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      A new species of Pristimantis (Amphibia, Anura, Strabomantidae) from the Pui Pui Protected Forest (central Peru), with comments on Pristimantis albertus Duellman & Hedges, 2007

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          Abstract

          We describe a new Pristimantis species from the eastern Andes, Región Junín, Peru following an integrative taxonomic approach. The description is based on three adult males (snout-vent length 25.7–28.8 mm) collected in two montane forests between 1615 and 1800 m a.s.l. in the Pui Pui Protected Forest and its close surroundings. The new species is mainly characterised by absence of tympanum, presence of inner tarsal fold, broad horizontal red band across iris, ventre mottled black and cream and ventral surfaces of thighs salmon and grey mottled. Amongst the Amazonian and montane forest Pristimantis that have the ventre and groin contrastingly black and cream mottled, P. sinschi sp. nov. is morphologically most similar to P. lindae and P. ventrimarmoratus . However, DNA barcoding revealed a clear distinction between these three species and placed P. sinschi sp. nov. as sister taxon of P. lindae . We designate a lectotype for P. ventrimarmoratus and restrict the type locality of this species to “El Topo, R. Pastaza, [Provincia Tungurahua,] E. Ecuador, 4200 feet”. Pristimantis albertus and P. sagittulus are recorded for the first time in the Región Junín. Additional data on morphology and systematics are provided for P. albertus .

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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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            MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

            Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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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
                17 November 2020
                : 994
                : 125-148
                Affiliations
                [1 ] Department of Zoology, National Museum, Cirkusová 1740, 193 00, Prague 9, Czech Republic National Museum Prague Czech Republic
                [2 ] Department of Biology, Illinois Wesleyan University, P.O. Box 2900, Bloomington, IL 61701, USA Illinois Wesleyan University Bloomington United States of America
                [3 ] Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Praha 2, Czech Republic Charles University Prague Czech Republic
                Author notes
                Corresponding author: Jiří Moravec ( jiri.moravec@ 123456nm.cz )

                Academic editor: A. Crottini

                Article
                56277
                10.3897/zookeys.994.56277
                7686219
                daf634df-cf7c-4b13-966d-68716e1a921b
                Jiří Moravec, Edgar Lehr, Karel Kodejš

                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
                : 07 July 2020
                : 06 October 2020
                Categories
                Research Article
                Anura
                Craugastoridae
                Biodiversity & Conservation
                Cenozoic
                Americas

                Animal science & Zoology
                andes,anuran diversity,montane rainforests,pristimantis sinschi sp. nov.,p. sagittulus,p. ventrimarmoratus

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