A comparative analysis of extraction protocol performance on degraded mammalian museum specimens

Hawkins, Melissa T. R.; Flores, Mary Faith C.; McGowen, Michael R.; Hinckley, Arlo

doi:10.3389/fevo.2022.984056

Cited by 10 publications

(11 citation statements)

References 32 publications

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“…Overall, these observations suggest that specimen preparation/storage by the collectors might have a greater impact on DNA quality than their age or the museum where they have been curated. These observations are in contrast with other studies that have statistically tested and found an effect of specimen age on DNA content or UCE recovery (Abreu et al, 2022; Hawkins et al, 2022).…”

Section: Resultscontrasting

confidence: 99%

“…Recent advances in high throughput sequencing in combination with natural history collection specimens provide a new, promising opportunity for the study of the IOK biogeographic transition (Hawkins et al, 2022; Lim et al, 2020; Mason et al, 2019; Patel et al, 2017). In this research, mitgenome evidence revealed deep phylogenetic breaks within each of our three study taxa across the IOK s.l .…”

Section: Discussionmentioning

confidence: 99%

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Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

Hinckley

Hawkins

Maldonado

et al. 2023

Journal of Biogeography

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Aim Understanding the biotic and abiotic mechanisms underlying the generation and maintenance of biogeographic transitions represent long‐standing topics in evolutionary biology. The Isthmus of Kra (IOK) divides Sundaland and Indochina and constitutes a poorly characterized terrestrial biogeographic transition. Here we looked at population genetic structure of three species that are distributed across the IOK to gain insights into the drivers that have shaped this transition and regional diversification patterns. Location Tropical east Asia: Sundaland and Indochina. Taxa Callosciurus caniceps, Tamiops mcclellandii, and Dremomys rufigenis‐ornatus species complex (Mammalia: Rodentia: Sciuridae). Methods We generated complete mitogenomes and sequences of 11 nuclear intron fragments from 61 and 67 museum specimen samples, respectively. We assessed population structure by constructing Maximum Likelihood mitogenome phylogenies (IQTREE2), and nuclear marker haplowebs and conspecificity matrices (HaplowebMaker and CoMa). We estimated divergence dates through Bayesian phylogenetic inference (BEAST2) and put these results in the context of climatic and geological history. Results High levels of mitochondrial and nuclear divergence were identified across the IOK in all three squirrels. Lineage turnover was consistent with the two major mammal species distribution transitions near the Kangar‐Pattani Line and at the juncture between the Thai‐Malay peninsula and the mainland. Divergence of mitochondrial lineages across Kra was estimated in the late Pliocene/ early Pleistocene for all three taxa. Older Miocene/Pliocene divergences were estimated within Indochina in D. rufigenis‐ornatus and T. mcclellandii, which were paraphyletic. Main Conclusions Sundaic and Indochinese populations have possibly diverged in allopatric habitat refugia in or around mountains during periods of increased aridity and evergreen forest contraction. Ecological differences and/or topography might have influenced genetic differentiation during periods of rainforest expansion. Alternative hypotheses remain to be tested with more informative nuclear markers and additional geographic sampling.

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Section: Resultscontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

Hinckley

Hawkins

Maldonado

et al. 2023

Journal of Biogeography

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“…obs. and, e.g., Hawkins et al, 2022;McDonough et al, 2018). The extraction buffer was freshly prepared to contain 150 μL Tris-HCL (20 mM), 150 μL NaCl (20 mM), 3 mg of SDS, 12 μL DTT (1 M) and 20 μL proteinase K (600 mAU/ml) per sample.…”

Section: Molecular Analysis and Genome Assemblymentioning

confidence: 99%

“…Museum collections are the most important archives of biodiversity on Earth and are used increasingly for various studies, including identification (Wannell et al, 2020), phylogenetics (Hawkins et al, 2016; Kehlmaier et al, 2020), population genomics (Castañeda‐Rico et al, 2022; Fry et al, 2020), conservation (Feigin et al, 2017; Jensen et al, 2022), biogeography (Irestedt et al, 2006; Lynch Alfaro et al, 2012; Pedersen et al, 2016), and ecology (Muff et al, 2023; Orlando & Cooper, 2014). However, molecular analysis of old museum material remains challenging because the historical DNA (the term coined by Raxworthy and Smith (2021) and adopted throughout this study) has degraded, is fragmented, and is of low quantity (Hagelberg et al, 2015; Hawkins et al, 2022). Nevertheless, there is a growing number of studies that have successfully used whole genome or target‐capture sequencing methods for acquiring complete (mitochondrial) genomes from museum material (e.g., Li et al, 2015; Straube, Lyra, et al, 2021), including of formalin‐preserved specimens (Hahn et al, 2022; Hykin et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

From historical expedition diaries to whole genome sequencing: A case study of the likely extinct Red Sea torpedo ray

Palandačić,

Kapun,

Greve

et al. 2023

Zoologica Scripta

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Torpedo rays (Torpedinidae, Torpediniformes) are small to moderately large batoids that produce an electric discharge. They are distributed worldwide in temperate and tropical seas and are, as a result of their bottom‐dwelling behaviour, susceptible to trawl fishing and often end up as victims of bycatch. The distribution ranges of most recognized species seem to be restricted; however, their species‐level systematics is not adequately resolved. In the genus Torpedo, in which many species require revision, there are possibly several undescribed species, while numerous misidentifications add to the complexity of the issue. In the latest lists of living rays, 13 species are accepted in the genus Torpedo, including three of doubtful validity and several recently discovered undescribed species. Among the valid species is the critically endangered, possibly extinct, Torpedo suessii Steindachner, 1898, the Red Sea torpedo, of which only four specimens have been recorded in the literature until now, three of which still exist in the fish collection of the Natural History Museum of Vienna. Museum collections are the most important archive of biodiversity on Earth, and are increasingly being used for various studies, including phylogenetics, population genomics, and biogeography. Nevertheless, molecular analysis of old museum material remains challenging because the genetic material has degraded, is fragmented, and of low quantity. In molecular taxonomy, the necessity of including type specimens as name‐bearing specimens is increasingly recognized. Here, the extended specimen approach was applied to re‐describe the lectotype of T. suessii. The approach included research of historical information and whole genome sequencing, followed by genome assembly and phylogenetic analysis.

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“…Thus far, the majority of research investigating how to maximize the recovery of genetic data from non-ancient museum specimens has focused on the influence of DNA source or extraction method on DNA yield (Hahn et al, 2022; Hawkins, Flores, McGowen, & Hinckley, 2022; McDonough et al, 2018; Pacheco et al, 2022; Straube et al, 2021; Tsai et al, 2020; Zacho et al, 2021). However, DNA yield does not necessarily predict sequencing success or efficiency (McDonough et al, 2018; Straube et al, 2021; Zacho et al, 2021) because it is not possible to estimate the proportions of endogenous versus exogenous extracted DNA.…”

Section: Introductionmentioning

confidence: 99%

Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens

Settlecowski

Marks

Manthey

2023

Preprint

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Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA source. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: 1) double-stranded, single tube (KAPA); 2) single-stranded, multi-tube (IDT); and 3) single-stranded, single-tube (Claret Bioscience). We found that the multi-tube ssDNA method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.

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A comparative analysis of extraction protocol performance on degraded mammalian museum specimens

Cited by 10 publications

References 32 publications

Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

From historical expedition diaries to whole genome sequencing: A case study of the likely extinct Red Sea torpedo ray

Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens

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