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      A new species of green-eyed Cordylus Laurenti, 1768 from the west-central highlands of Angola, and the rediscovery of Cordylus angolensis (Bocage, 1895) (Squamata: Cordylidae)

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      Vertebrate Zoology
      Pensoft Publishers

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          Abstract

          Cordylus angolensis (Bocage, 1895) was described 128 years ago on the basis of a single specimen collected at Caconda in the west-central highlands of Angola. Additional specimens referred to this species were collected at ‘Mombolo’ (also in the central highlands) during the Vernay Angola Expedition in 1925. As the holotype was apparently destroyed in the fire of 1978 at the Museu Bocage in Lisbon and no additional specimens have been collected, its taxonomic status and phylogenetic relationships has remained uncertain. The species has eluded all efforts aimed at its re-discovery in the vicinity of the type locality, with a single specimen from near Condé, north of Mombolo—collected in 1970 by Wulf Haacke—the only other specimen of Cordylus known from west-central Angola. Recent field work in the Angolan highlands resulted in the collection of a series of specimens from Taqueta Mountain (west of Caconda), Monte Verde (Sandula, ‘Mombolo’) and Uassamba (Vondo). A phylogenetic analysis, using three mitochondrial and six nuclear genes, indicated the existence of two distinct species-level lineages in the Angolan highlands. These two species are allopatric and morphologically distinct, differing especially in terms of their colour patterns, eye colour and certain scalation characteristics. We therefore confirm that C. angolensis is a valid species and designate a neotype, and describe a new species, Cordylus momboloensis sp. nov.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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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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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              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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                Author and article information

                Contributors
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                Journal
                Vertebrate Zoology
                VZ
                Pensoft Publishers
                2625-8498
                1864-5755
                July 14 2023
                July 14 2023
                : 73
                : 599-646
                Article
                10.3897/vz.73.e95639
                e19c97af-6636-4916-a892-7d388c25b168
                © 2023

                http://creativecommons.org/licenses/by/4.0/

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