Bomareapastazensis (Alstroemeriaceae), an exceptionally small new species from the eastern Andean slopes of Ecuador.

Recent field research on the eastern slopes of the Andes resulted in the discovery of a new species of Bomarea from the Cerro Candelaria Reserve in the Tungurahua province of Ecuador. Bomareapastazensis is the second smallest species in the genus and differs from the smallest by the presence of glutinous trichomes on the ovary, glabrous sepals, and greenish-yellow petals with purple spots. Based on IUCN guidelines, a preliminary conservation status is assigned as Vulnerable (VU).

ResumenRecientes investigaciones de campo en las estribaciones orientales de los Andes dieron como resultado el descubrimiento de una nueva especie de Bomarea en la Reserva Cerro Candelaria en la provincia de Tungurahua en Ecuador. Bomareapastazensis es la segunda especie más pequeña del género y se diferencia por la presencia de tricomas glutinosos en el ovario, sépalos glabros y pétalos verdes con amarillo y manchas moradas. Con base en los lineamientos de la IUCN, se le asigna un estado preliminar de conservación de Vulnerable (VU).

Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size.

We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size. Traditional rarefaction or extrapolation to equal-sized samples can misrepresent the relationships between the richnesses of the communities being compared because a sample of a given size may be sufficient to fully characterize the lower diversity community, but insufficient to characterize the richer community. Thus, the traditional method systematically biases the degree of differences between community richnesses. We derived a new analytic method for seamless coverage-based rarefaction and extrapolation. We show that this method yields less biased comparisons of richness between communities, and manages this with less total sampling effort. When this approach is integrated with an adaptive coverage-based stopping rule during sampling, samples may be compared directly without rarefaction, so no extra data is taken and none is thrown away. Even if this stopping rule is not used during data collection, coverage-based rarefaction throws away less data than traditional size-based rarefaction, and more efficiently finds the correct ranking of communities according to their true richnesses. Several hypothetical and real examples demonstrate these advantages.

Strong differentiation between amphibian communities on two adjacent mountains in the Upper Rio Pastaza watershed of Ecuador, with descriptions of two new species of terrestrial frogs.

We present the results of herpetological surveys in two adjacent mountains where the EcoMinga Foundation protects the cloud forest in the Upper Rio Pastaza watershed, in the Llanganates Sangay Ecological Corridor in Ecuador. A rapid assessment of the amphibian communities of the study sites reveals a diverse and heterogeneous composition, dominated by terrestrial frogs from the genus Pristimantis. We also identify a cryptic diversity with a significant number of candidate new species. We describe two new species of terrestrial frogs of the genus Pristimantis. Pristimantismaryanneae sp. nov. is characterised by not having tympanum externally visible and having 2-3 subconical tubercles in the upper eyelid; and Pristimantisburtoniorum sp. nov. is characterised by the presence of red colouration in hidden surfaces of the hind-limbs, tubercles on the upper eyelid, interorbital tubercle and a row of rounded tubercles along the snout to the tip and a pale red venter with dark brown mottled pattern. Our samples from the two Reserves do not share species between them, so the proportion of shared species seems to be relatively low. In addition, we highlight the importance of updating the knowledge of amphibians that are restricted to this important conservation region and comment about the threats and composition of the amphibian communities on the eastern slopes of the Upper Rio Pastaza watershed.

A spectacular new species of Hyloscirtus (Anura: Hylidae) from the Cordillera de Los Llanganates in the eastern Andes of Ecuador.

We have discovered a spectacular new species of frog in the genus Hyloscirtus, belonging to the H. larinopygion species group. The adult female is characterized by a mostly black body with large bright red spots on the dorsal and ventral surface, extremities, and toe pads. The adult male is unknown. Small juveniles are characterized by a yellow body with variable black markings on the flanks; while one larger juvenile displayed irregular orange or yellow marks on a black background color, with light orange or yellow toe pads. Additional distinctive external morphological features such as cloacal ornamentation are described, and some osteological details are imaged and analyzed. The performed phylogeny places the new species as the sister to a clade consisting of ten taxa, all of which are part of the H. larinopygion group. We use genetic distances to fit the new species into a published time-calibrated phylogeny of this group; our analysis based on the published chronology suggests that the divergence of the new species from its known congeners pre-dates the Quaternary period. The new species is currently only known only from Cerro Mayordomo, in Fundación EcoMinga´s Machay Reserve, at 2,900 m in the eastern Andes of Tungurahua province, Ecuador, near the southern edge of Los Llanganates National Park, but its real distribution may be larger.

New circumscriptions add two northern Andean species to Kohleria (Gesneriaceae).

Recent studies of type specimens and exploratory research expeditions in the northern Andes have resulted in an updated circumscription and recognition for two species of Kohleria (Gesneriaceae) in Ecuador and Colombia. A change in the rank from a variety to species is recognized for Kohleria anisophylla (Fritsch) Wiehler. The combination Kohleria andina (Fritsch) J.L. Clark & Jost, comb. nov. is provided here and a lectotype is designated. The updated circumscriptions of these two species are supported by morphology and geographic distribution. The presence of an epiphytic habit for Kohleria is discussed. Field images based on recent expeditions are provided to support the circumscriptions presented here.

ResumenLos estudios recientes de las colecciones tipo y las expediciones exploratorias en el norte de los Andes han dado como resultado la actualización en la circunscripción y reconocimiento de dos especies de Kohleria (Gesneriaceae) en Ecuador y Colombia. Se reconoce el cambio de rango de variedad a especie para Kohleria anisophylla (Fritsch) Wiehler. Se presenta la nueva combinación Kohleria andina (Fritsch) J.L. Clark & Jost, comb. nov. con la designación de su lectotipo. La circunscripción actualizada de estas dos especies está soportada por caracteres morfológicos y distribución geográfica. Se discute la presencia del hábito epífito en Kohleria. Se presentan imágenes obtenidas en las expediciones de campo para soportar las circunscripciones propuestas aquí.

A two-stage probabilistic approach to multiple-community similarity indices.

SUMMARY: A traditional approach for assessing similarity among N (N > 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N- 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.

Differentiation measures for conservation genetics.

We compare the two main classes of measures of population structure in genetics: (i) fixation measures such as FST,GST, and θ and (ii) allelic differentiation measures such as Jost's D and entropy differentiation. These two groups of measures quantify complementary aspects of population structure, which have no necessary relationship with each other. We focus especially on empirical aspects of population structure relevant to conservation analyses. At the empirical level, the first set of measures quantify nearness to fixation, while the second set of measures quantify relative degree of allelic differentiation. The two sets of measures do not compete with each other. Fixation measures are often misinterpreted as measures of allelic differentiation in conservation applications; we give examples and theoretical explanations showing why this interpretation can mislead. This misinterpretation has led to the mistaken belief that the absolute number of migrants determines allelic differentiation between demes when mutation rate is low; we show that in the finite island model, the absolute number of migrants determines nearness to fixation, not allelic differentiation. We show that a different quantity, the factor that controls Jost's D, is a good predictor of the evolution of the actual genetic divergence between demes at equilibrium in this model. We also show that when conservation decisions require judgments about differences in genetic composition between demes, allelic differentiation measures should be used instead of fixation measures. Allelic differentiation of fast-mutating markers can be used to rank pairs or sets of demes according to their differentiation, but the allelic differentiation at coding loci of interest should be directly measured in order to judge its actual magnitude at these loci.

Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales.

Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organization (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap, we present a unifying framework for the measurement of biodiversity across hierarchical levels of organization. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon's entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.), we applied the framework to a real data set on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics and eco-evolutionary dynamics.

Partitioning diversity into independent alpha and beta components.

Existing general definitions of beta diversity often produce a beta with a hidden dependence on alpha. Such a beta cannot be used to compare regions that differ in alpha diversity. To avoid misinterpretation, existing definitions of alpha and beta must be replaced by a definition that partitions diversity into independent alpha and beta components. Such a unique definition is derived here. When these new alpha and beta components are transformed into their numbers equivalents (effective numbers of elements), Whittaker's multiplicative law (alpha x beta = gamma) is necessarily true for all indices. The new beta gives the effective number of distinct communities. The most popular similarity and overlap measures of ecology (Jaccard, Sorensen, Horn, and Morisita-Horn indices) are monotonic transformations of the new beta diversity. Shannon measures follow deductively from this formalism and do not need to be borrowed from information theory; they are shown to be the only standard diversity measures which can be decomposed into meaningful independent alpha and beta components when community weights are unequal.

Two new species of endemic Ecuadorean Amaryllidaceae (Asparagales, Amaryllidaceae, Amarylloideae, Eucharideae).

New species of the genera Stenomesson and Eucharis (Amaryllidaceae) are described from Ecuador. Stenomessonecuadorense is the second species of the genus reported from that country, and the only endemic one. It is related to Stenomessonminiatum and Stenomessoncampanulatum, both from Peru, with which it shares orange flower color and the fusion of the staminal corona to the perianth tube. It differs from Stenomessonminiatum by the non-urceolate perianth, from Stenomessoncampanulatum by its shorter stamens and longer perianth, and from both by its lower montane, cloud forest habitat. Eucharisruthiana, found in the vicinity of Zamora, is related to Eucharismoorei from which it differs by the narrower leaves and tepals; short, deeply cleft staminal corona; the long teeth on either side of the free filaments; the narrowly subulate, incurved free filaments; and the shorter style. The green mature fruit and campanulate floral morphology place it in Eucharissubg.Heterocharis.

ResumenNuevas especies de los géneros Stenomesson y Eucharis (Amaryllidaceae) se describen para Ecuador. Stenomessonecuadorense es la segunda especie del género reportada de ese país y la única endémica. Está relacionada con Stenomessonminiatum y Stenomessoncampanulatum, ambos de Perú, con la que comparte el color naranja de la flor y la fusión de la copa estaminal al tubo del perianto. Se diferencia de Stenomessonminiatum por el perianto no urceolado, de Stenomessoncampanulatum por sus estambres más cortos y perianto más largo, yde ambos por su hábitat en bosque nuboso montano de baja altitud. Eucharisruthiana, que se encuentra en las cercanías de Zamora, está relacionada con Eucharismoorei, de cual difiere por las hojas y tépalos estrechos, copa estaminal corta y profundamente hendida, los dientes largos a ambos lados de los filamentos libres, filamentos libres encurvos y ligeramente subulados, y el estilo más corto. El fruto maduro verde y morfología floral campanulada lo posicionan en Eucharis subgénero Heterocharis.

Expected Shannon Entropy and Shannon Differentiation between Subpopulations for Neutral Genes under the Finite Island Model.

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Phylogenetic diversity measures based on Hill numbers.

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.

G(ST) and its relatives do not measure differentiation.

G(ST) and its relatives are often interpreted as measures of differentiation between subpopulations, with values near zero supposedly indicating low differentiation. However, G(ST) necessarily approaches zero when gene diversity is high, even if subpopulations are completely differentiated, and it is not monotonic with increasing differentiation. Likewise, when diversity is equated with heterozygosity, standard similarity measures formed by taking the ratio of mean within-subpopulation diversity to total diversity necessarily approach unity when diversity is high, even if the subpopulations are completely dissimilar (no shared alleles). None of these measures can be interpreted as measures of differentiation or similarity. The derivations of these measures contain two subtle misconceptions which cause their paradoxical behaviours. Conclusions about population differentiation, gene flow, relatedness, and conservation priority will often be wrong when based on these fixation indices or similarity measures. These are not statistical issues; the problems persist even when true population frequencies are used in the calculations. Recent advances in the mathematics of diversity identify the misconceptions, and yield mathematically consistent descriptive measures of population structure which eliminate the paradoxes produced by standard measures. These measures can be directly related to the migration and mutation rates of the finite-island model.