Deep learning as a tool for ecology and evolution

ML Borowiec, RB Dikow, PB Frandsen… - Methods in Ecology …, 2022 - Wiley Online Library
Deep learning is driving recent advances behind many everyday technologies, including
speech and image recognition, natural language processing and autonomous driving. It is …

Supervised machine learning for population genetics: a new paradigm

DR Schrider, AD Kern - Trends in Genetics, 2018 - cell.com
As population genomic datasets grow in size, researchers are faced with the daunting task
of making sense of a flood of information. To keep pace with this explosion of data …

Efficient ancestry and mutation simulation with msprime 1.0

F Baumdicker, G Bisschop, D Goldstein, G Gower… - Genetics, 2022 - academic.oup.com
Stochastic simulation is a key tool in population genetics, since the models involved are
often analytically intractable and simulation is usually the only way of obtaining ground-truth …

The importance of genomic variation for biodiversity, ecosystems and people

M Stange, RDH Barrett, AP Hendry - Nature Reviews Genetics, 2021 - nature.com
Abstract The 2019 United Nations Global assessment report on biodiversity and ecosystem
services estimated that approximately 1 million species are at risk of extinction. This …

Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships

FT Burbrink, FG Grazziotin, RA Pyron… - Systematic …, 2020 - academic.oup.com
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups.
For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes …

Multiple episodes of interbreeding between Neanderthal and modern humans

FA Villanea, JG Schraiber - Nature ecology & evolution, 2019 - nature.com
Neanderthals and anatomically modern humans overlapped geographically for a period of
over 30,000 years following human migration out of Africa. During this period, Neanderthals …

Using genomic data to infer historic population dynamics of nonmodel organisms

AC Beichman, E Huerta-Sanchez… - Annual Review of …, 2018 - annualreviews.org
Genome sequence data are now being routinely obtained from many nonmodel organisms.
These data contain a wealth of information about the demographic history of the populations …

The unreasonable effectiveness of convolutional neural networks in population genetic inference

L Flagel, Y Brandvain… - Molecular biology and …, 2019 - academic.oup.com
Population-scale genomic data sets have given researchers incredible amounts of
information from which to infer evolutionary histories. Concomitant with this flood of data …

Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random …

F Collin, G Durif, L Raynal, E Lombaert… - Molecular Ecology …, 2021 - Wiley Online Library
Simulation‐based methods such as approximate Bayesian computation (ABC) are well‐
adapted to the analysis of complex scenarios of populations and species genetic history. In …

A community-maintained standard library of population genetic models

JR Adrion, CB Cole, N Dukler, JG Galloway… - elife, 2020 - elifesciences.org
The explosion in population genomic data demands ever more complex modes of analysis,
and increasingly, these analyses depend on sophisticated simulations. Recent advances in …