Questioning the monophyly of Anthroherponina (Coleoptera: Leiodidae: Cholevinae: Leptodirini) and description of three new, ecologically ultraspecialized subterranean species

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The beetle subtribe Anthroherponina (Coleoptera: Leiodidae), including also ecologically specialized and semi-aquatic hygropetricolous genera, presents one of the most illustrative examples of morphological variability in cave-adapted animals. However, phylogenetic relations within the tribe remain dubious. Recent exploration of deep-phreatic caves of the Western Balkans Dinaric Karst enabled us to collect all known Anthroherponina genera and access new populations of hygropetricolous beetles, representatives of the iconic Hadesia and elusive Nauticiella. We studied the taxonomic structure of newly collected semi-aquatic beetle populations by using traditional morphology and deploying uni- and multilocus molecular species delimitation. In addition, we tested the monophyly of the subtribe Anthroherponina and set the group’s evolutionary development into a palaeogeographic context by reconstructing a multilocus calibrated phylogeny. As a result, three new species of specialized semi-aquatic beetles are described. The morphologically based monophyly of Anthroherponina was shown to be an artefact of evolutionary convergences, while the evolutionary development of the monophylum seems to be paired with the orogeny of the Dinarides. Finally, the new results raise more questions about our understanding of evolution in subterranean beetles and their adaptation to special ecological niches.

Related collections

Most cited references 70

Record: found
Abstract: found
Article: found

Is Open Access

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

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.

0 comments Cited 10924 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

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%.

0 comments Cited 7072 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

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.