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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 4, 2022

Abstract The change in allele frequencies within a population over time represents fundamental process of evolution. By monitoring frequencies, we can analyze the effects natural selection and genetic drift on populations. To efficiently track time-resolved change, large experimental or wild populations be sequenced as pools individuals sampled using high-throughput genome sequencing (called Evolve & Resequence approach, E&R). Here, present set experiments hundreds genotypes model plant Arabidopsis thaliana to showcase power this approach study rapid evolution at scale. First, validate that DNA directly extracted from flowers multiple plants -- organs are relatively consistent size easy sample produces comparable results other, more expensive state-of-the-art approaches such sampling individual leaves. Sequencing 25-50 ∼40X coverage recovers genome-wide diverse with accuracy r > 0.95. Secondly, enable analyses evolutionary adaptation E&R highly replicated environments, provide open source tools streamline data curation calculate various statistics two orders magnitude faster than current software. demonstrate usefulness our method, conducted two-year outdoor experiment A. show signals genomic regions. We how these laboratory computational Pool-seq-based methods scaled across many climates.

Language: Английский

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Genomic Responses to Climate Change: Making the Most of the Drosophila Model

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: July 13, 2021

It is pressing to understand how animal populations evolve in response climate change. We argue that new sequencing technologies and the use of historical samples are opening unprecedented opportunities investigate genome-wide responses changing environments. However, there important challenges interpreting emerging findings. First, it essential differentiate genetic adaptation from phenotypic plasticity. Second, extremely difficult map genotype, phenotype, fitness. Third, neutral demographic processes natural selection affect variation similar ways. Drosophila melanogaster , a classical model organism with decades research, uniquely suited overcome most these challenges. In near future, long-term time series datasets D. will provide exciting study recent change lay groundwork for related research non-model systems.

Language: Английский

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Genetic diversity loss in the Anthropocene

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Oct. 15, 2021

More species than ever before are at risk of extinction due to anthropogenic habitat loss and climate change. But even that not threatened have seen reductions in their populations geographic ranges, likely impacting genetic diversity. Although preserving diversity is key maintaining adaptability species, we lack predictive tools global estimates across ecosystems. By bridging theories biodiversity population genetics, introduce a mathematical framework understand the naturally occurring DNA mutations within decreasing species. Analysing genome-wide variation data 10,095 geo-referenced individuals from 20 plant animal show follows power law with area (the mutations-area relationship), which can predict spatial computer simulations local extinctions. Given pre-21 st century values ecosystem transformations, estimate over 10% may already be lost, surpassing United Nations targets for preservation. These estimated losses could rapidly accelerate advancing change destruction, highlighting need forecasting facilitate implementation policies protect resources globally.

Language: Английский

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A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Dec. 24, 2021

Abstract Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times study changes in allele frequencies can help clarify relative roles neutral and non-neutral short time scales. This compares whole-genome sequence variation recently collected natural population samples Drosophila melanogaster against collection made approximately 35 years prior from same locality – encompassing roughly 500 generations evolution. The frequency between these points would suggest relatively small local effective size order 10,000, significantly smaller than global species. Some loci display stronger be expected anywhere genome under neutrality most notably tandem paralogs Cyp6a17 Cyp6a23 , which are impacted by structural associated with resistance pyrethroid insecticides. We find genome-wide excess outliers for high differentiation old new samples, but larger number adaptation targets may have affected SNP-level versus window differentiation. also evidence strengthening latitudinal clines: northern-associated alleles increased an average nearly 2.5% at SNPs previously identified as clinal outliers, no such pattern is observed random SNPs. project underscores scientific potential using investigate how evolution operates populations, quantifying has changed over ecologically relevant timescales.

Language: Английский

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