Data from: Allergenic pollen production across a large city for common ragweed (Ambrosia artemisiifolia)
Contributors: Katz, Daniel S. W., Batterman, Stuart A.
... Predictions of airborne allergenic pollen concentrations at fine spatial scales require information on source plant location and pollen production. Such data are lacking at the urban scale, largely because manually mapping allergenic pollen producing plants across large areas is infeasible. However, modest-sized field surveys paired with allometric equations, remote sensing, and habitat distribution models can predict where these plants occur and how much pollen they produce. In this study, common ragweed (Ambrosia artemisiifolia) was mapped in a field survey in Detroit, MI, USA. The relationship between ragweed presence and habitat-related variables derived from aerial imagery, LiDAR, and municipal data were used to create a habitat distribution model, which was then used to predict ragweed presence across the study area (392 km2). The relationship between inflorescence length and pollen production was used to predict pollen production in the city. Ragweed occurs in 1.7% of Detroit and total pollen production is 312 × 1012 pollen grains annually, but ragweed presence was highly heterogeneous across the city. Ragweed was predominantly found in in vacant lots (75%) and near demolished structures (48%), and had varying associations with land cover types (e.g., sparse vegetation, trees, pavement) detected by remote sensing. These findings also suggest several management strategies that could help reduce levels of allergenic pollen, including appropriate post-demolition management practices. Spatially-resolved predictions for pollen production will allow mechanistic modeling of airborne allergenic pollen and improved exposure estimates for use in epidemiological and other applications.
Data from: Multi-scale habitat modeling identifies spatial conservation priorities for mainland clouded leopards (Neofelis nebulosa)
Contributors: Macdonald, David, Bothwell, Helen, Kaszta, Zaneta, Ash, Eric, Bolongon, Gilmoore, Burnham, Dawn, Can, Ozgun, Campos-Arceiz, Ahimsa, Channa, Phan, Clements, Gopalasamy
... Aim Deforestation is rapidly altering Southeast Asian landscapes, resulting in some of the highest rates of habitat loss worldwide. Among the many species facing declines in this region, clouded leopards rank notably for their ambassadorial potential and capacity to act as powerful levers for broader forest conservation programmes. Thus identifying core habitat and conservation opportunities are critical for curbing further Neofelis declines and extending umbrella protection for diverse forest biota similarly threatened by widespread habitat loss. Furthermore, a recent comprehensive habitat assessment of Sunda clouded leopards (N. diardi) highlights the lack of such information for the mainland species (N. nebulosa), and facilitates a comparative assessment. Location Southeast Asia. Methods Species-habitat relationships are scale-dependent, yet <5% of all recent habitat modeling papers apply robust approaches to optimize multivariate scale relationships. Using one of the largest camera trap datasets ever collected, we developed scale-optimized species distribution models for two con-generic carnivores, and quantitatively compared their habitat niches. Results We identified core habitat, connectivity corridors, and ranked remaining habitat patches for conservation prioritization. Closed canopy forest was the strongest predictor, with ~25% lower Neofelis detections when forest cover declined from 100 to 65%. A strong, positive association with increasing precipitation suggests ongoing climate change as a growing threat along drier edges of the species' range. While deforestation and land use conversion were deleterious for both species, N. nebulosa was uniquely associated with shrublands and grasslands. We identified 800km2 as a minimum patch size for supporting clouded leopard conservation. Main Conclusions We illustrate the utility of multi-scale modeling for identifying key habitat requirements, optimal scales of use, and critical targets for guiding conservation prioritization. Curbing deforestation and development within remaining core habitat and dispersal corridors, particularly in Myanmar, Laos, and Malaysia, is critical for supporting evolutionary potential of clouded leopards and conservation of associated forest biodiversity.
Data from: The complete genome sequence of the thermophilic bacterium Laceyella sacchari FBKL4.010 reveals the basis for tetramethylpyrazine biosynthesis in Moutai‐flavor Daqu
Contributors: Li, Dounan, Huang, Wei, Wang, Chunxiao, Qiu, Shuyi
... The genus Laceyella consists of a thermophilic filamentous bacteria. The pure isolate of Laceyella sacchari FBKL4.010 was isolated from Moutai‐flavor Daqu, Guizhou Province, China. In this study, the whole genome was sequenced and analyzed. The complete genome consists of one 3,374,379‐bp circular chromosome with 3,145 coding sequences (CDSs), seven clustered regularly interspaced short palindromic repeat (CRISPR) regions of 12 CRISPRs. Moreover, we identified that the genome contains genes encoding key enzymes such as proteases, peptidases, and acetolactate synthase (ALS) of the tetramethylpyrazine metabolic pathway. Metabolic pathways relevant to tetramethylpyrazine synthesis were also reconstructed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) PATHWAY database. Annotation and syntenic analyses using antiSMASH 4.0 also revealed the presence of two gene clusters in this strain that differ from known tetramethylpyrazine synthesis clusters, with one encoding amino acid dehydrogenase (ADH) and the other encoding transaminase in tetramethylpyrazine metabolism. The results of this study provide flavor and genomic references for further research on the flavor‐producing functions of strain FBKL4.010 in the Moutai liquor‐making process.
Contributors: Bélouard, Nadège, Paillisson, Jean-Marc, Oger, Adrien, Besnard, Anne-Laure, Petit, Eric
... Recent theoretical and experimental models have evidenced the role played by evolution during species spread, and particularly question the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences on genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwestern France). Despite the small spatial scale of our study (15 km²), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonisation through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a two-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights in the current context of profound rearrangements in species distributions due to global change.
Data from: Total-evidence approach reveals an extinct lineage of Paederinae rove beetles from Cretaceous Burmese amber
Contributors: Żyła, Dagmara, Yamamoto, Shuhei, Jenkins Shaw, Josh
... The fossil record contains vital information about the evolution of lineages and is a source of data that cannot be reconciled in any other way than by the direct observation of morphologies. Total-evidence phylogenetic reconstruction is being increasingly used to assess the position of extinct taxa by incorporating morphological data from extinct and extant taxa together with molecular data from extant taxa in a united framework. Here we apply the method to two Cretaceous Burmese amber inclusions belonging to the rove beetle subfamily Paederinae. To perform the total evidence analysis, we constructed the first morphological matrix and the most comprehensive molecular dataset for the subfamily. Our analyses reveal an extinct lineage of Paederinae rove beetles with a suite of unique morphological characters, resulting in the description of a new genus: Diminudon gen. nov. and two new species: D. schomannae sp. nov. and D. kachinensis sp. nov. Simultaneously our analyses provide new insights into the evolution and classification of the entire subfamily. We also discuss the unusually small size of the newly described Paederinae, which may represent an additional case for miniaturization in the Cretaceous.
Data from: Aragonite bias exhibits systematic spatial variation in the late Cretaceous Western Interior Seaway, North America
Contributors: Dean, Christopher, Allison, Peter, Hampson, Gary, Hill, Jon
... Preferential dissolution of the biogenic carbonate polymorph aragonite promotes preservational bias in shelly marine faunas. Whilst field studies have documented the impact of preferential aragonite dissolution on fossil molluscan diversity, its impact on regional and global biodiversity metrics is debated. Epicontinental seas are especially prone to conditions which both promote and inhibit preferential dissolution, which may result in spatially extensive zones with variable preservation. Here we present a multi-faceted evaluation of aragonite dissolution within the late Cretaceous Western Interior Seaway of North America. Occurrence data of molluscs from two time intervals (Cenomanian-Turonian boundary, early Campanian) are plotted on new high-resolution paleogeographies to assess aragonite preservation within the seaway. Fossil occurrences, diversity estimates and sampling probabilities for calcitic and aragonitic fauna were compared in zones defined by depth and distance from the seaway margins. Apparent range sizes, which could be influenced by differential preservation potential of aragonite between separate localities, were also compared. Our results are consistent with exacerbated aragonite dissolution within specific depth zones for both time slices, with aragonitic bivalves additionally showing a statistically significant decrease in range size compared to calcitic fauna within carbonate-dominated Cenomanian-Turonian strata. However, we are unable to conclusively show that aragonite dissolution impacted diversity estimates. Therefore, whilst aragonite dissolution is likely to have affected the preservation of fauna in specific localities, time averaging and instantaneous preservation events preserve regional biodiversity. Our results suggest that the spatial expression of taphonomic biases should be an important consideration for paleontologists working on paleobiogeographic problems.
Contributors: Suttner, Thomas James, Kido, Erika
... Conodont elements, consisting of crown and basal tissue are the well-known fossilized hard parts of Conodonta (extinct marine chordates), but the taphonomic processes leading to decomposition or remineralization of the basal tissue are not well understood. Here we focus on the taphonomy of basal tissue, reviewing the published record and describing new material from Asia and Europe (248 occurrences globally). These include crown and basal tissue in conjunction, and isolated basal bodies showing different stages of preservation. Some isolated specimens resemble phosphate rings similar to those assigned to Phosphannulus universalis. High-resolution biostratigraphy indicates that the lamellar type of conodont basal tissue is found in all facies and depositional environments. Other basal tissue types, described in the literature as tubular, mesodentine, spherulitic or lamellar with canalules, are limited to the early Palaeozoic and found exclusively in siliciclastic deposits (with the exception of spherulitic tissue). Although the stratigraphic record of basal tissue spans the range of Euconodonta (Cambrian–Triassic), this study shows that most of the isolated plate and ring-like structures are derived from early Palaeozoic coniform conodonts. Basal tissue of platform-type elements has a much more fragile shape and is therefore rarely preserved as a recognizable isolated unit.
Contributors: Soontararak, Sirikul, Chow, Lyndah, Johnson, Valerie, Coy, Jonathan, Webb, Craig, Wennogle, Sara, Dow, Steven
... Inflammatory bowel disease (IBD) in dogs is associated with clinical signs of intestinal dysfunction, as well as abnormal lymphocytic and myeloid cell infiltrates in the small and/or large intestine. Thus, in many respects IBD in dogs resembles IBD in humans. However, the factors that trigger intestinal inflammation in dogs with IBD are not well understood and have been variously attributed to immune responses against dietary antigens or intestinal antigens. Previous studies in humans with IBD have documented increased production of IgG and IgA antibodies specific to intestinal bacteria, and this abnormal immune response has been linked to disease pathogenesis. Therefore, we investigated the humoral immune response against gut bacteria in dogs with IBD, using flow cytometry to quantitate IgG and IgA binding. Studies were also done to investigate the source of these antibodies (locally produced versus systemic production) and whether greater antibody binding to bacteria is associated with increased inflammatory responses. We found that dogs with IBD had significantly higher percentages and overall amounts of IgG bound to their intestinal bacteria compared to healthy dogs. Similarly, significantly higher percentages of bacteria were IgA+ bacteria were also found in dogs with IBD. Serum antibody recognition of gut bacteria was not different between healthy dogs and dogs with IBD, suggesting that anti-bacterial antibodies were primarily produced locally in the gut rather than systemically. Importantly, bacteria in the Actinobacteria phylum and in particular the genus Collinsella had significantly greater levels of antibody binding in dogs with IBD. Based on these findings, we concluded that antibody binding to commensal gut bacteria was significantly increased in dogs with IBD, that particular phyla were preferential targets for gut antibodies, and that anti-bacterial antibody responses may play an important role in regulating gut inflammation.
Data from: New regionally modelled soil layers improve prediction of vegetation type relative to that based on global soil models
Contributors: Cramer, Michael, Wootton, Lara, van Mazijk, Ruan, Verboom, George
... Aim: High-resolution spatial soil data are crucial to species distribution modelling for fundamental research and conservation planning. Recent globally-modelled soil layers (e.g. SoilGrids) have transformed distribution modelling, but may fail to represent regional soil characteristics accurately. We hypothesize that in the Cape biodiversity hotspot of South Africa, the use of global soil layers has led to underestimation of the importance of edaphic factors as determinants of species’ and vegetation distributions. We present a series of new, regionally-modelled layers to address this deficiency. Location: Greater Cape Floristic Region (GCFR, South Africa) Methods: We georeferenced edaphic characteristics from literature and other sources and used boosted regression trees (BRT) to associate edaphic characteristics with spatially-explicit topographic, climatic, soil texture and biotic variables. Multinomial BRTs were used to predict mapped vegetation types from the collated edaphic and other data. Results: BRTs reliably predicted pH (92% of variance), Na (87%), K (85%), electrical conductivity (81%) and P (73%), but were less accurate for total N (55%) and total C (61%), for which data were sparser. Soil clay and pH values differed markedly in range and in spatial variation from those in SoilGrids. Using our new edaphic layers, we were able to accurately predict spatial distributions of vegetation types within the GCFR (multi-class AUC = 0.96). The multinomial BRT predicted vegetation less well when based on SoilGrids data alone (AUC = 0.84). Main conclusions: The more faithful representation of soil properties in our model is attributable both to its use of ca. 10-fold more samples, and to its regional focus. Our model of edaphic characteristics captures important edaphic variability that is vital for understanding plant and consequently faunal distributions, with wide-ranging conservation implications. Ongoing development of global syntheses of soil data requires more samples, especially in areas with high spatial heterogeneity and extreme edaphic conditions.
Contributors: Gee, Bryan, Reisz, Robert
... Nanobamus macrorhinus is a small amphibamiform temnospondyl from the early Permian Arroyo Formation of Texas. It is most readily characterized by an elongate and partially subdivided naris. This condition is superficially reminiscent of that seen in the coeval trematopids, the group to which N. macrorhinus was originally referred to under an interpretation of the holotype as a larval form. This was discounted by later workers, but the amphibamiform affinities of the specimen were not formalized until recently. The specimen has never been described in the context of its amphibamiform affinities and remains poorly characterized, never having been sampled in a phylogenetic analysis. Here we present a complete, updated osteological description of N. macrorhinus, including an improved characterization of its unique mosaic of plesiomorphic and apomorphic features and clarification of the taxon’s autapomorphies. Our analysis of the taxon’s phylogenetic position within Amphibamiformes shows that N. macrorhinus is recovered as diverging after basal amphibamiforms such the micropholids and before derived amphibamiforms such as the amphibamids. This is supported by the unique mixture of retained plesiomorphies such as non-foreshortened postparietals and an oval choana and apomorphies such as a narrow interorbital region and slender palatal rami of the pterygoid. These results reflect the complexity of terrestrial amphibamiform diversity and provide further insight into the evolutionary history of the lissamphibian stem in terrestrial environments.