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Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

TRABAJO PRCTICO: "Diversidad de especies. Anlisis mediante el uso de software" Objetivos: Estimar riqueza de especies con estimadores no paramtricos Obtener ndices ecolgicos, mediante el uso de software Discutir las interpretaciones de datos ecolgicos.

Introduccin: Se utilizarn los software libres EcoSim y EstimateS

EcoSim (http://garyentsminger.com/ecosim.htm) es un programa interactivo para anlisis de modelos nulos


en comunidades ecolgicas. Admite para los test, tanto datos experimentales como no-experimentales. Efecta simulaciones Monte Carlo para crear pseudocomunidades (Pianka 1986), y compara estadsticamente los datos de esas comunidades simuladas con los de la matriz real. Este test de modelo nulo puede tener aplicaciones en ecologa bsica y aplicada. A continuacin, se detallan las explicaciones de los anlisis de biodiversidad de especies, del software ECOSIM 2004, Versin 7.72 (traducidas al espaol). Para ms informacin, sugerimos visitar: http://garyentsminger.com/ecosim/ Algoritmos de muestreo. EcoSim le ofrece dos opciones para la forma en que se tomaron las muestras de su coleccin. 1) El muestreo independiente Supongamos que ha especificado muestras aleatorias con los niveles de abundancia de los 10, 20 y 40 especies. Con el muestreo independiente, EcoSim atraera a 10 especies, calculara la diversidad de especies, y luego volvera a colocar las 10 especies antes de sacar una muestra aleatoria de 20. Estas 20 tambin seran reemplazadas antes de extraer una muestra aleatoria de 40. En otras palabras, con muestreo independiente, EcoSim asegura que los estimadores de la diversidad para los diferentes niveles de abundancia son independientes el uno del otro. Casi siempre, este es el algoritmo de muestreo que se quiere utilizar. 2) Las curvas de acumulacin. Supongamos que ha especificado curvas de acumulacin de los niveles de abundancia de las 10, 20 y 40 especies. EcoSim en primer lugar extraer 10 especies elegidas al azar y calcular la diversidad de especies. A continuacin, sealar a otras 10 especies adicionales, agregar las de la primera muestra, y calcular la diversidad de especies de las 20 especies. Por ltimo, aadir 20 especies ms elegidas al azar y calcular la diversidad para el conjunto combinado de 40 especies. Esta curva de acumulacin podra ser importante si una de las muestras que se comparan est incluida dentro de otra muestra mayor. Este tipo de datos puede ser comn en los estudios de vegetacin. Para la mayora de los propsitos, sin embargo, tendr que utilizar el algoritmo de muestreo independiente.

EstimateS

(Website: http://purl.oclc.org/estimates or http://viceroy.eeb.uconn.edu/estimates). Estimacin estadstica de riqueza de especies y especies compartidas entre muestras. Es un software diseado por Robert Colwel para evaluar y comparar la diversidad y composicin de especies en ensambles o comunidades basadas en datos de muestreos. EstimateS computa una variedad de estadsticos de biodiversidad, incluyendo rarefaccin y extrapolacin, estimadores de riqueza de especies, ndices de diversidad y medidas de similitud (Anexo 1). Diversidad de especies La diversidad de especies sigue siendo uno de los principales objetos de estudio, tanto en Ecologa Bsica como Aplicada. Hay dos cuestiones a abordar en el estudio de la diversidad de especies. La primera es, cmo podemos cuantificar la diversidad de un ensamble? Y en segundo lugar, cmo podemos comparar

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

estadsticamente la diversidad de los dos conjuntos? Los datos de un estudio de la diversidad de especies constituyen una muestra de individuos que se clasifican en diferentes especies. Hiptesis de ndices de diversidad. Todos los ndices de diversidad de especies llevan consigo los siguientes supuestos implcitos (Peet 1974): 1) Todas las especies son igualmente importantes. En otras palabras, los ndices de la diversidad de las especies no se pueden utilizar para reconocer las diferentes combinaciones de especies o la presencia o ausencia de determinadas especies clave. 2) Todos los individuos asignados a una especie son iguales. Los ndices no distinguen entre diferentes clases de edad o diferentes etapas del ciclo vital de una especie. 3) La diversidad de especies se ha medido en las unidades apropiadas. Normalmente se mide por la diversidad de colecciones de individuos discretos, pero los datos tambin pueden ser recogidos en forma de biomasa o porcentaje cubierto. Debido a que el mdulo de la diversidad ECOSIM es un modelo estadstico de muestreo, la diversidad debe ser registrada como cuenta de individuos discretos (o colonias). Efectos de muestreo: Lamentablemente, rara vez se ha logrado recolectar exhaustivamente todos los organismos en una comunidad determinada, en parte porque es muy difcil definir los lmites espaciales y taxonmicos de la comunidad. A medida que ms especies estn incluidas en la muestra en un conjunto, la riqueza de especies se eleva hasta alcanzar una asntota, lo que significa que el nmero mximo de especies en el ensamble se ha alcanzado. Lamentablemente, cuando tenemos una muestra de la comunidad, incluso con varios grupos, no sabemos dnde exactamente llegamos a la asntota de la curva. En consecuencia, se hace muy difcil comparar la diversidad de especies de diferentes comunidades. Encontrar diferencias en la riqueza de especies o en la equitatividad representan diferencias biolgicas entre las comunidades? O son slo diferencias que podran desaparecer si se recogieran datos con ms intensidad de muestreo? La mayora de los ndices de la diversidad de las especies son sensibles al nmero de individuos recolectados, lo que hace difcil comparar la diversidad de especies en colecciones de diferentes tamaos. La rarefaccin. Sanders (1968) estaba interesado en comparar la riqueza de especies de diferentes ensambles de organismos marinos. l razon que la comparacin ms adecuada sera controlando las diferencias en la abundancia. En otras palabras, "enrareciendo" sus muestras a un nivel comn de abundancia y riqueza de especies. Por ejemplo, supongamos que una Comunidad A cuenta con 500 individuos y 40 especies; y una Comunidad B cuenta con 250 individuos y 30 especies. Rarefaccin dira que el nmero de especies que se encuentran en una muestra de 250 individuos extrados aleatoriamente de la Comunidad A. Usted podr entonces ver si este nmero es mayor o inferior al de 30 especies que se encontraron en B. La Rarefaccin utiliza la teora de la probabilidad de obtener las expresiones de la esperanza y la varianza de la riqueza de especies de una muestra de un determinado tamao (Hurlbert 1971, Heck et al. 1975). Este mdulo de ECOSIM proporciona un equipo de toma de muestras de algoritmo de rarefaccin, en la que un determinado nmero de individuos es procedente de una comunidad muestreada aleatoriamente. El proceso se repite muchas veces para generar una media y una varianza de la diversidad de especies. ECOSIM calcular la media de riqueza de especies, pero tambin permitir la construccin de estas curvas de muestreo para los distintos ndices de riqueza y la uniformidad. Supuestos de la rarefaccin: El "mtodo de rarefaccin" lleva consigo una serie de supuestos especficos (Tipper 1979, Gotelli & Graves 1996): 1) El muestreo ha sido suficiente para garantizar una adecuada caracterizacin de la distribucin real. 2) La distribucin espacial de los individuos es al azar (este supuesto no es necesario si la rarefaccin est basada en una muestra que preserva la heterogeneidad de la distribucin espacial de los individuos). 3) Las muestras que deben compararse son taxonmicamente "similares" y se han extrado del "mismo" tipo de comunidad. 4) las tcnicas de muestreo que se utilizan para todas las colecciones son estandarizadas. 2

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

5) La rarefaccin se puede utilizar para la interpolacin de un tamao de muestra ms pequeo, pero no para la extrapolacin de una muestra ms grande. El supuesto 4 es el ms crtico porque realmente no hay manera de comparar significativamente comunidades que no han sido incluidas en la muestra con mtodos comparables. Otra advertencia es que la metodologa de rarefaccin slo es adecuada para las cuestiones de la riqueza de especies (o uniformidad) - Cul es el nmero esperado de especies para un determinado nmero de individuos? Sin embargo, muchos investigadores estn realmente interesados en las densidades de las especies y el nmero esperado de especies por unidad de rea (o esfuerzo de muestreo). La densidad de especies depende tanto de la riqueza de especies y la densidad (nmero de organismos / unidad de rea). La curva de Rarefaccin. La Rarefaccin considera muestras de individuos al azar, lo cual es apropiado porque se trata de las unidades en que se mide la diversidad biolgica. Sin embargo, los eclogos que trabajan en el campo con organismos individuales, rara vez muestrean al azar. En lugar de ello, se recogen muestras (transectas, trampas, redes de niebla) que contienen un nmero determinado de individuos. Un muestreo aleatorio basado en la curva de los acumulados de la totalidad de las muestras, aumenta tanto la riqueza de especies como en las muestras posteriores que se aadan. Aclaracin: En ECOSIM-Diversidad de especies, los datos se cargan teniendo en cuenta que se considera un vector de abundancias, representado por una nica columna de datos. Cada fila en el vector es la abundancia de una especie en particular. Las entradas deben ser nmeros positivos o ceros. Se permite especificar que distintas columnas en una matriz de datos responden a distintas muestras o comunidades, a fin de que la diversidad en varios ensambles se pueda comparar en el mismo conjunto de datos. Si el usuario selecciona "Muestras" como la unidad de muestreo, EcoSim analizar toda la matriz de datos, realizando el tratamiento de cada columna como una muestra diferente.

ndices de Diversidad ecolgica: 1) La riqueza de especies es el nmero de especies ms natural indicador de diversidad de especies en un ensamble. 2) Indice de Hurlbert PIE (1971) calcula el ndice de probabilidad de un encuentro interespecfico (PIE). En otras palabras, este ndice da la probabilidad de que dos individuos de la muestra al azar el conjunto representan dos especies diferentes. Hay varias ventajas de utilizar PIE como un simple ndice de uniformidad. En primer lugar, el ndice es fcil de interpretar como una probabilidad. En segundo lugar, este ndice es uno de los pocos que es objetivo por el tamao de la muestra, aunque la diferencia aumenta en los pequeos N. En tercer lugar, tiene un importante PIE analgico en la gentica de poblaciones. Es equivalente al clculo de heterocigosidad (H), la probabilidad de que dos alelos no sean idnticos por descendencia. 3) Predominio de dominancia no es ms que la fraccin de la coleccin que est representada por las especies ms comunes. El dominio puede ser un ndice til de la monopolizacin de recursos por un competidor superior, sobre todo en comunidades que han sido invadidas por especies exticas. Al igual que la riqueza de especies, la posicin dominante es sensible al tamao de la muestra. En el caso extremo de una coleccin de slo 1 persona, siempre la igualdad de posicin dominante 1.0. 4) El ndice de diversidad de Shannon-Wiener considera la proporcin del nmero total de individuos que corresponde a cada una de las especies de la comunidad. Se basa en la Teora de la Informacin. Puede estimarse con distintas bases logartmicas (base 2 es el original, tambin se usa el de base neperiano o de base 10). La frmula que considera EcoSim utiliza ln. Estimadores no paramtricos de riqueza de especies Existen distintos estimadores no paramtricos para estimar de riqueza esperada y compararla con la observada, tales como Chao1, Chao 2 y Jackknife 1 y Jacknife 2, etc. Ni las curvas de rarefaccin ni la curva de acumulacin de especies esperada (MaoTau) son estimadores de la riqueza de especies en el mismo sentido que los otros estimadores, tales como Chao1, Chao2, Jack1 que estiman la riqueza total de especies, incluyendo las especies no presentes en cualquier muestra. Las curvas de 3

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

la rarefaccin estiman la riqueza de especies para una submuestra de la riqueza total basada en todas las especies registradas. En los ms simples estimadores de la riqueza (e.j. Chao1, Chao2, o estimadores Jackknife), las especies raras se clasifican como especies con una abundancia total de 1 (singletons) o 2 (doubletons) en una muestra basada en abundancia o que estn solamente en una unidad de muestreo (uniques, nicos) o en exactamente dos unidades de muestreo (duplicates, duplicados) en datos replicados de incidencia (Chao et al., 2005). Actividades: A) Ejercitacin con el software EcoSim. A partir de los datos registrados sobre la diversidad de rboles que fueron registrados en 2 transectas en el rea Sur de la Ciudad Universitaria, resuelve:
Cuadro 1. Nmero de individuos de rboles registrados en dos comunidades: Transecta 1 (margen de la Reserva Universitaria) y Transecta 2 (lmite con la Reserva Universitaria). ni = nmero de individuos de la especie i; pi = abundancia proporcional de la especie i (pi = ni /N). Transecta 1 Transecta 2 Especie ni pi ni pi

Nmero total de individuos (N)

(1) Carga los datos en el software ECOSIM (2) Analiza la diversidad de especies, en todos sus aspectos, para la comunidad de Transecta 1 y Transecta 2 (3) Completa la grilla con los resultados obtenidos:
Transecta 1 Riqueza de especies Diversidad de Shannon-Wiener Indice PIE Dominancia Transecta 2

B) Ejercitacin con el software EstimateS 1) Con los datos obtenidos, guarda la tabla en texto delimitado por tabulaciones siguiendo alguno de los formatos, por ej. El formato 1, donde en la primera lnea colocar el nombre que le asigne a la tabla, en la segunda el nmero de especies (filas) en la primera columna y en la segunda columna el nmero de hbitats, muestras, etc. (columnas). Aumenta el nmero de hbitats con datos aleatorios.

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

2) Del File menu en EstimateS, elige Load Input File y busca tu tabla en txt. Un dialogo de seleccin te aparece.

3) Clickea Ok. 4) Encontrar el Data Input File y abrirlo. Esto depende del formato de tabla que hayas cargado Si es Formato 1, 2, etc., mrcalo y Clickea Ok.

5) EstimateS completa la carga del set de datos y confirma que ha sido correctamente cargado.

6) Cuando clikeas Ok, aparece una segunda pantalla de confirmacin, explicando el set de datos que ser analizado automticamente y secuencialmente. Ej.

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

7) Setting and Running the Diversity Options Una vez que el Data input File ha sido cargado, ests listo para checkear las Diversity options y/o Shared Species options. 8) Del Diversity menu, elige Compute Diversity Stats para calcular Rarefaccin y estimadores de riqueza de especies. Los datos que aparecen en pantalla puedes exportarlo en Excel o txt. 9) Luego, elige la opcin Shared Species, Compute Shared Spp. Stats para calcular los indices de similitud. 10) De los resultados obtenidos grafica (en excel) las curvas de rarefaccin, y de estimadores de riqueza de especies por ej. Chao y Jacknife, relacionando nmero de muestras (samples) y de individuos. Ej.
nmero de especies

Cole Rarefaction Jack 1 Mean

numero de especies

6 4 2

6 4 2 0 0 100 200 nmero de individuos Cole Rarefaction Jack 1 Mean

Chao 1 Mean

0 0 2 4 6 8 nmero de muestras

11) Qu opinas sobre el efecto del tamao del muestreo realizado y los valores de obtenidos? 12) Cuntas especies sera posible encontrar si se aumenta el nmero de muestras? 13) Cmo interpretas los valores de Diversidad (RE, Shannon y PIE) obtenidos para ambas transectas?

Referencias Bibliogrficas:
Chao, A. 2005. Species richness estimation, Pages 7909-7916 in N. Balakrishnan, C. B. Read, and B. Vidakovic, eds. Encyclopedia of Statistical Sciences. New York, Wiley Colwell, R. K. 2013. EstimateS: Statistical estimation of species richness and shared species from samples. Version 9. User's Guide and application published at: http://purl.oclc.org/estimates Gotelli, N.J. & G.L. Entsminger. 2012. EcoSim 7.72. Acquired Intelligence, Inc. http://www.uvm.edu/ ngotelli/EcoSim/EcoSim.html Moreno, C. E. 2001. Mtodos para medir la biodiversidad. M&TManuales y Tesis SEA, vol. 1. Zaragoza, 84 pp. Pianka, E.R. 1986. Ecology and natural history of desert lizards. Princeton University Press, Princeton

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013

Anexo 1
EstimateS Samples and Species, Abundance and Incidence In this Guide, the term sample refers to any list of species or other taxa from a locality, site, quadrat, trap, time unit, clone library, or some other entity. Some estimators and indices require counts of individuals (or gene copies) for each species in single sample, or in each of a set of samples. Such data are called individual-based abundance data. Other estimators and indices require only presence/absence (occurrence) data for each species in each a set of related (or replicate) samples. (These related samples are sometimes called sampling units in the literature, and in this Guide.) Such data are called sample-based incidence data. When a dataset consists of species abundance data for a set of related samples (sample-based abundance data), the dataset can be treated, sample-by-sample, as individual-based abundance data, or converted to sample-based incidence data. When comparing the biotic (species or higher taxa) similarity of two or more localities (or habitats, treatments, seasons, etc.), you can do so either using abundance data or by using summed incidence data (frequencies of occurence, pooled among samples) for each or two or more sample sets. Single and Multiple Datasets EstimateS 9 allows you to analyze either a single dataset or a multiple datasets, one after another, in a single data input file (batch input). Each dataset may consist of either individual-based abundance data (a single sample of abundance data) or sample-based incidence or abundance data (several related samples of incidence or abundance data). The Fundamental Design of EstimateS: Diversity EstimateS helps you account for the inevitable confounding effects of sample size (or sampling effort) on biodiversity data by several different strategies. Consider a reference sample: either a single, individual-based abundance sample of n individuals, or a set of t related sampling units for which incidence data have been recorded. Richness estimators. Based on a reference sample (as defined above), EstimateS computes several widely-used statistical estimators of asymptotic species richness, the true number of species in the assemblage sampled. These estimators aim to reduce the effect of undersampling, which inevitably biases the observed species count. Rarefaction. Rarefaction is a resampling framework that selects, at random, 1, 2, ..., n individuals or i= 1, 2, ..., t sampling units (generally without replacement) until all individuals or sampling units in the reference sample have been accumulated. For each level of rarefaction, EstimateS computes a large number of biodiversity statistics. For species richness, exact analytical methods are used to compute the expected number of species (and its unconditional standard deviation) for each level of accumulation. For other diversity measures, EstimateS resamples individuals or sampling units stochastically, based on a random-number-driven algorithm. The resampling process is repeated many times, and the means (and conditional standard deviations) among resamples for each level of accumulation are reported. The effects of differences in sample size on diversity statistics for two or more samples can usually be substantially reduced by comparing a the same level of species accumulation. Extrapolation. Rarefaction, in effect, represents an interpolation betwen the value of a diversity measure assessed for the reference sample and zero (for individual-based abundance data) or between the value of the same divresity measure computed for an typical single sampling unit (for sample-based indidence data). For species richness (only) EstimateS 9 introduces extrapolation from a reference sample to the expected richness (and its unconditional standard deviation) for a user-specified, augmented number of individuals or sampling units. The methods that EstimateS uses for richness extrapolation rely on statistical sampling models, not on fitting mathematical functions.They require an estimator for asymptotic richness as a "target" for the extrapolation; EstimateS uses Chao1 for abundance data and Chao 2 for incidence data. The Fundamental Design of EstimateS: Shared Species and Similarity For sets of related sampling units, EstimateS computes several measures of compositional similarity, including traditional similarity indices as well as estimators of shared species and similarity indices that take shared, but unobserved species into account by statisical methods. These latter methods require species abundance data for a set of related samples (sample-based abundance data) or for summed incidence data for two or more sets of sampling units.

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 Preparing a Data Input File for EstimateS EstimateS Filetypes: The Load Data Input File Screen In EstimateS 9, the Load Data Input File command (from the File menu) presents a set of four filetype options. Specific data input formats for these filetype options are discussed ina later section of this Guide. This section describes the four filetypes and their uses.

Data Input Formats The Five Data Input Formats Once you have determined which of the four input filetypes you will be using, you need to decide which data input format you will use for the actual biodiversity data. Data input Formats 1 and 2 may be used with any input filetype. Data input Formats 3, 4, and 5 apply only to sample-based data (the first two input filetypes). Format 1. Species (rows) by Samples(columns). For sample-based input filetypes, you will have one row for each species, one column for each sample. For individual-based input filetypes, you will have one row for each species in a single column. The input file may contain any number of initial rows of column labels and/or initial columns of row labels, in which case you must tell EstimateS how many of each there are. (EstimateS simply skips over these specified label rows and columns.) Note on Format 1: If your file includes one or more rows of column labels, they must follow the required Title and Parameter records and precede the data. If your file includes one or more columns of row labels, the required Title and Parameter records nonetheless begin in the first column. Format 1 Example: Below is a simple example of an EstimateS sample-based Input File in Format 1, for a dataset called "My Input File" that includes data for 8 species (rows) in 10 samples (columns). The data are exactly the same as in the examples, below, for Formats 2 and 3. See the installed example filesSingle-Sample-Based-Data-Filetype.xlsx, SingleSample-Based-Example.txt, and Seedbank.txt.

Format 2. Samples (rows) by Species (columns). For sample-based input filetypes, you will have one row for each sample, one column for each species. For individual-based input filetypes, you will have one column for each species in a single row. The input file may contain any number of initial rows of column labels and/or initial columns of row labels, in which case you must tell EstimateS how many of each there are. (EstimateS simply skips over these specified label rows and columns.) Note on Format 2: If your file includes one or more rows of column labels, they must follow the required Title and Parameter records and precede the data. If your file includes one or more columns of row labels, the required Title and Parameter records nonetheless begin in the first column. Format 2 Example: Below is a simple example of an EstimateS sample-based Input File in Format 2, for a dataset called "My Input File" that includes data for 8 species (columns) in 10 samples (rows). The data are exactly the same as in the example, above, for Format 1, and the example, below, for Format 3. See the installed example files Single-IndividualBased-Data-Filetype.xlsx and Single-Individual-Based-Example.txt for individual-based examples in Format 2.

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Format 3 (Sample-based filetypes only). Species, Sample, Abundance triplets: the first column contains the species number, the second the sample number, and the third the number of individuals (abundance) of that species in that sample. A final (extra) record with "-1" in each of these three columsn indicates end of input. This "triplet" format a common input format for statistical programs (e.g. SYSTAT.) You can list one row for every sample/species combination, or rows for only those combinations that have non-zero abundances. (The rest are automatically set to zero.) Using the triplet format and storing only non-zero abundance values requires far less file space than storing the full matrix. In fact, this may be the most practical way to store files larger than your spreadsheet will accept. As an option (see below), EstimateS can export a data matrix in this format, after reading it in using one of the other four formats listed here. Note on Format 3: EstimateS expects no more than one record for each species x sample combination. If you have more than one, only the first is read. A special record must terminate triplet files, with "-1" in each of these three colums to indicate end of input, as shown in the example below. Format 3 Example: Below is a simple example of an EstimateS Input File in Format 3, for a dataset called "My Input File" that includes data for 8 species (columns) in 10 samples (rows). The data are exactly the same as in the examples, above, for Formats 1 and 2.

Format 4 (Sample-based filetypes only). Sample, Species, Abundance triplets. The formatis just as for Format 3, but the columns are ordered Sample, Species, Abundance. Note on Format 4: EstimateS expects no more than one record for each species x sample combination. If you have more than one, only the first is read. A special record must terminate triplet files, with "-1" in each of these three colums to indicate end of input, as shown in the example, above. Format 5 (Sample-based filetypes only). Biota format. This format is output automatically by Biota, with appropriate row and column labels. For other input files that include column or row labels, use Formats 1 or 2. Coleman Rarefaction Curves Like previous versions of EstimateS, Version 9 computes Coleman rarefaction curves (Coleman 1981, 1982) for samplebased abundance data (Filetypes 1 and 2). These curves estimate the number of species in 1, 2, ... T samples, on the assumption that all individuals in all samples are randomly mixed (Chazdon et al. 1998). In other words, the Coleman

Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 curve in EstimateS for Filetypes 1 and 2 is a form of individual-based rarefaction, applied to sample-based data. In fact, for individual-based rarefaction (Filetypes 3 and 4), EstimateS 9 follows a Poisson model for rarefaction, mathematically identical to Coleman's classic area-based sampling model (Colwell et al. 2012). If you summed abunances across samples in a sample-based abundance dataset (Filetype 1), and ran the totals as a single reference sample of Filetype 3 (indidividual-based rarefaction), the results would be indentical. Rarefaction and Extrapolation vs. Asympotic Richness Estimation Neither sample-based rarefaction curves nor individual-based rarefaction curves are estimators of the true species richness of the assemblage that a reference sample represents, in the same sense as the asympotic richness estimators that EstimateS computes. Whereas Chao1, Chao2, ACE, ICE or Jack1, for example, estimate total species richness, including species not present in any sample, rarefaction curves estimate species richness for a sub-sample of the pooled total species richness, based on an empirical reference sample. In contrast, the tools implemented in EstimateS 9 for extrapolation (Colwell et al. 2012) from a reference sample require a "target richness" that estimates the asymptotic number of species in the source assemblage, including species not documented by the reference sample. As explained in detail by Colwell et al. (2012), Chao1 was chosen to estimate the target richness for individual-based data and Chao 2 does so for sample-based data. For this reason, extrapolation may underestimate the expected richness of an augmented sample for hyperdiverse communities, for which Chao1 and Chao2 (and all other!) asymptotic richness estimators tend to increase with (reference) sample size. Asymptotic Species Richness Estimators The literature on species richness estimators continues to grow in several directions. Key reviews in the 1990s include Bunge & Fitzpatrick (1993) and Colwell & Coddington (1994). For a more recent review of the field, see Chao (2004), which, like most key papers cited in this User's Guide, can be downloaded as pdf file. Gotelli and Colwell (2011) also review the subject. Chao1 and Chao2 Richness Estimators. In EstimateS, the classic richness estimators Chao1 and Chao 2 are computed along with log-linear 95% confidence intervals, as suggested by Chao (1987). These asymmetrical confidence intervals, which are based on the assumption that log(Sest - Sobs) is normally distributed, have the common-sense property that the lower confidence bound cannot be less than the observed number of species, Sobs. See Appendix B for details. If you need a doubly-bounded richness estimator, with a fixed upper bound, see Eren et al. (in press) (not implemented in EstimateS). Coverage-Based Richness Estimators ICE and ACE.The species richness estimators, ICE (Incidence-based Coverage Estimator) and ACE (Abundance-base Coverage Estimator) are modifications of the Chao & Lee (1992) estimators discussed by Colwell & Coddington (1994). Chazdon et al. (1998) introduced ICE and ACE to the ecological literature. For that paper, they found it necessary and useful to change the notation for the variables involved in the other estimators, to allow a unified system of notation covering the new estimators. This new notation is referenced in Table 1 and detailed in the Appendix C of this User's Guide, replacing the notation of Colwell & Coddington (1994). See Chazdon et al. (1998), which can be downloaded as pdf file, for details and rationale. What EstimateS 9 Computes Table 1, below, lists the variables and statistics that EstimateS 9 computes from the Diversity menu. Table 2 lists the variable and statistics computed from the Shared Speciesmenu. Table 1: Diversity Statistics. Accumulated species and individuals, richness estimators, species diversity indices and related variables computed by EstimateS 9. In the output screen (and exported text files), values for accumulated species, richness estimators, and diversity indices appear for each level of accumulation, from a single sampling unit or a single individual up to the full reference sample. The statistics listed are reported as analytically computed expected values, or as mean values averaved over the number of randomizations you specify, for statistics that have no analytical rarefaction known. Formulas for the estimators appear in Appendix B . Filetype Variable Estimator Reference Samplebased Samplebased Samples (t) Number of sampling units accumulated m in Chazdon et al. (1998) h in Colwell et al. (2004) t in Colwell et al. (2012) Gotelli and Colwell (2001) Gotelli and Colwell (2011)

Individuals (computed)

[t/T]*N, where T is the number of sampling units in the reference sample and N is the total number of individuals in allT samples (makes sense for samplebased abundance date only)

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Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 Samplebased S(est) (analytical) Expected number of species int pooled samples, given the reference sample (analytical). Rarefaction: MaoTau in earlier versions of EstimateS (< v. 9), Eq. 5 in Colwell et al. (2004), Eq. 17 in Colwell et al. (2012)Extrapolation: Eq. 18 in Colwell et al. (2012) Rarefaction: Eq. 6 in Colwell et al. (2004) Extrapolation: Eq. 19 in Colwell et al. (2012) Rarefaction: Eq. 6 in Colwell et al. (2004) Extrapolation: Eq. 19 in Colwell et al. (2012) Rarefaction: Eq. 6 in Colwell et al. (2004) Extrapolation: Eq. 19 in Colwell et al. (2012) Sobs Mean in earlier versions of EstimateS (< v. 9) m in Colwell et al. (2012) Rarefaction: Eq. 6 in Colwell et al. (2012)Extrapolation: Eq. 9 in Colwell et al. (2012), slightly modified (to match Eq. 18, on Anne Chaos' advice) Rarefaction: Eq. 7 in Colwell et al. (2012) Extrapolation: Eq. 10 in Colwell et al. (2012) Rarefaction: Eq. 7 in Colwell et al. (2012) Extrapolation: Eq. 10 in Colwell et al. (2012) Rarefaction: Eq. 7 in Colwell et al. (2012) Extrapolation: Eq. 10 in Colwell et al. (2012)

Samplebased Samplebased Samplebased

S(est) 95% CI Lower Bound S(est) 95% CI Upper Bound S(est) SD (analytical)

Lower bound of 95% Confidence Interval for S(est) Upper bound of 95% Confidence Interval for S(est) Standard deviation of S(est) (analytical) (SD = SE)

Samplebased

S Mean (runs)

Number of species in t pooled samples, given the reference sample (mean among runs) Number of individuals Expected number of species represented among mindividuals, given the reference sample (analytical). Lower bound of 95% Confidence Interval for S(est) Upper bound of 95% Confidence Interval for S(est) Standard deviation of S(est) (analytical) (SD = SE)

Individual- Individuals (m) based Individual- S(est) based (analytical)

Individual- S(est) 95% CI based Lower Bound Individual- S(est) 95% CI based Upper Bound Individual- S(est) SD based (analytical)

Individual- S Mean based (runs) All filetypes All filetypes All filetypes All filetypes Samplebased Samplebased SampleSingletons Mean

Number of species represented among m individuals, given the reference sample (mean among runs) Number of singletons (species with only one individual) in tpooled samples or among mindividuals (mean among runs) Standard deviation of Singletons, among randomizations of sample order Number of doubletons (species with only two individuals) in tpooled samples or among mindividuals (mean among runs) Standard deviation of doubletons, among randomizations of sample order a in Colwell & Coddington (1994) F1 in Chazdon et al. (1998) f1 in Colwell et al. (2012) This is a bootstrap SD, based on variation in sample order among randomizations. b in Colwell & Coddington (1994) F2 in Chazdon et al. (1998) f2 in Colwell et al. (2012) This is a bootstrap SD, based on variation in sample order among randomizations.

Singletons SD (runs) Doubletons Mean

Doubletons SD (runs) Uniques Mean

Number of uniques (species that occur in a L in Colwell & Coddington (1994) only one sample) in t pooled samples Q1 in Chazdon et al. (1998) (mean among runs) Q1 in Colwell et al. (2012) This is a bootstrap SD, based on variation in sample order among randomizations.

Uniques SD (runs) Standard deviation of Uniques, among randomizations of sample order Duplicates Mean

Number of duplicates (species that occur in M in Colwell & Coddington (1994)

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Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 based Samplebased Duplicates SD (runs) a only two samples) in t pooled samples (mean among runs) Standard deviation of duplicates, among randomizations of sample order Abundance Coverage-based Estimator of species richness (mean among runs) Q2 in Chazdon et al. (1998) Q2 in Colwell et al. (2012) This is a bootstrap SD, based on variation in sample order among randomizations. Chao et al. (2000), Chazdon et al. (1998)

SampleACE Mean based & Individualbased SampleACE SD (runs) based & Individualbased Samplebased Samplebased All filetypes All filetypes All filetypes All filetypes ICE Mean ICE SD (runs) Chao1 Mean Chao1 95% CI Lower Bound Chao1 95% CI Upper Bound Chao1 SD(analytical)

Standard deviation of ACE, among randomizations of sample order or individual order Incidence Coverage-based Estimator of species richness (mean among runs) Standard deviation of ICE, among randomizations of sample order Chao 1 richness estimator (mean among runs)

This is a bootstrap SD, based on variation in sample order among randomizations.

Chao et al. (2000), Chazdon et al. (1998) This is a bootstrap SD, based on variation in sample order among randomizations. Chao (1984), with special cases as detailed in Appendix B.

Chao 1 log-linear confidence interval lower Chao (1987), see Appendix B. bound (mean among runs) Chao 1 log-linear confidence interval upper Chao (1987), see Appendix B. bound (mean among runs) Chao 1 standard deviation (by Chao's formulas) Chao (1987) (not Chao 1984). Note: The formula in Colwell & Coddington (1994) is incorrect. See Appendix B for the correct formula and for special cases. Chao (1984, 1987), with special cases as detailed in Appendix B.

Samplebased Samplebased Samplebased Samplebased

Chao2 Mean Chao2 95% CI Lower Bound Chao2 95% CI Upper Bound Chao2 SD(analytical)

Chao 2 richness estimator (mean among runs)

Chao 2 log-linear confidence interval lower Chao (1987), see Appendix B. bound (mean among runs) Chao 2 log-linear confidence interval upper Chao (1987), see Appendix B. bound (mean among runs) Chao 2 standard deviation (by Chao's formula) Chao (1987) Note: The formula in Colwell & Coddington is incorrect. See Appendix B for the correct formula and for special cases. Burnham & Overton(1978, 1979), Smith & van Belle (1984), Heltshe & Forrester (1983) This is a bootstrap SD, based on variation in sample order among randomizations. Burnham & Overton(1978, 1979), Smith & van Belle (1984), Palmer (1991) This is a bootstrap SD, based on variation in sample order among randomizations.

Samplebased Samplebased Samplebased Samplebased Samplebased Samplebased Samplebased

Jack1 Mean

First-order Jackknife richness estimator (mean among runs) First-order Jackknife standard deviation Second-order Jackknife richness estimator (mean among runs) Standard deviation of Jack2, among randomizations of sample order

Jack1 SD (runs) Jack2 Mean Jack2 SD (runs) Bootstrap Mean Bootstrap SD (runs) MMRuns Mean

Bootstrap richness estimator (mean among Smith & van Belle (1984) runs) Standard deviation of Bootstrap, among randomizations of sample order Michaelis-Menten richness estimator: estimators averaged over randomizations (mean among runs) This is a bootstrap SD, based on variation in sample order among randomizations. Raaijmakers (1987)

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Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 Samplebased MMMeans (1 run) Michaelis-Menten richness estimator: estimators computed once for analytica rarefaction curve, computed by Eq. 5 in Colwell et al. (2004) Cole Rarefaction Coleman rarefaction (number of species expected in t pooled samples, assuming individuals distributed at random among samples) Coleman standard deviation (analytical) Fisher's alpha diversity index Fisher's alpha standard deviation Shannon diversity index (mean among runs), natural logarithms Raaijmakers (1987), Colwell et al. (2004)

Samplebased

Coleman (1981), Coleman et al. (1982)

Samplebased All filetypes All filetypes All filetypes All filetypes All filetypes All filetypes All filetypes All filetypes

Cole SD Alpha Mean Alpha SD (analytical) Shannon Mean

Coleman (1981), Coleman et al. (1982) Magurran (2004), Hayek & Buzas (1996) Magurran (1988), Hayek & Buzas (1996) Magurran (2004, page 238) This is a bootstrap SD, based on variation in sample order among randomizations. Magurran (2004, page 149); Jost (2006)

Shannon SD (runs) Standard deviation of Shannon index among randomizations of sample order Shannon Exp Mean Shannon Exp SD (runs) Exponential Shannon diversity index (mean among runs)

Standard deviation of Exponential Shannon This is a bootstrap SD, based on variation index among randomizations of sample in sample order among randomizations. order Magurran (1988, eq. 2.27), Magurran (2004, p. 115), Hayek & Buzas (1996);Jost (2006) This is a bootstrap SD, based on variation in sample order among randomizations.

Simpson (Inverse) Simpson (inverse) diversity index (mean Mean among runs) Simpson (Inverse) Standard deviation of Simpson (inverse) SD (runs) index among randomizations of sample order

Table 2: Shared Species Statistics. Shared Species estimators, classic similarity indices, Chao's abundance-based Jaccard and Sorensen similarity indices and their estimators, and related variables computed by EstimateS 9. In the output screen (and exported text files), values for these statistics and variables appear for each possible pair of samples. The formula for the shared species estimator appears in Appendix C , and the formulas for Chao's abundance-based Jaccard and Sorensen similarity indices, and their estimators and variances appears in Appendix D . Note: The statisics in Table 2 are computed only for sample-based abundance data. Variable First Sample Second Sample Sobs First Sample Sobs Second Sample Shared Spp Observed ACE First ACE Second Observed number of species in the First Sample Observed number of species in the Second Sample Observed number of species shared by First and Second samples Estimated number of species in the First Sample: ACE Estimated number of species in the Second Sample: ACE Chao, Ma, and Yang (1993), Chazdon et al. (1998) Chao, Ma, and Yang (1993), Chazdon et al. (1998) Estimator Reference j in Appendix C k in Appendix C

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Facultad de Humanidades y Ciencias Universidad Nacional del Litoral Ecologa de Poblaciones y Comunidades 2013 Chao Shared Estimated Jaccard Classic Srensen Classic Chao-Jacc-Raw Abundance-based Chao-Jacc-Est Abundance-based Chao-Jacc-EstSD Abundance-based Chao-Jacc-Est Incidence-based Chao-Sor-EstSD Indidence-based Estimated number of species shared by First and Second samples: V(est) Classic Jaccard sample similarity index Classic Srensen incidence-based (qualitative) sample similarity index Chao's Jaccard Raw (uncorrected for unseen species) Abundance-based similarity index Chao's estimator (corrected for unseen species) for Chao's Jaccard Abundancebased similarity index Standard Deviation of Chao's estimator (corrected for unseen species) for Chao's Jaccard Abundance-based similarity index Chao's estimator (corrected for unseen species) for Chao's Jaccard similarity index for replicated Incidence-based data Standard Deviation of Chao's estimator (corrected for unseen species) for Chao's Jaccard similarity index for replicated Incidence-based data Chao's Srensen Raw (uncorrected for unseen species) Abundance-based similarity index Chao's estimator (corrected for unseen species) for Chao's Srensen Abundancebased similarity index Standard Deviation of Chao's estimator (corrected for unseen species) for Chao's Srensen Abundance-based similarity index Chao's estimator (corrected for unseen species) for Chao's Srensen similarity index for replicated Incidence-based data Standard Deviation of Chao's estimator (corrected for unseen species) for Chao's Srensen similarity index for replicated Incidence-based data Morisita-Horn sample similarity index Bray-Curtis (=Srensen quantitative) sample similarity index Chen et al. 1995 Chao et al. (2005, eq. 1) Chao et al. (2005, eq. 2) Chao et al. (2005, eq. 5) Chao et al. (2005, eq. 9)

Chao et al. (In press)

Chao et al. (2005, eq. 13)

Chao et al. (In press)

Chao-Sor-Raw Abundance-based Chao-Sor-Est Abundance-based Chao-Sor-EstSD Abundance-based Chao-Sor-Est Incidencebased Chao-Sor-EstSD Indidence-based

Chao et al. (2005, eq. 6)

Chao et al. (2005, eq. 10)

Chao et al. (In press)

Chao et al. (2005, eq. 14)

Chao et al. (In press)

Morisita- Horn Bray-Curtis

Magurran (1988, eq. 5.10), Magurran (2004, page ) Magurran (1988, eq. 5.9), Magurran (2004, page )

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