Mining museums for historical DNA: advances and challenges in museomics

Raxworthy, Christopher J.; Smith, Brian Tilston

doi:10.1016/j.tree.2021.07.009

Cited by 170 publications

(132 citation statements)

References 116 publications

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“…The ease of data collection will allow researchers to merge historical and contemporary datasets, providing more thorough analyses. This study joins many others demonstrating the key role of museums as repositories for key biological data [35][36][37].…”

Section: Ammophila Species Mean Prey Provisioned Per Offspring Sourcessupporting

confidence: 79%

A double-edged sword: parental care increases risk of offspring infection by a maternally vectored parasite

Millena

Rosenheim

2022

Biol. Lett.

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Parental care can protect offspring from predators but can also create opportunities for parents to vector parasites to their offspring. We hypothesized that the risk of infection by maternally vectored parasites would increase with the frequency of mother–offspring contact. Ammophila spp. wasps (Hymenoptera: Sphecidae) build nests in which they rear a single offspring. Ammophila species exhibit varied offspring provisioning behaviours: some species enter the nest once to provision a single, large caterpillar, whereas others enter the nest repeatedly to provision with many smaller caterpillars. We hypothesized that each nest visit increases the risk of offspring parasitism by Paraxenos lugubris (Strepsiptera: Xenidae), whose infectious stages ride on the mother wasp (phoresy) to reach the vulnerable Ammophila offspring. We quantified parasitism risk by external examination of museum-curated Ammophila specimens—the anterior portion of P. lugubris protrudes between the adult host's abdominal sclerites and reflects infection during the larval stage. As predicted, Ammophila species that receive larger numbers of provisions incur greater risks of parasitism, with nest provisioning behaviour explaining ca 90% of the interspecific variation in mean parasitism. These findings demonstrate that parental care can augment, rather than reduce, the risk of parasite transmission to offspring.

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Section: Ammophila Species Mean Prey Provisioned Per Offspring Sourcessupporting

confidence: 79%

A double-edged sword: parental care increases risk of offspring infection by a maternally vectored parasite

Millena

Rosenheim

2022

Biol. Lett.

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“…The reference genomes generated from tissue sequencing of collected samples will facilitate the shotgun sequencing of museum voucher specimens, thereby unlocking the vast genomic information preserved in the historical collections in Colombia’s zoos, museums, and universities ( 24 , 25 ). This is already taking place through the Andean Bear Project, and technological advances mean that many museum specimens may be of suitable quality for WGS ( 26 ).…”

Section: Ebp-colombia’s Contributions To the Nbsmentioning

confidence: 99%

“…This is already taking place through the Andean Bear Project, and technological advances mean that many museum specimens may be of suitable quality for WGS ( 26 ). Colombia’s extensive natural history collections can then provide valuable historical baselines for species genomics and comparisons with current populations ( 25 ).…”

Section: Ebp-colombia’s Contributions To the Nbsmentioning

confidence: 99%

EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development

Huddart

Crawford

Luna-Tapia³

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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The 2016 Peace Agreement has increased access to Colombia’s unique ecosystems, which remain understudied and increasingly under threat. The Colombian government has recently announced its National Bioeconomic Strategy (NBS), founded on the sustainable characterization, management, and conservation of the nation's biodiversity as a means to achieve sustainability and peace. Molecular tools will accelerate such endeavors, but capacity remains limited in Colombia. The Earth Biogenome Project's (EBP) objective is to characterize the genomes of all eukaryotic life on Earth through networks of partner institutions focused on sequencing either specific taxa or eukaryotic communities at regional or national scales. Colombia’s immense biodiversity and emerging network of stakeholders have inspired the creation of the national partnership “EBP-Colombia.” Here, we discuss how this Colombian-driven collaboration between government, academia, and the private sector is integrating research with sustainable, environmentally focused strategies to develop Colombia’s postconflict bioeconomy and conserve biological and cultural diversity. EBP-Colombia will accelerate the uptake of technology and promote partnership and exchange of knowledge among Colombian stakeholders and the EBP’s global network of experts; assist with conservation strategies to preserve Colombia’s vast biological wealth; and promote innovative approaches among public and private institutions in sectors such as agriculture, tourism, recycling, and medicine. EBP-Colombia can thus support Colombia’s NBS with the objective of sustainable and inclusive development to address the many social, environmental, and economic challenges, including conflict, inequality, poverty, and low agricultural productivity, and so, offer an alternative model for economic development that similarly placed countries can adopt.

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“…Therefore, we employed methods that minimized damage to herbarium specimens and insect samples. Museomics, a framework created to enhance research by integrating, sharing, and generalizing various sources of biological information (e.g., DNA, proteins, metabolomes, and isotopes, including data derived from museum specimens) has been rapidly progressing as a field of study (Matsumae, 2018;Raxworthy & Smith, 2021;Schaefer et al, 2009). DNA analysis of museum tissues has allowed evaluation of the classification, phylogeny, distribution, genetic diversity, and past bottlenecks of various organisms Satoh et al, 2018;Waku et al, 2016).…”

Section: Identification Of Seed-feeding Flies Using Nucleotide Sequencesmentioning

confidence: 99%

Molecular identification of seed‐feeding flies dissected from herbarium specimens clarifies the 100‐year history of parasitism by Japanagromyza tokunagai in Japan

Yamashita

Ogura‐Tsujita

Nagata

et al. 2021

Ecological Research

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Insect pests, particularly seed‐feeding flies, can cause serious damage to the fruits of many wild orchid species. Evidence of fly damage has been observed in 55 orchid species, belonging to 25 genera, distributed throughout Japan. Although some authors suggested that the observed increase in fly damage to orchids in recent years is related to the introduction of exotic species, the timing and route of spread remain unclear. We examined herbarium specimens of seven orchid species, collected between 1923 and 2016, to collect coarctate pupae and empty puparia, with minimal damage to the specimens. Genomic DNA was then extracted from the insect tissue and species were identified using mitochondrial cytochrome oxidase subunit 1 barcode regions. Long amplicons (660 base pairs [bp]) were obtained from 45.2% of samples and short amplicons (162 bp) were obtained from 90.3% of samples. In total, 51 of 62 samples had nucleotide sequences homologous to Japanagromyza tokunagai, with specimens distributed across collection years and geographic locations. Therefore, the severe damage to Japanese orchids observed in recent years is not related to the recent introduction of an exotic species; it may be related to a rapid increase in a native species. This work highlights the value of herbaria as important resources for elucidating the history and distribution of parasitic insects.

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Mining museums for historical DNA: advances and challenges in museomics

Cited by 170 publications

References 116 publications

A double-edged sword: parental care increases risk of offspring infection by a maternally vectored parasite

A double-edged sword: parental care increases risk of offspring infection by a maternally vectored parasite

EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development

Molecular identification of seed‐feeding flies dissected from herbarium specimens clarifies the 100‐year history of parasitism by Japanagromyza tokunagai in Japan

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