Description of a new thermal species of the genus Hyalella from Peru with molecular phylogeny of the family Hyalellidae (Crustacea, Amphipoda)

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Abstract

In recent years, the impact of rising water temperatures associated with global warming on cold-water freshwater organisms has become a major issue, and understanding the physiological and ecological elements that support temperature limits is essential for the conservation biology of freshwater organisms. We describe a new species of thermophilic hyalellid amphipod, Hyalella yashmara sp. nov. from the Peruvian hot spring Baños del Inca Cajamarca and this could potentially contribute to understanding the high temperature preference of these. We found that this new species can live in water temperatures ranging from 19.8 to 52.1°C, that, to our knowledge, is the highest recorded habitat temperature of amphipods. Hyalella yashmara sp. nov. is most similar to H. meinerti Stebbing, 1899 from Peru. However, this new species differs from the latter in features of gnathopods 1 and 2, sternal gills, uropod 3 and telson. A detailed morphological comparison between Hyalella yashmara sp. nov. and Peruvian species is also provided. Our molecular phylogenetic analyses based on the nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences strongly support the monophyly of Hyalellidae (=Hyalella). Since Hyalellidae was found to form a sister group with Chiltoniidae, these two families were expected to have originated from a common ancestor that invaded freshwater habitats from marine environments when the continents of South America, Africa and Australia were united as Gondwana. Our findings suggest that the South American species of Hyalella are not monophyletic and that the North American species are likely to share a most recent common ancestor with H. yashmara sp. nov. ZooBank: urn:lsid:zoobank.org:act:190CFB16-7BE4-4786-A97F-0AFD8CD72DEA

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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

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

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

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

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.