85 Works

Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen, Susanne Schulmeister, Debra L. Murray & Alexandr P. Rasnitsyn
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically,...

Data from: Widespread and persistent invasions of terrestrial habitats coincident with larval feeding behavior transitions during snail-killing fly evolution (Diptera: Sciomyzidae)

Eric G. Chapman, Andrey A. Przhiboro, James D. Harwood, Benjamin A. Foote & Walter R. Hoeh
Background: Transitions in habitats and feeding behaviors were fundamental to the diversification of life on Earth. There is ongoing debate regarding the typical directionality of transitions between aquatic and terrestrial habitats and the mechanisms responsible for the preponderance of terrestrial to aquatic transitions. Snail-killing flies (Diptera: Sciomyzidae) represent an excellent model system to study such transitions because their larvae display a range of feeding behaviors, being predators, parasitoids or saprophages of a variety of mollusks...

Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Hitoshi Suzuki, Mitsuo Nunome, Ghota Kinotshita, K. P. Aplin, Peter Vogel, Alexey P. Kryukov, Mei-Lei Jin, Sang-Hoon Han, Ibnu Maryanto, Kimiyuki Tsuchiya, Hidetoshi Ikeda, T. Shiroishi, Hiromichi Yonekawa & Kazuo Moriwaki
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges...

Data from: DNA barcoding and minibarcoding as a powerful tool for feather mite studies

Jorge Doña, Javier Diaz-Real, Sergey Mironov, Pilar Bazaga, David Serrano & Roger Jovani
Feather mites (Astigmata: Analgoidea and Pterolichoidea) are among the most abundant and commonly occurring bird ectosymbionts. Basic questions on the ecology and evolution of feather mites remain unanswered because feather mite species identification is often only possible for adult males, and it is laborious even for specialized taxonomists, thus precluding large-scale identifications. Here, we tested DNA barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of...

Data from: Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic

Sofie Smedegaard Mathiesen, Jakob Thyrring, Jakob Hemmer-Hansen, Jørgen Berge, Alexey Sukhotin, Peter Leopold, Michaël Bekaert, Mikael Kristian Sejr & Einar E. Nielsen
Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp....

Data from: Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

Sergey A. Naumenko, Maria D. Logacheva, Nina V. Popova, Anna V. Klepikova, Aleksey A. Penin, Georgii A. Bazykin, Anna E. Etingova, Nikolai S. Mugue, Alexey S. Kondrashov & Lev Y. Yampolsky
Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into...

Multituberculate mammals from the Middle Jurassic of Western Siberia, Russia, and the origin of Multituberculata

Alexander O. Averianov, Thomas Martin, Alexey V. Lopatin, Julia A. Schultz, Rico Schellhorn, Sergei Krasnolutskii, Pavel Skutschas & Stepan Ivantsov
Tashtykia primaeva gen. et sp. nov. and Tagaria antiqua gen. et sp. nov. (Multituberculata incertae sedis) are described based on isolated teeth from the Middle Jurassic (Bathonian) Itat Formation from the Berezovsk coal mine in Krasnoyarsk Territory, Western Siberia, Russia. Tashtykia primaeva gen. et sp. nov. is characterized by a P5 with three rows of cusps (cusp formula 2B:4M:6L) and a high sectorial p4 with two triangular lobes, five serrations associated with labial and lingual...

Vital rate estimates for the common eider Somateria mollissima, a data-rich exemplar of the seaduck tribe

Alex Nicol-Harper, Kevin Wood, Antony Diamond, Heather Major, Aevar Petersen, Grigori Tertitski, C. Patrick Doncaster, Thomas Ezard & Geoff Hilton
This database contains estimates of the following vital rates (as required to parameterise matrix population models), for the common eider (Somateria mollissima): 1st year survival (measured either from hatching, or from fledging, to 1 year old); 2nd year survival; adult annual survival; first breeding (both age-specific recruitment probability, and breeding propensity across potential recruitment ages); breeding propensity of established female breeders; clutch size; hatching success; and fledging success. These estimates are drawn from 134 studies,...

Geolocator tagging of east Siberian bluethroats

Staffan Bensch, Mikkel Willemoes, Stepan Ivanov, Sergey Vartanyan, Kristaps Sokolovskis & Diana Solovyeva
Many long-distance migratory bird species seem to retain the winter quarters their ancestors used during the last glacial maximum. Post-glacial colonization following the retreat of the ice sheets have then resulted in apparent suboptimal migration routes, since the expanding populations have failed to use more nearby, alternative and climatically suitable, wintering areas. The bluethroat subspecies Cyanecula svecica svecia occurs in the northern areas of the Palearctic from the Atlantic to Alaska. Because it is monotypic...

Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow

Diana Le Duc, Akhil Velluva, Molly Cassatt-Johnstone, Remi-Andre Olsen, Sina Baleka, Chen-Ching Lin, Johannes R. Lemke, John R. Southon, Alexander Burdin, Ming-Shan Wang, Sonja Grunewald, Wilfried Rosendahl, Ulrich Joger, Sereina Rutschmann, Thomas B. Hildebrandt, Guido Fritsch, James A. Estes, Janet Kelso, Love Dalén, Michael Hofreiter, Beth Shapiro & Torsten Schöneberg
Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse...

Future seasonal changes in habitat for Arctic whales during predicted ocean warming

Philippine Chambault, Kit M Kovacs, Christian Lydersen, Olga Shpak, Jonas Teilmann, Christoffer M. Albertsen & Mads Peter Heide-Jørgensen
Ocean warming is causing shifts in the distributions of marine species, but the location of suitable habitats in the future is unknown, especially in remote regions such as the Arctic. Using satellite tracking data from a 28-year long period, covering all three endemic Arctic cetaceans (227 individuals) in the Atlantic sector of the Arctic, together with climate models under two emission scenarios, species distributions were projected to assess responses of these whales to climate change...

Data from: Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal

Björn Stelbrink, Alena A. Shirokaya, Catharina Clewing, Tatyana Y. Sitnikova, Larisa A. Prozorova, Christian Albrecht & Tatiana Y. Sitnikova
Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake...

Data from: Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes

Laura S. Epp, Galina Gussarova, Sanne Boessenkool, Jesper Olsen, James Haile, Audun Schrøder-Nielsen, Anna Ludikova, Kristian Hassel, Hans K. Stenøien, Svend V. Funder, Eske Willerslev, Kurt Kjær & Christian Brochmann
High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA preservation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte,...

Data from: A new Cretaceous genus of xyelydid sawfly illuminating nygmata evolution in Hymenoptera

Wang Mei, Alexandr P. Rasnitsyn, Chungkun Shih & Dong Ren
Background: Nygmata are prominent glandular structures on the wings of insects. They have been documented in some extant insects, including several families of Neuroptera and Mecoptera, the majority of Trichoptera, and a few of the hymenopteran Symphyta. However, because nygmata are rarely preserved in compression fossils, their early development and evolution are still enigmatic. For example, the only documented nygmata in the Hymenoptera are on the forewings of the Triassic xyelids Asioxyela paurura and Madygenius...

Data from: Nature of the optical band shapes in polymethine dyes and H-aggregates: dozy chaos and excitons. Comparison with dimers, H*- and J-aggregates

Vladimir V. Egorov
Results on the theoretical explanation of the shape of optical bands in polymethine dyes, their dimers and aggregates are summarized. The theoretical dependence of the shape of optical bands for the dye monomers in the vinylogous series in line with a change in the solvent polarity is considered. A simple physical (analytical) model of the shape of optical absorption bands in H-aggregates of polymethine dyes is developed based on taking the dozy-chaos dynamics of the...

Data from: On polyphyly of the former section Ochlopoa Asch. et Graebn. and hybridogenic section Acroleucae Tzvelev et Prob. (Poa L., Poaceae): insights from the molecular phylogenetic analysis

Nikolai N. Nosov, Valery N. Tikhomirov, Eduard M. Machs & Alexander V. Rodionov
In this study, sequence data of the nuclear region ITS1-5.8S rDNA-ITS2 and the chloroplast region trnL-F as well as few morphological characters were examined trying to elucidate the relationships among known annual bluegrasses. It was shown that all taxa from the aggregate P. annua distinguished by lemma characters and growth form are identical according to ITS and trnL-trnF data wherein all ITS sequences of P. annua aggr. are the same as P. supina and all...

Data from: Genetic polymorphism in Chondrilla (Asteraceae) in the South of European Russia and the nature of Chondrilla juncea L.

Ivan Schanzer, Alexander Kashin, Tatyana Kritskaya & Alena Parkhomenko
We studied genetic diversity in 54 populations of nine species of the genus Chondrilla (C. acantholepis, C. ambigua, C. brevirostris, C. canescens, C. graminea, C. juncea, C. laticoronata, C. latifolia, and C. pauciflora) from SE European Russia and the neighboring territories of NW Kazakhstan. Analyses of the trnT–trnF region of plastid DNA and the internal transcribed spacer of ribosomal DNA (ITS1–5.8S–ITS2) using Statistical Parsimony, Maximum Likelihood and Neighbor Net methods revealed two major evolutionary lineages...

Data from: Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta: Sphagnaceae) relative to taxonomy and geography

Aaron Duffy, Blanka Aguero, Hans Stenoien, Kjell Ivar Flatberg, Michael S. Ignatov, Kristian Hassel & Jonathan Shaw
METHODS RADseq analyses were applied to a sample of 384 collections representing the European, North American, and (to a lesser extent) Asian ranges of the complex. The data were subjected to maximum likelihood phylogenetic analyses and analyses of genetic structure using the software, STRUCTURE, and multivariate ordination approaches. RESULTS Defined phylogenetically, the S. recurvum complex includes S. angustifolium , S. fallax , S. flexuosum , S. pacificum , and S. recurvum , as distinct clades...

Harrison’s rule scales up to entire parasite assemblages but is determined by environmental factors

Renan Maestri, Maico Fiedler, Georgy Shenbrot, Elena Surkova, Sergei Medvedev, Irina Khokhlova & Boris Krasnov
Harrison’s rule states that parasite body size and the body size of their hosts tend to be positively correlated. After it was proposed a century ago, a number of studies have investigated this trend, but the support level has varied greatly between parasite/host associations. Moreover, while the rule has been tested at the individual species level, we still lack knowledge on whether Harrison’s rule holds at the scale of parasite and host communities. Here, we...

Landscape genomics of a widely distributed snake (Dolichophis caspius, Gmelin, 1789) across Eastern Europe and Western Asia

Sarita Mahtani-Williams, William Fulton, Amelie Desvars-Larrive, Sara Lado, Jean Elbers, Bálint Halpern, Dávid Herczeg, Gergely Babocsay, Boris Lauš, Zoltán Tamás Nagy, Daniel Jablonski, Oleg Kukushkin, Pablo Orozco-TerWengel, Judit Vörös & Pamela Burger
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alterations. To understand population dynamics and the adaptive potential of this widespread but locally endangered snake, we investigated population structure, admixture and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms...

DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Gerard Talavera, Vladimir Lukhtanov, Naomi Pierce & Roger Vila
Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts...

Data from: The quiescent centre of the root apical meristem: Conceptual developments from Clowes to modern times

Joseph G. Dubrovsky & Victor B. Ivanov
This data for the review article "The quiescent centre of the root apical meristem: Conceptual developments from Clowes to modern times" published in Journal of Experimental Botany by Joseph G. Dubrovsky and Victor B. Ivanov (https://doi.org/10.1093/jxb/erab305) includes a complete bibliography of Frederick Albert Lionel Clowes in chronological order. The referred article is dedicated to the 100th anniversary of the birth of Clowes, who during his career investigated organization, function, and maintenance of the root apical...

Lophozia svalbardensis (Lophoziaceae) in continental North America, Greenland and Siberia, its identity, variation, and differentiation

Alexey Potemkin & Anna Vilnet
Lophozia excisa var. succulenta (≡ Lophoziopsis excisa var. succulenta) is a synonym of Lophozia svalbardensis. This conclusion is based on morphological investigation and a subsequent molecular-genetic study which revealed an absence of variability amon nucleotide sequences of ITS1-2 nrDNA and trnL-F cpDNA in specimens from Arctic Alaska, west Siberian Arctic and Svalbard. Lophozia svalbardensis is reported for the first time for continental North America, Greenland and Siberia based on revised data on the distribution of...

Data from: Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Robert H. S. Kraus, Pim Van Hooft, Hendrik-Jan Megens, Arseny Tsvey, Sergei Y. Fokin, Ronald C. Ydenberg & Herbert H. T. Prins
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority due to recent outbreaks of Avian Influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism (SNP) markers in combination with population genetics and phylogeographic approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations world-wide. Basic population genetic...

Data from: On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

Małgorzata Pilot, Tadeusz Malewski, Andre E. Moura, Tomasz Grzybowski, Kamil Oleński, Anna Ruść, Stanisław Kamiński, Fernanda Fadel, Daniel S. Mills, Abdulaziz N. Alagaili, Osama B. Mohammed, Grzegorz Kłys, Innokentiy M. Okhlopkov, Ewa Suchecka, Wieslaw Bogdanowicz & Fernanda Ruiz Fadel
Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our...

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