A Quantitative Test of the Neutral Theory Using Pooled Allozyme Data

Neutral theory predicts a positive correlation between the amount of polymorphism within species and evolutionary rate. Previous tests of this prediction using both allozyme and DNA data have led to conflicting conclusions about the influence of selection and mutation drift. It is argued here that quantitative conclusions about the adequacy of neutral theory can be obtained by analyzing genetic data pooled from many sources. Using this approach, a large database containing information on allozyme variation in over 1500 species is used to examine the relationship between heterozygosity and genetic distance. The results provide support for the hypothesis that a major percentage of protein variation can be explained by variation in neutral mutation rate, and a minor percentage by strong selection.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila Melanogaster. VI. Patterns and Processes of Genic Divergence between D. Melanogaster and Its Sibling Species, Drosophila Simulans

We present here an extensive set of data on allelic differences between homologous proteins of Drosophila melanogaster and its sibling species, Drosophila simulans, obtained by nondenaturing one-dimensional, and denaturing two-dimensional gel electrophoresis. The data suggest that, for these two species, (1) approximately 10% of protein-coding loci have no alleles in common in our sample, (2) the extent of genic variation at a locus (mean heterozygosity) within a species is not correlated with the extent of divergence (Nei's genetic distance) at that locus between species, and (3) significant heterogeneity of divergence rates exists for different structural/functional classes of loci. These results are discussed in the context of the dynamics of genetic variation within and between species.     

Hierarchical and spatially aggregated plant cover data

Most plant species are spatially aggregated and here the importance of taking the spatial variation into account when analyzing plant cover data is demonstrated in a general stochastic model where both the within-site and the among-site spatial variation of species cover data are parameterized. Using a generalised binomial distribution (or Pólya–Eggenberger distribution), where the among-site variation in mean cover is modeled by a zero-inflated beta distribution, it is possible to adequately analyze hierarchical plant cover data and link the estimates to the underlying ecological processes. The model is demonstrated in a case-study of pin-point cover data of Erica tetralix from 1148 wet heathland plots at 84 Danish sites, and it is shown that both parameter estimates and the conclusions of hypotheses testing critically depend on the correct modeling of the observed spatial variation. Finally, statistical power simulations of plant cover measurements are presented, which will be useful for planning ecological experiments and monitoring programs.     

Climate patterns and the stochastic dynamics of migratory birds

We analyse time series data of 17 bird species trapped at Ottenby Bird Observatory, Sweden, during spring migration 1972–1999. The species have similar demography but respond differently to variation in the North Atlantic Oscillation (NAO) – a strong determinant of winter climate in the northern Hemisphere. Species wintering in northern Europe, compared to species having winter quarters in the Mediterranean area, tend to respond positively to variation in NAO. The variation within each group is high due to wide-ranging winter-distribution in many species, probably smoothing out the effect of spatial variation in NAO. Whereas mild winters (high NAO) is benign for many – but not all – birds wintering in northern Europe, the effect of drier-than-normal conditions in the Mediterranean area during high NAO index winters are uncertain. The work presented here goes beyond simple correlative studies and help identifying which species that are most affected by variation in winter climate. This is a first important step that calls for a more mechanistic approach when analysing possible changes to climate change.     

Interspecific abundance–occupancy relationships of British mammals and birds: is it possible to explain the residual variation?

Aim The majority of studies concerning positive interspecific abundance–occupancy relationships have used broad‐scale and microcosm data to test the occurrence and correlates of the relationship to determine which of the proposed mechanisms give rise to it. It has been argued recently that studying the residual variation about abundance–occupancy relationships is a more logical analysis and may yield faster progress in identifying the relative roles of the mechanisms. However, to date this approach has been largely unsuccessful. Here we test if fundamental species traits such as the status (native and introduced), habitat and trophic group of mammal and bird species may explain any of the residual variation about their respective abundance–occupancy relationships. Location The study used British mammal and bird species. Methods We tested if species traits explained any of the variation about abundance–occupancy relationships using linear regression techniques both treating species as independent data points for analysis and controlling for phylogenetic association. Results None of the species traits could explain any residual variation about the positive interspecific abundance–occupancy relationships of British mammals and birds. This applied both when treating species as independent data points and after controlling for phylogenetic association. Conclusions Given the lack of explanatory power of the species traits here and in other studies using this approach it seems that the variation about positive interspecific abundance–occupancy relationships is not explicable in a simple fashion. Predicting the likely influence of traits that are independent of phylogeny is also problematic. Therefore, the general utility of this approach and its future role in understanding the mechanisms causing positive interspecific abundance–occupancy relationships is doubtful.     

Winter weather and waterfowl surveys in north-western Ontario, Canada

Abstract Aim An analysis is presented to examine whether variation in breeding waterfowl estimates can be explained by weather patterns prior to annual surveys. Location The location of the study is north‐western Ontario, Canada. Methods Annual, systematic survey data for breeding waterfowl are available from the 1950s to the present for north‐western Ontario. Regional monthly climate data for this area were compiled using weather data derived from interpolated annual climate surfaces. These data were analysed using stepwise multiple linear regression for each species and for waterfowl functional groups to assess whether monthly climate data accounted for some of the variation in waterfowl numbers. Results For all dabbling ducks pooled, 12% of the variation in annual abundance was explained by April temperatures, with more dabbling ducks observed in years when April was relatively cool. For diving ducks, 23% of the variation in pooled abundance was explained by April temperatures and February precipitation, where more diving ducks were observed in years when February had relatively less precipitation and April was cool. Patterns for individual species varied. Main conclusions Mean monthly weather data for months prior to surveys explained some of the variation in numbers of waterfowl observed in annual surveys. This suggests that future incorporation of weather data into waterfowl population models may help refine population estimates.     

Establishing a captive broodstock for the endangered bonytail chub (Gila elegans)

It is crucial for endangered species to retain as much genetic variation as possible to enhance recovery. Bonytail chub (Gila elegans) is one the most imperiled freshwater fish species, persisting as a declining population of large and old individuals primarily in Lake Mohave on the lower Colorado River. Establishment of a new captive broodstock from the 1981 F1 progeny of at most 10 wild fish plus any newly captured wild fish is evaluated and reviewed. The effective number of founders contributing to the 1981 F1 progeny appears quite small, varying from approximately 3.5, based on F1 allozyme data and supported by mtDNA data, to approximately 8.5, based on the original production records. Using a sample of these progeny to initiate a new broodstock further reduces the effective number of founders. With even the most optimistic evaluation of the amount of genetic variation in F1 progeny, it is obvious that including wild fish in the broodstock is essential to increase the amount of genetic variation. The approach given here could be applied to retain genetic variation in other endangered species in a captive broodstock until they have stable natural populations of adequate size.     

Genomics and conservation genetics

In large part, the relevance of genetics to conservation rests on the premise that neutral marker variation in populations reflects levels of detrimental and adaptive genetic variation. Despite its prominence, this tenet has been difficult to evaluate, until now. As we discuss here, genome sequence information and new technological and bioinformatics platforms now enable comprehensive surveys of neutral variation and more direct inferences of detrimental and adaptive variation in species with sequenced genomes and in 'genome-enabled' endangered taxa. Moreover, conservation schemes could begin to consider specific pathological genetic variants. A new conservation genetic agenda would utilize data from enhanced surveys of genomic variation in endangered species to better manage functional genetic variation.     

Genetic variation for outcrossing among Caenorhabditis elegans isolates

The evolution of breeding systems results from the existence of genetic variation and selective forces favoring different outcrossing rates. In this study we determine the extent of genetic variation for characters directly related to outcrossing, such as male frequency, male mating ability, and male reproductive success, in several wild isolates of the nematode Caenorhabditis elegans. This species is characterized by an androdioecious breeding system in which males occur with hermaphrodites that can either self-fertilize or outcross with males. We find genetic variation for all characters measured, but also find that environmental variation is a large fraction of the total phenotypic variance. We further determine the existence of substantial genetic variation for population competitive performance in several laboratory environments. However, these measures are uncorrelated with outcrossing characters. The data presented here contribute to an understanding of male maintenance in natural populations through their role in outcrossing.     

QUANTIFYING VARIATION IN SPECIATION AND EXTINCTION RATES WITH CLADE DATA

High‐level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name “clade data,” which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life‐history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented.     

Calibrating a molecular clock from phylogeographic data: moments and likelihood estimators

Abstract We present moments and likelihood methods that estimate a DNA substitution rate from a group of closely related sister species pairs separated at an assumed time, and we test these methods with simulations. The methods also estimate ancestral population size and can test whether there is a significant difference among the ancestral population sizes of the sister species pairs. Estimates presented in the literature often ignore the ancestral coalescent prior to speciation and therefore should be biased upward. The simulations show that both methods yield accurate estimates given sample sizes of five or more species pairs and that better likelihood estimates are obtained if there is no significant difference among ancestral population sizes. The model presented here indicates that the larger than expected variation found in multitaxa datasets can be explained by variation in the ancestral coalescence and the Poisson mutation process. In this context, observed variation can often be accounted for by variation in ancestral population sizes rather than invoking variation in other parameters, such as divergence time or mutation rate. The methods are applied to data from two groups of species pairs (sea urchins and Alpheus snapping shrimp) that are thought to have separated by the rise of Panama three million years ago.     

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

During the last couple of decades, an increasing number of studies use sequence clusters as units for taxonomic diversity. It is well known that such molecular operational taxonomic units (MOTUs) do not necessarily correspond to species, but they are treated as such when measuring diversity and testing theories. Here, I show that data from studies of molecular evolution and species diversification of fungi indicate that commonly used cut‐offs are likely to lump species in many cases. At the same time, empirical studies show that the mean within‐species variation is close to these cut‐offs. That the within‐species variation estimates are plausible is supported by coalescence modelling under a range of parameter settings. In addition, studies using crossing tests to delimit species show that there often is an overlap in within‐ and between‐species distances. The available data therefore indicate that sequence clusters are likely to misrepresent species. However, to keep a biological relevance, MOTUs should be kept in close agreement with species. Studies using them should therefore asses how sensitive the results are to differences between MOTUs and species – something that is rarely done. An even better solution is to directly include the uncertainty in species delimitation in the analyses, but in many cases, we need to increase our knowledge of taxonomy and evolution to do this accurately. Even if the empirical data referred to here pertain to the “barcoding” region of rDNA in fungi, there is nothing indicating that the situation is substantially better for other taxa or genes.     

Serum antioxidant levels in wild birds vary in relation to diet, season, life history strategy, and species

Micronutrient antioxidants are thought to be generally important for health in many animals, but factors determining levels in individuals and species are not well understood. Diet and season are obvious environmental variables that might predict the degree to which species can accumulate such nutrients. We analyzed antioxidant levels [Trolox-equivalent antioxidant capacity (TEAC), uric acid (UA), vitamin E, and four carotenoids] in 95 bird species and compared these to species-level data on diet from the literature. Using compositional principal components analysis, we identified two main axes of diet variation: invertebrate consumption and seed-to-fruit ratio. We then examined associations between diet axes and antioxidant measures, with and without control for life-history variation and phylogeny. We also analyzed a subset of 13 species for which we had data on seasonality of antioxidant levels and diet, assessing the variance in antioxidant levels explained by seasonality, diet, and species. Unsurprisingly, there were strong associations between antioxidant levels and diet. TEAC and UA concentration were consistently positively associated with invertebrate consumption and seed-to-fruit ratio, and carotenoid concentrations (e.g. zeaxanthin and β-carotene) were negatively associated with invertebrate consumption. However, vitamin E was not associated with diet as measured here. Importantly, there is much variation in antioxidants that is not explained by diet, and we are able to identify diet-independent effects of species, season/breeding stage, and life history on antioxidant levels. Circulating antioxidant concentrations within and across species can therefore be viewed as a function of multiple factors, including but not limited to diet, and antioxidant metabolism appears to differ across species and seasons irrespective of diet.     

Assessing latitudinal gradients in speciation rates and biodiversity at the global scale

The mechanisms responsible for latitudinal biodiversity gradients have fascinated and perplexed biologists since the time of Darwin. Ecological theory has yielded two general classes of mechanisms to account for variation in biodiversity: dispersal–assembly mechanisms that invoke differences in stochastic rates of speciation, extinction and dispersal; and niche–assembly mechanisms that invoke species differences, species interactions and environmental heterogeneity. Distinguishing between these two classes of mechanisms requires explicit consideration of macroevolutionary dynamics. Here, we assess the importance of dispersal–assembly mechanisms in the origin and maintenance of biodiversity using fossil data that encompass 30 million years of macroevolution for three distinct groups of ocean plankton: foraminifera, nannoplankton and radiolaria. Applying new methods of analysis to these fossil data, we show here for the first time that latitudinal biodiversity gradients exhibit strong positive correlations with speciation rates even after explicitly controlling for variation in sampling effort and for increases in habitat area towards the equator. These findings provide compelling evidence that geographical variation in macroevolutionary dynamics is a primary determinant of contemporary biodiversity gradients, as predicted by dispersal–assembly theory.     

Inter- and intraspecific variation in grass phytolith shape and size: a geometric morphometrics perspective

Background and AimsThe relative contributions of inter- and intraspecific variation to phytolith shape and size have only been investigated in a limited number of studies. However, a detailed understanding of phytolith variation patterns among populations or even within a single plant specimen is of key importance for the correct taxonomic identification of grass taxa in fossil samples and for the reconstruction of vegetation and environmental conditions in the past. In this study, we used geometric morphometric analysis for the quantification of different sources of phytolith shape and size variation.MethodsWe used landmark-based geometric morphometric methods for the analysis of phytolith shapes in two extant grass species (Brachypodium pinnatum and B. sylvaticum). For each species, 1200 phytoliths were analysed from 12 leaves originating from six plants growing in three populations. Phytolith shape and size data were subjected to multivariate Procrustes analysis of variance (ANOVA), multivariate regression, principal component analysis and linear discriminant analysis.Key ResultsInterspecific variation largely outweighed intraspecific variation with respect to phytolith shape. Individual phytolith shapes were classified with 83 % accuracy into their respective species. Conversely, variation in phytolith shapes within species but among populations, possibly related to environmental heterogeneity, was comparatively low.ConclusionsOur results imply that phytolith shape relatively closely corresponds to the taxonomic identity of closely related grass species. Moreover, our methodological approach, applied here in phytolith analysis for the first time, enabled the quantification and separation of variation that is not related to species discrimination. Our findings strengthen the role of grass phytoliths in the reconstruction of past vegetation dynamics.     

The second record of Diaphanosoma senegal Gauthier, 1951 (Crustacea : Daphniiformes : Sididae) in Africa,with a redescription of the species and ecological and distributional setes

The rare Diaphanosoma senegal has been found for the second time in Africa, in a water body North of Uagadugu (Burkina Faso). The species is here redescribed, with attention to individual and age variation. It combines primitive and evolutionarily advanced structural features, and inhabits temporary and intensely fluctuating water bodies of the equatorial and tropical zones. According to available data, its range is confined to West Africa and India.     

Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations

This paper describes DNA sequence variation within and among four populations of chinook salmon (Oncorhynchus tshawytscha) at the transferrin, somatolactin and p53 genes. Patterns of variation among salmon species at the transferrin gene have been hypothesized to be shaped by positive natural selection for new alleles because the rate of nonsynonymous substitution is significantly greater than the rate of synonymous substitution. The twin goals of this study were to determine if the history of selection among salmon species at the transferrin gene is also reflected in patterns of intraspecific variation in chinook salmon, and to look for evidence of local adaptation at the transferrin gene by comparing patterns of nonsynonymous and synonymous variation among chinook salmon populations. The analyses presented here show that unlike patterns of variation between species, there is no evidence of greater differentiation among chinook salmon populations at nonsynonymous compared to synonymous sites. There is also no evidence of a reduction of within-species variation due to the hitchhiking effect at the transferrin gene, although in some populations nonsynonymous and synonymous derived mutations are both at higher frequencies than expected under a simple neutral model. Population size weighted selection coefficients (4Ns) that are consistent with both the inter and intraspecific data range from approximately 10 to approximately 235, and imply that between 1 and 40% of new nonsynonymous mutations at the transferrin gene have been beneficial.     

Recombination rate predicts inversion size in Diptera.

Most species of the Drosophila genus and other Diptera are polymorphic for paracentric inversions. A common observation is that successful inversions are of intermediate size. We test here the hypothesis that the selected property is the recombination length of inversions, not their physical length. If so, physical length of successful inversions should be negatively correlated with recombination rate across species. This prediction was tested by a comprehensive statistical analysis of inversion size and recombination map length in 12 Diptera species for which appropriate data are available. We found that (1) there is a wide variation in recombination map length among species; (2) physical length of successful inversions varies greatly among species and is inversely correlated with the species recombination map length; and (3) neither the among-species variation in inversion length nor the correlation are observed in unsuccessful inversions. The clear differences between successful and unsuccessful inversions point to natural selection as the most likely explanation for our results. Presumably the selective advantage of an inversion increases with its length, but so does its detrimental effect on fertility due to double crossovers. Our analysis provides the strongest and most extensive evidence in favor of the notion that the adaptive value of inversions stems from their effect on recombination.     

The problem of movelength and turn definition in analysis of orientation data.

This study examines the analysis of arthropod orientation data. Three problems are discussed: (1) dealing with time as it applies to spatial data, (2) determining the appropriate movelength to be used in collecting and in analyzing data, and (3) defining a turn, to discriminate between "gait noise" and course changes. The main objective is to determine the solution to defining the most appropriate movelength for comparisons between variables and between species. The technique described here for selecting the appropriate movelength that has relevance to both the locomotory rate of the animal and its body length, reduces variation resulting from lateral translational movements, prevents the use of movelengths that lead to artifactual or unrealistic turning values per move, and permits comparisons of species and individuals under various stimulus conditions.