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      A new Andean genus, Lafontaineana, with descriptions of four new species and two new Neotropical species of Panthea (Noctuidae, Pantheinae)

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          Abstract

          Lafontaineana Martinez, gen. nov. is proposed as a new Neotropical genus of Pantheinae , forming a sister group to Gaujonia Dognin, 1891 based on a phylogenetic analysis. In addition, one new combination and four new species are proposed: Lafontaineana marmorifera (Walker, 1865), comb. nov. (Colombia), Lafontaineana alexandrae Martinez, sp. nov. (Ecuador), Lafontaineana imama Martinez, sp. nov. (Colombia), Lafontaineana puma Martinez, sp. nov. (Ecuador), and Lafontaineana thuta Martinez, sp. nov. (Ecuador). Two new Neotropical species of Panthea are described, Panthea hondurensis Martinez, sp. nov. and Panthea taina Martinez, sp. nov.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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            IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

            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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              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.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                2
                urn:lsid:arphahub.com:pub:45048D35-BB1D-5CE8-9668-537E44BD4C7E
                urn:lsid:zoobank.org:pub:91BD42D4-90F1-4B45-9350-EEF175B1727A
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2021
                06 April 2021
                : 1028
                : 113-134
                Affiliations
                [1 ] Entomology and Nematology Department, University of Florida, Gainesville, 32611, FL, USA
                [2 ] Agriculture and Agri-food Canada, Canadian National Collection of Insects, Arachnids and Nematodes, K.W. Neatby Bldg., 960 Carling Ave., K1A 0C6, Ottawa, ON, Canada
                [3 ] Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, 32611, FL, USA
                Author notes
                Corresponding author: Jose I. Martinez ( joemartinez@ 123456ufl.edu )

                Academic editor: E.J. van Nieukerken

                Author information
                https://orcid.org/0000-0003-4368-2729
                https://orcid.org/0000-0003-4160-7629
                Article
                56784
                10.3897/zookeys.1028.56784
                8044069
                33889048
                222ff0a8-3575-4860-b734-37718fff8134

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                : 21 July 2020
                : 03 March 2021
                Funding
                Funded by: National Geographic Society 100006363 http://doi.org/10.13039/100006363
                Categories
                Research Article
                Animalia
                Arthropoda
                Hexapoda
                Insecta
                Invertebrata
                Lepidoptera
                Systematics
                Taxonomy
                Americas
                South America

                Animal science & Zoology
                andes mountains,cloud forest, lichnoptera ,neotropics,south america,systematics

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