106 Works

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...

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: 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: 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...

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...

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...

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...

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...

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...

Обобщенная классификация интерфейсов транспортной инфраструктуры «умного города»

Павел Андреевич Курта & Максим Вадимович Коломеец
Рассматривается задача классификации интерфейсов транспортной инфраструктуры «умного города». На основе анализа научных исследований проводится обзор состояния данной области, включая существующие подходы к классификациям интерфейсов. Выделяются основные элементы: инфраструктура, беспилотное транспортное средство и окружение, которое дополнительно поделено на субъекты и объекты. Описывается схема взаимодействия элементов и указывается расположение на ней интерфейсов. В качестве подхода к классификации используется комбинация обмена информацией между элементами с учетом направления. В результате решения задачи выделяются 9 классов интерфейсов, которые характеризуются необходимостью...

Quantitative assessment of the terrain transformation in proglacial areas (the Djankuat River catchment case study, Caucuses)

Andrei Kedich
Proglacial areas are extremely unstable and characterized by highly intensive geomorphic processes. In this study, we consider a typical proglacial area on the Caucuses – Djankuat river catchment. This research presents the first results for the complex monitoring of exogenic geomorphic process rates within the selected catchment. A repeated UAV survey for selected sites conducted in September 2019 and in August 2020 was the primary method. Also, high-resolution DEMs derived from stereo satellite images and...

Multivariate statistical analysis of ecological communities (review)

Vladimir Shitikov & Т. D. Zinchenko
The modern approach to the study of communities’ ecology involves the integration and joint processing of large arrays of observations. This usually involves a variety of indicators (population, phenotypic, genetic, environmental, chemical, landscape and geographical) which are characterized by significant temporal and spatial variability. The purpose of the analysis is to identify significant statistical relationships of the taxonomic structure with the characteristics of biotopes and environmental factors. It is based on multivariate methods that allow...

Успехи петербургской школы горения и взрыва как области научно-технического прогресса. Вклад Санкт-Петербургского научного совета по горению и взрыву: 1999–2019 гг.

Вячеслав Борисович Улыбин, Татьяна Федоровна Пименова & Тарас Петрович Гайдей
Дан краткий анализ становления и развития современной науки о горении, показано, что основополагающие принципы были заложены в городе на Неве. Проанализированы успехи петербургской школы горения и взрыва, продолжающей оставаться одним из столпов развития данных исследований как в теоретическом плане, так и в прикладных аспектах. Описаны успехи петербургской школы в области энергетического горения, несанкционированного горения, технологического горения и взрыва, химической безопасности. Рассмотрен вклад Санкт-Петербургского научного совета по горению и взрыву за последние двадцать лет с момента...

On the deformation of a composite rod in the framework of gradient thermoelasticity

А.О. Vatulyan & S.А. Nesterov
The gradient thermoelasticity problem for a composite rod based on the applied one-parameter model is investigated. To find the Cauchy stresses, the Vishik-Lyusternik asymptotic approach is used, taking into account the presence of boundary-layer solutions in the vicinity of the rods' boundaries and interface. A new dimensionless parameter equal to the ratio of the second rod length and the gradient parameter are introduced. Simplified formulas are constructed in order to find the distribution of the...

STUDY OF THE INFLUENCE OF TECHNOLOGICAL FEATURES OF LASER STEREOLITHOGRAPHY PROCESS ON FUNCTIONAL CHARACTERISTICS OF PARTS

V.V. Vnuk, E.V. Ippolitov, S.V. Kamaev, M.A. Markov, A.A. Nikulenko, M.M. Novikov & S.A. Cherebylo
The article reports on the effect the building orientation of the part, produced by laser stereolithography technology, has on achieving its best functional characteristics. Based on the example of IPLIT-3 and IPLIT-4 resins, the study shows that in contrast to the literature data on other commercial photocurable resins (PCRs), there is no definite advantage of the vertical orientation of the test samples compared to their horizontal orientation for obtaining the best values of the manufactured...

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: 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...

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: 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...

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...

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...

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,...

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