Centennial clonal stability of asexual <i>Daphnia</i> in Greenland lakes despite climate variability

Dane, Maison; Anderson, Nicholas; Osburn, Christopher L.; Colbourne, John K.; Frisch, Dagmar

doi:10.1002/ece3.7012

Cited by 7 publications

(14 citation statements)

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“…Ephippia of Arctic, triploid populations of Daphnia pulicaria (asexually produced eggs) were collected in 2015 from sediment of two lakes in West Greenland (Kangerlussuaq area). Details on the lakes and sediment dating can be found in Dane et al (2020). Briefly, we sampled ephippia from sediment corresponding to several historical time periods in two lakes: Lake SS4 (Braya Sø): c .…”

Section: Methodsmentioning

confidence: 99%

Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs

O’Grady

Dhandapani

Colbourne

et al. 2021

Molecular Ecology Resources

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Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100‐year‐old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by‐product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.

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Section: Methodsmentioning

confidence: 99%

Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs

O’Grady

Dhandapani

Colbourne

et al. 2021

Molecular Ecology Resources

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“…We can extract DNA from these preserved diapausing eggs, and thereby reconstruct population genetic dynamics (Burge et al, 2018; Orsini et al, 2016). Although previous studies have revealed the evolutionary processes of Daphnia using diapausing eggs (e.g., Decaestecker et al, 2007; Hairston et al, 1999; Stoks et al, 2016), only three prior studies have observed long‐term genetic dynamics of Daphnia species including the early stage of colonisation (Conde‐Porcuna et al, 2021; Dane et al, 2020; Möst et al, 2015). Möst et al (2015) analysed 40 years of long‐term genetic dynamics of colonisation and establishment by Daphnia pulicaria that consisted of cyclic parthenogenetic lineages and possibly a few obligate parthenogenetic lineages.…”

Section: Introductionmentioning

confidence: 99%

“…Möst et al (2015) analysed 40 years of long‐term genetic dynamics of colonisation and establishment by Daphnia pulicaria that consisted of cyclic parthenogenetic lineages and possibly a few obligate parthenogenetic lineages. Dane et al (2020) and Conde‐Porcuna et al (2021) analysed long‐term genetic dynamics of an obligate parthenogenetic Daphnia pulex species complex. Dane et al (2020) observed the population genetic dynamics of obligate parthenogenetic D. pulicaria for three centuries including colonisation of three lakes in Greenland.…”

Section: Introductionmentioning

confidence: 99%

“…Dane et al (2020) and Conde‐Porcuna et al (2021) analysed long‐term genetic dynamics of an obligate parthenogenetic Daphnia pulex species complex. Dane et al (2020) observed the population genetic dynamics of obligate parthenogenetic D. pulicaria for three centuries including colonisation of three lakes in Greenland. Conde‐Porcuna et al (2021) observed the population genetic dynamics of obligate parthenogenetic D. pulex , which belonged to the North American lineage, for 65 years in a Spanish high‐mountain lake.…”

Section: Introductionmentioning

confidence: 99%

“…These three previous studies showed that limited haplotypes succeeded in colonisation, whereas population genetic dynamics after colonisation differed between the three cases. Although D. pulicaria populations with cyclic parthenogenetic lineages showed a rapid increase in genetic diversity after colonisation (Möst et al, 2015), obligate parthenogenetic populations were dominated by a single or a few genotypes without increasing genetic diversity over time (Conde‐Porcuna et al, 2021; Dane et al, 2020). Dane et al (2020) showed the dominance of a single genotype that had persisted for 250–300 years in two lakes despite substantial environmental changes during the period.…”

Section: Introductionmentioning

confidence: 99%

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Population genetic dynamics during colonisation and establishment of an obligate parthenogenetic Daphnia pulex population in a small lake of a continental archipelago

et al. 2022

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Population genetic diversity and structure are known to influence successful colonisation and establishment of a population in a novel habitat. However, our understanding of actual population genetic changes in the early stage of colonisation and detailed time‐series of genetic changes during the establishment of a new population is still limited due to the difficulty of making long‐term direct observations of a colonising population. Using a paleolimnological approach, we revealed the long‐term genetic dynamics of an obligate parthenogenetic panarctic Daphnia pulex population during the early stage of colonisation and subsequent establishment in Lake Fukami‐ike of Nagano, Japan. We collected diapausing eggs in ephippia of D. pulex from layers of sediment core samples (c. 370 cm long; dated 1662–2017) and then the mitochondrial DNA was sequenced using the markers designed for the NADH dehydrogenase 5 (ND5) gene and the control region. Daphnia pulex colonised and established a population in the early 2000s. Population genetic analysis showed that one colonising haplotype predominated in the population throughout the study period. Genetic diversity was consistently limited and there was no recovery of genetic diversity after colonisation. Clearly limited genetic diversity did not hamper population growth, possibly because phenotypic plasticity was used to cope with changes in predation pressure. Analysis using multivariate auto‐regressive models showed that responses to environmental and ecological factors varied depending on the haplotype, which may have contributed to successful colonisation of the lake by the different haplotypes. The present results suggest that an obligate parthenogenetic population can establish in a new habitat and be maintained for generations even though it has limited genetic diversity. We found that two independent lineages (JPN1 and JPN2) successfully established and coexisted toward the end of the study period. Although limited genetic diversity did not impede colonisation success, how the later colonising JPN1 lineage has successfully invaded a population consisting solely of the early colonising JPN2 deserves future attention to understand the population genetic dynamics revealed in this study.

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Refining the evolutionary time machine: an assessment of whole genome amplification using single historicalDaphniaeggs

O’Grady

Dhandapani

Colbourne

et al. 2021

Preprint

Self Cite

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Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimised workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10y and 300y old. Resulting genome coverage breadth in most samples was ~70%, including those from >100y old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with SNPs in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300y). The mtDNA provides an additional source for evolutionary studies of these populations. We provide an optimised workflow for WGA followed by whole genome sequencing including steps to minimise exogenous DNA.

show abstract

Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 7 publications

References 76 publications

Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs

Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs

Population genetic dynamics during colonisation and establishment of an obligate parthenogenetic Daphnia pulex population in a small lake of a continental archipelago

Refining the evolutionary time machine: an assessment of whole genome amplification using single historicalDaphniaeggs

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