Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene

Schmitt, Charlotte; Cook, Joseph A.; Zamudio, Kelly R.; Edwards, Scott V.

doi:10.1098/rstb.2017.0387

Cited by 83 publications

(68 citation statements)

References 140 publications

(189 reference statements)

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“…Given our results of widespread CMTV-like genomic fragments in wild FV3-like genomes, we speculate that either CMTV-like viruses were brought to North America as a consequence of the commercial pet trade since the intensification of global commercial trade in the past 50 years (32) or CMTV-like ranaviruses have leaked from ranaculture facilities in recent years. To test these hypotheses, we suggest testing museum specimens for Ranavirus to identify when the spread of ranaviruses started and which lineages were present in North America (33). A similar approach was used for Batrachochytrium dendrobatidis and confirmed B. dendrobatidis-positive amphibians in historic samples collected as early as 1888 in the United States (34).…”

Section: Discussionmentioning

confidence: 99%

Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada

Vilaça

Bienentreu

Brunetti

et al. 2019

J Virol

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Ranaviruses are pathogens associated with the decline of amphibian populations across much of their distribution. In North America, frog virus 3 (FV3) is a widely distributed pathogen with wild populations of amphibians harboring different lineages and putative recombinants between FV3 and common midwife toad virus (CMTV). These recombinants have higher pathogenicity, and CMTV-derived genes associated with virulence are reported in wild strains in Canada. However, while FV3 is linked to amphibian die-offs in North America, CMTVs have been reported only in commercial frog farms in North America. We sequenced complete genomes of 18 FV3 isolates from three amphibian species to characterize genetic diversity of the lineages in Canada and infer possible recombinant regions. The 18 FV3 isolates displayed different signals of recombination, varying from none to interspersed recombination with previously isolated CMTV-like viruses. In general, most recombination breakpoints were located within open reading frames (ORFs), generating new ORFs and proteins that were a mixture between FV3 and CMTV. A combined spatial and temporal phylogeny suggests the presence of the FV3 lineage in Canada is relatively contemporary (<100 years), corroborating the hypothesis that both CMTV- and FV3-like viruses spread to North America when the international commercial amphibian trade started. Our results highlight the importance of pathogen surveillance and viral dynamics using full genomes to more clearly understand the mechanisms of disease origin and spread. IMPORTANCE Amphibian populations are declining worldwide, and these declines have been linked to a number of anthropogenic factors, including disease. Among the pathogens associated with amphibian mortality, ranaviruses have caused massive die-offs across continents. In North America, frog virus 3 (FV3) is a widespread ranavirus that can infect wild and captive amphibians. In this study, we sequenced full FV3 genomes isolated from frogs in Canada. We report widespread recombination between FV3 and common midwife toad virus (CMTV). Phylogenies indicate a recent origin for FV3 in Canada, possibly as a result of international amphibian trade.

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Section: Discussionmentioning

confidence: 99%

Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada

Vilaça

Bienentreu

Brunetti

et al. 2019

J Virol

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“…Historical museum specimens have been used to explore various population genetics and evolutionary questions in both vertebrates (Palkovacs et al ., ; Austin & Melville, ; Schmitt et al ., ) and insects (Goldstein & Desalle, ; Harper et al ., ; Habel et al ., ; Saarinen & Daniels, ; Keyghobadi et al ., ; Heintzman et al ., ). Vertebrate specimens are often large in size when compared with invertebrates, and therefore tissues are relatively abundant, so getting sufficient tissue for analysis has generally not been an issue, but the quality of the DNA can be dependent on preservation technique (Bouzat et al ., ; Iudica et al ., ).…”

Section: Introductionmentioning

confidence: 99%

How old can we go? Evaluating the age limit for effective DNA recovery from historical insect specimens

Lalonde

Marcus

2019

Systematic Entomology

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Historical museum specimens are valuable for exploring population genetics and evolutionary questions because they can provide snapshots of morphological and genetic characteristics from populations over space and time. Unfortunately, DNA found in older museum specimens is frequently degraded, so obtaining genotypes from many individual samples necessary for rigorous molecular population genetic studies is challenging. Previous studies have varied greatly in their success at obtaining genotypes from older preserved insect material. Many well-intentioned collection curators have used research results showing poor preservation of DNA preserved in museum specimens to inform curatorial best practices, in some cases choosing not to allow DNA extraction by destructive sampling because, in their estimation, the likelihood of success would be low. Recent methodological advances in DNA extraction, amplification, and genotyping have allowed some researchers to include mid-19th century samples in molecular genetic analyses. Here we present a robust, high-throughput, and low-cost DNA extraction and genotyping protocol for historical insect specimens employing restriction digests of PCR products followed by high sensitivity electrophoresis. Using this technique, we obtained mitochondrial haplotypes for 100% of 48 New World Junonia butterfly specimens (Nymphalidae) ranging in age from pre-1813 to 1909 and show that the haplotype frequencies obtained are statistically indistinguishable from 20th-century and contemporary reference populations of Junonia (1632 specimens) matched by geographic region. As most extant insect specimens were collected after 1813, based on our findings we would expect that many or even most pinned specimens preserved in museum collections contain usable DNA for mitochondrial haplotyping.

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“…Species' occurrence data is important in many research fields, including systematics, biogeography, ecology, and global change biology. The power of museum collections, however, surprisingly remains largely untapped for study areas beyond systematics; they are just now being recognised for the possibilities they hold for long-term studies (e.g., Meineke et al 2018;Schmitt et al 2018). As always, accurate data garnered from real specimens are crucial to this venture.…”

Section: Discussionmentioning

confidence: 99%

Historical distribution data of New Zealand endemic families Callaeidae and Notiomystidae (Aves, Passeriformes)

Salvador¹,

Tomotani²,

Miskelly³

et al. 2019

CheckList

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Callaeidae (wattlebirds) and Notiomystidae (stitchbirds) are New Zealand-endemic sister-taxa; while widespread before human settlement, they subsequently became critically endangered or extinct. Aside from presently managed populations, information about them is scarce and actual specimens even scarcer. Herein, we provide a snapshot of these families’ historical distribution during the critical periods of European settlement and expansion in New Zealand (19th and early-20th centuries), exploring new data and insights resulting from this approach. We include an extensive catalogue of worldwide museum specimens to facilitate future research. We report the last known record/specimen of huia Heteralocha acutirostris (Gould, 1837) and late 19th century specimens of North Island saddleback Philesturnus rufusater (Lesson, 1828) from Cuvier Island that confirm its occurrence there. We failed to find specimens of North Island saddleback and stitchbird Notiomystis cincta (du Bus de Gisignies, 1839) (with one and two exceptions, respectively) from named locations on the mainland.

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Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene

Cited by 83 publications

References 140 publications

Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada

Frog Virus 3 Genomes Reveal Prevalent Recombination between Ranavirus Lineages and Their Origins in Canada

How old can we go? Evaluating the age limit for effective DNA recovery from historical insect specimens

Historical distribution data of New Zealand endemic families Callaeidae and Notiomystidae (Aves, Passeriformes)

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