DNA extraction and amplification methods for ephippial cases of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past

Ishida, Seiji; Ohtsuki, Hajime; Awano, Tamotsu; Tsugeki, Narumi K.; Makino, Wataru; Suyama, Yoshihisa; Urabe, Jotaro

doi:10.1007/s10201-012-0380-x

Cited by 18 publications

(19 citation statements)

References 33 publications

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“…Currently, the few contributions that included appendixes with photographs (Coronel et al, ; Brandão, ; Gerhard et al, ) helped to construct a list of 60 species identified for the region (Table ), improving future studies. Moreover, the use of molecular biological techniques, such as DNA extraction protocols, polymerase chain reaction (PCR), and ddRAD sequencing, might significantly improve our species identification capabilities (Hebert et al, ; Montero‐Pau et al, ; Ishida et al, , Peterson et al, ).…”

Section: Final Remarks/synthesismentioning

confidence: 99%

Current knowledge of South American cladoceran diapause: A brief review

Iglesias

Bonecker

Brandão

et al. 2016

Internat. Rev. Hydrobiol.

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The study of the structure and dynamics of cladoceran egg banks in South America began only 15 years ago and the amount of knowledge, in addition to being scarce, is widely spread over partially national journals, theses, and books, and thus partially unavailable. We conducted a review of the literature published for this region, focusing mainly on the methodological approaches that have been applied and describe the main findings already published. The different methodological approaches make data comparability difficult. However, a total of 77 egg morphotypes were identified in the published studies. Among the variety of methods used, we suggest to adopt as the standard procedure: 1) pre isolation of eggs from the sediments by the “Sugar Flotation Method;” 2) identification, enumeration, and sorting of egg morphotypes present in the sample; 3) individual hatching of each egg morphotype; 4) adult individual identification to the species level according to available keys; and 5) linking identified eggs to identified species’ adults. The absence of identification keys constitutes a challenge. Therefore, collaborative research with the aim of generating pictorial taxonomical support for Neotropical resting eggs are encouraged. We believe the adoption of the suggested protocol might facilitate this issue. An extremely low hatching success was reported for most studies and the factors triggering the break of dormancy in the resting eggs coming from permanent systems remain unknown. In conclusion, resting egg studies are a novel and promising field in South America, but with many challenges that need to be addressed.

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Section: Final Remarks/synthesismentioning

confidence: 99%

Current knowledge of South American cladoceran diapause: A brief review

Iglesias

Bonecker

Brandão

et al. 2016

Internat. Rev. Hydrobiol.

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“…Most daphniids are cyclical parthenogens with mainly asexual reproduction and a sexual phase, typically at the end of the growing season, that results in the production of sexual (dormant) eggs encased in a sclerotized structure (ephippium). Previous studies on Daphnia have utilized RE to infer adaptive responses to changes in ecological parameters (Cousyn et al., ; Decaestecker et al., ; Hairston et al., ; Weider, Lampert, Wessels, Colbourne, & Limburg, ) and to reconstruct population genetic profiles from resting eggs (Limburg & Weider, ; Mergeay, Vanoverbeke, Verschuren, & De Meester, ; Frisch et al., , 2017) or the ephippial casing (Ishida et al., ). Daphnia plays a pivotal role in lake ecosystems (Lehman, ), and the abundance of daphniids can control phytoplankton growth, not only via direct grazing but also indirectly via consumer‐driven nutrient recycling (Sterner, ), with important implications at the ecosystem level (Elser, Elser, MacKay, & Carpenter, ).…”

Section: Introductionmentioning

confidence: 99%

Whole genome amplification and sequencing of a Daphnia resting egg

Lack

Weider

Jeyasingh

2017

Molecular Ecology Resources

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“…Fortunately, whether empty or not, ephippial carapaces remain for a long time in lake sediments. Recently, we have developed methods for extracting and amplifying DNA from Daphnia ephippial carapaces [ 21 ]. These methods enabled us to reconstruct the genetic structure of past Daphnia populations without a large bias.…”

Section: Introductionmentioning

confidence: 99%

Historical Changes in the Ecosystem Condition of a Small Mountain Lake over the Past 60 Years as Revealed by Plankton Remains and Daphnia Ephippial Carapaces Stored in Lake Sediments

et al. 2015

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To examine if changes in species composition of a plankton community in the past due to anthropogenic activities can be clarified in lakes without any monitoring data, we analyzed genetically ephippial carapaces of Daphnia with plankton remains stored in the bottom sediments of Lake Hataya Ohunma in Japan. In the lake, abundance of most plankton remains in the sediments was limited and TP flux was at low levels (2–4 mg/m2/y) before 1970. However TP flux increased two-fold during the period from 1980s to 1990s. In parallel with this increase, abundance of most plankton remains increased although abundance of benthic testate amoebae’s remains decreased, indicating that the lake trophic condition had changed from oligo- to mesotrophic for the past 60 years. According to cluster analysis, the stratigraphic sediments were divided into two periods with different features of the phytoplankton composition. Chronological comparison with events in the watershed suggested that eutrophication occurred because of an increase in visitors to the watershed and deposition of atmospheric dust. In this lake more than 50% of resting eggs produced by Daphnia over the past 60 years hatched. However, genetic analysis of the ephippial carapaces (remains) showed that the Daphnia population was originally composed of D. dentifera but that D. galeata, or its hybrid with D. dentifera, invaded and increased the population density when the lake was eutrophied. Subsequently, large D. pulex established populations in the 1980s when largemouth bass were anonymously introduced. These results indicated that the Lake Hataya Ohunma plankton community underwent significant changes despite the fact that there were no notable changes in land cover or land use in the watershed. Since increases in atmospheric deposition and release of fish have occurred in many Japanese lakes, the changes in the plankton community described here may be widespread in these lakes.

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DNA extraction and amplification methods for ephippial cases of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past

Cited by 18 publications

References 33 publications

Current knowledge of South American cladoceran diapause: A brief review

Current knowledge of South American cladoceran diapause: A brief review

Whole genome amplification and sequencing of a Daphnia resting egg

Historical Changes in the Ecosystem Condition of a Small Mountain Lake over the Past 60 Years as Revealed by Plankton Remains and Daphnia Ephippial Carapaces Stored in Lake Sediments

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