Estimating Species Richness: The Michaelis-Menten Model Revisited

Keating, Kim A.; Quinn, James

doi:10.2307/3547060

Cited by 85 publications

(76 citation statements)

References 22 publications

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“…Rarefaction curves were calculated using EstimateS (http://viceroy.eeb.uconn.edu/estimates) using individual-based curves (sampling without replacement) (24) based on the Michaelis-Menten models (49). We note that the impact on the shape of species-accumulation curves of different community structures is an area of active research (50); with the data at hand (six samples), we are unable to satisfactorily explore this issue.…”

Section: Methodsmentioning

confidence: 99%

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

Juliano

Porter

Mwapasa

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

116

126

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Malaria infections commonly contain multiple genetically distinct variants. Mathematical and animal models suggest that interactions among these variants have a profound impact on the emergence of drug resistance. However, methods currently used for quantifying parasite diversity in individual infections are insensitive to lowabundance variants and are not quantitative for variant population sizes. To more completely describe the in-host complexity and ecology of malaria infections, we used massively parallel pyrosequencing to characterize malaria parasite diversity in the infections of a group of patients. By individually sequencing single strands of DNA in a complex mixture, this technique can quantify uncommon variants in mixed infections. The in-host diversity revealed by this method far exceeded that described by currently recommended genotyping methods, with as many as sixfold more variants per infection. In addition, in paired pre-and posttreatment samples, we show a complex milieu of parasites, including variants likely upselected and down-selected by drug therapy. As with all surveys of diversity, sampling limitations prevent full discovery and differences in sampling effort can confound comparisons among samples, hosts, and populations. Here, we used ecological approaches of species accumulation curves and capture-recapture to estimate the number of variants we failed to detect in the population, and show that these methods enable comparisons of diversity before and after treatment, as well as between malaria populations. The combination of ecological statistics and massively parallel pyrosequencing provides a powerful tool for studying the evolution of drug resistance and the in-host ecology of malaria infections.Plasmodium falciparum | next generation sequencing

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Section: Methodsmentioning

confidence: 99%

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

Juliano

Porter

Mwapasa

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

116

126

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“…However, caution should be exercised in equating the extrapolated S max with true total species richness. While certain studies have emphasized the Michaelis-Menten model's empirical accuracy and robustness (de Caprariis et al 1976(de Caprariis et al , 1981, others have demonstrated its bias in heterogeneous environments (Keating 1998). Yet, if species accumulation curves can be demonstrated to adequately represent uniform sampling of relatively homogenous environments, extrapolation to true species richness should still be possible (Colwell and Coddington 1994).…”

Section: Discussionmentioning

confidence: 99%

Testing a methodology for assessing plant communities in temperate inland lakes

Mikulyuk

Hauxwell

Rasmussen

et al. 2010

Lake and Reservoir Management

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“…An asymptotic equation is then fit to this curve, and the estimate of the asymptote parameter is the estimate of species richness. The function most often used, and the one used in this report, is the Michaelis-Menten equation (Clench 1979, Soberon and Llorente 1993, Colwell and Coddington 1994, Chazdon et al 1998, Keating and Quinn 1998. Parameter values were estimated using Raaijmakers' (1987) maximum likelihood estimators for the Eadie-Hofstee transformation, as outlined in Colwell and Coddington (1994).…”

Section: Richness Estimation and Evaluation Of Estimatorsmentioning

confidence: 99%

The Ant Fauna of a Tropical Rain Forest: Estimating Species Richness Three Different Ways

Longino¹,

Coddington²,

Colwell³

2002

Ecology

147

177

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Abstract. Species richness is an important characteristic of ecological communities, but it is difficult to quantify. We report here a thorough inventory of a tropical rain forest ant fauna and use it to evaluate species richness estimators. The study was carried out in ~ 1500 ha of lowland rain forest at La Selva Biological Station, Costa Rica. Diverse methods were used, including canopy fogging, Malaise traps, Berlese samples, Winkler samples, baiting, and manual search. Workers of 437 ant species were encountered. The abundance distribution was clearly lognormal, and the distribution emerged from a veil line with each doubling of sampling effort. Three richness estimates were calculated: the area under the fitted lognormal distribution, the asymptote of the Michaelis-Menten equation fit to the species accumulation curve, and the Incidence-based Coverage Estimator (ICE). The performance of the estimators was evaluated with sample-based rarefaction plots. The inventory was nearly complete because the species accumulation curve approached an asymptote, the richness estimates were very close to the observed species richness, and the uniques and duplicates curves were both declining. None of the richness estimators was stable in samplebased rarefaction plots, but regions of stability of estimators occurred. The explanation of rarity is one key to understanding why richness estimates fail. Fifty-one species (12% of the total) were still uniques (known from only one sample) at the end of the inventory. The rarity of 20 of these species was explained by "edge effects": "methodological edge species" (possibly abundant at the site but difficult to sample because of their microhabitat), and "geographic edge species," known to be common in habitats or regions outside of La Selva. Rarity of 31 species remained unexplained. Most of the 51 rare species were known from additional collections outside of La Selva, either in other parts of Costa Rica or in other countries. Only six species were "global uniques," known to date from only one sample on Earth. The study demonstrates that patterns of species occurrence early in an inventory may be inadequate to estimate species richness, but that relatively complete inventories of species-rich arthropod communities are possible if multiple sampling methods and extensive effort are applied.

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Estimating Species Richness: The Michaelis-Menten Model Revisited

Cited by 85 publications

References 22 publications

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing

Testing a methodology for assessing plant communities in temperate inland lakes

The Ant Fauna of a Tropical Rain Forest: Estimating Species Richness Three Different Ways

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