scholarly journals Environmental palaeogenomic reconstruction of an Ice Age algal population

2020 ◽  
Author(s):  
Youri Lammers ◽  
Peter D. Heintzman ◽  
Inger Greve Alsos
Keyword(s):  
Genomic Analysis ◽  
The Body ◽  
Genomic Variation ◽  
Ice Age ◽  
Ecological Change ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Population Genomic ◽  
Body Fossil ◽  
Major Haplogroups

AbstractPalaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve as fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and identified N. limnetica as the dominant taxon. We then reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed at least two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica. The approach presented here demonstrates the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

scholarly journals Environmental palaeogenomic reconstruction of an Ice Age algal population

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Youri Lammers ◽  
Peter D. Heintzman ◽  
Inger Greve Alsos
Keyword(s):  
Haplotype Diversity ◽  
Estimation Method ◽  
Genomic Analysis ◽  
The Body ◽  
Genomic Variation ◽  
Ice Age ◽  
Ecological Change ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Population Genomic

AbstractPalaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA.

scholarly journals Genes mirror migrations and cultures in prehistoric Europe – a population genomic perspective

2016 ◽  
Author(s):  
Torsten Günther ◽  
Mattias Jakobsson
Keyword(s):  
Bronze Age ◽  
Genomic Variation ◽  
Full Potential ◽  
Genomic Information ◽  
The North ◽  
Population Genomic ◽  
The Last Glacial Maximum ◽  
Stable Populations ◽  
The Bronze Age ◽  
The Last Glacial

AbstractGenomic information from ancient human remains is beginning to show its full potential for learning about human prehistory. We review the last few years' dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. The early times, the Upper Palaeolithic, appears to contain several population turn-overs followed by more stable populations after the Last Glacial Maximum and during the Mesolithic. Some 11,000 years ago the migrations driving the Neolithic transition start from around Anatolia and reach the north and the west of Europe millennia later followed by major migrations during the Bronze age. These findings show that culture and lifestyle were major determinants of genomic differentiation and similarity in pre-historic Europe rather than geography as is the case today.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

scholarly journals Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History

2009 ◽  
Vol 26 (6) ◽  
pp. 1357-1367 ◽  
Author(s):  
Laura B. Scheinfeldt ◽  
Shameek Biswas ◽  
Jennifer Madeoy ◽  
Caitlin F. Connelly ◽  
Eric E. Schadt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Population Genomic ◽  
Complex Evolutionary History

scholarly journals Associations between Socio-Economic Status and Unfavorable Social Indicators of Child Wellbeing; a Neighbourhood Level Data Design

2021 ◽  
Vol 18 (23) ◽  
pp. 12661
Author(s):  
Minke R. C. van Minde ◽  
Marlou L. A. de Kroon ◽  
Meertien K. Sijpkens ◽  
Hein Raat ◽  
Eric A. P. Steegers ◽  
...  
Keyword(s):  
Economic Status ◽  
Social Indicators ◽  
Cubic Splines ◽  
Repeated Measurements ◽  
The Body ◽  
Full Potential ◽  
Child Wellbeing ◽  
Socio Economic Status ◽  
Level Data ◽  
Health Differences

Background: Living in deprivation is related to ill health. Differences in health outcomes between neighbourhoods may be attributed to neighbourhood socio-economic status (SES). Additional to differences in health, neighbourhood differences in child wellbeing could also be attributed to neighbourhood SES. Therefore, we aimed to investigate the association between neighbourhood deprivation, and social indicators of child wellbeing. Methods: Aggregated data from 3565 neighbourhoods in 390 municipalities in the Netherlands were eligible for analysis. Neighbourhood SES scores and neighbourhood data on social indicators of child wellbeing were used to perform repeated measurements, with one year measurement intervals, over a period of 11 years. Linear mixed models were used to estimate the associations between SES score and the proportion of unfavorable social indicators of child wellbeing. Results: After adjustment for year, population size, and clustering within neighbourhoods and within a municipality, neighbourhood SES was inversely associated with the proportion of ‘children living in families on welfare’ (estimates with two cubic splines: −3.59 [CI: −3.99; −3.19], and −3.00 [CI: −3.33; −2.67]), ‘delinquent youth’ (estimate −0.26 [CI: −0.30; −0.23]) and ‘unemployed youth’ (estimates with four cubic splines: −0.41 [CI: −0.57; −0.25], −0.58 [CI: −0.73; −0.43], −1.35 [−1.70; −1.01], and −0.96 [1.24; −0.70]). Conclusions: In this study using repeated measurements, a lower neighbourhood SES was significantly associated with a higher prevalence of unfavorable social indicators of child wellbeing. This contributes to the body of evidence that neighbourhood SES is strongly related to child health and a child’s ability to reach its full potential in later life. Future studies should consist of larger longitudinal datasets, potentially across countries, and should attempt to take the interpersonal variation into account with more individual-level data on SES and outcomes.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

2021 ◽  
Author(s):  
Yanqing Sun ◽  
Enhui Shen ◽  
Yiyu Hu ◽  
Dongya Wu ◽  
Yu Feng ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Population Genomic

Excerpt from “Women Mystics and Eucharistic Devotion in the Thirteenth Century”

2017 ◽  
Author(s):  
Caroline Walker Bynum
Keyword(s):  
Thirteenth Century ◽  
The Body ◽  
Body Of Christ ◽  
Full Potential ◽  
Christian Women ◽  
Imitatio Christi ◽  
Life And Death ◽  
The World ◽  
Embodied Practice ◽  
Women Mystics

In this chapter the renowned medievalist scholar Caroline Walker Bynum brings our attention to a striking historical occurrence: in twelfth- and thirteenth-century Europe the concern with and attachment to Eucharistic devotion was overwhelmingly female. Why this gender bias, and at that time? Christian women were predominantly “inspired, compelled, comforted and troubled by the Eucharist” and in many different forms—from miraculous apparitions, to experiences of ecstasy connected to the attendance and ingestion of the Eucharist, to the showing of sensorial excesses in its presence. Bynum shows how material and physical receptions of the body of Christ were expressed not only as forms of ecstasy but also as gendered modes of living the Imitatio Christi. This thirteenth-century corporeal, female experience of the Eucharist is connected to a particular moment in the life of Christ—the transition between life and death. Positioned as “brides” and hence as the erotic counterparts of Christ, women and female mystics exploited the full potential of Christ’s own corporeality rather than his otherworldly nature. Bynum’s work constitutes a formative reference point for scholars of Catholicism across a range of disciplines for the obvious reason that it deals so elegantly with themes of substance, gender, bodies, and devotional forms of Catholic practice. Her work continues to be an original source of inspiration for anthropologists because of its remarkable sensitivity to religion as an embodied, practice-generative engagement with the world. Bynum should also be considered as important for the “new” anthropology of Catholicism for her pioneering work on the gymnasticity of gender and for the attention it draws to the sublimated erotic tension that exists between institutional doxa and mystical aesthetics.2 In Bynum’s work, gender is not presented as merely one among a number of potential analytical foci for elaboration of Catholicism; rather, it is the very ontological architecture of the religious, and hence an essential topic for scholars seeking to understand Catholicism as a translocal force.

Into the Icehouse

2012 ◽  
Author(s):  
Jan Zalasiewicz ◽  
Mark Williams
Keyword(s):  
The Body ◽  
Ice Age ◽  
Polar Regions ◽  
Earth System ◽  
The North ◽  
The World ◽  
The Face ◽  
Ancient Times ◽  
Almost All ◽  
Popular Image

The frozen lands of the north are an unforgiving place for humans to live. The Inuit view of the cosmos is that it is ruled by no one, with no gods to create wind and sun and ice, or to provide punishment or forgiveness, or to act as Earth Mother or Father. Amid those harsh landscapes, belief is superfluous, and only fear can be relied on as a guide. How could such a world begin, and end? In Nordic mythology, in ancient times there used to be a yet greater kingdom of ice, ruled by the ice giant, Ymir Aurgelmir. To make a world fit for humans, Ymir was killed by three brothers—Odin, Vilje, and Ve. The blood of the dying giant drowned his own children, and formed the seas, while the body of the dead giant became the land. To keep out other ice giants that yet lived in the far north, Odin and his brothers made a wall out of Ymir’s eyebrows. One may see, fancifully, those eyebrows still, in the form of the massive, curved lines of morainic hills that run across Sweden and Finland. We now have a popular image of Ymir’s domain—the past ‘Ice Age’—as snowy landscapes of a recent past, populated by mammoths and woolly rhinos and fur-clad humans (who would have been beginning to create such legends to explain the precarious world on which they lived). This image, as we have seen, represents a peculiarly northern perspective. The current ice age is geologically ancient, for the bulk of the world’s land-ice had already grown to cover almost all Antarctica, more than thirty million years ago. Nevertheless, a mere two and a half million years ago, there was a significant transition in Earth history—an intensification of the Earth’s icehouse state that spread more or less permanent ice widely across the northern polar regions of the world. This intensification— via those fiendishly complex teleconnections that characterize the Earth system—changed the face of the entire globe. The changes can be detected in the sedimentary strata that were then being deposited around the world.

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