PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2

Rosenberg, Michael S.; Anderson, Corey Devin

doi:10.1111/j.2041-210x.2010.00081.x

Cited by 676 publications

(516 citation statements)

References 5 publications

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“…developed by Rosenberg and Anderson (2011). This test corrects the degrees of freedom based on the amount of auto-correlation in the data (e.g., Wang et al 2007c).…”

Section: Resultsmentioning

confidence: 99%

Ecosystem-scale spatial heterogeneity of stable isotopes of soil nitrogen in African savannas

et al. 2012

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“…developed by Rosenberg and Anderson (2011). This test corrects the degrees of freedom based on the amount of auto-correlation in the data (e.g., Wang et al 2007c).…”

Section: Resultsmentioning

confidence: 99%

Ecosystem-scale spatial heterogeneity of stable isotopes of soil nitrogen in African savannas

et al. 2012

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“…We analyzed isolation by distance with a Mantel test correlating F st and physical distance matrices within PASSaGE [61]. We used Fast UniFrac [62] to test for significant differentiation among Bradyrhizobium communities at different collection sites.…”

Section: Community Structurementioning

confidence: 99%

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

et al. 2015

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The patterns and drivers of bacterial strain dominance remain poorly understood in natural populations. Here, we cultured 1292 Bradyrhizobium isolates from symbiotic root nodules and the soil root interface of the host plant Acmispon strigosus across a >840-km transect in California. To investigate epidemiology and the potential role of accessory loci as epidemic drivers, isolates were genotyped at two chromosomal loci and were assayed for presence or absence of accessory Bsymbiosis island^loci that encode capacity to form nodules on hosts. We found that Bradyrhizobium populations were very diverse but dominated by few haplotypeswith a single Bepidemic^haplotype constituting nearly 30 % of collected isolates and spreading nearly statewide. In many Bradyrhizobium lineages, we inferred presence and absence of the symbiosis island suggesting recurrent evolutionary gain and or loss of symbiotic capacity. We did not find statistical phylogenetic evidence that the symbiosis island acquisition promotes strain dominance and both symbiotic and nonsymbiotic strains exhibited population dominance and spatial spread. Our dataset reveals that a strikingly few Bradyrhizobium genotypes can rapidly spread to dominate a landscape and suggests that these epidemics are not driven by the acquisition of accessory loci as occurs in key human pathogens.

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“…Two different distance classes were used (Legendre and Legendre, 1998): equal distance and equal count (Supplementary Table S2). The Mantel test and Mantel correlogram analysis were performed using PASSaGE v2 (Pattern Analysis, Spatial Statistics and Geographic Exegesis) software (http://www.passagesoftware.net/, Rosenberg and Anderson, 2011). Statistical significance of the correlation coefficient for the Mantel test and Mantel statistics for the correlogram analysis was tested by 10,000 permutations.…”

Section: Methodsmentioning

confidence: 99%

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

et al. 2017

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Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (α-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao1 index = 6,862) than in forests in Singapore and Sarawak (~1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chao1 indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest-specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (β-diversity) and direct distance between forests. Both α-and β-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.

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PASSaGE: Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2

Cited by 676 publications

References 5 publications

Ecosystem-scale spatial heterogeneity of stable isotopes of soil nitrogen in African savannas

Ecosystem-scale spatial heterogeneity of stable isotopes of soil nitrogen in African savannas

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

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