Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity

Sefc, Kristina M.; Payne, Robert B.; Sorenson, Michael D.

doi:10.1007/s10592-006-9240-8

Cited by 38 publications

(43 citation statements)

References 34 publications

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“…C to T transitions are the main type of such alterations that occur when an erroneous DNA strand is replicated during the first cycle of a PCR. Initially thought to be limited to ancient DNA, nucleotide misincorporations have recently been reported in studies based on specimens from NHC [15,52,53]. Estimates so far range from 17% to 21% of sequences that show one or more errors [15,53].…”

Section: Reviewmentioning

confidence: 99%

“…Initially thought to be limited to ancient DNA, nucleotide misincorporations have recently been reported in studies based on specimens from NHC [15,52,53]. 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].…”

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

545

523

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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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Section: Reviewmentioning

confidence: 99%

Section: Reviewmentioning

confidence: 99%

Back to the future: museum specimens in population genetics

Wandeler

Hoeck

Keller

2007

Trends in Ecology & Evolution

545

523

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“…Our study highlights the importance of including historical DNA; however, caution should be taken when working with historical specimens as the degraded nature of the DNA not only hampers the successful amplification of the specimens (Sefc, Payne, & Sorenson, 2003; Sefc et al., 2007), but also renders it susceptible to genotyping discrepancies. Despite this, we recommend that future studies attempting to infer the demographic history of invasive species should incorporate native historical samples.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, the resulting PCR products for each multiplex were diluted with distilled water to obtain a 1/10 PCR product which, in turn, served as template in the subsequent PCR. To ensure amplification and to avoid the overestimation of genetic diversity often associated with the amplification of ancient‐ and formalin‐fixed DNA (Buchan, Archie, Van Horn, Moss, & Alberts, 2005; Sefc et al., 2007), historical samples were amplified twice for each microsatellite locus. All microsatellite genotyping was performed on an ABI 3730 XL DNA Analyzer (Applied Biosystems, CAF, Stellenbosch, South Africa), using LIZ as an internal size marker, and scoring was conducted in Geneious ® 10.0.2 (Biomatters, Auckland, New Zealand).…”

Section: Methodsmentioning

confidence: 99%

“…Historic DNA serves as a valuable reference when examining contemporary genetic diversity (Bouzat, 2000; Dormontt et al., 2014; Guinand, Scribner, & Page, 2003; Lozier & Cameron, 2009), as it allows for the monitoring of temporal changes in genetic diversity across generations (Guinand et al., 2003; Sefc, Payne, & Sorenson, 2007). This temporal approach increases the chance of detecting subtle changes frequently overlooked by studies focussing only on contemporary data (Lozier & Cameron, 2009) and thus allows us to delineate the most likely invasion scenario (Gillis et al., 2009; Thompson et al., 2011; Van Kleunen, Weber, & Fischer, 2010) and reveal connectivity levels among invasive populations (Beneteau, Walter, Mandrak, & Heath, 2012; Funk, Garcia, Cortina, & Hill, 2011; Snyder & Stepien, 2017).…”

Section: Introductionmentioning

confidence: 99%

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The ghost of introduction past: Spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Diedericks

Henriques

Heyden

et al. 2018

Evolutionary Applications

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Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three‐way comparison of the genetic diversity of native (historic and contemporary) and invasive (contemporary) smallmouth bass (Micropterus dolomieu) populations. Analyses of a total of 572 M. dolomieu samples, representing the contemporary invasive South African range, contemporary and historical native USA range (dating back to the 1930s when these fish were first introduced into South Africa), revealed that the historical native range had higher genetic diversity levels when compared to both contemporary native and invasive ranges. These results suggest that both contemporary populations experienced a recent genetic bottleneck. Furthermore, the invasive range displayed significant population structure, whereas both historical and contemporary native US populations revealed higher levels of admixture. Comparison of contemporary and historical samples showed both a historic introduction of M. dolomieu and a more recent introduction, thereby demonstrating that undocumented introductions of this species have occurred. Although multiple introductions might have contributed to the high levels of genetic diversity in the invaded range, we discuss alternative factors that may have been responsible for the elevated levels of genetic diversity and highlight the importance of incorporating historic specimens into demographic analyses.

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Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change

Kuhn

Schwenk

Both

et al. 2013

Ecology and Evolution

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Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.

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Single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity

Cited by 38 publications

References 34 publications

Back to the future: museum specimens in population genetics

Back to the future: museum specimens in population genetics

The ghost of introduction past: Spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change

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