Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees

MOTIVATION: In the maximum parsimony (MP) method, the tree requiring the minimum number of changes (discrepancy) to explain the given set of DNA or amino acid sequences is chosen to represent their evolutionary relationships. To find the MP tree, the branch-and-bound algorithm is normally used. For a partial phylogenetic-tree (one that has a subset of the organisms) the traditional algorithm assigns a cost equal to the discrepancy of the partial phylogenetic-tree. We propose a single column discrepancy heuristic which increases this cost by predicting a minimum additional discrepancy needed to attach the sequences yet to be added to the partial phylogenetic-tree. A dynamic Max-mini order of sequence addition is also proposed to quickly terminate branch-and-bound search paths that are guaranteed to lead to suboptimal solutions. RESULTS: We studied the running time of 47 problems generated from 17 data sets. The use of single column discrepancy heuristic speeded up the computation to 2.4-fold for static and 18.2-fold for dynamic search order. The improvement appeared to increase exponentially with the number of sequences. The proposed strategies are also likely to be useful in speeding up the MP tree search using heuristic searches that are based on branch-and-bound-like algorithms.CONTACT: s.kumar@asu.edu     

Biodiversity and ecosystem productivity: implications for carbon storage

Recent experiments have found that Net Primary Productivity (NPP) can often be a positive saturating function of plant species and functional diversity. These findings raised the possibility that more diverse ecosystems might store more carbon as a result of increased photosynthetic inputs. However, carbon inputs will not only remain in plant biomass, but will be translocated to the soil via root exudation, fine root turnover, and litter fall. Thus, we must consider not just plant productivity (NPP), but also net productivity of the whole ecosystem (NEP), which itself measures net carbon storage. We currently know little about how plant diversity could influence soil processes that return carbon back to the atmosphere, such as heterotrophic respiration and decomposition of organic matter. Nevertheless, it is clear that any effects on such processes could make NPP a poor predictor of whole-ecosystem productivity, and potentially the ability of the ecosystem to store carbon. We examine the range of mechanisms by which plant diversity could influence net ecosystem productivity, incorporating processes involved with carbon uptake (productivity), loss (autotrophic and heterotrophic respiration), and residence time within the system (decomposition rate). Understanding the relationship between plant diversity and ecosystem carbon dynamics must be made a research priority if we wish to provide information relevant to global carbon policy decisions. This goal is entirely feasible if we utilize some basic methods for measuring the major fluxes of carbon into and out of the ecosystem.     

Mutualism fails when climate response differs between interacting species

Successful species interactions require that both partners share a similar cue. For many species, spring warming acts as a shared signal to synchronize mutualist behaviors. Spring flowering plants and the ants that disperse their seeds respond to warming temperatures so that ants forage when plants drop seeds. However, where warm‐adapted ants replace cold‐adapted ants, changes in this timing might leave early seeds stranded without a disperser. We investigate plant seed dispersal south and north of a distinct boundary between warm‐ and cold‐adapted ants to determine if changes in the ant species influence local plant dispersal. The warm‐adapted ants forage much later than the cold‐adapted ants, and so we first assess natural populations of early and late blooming plants. We then transplant these plants south and north of the ant boundary to test whether distinct ant climate requirements disrupt the ant–plant mutualism. Whereas the early blooming plant's inability to synchronize with the warm‐adapted ant leaves its populations clumped and patchy and its seedlings clustered around the parents in natural populations, when transplanted into the range of the cold‐adapted ant, effective seed dispersal recovers. In contrast, the mutualism persists for the later blooming plant regardless of location because it sets seed later in spring when both warm‐ and cold‐adapted ant species forage, resulting in effective seed dispersal. These results indicate that the climate response of species interactions, not just the species themselves, is integral in understanding ecological responses to a changing climate. Data linking phenological synchrony and dispersal are rare, and these results suggest a viable mechanism by which a species' range is limited more by biotic than abiotic interactions – despite the general assumption that biotic influences are buried within larger climate drivers. These results show that biotic partner can be as fundamental a niche requirement as abiotic resources.     

Predicting the timing of maturational spurts in skeletal age

Measures of maturity provide windows into the timing and tempo of childhood growth and maturation. Delayed maturation in a single child, or systemically in a population, can result from either genetic or environmental factors. In terms of the skeleton, delayed maturation may result in short stature or indicate another underlying issue. Thus, prediction of the timing of a maturational spurt is often desirable in order to determine the likelihood that a child will catch up to their chronological age peers. Serial data from the Fels Longitudinal Study were used to predict future skeletal age conditional on current skeletal age and to predict the timing of maturational spurts. For children who were delayed relative to their chronological age peers, the likelihood of catch‐up maturation increased through the average age of onset of puberty and decreased prior to the average age of peak height velocity. For boys, the probability of an imminent maturational spurt was higher for those who were less mature. For girls aged 11 to 13 years, however, this probability was higher for those who were more mature, potentially indicating the presence of a skeletal maturation plateau between multiple spurts. The prediction model, available on the web, is most relevant to children of European ancestry living in the Midwestern US. Our model may also provide insight into the tempo of maturation for children in other populations, but must be applied with caution if those populations are known to have high burdens of environmental stressors not typical of the Midwestern US. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Mapping macroecology

Although macroecology arose from geographical ecology, it has diverted from a geographical perspective. At present, most macroecological studies use a statistical approach that adopts an 'individual species focus' and relies on comparisons between species to test for broad-scale ecological patterns. Sometimes, space is included as part of the analysis, but almost always in a single dimension. In both situations, observed relationships are depicted using bivariate scatter-plots. We argue that current macroecological approaches may interfere with our perception of patterns and have important implications for their biological interpretation. We use the literature concerned with spatial variation in the range sizes of species (Rapoport's rule) to illustrate our point of view. Given the current lack of maps actually showing the patterns we are trying to explain, we contend that macroecology could benefit greatly by returning to its geographical roots, at least when data contain spatial structure.     

A catastrophic meltwater flood event and the formation of the Hudson Shelf Valley

The Hudson Shelf Valley (HSV) is the largest physiographic feature on the U.S. mid-Atlantic continental shelf. The 150-km long valley is the submerged extension of the ancestral Hudson River Valley that connects to the Hudson Canyon. Unlike other incised valleys on the mid-Atlantic shelf, it has not been infilled with sediment during the Holocene. Analyses of multibeam bathymetry, acoustic backscatter intensity, and high-resolution seismic reflection profiles reveal morphologic and stratigraphic evidence for a catastrophic meltwater flood event that formed the modern HSV. The valley and its distal deposits record a discrete flood event that carved 15-m high banks, formed a 120-km² field of 3- to 6-m high bedforms, and deposited a subaqueous delta on the outer shelf. The HSV is inferred to have been carved initially by precipitation and meltwater runoff during the advance of the Laurentide Ice Sheet, and later by the drainage of early proglacial lakes through stable spillways. A flood resulting from the failure of the terminal moraine dam at the Narrows between Staten Island and Long Island, New York, allowed glacial lakes in the Hudson and Ontario basins to drain across the continental shelf. Water level changes in the Hudson River basin associated with the catastrophic drainage of glacial lakes Iroquois, Vermont, and Albany around 11,450 ¹⁴C year BP (∼ 13,350 cal BP) may have precipitated dam failure at the Narrows. This 3200 km³ discharge of freshwater entered the North Atlantic proximal to the Gulf Stream and may have affected thermohaline circulation at the onset of the Intra-Allerød Cold Period. Based on bedform characteristics and fluvial morphology in the HSV, the maximum freshwater flux during the flood event is estimated to be ∼ 0.46 Sv for a duration of ∼ 80 days.     

Mechanisms of acrolein-induced myocardial dysfunction: implications for environmental and endogenous aldehyde exposure

Aldehydes are ubiquitous pollutants generated during the combustion of organic materials and are present in air, water, and food. Several aldehydes are also endogenous products of lipid peroxidation and by-products of drug metabolism. Despite well-documented high reactivity of unsaturated aldehydes, little is known regarding their cardiovascular effects and their role in cardiac pathology. Accordingly, we examined the myocardial effects of the model unsaturated aldehyde acrolein. In closed-chest mice, intravenous acrolein (0.5 mg/kg) induced rapid but reversible left ventricular dilatation and dysfunction. In mouse myocytes, micromolar acrolein acutely depressed myofilament Ca(2+) responsiveness without altering catecholamine sensitivity, similar to the phenotype of stunned myocardium. Immunoblotting revealed increased acrolein-protein adducts and protein-carbonyls in both acrolein-exposed myocardium (1.8-fold increase, P < 0.002) and myocytes (6.4-fold increase, P < 0.02). Both the contractile dysfunction and adduct formation were markedly attenuated by pretreatment with the thiol donor N-acetylcysteine (5 mM). Two-dimensional gel electrophoresis and mass-assisted laser desorption/ionization time-of-flight mass spectrometry analysis revealed two groups of adducted proteins, sarcomeric/cytoskeletal proteins (cardiac alpha-actin, desmin, myosin light polypeptide 3) and energy metabolism proteins (mitochondrial creatine kinase-2, ATP synthase), indicating site-specific protein modification that was confirmed by immunohistochemical colocalization. We conclude that direct exposure to acrolein induces selective myofilament impairment, which may be, in part, related to the modification of proteins involved in myocardial contraction and energy metabolism. Myocardial dysfunction induced by acrolein and related aldehydes may be symptomatic of toxicological states associated with ambient or occupational exposures or drug toxicity. Moreover, aldehydes such as acrolein may mediate cardiac dysfunction in pathologies characterized by high-oxidative stress.     

Neogenin: A multi-functional receptor regulating diverse developmental processes

Neogenin, a close relative of the axon guidance receptor Deleted in Colorectal Cancer (DCC), has been shown to be a receptor for members of the Netrin and Repulsive Guidance Molecule (RGM) families. While Netrin-1-Neogenin interactions result in a chemoattractive axon guidance response, the interaction between Neogenin and RGMa induces a chemorepulsive response. Evidence is now accumulating that Neogenin is a multi-functional receptor regulating many diverse developmental processes, including neural tube and mammary gland formation, myogenesis and angiogenesis. Little is known of the function of Neogenin in the adult, however, a novel role in the regulation of iron homeostasis is now emerging. While the signal transduction pathways activated by Neogenin are poorly understood, it is clear that the functional outcome of Neogenin activation, at least in the embryo, depends on both the developmental context as well as the nature of the ligand.     

Sungear: interactive visualization and functional analysis of genomic datasets

Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY: A live online version of Sungear can be found at http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi