Karen Meusemann

Bio: Karen Meusemann is an academic researcher from University of Freiburg. The author has contributed to research in topics: Phylogenetic tree & Sister group. The author has an hindex of 32, co-authored 78 publications receiving 5568 citations. Previous affiliations of Karen Meusemann include Commonwealth Scientific and Industrial Research Organisation & Leibniz Institute for Neurobiology.

Phylogenomics resolves the timing and pattern of insect evolution

Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

Abstract: Arthropods were the first animalsto conquer land and air. They encompass more than three quarters of all described living species.Thisextraordinaryevolutionarysuccessisbasedonanastoundinglywidearrayofhighly adaptivebody organizations. A lackofrobustlyresolvedphylogeneticrelationships,however,currentlyimpedesthereliablereconstructionoftheunderlyingevolutionaryprocesses.Here,weshowthatphylogenomicdatacansubstantiallyadvanceourunderstandingofarthropod evolution and resolve several conflicts among existinghypotheses. We assembled a data set of 233 taxa and 775 genes from which an optimally informative data set of 117 taxa and 129 genes was finally selected using new heuristics and compared with the unreduced data set.We included novelexpressed sequencetag (EST) data for 11 species and allpublished phylogenomic data augmentedbyrecentlypublishedESTdata ontaxonomicallyimportantarthropodtaxa.This thorough sampling reduces the chance of obtainingspurious results due to stochastic effects of undersampling taxa and genes. Orthology prediction of genes, alignmentmasking tools, and selection of most informativegenes due to a balanced taxa–gene ratio using new heuristics were established.Our optimizeddata setrobustly resolves major arthropod relationships.We received strong supportforasistergrouprelationshipofonychophoransandeuarthropodsandstrongsupportforacloseassociationoftardigrades andcycloneuralia.Withinpancrustaceans,our analysesyieldedparaphyleticcrustaceansandmonophyletichexapods and robustly resolved monophyletic endopterygoteinsects.However, our analysesalsoshowed for few deep splitsthat were recently thought to be resolved,for example,the positionofmyriapods, a remarkable sensitivitytomethods of analyses.

Phylogenomics Reveals the Evolutionary Timing and Pattern of Butterflies and Moths

Abstract: Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths' evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.

UFBoot2: Improving the Ultrafast Bootstrap Approximation.

Abstract: The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.

Abstract: Summary After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users The release of version 50 has marked a leap towards a modern software for evolutionary analyses Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity Availability and implementation ape is distributed through the Comprehensive R Archive Network: http://cranr-projectorg/package=ape Further information may be found at http://ape-packageirdfr/

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

Abstract: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.