Extraction of nuclear DNA from bone of skeletonized and fluid‐preserved museum specimens

Stuart, Bryan L.; Dugan, Kerri A.; Allard, Marc W.; Kearney, Maureen

doi:10.1017/s1477200005001891

Cited by 24 publications

(18 citation statements)

References 32 publications

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“…DNA extraction and PCR amplification from formalin-fixed specimens, however, is particularly difficult [50,54]. Formalin storage can cause frequent nucleotide misincorporations [50,55].…”

Section: Fluid Specimensmentioning

confidence: 99%

“…Estimates so far range from 17% to 21% of sequences that show one or more errors [15,53]. Special cases are formalin-preserved specimens, in which sequence alterations can occur at even higher frequencies [50,54,55]. Misincorporations might look like new alleles or new sequences and can therefore lead to systematic overestimation of the genetic diversity of past populations [53].…”

Section: Reviewmentioning

confidence: 99%

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Back to the future: museum specimens in population genetics

Wandeler

Hoeck

Keller

2007

Trends in Ecology & Evolution

529

513

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Museums and other natural history collections (NHC) worldwide house millions of specimens. With the advent of molecular genetic approaches these collections have become the source of many fascinating population studies in conservation genetics that contrast historical with present-day genetic diversity. Recent developments in molecular genetics and genomics and the associated statistical tools have opened up the further possibility of studying evolutionary change directly. As we discuss here, we believe that NHC specimens provide a largely underutilized resource for such investigations. However, because DNA extracted from NHC samples is degraded, analyses of such samples are technically demanding and many potential pitfalls exist. Thus, we propose a set of guidelines that outline the steps necessary to begin genetic investigations using specimens from NHC. Museums and other natural history collections (NHC) worldwide house millions of specimens. With the advent of molecular genetic approaches these collections have become the source of many fascinating population studies in conservation genetics that contrast historical with present-day genetic diversity. Recent developments in molecular genetics and genomics and the associated statistical tools have opened up the further possibility of studying evolutionary change directly. As we discuss here, we believe that NHC specimens provide a largely underutilized resource for such investigations. However, because DNA extracted from NHC samples is degraded, analyses of such samples are technically demanding and many potential pitfalls exist. Thus, we propose a set of guidelines that outline the steps necessary to begin genetic investigations using specimens from NHC. IntroductionGiven that evolution is change over time, documenting and understanding temporal patterns has long been at the heart of evolutionary studies. In disciplines such as palaeontology, inferences about evolutionary processes are drawn from the analyses of temporal patterns in the fossil record. Similarly, our understanding of microevolutionary processes (i.e. changes in gene frequencies over time) has often involved the analyses of records taken over several years; Dobzhanksy's [1] early studies of microevolution among Drosophila used this approach, a tradition that continues among students of this model organism today [2]. However, such microevolutionary studies were often limited to certain taxa and questions because the time available to document temporal changes was often limited to a few generations. How can these limitations be overcome? Long term studies, running over several decades, are one possibility and they are yielding fascinating insights, for example, into the role of reinforcement and character displacement in adaptive radiation and speciation [3,4]. Another approach, which gives longer time series, is to extend the data back in time using well preserved fossil samples or specimens from natural history collections (NHC). Here, we review the use of specimens from NHC for the ...

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“…DNA extraction and PCR amplification from formalin-fixed specimens, however, is particularly difficult [50,54]. Formalin storage can cause frequent nucleotide misincorporations [50,55].…”

Section: Fluid Specimensmentioning

confidence: 99%

Section: Reviewmentioning

confidence: 99%

Back to the future: museum specimens in population genetics

Wandeler

Hoeck

Keller

2007

Trends in Ecology & Evolution

529

513

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“…The added value of museum specimens becomes even more important when considering morphological groups with 'fuzzy' species delimitations (e.g. species complexes), and extinct or very elusive taxa (Chakraborty et al 2006;Stuart et al 2006;Wandeler et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Garrigos

Hugueny²,

Koerner³

et al. 2013

Zootaxa

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Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphologybased taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in-and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as on...

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“…As a result, many previous identifications of old samples appear questionable-at least in some groups-and their value for science becomes limited (Graham et al 2004). Advances in molecular techniques allow DNA extraction from rather old samples (Stuart et al 2006;Wandeler et al 2007), but only if the latter were preserved properly. This is usually not the case with old crustacean samples; to our knowledge DNA extraction has been unsuccessful in many such cases (authors' experience; pers.…”

Section: Introductionmentioning

confidence: 99%

Old museum samples and recent taxonomy: A taxonomic, biogeographic and conservation perspective of the Niphargus tatrensis species complex (Crustacea: Amphipoda)

Coleman

Zagmajster

Zwittnig³

et al. 2010

Org Divers Evol

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Natural history museum collections harbour valuable information on species. The usefulness of such data critically depends on the accurate identification of species, which has been challenged by introduction of molecular techniques into taxonomy. However, most collections may suffer from DNA degradation, due to age and/or improper preservation; hence the identification of specimens depends solely on morphological features. This study explores how and to what extent morphological data can help to solve ambiguous taxonomic cases based on selected species concepts and with the use of operational criteria in a species-hypothesis testing procedure. The studied taxon, the Niphargus tatrensis species complex, comprises freshwater subterranean amphipods, distributed across Central Europe, the taxonomic status of which was debated extensively between 1930 and 1960. Using the general species concept, character-and tree-based operational criteria reveal northern and southern diagnosable and exclusive lineages identified here as N. tatrensis Wrześniowski, 1888 and N. scopicauda sp. n., respectively. The remaining populations represent the non-exclusive N. aggtelekiensis Dudich, 1932, which occurs from the eastern Alps to Hungary. In the entire complex, altitudinal distribution is largely limited to areas above 400 m, where the mean annual temperature never exceeds 9°C. Seemingly well-defined distributional ranges of N. tatrensis and N. aggtelekiensis are fragmented in an ecological sense, which raises the question whether two of the three species recognised here actually consist of several unidentified taxa. Morphological similarity between the species, numerous polymorphic features, and the association with cool temperatures lead to a hypothesis in which fragmentation of the ancestral range occurred during post-Pleistocene climate warming, reducing gene flow across lowland populations due to niche conservatism of the ancestral species and/or to invasion of competitive species along the Danube and Drava rivers. The results are discussed regarding how old museum samples are conducive to more detailed moleculartaxonomic and conservation studies.

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Extraction of nuclear DNA from bone of skeletonized and fluid‐preserved museum specimens

Cited by 24 publications

References 32 publications

Back to the future: museum specimens in population genetics

Back to the future: museum specimens in population genetics

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus <i>Orestias</i> (Teleostei: Cyprinodontidae)

Old museum samples and recent taxonomy: A taxonomic, biogeographic and conservation perspective of the Niphargus tatrensis species complex (Crustacea: Amphipoda)

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