Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis

Kruskal, Joseph B.

doi:10.1007/bf02289565

Cited by 6,285 publications

(3,198 citation statements)

References 13 publications

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“…The STATISTICA package (StatSoft Inc., Tulsa, OK, USA) was used for multi-dimensional scaling (MDS) analysis. 29 BSPs were produced from the coding region sequences (positions 577-16023) using MCMC sampling in version 5.1 of the program BEAST. 30 The plots were obtained with a piecewise linear model and ancestral gene trees were based on a general time-reversible substitution model with invariant sites (GTR+I).…”

Section: Resultsmentioning

confidence: 99%

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

Schönberg

Theunert

et al. 2011

Eur J Hum Genet

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To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used highthroughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40-50 kya, followed by a constant population size, and then another expansion around 15-18 kya for the groups from the Caucasus and Iran. The BSP for Turkey differs the most from the others, with an increase from 35 to 50 kya followed by a prolonged period of constant population size, and no indication of a second period of growth. An approximate Bayesian computation approach was used to estimate divergence times between each pair of populations; the oldest divergence times were between Turkey and the other four groups from the South Caucasus and Iran (B400-600 generations), while the divergence time of the three Caucasus groups from each other was comparable to their divergence time from Iran (average of B360 generations). These results illustrate the value of random sampling of complete mtDNA genome sequences that can be obtained with high-throughput sequencing platforms.

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Section: Resultsmentioning

confidence: 99%

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

Schönberg

Theunert

et al. 2011

Eur J Hum Genet

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“…Occurrence of pest species was compared first with an ordination method, non-metric multidimensional scaling (NMS, Kruskal, 1964), and then with a multiple response permutation procedure (MRPP, Zimmerman et al, 1985). Possible associations between taxa and habitats were defined using indicator species analysis (ISA, Dufrene and Legendre, 1997).…”

Section: Resultsmentioning

confidence: 99%

Shared flowering phenology, insect pests, and pathogens among wild, weedy, and cultivated rice in the Mekong Delta, Vietnam: implications for transgenic rice

Cohen

Arpaia

Lan

et al. 2008

Environ. Biosafety Res.

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Many varieties of transgenic rice are under development in countries where wild and weedy relatives co-occur with the crop. To evaluate possible risks associated with pollen-mediated transgene dispersal, we conducted a two-year survey in Vietnam to examine overlapping flowering periods of rice (Oryza sativa L.), weedy rice (O. sativa), and wild rice (O. rufipogon Griff.), all of which are inter-fertile. We surveyed populations in two regions of the Mekong Delta, northern and southern, and at three sites in each of three habitats per region: fresh water, saline water, and acid sulfate soil. Weedy rice frequently flowered simultaneously with neighboring cultivated rice plants. Flowering was more seasonal in wild rice and often peaked in November and December. Peak flowering times of wild rice overlapped with adjacent rice fields at all of the saline sites and half of the acid sulfate sites. The longer flowering season of wild rice ensured that crop-to-wild gene flow was possible in fresh water habitats as well. Our second objective was to determine whether wild and weedy rice populations are exposed to pests that could be targeted by future transgenes, which may then provide fitness benefits. These populations shared many pathogen and insect herbivore species with cultivated rice (leaffolder, locust, cricket, planthoppers, rice bug, stem borer, sheath blight, blast, bacterial leaf blight, and brown spot). Damage by leaffolders and locusts was the most frequently observed insect feeding damage on all three rice types. Indicator species analysis revealed that most of the insect herbivores were associated with particular habitats, demonstrating the importance of broad geographic sampling for transgenic rice risk assessment. These survey data and the strong likelihood of gene flow from cultivated rice suggest that further studies are needed to examine the effects of transgenic traits such as resistance to pests on the abundance of wild and weedy rice.

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“…To make the intensive plot data set parallel to the rapid assessment data, we normalized the intensive sample plot data to only include trees, shrubs, and up to three dominant herbaceous species in each plot. We then ran ordination analyses using nonmetric multidimensional scaling (NMS; Kruskal, 1964) with Sørensen distance, first on all the plots, then just on the intensively sampled plots. The cluster analysis and ordinations were performed in PC‐ORD 5.0 (McCune & Mefford, 1999).…”

Section: Methodsmentioning

confidence: 99%

Local patterns of diversity in California northern coastal scrub

Wrubel

Parker

2018

Ecology and Evolution

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Within global biodiversity hotspots such as the California Floristic Province, local patterns of diversity must be better understood to prioritize conservation for the greatest number of species. This study investigates patterns of vascular plant diversity in relation to coast–inland environmental gradients in the shrublands of Central California known as northern coastal scrub. We sampled coastal shrublands of the San Francisco Bay Area at coastal and inland locations, modeled fine‐scale climatic variables, and developed an index for local exposure to maritime salts. We compared diversity, composition, and structure of the coastal and inland plots using indirect gradient analysis and estimated species accumulation using rarefaction curves. Coastal plots were significantly higher in alpha, beta, and gamma diversity than inland plots. Plant diversity (effective species number) in coastal plots was 2.1 times greater than inland plots, and beta diversity was 1.9 times greater. Estimated richness by rarefaction was 2.05 times greater in coastal sites than inland sites. Salt deposition and water availability were the abiotic process most strongly correlated with increased maritime plant diversity and compositional differences. Stands of northern coastal scrub on the immediate coast with higher maritime influence exhibit markedly higher plant diversity than most interior stands, paralleling previous work in other vegetation types in this region. These studies suggest that the California coastline deserves special consideration for botanical conservation. Fine‐scale climatic models of cloud frequency, water availability, and the salt deposition index presented here can be used to define priority areas for plant conservation in California and other coastal regions worldwide.

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Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis

Cited by 6,285 publications

References 13 publications

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences

Shared flowering phenology, insect pests, and pathogens among wild, weedy, and cultivated rice in the Mekong Delta, Vietnam: implications for transgenic rice

Local patterns of diversity in California northern coastal scrub

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