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opennotspecifiedDec 2001View details →

................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.

................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.

opencc-zeroNov 2020View details →

Data from: Contribution of small isolated habitats in creating refuges from biological invasions along a geomorphological gradient of floodplain waterbodies

1. Habitat fragmentation, which involves habitat size reduction and isolation, is a major cause of biodiversity decline. However, interest in small isolated habitats has increased among ecosystem managers because these fragments can serve as remnant refuges for unique and/or endangered species in human-altered landscapes. 2. In a fragmented floodplain of northern Japan, we demonstrate how habitat fragmentation and habitat quality shape the refuges for a unique endangered minnow (Rhynchocypris percnurus sachalinensis) from biological invasions. We focused on two invasive minnows, topmouth gudgeon (Pseudorasbora parva) and rosy bitterling (Rhodeus ocellatus ocellatus), which are the dominant invasive species. By using a graph theoretical approach and structural equation modeling, we elucidated the relationships among habitat fragmentation, habitat quality and the abundance of invasive minnows with the endangered swamp minnow. 3. We found that the invasion of topmouth gudgeon, which has a high mobility and environmental tolerance, negatively affected swamp minnow populations. The invasive species may outcompete the native species in their overlapping trophic niche. 4. Analyses indicated that habitat fragmentation (decreasing habitat size and connectivity) indirectly and positively affected the population abundance of swamp minnow by reducing the potential for invasion by topmouth gudgeon. We further found an interaction between the indirect effects of habitat fragmentation and local habitat quality: the indirect effects became more apparent in the relatively deeper habitats that were of better quality for natives. This result was likely attributed to the strong control effect of the abiotic stressor. Interspecific competition between the two minnows would be masked in shallow ponds because the native populations are primarily restricted by the abiotic factor, and its abundance is inherently limited regardless of pressure by invaders. 5. In fragmented landscapes, evenly conserving all small fragments within a limited budget is difficult. The change in importance of small isolated ponds across a pond-depth gradient suggests that conservation priorities for small fragments should be established by considering local habitat quality. Our findings do not justify habitat fragmentation but suggest that both landscape-scale and local-scale perspectives synergistically aid in the management of biological invasions in modified habitat networks.

opencc-zeroNov 2020View details →

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

opencc-by-4.0Dec 2020View details →

Nonresonant Raman spectroscopy of isolated human retina samples complying with laser safety regulations for in vivo measurements

Raman raw data for the paper "Nonresonant Raman spectroscopy of isolated human retina samples complying with laser safety regulations for in vivo measurements" <ul> <li>two sets of unprocessed Raman spectra recorded under restricted conditions as seen in Figure 5(b)</li> <li>each spectrum was recorded at 785 nm with 1 mW laser power and 10 s integration time</li> </ul>

opencc-zeroDec 2020View details →

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

opencc-by-4.0Dec 2020View details →

Social isolation induces hyperactivity and exploration in aged female mice - Raw Data

Raw data for the publication Social isolation induces hyperactivity and exploration in aged female mice accepted in PLOS One. Data is public for transparency and future utilization.

opencc-zeroOct 2021View details →

Data from: Phylogenetic diversity of two geographically overlapping species in the lichen genus Sticta (Ascomycota: Peltigeraceae): isolation by distance, environment, or fragmentation?

Aim: To test whether the degree of phylogenetic diversity differs in two congeneric, morphologically similar lichens that are both widespread and with a similar geographical range (Neotropics and Hawaii), but differ in altitudinal and habitat preferences, and whether the two species underwent isolation by distance (IBD), environment (IBE), or fragmentation (IBF). Location: South and Central America, Caribbean, Hawaii, Azores. Taxon: Sticta (Peltigeraceae). Methods: Analysis of 395 specimens across the study area; ITS barcoding marker; maximum likelihood tree reconstruction within a broad taxonomic framework; TCS haplotype networks; Mantel test of genetic vs. geographic, environmental, and fragmentation distances; statistical comparison of BIOclim variables. Results: Sticta andina exhibited high phenotypic variation and high reticulate phylogenetic diversity across its range, whereas the phenotypically more uniform S. scabrosa contained two main haplotypes, one unique to Hawaii (subsp. hawaiiensis). Sticta andina was restricted to well-preserved andine forests and paramos, habitats fragmented due to disruptive topology, whereas S. scabrosa was found in lowland to lower montane forests in rather exposed microsites, representing a more continuous habitat. These differences were statistically significant for several BIOclim variables. Mantel tests on genetic vs. geographic and environmental distances demonstrated that S. scabrosa followed a pattern of IBD across its full range but not within continental Central and South America. In contrast, S. andina did not exhibit IBD but showed weak, yet significant patterns of IBE at continental level and IBF in the northern Andes. Main Conclusions: Autecology indirectly drives phylogenetic diversity in the two studied species. In the low altitude species, S. scabrosa, phylogenetic diversity is low and shows no correlation with geographic or environmental distances, except for the differentiation of the Hawaiian subspecies. We attribute this to rapid expansion and effective gene flow between populations across a more or less continuously distributed niche representing partially exposed microsites, including disturbed and anthropogenic vegetation, such as planted trees. In contrast, in the high altitude species, S. andina, phylogenetic diversity is high and correlated with both environmental niche differentiation (IBE) and fragmentation caused by the final Andean uplift (IBF). Therefore, an autoecological preference for high altitudes increases the likelihood for higher phylogenetic diversity.

FIGURE 1 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 1. PCA of different populations of Heterorhabditis bacteriophora based on infective juvenile morphological characters.

FIGURE 4 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 4. Phylogenetic relationships of Heterorhabditis isolates DH7, DH8 and CH21 based on ITS rDNA sequences. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (10.000 replicates) is shown next to the branches. Branch lengths indicate evolutionary distances and are expressed in units of the number of base differences per site.

FIGURE 3 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 3. PCA of different populations of Heterorhabditis bacteriophora based on male morphological characters.

FIGURE 7 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 7. Percentage mortality (mean and SD) of Spodoptera litura (A and B), Helicoverpa armigera (C and D) and Holotrichia serrata (E and F) larvae with different doses of Heterorhabditis bacteriophora isolates DH7 and DH8.

FIGURE 2 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 2. PCA of different populations of Heterorhabditis bacteriophora based on hermaphroditic female morphological characters.

FIGURE 6 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 6. Phylogenetic relationships of Photorhabdus species based on the analysis of 16S rDNA gene sequences. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1.000 replicates) are shown next to the branches. Branch lengths indicate evolutionary distances and are expressed in units of the number of base differences per site.

FIGURE 5 in Morphological and molecular characterization of Heterorhabditis bacteriophora isolated from Indian soils and their biocontrol potential

FIGURE 5. Phylogenetic relationships of Heterorhabditis isolates DH7, DH8 and CH21 based on the analysis of the D2D3 region of the 28S rDNA. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (10.000 replicates) is shown next to the branches. Branch lengths indicate evolutionary distances and are expressed in units of the number of base differences per site.

opencc-zeroJan 2021View details →

Data from: Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies

Landscape features shape patterns of gene flow among populations, ultimately determining where taxa lay along the continuum between panmixia to complete reproductive isolation. Gene flow can be restricted leading to population differentiation in two non-exclusive ways: "physical isolation", in which geographic distance in combination with the landscape features restricts movement of individuals promoting genetic drift, and "ecological isolation", in which adaptive mechanisms constrain gene flow between different environments via divergent natural selection. In central Iberia, two fire salamander subspecies occur in parapatry across elevation gradients along the Iberian Central System mountains, while in adjacent Mountains of Toledo Region only one of them occurs. By integrating population and landscape genetic analyses, we show a ubiquitous role of physical isolation between and within mountain ranges, with unsuitable landscapes increasing differentiation between populations. However, across the Iberian Central System, we found strong support for a significant contribution of ecological isolation, with low genetic differentiation in environmentally homogeneous areas, but high differentiation across sharp transitions in precipitation seasonality. These patterns are consistent with a significant contribution of ecological isolation in restricting gene flow among subspecies. Overall, our results suggest that ecological divergence contributes to reduce genetic admixture, creating an opportunity for lineages to follow distinct evolutionary trajectories.

opencc-zeroJan 2021View details →

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and USA to hindcast the potential range of Larix laricina during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of broadest areas of past climate suitability for Larix laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of Larix laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM, suggest that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.

opencc-by-4.0Jan 2021View details →

Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Optical DNA mapping (ODM) data related to the study, presented in figures 2-6 in the paper.

opencc-zeroJan 2021View details →

Limited phenological and pollinator-mediated isolation among selfing and outcrossing Arabidopsis lyrata populations

Transitions from outcrossing to selfing have been a frequent evolutionary shift in plants and clearly play a role in species divergence. However, many questions remain about the initial mechanistic basis of reproductive isolation during the evolution of selfing. For instance, how important are pre-zygotic pre-pollination mechanisms (e.g. changes in phenology and pollinator visitation) in maintaining reproductive isolation between newly arisen selfing populations and their outcrossing ancestors? To test whether changes in phenology and pollinator visitation isolate selfing populations of Arabidopsis lyrata from outcrossing populations, we conducted a common garden experiment with plants from selfing and outcrossing populations as well as their between-population hybrids. Specifically, we asked whether there was isolation between outcrossing and selfing plants and their between-population hybrids through differences in (1) the timing or intensity of flowering; and/or (2) pollinator visitation. We found that phenology largely overlapped between plants from outcrossing and selfing populations. There were also no differences in pollinator preference related to mating system. Additionally, pollinators preferred to visit flowers on the same plant rather than exploring nearby plants, creating a large opportunity for self-fertilization. Overall, this suggests that pre-zygotic pre-pollination mechanisms do not strongly reproductively isolate plants from selfing and outcrossing populations of Arabidopsis lyrata.

opencc-by-4.0Jan 2021View details →

The Formation of Isolated Ultra-Diffuse Galaxies in Romulus25

Ultra-diffuse galaxies (UDGs) are a subset of the low surface brightness (LSB) galaxy population characterized by dwarf-like luminosities but light profiles that can extend as far as those of Milky-Way-mass galaxies. Although thousands of these objects have been discovered in cluster and group environments, fewer than 200 have thus far been confirmed in the field. We use the Romulus25 cosmological simulation to study the methods by which isolated UDGs form and evolve. Beyond their low central surface brightnesses and large effective radii, these galaxies have fairly typical global properties for their masses and environments. However, their central star formation rates are systematically low, leading to lower central stellar densities and older, fainter central stellar populations. We find that isolated UDGs are the products of early major mergers that produce a temporary boost in spin and cause star-forming gas to migrate from the centers of the galaxies to larger radii. Although our simulated UDGs are consistent with the few existent observations of isolated UDGs, we predict that many isolated UDGs have been missed by current surveys. The Nancy Grace Roman Telescope’s ability to provide deep, wide-field photometry will make it an ideal instrument for future discovery and study of these extreme LSB galaxies.