36 Works

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Barcoding snakeheads (Teleostei, Channidae) revisited: discovering greater species diversity and resolving perpetuated taxonomic confusions

Cecilia Conte-Grand, Ralf Britz, Neelesh Dahanukar, Rajeev Raghavan, Rohan Pethiyagoda, Hoek Hui Tan, Renny Kurnia Hadiaty, Norsham S. Yaakob, Lukas Rüber & Heok Hui Tan
Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group...

Fermur lengths of Drosophila melanogaster at different developmental temperatures and Wolbachia-infection types

Martin Kapun & Sina Lerch
To estimate the influence of developmental temperature and Wolbachia infections on body size in Drosophila melanogaster, we disected female flies and mounted left forelegs. Pictures were taken under a Leica DFC 490 microscope. Femur lengths, wich have proven to be a good proxy for bodysize, were measured in ImageJ. Our analyses revealed that temperature, but not Wolbachia infections strongly influenced female body size. See also the corresponing README.txt and the table "FullData.xlsx" within SupplementaryData.zip in...

Data from: Multiple independent colonizations into the Congo Basin during the continental radiation of African Mastacembelus spiny eels

Julia J. Day, Antonie Fages, Katherine J. Brown, Emmanuel J. Vreven, Melanie L. J. Stiassny, Roger Bills, John P. Friel, Lukas Rüber & Antoine Fages
Aim: There has been recent interest in the origin and assembly of continental biotas based on densely sampled species-level clades, however, studies from African freshwaters are few so that the commonality of macroevolutionary patterns and processes among continental clades remain to be tested. Within the Afrotropics, the Congo Basin contains the highest diversity of riverine fishes, yet it is unclear how this fauna was assembled. To address this, and the diversification dynamics of a continental...

Data from: Sexual dimorphism in shells of Cochlostoma septemspirale (Caenogastropoda, Cyclophoroidea, Diplommatinidae, Cochlostomatinae)

Fabian Reichenbach, Hannes Baur & Eike Neubert
Sexual dimorphisms in shell-bearing snails expressed by characteristic traits of their respective shells would offer the possibility for a lot of studies about gender distribution in populations, species, etc. In this study, the seven main shell characters of the snail Cochlostoma septemspirale were measured in both sexes: (1) height and (2) width of the shell, (3) height and (4) width of the aperture, (5) width of the last whorl, (6) rib density on the last...

Data from: Morphometric analysis and taxonomic revision of Anisopteromalus Ruschka (Hymenoptera: Chalcidoidea: Pteromalidae) – an integrative approach

Hannes Baur, Yvonne Kranz-Baltensperger, Astrid Cruaud, Jean-Yves Rasplus, Alexander V. Timokhov & Vladimir E. Gokhman
We use an integrative taxonomic approach to revise the genus Anisopteromalus. In particular, we apply multivariate ratio analysis (MRA), a rather new statistical method based on principal component analysis (PCA) and linear discriminant analysis (LDA), to numerous body measurements and combine the data with those from our molecular analysis of Cytb and ITS2 genetic markers (on a subset of species) and all available published data on morphology, karyology, behavior, host associations, and geographic distribution. We...

Data from: Genetic structure and effective population sizes in European red deer (Cervus elaphus) at a continental scale: insights from microsatellite DNA

Frank E. Zachos, Alain C. Frantz, Ralph Kuehn, Sabine Bertouille, Marc Colyn, Magdalena Niedzialkowska, Javier Pérez-González, Anna Skog, Nikica Šprem & Marie-Christine Flamand
We analysed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall FST = 0.166, Jost’s Dest = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only three genetic clusters our data set produced a very similar geographic pattern as previously...

Data from: Phylogeography and demographic history of two widespread Indo-Pacific mudskippers (Gobiidae: Periophthalmus)

Gianluca Polgar, Lorenzo Zane, Massimiliano Babbucci, Federica Barbisan, Tomaso Patarnello, Lukas Rüber & Chiara Papetti
This study provides a first description of the phylogeographic patterns and evolutionary history of two species of the mudskipper genus Periophthalmus. These amphibious gobies are distributed throughout the whole Indo-Pacific region and Atlantic coast of Africa, in peritidal habitats of soft-bottom coastal ecosystems. Three sequence datasets of two widely distributed species, Periophthalmus argentilineatus and P. kalolo, were obtained by amplifying and sequencing two mtDNA markers (D-loop and 16S rDNA) and the nDNA rag1 region. The...

Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Nicolás Mongiardino Koch, Jeffrey R Thompson, Avery S Hatch, Marina F McCowin, A Frances Armstrong, Simon E Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi & Greg W Rouse
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ eighteen novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise...

Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

Christian Kehlmaier, Eva Graciá, Patrick D. Campbell, Margaretha D. Hofmeyr, Silke Schweiger, Albert Martínez-Silvestre, Walter Joyce & Uwe Fritz
The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage...

Data from: High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Antonia G. P. Ford, Kanchon K. Dasmahapatra, Lukas Rüber, Karim Gharbi, Timothée Cezard & Julia J. Day
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found...

Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

Yoshan Moodley, Isa-Rita M. Russo, Desiré L. Dalton, Antoinette Kotzé, Shadrack Muya, Patricia Haubensak, Boglárka Bálint, Gopi K. Munimanda, Caroline Deimel, Andrea Setzer, Kara Dicks, Barbara Herzig-Straschil, Daniela C. Kalthoff, Hans R. Siegismund, Jan Robovský, Paul O’Donoghue & Michael W. Bruford
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide...

Data from: Multivariate ratio analysis reveals Trigonoderus pedicellaris Thomson (Hymenoptera, Chalcidoidea, Pteromalidae) as a valid species

Zoltán László, Hannes Baur & Béla Tóthmérész
We demonstrate by multivariate ratio analysis (MRA) the validity of two female colour morphs as separate species in what was previously regarded as a single species, Trigonoderus cyanescens (Förster, 1841) (Hymenoptera: Pteromalidae). As a result, T. pedicellaris Thomson, 1878 stat.r., is resurrected from synonymy under T. cyanescens and T. filatus binubilatus Erdős, 1960 syn.n. is synonymized with T. cyanescens. More than 20 characters were measured as part of two MRA dataset analyses. The first analysis...

Data from: A new ammonoid fauna from the Carnian (Upper Triassic) Kasimlar Formation of the Taurus Mountains (Anatolia, Turkey)

Susanne Lukeneder & Alexander Lukeneder
We describe a new ammonoid fauna from the Taurus Mountains of southern Turkey. The Carnian ammonoid fauna from Aşağiyaylabel is presented for the first time. Ammonoids were obtained from limestone to marl beds of an approximately 35-m-thick section, which depicts the scarce possibility to investigate ammonoid faunas across the Lower–Upper Carnian boundary. Intense sampling near the village of Aşağiyaylabel led to the recognition of a new Lower Carnian (Julian 2) to Upper Carnian (Tuvalian 1)...

Data from: Mosaic patterns of diversification dynamics following the colonization of Melanesian islands

Emmanuel F. A. Toussaint, L Hendrich, Helen Shaverdo & Michael Balke
The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to...

Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Jonathan Silvertown, Laurence Cook, Robert Cameron, Mike Dodd, Kevin McConway, Jenny Worthington, Peter Skelton, Christian Anton, Oliver Bossdorf, Bruno Baur, Menno Schilthuizen, Benoît Fontaine, Helmut Sattmann, Giorgio Bertorelle, Maria Correia, Cristina Oliveira, Beata Pokryszko, Małgorzata Ożgo, Arturs Stalažs, Eoin Gill, Üllar Rammul, Péter Sólymos, Zoltan Féher & Xavier Juan
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern...

Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds

Manuel Schweizer, Raffael Ayé, Roman Kashkarov & Tobias Roth
Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument...

Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.

Saskia Brix, Eva Paulus, Pedro Martinez Arbizu, Sven Rossel, Janna Peters & Martin Schwentner
The crustacean marine isopod species Haploniscus bicuspis (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus...

Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

Martin Kapun, Athene Giesen, Wolf U Blanckenhorn, Martin A Schäfer, Kentaro K Shimizu, Rie Shimizu-Inatsugi, Bernhard Misof, Oliver Niehuis, Lars Podsiadlowski, Heidi E L Liescher & Simon Aeschbacher
Interspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but can also initiate reinforcement of reproductive isolation through natural and sexual selection. However, the extent of interspecific gene flow and its consequences for the initiation and maintenance of species barriers in natural systems remain poorly understood. We first applied coalescence simulations and approximate Bayesian calculations based on microsatellite data to infer the yet unknown demographic history of the two closely related European...

Data from: Plant interactions shape pollination networks via nonadditive effects

Gianalberto Losapio, Miguel A. Fortuna, Jordi Bascompte, Bernhard Schmid, Richard Michalet, Rainer Neumeyer, Leopoldo Castro, Pierfilippo Cerretti, Christoph Germann, Jean-Paul Haenni, Seraina Klopfstein, Francisco Javier Ortiz-Sánchez, Adrian C. Pont, Pascal Rousse, Jürg Schmid, Daniele Sommaggio & Christian Schöb
Plants grow in communities where they interact with other plants and with other living organisms such as pollinators. On the one hand, studies of plant–plant interactions rarely consider how plants interact with other trophic levels such as pollinators. On the other, studies of plant–animal interactions rarely deal with interactions within trophic levels such as plant–plant competition and facilitation. Thus, to what degree plant interactions affect biodiversity and ecological networks across trophic levels is poorly understood....

Data from: Natural and anthropogenic influences on the population structure of white-tailed eagles in the Carpathian Basin and Central Europe

Edina Nemesházi, Szilvia Kövér, Frank E. Zachos, Zoltán Horváth, Gábor Tihanyi, Attila Mórocz, Tibor Mikuska, István Hám, Ivan Literák, Suvi Ponnikas, Tadeusz Mizera & Krisztián Szabó
European populations of the white-tailed eagle (Haliaeetus albicilla) suffered a drastic decline during the 20th century. In many countries, only a few dozen breeding pairs survived or the species disappeared completely. By today, the populations have recovered, naturally or through restocking (e.g. in Scotland or the Czech Republic). In the Carpathian Basin, which is now a stronghold in southern Europe for the species in the southern part of the distribution range with more than 500...

Data from: Oncological and surgical outcome after treatment of pelvic sarcomas

Stephan Puchner, Philipp T. Funovics, Christoph Böhler, Alexandra Kaider, Christoph Stihsen, Gerhard M. Hobusch, Joannis Panotopoulos, Reinhard Windhager & Stephan E. Puchner
Background and Objectives. Treatment of pelvic tumors remains challenging due to complex anatomy, poor oncological outcome and high complication rates. We sought to investigate the long-term oncological and surgical outcome of these patients. Methods. Between 1980 and 2012, 147 patients underwent surgical treatment for pelvic sarcoma. Histological diagnosis was Chondrosarcoma in 54, Ewing's Sarcoma/PNET in 37, Osterosarcoma in 32 and others in 24 patients. Statistical analysis for the evaluation of oncological and surgical outcome was...

Data from: Evolutionary divergence in life history traits among populations of the Lake Malawi cichlid fish Astatotilapia calliptera

Paul J. Parsons, Jon R. Bridle, Lukas Rüber & Martin J. Genner
During the early stages of adaptive radiation, populations diverge in life history traits such as egg size and growth rates, in addition to eco-morphological and behavioral characteristics. However, there are few studies of life history divergence within ongoing adaptive radiations. Here, we studied Astatotilapia calliptera, a maternal mouthbrooding cichlid fish within the Lake Malawi haplochromine radiation. This species occupies a rich diversity of habitats, including the main body of Lake Malawi, as well as peripheral...

Data from: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

Alain C. Frantz, Frank E. Zachos, Sabine Bertouille, Marie-Christine Eloy, Marc Colyn & Marie-Christine Flamand
Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large-scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non-autochthonous animals and...

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