grenedalf: Population genetic statistics for the next generation of Pool sequencing

Bioinformatics, Год журнала: 2024, Номер 40(8)

Опубликована: Авг. 1, 2024

Abstract Summary 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-Resequence experiments, monitoring of genetic diversity wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written C++ that implements common population statistics θ, Tajima’s D, FST sequencing. It orders magnitude faster than current tools, focused on providing usability scalability, while also offering plethora input file formats convenience options. Availability implementation grenedalf published under the GPL-3, freely available at github.com/lczech/grenedalf.

Язык: Английский

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On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)

Peer Community Journal, Год журнала: 2025, Номер 5

Опубликована: Апрель 9, 2025

It is vital to understand the genomic basis of differences in ecologically important traits if we are impact global change on biodiversity and enhance our ability for targeted intervention. This study explores potential a novel genome-wide association (GWAS) approach identifying loci underlying quantitative polygenic natural populations, based phenotypic population means allele frequency data as obtained e.g. by PoolSeq approaches. Extensive genetic forward simulations demonstrate that generally effective oligogenic moderately relatively insensitive low heritability. However, applicability limited highly architectures pronounced structure. The required sample size moderate with very good results being already few dozen populations scored. When combined machine learning feature selection, method performs well predicting means. efficiency method, particularly when using pooled sequencing bulk phenotyping, makes GWAS studies more accessible research genomics. Moreover, direct comparison individual GWAS, proposed performed constistently better regard number true positive identified prediction accuracy. Overall, this highlights promise popGWAS dissecting complex populations.

Язык: Английский

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Re-focusing sampling, design and experimental methods to assess rapid evolution by non-native plant species

Biological Invasions, Год журнала: 2024, Номер 26(5), С. 1327 - 1343

Опубликована: Фев. 12, 2024

Abstract Evolution can occur over contemporary timescales, which may be crucial for the invasive success of non-native plant species. Many studies have shown rapid evolution by comparing native and populations in common gardens. However, our understanding mechanisms underpinning is still incomplete. Here, we identify progress, applications, limitations on plants with respect to sampling, experimental design methods. To encompass broad variation within between ranges, recommend sampling across large-scale environmental gradients. We also suggest careful consideration pitfalls related choice seed families biotic interaction under focus. The latter should chosen a view both treatment corresponding field data estimate population history. Furthermore, exploiting multiple omics approaches address complexity interactions, account non-adaptive molecular demographic history populations. reviewed papers that studied quantified how many these met criteria. anticipate disentangling adaptive drivers among-population increase accuracy research evolution, integrating phenotypic, metabolomic genomic bring opportunities studying complex interactions. illustrate importance large collaborative networks present scientific network iCONNECT (integrative CONyza NEtwork Contemporary Trait evolution), goal motivating similar mechanistic evolution.

Язык: Английский

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Repeatability of evolution and genomic predictions of temperature adaptation in seed beetles

Nature Ecology & Evolution, Год журнала: 2025, Номер unknown

Опубликована: Май 16, 2025

Climate warming is threatening biodiversity by increasing temperatures beyond the optima of many ectotherms. Owing to inherent non-linear relationship between temperature and rate cellular processes, such shifts towards hot are predicted impose stronger selection compared with corresponding cold temperature. This suggests that when adaptation occurs, it should be relatively rapid predictable. Here we tested this hypothesis from level single-nucleotide polymorphisms life-history traits in beetle Callosobruchus maculatus. We conducted an evolve-and-resequence experiment on three genetic backgrounds reared at or Indeed, find phenotypic evolution was faster more repeatable However, genomic level, heat less across backgrounds. As a result, predictions populations exposed were accurate within, but not between, These results seem best explained redundancy increased importance epistasis during heat, imply same mechanisms exert strong increase repeatability reduce level. Thus, key phenotypes data may become increasingly difficult as climates warm.

Язык: Английский

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Understanding local plant extinctions before it is too late: bridging evolutionary genomics with global ecology

New Phytologist, Год журнала: 2023, Номер 237(6), С. 2005 - 2011

Опубликована: Янв. 6, 2023

Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant before it too late. However, most models biodiversity risk under global change do not account for genetic variation local adaptation different populations. Population diversity critical understanding because populations may be more or less susceptible and, if lost, would reduce total species. Two new modeling frameworks advance our from angle: Rapid climate change-driven disruptions in are predicted associations between genomes climates. Furthermore, losses land-use transformations estimated by scaling relationships species' with habitat area. Overall, these eco-evolutionary methods predictability - possibly preventability ongoing

Язык: Английский

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Phylogenetically‐conserved candidate genes unify biodiversity–ecosystem function relationships and eco‐evolutionary dynamics across biological scales

Molecular Ecology, Год журнала: 2023, Номер 32(16), С. 4467 - 4481

Опубликована: Июнь 9, 2023

Abstract The intra‐ and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding how evolution has shaped biodiversity, (as a whole) alters ecological dynamics hence eco‐evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically‐conserved across species sustaining functional traits as an inclusive unit transcending boundaries. This framework merges knowledge from genomics ecology, first provide guidelines concrete example for identifying (PCCGs) within communities measuring PCCGs. We then explain measured PCCGs can be linked to ecosystem functions, which unifies recent observations that both are important functions. highlight processes shaping PCCG diversity patterns argue their respective role inferred concepts derived population genetics. Finally, may shift field focal‐species approach more realistic focal‐community approach. provides novel perspective investigate global consequences loss biological scales, these changes further alter evolution.

Язык: Английский

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A New Dawn for Protist Biogeography

Global Ecology and Biogeography, Год журнала: 2024, Номер 33(12)

Опубликована: Окт. 7, 2024

ABSTRACT Aim Biogeographers have believed for a long time that the geographical distributions of protists are only determined by environmental conditions, because dispersal is not limited. During past two decades, field has come way to show historical and spatial factors also significantly contribute shaping protist distributions, calling reappraisal our understanding biogeography. Methods We review current state‐of‐the‐art on biogeography, highlighting several outstanding questions opportunities. Our brings together insights from different disciplines, ranging morphology‐based research environmental, population speciation genomics. Results Protist communities harbour cosmopolitan geographically restricted species shaped both local conditions processes, yet relative contributions these patterns processes likely differs depending geographic scale, lineage habitat being investigated. The ready move beyond decades‐long ubiquity versus (moderate) endemicity discourse instead ask why where specific clades more prone widespread or distributions. With advent next‐generation sequencing technologies, whole‐genome ancient DNA surveys, it now possible integrate multiple lines evidence investigate communities, populations at an unprecedented scale detail. Outlook To further advance field, community needs focus understudied habitats lineages, study impact traits biogeographical patterns, perform targeted experimental work disentangle underlie biogeographies expand develop databases with sequence, trait, distributional phylogenetic information protists. Given good boundaries central unravelling remains crucial invest in polyphasic taxonomic research.

Язык: Английский

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Impact of Fog on Physiology and Growth of Plant Species

Опубликована: Янв. 1, 2025

Язык: Английский

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On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 14, 2024

ABSTRACT It is vital to understand the genomic basis of differences in ecologically important traits if we are impact global change on biodiversity and enhance our ability for targeted intervention. This study explores potential a novel genome-wide association (GWAS) approach identifying loci underlying quantitative polygenic natural populations, based phenotypic population means allele frequency data as obtained e.g. by PoolSeq approaches. Extensive genetic forward simulations demonstrate that generally effective oligogenic moderately relatively insensitive low heritability. However, applicability limited highly architectures pronounced structure. The required sample size moderate with very good results being already few dozen populations scored. When combined machine learning feature selection, method performs well predicting means. efficiency method, particularly when using pooled sequencing bulk phenotyping, makes GWAS studies more accessible research genomics. Moreover, direct comparison individual GWAS, proposed performed constistently better regard number true positive identified prediction accuracy. Overall, this highlights promise popGWAS dissecting complex populations.

Язык: Английский

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Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

Journal of Evolutionary Biology, Год журнала: 2023, Номер 36(3), С. 550 - 562

Опубликована: Янв. 31, 2023

Abstract While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree parallelism evolutionary responses to is limited. In this study, combined resurrection approach with an evolve‐and‐resequence design examine genome‐wide changes following drought. We exposed genetically similar replicate populations annual plant Brassica rapa derived from a field population in southern California four generations experimental drought or watered conditions greenhouse. Genome‐wide sequencing ancestral descendant pools identified hundreds SNPs showed evidence rapidly evolving response Several these were stress genes, two prior study species. However, almost all unique among populations, indicating largely nonparallel, despite fact replicates same founder had experienced controlled consistent selection regimes. This nonparallelism evolution at level because polygenetic adaptation allowing for multiple different routes outcomes. Our findings help elucidate relationship between genomic shed light on predictability environmental change.

Язык: Английский

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