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FIGURE 5. Map showing the zones I, II in Ecological study based on the distribution of recent foraminifers from southeast of Buenos Aires province, Argentinean Continental Shelf
FIGURE 5. Map showing the zones I, II, III recognized in the study area.
Data from: Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist
While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.
Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi's three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (~1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Data from: A time-calibrated species tree of Crocodylia reveals a recent radiation of the true crocodiles
True crocodiles (Crocodylus) are the most broadly distributed, ecologically diverse, and species-rich crocodylian genus, comprising about half of extant crocodylian diversity and exhibiting a circumtropical distribution. Crocodylus traditionally has been viewed as an ancient group of morphologically conserved species that originated in Africa prior to continental breakup. In this study, these long-held notions about the temporal and geographic origin of Crocodylus are tested using DNA sequence data of 10 loci from 76 individuals representing all 23 crocodylian species. I infer a time-calibrated species tree of all Crocodylia and estimate the spatial pattern of diversification within Crocodylus. For the first time, a fully resolved phylogenetic estimate of all Crocodylia is well-supported. The results overturn traditional views of the evolution of Crocodylus by demonstrating that the true crocodiles are not "living-fossils" that originated in Africa. Rather, Crocodylus originated from an ancestor in the tropics of the Late Miocene Indo-Pacific, and rapidly radiated and dispersed around the globe during a period marked by mass extinctions of fellow crocodylians. The findings also reveal more diversity within the genus than is recognized by current taxonomy.
Data from: Molecular data and distribution dynamics indicate a recent and incomplete separation of manakins species of the genus Antilophia (Aves: Pipridae) in response to Holocene climate change
To determine a hypothetical scenario that accounts for the diversification of the two species of the genus Antilophia, we conducted multilocus molecular comparisons and species distribution modeling for the two taxa, which have distinct male plumage coloration patterns and allopatric geographic distributions, despite the high degree of genetic similarity indicated by recent studies. Three mitochondrial and three nuclear fragments were analyzed. The results indicate clear differences in the genetic diversity of the two species, but with ample sharing of haplotypes in all the markers analyzed, reflecting the absence of reciprocal monophyly, presumably due to the relatively recent and still incomplete separation of the two species. The paleoclimatic distribution models, together with the observed genetic profile indicate a recent process of divergence by geographic isolation in the ancestral populations of the two species. This scenario coincides with the recent climatic events of the South American dry diagonal, which involves the gallery forests of the Cerrado biome and the cloud forest enclaves of the seasonal tropical dry forest of the Caatinga between the late Pleistocene and the mid Holocene.
Data from: A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata
Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering, and in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life-history traits as it perceives changes in daylength. We asked, whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search for signals of directional selection at the PHYA locus, we resequenced PHYA and 9 short fragments around PHYA from a 57 kb region from a German (Plech) and a Norwegian (Spiterstulen) population and compared patterns of differentiation and diversity to a set of 19 reference loci around the genome. First, we found that the populations were highly differentiated: there were three nonsynonymous fixed differences at the PHYA locus, which was in stark contrast with the total four fixed differences in the 19 reference loci. Compatible with a sweep hypothesis, variation was almost completely removed from the 9.4 kb region around PHYA in the northern Spiterstulen population. The overall level of linkage disequilibrium (LD) was higher in Spiterstulen, but there was no LD across the PHYA locus in the population, which is also a known consequence of a selective sweep. The sweep has likely occurred after the last glacial maximum, which suggests that it has contributed to adaptation to the northern conditions.
Data from: Host-jump drives rapid and recent ecological speciation of the emergent fungal pathogen Colletotrichum kahawae
Ecological speciation through host-shift has been proposed as a major route for the appearance of novel fungal pathogens. The growing awareness of their negative impact on global economies and public health created an enormous interest in identifying the factors that are most likely to promote their emergence in nature. In this work, a combination of pathological, molecular and geographic data was used to investigate the recent emergence of the fungus Colletotrichum kahawae (Ck). Ck emerged as a specialist pathogen causing Coffee Berry Disease in Coffea arabica, due to its unparalleled adaptation of infecting green coffee berries. Contrary to current hypotheses, our results suggest that a recent host-jump underlay the speciation of Ck from a generalist group of fungi seemingly harmless to coffee berries. We posit that immigrant inviability and a predominantly asexual behavior could have been instrumental in driving speciation by creating pleiotropic interactions between local adaptation and reproductive patterns. Moreover, we estimate that Ck began its diversification at less than 2,200 yrs leaving a very short time frame since the divergence from its sibling lineage (∼5,600 yrs), during which a severe drop in Ck's effective population size occurred. This further supports a scenario of recent introduction and subsequent adaptation to C. arabica. Phylogeographic data revealed low levels of genetic polymorphism but provided the first geographically consistent population structure of Ck, inferring the Angolan population as the most ancestral and the East African populations as the most recently derived. Altogether, these results highlight the significant role of host specialization and asexuality in the emergence of fungal pathogens through ecological speciation.
Data from: Evidence for a recent horizontal transmission and spatial spread of Wolbachia from endemic Rhagoletis cerasi (Diptera: Tephritidae) to invasive Rhagoletis cingulata in Europe
The widespread occurrence of Wolbachia in arthropods and nematodes suggests that this intracellular, maternally inherited endosymbiont has the ability to cross species boundaries. However, direct evidence for such a horizontal transmission of Wolbachia in nature is scarce. Here, we compare the well-characterized Wolbachia infection of the European cherry fruit fly, Rhagoletis cerasi, with that of the North American eastern cherry fruit fly, Rhagoletis cingulata, recently introduced to Europe. Molecular genetic analysis of Wolbachia based on multilocus sequence typing and the Wolbachia surface protein wsp showed that all R. cingulata individuals are infected with wCin2 identical to wCer2 in R. cerasi. In contrast, wCin1, a strain identical to wCer1 in R. cerasi, was present in several European populations of R. cingulata, but not in any individual from the United States. Surveys of R. cingulata from Germany and Hungary indicated that the frequency of wCin1 infection increased dramatically in just a few years with at least two independent horizontal transmission events in Germany and Hungary. This is further corroborated by the analysis of the mitochondrial cytochrome oxidase II gene that showed linkage of wCin1 with two distinct haplotypes in Germany, one of which is also infected with wCin1 in Hungary. In summary, our study provides strong evidence for a very recent interspecific Wolbachia transmission with a subsequent spatial spread in field populations.
Substantial genetic divergence and lack of recent gene flow support cryptic speciation in a colour polymorphic bumble bee (Bombus bifarius) species complex
<p>Phenotypic polymorphism can constitute an inherent challenge for species delimitation. This issue is exemplified in bumble bees (<i>Bombus</i>), where species can exhibit high colour variation across their range, but otherwise exhibit little morphological variation to distinguish them from close relatives. We examine the species status of one of the most abundant North American bumble bees, <i>Bombus bifarius</i> Cresson, which historically was comprised of two major taxa, <i>bifarius</i> <i>s.s.</i> (<i>sensu stricto</i>) and <i>nearcticus</i>. These sublineages are recognized primarily by red and black variation in their mid-abdominal coloration, however, a continuum from black (<i>nearcticus</i>) to red (<i>bifarius s.s.</i>) variation has led to their historic synonymisation. Integrating mitochondrial and nuclear data and whole-genome sequencing, we reveal a high level of both mitochondrial and nuclear divergence delimiting two morphologically cryptic species – the red <i>bifarius s.s.</i> and the color variable (black to red) <i>nearcticus</i>. Population genomic analysis supports an absence of recent genomic admixture and a strong population structure between the two clades even in sympatry. Species distribution models predict partially differentiated niches between the genetically-inferred clades with annual precipitation being a leading differentiating variable. The<i> bifarius</i> <i>s.s. </i>lineage also occupies significantly higher elevations, with regions of sympatry being among the highest elevations in <i>nearcticus</i>. Our data also support a subspecies-level divergence between the broadly distributed <i>nearcticus</i> and the island population <i>vancouverensis</i>. In this paper, we formally recognize the two species, <i>Bombus</i> <i>bifarius</i> Cresson and <i>Bombus</i> <i>vancouverensis </i>Cresson, the latter including the subspecies <i>B. vancouverensis vancouverensis</i> <b>comb. n.</b> and <i>B. vancouverensis nearcticus</i> <b>comb. n</b>., with <i>vancouverensis </i>the name bearer due to year priority.</p> <p> </p>
Data from: Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into southeastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g., Australian populations) and allopatric (e.g., northern-hemisphere Mytilus taxa) ranges are necessary to accurately (i) interpret patterns of intraspecific differentiation and to (ii) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well-defined.
Data from: Species richness and the temporal stability of biomass production: a new analysis of recent biodiversity experiments
The relationship between biological diversity and ecological stability has fascinated ecologists for decades. Determining the generality of this relationship, and discovering the mechanisms that underlie it, are vitally important for ecosystem management. Here, we investigate how species richness affects the temporal stability of biomass production by re-analyzing 27 recent biodiversity experiments conducted with primary producers. We find that, in grasslands, increasing species richness stabilizes whole-community biomass but destabilizes the dynamics of constituent populations. Community biomass is stabilized because species richness impacts mean biomass more strongly than its variance. In algal communities, species richness has a minimal effect on community stability because richness affects the mean and variance of biomass nearly equally. Using a new measure of synchrony among species, we find that for both grasslands and algae, temporal correlations in species biomass are lower when species are grown together in polyculture than when grown alone in monoculture. These results suggest that interspecific interactions tend to stabilize community biomass in diverse communities. Contrary to prevailing theory, we found no evidence that species' responses to environmental variation in monoculture predicted the strength of diversity's stabilizing effect. Together, these results deepen our understanding of when and why increasing species richness stabilizes community biomass.
Data from: Three-dimensional morphological variability of recent rhynchonellide brachiopod crura
Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations. Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.
Data from: Phylogeny, ecology and deep time: 2D outline analysis of anuran skulls from the Early Cretaceous to Recent
Anurans have a long fossil record, spanning from the Early Jurassic to Recent. However, specimens are often severely flattened, limiting their inclusion in quantitative analyses of morphological evolution. We perform a two-dimensional morphometric analysis of anuran skull outlines, incorporating 42 Early Cretaceous to Miocene species, as well as 93 extant species in 32 families. Outlines were traced in tpsDig2 and analysed with elliptical Fourier analysis. Fourier coefficients were used in MANOVAs, phylogenetic MANOVAs (as significant phylogenetic signal was found) and disparity analyses across multiple ecological and life history groupings. The Neotropical realm showed higher disparity than the Australian, Palearctic and Oriental realms (p = 0.007, 0.013, 0.038, respectively), suggesting concordance of disparity and diversity. Developmental strategy had a weak effect on skull shape (R2 = 0.02, p = 0.039), and disparity was similar in metamorphosing and direct developing frogs. Ecological niche was a significant discriminator of skull shape (F = 1.43, p = 0.004), but not after phylogenetic correction. Evolutionary allometry had a small but significant influence on the cranial outlines of the combined extant and fossil dataset (R2 = 0.05, p = 0.004). Finally, morphospace occupation appears to have changed over time (F = 1.59, p = 5 × 10-10). However, as with ecological signal, this shift appears to be largely driven by phylogeny and was not significant after phylogenetic correction (R2 = 0.26, p = 0.22). This study thus suggests that frog skull evolution is shaped more by phylogenetic constraints than by ecology.
Data from: Insular biogeographic origins and high phylogenetic distinctiveness for a recently depleted lizard fauna from Christmas Island, Australia
Striking faunal turnover across Asia and Australasia, most famously along the eastern edge of the Sunda Shelf or 'Wallace's Line', has been a focus of biogeographic research for over 150 years. Here we investigate the origins of a highly threatened endemic lizard fauna (4 species) on Christmas Island. Despite occurring less 350 km south of the Sunda Shelf, this fauna mostly comprises species from clades centred on the more distant regions of Wallacea, the Pacific and Australia (> 1000 km east). The three most divergent lineages show Miocene (~23–5mya) divergences from sampled relatives; and have recently become extinct or extinct in the wild, likely due to the recent introduction of a south-east Asian snake (Lycodon capucinus). Insular distributions, deep phylogenetic divergence and recent decline, suggest that rather than dispersal ability or recent origins, environmental and biotic barriers have impeded these lineages from diversifying on the continental Sunda Shelf, and thereby, reinforced faunal differentiation across Wallace's Line. Our new phylogenetically informed perspective further highlights the rapid loss of ancient lineages that has occurred on Christmas Island, and underlines how the evolutionary divergence and vulnerability of many island-associated lineages may continue to be underestimated.
Data from: Extant primitively segmented spiders have recently diversified from an ancient lineage
Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39–58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4–24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.
Industrial relations in central public administration: recent trends and features
<p>This report maps current developments in industrial relations systems in the central public administration secrtor across the Member States, covering all EU Member States except Croatia, which joined the EU in mid-2013. The report explores to what extent there is formal industrial relations processes within the sector, including the organisation of unions and employer representatives, and the role of collective bargaining and consultation. It also examines the specific features of the sector in terms of both industrial relations processes and worker outcomes and charts reforms that have been carried out since 2008: changes in collective bargaining and in the balance of negotiation versus unilateral imposition of change by the employer, and the responses of trade unions. Finally, the report addresses the role of the social partners regarding the outcomes for employees of the recent austerity measures on issues such as wages, job security, working time and pensions.</p> <p>[Google](http://www.google.com)<br /> <br /> http://www.eurofound.europa.eu/eiro/studies/tn1307019s/index.htm </p>
FIGURE 50 in A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species
FIGURE 50. Comparison of the Type A bracts of Erenna species at the same scale. Scale bar 5 mm.
FIGURE 20. Erenna cornuta Pugh, 2001. Type B bracts. Scale bar 5 in A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species
FIGURE 20. Erenna cornuta Pugh, 2001. Type B bracts. Scale bar 5 mm.
FIGURE 14 in A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species
FIGURE 14. In situ photograph of Erenna cornuta taken during Tiburon Dive 1155 at 1628m. MBARI.
FIGURE 18 in A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species
FIGURE 18. Detail of siphosome of Erenna cornuta Pugh, 2001 from Tiburon Dive 1155. MBARI.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.