The great greenbriers gall mystery resolved? New species of Aprostocetus Westwood (Hymenoptera, Eulophidae) gall inducer and two new parasitoids (Hymenoptera, Eurytomidae) associated with Smilax L. in southern Florida, USA

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Abstract

Aprostocetus smilax Gates & Zhang, sp. nov., is described from stem and leaf galls on Smilax havanensis Jacq. in southern Florida, USA. It is the third species of Aprostocetus Westwood known to induce plant galls. Two parasitoids of A. smilax are also described: Phylloxeroxenus smilax Gates & Zhang sp. nov. and Sycophila smilax Gates & Zhang, sp. nov. We conclude that A. smilax is the true gall inducer on Smilax L., and thus the host records of Diastrophus smilacis Ashmead and its inquiline Periclistus smilacis Ashmead, both from Smilax, are erroneous.

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ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

Subha Kalyaanamoorthy, Bui Minh, Thomas Wong … (2017)

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)

Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

K Katoh (2002)

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.