Weighting species abundance estimates for marine resource assessment

Mumby, Peter J.; Clarke, K.R.; Harborne, Alastair R.

doi:10.1002/(sici)1099-0755(199609)6:3<115::aid-aqc188>3.0.co;2-t

Cited by 16 publications

(10 citation statements)

References 13 publications

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“…To investigate the effects of disturbance on the structure of recruit cornrnunities at each site, comrnunity distance was measured using the Bray-Curt1.s similarity coefficient and represented using non-metric multidimensional scaling (MDS). The Bray-Curtis similarity coefficient has a number of desirable properties for measuring community similarities, such as ignoring joint absences of species (Mumby et al 1996), and. is a robust measure of ecological distance (Faith et al 1987).…”

Section: Methodsmentioning

confidence: 99%

Bleaching and hurricane disturbances to populations of coral recruits in Belize

Mumby¹

1999

Mar. Ecol. Prog. Ser.

139

111

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In 1998, coral populations in Belize were disturbed sirnultaneously by a severe coral bleaching event and Hurricane Mitch. The impact of these disturbances was assessed for naturally occurring populations of coral recruits (2 to 20 mm diameter), at a depth of 8 to 10 m on the forereef of Glovers Atoll. Bleaching took place at aii 4 study sites but the hurricane only affected 2 sites, enabling the effects of bleaching to be compared to those arising from bleaching plus hurncane damage. Predisturbance recruit density, size-frequency distribution, and cornmunity structure were similar between sites (at kiiometre scales). The bleaching event lasted ca 3.5 mo. From 70 to 90% of adult colonies bleached and at least 25% of recruits exhibited signs of bleaching. A month after adult colonies had regained usual colouration, only 1 % of recruits showed even partial bleaching. Surprisingly, coral bleaching alone had no measurable effect on either recruit density or community structure. The combination of bleaching and hurricane disturbance reduced total recruit densities to 20% of pre-&stur-bance levels. Effects of bleaching/hurricane disturbance on community structure were spatially patchy, and I suggest that such patchiness may arise from variable Cover of protective rnicrohabitat and/or different storm conditions mediated by proximity to reef cuts (breaks in the reef crest).

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Section: Methodsmentioning

confidence: 99%

Bleaching and hurricane disturbances to populations of coral recruits in Belize

Mumby¹

1999

Mar. Ecol. Prog. Ser.

139

111

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“…2 ). The BC dissimilarity index [ 53 ] compares two microbiomes and quantifies the differences between them. A BC index equal to 100 indicates perfect similarity in species identity and abundance between two microbiomes, and a BC index equal to 0 indicates that there are no species in common between the microbiomes.…”

Section: Analysesmentioning

confidence: 99%

“…These approaches are complimentary. While MDS plots, based on Euclidian distances, globally visualize how similar samples are within a potentially very large dataset, BC indices [ 53 ] provide a quantifiable metric for similarity between specific pairs of samples.…”

Section: Analysesmentioning

confidence: 99%

Metabolome of human gut microbiome is predictive of host dysbiosis

Larsen

Dai

2015

Gigascience

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BackgroundHumans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome.ResultsUsing data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles.ConclusionsSpecific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0084-3) contains supplementary material, which is available to authorized users.

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“…Se utilizó el modelo Fundy 6.5.1 (Lynch y Werner 1987, Lynch et al 1992, Greenberg et al 1998) con coordenadas esféricas para obtener las soluciones de elevación y corriente forzadas por condiciones de frontera. El modelo Fundy es un connectivity among populations, especially of sessile or limited-mobility species (Mumby et al 1996, Metaxas 2001, Hart and Chute 2004.…”

Section: El Modelounclassified

“…One way of attacking this subject is to construct Lagrangian circulation models using key information of the early life stages of the species and identify the most influential oceanographic processes in the time scales related to the population dynamics. Examples of this are the assessment of settling probabilities at the end of the larval period of some species, coincidence of areas of food concentration (phytoplankton) with organism retention in a suitable habitat during the critical larval period (just after consumption of the food reserve), and the potential periodo crítico larval (justo después del consumo de la reserva alimenticia) y la conectividad potencial entre poblaciones, especialmente de especies sésiles o de locomoción limitada (Mumby et al 1996, Metaxas 2001, Hart y Chute 2004.…”

Section: Introductionmentioning

confidence: 99%

Modeling winter circulation and particle retention in the Magdalena-Almejas Bay lagoon system (Baja California Sur, Mexico)

Morales-Zárate¹,

Aretxabaleta

Wermer³

et al. 2006

CiencMar

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ResumenSe describe la circulación y el transporte pasivo de partículas en las inmediaciones del sistema lagunar Bahía Magdalena-Almejas mediante un modelo lineal de circulación en el dominio de la frecuencia con el que se obtuvieron los campos básicos de flujo. El modelo está forzado por mareas, marea residual, viento medio, viento periódico para simular el efecto de la brisa marina y una simulación aproximada del efecto de la Corriente de California. Se realizaron dos experimentos principales, uno enfocado a detectar zonas de retención en el interior del sistema lagunar, y el segundo para observar el intercambio de partículas entre el sistema y el océano abierto adyacente. Se encontró que las partículas sembradas en el sistema tienden a quedarse dentro y concentrarse en regiones particulares que se correspondieron con la distribución real de bancos pesqueros de recursos bentónicos y, en segundo término, que durante condiciones poco comunes de viento se pueden presentar intrusiones importantes de partículas de la plataforma continental al interior del sistema lagunar. Los resultados son de importancia para el estudio de la zona en general, y particularmente para la modelación y desarrollo de pronósticos de procesos de deriva larval de recursos pesqueros importantes.Palabras clave: modelación, deriva larval, Bahía Magdalena, retención de partículas. AbstractWe describe circulation and passive particle transport in the Magdalena-Almejas Bay lagoon system through a linear circulation model in the frequency domain to obtain basic flux fields. The model is forced by tides, residual tides, mean wind speed, periodic winds (to simulate sea breeze), and an approximation of advection in the California Current. Two main experiments were performed: one to detect retention zones within the lagoon system and another to evaluate particle exchange between the lagoon system and the open ocean. We found that particles seeded within the system tend to remain inside and concentrate in restricted areas that correspond to the real distribution of benthic fish and that, under rare wind conditions, masses of particles seeded on the continental shelf could enter the lagoon system. The results are relevant for the general study of the system and for modeling and developing forecasts of the larval drift of important fish resources.

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Weighting species abundance estimates for marine resource assessment

Cited by 16 publications

References 13 publications

Bleaching and hurricane disturbances to populations of coral recruits in Belize

Bleaching and hurricane disturbances to populations of coral recruits in Belize

Metabolome of human gut microbiome is predictive of host dysbiosis

Modeling winter circulation and particle retention in the Magdalena-Almejas Bay lagoon system (Baja California Sur, Mexico)

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