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Currently indexing 62,747 bioRxiv papers from 278,434 authors.

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Results 1 through 20 out of 4155

in category evolutionary biology

 

1: Population Replacement in Early Neolithic Britain

Selina Brace, Yoan Diekmann et al.

9,125 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 transition remains unclear. We assembled genome-wide data from six Mesolithic and 67 Neolithic individuals found in Britain, dating from 10.5-4.5 kBP, a dataset that includes 22 newly reported individuals and the first genomic data from British Mesolithic hunter-gatherers. Our analyses reveals persistent genetic affinities between Mesolithic British and Western European hunter-gatherers over a period spanning Britain's separation from continental Europe. We find overwhelming support for agriculture being introduced by incoming continental farmers, with small and geographically structured levels of additional hunter-gatherer introgression. We find genetic affinity between British and Iberian Neolithic populations indicating that British Neolithic people derived much of their ancestry from Anatolian farmers who originally followed the Mediterranean route of dispersal and likely entered Britain from northwestern mainland Europe.

https://rxivist.org/papers/24852
https://doi.org/10.1101/267443

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

Dejian Yuan, Xiaoyun Lei et al.

7,405 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...

https://rxivist.org/papers/24615
https://doi.org/10.1101/101410

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

Joseph K. Pickrell, David Reich

7,283 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...

https://rxivist.org/papers/26664
https://doi.org/10.1101/003517

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

Hang Zhou, Sile Hu et al.

6,810 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...

https://rxivist.org/papers/26420
https://doi.org/10.1101/018929

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

Hugh McColl, Fernando Racimo et al.

6,627 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...

https://rxivist.org/papers/24790
https://doi.org/10.1101/278374

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

Carina M Schlebusch, Helena Malmström et al.

6,572 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...

https://rxivist.org/papers/25500
https://doi.org/10.1101/145409

7: 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.

5,538 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...

https://rxivist.org/papers/25468
https://doi.org/10.1101/052761

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

Jeremy J. Berg, Arbel Harpak et al.

4,912 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...

https://rxivist.org/papers/24367
https://doi.org/10.1101/354951

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

Benjamin M Peter, Desislava Petkova et al.

4,818 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...

https://rxivist.org/papers/24724
https://doi.org/10.1101/233486

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

David Labonte

4,410 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...

https://rxivist.org/papers/26226
https://doi.org/10.1101/033845

11: The infinitesimal model

N H Barton, A M Etheridge et al.

4,345 downloads (posted 15 Feb 2016)

Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. We first review the long history of the infinitesimal model in quantitative genetics. Then we provide a definition of the model at the phenotypic level in terms of individual trait values and...

https://rxivist.org/papers/26196
https://doi.org/10.1101/039768

12: The hidden elasticity of avian and mammalian genomes

Aurélie Kapusta, Alexander Suh et al.

4,227 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...

https://rxivist.org/papers/25885
https://doi.org/10.1101/081307

13: Adaptive evolution within the gut microbiome of individual people

Shijie Zhao, Tami D. Lieberman et al.

4,115 downloads (posted 24 Oct 2017)

Individual bacterial lineages stably persist for years in the human gut microbiome. However, it is unknown if these lineages adapt during colonization of healthy people. Here, we assess evolution within individual microbiomes by sequencing the genomes of 602 Bacteroides fragilis isolates cultured from 12 healthy subjects. We find that B. fragilis within-subject populations contain significant de novo nucleotide and mobile element diversity, which preserve years of within-person evolutionary history. This evolutionary hi...

https://rxivist.org/papers/24784
https://doi.org/10.1101/208009

14: A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage

Juan Manuel Vazquez, Michael Sulak et al.

4,097 downloads (posted 12 Sep 2017)

Among the evolutionary and developmental constraints on the evolution of very large body sizes is an increased risk of developing cancer because large bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms with fewer cells. This expectation predicts a positive correlation between body size and cancer risk, however, there is no correlation between body size and cancer risk across species; this lack of correlation is often referred to as "Peto's Paradox". Here we show that elephan...

https://rxivist.org/papers/24381
https://doi.org/10.1101/187922

15: Independent evolution of ab- and adaxial stomatal density enables adaptation

Christopher David Muir

4,043 downloads (posted 15 Dec 2015)

Are organisms free to reach their adaptive optima or constrained by hard-wired developmental programs? Recent evidence suggests that the arrangement of stomata on abaxial (lower) and adaxial (upper) leaf surfaces may be an important adaptation in plants, but stomatal traits on each surface likely share developmental pathways that could hamper evolution. We reviewed the quantitative genetics of stomatal density to look for loci that (1) affected ab- or adaxial density independently or (2) pleiotropically affected stomata...

https://rxivist.org/papers/26243
https://doi.org/10.1101/034355

16: Niche construction in evolutionary theory: the construction of an academic niche?

Manan Gupta, N G Prasad et al.

3,961 downloads (posted 19 Feb 2017)

In recent years, fairly far-reaching claims have been repeatedly made about how niche construction, the modification by organisms of their environment, and that of other organisms, represents a vastly neglected phenomenon in ecological and evolutionary thought. The proponents of this view claim that the niche construction perspective greatly expands the scope of standard evolutionary theory and that niche construction deserves to be treated as a significant evolutionary process in its own right, almost at par with natur...

https://rxivist.org/papers/25699
https://doi.org/10.1101/109793

17: The Genetic Cost of Neanderthal Introgression

Kelley Harris, Rasmus Nielsen

3,878 downloads (posted 30 Oct 2015)

Approximately 2-4\% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% ...

https://rxivist.org/papers/26132
https://doi.org/10.1101/030387

18: Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

Stephen E. Harris, Jason Munshi-South

3,806 downloads (posted 28 Jan 2016)

Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified...

https://rxivist.org/papers/25238
https://doi.org/10.1101/038141

19: Trees, Population Structure, F-statistics!

Benjamin M Peter

3,765 downloads (posted 09 Oct 2015)

Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose are F-statistics, that measure shared genetic drift between sets of two, three and four populations, and can be used to test simple and complex hypotheses about admixture between populations. Here, we put these statistics in context of phylogenetic and population genetic theory. We show how measures of genetic drift can be interp...

https://rxivist.org/papers/26306
https://doi.org/10.1101/028753

20: Unravelling the diversity behind Ophiocordyceps unilateralis complex: Three new species of Zombie-Ant fungus from Brazilian Amazon

João P. M. Araújo, Harry C Evans et al.

3,760 downloads (posted 03 Apr 2014)

In tropical forests, one of the most common relationships between parasites and insects is that between the fungus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Ascomycota) and ants, especially within the tribe Camponotini. These fungi have the ability to penetrate the exoskeleton of the ant and to manipulate the behavior of the host, making it leave the nest and ascend understorey shrubs, to die biting onto the vegetation: hence, the term zombie-ant fungi to describe this behavioral changes on the host. It is posi...

https://rxivist.org/papers/26588
https://doi.org/10.1101/003806