An optimality criterion to determine areas of endemism

A formal method was developed to determine areas of endemism. The study region is divided into cells, and the number of species that can be considered as endemic is counted for a given set of cells (= area). Thus, the areas with the maximum number of species considered endemic are preferred. This is the first method for the identification of areas of endemism that implements an optimality criterion directly based on considering the aspects of species distribution that are relevant to endemism. The method is implemented in two computer programs, NDM and VNDM, available from the authors.     

Predictive optimality criterion for idealization of ion channel data and exact Akaike's criterion

Different statistical or low-pass filters may be used for the idealization of ion channel data. We address the problem of predicting optimal filter parameters, represented by a threshold test-value for statistical filters and by a cut-off frequency for low-pass filters. Optimal idealization is understood in the sense of maximal similarity between recovered and real signals. Special procedures are suggested to quantitatively characterize the difference between the recovered and the real signals, the latter being known for simulated data. These procedures, called objective criteria, play the role of referees in estimating the performance of different predictive optimality criteria. We have tested standard Akaike's AIC and its modification by Rissanen, MDL. Both gave unsatisfactory results. We have shown analytically, that the Akaike-type criterion, based on the use of a certain penalty for the log likelihood function per transition, indicates the correct optimum point only if the penalty is set equal to half the optimal threshold. As the latter varies significantly for different data sets, this criterion is not particularly helpful. A new universal predictive optimality criterion, valid for real data and any idealization method, is suggested. It is formally similar to AIC, but instead of log likelihood it uses the doubled number of false transitions. The predictive power of the new criterion is demonstrated with different types of data for Hinkley and 50% amplitude methods. Received: 23 July 1996 / Accepted: 9 May 1997     

Simultaneously mapping and superimposing landmark configurations with parsimony as optimality criterion

All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark configurations along the tree as changes in shape, the metric chosen to define the ancestral assignments should also form the basis to superimpose the configurations. Thus, we present here a method that merges both steps, map and align, into a single procedure that (for the given tree) produces a multiple alignment and ancestral assignments such that the sum of the Euclidean distances between the corresponding landmarks along tree nodes is minimized. This approach is an extension of the method proposed by Catalano et al. (2010. Phylogenetic morphometrics (I): the use of landmark data in a phylogenetic framework. Cladistics. 26:539-549) for mapping landmark data with parsimony as optimality criterion. In the context of phylogenetics, this method allows maximizing the degree to which similarity in landmark positions can be accounted for by common ancestry. In the context of morphometrics, this approach guarantees (heuristics aside) that all the transformations inferred on the tree represent changes in shape. The performance of the method was evaluated on different data sets, indicating that the method produces marked improvements in tree score (up to 5% compared with generalized superimpositions, up to 11% compared with ordinary superimpositions). These empirical results stress the importance of incorporating the phylogenetic information into the alignment step.     

Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.     

Areas of endemism in the Espinhaço Range in Minas Gerais, Brazil

The Espinhaço Range, a mountain chain located in the Brazilian states of Minas Gerais and Bahia, contains one of the richest floras in Brazil, with a high frequency of endemic species. Since 2005 it is designated as UNESCO biosphere reserve and is situated at the joint border of two global hotspots for biodiversity conservation. Endemic species with congruent occurrence patterns were identified in order to establish areas of higher endemism within the Espinhaço Range. Taxonomic reviews were analyzed in order to identify endemic taxa and a dataset was elaborated containing 1765 records from 178 endemic species of vascular plants, representing 17 families and including the geographic coordinates for each record. Two maps were produced showing species richness and collection effort in 15′ quadrats. The congruent occurrences were identified and a third map was provided, delimiting 10 candidate areas of endemism for a “parsimony analysis of endemicity” (PAE). One most parsimonious cladogram is then retrieved, evidencing three major clades corresponding to the northern, central and southern portions of the Espinhaço, in addition to four subclades included into the central clade. We finally identified six major areas of endemism. Furthermore, there is a strong correlation between species richness and collector effort, revealing which areas are in need of further field inventories.     

Prediction of phylogeographic endemism in an environmentally complex biome

Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current and past climatic variation on the genetic diversity of 25 vertebrates in the Brazilian Atlantic rainforest. We identify two divergent bioclimatic domains within the forest and high turnover around the Rio Doce. Independent modelling of these domains demonstrates that endemism patterns are subject to different climatic drivers. Past climate dynamics, specifically areas of relative stability, predict phylogeographic endemism in the north. Conversely, contemporary climatic heterogeneity better explains endemism in the south. These results accord with recent speleothem and fossil pollen studies, suggesting that climatic variability through the last 250 kyr impacted the northern and the southern forests differently. Incorporating sub-regional differences in climate dynamics will enhance our ability to understand those processes shaping high phylogeographic and species endemism, in the Neotropics and beyond.     

The scaling of diving time budgets: insights from an optimality approach

Simple scaling arguments suggest that, among air-breathing divers, dive duration should scale approximately with mass to the one-third power. Recent phylogenetic analyses appear to confirm this. The same analyses showed that duration of time spent at the surface between dives has scaling very similar to that of dive duration, with the result that the ratio of dive duration to surface pause duration is approximately mass invariant. This finding runs counter to other arguments found in the diving literature that suggest that surface pause duration should scale more positively with mass, leading to a negative scaling of the dive-pause ratio. We use a published model of optimal time allocation in the dive cycle to show that optimal decisions can predict approximate mass invariance in the dive-pause ratio, especially if metabolism scales approximately with mass to the two-thirds power (as indicated by some recent analyses) and oxygen uptake is assumed to have evolved to supply the body tissues at the required rate. However, emergent scaling rules are sensitive to input parameters, especially to the relationship between the scaling of metabolism and oxygen uptake rate at the surface. Our results illustrate the utility of an optimality approach for developing predictions and identifying key areas for empirical research on the allometry of diving behavior.     

On areas of endemism,with an example from the African Restionaceae

Areas of endemism are central to cladistic biogeography. The concept has been much debated in the past, and from this has emerged the generally accepted definition as an area to which at least two species are endemic. Protocols for locating areas of endemism have been neglected, and to date no attempt has been made to develop optimality criteria against which to evaluate competing hypotheses of areas of endemism. Here various protocols for finding areas of endemism are evaluated--protocols based on both phonetic and parsimony analyses, on both unweighted data and data weighted by various criteria. The optimality criteria used to compare the performance of the methods include the number of species included in the areas of endemism, the number of areas delimited, and the degree of distributional congruency of the species restricted to each area of endemism. These methods are applied to the African Restionaceae in the Cape Floristic Region. Parsimony methods using weighted data are shown to perform best on the combination of all three optimality criteria. By varying the weighting parameters, the size of the areas of endemism can be varied. This provides a very useful tool for locating areas of endemism that satisfy prespecified scale criteria.     

Genetic endemism of Galapagos Pteridium

Hybridization experiments indicate that Pteridium aquilinum from Hawaii and P. aquilinum from the Galapagos Isles are intersterile. Both of these populations will cross readily with other New World collections of Pteridium. Evidence suggests that the Galapagos populations are genetically distinct from the South American populations. The genetic divergence of the Galapagos populations has not been accompanied by morphological divergence.     

Iterative species distribution modelling and ground validation in endemism research: an Alpine jumping bristletail example

Endemic species play an important role in conservation ecology. However, knowledge of the real distribution and ecology is still scarce for many endemics. The aims of this study were to predict the distribution of the short-range endemic Alpine jumping bristletail Machilis pallida; to evaluate the actual level of endemism via ground validation using an iterative approach for testing the models in field trips and increasing the quality of the prediction step by step; and to test the potential of species distribution modelling for increasing the knowledge about the ecological niche. Based on seven known locations of M. pallida, we used species distribution modelling via Maxent. After a set of seven field trips a new model was built if new locations were found. Three such iterations were performed to increase model quality. We discovered four new locations of M. pallida, increasing the area of known distribution from 470 to 4,890?km². The distribution of M. pallida is thus wider than formerly known, but our results support Eastern Alpine endemism of the species. The knowledge about the ecological niche could be increased due to the newly found locations. Our study showcases the potential of the iterative approach of modelling and ground validation to evaluate the actual level of endemism and the ecological niche in Alpine species and beyond.     

Estradiol 17 -hemisuccinate: an improved procedure

A simple, rapid, high-yield, and relatively inexpensive procedure for the preparation of estradiol 17beta-hemisuccinate is described. The synthesis can be done conveniently in the ordinary biological laboratory.     

Quantitative chemobehavior of fish: an improved methodology

Synopsis A new behavioral monitoring system, an octagonal fluviarium, and associated time-series analytical techniques were developed to quantitatively examine and assess the chemobehavior of fish to waterborne chemicals. Together they aid in the solution of many of the quantitative behavioral and physical problems inherent in earlier experimental approaches. The fluviarium utilizes a quasi-circular channel in which fish are able to move freely through any of eight areas, any of which can receive a predetermined concentration of a chemical stimulus. Movements and preferential stays of animals monitored with a video system are analyzed to determine spatial and temporal preference in their distributions within the system in response to introduced chemicals. The advantages of these designs include precise control of the water flow dynamics affecting the odor plume, virtual elimination of the wall-hugging tendency of animals due to the quasicircular construction of the octagonal trough, and the assessment of temporal changes in the behavioral responses of the animals which can be correlated with the presence of odoriferous cues. The efficacy of the fluviarium and statistical analysis is illustrated with data on the chemoresponse of zebrafish, Brachydanio rerio, to 1 × 10^–3 M L-alanine. Our system should have extensive application in investigating the chemoresponses of aquatic organisms to waterborne chemicals (presented singularly and in combinations) such as food substances, pheromones or pollutants.     

Biological optimality: Comparison of generalized feasibility and optimality conditions for linear,error-minimizing systems

An attempt is made to compare the conditions for the general error-optimality of linear systems developed by Kalman with the conditions for feasibility of linear models of neuromuscular and physiological control systems. Models of three actual physiological systems are tested for both the above criteria. Theoretical analysis presented here shows that there are no simple relationships between the two sets of conditions. Analysis carried out on the physiological systems models suggests the need for a general set of conditions for other optimality criteria, such as time and energy minimization, similar to Kalman's condition for error minimization.     

Hidden areas of endemism: Small units in the South-eastern Neotropics

This study aimed to establish if the Lower Río de la Plata Basin (LRPB) wetlands can be considered a biogeographic unit. The species of this area were compiled and segregated according to the habitat, selecting only 87 endemic taxa restricted to the LRPB and linked to wetlands. Distributional data of species obtained from the literature, web databases, biological collections, and field trips were georeferenced. The areas of endemism were established as those areas where the distribution of two or more taxa overlaps in groups of rivers’ sections with geographic continuity and were tested with a cluster analysis. This congruence is due to ecological, geomorphological, and historical factors. Four areas of endemism were found: a broad area that comprises the whole study area (Riverine district), which is divided into three nested smaller areas (Paraguay–Paraná Flooding Valleys, Uruguay Basin, and Paraná Delta subdistricts). Then, we analysed 170 taxa distributions to evaluate the relationship between the study area and the neighbouring biogeographic units. According to the results, the study area belongs to the Paraná biogeographic province. Some areas of endemism are hidden inside broader areas and are hardly detected with the currently used biogeographic grid-methods. We propose to combine the information about ecological requirements of each taxon with its georeferenced records to estimate their areas of distribution as a primary step for searching areas of endemism in intracontinental studies.     

Polyacrylamide slab gel electrophoresis: an improved design

An apparatus for polyacrylamide slab gel electrophoresis is decribed which combines all parts into one integral unit. It eliminates several steps in the process of sealing, pouring, and setting the gels. Construction is easy with modest workshop facilities and the design easily adapted to suit most requirements. The apparatus provides a high degree of versatility and is suitable for use with many slab gel electrophoretic techniques.