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      Three new species of frogs of the genus Pristimantis (Anura, Strabomantidae) with a redefinition of the P. lacrimosus species group

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          Abstract

          A new phylogeny for the Pristimantis lacrimosus species group is presented, its species content reviewed, and three new species described from the eastern slopes of the Ecuadorian Andes. Our phylogeny includes, for the first time, samples of P. aureolineatus , P. bromeliaceus , and P. lacrimosus . The morphology of hyperdistal subarticular tubercles is also assessed among 21 species of Pristimantis . The P. lacrimosus species group is composed of 36 species distributed in the Chocó, Guiana, and Amazon regions of tropical South America with a single species reaching Central America. Ancestral area reconstruction indicates that, despite its high diversity in the Amazon region, the P. lacrimosus group originated in the Pacific basin, Chocó region of Ecuador and Colombia. Pristimantis amaguanae sp. nov. is most closely related to P. bromeliaceus . It differs from P. bromeliaceus by being smaller, having transversal dark bands in the hindlimbs (absent or faint in P. bromeliaceus ) and the absence of discoidal fold (present in P. bromeliaceus ). Pristimantis nankints sp. nov. and P. romeroae sp. nov. are part of a clade of predominantly light-green frogs that includes P. acuminatus , P. enigmaticus , P. limoncochensis , and P. omeviridis . Pristimantis nankints sp. nov. and P. romeroae sp. nov. can be distinguished from all of them by the presence of a dark dorsolateral stripe that borders a light green band on a green background. Hyperdistal tubercles are present in all examined species of the P. lacrimosus species group and its sister clade. Species with hyperdistal tubercles are characterized by having relatively long terminal phalanges and narrow T-shaped expansion at the end of the terminal phalange. We discuss the phylogenetic distribution of these characters and their potential diagnostic significance.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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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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              MUSCLE: multiple sequence alignment with high accuracy and high throughput.

              We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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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
                2020
                16 November 2020
                : 993
                : 121-155
                Affiliations
                [1 ] Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre y Roca, Aptdo. 17-01-2184, Quito, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
                Author notes
                Corresponding author: Santiago R. Ron (santiago.r.ron@gmail.com)

                Academic editor: A. Crottini

                Author information
                https://orcid.org/0000-0001-6300-9350
                https://orcid.org/0000-0002-5827-7462
                Article
                53559
                10.3897/zookeys.993.53559
                7683497
                33262676
                91f3012f-cfcd-40d0-9dc6-7798930e1aef
                Santiago R. Ron, Julio Carrión, Marcel A. Caminer, Yerka Sagredo, María J. Navarrete, Jhael A. Ortega, Andrea Varela-Jaramillo, Gabriela A. Maldonado-Castro, Claudia Terán

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 April 2020
                : 05 September 2020
                Funding
                Funded by: Secretaría de Educación Superior, Ciencia, Tecnología e Innovación 501100004299 http://doi.org/10.13039/501100004299
                Categories
                Research Article
                Amphibia
                Animalia
                Anura
                Biodiversity & Conservation
                Biogeography
                Evolutionary biology
                Genetics
                Molecular systematics
                Systematics
                Cenozoic
                Americas
                Central America and the Caribbean
                South America

                Animal science & Zoology
                amazon,andes, brachycephaloidea ,morphology,phalanges,phylogeny,pristimantis amaguanae sp. nov.,pristimantis nankints sp. nov.,pristimantis romeroae sp. nov.,subarticular tubercles,systematics,taxonomy, terrarana

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