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opencc-by-4.0Jun 2022View details →

Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn

The 132 bathymetric data from the lake while lake samples were taken on board. We created a bathymetric contour map in ArcGIS 10.2 using the natural neighborhood method to reflect the overall bathymetry of the lake through 116 randomly selected bathymetric data. The size of the Landsat 8 image was used as the basic unit (30*30 m) to divide the lake into 30*30 m areas and read data from 16 other bathymetric points that were not involved in the production of the bathymetric map.

opencc-by-4.0Jun 2022View details →

Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn

Wind speed data were collected from the Shishou weather station monitored by the China Meteorological Network (http://data.cma.cn/dataService/cdcindex/datacode/A.0012.0001/show_value/normal.html).

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Spatial pattern of genetic diversity in field populations of Fusarium incarnatum-equiseti species complex

Fusarium is associated with a number of wilt, blight, scab and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of Fusarium incarnatum-equiseti species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on inter-simple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intra-population genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.

opencc-zeroJul 2022View details →

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Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands

Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of Cyperus papyrus in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream of the Zambezi river basin. Our results also point to the very low genetic diversity of C. papyrus populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.

opencc-zeroSep 2022View details →

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Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal

The major histocompatibility complex (MHC) has been intensively studied to test for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing the variation of microsatellites and the diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g. immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely-distributed wild mammal.

opencc-zeroOct 2022View details →

opencc-by-4.0Jul 2024View details →

Data and figure production code for 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry'

Time mean data, and python code, used to create figures in 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry', Biogeosciences, Hogikyan and Resplandy 2024

opencc-by-4.0Jul 2018View details →

Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion

KGS conformational ensembles of 100 substates from sampling ADK starting from the open conformation (PDB ID 4ake). Hydrogen bonds were included at thresholds of -1, -2, and -4 kcal/mol. Hydrogen bond network constraint relaxation was set to 1e-10 (nullspace floppy modes) and 1e-2 (kinematic flexibility modes)

opencc-zeroJun 2019View details →

Supplementary material 5 from: Cabezas MP, Ros M, Santos AM, Martínez-Laiz G, Xavier R, Montelli L, Hoffman R, Fersi A, Dauvin JC, Guerra-García JM (2019) Unravelling the origin and introduction pattern of the tropical species Paracaprella pusilla Mayer, 1890 (Crustacea, Amphipoda, Caprellidae) in temperate European waters: first molecular insights from a spatial and temporal perspective. NeoBiota 47: 43-80. https://doi.org/10.3897/neobiota.47.32408

: Explanation note: A Phylogenetic tree of nuclear 28S rRNA. Unfortunately, this gene could not be amplified in P.tenuis species. In P.pusilla, only two haplotypes were detected, differing only by the presence of an indel. B Phylogenetic tree of nuclear ribosomal internal transcribed spacer (ITS). No variation was observed among P.pusilla sequences. Trees were rooted with Caprelladanilevskii and Caprellaliparotensis. Values at the nodes correspond to ML bootstrap support and Bayesian posterior probabilities, respectively.

opencc-by-4.0Oct 2019View details →

data and code for "Nest entrances, spatial fidelity, and foraging patterns in the red ant Myrmica rubra: a field and theoretical study"

Data set and codes used for the results, figures and simulation of the paper "Nest entrances, spatial fidelity, and foraging patterns in the red ant Myrmica rubra: a field and theoretical study".

Fig. 3 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)

Fig. 3 Bythinella pannonica COI haplotype network. Circles Haplotypes occurring in the Karst (white) and in the Bükk Mts. (black). Circle sizes are proportional to the frequencies of the haplotypes. Haplotypes were nested into hierarchical clades following the rules of Templeton et al. (1987) and Templeton and Sing (1993). The two main clades, which could not be connected at the 95 % confidence level, are considered as distinct 4-step clades. For reasons of simplicity, only 2nd and higher step clades are indicated here. See Table 4 for phylogeographic inferences

Fig. 2 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)

Fig. 2 Constrained Bayesian tree of Bythinella pannonica mitochondrial cytochrome c oxidase subunit I gene (COI) haplotypes. The tree was rooted by Bythinella austriaca (FJ028978) (not illustrated). Numbers at branches are Bayesian posterior probabilities. For reasons of comparability, 2nd and higher step clades, defined by nested clade analysis, are indicated. Posterior probabilities above 95 % are given only for 2nd and higher step clades (see Fig. 3 for nested clade structure). Note that clade 2–7 is inferred to be paraphyletic by this analysis. This tree has been deposited in the TreeBase (http://purl.org/ phylo/treebase/phylows/study/ TB2:S10789)

Fig. 4 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)

Fig. 4 Mismatch frequency distributions of pairwise mutational differences for different datasets of Bythinella pannonica samples. a Whole dataset, b clade-A (see Figs. 2 and 3) c Clade-B d Subset of Clade-A sampled in the Karst, e Subset of Clade-A sampled in the Bükk Mts. Thick solid lines Observed frequency of pairwise differences, dashed lines expected distribution under the sudden expansion model, thin lines lower and upper bounds of the 95 % confidence interval

Fig. 1 in Spatial pattern of intraspecific mitochondrial diversity in the Northern Carpathian endemic spring snail, Bythinella pannonica (Frauenfeld, 1865) (Gastropoda: Hydrobiidae)

Fig. 1 Relief map of the northeastern part of the Carpathian Basin showing collection sites and the geographic distribution of intraspecific clades [at the level at which significant phylogenetic structure was found by nested clade phylogeographic analysis (NCPA)]. Clade names correspond to those in Figs. 2 and 3. More precise locality data are given in Table 1. Thick solid line Political border between Hungary and Slovakia

Fig. 7 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 7 Climatic niche comparisons along the environmental space using hypervolumes for delimited lineages of South American Physamia. (a–c) Hypervolumes (point density and alpha-hull contour boundary) for delimited lineages of South American Physamia representing their climatic niches, and estimated using the values extracted from the components of the PCA-env (first three components). (a) PCenv1 vs PCenv2. (b) PCenv1 vs PCenv3. (c) PCenv2 vs PCenv3. (d) Phylomorphospace plot showing niche position between delimited lineages obtained using centroid distances between each pair of hypervolumes and multidimensional scaling

Fig. 4 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 4 Phylogenetic placement of sampled specimens of South American Physamia. (a–c) Maximum clade credibility (MCC) tree generated by Bayesian inference with BEAST 1.8.4. (a) nrITS dataset. (b) cpDNA dataset (tmnL-F/tmnH-psbA/tmnG intron/tmnS-tmnG). (c) Concatenated ITS + cpDNA datasets. (d) MCC tree estimated from ITS and cpDNA datasets using the multispecies coalescent method implemented in *BEAST v.1.8.4. The small circles on nodes indicate posterior probability (pp): black circles pp≥0.9, gray circles 0.9>pp≥0.7, white circles

Fig. 1 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 1 Representatives of South American Physamia. a–c P. cmassistigma. a Plant with flowers. b Plant with fruits. c Detail of fruits. d–e P. latemalis. d Plant with flowers and fruits. e Detail of fruits. f–g P. mendocina. f Plant with flowers. g Plant with fruits. h–i P. pygmaea. h Plant with flowers and fruits. i Details of fruits. j–l P. umbaniana. j Plant with flowers. k Plant with fruits. l Detail of fruits. a–c from Salamiato et al.

Fig. 6 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 6 Geographic and climatic niche distribution for delimited lineages of South American Physamia. (a) Maximum clade credibility (MCC) species tree estimated from ITS and cpDNA datasets using the multispecies coalescent method implemented in *BEAST 1.8.4 and the hypothesis of six independently evolving lineages. Numbers on branches correspond to posterior probability. (b) Geographic distribution of lineages: green,

Fig. 5 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 5 Results of species delimitation analyses. (a) Results from GMYC (discovery approach), BPP, and BFD (validation approaches) plotted onto the MCC tree obtained with the concatenated ITS+cpDNA dataset. GMYC analyses were conducted using MCC trees obtained with nrITS, cpDNA, concatenated nrITS+cpDNA, and coalescence nrITS–cpDNA analyses. BPP analyses were conducted using six different combinations

Fig. 3 in Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species

Fig. 3 Median-joining networks of a, nrITS dataset; b, cpDNA dataset (tmnLF, tmnH-psbA, tmnG intron, tmnS-tmnG spacer). Six morphologically defined species are distinguished by different colors: blue, P. cmassistigma; pink, P. latemalis; red, P. mendocina; black, P. okanensis; yellow, P. pygmaea; green: P. umbaniana. Intermediate (unobserved) haplotypes are distinguished by small gray circles. Circle sizes correspond to relative numbers of in- dividuals sharing a particular haplotype