Preservation-Induced Morphological Change in Salamanders and Failed DNA Extraction from a Decades-Old Museum Specimen: Implications for Plethodon ainsworthi

Pierson, Todd W.; Kieran, Troy J.; Clause, Adam G.; Castleberry, Nikole L.

doi:10.1670/19-012

Cited by 17 publications

(21 citation statements)

References 31 publications

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“…Preservation is known to alter morphology in amphibians (e.g., Pierson et al 2020). However, a previous study found little difference in anuran evolutionary eye-body allometry based on fresh vs. preserved specimens and found similar patterns of eye scaling compared to SVL or wet mass (Thomas et al 2020).…”

Section: Morphological Measurementsmentioning

confidence: 99%

Eye‐body allometry across biphasic ontogeny in anuran amphibians

et al. 2021

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Animals with biphasic lifecycles often inhabit different visual environments across ontogeny. Many frogs and toads (Amphibia: Anura) have free-living aquatic larvae (tadpoles) that metamorphose into adults that inhabit a range of aquatic and terrestrial environments. Ecological differences influence eye size across species, but these relationships have not yet been explored across life stages in an ontogenetic allometric context. We examined eye-body size scaling in a species with aquatic larvae and terrestrial adults, the common frog Rana temporaria, using a well-sampled developmental series. We found a shift in ontogenetic allometric trajectory near metamorphosis indicating prioritized growth in tadpole eyes. To explore the effects of different tadpole and adult ecologies on eye-body scaling, we expanded our taxonomic sampling to include developmental series of eleven additional anuran species. Intraspecific eye-body scaling was variable among species, with 8/12 species exhibiting a significant change in allometric slope between tadpoles and adults. Traits categorizing both tadpole ecology (microhabitat, eye position, mouth position) and adult ecology (habitat, activity pattern) across species had significant effects on allometric slopes among tadpoles, but only tadpole eye position had a significant effect among adults. Our study suggests that relative eye growth in the preliminary stages of biphasic anuran ontogenies is somewhat decoupled and may be shaped by both immediate ecological need (i.e. tadpole visual requirements) and what will be advantageous during later adult stages.

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Section: Morphological Measurementsmentioning

confidence: 99%

Eye‐body allometry across biphasic ontogeny in anuran amphibians

et al. 2021

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“…Head width (HW; maximum width of the head), snout–gular length (tip of snout to gular fold), snout–vent length (SVL; tip of snout to posterior margin of vent), axilla–groin (AG) or trunk length (distance between limbs), and tail length (posterior edge of vent to tail tip) were measured using 823 A. hardii , 452 A. aeneus , 358 A. ferreus , 426 A. flavipunctatus , and 363 A. lugubris specimens from the collections of the Museum of Vertebrate Zoology (MVZ), University of California at Berkeley, Field Museum of Natural History (FMNH), University of Michigan Museum of Zoology (UMMZ), the American Museum of Natural History (AMNH), and specimens from the personal collections of R. Highton, J. Beatty, and the author (NLS) (see Supplementary Appendix S1). Specimens were only used if they had been fixed and processed in the same way (fixed in 10% neutral buffered formalin, rinsed in water, stored in 70% ethanol) to avoid inconsistent distortion of morphology ( Pierson et al. 2020 ).…”

Section: Methodsmentioning

confidence: 99%

The Evolution of Derived Monomorphism From Sexual Dimorphism: A Case Study on Salamanders

Staub

2020

Integrative Organismal Biology

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While sexual dimorphism has long received special attention from biologists, derived monomorphism, the condition in which both males and females express similar derived features, has been less well studied. Historically, the appearance of “male-like” features in females has been explained by the genetic correlation between the sexes. Recent work emphasizes the importance of studying the independent selective forces on both females and males to understand sexual dimorphism. Sexual dimorphism and derived monomorphism in the genus Aneides are examined in light of predictions of social selection. Aneides hardii shows the greatest degree of sexual dimorphism in snout-vent length and head width, with the other species of Aneides less sexually dimorphic. This reduced dimorphism, however, is not a return to an ancestral monomorphic state, but rather exemplifies derived monomorphism because females express traits that were limited in expression to males of ancestral species. Instead of calling these “male-typical” traits in females, I suggest the term “derived monomorphic” traits, as these traits are typical in these females and “derived monomorphic” can apply to both sexes. Increased attention to studying the patterns and ecological significance of derived monomorphism will shed light on the underlying selective forces, including sexual selection, on both females and males.

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“…Another factor that may impact sample outcomes is the tissue type used for extractions. Studies seeking to extract DNA from formalin-fixed samples typically sample liver or muscle tissue (Hykin et al 2015, Ruane & Austin, 2017Pierson et al 2020). Hykin et al (2015) compared extraction success between these two tissue types and extracted higher yields from the liver replicates of Anolis lizard samples.…”

Section: Predictors Of Formalin-fixed Sample Successmentioning

confidence: 99%

“…Hykin et al (2015) compared extraction success between these two tissue types and extracted higher yields from the liver replicates of Anolis lizard samples. Ruane and Austin (2017) successfully extracted DNA from snake liver tissues, while Pierson et al (2020) were unable to extract suitable DNA for PCR or library preparation from salamander tail muscle. Here we compared success between muscle and liver replicates of specimen USNM 525133.…”

Section: Predictors Of Formalin-fixed Sample Successmentioning

confidence: 99%

“…Researchers have only just begun to apply this class of methods to fluid-preserved specimens that are formalin-or ethanol-fixed, often with mixed success (Hykin et al 2015;Ruane & Austin, 2017;Hedin et al 2018;McGuire et al 2018;Wood et al 2018;Derkarabetian et al 2019;Turvey et al 2019;Lyra et al 2020). Formalin damages DNA in several ways (Campos & Gilbert, 2012;Cook et al 2014), making the extraction and sequencing of genomic DNA from formalin-fixed specimens more challenging than other specimen preparation types (Stuart et al 2006;Pierson et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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The utility of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based SNP datasets

O’Connell¹,

Mulder

Wynn³

et al. 2021

Preprint

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Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from ten specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected 1985–1990: allozyme supernatants, allozyme homogenate pellets, and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated (RADseq) sequencing derived loci from seven of the specimens and assessed the success and consistency of capture and RADseq technical replicates. This study design enabled direct comparisons of data quality and potential biases among the different datasets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all replicates for a given specimen clustered together, but in principal component space, RADseq replicates did not cluster with corresponding capture-based replicates. SNP calls were on average 18.3% different between technical replicates, but these discrepancies were primarily due to differences in heterozygous/homozygous SNP calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

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Preservation-Induced Morphological Change in Salamanders and Failed DNA Extraction from a Decades-Old Museum Specimen: Implications for Plethodon ainsworthi

Cited by 17 publications

References 31 publications

Eye‐body allometry across biphasic ontogeny in anuran amphibians

Eye‐body allometry across biphasic ontogeny in anuran amphibians

The Evolution of Derived Monomorphism From Sexual Dimorphism: A Case Study on Salamanders

The utility of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based SNP datasets

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