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Applications in Plant Sciences
Scopus
ISSN 2168-0450 · Wiley · 578 articles in the index
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Journal Article
Are they two seeds in a pod? Comparing seed rain recovery in grasslands using artificial grass carpets versus sticky traps
Abstract Premise Seed dispersal is a critical process for plant community assembly; however, natural rates of seed arrival are rarely quantified compared with other assembly mechanisms, especially in herbaceous communities. Methods Here we compare the utility of artificial grass carpet squares…
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Journal Article
DNA metabarcoding reveals greater plant diversity than morphological seed analysis of bird feces
Abstract Premise Fruit‐eating birds drive seed dispersal in recovering tropical ecosystems, shaping forest regeneration. Molecular techniques, such as DNA metabarcoding, enable diet analysis from feces and can provide complementary frugivory data where dispersal is infrequent, as well as aid in…
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Journal Article
Fern spore dispersal: A methodological review and experimental field study
Abstract Spore dispersal is one of the most important but perhaps the least investigated and understood processes in determining the geographical distribution of fern species. After a methodological review of the aerobiology of fern spores, we examined the impact of spore characteristics and…
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Journal Article
Animal‐mediated seed dispersal: A review of study methods
Abstract By dispersing seeds, animals provide ecological functions critical for the ecology, evolution, and conservation of plants. We review quantitative and empirical approaches and emerging technologies to quantify processes and patterns of animal‐mediated seed dispersal (zoochory) across its…
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Journal Article
Unlocking fruit dimensions: Quantification of functional traits driving plant–frugivore interactions
Abstract Fleshy fruits attract animals to ingest fruit, swallow the seeds, and release them in the landscape, thus facilitating seed dispersal and plant regeneration. Attraction of animal dispersers is achieved via attractants such as color or scent, and rewards like sugars, lipids, and…
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Journal Article
A simple and affordable protocol to assess censer seed dispersal: First confirmation of the mechanism in the genus Solanum
Abstract Premise The censer seed dispersal mechanism, whereby mature fruits are retained on plants and seeds dispersed by mechanical shaking, is among the most specialized wind‐aided seed dispersal strategies employed by the flowering plants. An efficient, affordable, and easily repeatable protocol…
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Journal Article
Experimental methods for wind tunnel studies of seed dispersal by wind
Abstract The complexity and variability of natural environments make quantitative studies of seed wind dispersal challenging. Wind tunnel experiments offer a controlled alternative to investigate the mechanisms of seed wind dispersal. This review focuses on wind tunnels and the associated…
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Journal Article
Detecting introgression from phylogenetic invariant site patterns using machine learning
Abstract Premise Detecting historical introgression among populations or species from genomic data is a common goal in evolutionary genetics. Most current methods fall into two major categories: network inference and admixture inference. Network inference (e.g., SNaQ) is computationally challenging…
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Journal Article
Ancient hybridization and phylogenetic discordance: Exploring evolutionary complexity in Asteraceae
Abstract Premise Conflicting phylogenetic signals are common in plant phylogenomics and often reflect evolutionary histories shaped by processes like hybridization, incomplete lineage sorting, and whole‐genome duplication (WGD). We aimed to identify and assess these complex processes in the…
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Journal Article
tanggle: An R package for the visualization of phylogenetic networks
Abstract Premise Phylogenetic trees depict evolutionary relationships among taxa. However, they are strictly bifurcating structures that do not take into account several types of evolutionary events such as horizontal gene transfer, hybridization, or introgression. Although the development of new…
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Journal Article
Leveraging target enrichment and genome skimming (Hyb‐Seq) of herbarium collections to unlock timber DNA barcoding
Abstract Premise DNA barcoding for timber species identification requires comprehensive reference datasets, informative DNA barcodes, and cost‐effective protocols. We developed a workflow leveraging Hyb‐Seq (target capture sequencing and genome skimming) to address these challenges, and we tested…
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Journal Article
HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees
Abstract Premise Hybrid capture sequencing (Hyb‐Seq) is a widely used approach in phylogenomics, providing efficient access to targeted genomic regions. However, deriving high‐quality phylogenetic trees from raw sequencing reads requires extensive bioinformatics processing, which increases…
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Journal Article
Off‐target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica
Abstract Premise The recovery of non‐target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker‐based pipelines enable the use of short…
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Journal Article
Detecting cryptic ghost lineage introgression in four‐taxon genomic datasets
Abstract Premise Hybridization and introgression are pervasive evolutionary forces that have played fundamental roles in shaping the diversity of wild and domesticated plants. Four‐taxon tests for introgression provide a reliable framework for detecting signatures of ancient introgression from…
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Journal Article
HapAsmbl: A reference‐aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations
Abstract Premise Advances in long‐read sequencing offer new possibilities to investigate haplotype diversity across multiple genes in plants and other taxa through multi‐locus, long‐read amplicon sequencing (multi‐locus LRAS). Despite this progress, there is a notable absence of dedicated…
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Journal Article
Pearl's causality for integrating ecological datasets: A case study on Myricaria germanica in northern Italy
Abstract Premise Applied ecology can significantly influence policy decisions on environmental issues. Therefore, research in this field should be as transparent and reproducible as possible. Existing expertise from a broad range of disciplines should also be integrated into ecological research to…
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Journal Article
Enabling the study of gene function in gymnosperms: Virus‐induced gene silencing in Ephedra tweedieana
Abstract Premise As the sister clade to angiosperms, extant gymnosperms are crucial for reconstructing ancestral gene regulatory networks in seed plants. This highlights the need for model systems representing each of their distinct lineages. However, tools to quickly and effectively investigate…