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Dataset: Employing the Generalized Pareto Distribution to Analyze Extreme Rainfall Events on Consecutive Rainy Days in Thailand's Chi Watershed: Implications for Flood Management

This data set is used to employing the generalized Pareto distribution to analyze extreme rainfall events on consecutive rainy days in Thailand's Chi watershed. A case of implications for flood management. Observational raw data from Thailand were provided by the Climate Information Services (CIS) at https://www.tmd.go.th/cis/main.php.

opencc-zeroJan 2024View details →

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Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation

When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

opencc-by-4.0Feb 2018View details →

Fig. 1. A in A new Mississippian hexactinellid sponge from the western Gondwana: Taxonomic and paleobiogeographic implications

Fig. 1. A. Geographic location of the studied area. B. Geological map and location of the studied section. The west flank of the Agua Quemada Syncline is divided in some tectonic blocks (1 and 2) by inverse and dextral strip faults. Sponges come from nodules of equivalent fine-grained dark stratigraphical intervals of the Agua de Lucho Formation (Tournaisian), cropping out under glacigenic diamictitic in both tectonic blocks. C. Stratigraphic column of the Agua de Lucho Formation and the location of the sponge-bearing levels.

opencc-by-4.0Jan 2020View details →

Fig. 1. A in The first ornithosuchid from Brazil and its macroevolutionary and phylogenetic implications for Late Triassic faunas in Gondwana

Fig. 1. A. Location map of the Janner site and the surface distribution of the geologic units in the area (modified from Müller et al. 2017). B. Stratigraphic column of the Janner site (modified from Da-Rosa 2015) depicting its fossiliferous content: 1, Exaeretodon; 2, Hyperodapedon; 3, Pampadromaeus; 4, Trucidocynodon; 5, Bagualosaurus; and 6, the new ornithosuchid.

opencc-by-4.0Feb 2018View details →

Fig. 2 in A new Mississippian hexactinellid sponge from the western Gondwana: Taxonomic and paleobiogeographic implications

Fig. 2. Hexactinellid sponge Minitaspongia parvis gen. et sp. nov. from the Tournaisian Carboniferous, Sierra de las Minitas section, La Rioja Province, Argentina. A. Holotype PULR-I 4, complete obconical specimen, showing the cylindrical acute base. External surface of the holotype showing deep impressions of vertical and horizontal tracts and cross-shaped spicule molds as second order elements in the middle of first order quadrules (A2). B. Paratype PULR-I 5, external impression with original spicules forming the reticulate skeleton (B1); detail showing a well preserved external area of the second order quadrules (B2); detail of the first order quadrules showing preserved hexactine-based spicules aligned (B3); detail of the tract with vertically oriented, main long axis hexactine- based spicules, bundles of two or three long spicule axis occur in the tract (B4); enlarged section of B4 showing nodes of the perpendicular axis of the hexactins (B5); details of the spicules in the tracts, long rayed hexactins, and small second order hexactins with equal-ray dimensions (B6, B7).

opencc-by-4.0Feb 2018View details →

Fig. 3. A in A new Mississippian hexactinellid sponge from the western Gondwana: Taxonomic and paleobiogeographic implications

Fig. 3. A. Schematic reconstruction of the complete sponge Minitaspongia parvis gen et. sp. nov. B. The spicule framework of the wall as main parts of the vertical and horizontal bands.

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Data from: In vitro competition between two transmissible cancers, and potential implications for their host, the Tasmanian devil

Since the emergence of a transmissible cancer, devil facial tumour disease (DFT1), in the 1980s, wild Tasmanian devil populations have been in decline. In 2016, a second, independently evolved transmissible cancer (DFT2) was discovered raising concerns for survival of the host species. Here, we applied experimental and modelling frameworks to examine competition dynamics between the two transmissible cancers in vitro. Using representative cell lines for DFT1 and DFT2, we have found that in monoculture, DFT2 grows twice as fast as DFT1 but reaches lower maximum cell densities. Using co-cultures, we demonstrate that DFT2 outcompetes DFT1: the number of DFT1 cells decreasing over time, never reaching exponential growth. This phenomenon could not be replicated when cells were grown separated by a semi-permeable membrane, consistent with exertion of mechanical stress on DFT1 cells by DFT2. A logistic model and a Lotka-Volterra competition model were used to interrogate monoculture and co-culture growth curves respectively, suggesting DFT2 is a better competitor than DFT1, but also showing that competition outcomes might depend on the initial number of cells, at least in the laboratory. We provide theories how the in vitro results could be translated to observations in the wild and propose that these results may indicate that although DFT2 is currently in a smaller geographic area than DFT1, it could have the potential to outcompete DFT1. Further, we provide a framework for improving the parameterization of epidemiological models applied to these cancer lineages, which will inform future disease management.

opencc-zeroFeb 2024View details →

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Data from: Seasonal bee communities vary in their responses to resources at local and landscape scales: Implication for land managers

Context: There is great interest in land management practices for pollinators; however, a quantitative comparison of landscape and local effects on bee communities is necessary to determine if adding small habitat patches can increase bee abundance or species richness. The value of increasing floral abundance at a site is undoubtedly influenced by the phenology and magnitude of floral resources in the landscape, but due to the complexity of measuring landscape-scale resources, these factors have been understudied. Objectives: To address this knowledge gap, we quantified the relative importance of local versus landscape scale resources for bee communities, identified the most important metrics of local and landscape quality, and evaluated how these relationships vary with season. Methods: We studied season-specific relationships between local and landscape quality and wild-bee communities at 33 sites in the Finger Lakes region of New York, USA. We paired site surveys of wild bees, plants, and soil characteristics with a multi-dimensional assessment of landscape composition, configuration, insecticide toxic load, and a spatio-temporal evaluation of floral resources at local and landscape scales. Results: We found that the most relevant spatial scale and landscape factor varied by season. Early-season bee communities responded primarily to landscape resources, including the presence of flowering trees and wetland habitats. In contrast, mid to late-season bee communities were more influenced by local conditions, though bee diversity was negatively impacted when sites were embedded in highly agricultural landscapes. Soil composition had complex impacts on bee communities, and likely reflects effects on plant community flowering. Conclusions: Early-season bees can be supported by adding flowering trees and wetlands, while mid to late-season bees can be supported by local addition of summer and fall flowering plants. Sites embedded in landscapes with a greater proportion of natural areas will host a greater bee species diversity.

opencc-zeroMar 2024View details →

opencc-by-4.0Mar 2024View details →

Research Data for Comparative Evaluation of RT-PCR and Antigen-based Rapid Diagnostic Tests (Ag-RDTs) for SARS-CoV-2 Detection: Performance, Variant Specificity, and Clinical Implications

This dataset represents laboratory findings for the comparative evaluation of the diagnostic performance of Ag-RDTs (Flourescence Immunoassay and Lateral Flow Immunoassay) with RT-PCR

FIGURE 4 in Confirming the identity of the Hypogeococcus species (Hemiptera: Pseudococcidae) associated with Harrisia martinii (Labour.) Britton (Cactaceae) in Australia: implications for biological control

FIGURE 4 Mean (± SE) development time in days of the first- and second-generation females, from the first nymph to adult emergence of the Australian Hypogeococcus (W = 39, p = 0.0545).

FIGURE 3 in Confirming the identity of the Hypogeococcus species (Hemiptera: Pseudococcidae) associated with Harrisia martinii (Labour.) Britton (Cactaceae) in Australia: implications for biological control

FIGURE 3 Phylogenetic trees based on COI sequence data (a) maximum likelihood (IQ-TREE) and (b) Bayesian (Mr. Bayes). Branch labels indicate the ultrafast bootstrap and SH-aLRT values for the maximum likelihood tree and posterior probabilities for the Bayesian tree. Paracoccus marginatus was used as the outgroup for both trees. The host plant family is followed by the country of collection. See Table S1 for further details on host plant species and specimen collection codes for Hypogeococcus. **Country of collection includes Argentina, Brazil, Puerto Rico, and the United States.

FIGURE 2 in Confirming the identity of the Hypogeococcus species (Hemiptera: Pseudococcidae) associated with Harrisia martinii (Labour.) Britton (Cactaceae) in Australia: implications for biological control

FIGURE 2 Phylogenetic trees based on EF1α sequence data (a) maximum likelihood (IQ-TREE) and (b) Bayesian (Mr. Bayes). Branch labels indicate the ultrafast bootstrap and SH-aLRT values for the maximum likelihood tree and posterior probabilities for the Bayesian tree. Planococcus ficus was used as the outgroup for both trees. The host plant family is followed by the country of collection. See Table S1 for further details on host plant species and specimen collection codes for Hypogeococcus.

FIGURE 5 in Confirming the identity of the Hypogeococcus species (Hemiptera: Pseudococcidae) associated with Harrisia martinii (Labour.) Britton (Cactaceae) in Australia: implications for biological control

FIGURE 5 (a) Mean (± SE) pre-oviposition period (days) of the first virgin females, the second virgin, and second mated female generations (H = 19.491, p <0.0001), means labelled with similar letters are not significantly different (Dunn's test, p <0.05); (b) realised fecundity of the first virgin females, the second virgin and second mated female generations (H = 1.2429, p = 0.5372).

FIGURE 1 in Confirming the identity of the Hypogeococcus species (Hemiptera: Pseudococcidae) associated with Harrisia martinii (Labour.) Britton (Cactaceae) in Australia: implications for biological control

FIGURE 1 The different morphological features of the Australian Hypogeococcus: Panels (a) and (b) show that the abdominal region has three circuli (1–3); panel (c) shows that the head region has two antennae (4), numerous slender capitate setae (5), and numerous multilocular pores (6); panel (d) shows the presence of numerous slender capitate setae (5) and numerous multilocular pores (6) in the abdominal region; panels (e) and (f) show that the posterior ventral area possess numerous multilocular pores (6) and numerous conical setae (7); panels (g) and (h) show the foreleg (8) with the curvature attachment point, mid-leg (9) and hindleg (10), both with attachment points ending in a bifurcation. These characters are consistent with Hypogeococcus pungens s.s.

FIGURE 15 in Comparison of Miocene to early Pleistocene-aged Castor californicus (Rodentia: Castoridae) to extant beavers and implications for the evolution of Castor in North America

FIGURE 15. Comparison of the skull and dentary of extant Castor canadensis (MVZ 80744) and C. fiber (USNM 248154) to fossil C. californicus (USNM 26154). Note that the North American species C. canadensis and C. californicus share shorter nasals, wider occiput, and more posteriorly positioned orbits than Eurasian C. fiber; both also display more anterior placement of the anterior margin of the pterygoid insertion and greater spread of the posterior processes (coronoid, condylar, angular) than C. fiber.

FIGURE 14 in Comparison of Miocene to early Pleistocene-aged Castor californicus (Rodentia: Castoridae) to extant beavers and implications for the evolution of Castor in North America

FIGURE 14. Variation line graph calculated by coefficients of variation with sample size correction for Castor canadensis and C. californicus postcranial measurements. Note that C. fiber is excluded due to limited sampling. Castor canadensis and C. californicus both contains high levels of variation in postcranial elements. See Table 17 for descriptive statistics, coefficients of variation, and ANOVA results.

FIGURE 13 in Comparison of Miocene to early Pleistocene-aged Castor californicus (Rodentia: Castoridae) to extant beavers and implications for the evolution of Castor in North America

FIGURE 13. Boxplots for (A) articular width of humeral distal end (HDAW), (B) femoral epicondylar breadth (FeEB), (C) anteroposterior diameter of tibia distal epiphysis (TDEAPD), (D) anteroposterior diameter of third metatarsal (MT3APD), and (E) mediolateral diameter of fourth metatarsal (MT4MLD) of Castor canadensis and C. californicus, which exhibit differences in mean values and no overlap in range values. See Table 17 for descriptive statistics, coefficients of variation, and ANOVA results.

FIGURE 12 in Comparison of Miocene to early Pleistocene-aged Castor californicus (Rodentia: Castoridae) to extant beavers and implications for the evolution of Castor in North America

FIGURE 12. Boxplots for (A) anteroposterior diameter of femur (FeAPD) and (B) mediolateral diameter of tibia distal epiphysis (TDEMLD) of Castor canadensis and C. californicus, which exhibit differences in mean values and minimal overlap in range values. See Table 17 for descriptive statistics, coefficients of variation, and ANOVA results.

FIGURE 9 in Comparison of Miocene to early Pleistocene-aged Castor californicus (Rodentia: Castoridae) to extant beavers and implications for the evolution of Castor in North America

FIGURE 9. Canonical variate plot for analysis of dentary data with Castor californicus treated as a distinct taxon a priori. Axes depict shape variation, associated with landmark deformations, indicated by thin plate splines deformation grids.