Genetic diversity loss in the Anthropocene

M Exposito-Alonso, TR Booker, L Czech, L Gillespie… - Science, 2022 - science.org
Anthropogenic habitat loss and climate change are reducing species' geographic ranges,
increasing extinction risk and losses of species' genetic diversity. Although preserving …

Genomics and conservation: Guidance from training to analyses and applications

LM Schiebelhut, AS Guillaume, A Kuhn… - Molecular Ecology …, 2024 - Wiley Online Library
Environmental change is intensifying the biodiversity crisis and threatening species across
the tree of life. Conservation genomics can help inform conservation actions and slow …

A fast, reproducible, high-throughput variant calling workflow for population genomics

CD Mirchandani, AJ Shultz… - Molecular Biology …, 2024 - academic.oup.com
The increasing availability of genomic resequencing data sets and high-quality reference
genomes across the tree of life present exciting opportunities for comparative population …

Wide-ranging consequences of priority effects governed by an overarching factor

CR Chappell, MK Dhami, MC Bitter, L Czech… - Elife, 2022 - elifesciences.org
Priority effects, where arrival order and initial relative abundance modulate local species
interactions, can exert taxonomic, functional, and evolutionary influences on ecological …

Maroon rice genomic diversity reflects 350 years of colonial history

MS Van De Loosdrecht, NM Pinas… - Molecular Biology …, 2024 - academic.oup.com
Abstract Maroons in Suriname and French Guiana descend from enslaved Africans who
escaped the plantations during colonial times. Maroon farmers still cultivate a large diversity …

grenedalf: population genetic statistics for the next generation of pool sequencing

L Czech, JP Spence, M Expósito-Alonso - Bioinformatics, 2024 - academic.oup.com
Pool sequencing is an efficient method for capturing genome-wide allele frequencies from
multiple individuals, with broad applications such as studying adaptation in Evolve-and …

[HTML][HTML] Population genomic analysis reveals key genetic variations and the driving force for embryonic callus induction capability in maize

P Liu, L Ma, S Jian, Y He, G Yuan, F Ge, Z Chen… - Journal of Integrative …, 2024 - Elsevier
Genetic transformation has been an effective technology for improving the agronomic traits
of maize. However, it is highly reliant on the use of embryonic callus (EC) and shows a …

Monitoring rapid evolution of plant populations at scale with Pool-Sequencing

L Czech, Y Peng, JP Spence, PLM Lang, T Bellagio… - BioRxiv, 2022 - biorxiv.org
The change in allele frequencies within a population over time represents a fundamental
process of evolution. By monitoring allele frequencies, we can analyze the effects of natural …

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

AR Vieira, F de Sousa, J Bilro, MB Viegas… - Scientific Reports, 2024 - nature.com
The development of management strategies for the promotion of sustainable fisheries relies
on a deep knowledge of ecological and evolutionary processes driving the diversification …

ARA: a flexible pipeline for automated exploration of NCBI SRA datasets

A Maurya, M Szymanski, WM Karlowski - GigaScience, 2023 - academic.oup.com
Background One of the most effective and useful methods to explore the content of
biological databases is searching with nucleotide or protein sequences as a query …