The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV

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Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

Elia Vajana

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive gene ...

WILEY2021

HIV-1 and human genetic variation

Jacques Fellay

Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV i ...

NATURE RESEARCH2021

Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

Christoph Bachofen

Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whe ...

WILEY2021

A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Jacques Fellay

A high-resolution reference panel based on whole-genome sequencing data enables accurate imputation of HLA alleles across diverse populations and fine-mapping of HLA association signals for HIV-1 host response. ...

NATURE PORTFOLIO2021

Stabilization of cultural innovations depends on population density: Testing an epidemiological model of cultural evolution against a global dataset of rock art sites and climate-based estimates of ancient population densities

Francesco Casalegno, Taylor Howard Newton

Demographic models of human cultural evolution have high explanatory potential but weak empirical support. Here we use a global dataset of rock art sites and climate and genetics-based estimates of ancient population densities to test a new model based on ...

2021

Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment

Anne-Florence Raphaëlle Bitbol

We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the absence of mutan ...

2020

Rapid Progression of Kidney Dysfunction in People Living With HIV: Use of Polygenic and Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) Risk Scores

Jacques Fellay, Christian Axel Wandall Thorball

Background In people with human immunodeficiency virus (PWH), it is unknown whether genetic background associates with rapid progression of kidney dysfunction (ie, estimated glomerular filtration rate [eGFR] decrease of >5mL/min/1.73m(2) per year for >= 3 ...

OXFORD UNIV PRESS INC2021

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Kristen Kay Irwin, Jeffrey David Jensen, Susanne Petra Pfeifer, Stefan Jean Laurent

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on backgr ...

NATURE PUBLISHING GROUP2020

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Tamar Kohn, Timothy R. Julian, Xavier Fernandez Cassi, Federica Cariti, Alex Tunas Corzon

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Swi ...

2022

Limits on amplifiers of natural selection under death-Birth updating

Andreas Pavlogiannis

The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advanta ...

2020

Naming CHO cells for bio-manufacturing: Genome plasticity and variant phenotypes of cell populations in bioreactors question the relevance of old names

Florian Maria Wurm

Chinese Hamster Ovary [CHO] cells are the workhorse for production of modern biopharmaceuticals. They are however immortalized cells with a high propensity for genetic change. Judging from published culture records, CHO cell populations have undergone hund ...

2021