Weigert A.,University of Leipzig |
Helm C.,University of Leipzig |
Meyer M.,Max Planck Institute for Evolutionary Anthropology |
Nickel B.,Max Planck Institute for Evolutionary Anthropology |
And 7 more authors.
Molecular Biology and Evolution | Year: 2014
Annelida is one of three animal groups possessing segmentation and is central in considerations about the evolution of different character traits. It has even been proposed that the bilaterian ancestor resembled an annelid. However, a robust phylogeny of Annelida, especially with respect to the basal relationships, has been lacking. Our study based on transcriptomic data comprising 68,750-170,497 amino acid sites from 305 to 622 proteins resolves annelid relationships, including Chaetopteridae, Amphinomidae, Sipuncula, Oweniidae, and Magelonidae in the basal part of the tree. Myzostomida, which have been indicated to belong to the basal radiation as well, are now found deeply nested within Annelida as sister group to Errantia in most analyses. On the basis of our reconstruction of a robust annelid phylogeny, we show that the basal branching taxa include a huge variety of life styles such as tube dwelling and deposit feeding, endobenthic and burrowing, tubicolous and filter feeding, and errant and carnivorous forms. Ancestral character state reconstruction suggests that the ancestral annelid possessed a pair of either sensory or grooved palps, bicellular eyes, biramous parapodia bearing simple chaeta, and lacked nuchal organs. Because the oldest fossil of Annelida is reported for Sipuncula (520 Ma), we infer that the early diversification of annelids took place at least in the Lower Cambrian. © 2014 The Author.
Potamitis I.,Technological Educational Institute of Crete |
Ntalampiras S.,Polytechnic of Milan |
Jahn O.,Zoological Research Museum Alexander Koenig |
Riede K.,Zoological Research Museum Alexander Koenig
Applied Acoustics | Year: 2014
The primary purpose for pursuing this research is to present a modular approach that enables reliable automatic bird species identification on the basis of their sound emissions in the field. A practical and complete computer-based framework is proposed to detect and time-stamp particular bird species in continuous real field recordings. Acoustic detection of avian sounds can be used for the automatized monitoring of multiple bird taxa and querying in long-term recordings for species of interest for researchers, conservation practitioners, and decision makers, such as environmental indicator taxa and threatened species. This work describes two novel procedures and offers an open modular framework that detects and time-stamps online calls and songs of target bird species and is fast enough to report results in reasonable time for non-processed field recordings of many thousands files and is generic enough to accommodate any species. The framework is evaluated on two large corpora of real field data, targeting the calls and songs of American Robin Turdus migratorius, a Northamerican oscine passerine (true songbird) and the Common Kingfisher Alcedo atthis, a non-passerine species with a wide distribution throughout Eurasia and North Africa. With the aim of promoting the widespread use of digital autonomous recording units (ARUs) and species recognition technologies the processing code and a large corpus of audio recordings is provided in order to enable other researchers to perform and assess comparative experiments. © 2014 Elsevier Ltd. All rights reserved.
News Article | November 10, 2016
No scales or eyes: together with a team of Iraqi scientists, researchers from the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) and the Zoological Research Museum Alexander Koenig (ZFMK) have described a strange new species of fish, Eidinemacheilus proudlovei. The species was first discovered in the Kurdish region of Iraq at the end of March 2016. The blind fish, belonging to the stone loach family, lives in inaccessible subterranean streams. The heavy rainfall and flooding that hit the northern Zagros mountains in Iraq in March 2016 were anything but a blessing to the local population. Nor to the blind fish washed up onto Earth's surface from a newly formed source following a rise in the groundwater table: most of the helpless creatures fell victim to birds. However, Korsh Ararat, biologist at the University of Sulaimani in the Kurdish cultural capital of Sulaymaniyah in the autonomous region of Kurdistan, was quick to grasp the enormity of the event. He succeeded in securing a few specimens of the curious fish, which for several days had continued to be flushed out of a hole in the ground and into a nearby brook. In a bid to find out more about the species, the biologist contacted Dr. Jörg Freyhof, ichthyologist at IGB. Whilst Freyhof studied the morphological features of the fish and compared them to the only other known representative of blind loaches in the Middle East, Dr. Matthias Geiger analysed the creatures' DNA at ZFMK in Bonn and had the DNA barcode developed. When the scientists then brought together their findings on the body structure and considered the extent to which the species differed genetically from all other known species of fish, they realised that it had to be a new species, now seen alive for the first time ever. The fish is most closely related to Eidinemacheilus smithi, another subterranean species of fish from Iran. Until then, E. smithi was the only known species of a genus that was described only recently. The new species was given the name Eidinemacheilus proudlovei. Freyhof and his team chose this name in honour of the scientist Graham S. Proudlove, a globally acclaimed cave fish expert. "E. proudlovei has no eyes or scales, its skin has no pigments whatsoever. The fish probably graze bacterial films from cave walls, but nothing is known about the biology of this unusual loach," explained Jörg Freyhof. The spontaneously created source soon dried up, and the fish are now once again inaccessible underground. Not only were the extremely unusual circumstances of the find very special, the site where the new species of fish was discovered was also exceptional. "We did not expect anyone to concern themselves with such small fish in Iraq. But research and nature conservation are still being conducted in this war-torn country," stated Freyhof. Today, subterranean fish are endangered species, especially on account of dam projects, the implementation of which destroys these specialised creatures' habitats. "The problem also exists in Europe, where subterranean animal species are at great risk from dam projects, particularly in Croatia and Bosnia-Herzegovina," emphasised Jörg Freyhof. Little is known about subterranean ecosystems because they are difficult to access.
Wesener T.,Zoological Research Museum Alexander Koenig |
Raupach M.J.,AG Molekulare Taxonomie Mariner Organismen |
Decker P.,Metadatenbank Myriapoda
PLoS ONE | Year: 2011
To elucidate the speciation mechanisms prevalent within hotspots of biodiversity, and the evolutionary processes behind the rise of their species-rich and endemic biota, we investigated the phylogeny of the giant fire-millipede genus Aphistogoniulus Silvestri, 1897, a Malagasy endemic. This study is the first comprehensive (molecular and morphological) phylogenetic study focusing on millipede (class Diplopoda) speciation on Madagascar. The morphological analysis is based on 35 morphological characters and incorporates ten described as well as two newly described species (A. rubrodorsalis
Fourcade Y.,University of Angers |
Engler J.O.,University of Gottingen |
Engler J.O.,Zoological Research Museum Alexander Koenig |
Rodder D.,Zoological Research Museum Alexander Koenig |
Secondi J.,University of Angers
PLoS ONE | Year: 2014
MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one "virtual" derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases. © 2014 Fourcade et al.
Rodder D.,University of Trier |
Rodder D.,Zoological Research Museum Alexander Koenig |
Engler J.O.,University of Trier |
Engler J.O.,Zoological Research Museum Alexander Koenig
Global Ecology and Biogeography | Year: 2011
Aim Studies of environmental niche shift/niche conservatism that are based on species distribution modelling require a quantification of niche purity and potential overlap. Although various metrics have been proposed for this task, no comparisons of their performance are available yet that express the linearity of range shifts and error-proneness. Herein, we assess the performance of six niche overlap metrics using three sister pairs of plethodontid salamanders as well as artificial species to test for linearity of overlap curves, impacts of varying potential distribution sizes and study area sizes. Location North America, artificial environments. Methods Species distribution models for the salamanders were performed with Maxent, and artificial species were created in the R environment. Potential distributions of species with varying range sizes and extents of the study area were compared using the Bray-Curtis distance BC, Schoener's D, two different modifications of the Hellinger distance I mod, I cor, Pianka's O and Horn's R. Niche overlaps in ecological space were compared using linear discriminant analyses based on principal components. Results Simulations of niche overlaps revealed strong variations in the performance of the niche overlap metrics. In artificial species, BC and D performed best, followed by O, R and I cor, but the modified Hellinger distance I mod showed a nonlinear slope and a truncated range. Furthermore, the simulations suggest that, in proportionally small potential distributions on large grids, an inclusion of a high proportion of grid cells with low occurrence probabilities representing background noise may bias assessments of niche overlaps. Main conclusions Both the salamander examples and simulations suggest that Schoener's D and the Bray-Curtis distance BC are best suited to compute niche overlaps from potential distributions derived from species distribution models. However, like all analysed metrics, both D and BC are seriously affected by the inclusion of high numbers of grid cells where the species are probably absent, i.e. with low occurrence probabilities. Therefore, pre-processing to eliminate background noise in the potential distribution grids is highly recommended. © 2011 Blackwell Publishing Ltd.
Kuck P.,Zoological Research Museum Alexander Koenig |
Struck T.H.,Zoological Research Museum Alexander Koenig
Molecular Phylogenetics and Evolution | Year: 2014
BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions. As a result of its speed and flexibility, the program provides the possibility to analyze hundreds of pre-defined gene partitions and taxon subsets in one single process run. BaCoCa is command-line driven and can be easily integrated into automatic process pipelines of phylogenomic studies. Moreover, given the tab-delimited output style the results can be easily used for further analyses in programs like Excel or statistical packages like R. A built-in option of BaCoCa is the generation of heat maps with hierarchical clustering of certain results using R. As input files BaCoCa can handle FASTA and relaxed PHYLIP, which are commonly used in phylogenomic pipelines. BaCoCa is implemented in Perl and works on Windows PCs, Macs and Linux operating systems. The executable source code as well as example test files and a detailed documentation of BaCoCa are freely available at http://software.zfmk.de. © 2013 Elsevier Inc.
Struck T.H.,Zoological Research Museum Alexander Koenig
PLoS ONE | Year: 2013
Phylogenomic studies based on hundreds of genes derived from expressed sequence tags libraries are increasingly used to reveal the phylogeny of taxa. A prerequisite for these studies is the assignment of genes into clusters of orthologous sequences. Sophisticated methods of orthology prediction are used in such analyses, but it is rarely assessed whether paralogous sequences have been erroneously grouped together as orthologous sequences after the prediction, and whether this had an impact on the phylogenetic reconstruction using a super-matrix approach. Herein, I tested the impact of paralogous sequences on the reconstruction of annelid relationships based on phylogenomic datasets. Using single-partition analyses, screening for bootstrap support, blast searches and pruning of sequences in the supermatrix, wrongly assigned paralogous sequences were found in eight partitions and the placement of five taxa (the annelids Owenia, Scoloplos, Sthenelais and Eurythoe and the nemertean Cerebratulus) including the robust bootstrap support could be attributed to the presence of paralogous sequences in two partitions. Excluding these sequences resulted in a different, weaker supported placement for these taxa. Moreover, the analyses revealed that paralogous sequences impacted the reconstruction when only a single taxon represented a previously supported higher taxon such as a polychaete family. One possibility of a priori detection of wrongly assigned paralogous sequences could combine 1) a screening of single-partition analyses based on criteria such as nodal support or internal branch length with 2) blast searches of suspicious cases as presented herein. Also possible are a posteriori approaches in which support for specific clades is investigated by comparing alternative hypotheses based on differences in per-site likelihoods. Increasing the sizes of EST libraries will also decrease the likelihood of wrongly assigned paralogous sequences, and in the case of orthology prediction methods like HaMStR it is likewise decreased by using more than one reference taxon. © 2013 Torsten H.
Struck T.H.,Zoological Research Museum Alexander Koenig
Evolutionary Bioinformatics | Year: 2014
Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. Te program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html. © the authors, publisher and licensee libertas academica limited.
News Article | April 9, 2016
Six new species of dragon millipedes have been discovered by scientists in the deep, dark caves of China. These cave-dwelling creepy crawlies were found in the caves of Guangdong and Guangxi Zhuang, by a diverse team of researchers from South China Agricultural University, the Russian Academy of Sciences and Zoological Research Museum Alexander Koenig. Dragon millipedes are native to southeastern Asia and these extraordinary creatures are characterized by a fish bone-like body with spiny projections such as that on a dragon. Given that their natural habitat is the cave, they exhibit loss of pigmentation and usually appear a dirty white in color or are translucent by nature. Their legs and antennas are unusually elongated, setting them apart from the other species of millipedes. Four out of the six species that were discovered, live exclusively in caves. "This genus is conspicuous in its species generally showing a dragon-like appearance, with strongly wing, spine or antler-shaped paraterga," wrote the researchers in their published study. An interesting fact about the dragon millipedes is that they come equipped with a deadly toxin namely hydrogen cyanide to ward off dangerous predators. Dragon millipedes belong to a genus of millipedes called the Desmoxytes, which are rampant in southeastern Asia. The findings of the study published on ZooKeys is an add-on to the already existing 2007 study based on the discovery of several new species of Desmoxytes. Wide attention was particularly received at the discovery of a dragon millipede in a shocking pink avatar in Thailand. These millipede species are found prevalent in the Mekong Delta, and several other places across Thailand and Myanmar. The team of researchers from China, Russia and Germany chanced upon these new species in two separate regions of Guangdong and Guangxi Zhuang. Both these places comprise of incredible caves that shelter a wide variety of extraordinary species that are still yet to be discovered. © 2016 Tech Times, All rights reserved. Do not reproduce without permission.