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.

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 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 Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

scholarly journals Inferring number of populations and changes in connectivity under the n-island model

Heredity ◽  
2021 ◽  
Author(s):  
Armando Arredondo ◽  
Beatriz Mourato ◽  
Khoa Nguyen ◽  
Simon Boitard ◽  
Willy Rodríguez ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Demographic History ◽  
Simulated Data ◽  
Fixed Number ◽  
Ancestral Population ◽  
Demographic Model ◽  
History Of ◽  
Time Periods

AbstractInferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

scholarly journals Inferring number of populations and changes in connectivity under the n-island model

2020 ◽  
Author(s):  
Armando Arredondo ◽  
Beatriz Mourato ◽  
Khoa Nguyen ◽  
Simon Boitard ◽  
Willy Rodríguez ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
A Priori ◽  
Simulated Data ◽  
Fixed Number ◽  
Ancestral Population ◽  
Demographic Model ◽  
Automated Method ◽  
History Of ◽  
Diploid Individual

AbstractInferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, thus ignoring population structure. Alternatively, structure is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate), which can be estimated using the PSMC method of Li and Durbin (2011) for a single diploid individual. For an isolated population, the IICR matches the population size history, which is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme. Our automated method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise-stationary symmetrical island models, in which we assume a fixed number of time periods during which gene flow is constant. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the widely accepted view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.

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 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 Modern wolves trace their origin to a late Pleistocene expansion from Beringia

2018 ◽  
Author(s):  
Liisa Loog ◽  
Olaf Thalmann ◽  
Mikkel-Holger S. Sinding ◽  
Verena J. Schuenemann ◽  
Angela Perri ◽  
...  
Keyword(s):  
Northern Hemisphere ◽  
Late Pleistocene ◽  
Demographic History ◽  
Geographic Origin ◽  
Population History ◽  
Ancestral Population ◽  
Modeling Framework ◽  
Ecological Changes ◽  
History Of ◽  
Continuous Presence

ABSTRACTGrey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

scholarly journals Demographic History of the Human Commensal Drosophila melanogaster

2019 ◽  
Vol 11 (3) ◽  
pp. 844-854 ◽  
Author(s):  
J Roman Arguello ◽  
Stefan Laurent ◽  
Andrew G Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
History Of

scholarly journals The Demographic History of African Drosophila melanogaster

2018 ◽  
Vol 10 (9) ◽  
pp. 2338-2342 ◽  
Author(s):  
Adamandia Kapopoulou ◽  
Susanne P Pfeifer ◽  
Jeffrey D Jensen ◽  
Stefan Laurent
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
History Of
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