Fredrik Ronquist
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View article: HAPP: High-accuracy pipeline for processing deep metabarcoding data
HAPP: High-accuracy pipeline for processing deep metabarcoding data Open
Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel alg…
View article: Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring
Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring Open
Obtaining genome‐wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenom…
View article: Moving towards better risk assessment for invertebrate conservation
Moving towards better risk assessment for invertebrate conservation Open
Global change threatens a vast number of species with severe population declines or even extinction. The threat status of an organism is often designated based on geographic range, population size, or declines in either. However, invertebr…
View article: High-throughput biodiversity surveying sheds new light on the brightest of insect taxa
High-throughput biodiversity surveying sheds new light on the brightest of insect taxa Open
DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored re…
View article: The business case for investing in biodiversity data
The business case for investing in biodiversity data Open
1. The private sector is increasingly aware of its dependence on biodiversity and the financial risks and opportunities involved. This has generated a lot of demand for investing in nature-positive solutions. There is an obvious and non-ne…
View article: HAPP: High-Accuracy Pipeline for Processing deep metabarcoding data
HAPP: High-Accuracy Pipeline for Processing deep metabarcoding data Open
We introduce HAPP, a high-accuracy pipeline for processing deep metabarcoding data, leveraging data richness to enhance the signal-to-noise-ratio. Starting with denoised amplicon sequence variants, the pipeline consists of four steps: (1) …
View article: Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar
Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar Open
We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, weekly Malaise trap samples were collected at 203 locations within 100 sites in Sweden…
View article: High-throughput biodiversity surveying sheds new light on the brightest of insect taxa
High-throughput biodiversity surveying sheds new light on the brightest of insect taxa Open
Sampling of species-rich taxa followed by DNA metabarcoding is quickly becoming a popular high-throughput method for biodiversity inventories. Unfortunately, we know little about its accuracy and efficiency, as the results mostly pertain t…
View article: Temperature and water availability drive insect seasonality across a temperate and a tropical region
Temperature and water availability drive insect seasonality across a temperate and a tropical region Open
The more insects there are, the more food there is for insectivores and the higher the likelihood for insect-associated ecosystem services. Yet, we lack insights into the drivers of insect biomass over space and seasons, for both tropical …
View article: Biotic and abiotic drivers of ecosystem functioning differ between a temperate and a tropical region
Biotic and abiotic drivers of ecosystem functioning differ between a temperate and a tropical region Open
Any single ecosystem will provide many ecosystem functions. Whether these functions tend to increase in concert or trade off against each other is a question of much current interest. Equally topical are the drivers behind ecosystem functi…
View article: The rarity of Invertebrates prevents reliable application of IUCN Red-List criteria.
The rarity of Invertebrates prevents reliable application of IUCN Red-List criteria. Open
Among the most widely used information underpinning international conservation efforts is the IUCN Red List of endangered species. The Red List designates species extinction risk based on geographic range, population size, or declines in e…
View article: TreePPL: A Universal Probabilistic Programming Language for Phylogenetics
TreePPL: A Universal Probabilistic Programming Language for Phylogenetics Open
We present TreePPL, a universal probabilistic programming language (PPL) designed for probabilistic modeling and inference in phylogenetics. In TreePPL, the model is expressed as a computer program, which can generate simulations from the …
View article: Phylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships
Phylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships Open
Gall wasps (Hymenoptera: Cynipidae) comprise 13 distinct tribes whose interrelationships remain incompletely understood. Recent analyses of ultra‐conserved elements (UCEs) represent the first attempt at resolving these relationships using …
View article: Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating
Skyline Fossilized Birth–Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating Open
Several total-evidence dating studies under the fossilized birth–death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed “deep root attraction (DRA).” For two sp…
View article: The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas
The ASV Portal Allows for Efficient Handling of DNA Derived Data in the Living Atlas Open
The Living Atlas platform functions as the national hub for integration of biodiversity data with environmental and contextual information in many countries, but it has had limited functionality for species occurrence data derived from DNA…
View article: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating Open
Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed “deep root attraction (DRA)”. For two sp…
View article: FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples
FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples Open
Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcodin…
View article: Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating Open
sup_tables_figs.pdf: supplementary tables and figures simulations: results under different simulation settings hymenoptera: xml and tree files by analyzing the hymenoptera data eutheria: xml and tree files by analyzing the placental mammal…
View article: Optimizing insect metabarcoding using replicated mock communities
Optimizing insect metabarcoding using replicated mock communities Open
Metabarcoding (high‐throughput sequencing of marker gene amplicons) has emerged as a promising and cost‐effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has…
View article: Automatic Alignment in Higher-Order Probabilistic Programming Languages
Automatic Alignment in Higher-Order Probabilistic Programming Languages Open
Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and M…
View article: Automatic Alignment in Higher-Order Probabilistic Programming Languages
Automatic Alignment in Higher-Order Probabilistic Programming Languages Open
Probabilistic Programming Languages (PPLs) allow users to encode statistical inference problems and automatically apply an inference algorithm to solve them. Popular inference algorithms for PPLs, such as sequential Monte Carlo (SMC) and M…
View article: Optimizing insect metabarcoding using replicated mock communities
Optimizing insect metabarcoding using replicated mock communities Open
Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has…
View article: Phylogenomic Analysis of Protein-Coding Genes Resolves Complex Gall Wasp Relationships
Phylogenomic Analysis of Protein-Coding Genes Resolves Complex Gall Wasp Relationships Open
The phylogeny of gall wasps (Cynipidae) and their parasitic relatives has attracted considerable attention in recent years. The family is now widely recognized to fall into thirteen natural lineages, designated tribes, but the relationship…
View article: Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better
Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better Open
DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specime…
View article: Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better
Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better Open
Raw data from metabarcoding of mock communities sequencing on Illumina MiSeq (COI + 16S markers), from the article "Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better", Metabarcod…