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Results 1 through 20 out of 5169

in category evolutionary biology


1: Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

Prashant Pradhan, Ashutosh Kumar Pandey et al.

364,198 downloads (posted 31 Jan 2020)

This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author.


2: Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

Bette T. Korber, WM Fischer et al.

184,499 downloads (posted 30 Apr 2020)

We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages i...


3: Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity

Yong Jia, Gangxu Shen et al.

29,776 downloads (posted 11 Apr 2020)

Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural...


4: Quantitative translation of dog-to-human aging by conserved remodeling of epigenetic networks

Tina Wang, Jianzhu Ma et al.

19,931 downloads (posted 04 Nov 2019)

Mammals progress through similar physiological stages during life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects conserved molecular events is unclear. Here, we map common epigenetic changes experienced by mammalian genomes as they age, focusing on evolutionary comparisons of humans to dogs, an emerging model of aging. Using targeted sequencing, we characterize the methylomes of 104 Labrador retrievers spanning a 16 year age range, achieving >150X covera...


5: SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?

Shing Hei Zhan, Benjamin E. Deverman et al.

16,138 downloads (posted 02 May 2020)

In a side-by-side comparison of evolutionary dynamics between the 2019/2020 SARS-CoV-2 and the 2003 SARS-CoV, we were surprised to find that SARS-CoV-2 resembles SARS-CoV in the late phase of the 2003 epidemic after SARS-CoV had developed several advantageous adaptations for human transmission. Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. However, no precursors or parallel branches of...


6: Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Maciej F. Boni, Philippe Lemey et al.

11,129 downloads (posted 31 Mar 2020)

There are outstanding evolutionary questions on the recent emergence of coronavirus SARS-CoV-2/hCoV-19 in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses -- the viral subgenus responsible for the emergence of SA...


7: Population Replacement in Early Neolithic Britain

Selina Brace, Yoan Diekmann et al.

10,286 downloads (posted 18 Feb 2018)

The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Anatolian ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain c. 6000 years ago (kBP), a millennium after they appear in adjacent areas of northwestern continental Europe. However, the pattern and process of the British Neolithic transitio...


8: Modern human origins: multiregional evolution of autosomes and East Asia origin of Y and mtDNA

Dejian Yuan, Xiaoyun Lei et al.

8,611 downloads (posted 18 Jan 2017)

The neutral theory has been used as a null model for interpreting nature and produced the Recent Out of Africa model of anatomically modern humans. Recent studies, however, have established that genetic diversities are mostly at maximum saturation levels maintained by selection, therefore challenging the explanatory power of the neutral theory and rendering the present molecular model of human origins untenable. Using improved methods and public data, we have revisited human evolution and found sharing of genetic variat...


9: Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia

Hugh McColl, Fernando Racimo et al.

7,658 downloads (posted 08 Mar 2018)

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contex...


10: Towards a new history and geography of human genes informed by ancient DNA

Joseph K. Pickrell, David Reich

7,403 downloads (posted 21 Mar 2014)

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migratio...


11: A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years

Hang Zhou, Sile Hu et al.

6,969 downloads (posted 05 May 2015)

The spatiotemporal distribution of recent human adaptation is a long standing question. We developed a new coalescent-based method that collectively assigned human genome regions to modes of neutrality or to positive, negative, or balancing selection. Most importantly, the selection times were estimated for all positive selection signals, which ranged over the last half million years, penetrating the emergence of anatomically modern human (AMH). These selection time estimates were further supported by analyses of the ge...


12: Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago

Carina M. Schlebusch, Helena Malmström et al.

6,911 downloads (posted 05 Jun 2017)

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Ag...


13: Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations

Yann X.C. Bourgeois, Khaled M Hazzouri et al.

6,265 downloads (posted 12 May 2016)

1. Characterizing species history and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species. 2. The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes. Po...


14: The hidden elasticity of avian and mammalian genomes

Aurélie Kapusta, Alexander Suh et al.

5,669 downloads (posted 16 Oct 2016)

Genome size in mammals and birds shows remarkably little interspecific variation compared to other taxa. Yet, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been co-variation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome si...


15: Genetic landscapes reveal how human genetic diversity aligns with geography

Benjamin Marco Peter, Desislava Petkova et al.

5,428 downloads (posted 13 Dec 2017)

Summarizing spatial patterns in human genetic diversity to understand population history has been a persistent goal for human geneticists. Here, we use a recently developed spatially explicit method to estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured (the EEMS method). The resulting surfaces are "rugged", which indicates the relationship between genetic and geographic distance is heterogenous and distorted as a rule. Most prominently, topographic and marine fe...


16: Reduced signal for polygenic adaptation of height in UK Biobank

Jeremy J. Berg, Arbel Harpak et al.

5,174 downloads (posted 25 Jun 2018)

Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used height effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based on the the UK Biobank (UKB), a large, independent dataset. We find that the signals of selection using UKB effect-size estimates for height are strongly attenuated or absent. We also provide evidence that previous analyses were confounded by population stratification Therefore, the conclus...


17: Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2

Juan Ángel Patiño-Galindo, Ioan Filip et al.

4,925 downloads (posted 18 Feb 2020)

The recent outbreak of a new coronavirus (SARS-CoV-2) in Wuhan, China, underscores the need for understanding the evolutionary processes that drive the emergence and adaptation of zoonotic viruses in humans. Here, we show that recombination in betacoronaviruses, including human-infecting viruses like SARS-CoV and MERS-CoV, frequently encompasses the Receptor Binding Domain (RBD) in the Spike gene. We find that this common process likely led to a recombination event at least 11 years ago in an ancestor of the SARS-CoV-2 ...


18: Extreme positive allometry of animal adhesive pads and the size limits of adhesion-based climbing.

David Labonte

4,703 downloads (posted 07 Dec 2015)

Organismal functions are size-dependent whenever body surfaces supply body volumes. Larger organisms can develop strongly folded internal surfaces for enhanced diffusion, but in many cases areas cannot be folded so that their enlargement is constrained by anatomy, presenting a problem for larger animals. Here, we study the allometry of adhesive pad area in 225 climbing animal species, covering more than seven orders of magnitude in weight. Across all taxa, adhesive pad area showed extreme positive allometry and scaled w...


19: A SARS-CoV-2 vaccine candidate would likely match all currently circulating strains

Bethany L. Dearlove, Eric Lewitus et al.

4,695 downloads (posted 27 Apr 2020)

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective vaccine. Here we analyzed SARS-CoV-2 sequence diversity across 5,700 sequences sampled since December 2019. The Spike protein, which is the target immunogen of most vaccine candidates, showed 93 sites with shared polymorphisms; only one of these mutations was found in more than 1% of currently circulating sequences. The minimal diversity found among SARS-CoV-2 sequences can be explained by drift and bottleneck events as the virus spr...


20: Evidence supporting a viral origin of the eukaryotic nucleus

Philip JL Bell

4,659 downloads (posted 21 Jun 2019)

The defining feature of the eukaryotic cell is the possession of a nucleus that uncouples transcription from translation. This uncoupling of transcription from translation depends on a complex process employing hundreds of eukaryotic specific genes acting in concert and requires the 7-methylguanylate (m7G) cap to prime eukaryotic mRNA for splicing, nuclear export, and cytoplasmic translation. The origin of this complex system is currently a paradox since it is not found or needed in prokaryotic cells which lack nuclei, ...