snakes, a recent synthesis of museum specimens and verified localities offers a fine-grained perspective on their ecogeographic distribution in Central and South America, and the Caribbean (Guedes et al., 2018).

scholarly journals Revisiting Ophidiomycosis (Snake Fungal Disease) After a Decade of Targeted Research

2021 ◽  
Vol 8 ◽  
Author(s):  
Christina M. Davy ◽  
Leonard Shirose ◽  
Doug Campbell ◽  
Rachel Dillon ◽  
Christina McKenzie ◽  
...  
Keyword(s):  
Large Scale ◽  
Sublethal Effects ◽  
Clinical Signs ◽  
Fungal Disease ◽  
Host Susceptibility ◽  
Current Evidence ◽  
Molecular Testing ◽  
Population Declines ◽  
Snake Fungal Disease ◽  
Free Ranging

Emerging infectious diseases (EIDs) are typically characterized by novelty (recent detection) and by increasing incidence, distribution, and/or pathogenicity. Ophidiomycosis, also called snake fungal disease, is caused by the fungus Ophidiomyces ophidiicola (formerly “ophiodiicola”). Ophidiomycosis has been characterized as an EID and as a potential threat to populations of Nearctic snakes, sparking over a decade of targeted research. However, the severity of this threat is unclear. We reviewed the available literature to quantify incidence and effects of ophidiomycosis in Nearctic snakes, and to evaluate whether the evidence supports the ongoing characterization of ophidiomycosis as an EID. Data from Canada remain scarce, so we supplemented the literature review with surveys for O. ophidiicola in the Canadian Great Lakes region. Peer-reviewed reports of clinical signs consistent with ophidiomycosis in free-ranging, Nearctic snakes date back to at least 1998, and retrospective molecular testing of samples extend the earliest confirmed record to 1986. Diagnostic criteria varied among publications (n = 33), confounding quantitative comparisons. Ophidiomycosis was diagnosed or suspected in 36/121 captive snakes and was fatal in over half of cases (66.7%). This result may implicate captivity-related stress as a risk factor for mortality from ophidiomycosis, but could also reflect reporting bias (i.e., infections are more likely to be detected in captive snakes, and severe cases are more likely to be reported). In contrast, ophidiomycosis was diagnosed or suspected in 441/2,384 free-ranging snakes, with mortality observed in 43 (9.8 %). Ophidiomycosis was only speculatively linked to population declines, and we found no evidence that the prevalence of the pathogen or disease increased over the past decade of targeted research. Supplemental surveys and molecular (qPCR) testing in Ontario, Canada detected O. ophidiicola on 76 of 657 free-ranging snakes sampled across ~136,000 km2. The pathogen was detected at most sites despite limited and haphazard sampling. No large-scale mortality was observed. Current evidence supports previous suggestions that the pathogen is a widespread, previously unrecognized endemic, rather than a novel pathogen. Ophidiomycosis may not pose an imminent threat to Nearctic snakes, but further research should investigate potential sublethal effects of ophidiomycosis such as altered reproductive success that could impact population growth, and explore whether shifting environmental conditions may alter host susceptibility.

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