4.2 Article

Weak seed banks influence the signature and detectability of selective sweeps

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis

William R. Shoemaker et al.

Summary: Fluctuations in resource availability can constrain individual growth and reproduction, and thus impact population evolution. Dormancy can act as an evolutionary buffer, altering the accumulation of genetic diversity and mutation trajectories in bacteria.

GENETICS (2022)

Article Biochemistry & Molecular Biology

Limits and convergence properties of the sequentially Markovian coalescent

Thibaut Paul Patrick Sellinger et al.

Summary: Various methods based on SMC have been developed to infer population demographic history using full genome sequence data, but a comprehensive investigation into the limitations of these methods is lacking. Researchers have introduced a tool to infer the best case convergence of SMC methods and evaluated the inference accuracy when assumptions are violated. Additionally, they emphasize the importance of the transition matrix in SMC methods.

MOLECULAR ECOLOGY RESOURCES (2021)

Review Multidisciplinary Sciences

Principles of seed banks and the emergence of complexity from dormancy

Jay T. Lennon et al.

Summary: Populations across the tree of life have evolved the ability to contend with suboptimal conditions through dormancy, entering a reversible state of reduced metabolic activity to form complex seed banks storing information and imparting memory that give rise to multi-scale structures and networks in ecosystems. Dormancy not only exists among diverse taxa but is also found in stem cells, brains, and tumors.

NATURE COMMUNICATIONS (2021)

Article Genetics & Heredity

Sweeps in time: leveraging the joint distribution of branch lengths

Gertjan Bisschop et al.

Summary: Current methods for identifying positively selected regions in the genome have limitations in accounting for the timing of adaptive events and comparing models of selective sweeps and sequence data. This study introduces a new method that explicitly models the effect of positive selection on genealogical histories, providing higher power to identify old selective sweeps and accurately infer the time and strength of selection. Additionally, the framework allows analysis beyond polymorphism data, leveraging information in patterns of linked variants and providing a link between analytic understanding of sweeps on sequence variation and recent advances in simulation and heuristic inference procedures.

GENETICS (2021)

Article Ecology

Statistical tools for seed bank detection

Jochen Blath et al.

THEORETICAL POPULATION BIOLOGY (2020)

Article Genetics & Heredity

Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Thibaut Paul Patrick Sellinger et al.

PLOS GENETICS (2020)

Article Biology

Structural properties of the seed bank and the two island diffusion

Jochen Blath et al.

JOURNAL OF MATHEMATICAL BIOLOGY (2019)

Article Genetics & Heredity

Selective Sweeps

Wolfgang Stephan

GENETICS (2019)

Article Biochemistry & Molecular Biology

SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model

Benjamin C. Haller et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Biochemistry & Molecular Biology

McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes

Remi Tournebize et al.

MOLECULAR ECOLOGY RESOURCES (2019)

Review Evolutionary Biology

Evolution with a seed bank: The population genetic consequences of microbial dormancy

William R. Shoemaker et al.

EVOLUTIONARY APPLICATIONS (2018)

Article Biochemical Research Methods

Efficient pedigree recording for fast population genetics simulation

Jerome Kelleher et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Ecology

Fisher-Wright model with deterministic seed bank and selection

Bendix Koopmann et al.

THEORETICAL POPULATION BIOLOGY (2017)

Article Statistics & Probability

A NEW COALESCENT FOR SEED-BANK MODELS

Jochen Blath et al.

ANNALS OF APPLIED PROBABILITY (2016)

Article Multidisciplinary Sciences

DNA damage checkpoint kinase ATM regulates germination and maintains genome stability in seeds

Wanda M. Waterworth et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Biochemical Research Methods

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

Paul R. Staab et al.

BIOINFORMATICS (2015)

Article Genetics & Heredity

Genetic Variability Under the Seedbank Coalescent

Jochen Blath et al.

GENETICS (2015)

Article Biochemistry & Molecular Biology

Population genetic dynamics of an invasion reconstructed from the sediment egg bank

Markus Moest et al.

MOLECULAR ECOLOGY (2015)

Article Genetics & Heredity

Genetic Variability Under the Seedbank Coalescent

Jochen Blath et al.

GENETICS (2015)

Article Biochemistry & Molecular Biology

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

Pavlos Pavlidis et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemical Research Methods

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets

N. Alachiotis et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

Germ banks affect the inference of past demographic events

Daniel Zivkovic et al.

MOLECULAR ECOLOGY (2012)

Article Multidisciplinary Sciences

Inference of seed bank parameters in two wild tomato species using ecological and genetic data

Aurelien Tellier et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Editorial Material Plant Sciences

Spores of ectomycorrhizal fungi: ecological strategies for germination and dormancy

Kazuhide Nara

NEW PHYTOLOGIST (2009)

Article Genetics & Heredity

The distribution of beneficial mutant effects under strong selection

Rowan D. H. Barrett et al.

GENETICS (2006)

Review Biology

Germ banking: Bet-hedging and varlable release from egg and seed dormancy

MEK Evans et al.

QUARTERLY REVIEW OF BIOLOGY (2005)