Making sense of genomic islands of differentiation in light of speciation

JBW Wolf, H Ellegren - Nature Reviews Genetics, 2017 - nature.com
As populations diverge, genetic differences accumulate across the genome. Spurred by
rapid developments in sequencing technology, genome-wide population surveys of natural …

[HTML][HTML] Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

JF Gui, L Zhou, XY Li - Water Biology and Security, 2022 - Elsevier
Fish biology has been developed for more than 100 years, but some important
breakthroughs have been made in the last decade. Early studies commonly concentrated on …

Drivers and dynamics of a massive adaptive radiation in cichlid fishes

F Ronco, M Matschiner, A Böhne, A Boila, HH Büscher… - Nature, 2021 - nature.com
Adaptive radiation is the likely source of much of the ecological and morphological diversity
of life,,–. How adaptive radiations proceed and what determines their extent remains unclear …

Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files

M Malinsky, M Matschiner… - Molecular ecology …, 2021 - Wiley Online Library
Patterson's D, also known as the ABBA‐BABA statistic, and related statistics such as the f4‐
ratio, are commonly used to assess evidence of gene flow between populations or closely …

Natural hybridization reduces vulnerability to climate change

CJ Brauer, J Sandoval-Castillo, K Gates… - Nature Climate …, 2023 - nature.com
Under climate change, species unable to track their niche via range shifts are largely reliant
on genetic variation to adapt and persist. Genomic vulnerability predictions are used to …

Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice

B Wu, J Meng, H Liu, D Mao, H Yin, Z Zhang, X Zhou… - Nature Genetics, 2023 - nature.com
One-step and two-step pathways are proposed to synthesize cytokinin in plants. The one-
step pathway is mediated by LONELY GUY (LOG) proteins. However, the enzyme for the two …

Deriving genotypes from RAD-seq short-read data using Stacks

NC Rochette, JM Catchen - Nature protocols, 2017 - nature.com
Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

M Malinsky, H Svardal, AM Tyers, EA Miska… - Nature ecology & …, 2018 - nature.com
The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent
vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 …

Contrasting signatures of genomic divergence during sympatric speciation

AF Kautt, CF Kratochwil, A Nater… - Nature, 2020 - nature.com
The transition from 'well-marked varieties' of a single species into 'well-defined species'—
especially in the absence of geographic barriers to gene flow (sympatric speciation)—has …

Recombination rate variation shapes barriers to introgression across butterfly genomes

SH Martin, JW Davey, C Salazar, CD Jiggins - PLoS biology, 2019 - journals.plos.org
Hybridisation and introgression can dramatically alter the relationships among groups of
species, leading to phylogenetic discordance across the genome and between populations …