Fredrik Ronquist

Fredrik Ronquist
Swedish Museum of Natural History · Department of Bioinformatics and Genetics

Professor

About

270
Publications
69,087
Reads
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103,328
Citations
Additional affiliations
January 2013 - September 2015
Swedish Museum of Natural History
Position
  • Head of Department
January 2013 - October 2015
Swedish Museum of Natural History
Position
  • Head of Department
August 2003 - June 2007
Florida State University
Position
  • Professor (Associate)

Publications

Publications (270)
Preprint
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 not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resol...
Article
Full-text available
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 specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, alth...
Article
Full-text available
New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling "dark taxa", here defined as groups for which <10% of all species are described and the estimated diversity exceeds 1000 species. Species delimitation for these taxa should be based on multiple data sources ("integrative taxonomy")...
Chapter
Probabilistic programming languages (PPLs) allow users to encode arbitrary inference problems, and PPL implementations provide general-purpose automatic inference for these problems. However, constructing inference implementations that are efficient enough is challenging for many real-world problems. Often, this is due to PPLs not fully exploiting...
Preprint
Full-text available
Probabilistic programming languages (PPLs) allow for natural encoding of arbitrary inference problems, and PPL implementations can provide automatic general-purpose inference for these problems. However, constructing inference implementations that are efficient enough is challenging for many real-world problems. Often, this is due to PPLs not fully...
Article
Full-text available
The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms races. To learn more about the coevolution of these two clades, we reconstructed ancestral ecological networks using...
Preprint
Full-text available
New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling 'dark taxa', that we here define as clades for which <10% of all species are described and the estimated diversity exceeds 1000 species. Species delimitation should be based on multiple data sources ('integrative taxonomy') but coll...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s42003-021-01922-8
Article
Full-text available
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here, we...
Article
Full-text available
Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed...
Preprint
Full-text available
The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms-races. To learn more about how the two lineages co-evolved over time, we reconstructed ecological networks and netwo...
Article
Full-text available
High‐throughput sequencing (HTS) is increasingly being used for the characterisation and monitoring of biodiversity. If applied in a structured way, across broad geographic scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated indepe...
Article
Full-text available
Background: Despite Sweden's strong entomological tradition, large portions of its insect fauna remain poorly known. As part of the Swedish Taxonomy Initiative, launched in 2002 to document all multi-cellular species occurring in the country, the first taxonomically-broad inventory of the country's insect fauna was initiated, the Swedish Malaise T...
Article
Full-text available
The genus Megaselia Rondani (Diptera: Phoridae) is one of the largest in the animal kingdom, with nearly 1700 described species and many remaining to be discovered. Work on this group is notoriously challenging due to the extreme species diversity, poor knowledge of higher‐level relationships and lack of molecular data. In this paper, we present th...
Preprint
Full-text available
Statistical phylogenetic analysis currently relies on complex, dedicated software packages, making it difficult for evolutionary biologists to explore new models and inference strategies. Recent years have seen more generic solutions based on probabilistic graphical models, but this formalism can only partly express phylogenetic problems. Here we s...
Article
Full-text available
Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such interactions make the simplifying assumption that parasites have a single host. Many methods also focus on...
Preprint
Full-text available
1. Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70 % ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA. Highly concentrated ethanol (95 - 100 %), preferred as a DNA preservative, has generally been assumed to make specime...
Article
Full-text available
Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish i...
Article
Full-text available
Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such...
Article
Full-text available
The Swedish Malaise Trap Project (SMTP) is one of the most ambitious insect inventories ever attempted. The project was designed to target poorly known insect groups across a diverse range of habitats in Sweden. The field campaign involved the deployment of 73 Malaise traps at 55 localities across the country for three years (2003-2006). Over the p...
Article
Full-text available
Rapid and reliable identification of insects is important in many contexts, from the detection of disease vectors and invasive species to the sorting of material from biodiversity inventories. Because of the shortage of adequate expertise, there has long been an interest in developing automated systems for this task. Previous attempts have been bas...
Preprint
Full-text available
Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such...
Article
Full-text available
DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers...
Conference Paper
Full-text available
The DINA Consortium (“ DI gital information system for NA tural history data”, https://dina-project.net ) was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate through a distributed Open Source development model to produce a flexible and sustainable collection management syst...
Preprint
Full-text available
We consider probabilistic programming for birth-death models of evolution and introduce a new widely-applicable inference method that combines an extension of the alive particle filter (APF) with automatic Rao-Blackwellization via delayed sampling. Birth-death models of evolution are an important family of phylogenetic models of the diversification...
Preprint
Full-text available
Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish i...
Preprint
Full-text available
Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such associations make the simplifying assumption that parasites have a single host. Many methods also focus on...
Presentation
Full-text available
Background: Metabarcoding of the DNA extracted from preservative ethanol of insect bulk samples, instead of homogenized tissue, could bring a series of advantages such as reducing processing time and handling (reducing risk of cross-contamination). But, more importantly, it would allow researchers to conduct further work on intact insects (taxonomy...
Preprint
Full-text available
DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several alternative approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two differ...
Preprint
Full-text available
Probabilistic programming is a programming paradigm for expressing flexible probabilistic models. Implementations of probabilistic programming languages employ a variety of inference algorithms, where sequential Monte Carlo methods are commonly used. A problem with current state-of-the-art implementations using sequential Monte Carlo inference is t...
Article
Full-text available
Insect metabarcoding has been mainly based on PCR amplification of short fragments within the ‘barcoding region’ of the gene COI. However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make t...
Article
Full-text available
By mechanisms that are still unknown, gall wasps (Cynipidae) induce plants to form complex galls, inside which their larvae develop. The family also includes inquilines (phytophagous forms that live inside the galls of other gall inducers) and possibly also parasitoids of gall inducers. The origin of cynipids is shrouded in mystery, but it has been...
Conference Paper
Full-text available
The DINA Consortium ( “ DI gital information system for NA tural history data”, https://dina-project.net, Fig. 1 ) was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate through a distributed Open Source development model to produce a flexible and sustainable collection manage...
Preprint
Full-text available
Insect metabarcoding has been mainly based on PCR amplification of short fragments within the 'barcoding region' of the gene COI. However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make t...
Presentation
Full-text available
Background: Many universal primers for insect metabarcoding have been reported to introduce amplification bias due to mismatches with the templates. In a diverse sample, such as a soil or Malaise trap sample of insects, this may result in some species being less efficiently amplified or not detected at all. We explored the potential of solving this...
Article
Full-text available
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also...
Article
Full-text available
Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may...
Article
Full-text available
Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, mor...
Article
Full-text available
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed...
Article
Full-text available
The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circula...
Article
Full-text available
Directional evolution has played an important role in shaping the morphological, ecological and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus hampering the study of directionality. Here we explore a simple, non-stationary model of evolution for d...
Article
Full-text available
Sampling tree space is the most challenging aspect of Bayesian phylogenetic inference. The sheer number of alternative topologies is problematic by itself. In addition, the complex dependency between branch lengths and topology increases the difficulty of moving efficiently among topologies. Current tree proposals are fast but sample new trees usin...
Article
Full-text available
With 1,400 described species, Megaselia is one of the most species-rich genera in the animal kingdom, and at the same time one of the least studied. An important obstacle to taxonomic progress is the lack of knowledge concerning the phylogenetic structure within the genus. Classification of Megaselia at the level of subgenus is incomplete although...
Data
Figure S2. Majority rule consensus tree from a Bayesian analysis of lucifrons group relationships based on 28S D2 data
Data
Figure S1. Majority rule consensus tree from a Bayesian analysis of lucifrons group relationships based on COI data
Article
Full-text available
Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relat...
Article
Full-text available
Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomi...
Article
The braconid subfamily Euphorinae is a large, cosmopolitan group of endoparasitoid wasps. The majority of species attack adult hosts, a strategy that is rare among parasitic wasps, but there are also many species that attack nymphs and larval stages. Euphorine hosts may belong to a variety of insect orders (Coleoptera, Hemiptera, Hymenoptera, Neuro...
Article
Full-text available
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software...
Article
Full-text available
Variation in the evolutionary process across the sites of nucleotide sequence alignments is well established, and is an increasingly pervasive feature of datasets composed of gene regions sampled from multiple loci and/or different genomes. Inference of phylogeny from these data demands that we adequately model the underlying process heterogeneity;...
Conference Paper
Natural history collections constitute the major source of data for research in phylogenetics and systematics, and provide crucial information for analyses of long-term trends in ecology and environmental sciences. Recent mass-digitization efforts have opened up such collections abroad for transformative e-science approaches, but research dependent...