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.

https://science.sciencemag.org/content/sci/346/6210/763.full.pdf

Phylogenomics resolves the timing and pattern of insect evolution

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary model. Although partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search algorithms due to the existence of phylogenetic (partial) terraces. Here, we introduce the phylogenetic terrace aware (PTA) data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic inference software.

/pdf/terrace-aware-data-structure-for-phylogenomic-inference-from-1uhmj47jh4.pdf

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

/pdf/applications-of-next-generation-sequencing-in-molecular-3x2xhuh15b.pdf

Applications of next generation sequencing in molecular ecology of non-model organisms

In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2]–[4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies.

https://epub.ub.uni-muenchen.de/13699/1/woerheide_13699.pdf

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4-20% complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291-347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. (Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.)

/pdf/a-total-evidence-approach-to-dating-with-fossils-applied-to-4zt7zn0fxx.pdf

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

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.

/pdf/a-phylogenomic-approach-to-resolve-the-arthropod-tree-of-3nxzrze8l6.pdf

Falko Roeding

Papers

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator).

EST sequencing of Onychophora and phylogenomic analysis of Metazoa.