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Non-additive interaction between genotypes: implications for competitive fitness assays
<p>Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged <em>Drosophila simulans</em> populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: 1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. 2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype x environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.</p>
The interplay between abiotic and biotic factors on dispersal decisions: evidence and implications for metacommunities
<p>Suitable conditions for species to survive and reproduce constitute their ecological niche, which is built by abiotic conditions and interactions with conspecifics and heterospecifics. Organisms should ideally assess and use information about all these environmental dimensions to adjust their dispersal decisions depending on their own internal conditions. Dispersal plasticity is often considered through its dependence to abiotic conditions or conspecifics density, and to a lesser extent with the effects of interactions with heterospecifics, potentially leading to misinterpretation of dispersal drivers. Here, we first review the evidence for effects of, and the potential interplays between abiotic factors, biotic interactions with conspecifics and heterospecifics, and phenotype on dispersal decisions. We then present an experimental test of these potential interplays, testing the effects of density and interactions with conspecifics and heterospecifics on temperature-dependent dispersal in microcosms of <i>Tetrahymena </i>ciliates. We found significant differences in dispersal rates depending on temperature, density, and presence of another strain or species. However, the presence and density of conspecifics and heterospecifics had no effects on the thermal-dependency of dispersal. We discuss the causes and consequences of the (lack of) interplay between the different environmental dimensions and the phenotype for metacommunity assembly and dynamics.</p>
Figure 1 in Oviposition of Quesada gigas in weed no hostess: implication in pest management
Figure 1 - Oviposition of Quesada gigas in weed Conyza spp. A. Eggs nests into side branch B. Eggs with fusiform format and white milky color.
Dataset for "Plume-driven weakening of the lithosphere and geodynamic implications"
<p><strong>Dataset for numerical modeling results of "Plume-driven weakening of the lithosphere and geodynamic implications". These data can be used for reproducing all the numerical figures.</strong></p>
Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity
<ul> <li>Background and Aims: The tribe Paullinieae have the highest diversity of vascular variants among the seed plants. The developmental diversity is better understood in the speciose genera <em>Paullinia </em>and <em>Serjania, </em>however, the phylogeny and diversity of vascular variants in the smaller genera of Paullinieae remain understudied. Here we investigate the evolution of development of stem vasculatures in the small genus <em>Urvillea.</em></li> <li>Methods: We generate the first molecular phylogeny of <em>Urvillea </em>derived from 11 markers using a maximum likelihood and Bayesian approach. In combination with phylogenetic reconstruction, stochastic character mapping is used to assess evolutionary changes in stem ontogenies, determined from developmental anatomy of stems collected in the field or from herbarium and wood collections. </li> <li>Key Results: <em>Urvillea </em>is supported as a monophyletic group and sister to <em>Serjania. </em>There are five stem ontogenies in <em>Urvillea, </em>including a regular anatomy and four vascular variants. Most stem ontogenies initiate with lobed stems. Lobed adult stems are conserved in <em>Urvillea</em>, but this ontogeny was lost multiple times. A reversal to regular anatomy occurred in non-climbing species. Phloem wedges, fissured stems and ectopic cambia evolved independently once. Phloem wedges is an intermediate developmental stage in the formation of fissured stems, which is characterized by a continuous fragmentation of vascular tissues. Lobed stems may generate constriction zones and lobes may split or not. </li> </ul> <ul> <li>Conclusions: <em>Urvillea </em>stands out as the third most diverse genus in number of vascular variants within Paullinieae, but only one ontogeny (fissured stems) is exclusive for the genus. Differential cambial activity and ectopic cambia are the main ontogenetic processes generating stem diversity. The evolutionary history of vascular variants demonstrates the large developmental lability of the cambium in such a small genus and corroborates a scenario of repeated evolution of complex anatomies within Paullinieae lianas.</li> </ul>
Implications of headwater contact zones for the riverine barrier hypothesis: a case study of the Blue-capped Manakin (Lepidothrix coronata)
<p>Rivers frequently delimit the geographic ranges of species in the Amazon Basin. These rivers also define the boundaries between genetic clusters within many species, yet river boundaries have been documented to break down in headwater regions where rivers are narrower. To explore the evolutionary implications of headwater contact zones in Amazonia, we examined genetic variation in the Blue-capped Manakin (<em>Lepidothrix coronata</em>), a species previously shown to contain several genetically and phenotypically distinct populations across the western Amazon Basin. We collected restriction site-associated DNA sequence data (RADcap) for 706 individuals and found that spatial patterns of genetic structure indicate rivers, particularly the Amazon and Ucayali, are major dispersal barriers for <em>L. coronata</em> along a distance of more than 3000 km. We also found evidence that genetic connectivity is elevated across several headwater regions, highlighting the importance of headwater gene flow for models of Amazonian diversification. The headwaters of the Ucayali River provide a notable exception to findings of headwater gene flow by harboring non-admixed populations of <em>L. coronata</em> on opposite sides of a <1 km-wide river channel with a known dynamic history, potentially suggesting that additional prezygotic barriers are limiting gene flow in this region. </p>
Figure 2 in On cosmine: its origins, biology and implications for sarcopterygian interrelationships
Figure 2. – Phylogenetic implications and evolutionary scenario of cosmine development in osteichthyans. Numbers 1-4 detailed in the text (Development of cosmine). A: phylogenetic interrelationships of selected osteichthyans (after Lu et al., 2017) and interpretative reconstructions of taxa; B: histological cross sections; C: illustrations of the histological structures from the cross sections; D: virtual and ideal- ized reconstructions of the pore-canal system of the cosmine. Sources of cross sections and drawings: Andreolepis: Zhu et al., 2010, Qu et al., 2013b, 2016; Psarolepis: Qu et al., 2013a, 2016; Meemannia: Zhu et al., 2010; Styloichthys: Zhu et al., 2006; Porolepis: Gross, 1956; Mondéjar-Fernández and Clément, 2012; Dipterus: Gross, 1956; Osteolepis: Gross, 1956, Schultze, 2015; Megalichthys: Gross, 1956; Thomson, 1975. Scale bar = 100 µm. Abbreviations: ba, basal extension; cc, cross canal; d, dentine; dt, dentinal tubules; e, enamel; lmc, lower mesh canal; mc, mesh canal; od, odontode; pc, pore cavity; po, pore opening; puc, pulp cavity.
Figure 1 in On cosmine: its origins, biology and implications for sarcopterygian interrelationships
Figure 1. – Interrelationships and geological time range of selected osteichthyans (histologically surveyed taxa or with important phylogenetic implications). Phylogenetic hypothesis after Ahlberg and Johanson, 1998; Johanson and Ahlberg, 2001; Zhu et al., 2001, 2006, 2009, 2017; Friedman, 2007; Snitting, 2008; Lu and Zhu, 2010; Coates and Friedman, 2010; Lu et al., 2012, 2017; Choo et al., 2017, among others. The dates of origin of clades are hypothetical. Abbreviations: A: Actinopterygii, D: Dipnomorpha, R: Rhipidistia, S: Sarcopterygii, T: Tetrapodomorpha. Legends: light grey with large dots: primitive type of cosmine as described in early osteichthyans (presence of large pores associated with a variably developed pore-canal system in the dentine and superimposed odontodes); light grey with fine dots: eucosmine (presence of minute pores associated with a pore-canal system in the dentine overlaid by a single layer of enamel); light grey: odontogenic derivatives of cosmine: ganoine (in actinopterygians), tubercles solely made of dentine or a combination of enamel and dentine (early osteichthyans and sarcopterygians); white: bony ornamentation (absence of odontogenic tissues in the dermoskeleton).
Figure 4 in On cosmine: its origins, biology and implications for sarcopterygian interrelationships
Figure 4. – Histological cross sections of Russian tetrapodomorph scale material. A: Lamprotolepis ('Osteolepiformes'), fragment of a scale ornamented with dentine tubercles. B: Inset of a tubercle (odontode). Note the absence of a pore-canal system and of enamel capping the dentine tubercle. The odontodes lie on a thin and irregularly developed layer of vascular bone (spongiosa). The basal lamellar bone layer (isopedine) is thick and well developed. C: Thysanolepis (?Rhizodontida), upper portion of a scale in cross section. Note the presence of cosmine formed by the association of enamel and dentine pervaded by a pore-canal system. The middle vascular bone layer (spongiosa) is well developed and rests on the basal layer of lamellar bone (isopedine). D: Megistolepis ('Osteolepiformes'), upper portion of a scale in cross section. Note the presence cosmine and a well developed and cancellous spongiosa. The inferior part of the pore-canal system of the cosmine prolongs itself into the vascular canals of the spongiosa. Basal bony layer not visible. Abbreviations: d, dentine; e, enamel; lb, lamellar bone; mc, mesh canal; pc, pore cavity; vb, vascular bone; vc, vascular canal. Pictures courtesy of François Meunier. Scale bars: A = 1 mm; B = 500 μm; C, D = 100 μm.
Figure 3 in On cosmine: its origins, biology and implications for sarcopterygian interrelationships
Figure 3. – Morphology and histology of porolepiform holoptychiid scales. A: Holoptychius nobilissimus (MB.f. 1994.1) and B: Laccognathus panderi (MB.f. 1833,2) from the Middle – Late Devonian of Latvia. 1: External view of the scales (arrow points anteriorly); 2: Internal view of the scales; 3: General view of the cross section; 4: Inset from the cross section showing the arrangement of the histological layers. Note the ornamental and histological differences between both scales: in Holoptychius the exposed area is ornamented with thick longitudinal ridges solely made of dense bone resting upon the spongiosa (vascular bone); in Laccognathus the exposed area shows numerous dentine tubercles, capped with a thin enamel layer (i.e. odontodes), older odontodes from previous generations are embedded in the underlying spongiosa (black arrowheads). In both scales, the internal surface is flat and smooth and is solely formed by the isopedine (lamellar bone) layer, which is relatively thicker in Holoptychius than in Laccognathus. Abbreviations: d, dentine; e, enamel; lb, lamellar bone; vb, vascular bone. Scale bars: A/B2 = 1 cm; A/B3 = 5 mm; A/B4 = 500 μm.
Figure 3 in Histology of ganoid scales from the early Late Cretaceous of the Kem Kem beds , SE Morocco : systematic and evolutionary implications
Figure 3. - Scales of Adrianaichthys pankowski (MNHN-Histos 1959). A: Cross section of a scale (transmitted natural light) showing two superimposed layers: pluristratified ganoine (black arrow), and basal plate (bp) constituted of an avascular bony tissue. Dentine is lacking; B-D: Cross sections of scales (transmitted natural light); B: Detail of pluristratified ganoine (g). In the underlying bony basal plate (bp) one can see canaliculi of Williamson (cw) and a growth mark (gm); C: Detail of the bony basal plate showing numerous Sharpey's fibres and two canaliculi of Williamson (arrow) and a growth mark (gm); D: Detail of the bony basal plate showing a dichotomy on a canaliculus of Williamson (arrowhead). Scale bars: A = 1 mm; B = 100 µm; C = 50 µm; D = 20 µm).
Fig. 7. A. Clidastes propython Cope, 1869 in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 7. A. Clidastes propython Cope, 1869. Belemnellocamax mammillatus zone, Åsen, Kristianstad Basin, southern Sweden, × 2.0. RM PZ R1779, most likely the sixth or seventh cervical vertebra (the same animal as RM PZ R1778); ventral (A1, stereo pair), posterior (A2, stereo pair), and lateral (A3, stereo pair) views. B. Clidastes propython Cope, 1869, earliest Campanian part of the Smoky Hill Chalk Member of the Niobrara Formation in western Kansas, USA, × 2.0. YPM 40354, most likely the sixth or seventh cervical vertebra; ventral (B1), posterior (B2), and lateral (B3) views.
Fig. 1. A in The first record of the mosasaur Clidastes from Europe and its palaeogeographical implications
Fig. 1. A. Localization of Kristianstad Basin, Southern Sweden. B. Map of the Kristianstad Basin with the localities yielding remains of Clidastes propython Cope, 1869. The term "other bedrock" refers to both Precambrian and Phanerozoic rocks covered by Quaternary deposits. Slightly modified from Lindgren and Siverson (2002: fig. 1).
Data and analysis scripts for: Co-occurrence patterns at four spatial scales implicate reproductive processes in shaping community assembly in clovers
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Data from: Conodont faunas across the Kasimovian–Gzhelian boundary (Late Pennsylvanian) in South China and implications for the selection of the stratotype for the base of the global Gzhelian Stage
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Data from: Evolutionary lability of sexual selection and its implications for speciation and macroevolution
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Larval dispersal patterns and connectivity of Acropora on Florida’s Coral Reef and its implications for restoration
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Data from: Diversity among rare and common congeneric plant species from the Garry oak and Okanagan shrub-steppe ecosystems in British Columbia: implications for conservation
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Data from: Effect of culling on individual badger Meles meles behaviour: potential implications for bovine tuberculosis transmission
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Blood variation implicates respiratory limits on elevational ranges of Andean birds
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.