Parallel selection on a dormancy gene during domestication of crops from multiple families

Nature Genetics, Journal Year: 2018, Volume and Issue: 50(10), P. 1435 - 1441

Published: Sept. 21, 2018

Language: Английский

---

Contrasting signatures of genomic divergence during sympatric speciation

Nature, Journal Year: 2020, Volume and Issue: 588(7836), P. 106 - 111

Published: Oct. 28, 2020

Abstract The transition from ‘well-marked varieties’ of a single species into ‘well-defined species’—especially in the absence geographic barriers to gene flow (sympatric speciation)—has puzzled evolutionary biologists ever since Darwin 1,2 . Gene counteracts buildup genome-wide differentiation, which is hallmark speciation and increases likelihood evolution irreversible reproductive (incompatibilities) that complete process 3 Theory predicts genetic architecture divergently selected traits can influence whether sympatric occurs 4 , but empirical tests this theory are scant because comprehensive data difficult collect synthesize across species, owing their unique biologies histories 5 Here, within young complex neotropical cichlid fishes ( Amphilophus spp.), we analysed genomic divergence among populations species. By generating new genome assembly re-sequencing 453 genomes, uncovered have been suggested be important for divergence. Species differ monogenic or oligogenic affect ecological performance and/or mate choice show remarkably localized differentiation. contrast, differentiation diverged polygenic genomically widespread much higher overall, consistent with effective stable flow. Thus, conclude simple trait architectures not always as conducive previously suggested, whereas promote rapid sympatry.

Language: Английский

---

Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: May 26, 2022

Abstract We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, identify 81.5 million SNPs INDELs, of which 38.5% are absent in dbSNP Build 151. provide a population-specific reference panel an online imputation server ( https://wbbc.westlake.edu.cn/ ) could yield substantial improvement performance population, especially low-frequency rare variants. By analyzing singleton density WGS data, we find selection signatures SNX29 , DNAH1 WDR1 genes, derived alleles alcohol metabolism genes ADH1A ADH1B emerge around 7,000 years ago tend to be more common from 4,000 East Asia. Genetic evidence supports corresponding geographical boundaries Qinling-Huaihe Line Nanling Mountains, separate Han into subgroups, reveal that North was homogeneous than South Han.

Language: Английский

---

Parallel gene expansions drive rapid dietary adaptation in herbivorous woodrats

Science, Journal Year: 2025, Volume and Issue: 387(6730), P. 156 - 162

Published: Jan. 9, 2025

How mammalian herbivores evolve to feed on chemically defended plants remains poorly understood. In this study, we investigated the adaptation of two species woodrats ( Neotoma lepida and N. bryanti ) creosote bush Larrea tridentata ), a toxic shrub that expanded across southwestern United States after Last Glacial Maximum. We found creosote-adapted have elevated gene dosage multiple biotransformation enzyme families. These duplication events occurred independently substantially increase expression genes, especially within glucuronidation pathway. propose increased resulting from is an important mechanism by which animals initially adapt novel environmental pressures.

Language: Английский

---

A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication

Nature Plants, Journal Year: 2017, Volume and Issue: 3(6)

Published: May 8, 2017

Language: Английский

---

Signatures of selection and environmental adaptation across the goat genome post-domestication

Genetics Selection Evolution, Journal Year: 2018, Volume and Issue: 50(1)

Published: Nov. 14, 2018

Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of breeds and these are classified mainly into two types: (i) adaptation different breeding systems and/or purposes (ii) environments. As a result, approximately 600 developed worldwide; they differ considerably from one another in terms phenotypic characteristics adapted wide range climatic conditions. In this work, we analyzed AdaptMap dataset, which is composed data more than 3000 animals collected worldwide genotyped with CaprineSNP50 BeadChip. These were partitioned groups based on geographical area, production uses, available records solid coat color environmental variables including sampling coordinates, investigate role natural artificial selection shaping genome breeds.Several signatures chromosomal regions detected across breeds, sub-geographical clusters, groups. contain genes that involved important biological processes, such as milk-, meat- or fiber-related production, color, glucose pathway, oxidative stress response, size, circadian clock differences. Our results confirm previous findings other species extreme environments human provide new could explain some differences between according their distribution environments.These analyses comprehensive first picture global domestication process highlight possible may worldwide.

Language: Английский

---

The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: April 30, 2020

Abstract The Democratic Republic of the Congo (DRC) harbors 11% global malaria cases, yet little is known about spatial and genetic structure parasite population in that country. We sequence 2537 Plasmodium falciparum infections, including a nationally representative sample from DRC samples surrounding countries, using molecular inversion probes - high-throughput genotyping tool. identify an east-west divide haplotypes to confer resistance chloroquine sulfadoxine-pyrimethamine. Furthermore, we highly related parasites over large geographic distances, indicative gene flow migration. Our results are consistent with background isolation by distance combined effects selection for antimalarial drug resistance. This study provides high-resolution view across country Africa baseline how implementation programs may impact populations.

Language: Английский

---

Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 20, 2021

Urbanisation is increasing worldwide, and there now ample evidence of phenotypic changes in wild organisms response to this novel environment. Yet, the genetic genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, address major knowledge gap our understanding wildlife urban adaptation. We find that a combination polygenic allele frequency shifts recurrent selective sweeps associated adaptation environments. While haplotypes under selection rarely shared across populations, occur within same genes, mostly linked neural function development. Collectively, show widespread songbird occurs through unique core-set behaviour-linked genes.

Language: Английский

---

MOTHER‐OF‐FT‐AND‐TFL1 regulates the seed oil and protein content in soybean

New Phytologist, Journal Year: 2023, Volume and Issue: 239(3), P. 905 - 919

Published: Feb. 6, 2023

Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed are regulated by complex quantitative trait loci (QTLs) have undergone intensive selections during the domestication of soybean. It essential to identify genetic components understand their mechanism behind in We report MOTHER-OF-FT-AND-TFL1 (GmMFT) gene classical QTL has been reported regulate content many studies. Mutation MFT decreased seeds weight both Arabidopsis soybean, whereas increased expression GmMFT enhanced weight. Haplotype analysis showed selection, which resulted extended haplotype homozygosity cultivated soybean enriching oil-favorable allele modern cultivars. This work unraveled GmMFT-mediated regulating weight, revealed previously unknown function provides new insights into targeted improvement breeding.

Language: Английский

---

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

ABSTRACT Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European ( Anguilla anguilla ) American eel A. rostrata represent a remarkable case hybridisation. Both are panmictic spawn partial sympatry Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found Iceland. We studied from into using whole‐genome sequences 78 individuals, including European, 21 putative hybrid eels. Previous studies few genetic markers could not resolve whether involved simple unidirectional backcrossing or more complex swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were F1 first‐generation backcrosses towards eel, with some showing backcrossing. All eels outside Iceland contained short chromosomal blocks indicating porous genome. no evidence for previously hypothesised geographical gradients introgression Several regions showed high divergence, but haplotype identified both within these regions. There was little correspondence between relative F ST absolute divergence d XY ), former reflecting selective sweeps species reduced recombination rather than barrier loci. A single genomic region repeated under positive selection species. The study illustrates can maintain integrity despite genomes standing one potentially be available future adaptive responses other

Language: Английский

---