scholarly journals Discovery of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2018 ◽  
Author(s):  
Quentin D. Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D. Lange ◽  
Daniel R. Matute ◽  
Brandon S. Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Historical Context ◽  
Model Organism ◽  
Widespread Species ◽  
Wilderness Areas ◽  
Genomic Studies ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster, a globally widespread species [1] which “has invariably appeared to be a strict human commensal” [2]. In spite of its sub-Saharan origins, this species has never been reported from undisturbed wilderness environments that might reflect its pre-commensal niche [3]. Here, we document the collection of 288 D. melanogaster individuals from African wilderness areas in Zambia, Zimbabwe, and Namibia. After sequencing the genomes of 17 flies collected from Kafue National Park, Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these new genomes with prior data enabled us to gain novel insights into the history of this species’ geographic expansion. Our demographic estimates indicated that an expansion from southern Africa began approximately 10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide a critical resource for future evolutionary and genomic studies of this key model organism. Our results add historical context to the species’ human association, and the opportunity to study wilderness populations opens the door for future studies on the biological basis of its adaptation to human environments.

scholarly journals Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History

2019 ◽  
Vol 37 (3) ◽  
pp. 627-638 ◽  
Author(s):  
Quentin D Sprengelmeyer ◽  
Suzan Mansourian ◽  
Jeremy D Lange ◽  
Daniel R Matute ◽  
Brandon S Cooper ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Central Africa ◽  
Model Organism ◽  
Sub Saharan Africa ◽  
Wilderness Areas ◽  
Southern Central ◽  
History Of ◽  
Sub Saharan ◽  
Improved Model

Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼13,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,800 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.

scholarly journals Demographic history and admixture dynamics in African Sahelian populations

2020 ◽  
Author(s):  
Viktor Černý ◽  
Cesar Fortes-Lima ◽  
Petr Tříska
Keyword(s):  
Demographic History ◽  
Distribution Patterns ◽  
Human Populations ◽  
African Region ◽  
Genetic Studies ◽  
Genomic Studies ◽  
History Of ◽  
Sub Saharan ◽  
High Degree ◽  
The Impact

Abstract The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterised by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure as well as the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity, and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.

scholarly journals The demographic history of African Drosophila melanogaster

2018 ◽  
Author(s):  
Adamandia Kapopoulou ◽  
Susanne P. Pfeifer ◽  
Jeffrey D. Jensen ◽  
Stefan Laurent
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
Research Question ◽  
Model Organism ◽  
Quantitative Model ◽  
Population History ◽  
Parameter Estimates ◽  
Demographic Model ◽  
African Populations ◽  
History Of

ABSTRACTAs one of the most commonly utilized organisms in the study of local adaptation, an accurate characterization of the demographic history of Drosophila melanogaster remains as an important research question. This owes both to the inherent interest in characterizing the population history of this model organism, as well as to the well-established importance of an accurate null demographic model for increasing power and decreasing false positive rates in genomic scans for positive selection. While considerable attention has been afforded to this issue in non-African populations, less is known about the demographic history of African populations, including from the ancestral range of the species. While qualitative predictions and hypotheses have previously been forwarded, we here present a quantitative model fitting of the population history characterizing both the ancestral Zambian population range as well as the subsequently colonized west African populations, which themselves served as the source of multiple non-African colonization events. These parameter estimates thus represent an important null model for future investigations in to African and non-African D. melanogaster populations alike.

scholarly journals Corrigendum to: Demographic history of the human commensal Drosophila melanogaster

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
J Roman Arguello ◽  
Stefan Laurent ◽  
Andrew G Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
History Of

scholarly journals Moose genomes reveal past glacial demography and the origin of modern lineages

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicolas Dussex ◽  
Federica Alberti ◽  
Matti T. Heino ◽  
Remi-Andre Olsen ◽  
Tom van der Valk ◽  
...  
Keyword(s):  
North America ◽  
De Novo ◽  
Demographic History ◽  
Glacial Refugia ◽  
Population Declines ◽  
Glacial Cycles ◽  
Climate Fluctuations ◽  
Northern Latitudes ◽  
Genomic Studies ◽  
History Of

Abstract Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

scholarly journals Monitoring food preference in Drosophila by oligonucleotide tagging

2018 ◽  
Vol 115 (36) ◽  
pp. 9020-9025 ◽  
Author(s):  
Annie Park ◽  
Tracy Tran ◽  
Nigel S. Atkinson
Keyword(s):  
Drosophila Melanogaster ◽  
Mushroom Body ◽  
Food Preference ◽  
Model Organism ◽  
Food Choices ◽  
Sexually Dimorphic ◽  
History Of ◽  
Ad Libitum ◽  
Independent Assay

Drosophila melanogaster is a powerful model organism for dissecting the neurogenetic basis of appetitive and aversive behaviors. However, some methods used to assay food preference require or cause starvation. This can be problematic for fly ethanol research because it can be difficult to dissociate caloric preference for ethanol from pharmacological preference for the drug. We designed BARCODE, a starvation-independent assay that uses trace levels of oligonucleotide tags to differentially mark food types. In BARCODE, flies feed ad libitum, and relative food preference is monitored by qPCR of the oligonucleotides. Persistence of the ingested oligomers within the fly records the feeding history of the fly over several days. Using BARCODE, we identified a sexually dimorphic preference for ethanol. Females are attracted to ethanol-laden foods, whereas males avoid consuming it. Furthermore, genetically feminizing male mushroom body lobes induces preference for ethanol. In addition, we demonstrate that BARCODE can be used for multiplex diet measurements when animals are presented with more than two food choices.

scholarly journals Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared to mice and Drosophila melanogaster

2018 ◽  
Author(s):  
Ying Zhen ◽  
Christian D. Huber ◽  
Robert W. Davies ◽  
Kirk E. Lohmueller
Keyword(s):  
Drosophila Melanogaster ◽  
Adaptive Evolution ◽  
Demographic History ◽  
Composite Likelihood ◽  
Ancestral Population ◽  
Beneficial Mutations ◽  
Outgroup Species ◽  
Biased Gene Conversion ◽  
History Of ◽  
Adaptive Walks

ABSTRACTQuantifying and comparing the amount of adaptive evolution among different species is key to understanding evolutionary processes. Previous studies have shown differences in adaptive evolution across species; however, their specific causes remain elusive. Here, we use improved modeling of weakly deleterious mutations and the demographic history of the outgroup species and ancestral population and estimate that at least 20% of nonsynonymous substitutions between humans and an outgroup species were fixed by positive selection. This estimate is much higher than previous estimates, which did not correct for the sizes of the outgroup species and ancestral population. Next, we directly estimate the proportion and selection coefficients (p+ and s+, respectively) of newly arising beneficial nonsynonymous mutations in humans, mice, and Drosophila melanogaster by examining patterns of polymorphism and divergence. We develop a novel composite likelihood framework to test whether these parameters differ across species. Overall, we reject a model with the same p+ and s+ of beneficial mutations across species, and estimate that humans have a higher p+s+ compared to D. melanogaster and mice. We demonstrate that this result cannot be caused by biased gene conversion or hypermutable CpG sites. In summary, we find the proportion of beneficial mutations to be higher in humans than in D. melanogaster or mice, suggesting that organismal complexity, which increases the number of steps required in adaptive walks, may be a key predictor of the amount of adaptive evolution within a species.

Constructing Identity: Sixteenth- and Seventeenth-Century Architecture in the Gambia-Geba Region and the Articulation of Luso-African Ethnicity

1995 ◽  
Vol 22 ◽  
pp. 307-327 ◽  
Author(s):  
Peter Mark
Keyword(s):  
Seventeenth Century ◽  
Building Materials ◽  
Historical Context ◽  
The Gambia ◽  
Sub Saharan Africa ◽  
Cultural Interaction ◽  
European Contact ◽  
Living Space ◽  
History Of ◽  
Sub Saharan

The precolonial architectural history of the northern Upper Guinea coast from the Gambia to the Geba rivers has yet to be studied in depth. Yet this region, the first to be visited and described by European travelers in the fifteenth and early sixteenth centuries, is among the best-documented parts of sub-Saharan Africa for the four centuries of precolonial African-European contact. The establishment of communities of Luso-African traders in the sixteenth and seventeenth century makes the Gambia-Casamance-Bissau area important to the study of early sustained cultural interaction between Europeans and West Africans.One result of the establishment of Portuguese and Luso-African trading communities was the development of a distinctive style of architecture, suited to the climate and making use of locally-available building materials. The history of the trade itself has been extensively studied by George Brooks. His work, along with that of Jean Boulègue, provides a firm foundation for the study of local architecture and living space. It is not my intention to rewrite these excellent sources, although much of my material is drawn from the same primary documents they have used, and although, in presenting the historical context from which seventeenth-century coastal architecture developed, I necessarily cover some ground that Brooks has already trod.In addition to the history of building styles, several related questions that are highly significant to the history of European-African cultural interaction need to be addressed. These questions include: what were the respective roles of Africans, Europeans, and Luso-Africans in the development of a distinctive architectural style? Is it possible to discern the influence of evolving Luso-African construction on local African architecture? And of local building styles on Afro-European construction? In other words, to what extent does architecture reflect mutual, two-way interaction between European and African society?

The Journal Korall and Hungarian Social History: Between International and National Contexts

2008 ◽  
Vol 34-35 (1-2) ◽  
pp. 327-353
Author(s):  
Anders Blomqvist
Keyword(s):  
Cultural History ◽  
Environmental History ◽  
Social History ◽  
Review Essay ◽  
Demographic History ◽  
Historical Context ◽  
Research Programme ◽  
Historical Sociology ◽  
The Social ◽  
History Of

This review essay evaluates the evolution of the Hungarian journal of social history, Korall társadalomtörténeti folyóirat (Coral: A journal of social history), founded in 1999 as a new forum of social history research. Korall promoted two distinct understandings of social history, stated only implicitly in the first years of the journal, but later elaborated more explicitely by the editors, as core definitions of their research programme. A first, narrow acceptation places social history within the field of (historical) sociology and favours structural approaches and concepts specific to the social sciences rather than the actual historical context. A second definition is wider, including a variety of topics such as environmental history, cultural history, economic, and demographic history, being meant to function as a powerful counter-discourse against positivistic, traditional and political-orientated history, still dominant in contemporary Hungarian historiography. Based on a combination of qualitative and quantitative content analysis, the review essay argues that, during its eight years of existance to date, Korall has undergone a process of internationalization. Although most articles published in the journal continue to focus on topics pertaining to the history of Hungary—especially during the “dualist period,” 1867-1918—references to international events, authors, and theories have lately acquired a greater importance.

scholarly journals Fine-scale Inference of Ancestry Segments without Prior Knowledge of Admixing Groups

2018 ◽  
Author(s):  
Michael Salter-Townshend ◽  
Simon Myers
Keyword(s):  
Natural Selection ◽  
Prior Knowledge ◽  
Markov Models ◽  
Demographic History ◽  
Eastern European ◽  
North African ◽  
Local Ancestry ◽  
History Of ◽  
Sub Saharan ◽  
The Relationship

ABSTRACTWe present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary number of genetically differentiated groups coming together. This allows inference of the demographic history of the species, properties of admixing groups, identification of signatures of natural selection, and may aid disease gene mapping. The algorithm employs nested hidden Markov models to obtain local ancestry estimation along the genome for each admixed individual. In a range of simulations, the accuracy of these estimates equals or exceeds leading existing methods that return local ancestry. Moreover, and unlike these approaches, we do not require any prior knowledge of the relationship between sub-groups of donor reference haplotypes and the unseen mixing ancestral populations. Instead, our approach infers these in terms of conditional “copying probabilities”. In application to the Human Genome Diversity Panel we corroborate many previously inferred admixture events (e.g. an ancient admixture event in the Kalash). We further identify novel events such as complex 4-way admixture in San-Khomani individuals, and show that Eastern European populations possess 1 – 5% ancestry from a group resembling modern-day central Asians. We also identify evidence of recent natural selection favouring sub-Saharan ancestry at the HLA region, across North African individuals. We make available an R and C++ software library, which we term MOSAIC (which stands for MOSAIC Organises Segments of Ancestry In Chromosomes).

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