Can patterns of spatial autocorrelation reveal population processes? An analysis with the fire salamander

Spatial autocorrelation (SAC) is often observed in species distribution data, and can be caused by exogenous, autocorrelated factors determining species distribution, or by endogenous population processes determining clustering such as dispersal. However, it remains debated whether SAC patterns can actually reveal endogenous processes. We reviewed studies measuring dispersal of the salamander Salamandra salamandra, to formulate a priori hypotheses on the scale at which dispersal is expected to determine population distribution. We then tested the hypotheses by analysing SAC in distribution data, and evaluating whether controlling for the effect of environmental variables can reveal endogenous processes. We surveyed 565 streams to obtain species distribution data; we also recorded landscape and microhabitat features known to affect the species. We used multiple approaches to tease apart endogenous and exogenous SAC: the analysis of residuals of logistic regression models considering different environmental variables; the analysis of eigenvectors extracted by several implementations of spatial eigenvector mapping. In capture–mark–recapture studies, 98% of individuals moved 500 m or less. Both species distribution and environmental features were strongly autocorrelated. The residuals of logistic regression relating species to environmental variables were autocorrelated at distances up to 500 m; analyses considering different sets of environmental variables, or assuming non‐linear species habitat relationships, yielded identical results. The results of spatial eigenvector mapping strongly depended on the matrix of distances used. Nevertheless, the eigenvectors of models with best fit were autocorrelated at distances up to 200–500 m. The concordance between multiple approaches suggests that 500 m is the scale at which dispersal connects breeding localities, increasing probability of occurrence. If exogenous variables are correctly identified, the analysis of SAC can provide important insights on endogenous population processes, such as the flow of individuals. SAC analysis can also provide important information for conservation, as the existence of metapopulations or population networks is essential for long term persistence of amphibians.     

Where does fission yeast sit on the tree of life?

The budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe are as different from each other as either is from animals: their ancestors separated about 420 to 330 million years ago. Now that S. pombe is poised to join the post-genome era, its evolutionary position should become much clearer.     

The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?

It is a basis of darwinian evolution that the microevolutionary mechanisms that can be studied in the present are sufficient to account for macroevolution. However, this idea needs to be tested explicitly, as highlighted here by the example of the superceding of dinosaurs and pterosaurs by birds and placental mammals that occurred near the Cretaceous/Tertiary boundary approximately 65 million years ago. A major problem for testing the sufficiency of microevolutionary processes is that independent ideas (such as the existence of an extraterrestrial impact, and the extinction of dinosaurs) were linked without the evidence for each idea being evaluated separately. Here, we suggest and discuss five testable models for the times and divergences of modern mammals and birds. Determination of the model that best represents these events will enable the role of microevolutionary mechanisms to be evaluated. The question of the sufficiency of microevolutionary processes for macroevolution is solvable, and available evidence supports an important role for biological processes in the initial decline of dinosaurs and pterosaurs.     

Is the microbial tree of life verificationist?

The field of microbial phylogenetics has questioned the feasibility of using a tree‐like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree‐like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree‐like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.     

What drives the evolution of body size in ectotherms? A global analysis across the amphibian tree of life

Aim

The emergence of large-scale patterns of animal body size is the central expectation of a wide range of (macro)ecological and evolutionary hypotheses. The drivers shaping these patterns include climate (e.g. Bergmann's rule), resource availability (e.g. ‘resource rule’), biogeographic settings and niche partitioning (e.g. adaptive radiation). However, these hypotheses often make opposing predictions about the trajectories of body size evolution. Therefore, whether underlying drivers of body size evolution can be identified remains an open question. Here, we employ the most comprehensive global dataset of body size in amphibians, to address multiple hypotheses that predict patterns of body size evolution based on climatic factors, ecology and biogeographic settings to identify underlying drivers and their generality across lineages.

Location

Global.

Time Period

Present.

Major Taxa Studied

Amphibians.

Methods

Using a global dataset spanning 7270 (>87% of) species of Anura, Caudata and Gymnophiona, we employed phylogenetic Bayesian modelling to test the roles of climate, resource availability, insularity, elevation, habitat use and diel activity on body size.

Results

Only climate and elevation drive body size patterns, and these processes are order-specific. Seasonality in precipitation and in temperature predict body size clines in anurans, whereas caecilian body size increases with aridity. However, neither of these drivers explained variation in salamander body size. In both anurans and caecilians, size increases with elevational range and with midpoint elevation in caecilians only. No effects of mean temperature, resource abundance, insularity, time of activity or habitat use were found.

Main Conclusions

Precipitation and temperature seasonality are the dominant climatic drivers of body size variation in amphibians overall. Bergmann's rule is consistently rejected, and so are other alternative hypotheses. We suggest that the rationale sustaining existing macroecological rules of body size is unrealistic in amphibians and discuss our findings in the context of the emerging hypothesis that climate change can drive body size shifts.     

Are the fusion processes involved in birth, life and death of the cell depending on tilted insertion of peptides into membranes?

Various peptide segments have been modeled as asymmetric amphipathic alpha-helices. Theoretical calculations have shown that they insert obliquely into model membranes. They have been named "tilted peptides". Molecular modeling results reported here also evidence the presence of tilted peptides in ADM-1 protein of Caenorhabditis elegans that may be involved in fusion events, in meltrin alpha, a protein implicated in myoblast fusion, in hemagglutinin of influenza virus, in the E2 glycoprotein of rubella virus, in the S protein of hepatitis B virus, in a subdomain of Ebola virus and in the malaria CS protein. Experimental results have indicated that tilted peptide fragments may be involved in cellular life events like sperm-egg fecondation, muscle development, protein translocation through signal sequences and cellular death caused by viral infection or parasite infestation. We speculate that membrane destabilization by these tilted peptides may be an important common step in life processes involving fusion phenomena.     

Computational analysis of the oscillatory dynamics in the processes of CO₂ assimilation and photorespiration

The computational analysis of the model system consisting of the processes of CO₂ assimilation and photorespiration shows the appearance of sustained oscillations in the system which might reflect their presence in photosynthesizing cells. Concentrations of CO₂ and O₂ oscillate in opposite phases causing Rubisco switching continuously between the carboxylase (CO₂ assimilation) and the oxygenase (photorespiration) reactions. The results of modeling are consistent with carbon isotopic and other observed data. They show that the oscillation period varies from about 1 s to 3 s depending on the values of parameters taken. Too high concentrations of O₂ suppress the oscillations.     

Do landscape processes predict phylogeographic patterns in the wood frog?

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high-resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape-free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.     

A spatial model of tree α-diversity and tree density for the Amazon

Large-scale patterns of Amazonian biodiversity have until now been obscured by a sparse and scattered inventory record. Here we present the first comprehensive spatial model of tree -diversity and tree density in Amazonian rainforests, based on the largest-yet compilation of forest inventories and bolstered by a spatial interpolation technique that allows us to estimate diversity and density in areas that have never been inventoried. These data were then compared to continent-wide patterns of rainfall seasonality. We find that dry season length, while only weakly correlated with average tree -diversity, is a strong predictor of tree density and of maximum tree -diversity. The most diverse forests for any given DSL are concentrated in a narrow latitudinal band just south of the equator, while the least diverse forests for any given DSL are found in the Guayana Shield and Amazonian Bolivia. Denser forests are more diverse than sparser forests, even when we used a measure of diversity that corrects for sample size. We propose that rainfall seasonality regulates tree -diversity and tree density by affecting shade tolerance and subsequently the number of different functional types of trees that can persist in an area.     

Age-specific life history tactics in organisms with determinate growth: Optimal models for non-optimal behavior?

Among organisms with determinate growth, optimization models predict that reproductive effort should increase as individuals approach old age, but the assumptions of these models may be inappropriate because the senescence that generates the necessary selective pressure may be not itself be optimal. Population genetics models were constructed to examine whether genes for age-specific changes in reproductive effort could invade a population in which senescence was maintained at equilibrium levels by a balance between mutation and selection. In asexually reproducing organisms, it was found that strategies of increasing reproductive effort could not normally invade the population. In sexually reproducing organisms, however, recombination was found to be important and genes for age-specific changes in effort could spread in the population under most circumstances.     

A barcode of life database for the Cephalopoda? Considerations and concerns

The concept of a Barcode of Life Database (BoLD) for the Class Cephalopoda (Phylum Mollusca) was introduced at the Cephalopod International Advisory Council (CIAC) symposium in Hobart, Australia, February 2006. This suggestion was met with significant interest, concern and debate. This review attempts to describe the concept of the BoLD initiative and to outline considerations and concerns specific to a cephalopod BoLD. Jan M. Strugnell and Annie R. Lindgren contributed equally to this work.     

A comparative analysis of the molecular genetic processes in the pathogenesis of psoriasis and Crohn’s disease

Molecular Biology - A comparative bioinformatics analysis of the molecular genetic processes in the pathogenesis of multifactorial diseases—psoriasis and Crohn’s disease—was...     

The tree of life and the rock of ages: Are we getting better at estimating phylogeny?

In a recent paper,(1) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad "black box" science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating "yardstick" may be more appropriate for some groups than others.     

Diversity of the Southeast Asian leaf turtle genus Cyclemys: how many leaves on its tree of life?

In the present study, we use mtDNA sequence data (cyt b gene) in combination with nuclear DNA sequences (C-mos, Rag2 genes, R35 intron), nuclear genomic fingerprints (ISSR) and morphological data to reveal species diversity within the Southeast Asian leaf turtle genus Cyclemys , a morphologically difficult group comprising cryptic species. Two morphologically distinct major groupings exist, a yellow-bellied species group with three taxa ( Cyclemys atripons , C. dentata , C. pulchristriata ) and a dark-bellied species group. The latter contains besides the morphologically variable C. oldhamii three additional new species ( C. enigmatica n. sp., C. fusca n. sp., C. gemeli n. sp.). According to mtDNA data, C. fusca and C. gemeli constitute with high support the sister group of a clade comprising all other species, indicating that the dark-bellied species are not monophyletic, despite morphological similarity. mtDNA sequences of C. enigmatica , being highly distinct in nuclear genomic markers, do not differ from the sympatric C. dentata , suggesting that the original mitochondrial genome of C. enigmatica was lost due to introgressive hybridization. Morphological discrimination of Cyclemys species is possible using multivariate methods. However, gross morphology of most dark-bellied species on the one hand and of C. atripons and C. pulchristriata on the other is so similar that reliable species determination is only possible when genetic markers are used. The high diversity within Cyclemys requires revision of the IUCN Red List Categories for leaf turtles because the former assessment was based on the wrong assumption that in the entire range of the genus occurs only a single species.