Potamophylax coronavirus sp. n. (Trichoptera: Limnephilidae), a new species from Bjeshkët e Nemuna National Park in the Republic of Kosovo, with molecular and ecological notes

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Abstract

The Western Balkans are an important hotspot of caddisfly diversity in Europe, with several microscale endemics, many of whom were discovered during the recent years. The genus Potamophylax Wallengren, 1891 likely originated and diversified in Europe, with the Balkan Peninsula being one of the most important diversity hotspots. In this paper, we describe the new species Potamophylax coronavirusi sp. n. from Bjeshkët e Nemuna National Park in the Republic of Kosovo. The new species belongs to the Potamophylax winneguthi species group and is morphologically most similar to Potamophylax juliani Kumanski 1999, currently known only from Bulgaria, and Potamophylax winneguthi Klapalek, 1902, known from Bosnia and Herzegovina and Serbia. The male of the new species differs from its most similar congeners mainly in exhibiting (1) elongated subrectangular superior appendages in lateral view; (2) hardly acuminate, almost rounded apex of intermediate appendages; (3) differently shaped, irregular and higher inferior appendages; (4) narrow spinate area, roughly rectangular in dorsal view, slightly wider at the base, and (5) paramere shape and/or spine pattern. The new species also differs by its considerably smaller size and association with open, high altitude eucrenal zones. In the phylogenetic analysis, the relatively long branch leading to P. coronavirusi sp. n. shows that this species' divergence is on par with those among the other species in the P. winneguthi species group.The new species is most probably a microendemic of Bjeshkët e Nemuna, thus highlighting further this area as an important hotspot of caddisfly biodiversity in Europe.

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We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

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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.