AN “ENVIRO‐INFORMATIC” ASSESSMENT OF SAGINAW BAY (LAKE HURON,USA) PHYTOPLANKTON: DATA‐DRIVEN CHARACTERIZATION AND MODELING OF MICROCYSTIS (CYANOPHYTA)1

Phytoplankton and Microcystis aeruginosa (Kütz.) Kütz. biovolumes were characterized and modeled, respectively, with regard to hydrological and meteorological variables during zebra mussel invasion in Saginaw Bay (1990–1996). Total phytoplankton and Microcystis biomass within the inner bay were one and one‐half and six times greater, respectively, than those of the outer bay. Following mussel invasion, mean total biomass in the inner bay decreased 84% but then returned to its approximate initial value. Microcystis was not present in the bay during 1990 and 1991 and thereafter occurred at/in 52% of sample sites/dates with the greatest biomass occurring in 1994–1996 and within months having water temperatures >19°C. With an overall relative biomass of 0.03 ± 0.01 (mean + SE), Microcystis had, at best, a marginal impact upon holistic compositional dynamics. Dynamics of the centric diatom Cyclotella ocellata Pant. and large pennate diatoms dominated compositional dissimilarities both inter‐ and intra‐annually. The environmental variables that corresponded with phytoplankton distributions were similar for the inner and outer bays, and together identified physical forcing and biotic utilization of nutrients as determinants of system‐level biomass patterns. Nonparametric models explained 70%–85% of the variability in Microcystis biovolumes and identified maximal biomass to occur at total phosphorus (TP) concentrations ranging from 40 to 45 μg · L^?1. From isometric projections depicting modeled Microcystis/environmental interactions, a TP concentration of <30 μg · L^?1 was identified as a desirable contemporary “target” for management efforts to ameliorate bloom potentials throughout mussel‐impacted bay waters.     

Nonidentifiability of population size from capture-recapture data with heterogeneous detection probabilities

Heterogeneity in detection probabilities has long been recognized as problematic in mark-recapture studies, and numerous models developed to accommodate its effects. Individual heterogeneity is especially problematic, in that reasonable alternative models may predict essentially identical observations from populations of substantially different sizes. Thus even with very large samples, the analyst will not be able to distinguish among reasonable models of heterogeneity, even though these yield quite distinct inferences about population size. The problem is illustrated with models for closed and open populations.     

An alternative method for assessing early mortality in contemporary populations

Biological anthropologists are interested in a population's early mortality rates for a variety of reasons. Early mortality (infant or juvenile) is of obvious importance to those interested in demography, but early mortality statistics are useful for life history analysis, paleodemography, and human adaptability studies, among others. In general, the form of mortality statistics is derived from demography, where chronological age is the gold standard for statistical calculation and comparison. However, there are numerous problems associated with the collection, analysis, and interpretation of early mortality statistics based on age, particularly for anthropological research, which is often conducted in small or non-calendrical-age numerate populations. The infant mortality rate (IMR), for example, is notoriously difficult to determine in populations where accurate accounting of age is not routine, and yet it is widely used in demography, public health, medicine, and social science research. Here we offer an alternative to age-based early mortality statistics that makes use of human biologists' interest in, and skill at, assessing human growth and development. Our proposal is to use developmental stages of juveniles instead of relying exclusively on age as the basis for mortality statistics. Death or survival according to a developmental stage (such as crawling or weaning) may provide more accurate data that are also more closely related to the cause of death. Developmental stages have the added advantage of putting infants and children back at the center of the discussion of early mortality by focusing on their activities in relation to their environment. A case study from the Turkana population of Kenya illustrates the use of developmental stages in describing early mortality. Am J Phys Anthropol 107:315–330, 1998. © 1998 Wiley-Liss, Inc.     

Craniometric allometry in the thicktailed bushbabyOtolemur Crassicaudatus

Static adult craniometric allometry was evaluated in a sample of 66Otolemur crassicaudatus skulls (34 males, 32 females). Although cranial measures were equally well correlated to skull length in males and females, there were noteworthy differences in the exponential values between the sexes. These results underlined the need for caution when allometric analyses are based on pooled data. From the cranial allometric analyses it is concluded that the longer the skull, the shorter and the narrower the maxilla, and the broader the bizygomatic distance. Although cranial length increased proportionately to the increase in skull length, the cranial width in females was positively allometric whilst in males it was negatively allometric. Allometric analyses of mandibular dimensions suggest that larger animals will have proportionately longer mandibulae, which will, in turn, be relatively wider across the gonia, yet shallower behind the first molars. It is postulated that the disproportionate widening of the zygomata might be related to the widening across the gonia.     

Observations on the Staining of Corynebacterium Diphtheriae

Albert's method, of staining diphtheria cultures consists of staining a fixed smear for one minute (some laboratories stain for five minutes) with a solution containing toluidine blue and malachite (or methyl) green, washing with water, and applying Albert's iodine for one minute. This procedure is discussed and criticized, and in addition the mechanism of the stain is elucidated. Also, the procedure which involves staining a fixed smear for one minute with Loeffler's alkaline methylene blue solution is discussed and criticized.

To overcome the objections to the above staining methods, a different method is proposed. This consists of staining a fixed smear with an acid solution of toluidine blue, washing with water, applying Albert's iodine for one minute, washing with water, and finally applying a safranin solution for 15-20 seconds. The theoretical basis for this method is presented.     

Estimating population structure from AFLP amplification intensity

In the last decade, amplified fragment length polymorphisms (AFLPs) have become one of the most widely used molecular markers to study the genetic structure of natural populations. Most of the statistical methods available to study the genetic structure of populations using AFLPs consider these markers as dominant and are thus unable to distinguish between individuals being heterozygous or homozygous for the dominant allele. Some attempts have been made to treat AFLPs as codominant markers by using AFLP band intensities to infer the most likely genotype of each individual. These two approaches have some drawbacks, the former discarding potentially valuable information and the latter being sometimes unable to correctly assign genotypes to individuals. In this study, we propose an alternative likelihood‐based approach, which does not attempt at inferring the genotype of each individual, but rather incorporate the uncertainty about genotypes into a Bayesian framework leading to the estimation of population‐specific F_IS and F_ST coefficients. We show with simulations that the accuracy of our method is much higher than one using AFLP as dominant markers and is generally close to what would be obtained by using the same number of Single‐Nucleotide Polymorphism (SNP) markers. The method is applied to a data set of four populations of the common vole (Microtus arvalis) from Grisons in Switzerland, for which we obtained 562 polymorphic AFLP markers. Our approach is very general and has the potential to make AFLP markers as useful as SNP data for nonmodel species.     

Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees

We present fast new algorithms for evaluating trees with respectto least squares and minimum evolution (ME), the most commonlyused criteria for inferring phylogenetic trees from distancedata. The new algorithms include an optimal O(N2) time algorithmfor calculating the edge (branch or internode) lengths on atree according to ordinary or unweighted least squares (OLS);an O(N3) time algorithm for edge lengths under weighted leastsquares (WLS) including the Fitch-Margoliash method; and anoptimal O(N4) time algorithm for generalized least-squares (GLS)edge lengths (where N is the number of taxa in the tree). TheME criterion is based on the sum of edge lengths. Consequently,the edge lengths algorithms presented here lead directly toO(N2), O(N3), and O(N4) time algorithms for ME under OLS, WLS,and GLS, respectively. All of these algorithms are as fast asor faster than any of those previously published, and the algorithmsfor OLS and GLS are the fastest possible (with respect to orderof computational complexity). A major advantage of our new methodsis that they are as well adapted to multifurcating trees asthey are to binary trees. An optimal algorithm for determiningpath lengths from a tree with given edge lengths is also developed.This leads to an optimal O(N2) algorithm for OLS sums of squaresevaluation and corresponding O(N3) and O(N4) time algorithmsfor WLS and GLS sums of squares, respectively. The GLS algorithmis time-optimal if the covariance matrix is already inverted.The speed of each algorithm is assessed analytically—thespeed increases we calculate are confirmed by the dramatic speedincreases resulting from their implementation in PAUP* 4.0.The new algorithms enable far more extensive tree searches andstatistical evaluations (e.g., bootstrap, parametric bootstrap,or jackknife) in the same amount of time. Hopefully, the fastalgorithms for WLS and GLS will encourage the use of these criteriafor evaluating trees and their edge lengths (e.g., for approximatedivergence time estimates), since they should be more statisticallyefficient than OLS.