Segregating the Effects of Seed Traits and Common Ancestry of Hardwood Trees on Eastern Gray Squirrel Foraging Decisions

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27–73%), and combined effects of seed traits and phylogeny of hardwood trees (5–55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 “global” axes of traits that were phylogenetically autocorrelated at the family and genus level and a third “local” axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30–76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.     

Global Value Trees

The fragmentation of production across countries has become an important feature of the globalization in recent decades and is often conceptualized by the term “global value chains” (GVCs). When empirically investigating the GVCs, previous studies are mainly interested in knowing how global the GVCs are rather than how the GVCs look like. From a complex networks perspective, we use the World Input-Output Database (WIOD) to study the evolution of the global production system. We find that the industry-level GVCs are indeed not chain-like but are better characterized by the tree topology. Hence, we compute the global value trees (GVTs) for all the industries available in the WIOD. Moreover, we compute an industry importance measure based on the GVTs and compare it with other network centrality measures. Finally, we discuss some future applications of the GVTs.     

Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.     

Searching for the Oldest Baobab of Madagascar: Radiocarbon Investigation of Large Adansonia rubrostipa Trees

We extended our research on the architecture, growth and age of trees belonging to the genus Adansonia, by starting to investigate large individuals of the most widespread Malagasy species. Our research also intends to identify the oldest baobabs of Madagascar. Here we present results of the radiocarbon investigation of the two most representative Adansonia rubrostipa (fony baobab) specimens, which are located in south-western Madagascar, in the Tsimanampetsotse National Park. We found that the fony baobab called “Grandmother” consists of 3 perfectly fused stems of different ages. The radiocarbon date of the oldest sample was found to be 1136 ± 16 BP. We estimated that the oldest part of this tree, which is mainly hollow, has an age close to 1,600 yr. This value is comparable to the age of the oldest Adansonia digitata (African baobab) specimens. By its age, the Grandmother is a major candidate for the oldest baobab of Madagascar. The second investigated specimen, called the “polygamous baobab”, consists of 6 partially fused stems of different ages. According to dating results, this fony baobab is 1,000 yr old. This research is the first investigation of the structure and age of Malagasy baobabs.     

Solutions for transients in arbitrarily branching cables: II. Voltage clamp theory

Analytical solutions are derived for arbitrarily branching passive neurone models with a soma and somatic shunt, for synaptic inputs and somatic voltage commands, for both perfect and imperfect somatic voltage clamp. The solutions are infinite exponential series. Perfect clamp decouples different dendritic trees at the soma: each exponential component exists only in one tree; its time constant is independent of stimulating and recording position within the tree; its amplitude is the product of a factor constant over that entire tree and factors dependent on stimulating and recording positions. Imperfect clamp to zero is mathematically equivalent to voltage recording with a shunt. As the series resistance increases, different dendritic trees become more strongly coupled. A number of interesting response symmetries are evident. The solutions reveal parameter dependencies, including an insensitivity of the early parts of the responses to specific membrane resistivity and somatic shunt, and an approximately linear dependence of the slower time constants on series resistance, for small series resistances. The solutions are illustrated using a “cartoon” representation of a CA1 pyramidal cell and a two-cylinder + soma model.     

Tree Diversity Limits the Impact of an Invasive Forest Pest

The impact of invasive herbivore species may be lower in more diverse plant communities due to mechanisms of associational resistance. According to the “resource concentration hypothesis” the amount and accessibility of host plants is reduced in diverse plant communities, thus limiting the exploitation of resources by consumers. In addition, the “natural enemy hypothesis” suggests that richer plant assemblages provide natural enemies with more complementary resources and habitats, thus promoting top down regulation of herbivores. We tested these two hypotheses by comparing crown damage by the invasive Asian chestnut gall wasp (Dryocosmus kuriphilus) on chestnut trees (Castanea sativa) in pure and mixed stands in Italy. We estimated the defoliation on 70 chestnut trees in 15 mature stands sampled in the same region along a gradient of tree species richness ranging from one species (chestnut monocultures) to four species (mixtures of chestnut and three broadleaved species). Chestnut defoliation was significantly lower in stands with higher tree diversity. Damage on individual chestnut trees decreased with increasing height of neighboring, heterospecific trees. These results suggest that conservation biological control method based on tree species mixtures might help to reduce the impact of the Asian chestnut gall.     

Genealogical Trees of Scientific Papers

Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a “dying” paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing “offspring”. Practically, this might be used to trace the successive published milestones of a research field.     

Darwin's Manufactory Hypothesis Is Confirmed and Predicts the Extinction Risk of Extant Birds

In the Origin of Species Darwin hypothesized that the “manufactory” of species operates at different rates in different lineages and that the richness of taxonomic units is autocorrelated across levels of the taxonomic hierarchy. We confirm the manufactory hypothesis using a database of all the world''s extant avian subspecies, species and genera. The hypothesis is confirmed both in correlations across all genera and in paired comparisons controlling for phylogeny. We also find that the modern risk of extinction, as measured by “Red List” classifications, differs across the different categories of genera identified by Darwin. Specifically, species in “manufactory” genera are less likely to be threatened, endangered or recently extinct than are “weak manufactory” genera. Therefore, although Darwin used his hypothesis to investigate past evolutionary processes, we find that the hypothesis also foreshadows future changes to the evolutionary tree.     

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes

How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.     

Applicants to Canadian Medical Schools for 1966-67

An examination of applicants to Canadian medical schools for 1966-67 revealed that 4534 applications were received for the approximately 974 available places. The number of Canadian applications was 2866 and these were made by 1815 individual applicants, an increase of 48 over 1965-66. United States applicants declined from 1143 to 1013.Evaluations made by the schools concerning the acceptability of the Canadian applicants disclosed that 55 applicants who rated as “acceptable” by one or more schools failed to gain admission to any medical school in 1966-67 (as compared to 36 in 1965-66). However, of those applicants who did find a place 76 were evaluated as “marginal” or “unacceptable”, while another 126 were rated as “acceptable” by one school but “marginal” and/or “acceptable” by one or more other schools.These results were interpreted to imply that the Canadian medical schools were still experiencing difficulty in attracting well-qualified applicants for study in medicine.     

Canadian Applicants to Medical Schools in Canada for 1965-66

An examination of applicants to Canadian medical schools for 1965-66 revealed that 4660 applications were received by the 12 schools for approximately 900 places available; 2852 of these were from Canadians, but because many applicants applied to more than one school, these 2852 applications represented only 1767 individuals. Evaluations made by the schools concerning the acceptability of these applicants showed that only 36 persons rated as “acceptable” by one or more schools failed to gain admission to any Canadian school for 1965-66. Furthermore, 66 “marginal” applicants were accepted, as were 130 multiple applicants who were rated as “acceptable” by one school but “marginal” and/or “unacceptable” by one or more other schools. Of the 464 multiple applicants, only 40% received the same evaluation from all schools to which they applied. If those multiple applicants who were rated as acceptable by all schools to which they applied are added to single applicants rated as acceptable, the pool of these clearly acceptable candidates (40% of all Canadian applicants) is sufficient only to fill 78% of places available. It was thus concluded that it is erroneous to speak of a surplus of well-qualified Canadian applicants at the present time.     

Memory for Expectation-Violating Concepts: The Effects of Agents and Cultural Familiarity

Previous research has shown that ideas which violate our expectations, such as schema-inconsistent concepts, enjoy privileged status in terms of memorability. In our study, memory for concepts that violate cultural (cultural schema-level) expectations (e.g., “illiterate teacher”, “wooden bottle”, or “thorny grass”) versus domain-level (ontological) expectations (e.g., “speaking cat”, “jumping maple”, or “melting teacher”) was examined. Concepts that violate cultural expectations, or counter-schematic, were remembered to a greater extent compared with concepts that violate ontological expectations and with intuitive concepts (e.g., “galloping pony”, “drying orchid”, or “convertible car”), in both immediate recall, and delayed recognition tests. Importantly, concepts related to agents showed a memory advantage over concepts not pertaining to agents, but this was true only for expectation-violating concepts. Our results imply that intuitive, everyday concepts are equally attractive and memorable regardless of the presence or absence of agents. However, concepts that violate our expectations (cultural-schema or domain-level) are more memorable when pertaining to agents (humans and animals) than to non-agents (plants or objects/artifacts). We conclude that due to their evolutionary salience, cultural ideas which combine expectancy violations and the involvement of an agent are especially memorable and thus have an enhanced probability of being successfully propagated.     

Categorical Biases in Perceiving Spatial Relations

We investigate the effect of spatial categories on visual perception. In three experiments, participants made same/different judgments on pairs of simultaneously presented dot-cross configurations. For different trials, the position of the dot within each cross could differ with respect to either categorical spatial relations (the dots occupied different quadrants) or coordinate spatial relations (the dots occupied different positions within the same quadrant). The dot-cross configurations also varied in how readily the dot position could be lexicalized. In harder-to-name trials, crosses formed a “+” shape such that each quadrant was associated with two discrete lexicalized spatial categories (e.g., “above” and “left”). In easier-to-name trials, both crosses were rotated 45° to form an “×” shape such that quadrants were unambiguously associated with a single lexicalized spatial category (e.g., “above” or “left”). In Experiment 1, participants were more accurate when discriminating categorical information between easier-to-name categories and more accurate at discriminating coordinate spatial information within harder-to-name categories. Subsequent experiments attempted to down-regulate or up-regulate the involvement of language in task performance. Results from Experiment 2 (verbal interference) and Experiment 3 (verbal training) suggest that the observed spatial relation type-by-nameability interaction is resistant to online language manipulations previously shown to affect color and object-based perceptual processing. The results across all three experiments suggest that robust biases in the visual perception of spatial relations correlate with patterns of lexicalization, but do not appear to be modulated by language online.     

Understanding 3D structural complexity of individual Scots pine trees with different management history

Tree functional traits together with processes such as forest regeneration, growth, and mortality affect forest and tree structure. Forest management inherently impacts these processes. Moreover, forest structure, biodiversity, resilience, and carbon uptake can be sustained and enhanced with forest management activities. To assess structural complexity of individual trees, comprehensive and quantitative measures are needed, and they are often lacking for current forest management practices. Here, we utilized 3D information from individual Scots pine (Pinus sylvestris L.) trees obtained with terrestrial laser scanning to, first, assess effects of forest management on structural complexity of individual trees and, second, understand relationship between several tree attributes and structural complexity. We studied structural complexity of individual trees represented by a single scale‐independent metric called “box dimension.” This study aimed at identifying drivers affecting structural complexity of individual Scots pine trees in boreal forest conditions. The results showed that thinning increased structural complexity of individual Scots pine trees. Furthermore, we found a relationship between structural complexity and stem and crown size and shape as well as tree growth. Thus, it can be concluded that forest management affected structural complexity of individual Scots pine trees in managed boreal forests, and stem, crown, and growth attributes were identified as drivers of it.     

Endless forms most stupid,icky, and small: The preponderance of noncharismatic invertebrates as integral to a biologically sound view of life

Big, beautiful organisms are useful for biological education, increasing evolution literacy, and biodiversity conservation. But if educators gloss over the ubiquity of streamlined and miniaturized organisms, they unwittingly leave students and the public vulnerable to the idea that the primary evolutionary plot of every metazoan lineage is “progressive” and "favors" complexity. We show that simple, small, and intriguingly repulsive invertebrate animals provide a counterpoint to misconceptions about evolution. Our examples can be immediately deployed in biology courses and outreach. This context emphasizes that chordates are not the pinnacle of evolution. Rather, in the evolution of animals, miniaturization, trait loss, and lack of perfection are at least as frequent as their opposites. Teaching about invertebrate animals in a “tree thinking” context uproots evolution misconceptions (for students and the public alike), provides a mental scaffold for understanding all animals, and helps to cultivate future ambassadors and experts on these little‐known, weird, and fascinating taxa.     

Horizontal Gene Transfer and the History of Life

Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.The discovery of the existence of prokaryotic microbes dates back more than 300 years. Since then, our picture of our distant microscopic relatives has undergone several revolutions: from being the living “proofs” of the existence of spontaneous generation, they became later the “archaic” representatives of our distant ancestors, to finally be legitimately recognized as exceptionally diverse organisms, keystone to any ecosystem, including the most familiar and the most hostile environments on Earth. Similarly, although they were first seen as elementary and unbreakable bricks of life, they are now seen as genetically composite bodies, heavyweight champions of “gene robbery.” The most recent of these revolutions has indeed been the realization of their unparalleled ability to integrate genetic material coming from more or less evolutionarily distant organisms. This mechanism is called “horizontal gene transfer” as opposed to vertical transmission from mother to daughter cell.     

Optimization of Analytical Parameters for Inferring Relationships among Escherichia coli Isolates from Repetitive-Element PCR by Maximizing Correspondence with Multilocus Sequence Typing Data

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a “gold standard” to optimize the analytical parameters for inferring relationships among Escherichia coli isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles (“curve-based” methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were “band-sharing coefficient” methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among E. coli isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.     

Buffeted by harsh economic winds,medical schools turn a wary eye to the future

All parts of Canada''s health care system are facing fiscal pressures these days, but they are particularly great at Canada''s medical schools. However, Dr. David Hawkins of the Association of Canadian Medical Colleges is optimistic that all 16 of Canada''s medical schools will remain open, mainly because of the huge impact they have on health care in their local communities. “We don''t just turn out students — we raise the standard of health care in a whole community,” he says.     

Are our phylomorphospace plots so terribly tangled? An investigation of disorder in data simulated under adaptive and nonadaptive models

Contemporary methods for visualizing phenotypic evolution, such as phylomorphospaces, often reveal patterns which depart strongly from a naïve expectation of consistently divergent branching and expansion. Instead, branches regularly crisscross as convergence, reversals, or other forms of homoplasy occur, forming patterns described as “birds’ nests”, “flies in vials”, or less elegantly, “a mess”. In other words, the phenotypic tree of life often appears highly tangled. Various explanations are given for this, such as differential degrees of developmental constraint, adaptation, or lack of adaptation. However, null expectations for the magnitude of disorder or “tangling” have never been established, so it is unclear which or even whether various evolutionary factors are required to explain messy patterns of evolution. I simulated evolution along phylogenies under a number of varying parameters (number of taxa and number of traits) and models (Brownian motion, Ornstein–Uhlenbeck (OU)-based, early burst, and character displacement (CD)] and quantified disorder using 2 measures. All models produce substantial amounts of disorder. Disorder increases with tree size and the number of phenotypic traits. OU models produced the largest amounts of disorder—adaptive peaks influence lineages to evolve within restricted areas, with concomitant increases in crossing of branches and density of evolution. Large early changes in trait values can be important in minimizing disorder. CD consistently produced trees with low (but not absent) disorder. Overall, neither constraints nor a lack of adaptation is required to explain messy phylomorphospaces—both stochastic and deterministic processes can act to produce the tantalizingly tangled phenotypic tree of life.     

“Trees Live on Soil and Sunshine!”- Coexistence of Scientific and Alternative Conception of Tree Assimilation

Successful learning is the integration of new knowledge into existing schemes, leading to an integrated and correct scientific conception. By contrast, the co-existence of scientific and alternative conceptions may indicate a fragmented knowledge profile. Every learner is unique and thus carries an individual set of preconceptions before classroom engagement due to prior experiences. Hence, instructors and teachers have to consider the heterogeneous knowledge profiles of their class when teaching. However, determinants of fragmented knowledge profiles are not well understood yet, which may hamper a development of adapted teaching schemes. We used a questionnaire-based approach to assess conceptual knowledge of tree assimilation and wood synthesis surveying 885 students of four educational levels: 6^th graders, 10^th graders, natural science freshmen and other academic studies freshmen. We analysed the influence of learner’s characteristics such as educational level, age and sex on the coexistence of scientific and alternative conceptions. Within all subsamples well-known alternative conceptions regarding tree assimilation and wood synthesis coexisted with correct scientific ones. For example, students describe trees to be living on “soil and sunshine”, representing scientific knowledge of photosynthesis mingled with an alternative conception of trees eating like animals. Fragmented knowledge profiles occurred in all subsamples, but our models showed that improved education and age foster knowledge integration. Sex had almost no influence on the existing scientific conceptions and evolution of knowledge integration. Consequently, complex biological issues such as tree assimilation and wood synthesis need specific support e.g. through repeated learning units in class- and seminar-rooms in order to help especially young students to handle and overcome common alternative conceptions and appropriately integrate scientific conceptions into their knowledge profile.