Branch Widths Research Articles

Optimization of heat dissipation in novel design wavy channel heat sinks for better performance

This research presents a novel design in wavy channel heat sinks, crucial for the thermal management of electronic devices. The design features secondary branches with progressively decreasing spacing and a reduced channel height, enhancing flow mixing and uniform temperature distribution. The novelty of this research lies in the integration of a wavy channel, an innovative secondary branch pattern, lowered channel height, and optimized branch angles and widths. The study examines the impact of the design parameters across flow rates (0.004–0.014 kg/s) under a constant heat flux of 5.17 W/cm2. Key findings reveal that a 90-degree branch angle with a 1 mm width achieves a 5.27% temperature reduction compared to the basic wavy channel heat sinks, reducing the surface temperature by 1.4 °C over 45-degree configurations. Additionally, 45-degree and 90-degree configurations with a 1.5 mm width show pressure drop increases of 12.13% and 20.60%, respectively. Using factorial designs and response optimization, the study identifies an optimal configuration at a 90-degree angle and 2 mm width for a flow rate of 0.008 kg/s, balancing heat transfer enhancement, and hydraulic performance. This design marks a significant advancement in efficient and effective cooling technologies for electronic devices.

DSNUNet: An Improved Forest Change Detection Network by Combining Sentinel-1 and Sentinel-2 Images

The use of remote sensing images to detect forest changes is of great significance for forest resource management. With the development and implementation of deep learning algorithms in change detection, a large number of models have been designed to detect changes in multi-phase remote sensing images. Although synthetic aperture radar (SAR) data have strong potential for application in forest change detection tasks, most existing deep learning-based models have been designed for optical imagery. Therefore, to effectively combine optical and SAR data in forest change detection, this paper proposes a double Siamese branch-based change detection network called DSNUNet. DSNUNet uses two sets of feature branches to extract features from dual-phase optical and SAR images and employs shared weights to combine features into groups. In the proposed DSNUNet, different feature extraction branch widths were used to compensate for a difference in the amount of information between optical and SAR images. The proposed DSNUNet was validated by experiments on the manually annotated forest change detection dataset. According to the obtained results, the proposed method outperformed other change detection methods, achieving an F1-score of 76.40%. In addition, different combinations of width between feature extraction branches were analyzed in this study. The results revealed an optimal performance of the model at initial channel numbers of the optical imaging branch and SAR image branch of 32 and 8, respectively. The prediction results demonstrated the effectiveness of the proposed method in accurately predicting forest changes and suppressing cloud interferences to some extent.

Gracilaria parva sp. nov. (Gracilariales, Rhodophyta) a Diminutive Species from the Tropical Eastern Pacific

DNA sequencing of the plastid encoded rbcL gene supported by morpho-anatomical features reveals Gracilaria parva sp. nov. from Panama and Ecuador in the tropical eastern Pacific Ocean. In the rbcL phylogram, G. parva occurs in a clade sister to the western Atlantic species G. galatensis. Morphologically and anatomically, G. parva is distinguished from two similar, described tropical eastern Pacific species, G. brevis and G. veleroae by its small size, to 2.5 cm tall with branch widths mostly <2 mm occasionally to 4 mm, and by its two to three cell layered cortex. Gracilaria brevis and G. veleroae are taller, have wider branches, and a one cell layered cortex. DNA sequencing is needed to resolve the many diminutive species in the tropical eastern Pacific, particularly those occurring in turf communities. DNA sequencing of historical type specimens from the 19th and 20th centuries is also needed to correctly apply names in this region.

A study on buoyancy-driven maximum ceiling gas temperature of T-shaped bifurcated channel-like structure in fire environment

A study mainly concerning the fire-induced maximum ceiling smoke temperature in T-shaped bifurcated channel-like structure was conducted. A series of model-scale fire tests and full-scale numerical simulations were performed to obtain the maximum ceiling smoke temperature with various heat release rates and branch widths. Results shown that the branch could affect plume entrainment flow in vicinity of fire source. Flame plume would tilt to the proximal sidewall to some extent. With the increase of branch opening, flame plume tilt seems to be greater. The growth trend of central ceiling smoke temperature directly above fire source with burning time can be effectively characterized by power function (Ts∝n1tn2). In current research range of model structure scale and heat release rate, maximum ceiling smoke temperature of T-shaped bifurcated channel slightly decreases with the increase of dimensionless branch width. A corresponding empirical correlation for maximum ceiling smoke temperature in such fire scenario is proposed by associating dimensionless branch width and dimensionless heat release rate. The prediction of empirical correlation could be supported by current measured results in model-scale fire tests and full-scale numerical simulations, as well as the previous scholars' model-scale and full-scale data.

Shaping surfaces and interfaces of 2D materials on mica with intercalating water and ethanol

Interfaces between mica and graphene, as well as the transition metal dichalcogenides (TMDCs) MoS2 and WS2, were wetted with water and ethanol, and investigated employing scanning force microscopy and molecular dynamics (MD) simulations. Below 25% RH, water wets the graphene-mica interface with labyrinthine structures, exhibiting branch widths of about 50 nm for single layers of graphene, increasing to almost an order of magnitude more for four graphene layers. At mica-TMDC interfaces, water films exhibit a transition from labyrinthine to compact morphology upon going from single- to multi-layers of the TMDCs. Ethanol films show a compact morphology at all the interfaces, regardless of the number of 2D material layers on top. The film morphologies are attributed to an equilibrium between electrostatic repulsion of preferentially oriented molecular dipoles, and the line tension of the wetted areas, which is dominated by the deformation of the 2D materials at the edges of the wet areas. The compact front of the water wetting film under multilayers of TMDCs is attributed to a much larger bending stiffness of these materials than of graphene multilayers. The thickness dependent stiffness of the 2D materials may be employed to shape their surfaces from the nano- to the micrometer scale.

Simulation analysis of mixing in passive microchannel with fractal obstacles based on Murray's law

In this paper, we designed fractal obstacles according to Murray’s law and set them in a microchannel. We study the influence of the numbers of fractal obstacles, channel widths, branch widths, and the distance between fractal obstacles on mixing efficiency. The optimized micromixer has a high mixing efficiency of more than 90% at all velocities. This paper focuses on the analysis of the variation of mixing efficiency and pressure drop in the range of Reynolds number (Re) 0.1–150. The simulation results show that when the fluid velocity is low, the mixing efficiency of the fluids is mainly improved by molecular diffusion, when the fluid velocity is high, the microchannel with fractal obstacles can promote chaotic convection of the fluids and improve the mixing efficiency. The fractal structure based on Murray's law can be widely used in the design of passive micromixer.

A higher-order tensor voting-based approach for road junction detection and delineation from airborne LiDAR data

The location and delineation of road junctions produce valuable inputs for road network understanding and topology reconstruction; the results also serve as basic information for road construction planning, emergency rescue, and large-scale data registration. This study addresses fully automatic road junction detection and delineation from airborne lidar (or LiDAR – light detection and ranging) data. For this purpose, a higher-order tensor voting-based approach is developed, which can locate road junctions by identifying multidirectional features in encoded higher-order tensor models. This approach comprises three main steps. First, a roughness-enhanced Gabor filter is implemented to process both the lidar-derived intensity image and the normalized digital surface model to extract homogeneous elongated structural keypoints. Second, these keypoints are fed into a higher-order tensor voting algorithm to recognize road junction candidates. We modified the method for encoding higher-order tensor models to enable the algorithm to deal with both antipodal symmetric and nonsymmetric junctions. After a higher-order tensor decomposition, the number of road branches and their directions are obtained; road junction candidates were then located. Third, by matching the results with a geometric template, road junction delineation is performed to retrieve the junction center position and the road branch directions and widths. We tested our method in two study areas and assessed the quality of the results by comparing them with ground-truth data. The results proved the validity of this approach in both urban and semiurban scenarios. We also compared our method with other junction detection algorithms and analyzed the parameter influence of the approach to essential parameters.

Pedestrian merging behavior analysis: An experimental study

Merging flows involve complex interactions between pedestrians, which will restrict the efficiency of the evacuation process in emergency situations, such as fires. However, experimental research on merging behavior is limited. This paper describes pedestrian behavior in a merging channel where the branch flow joins the main flow at a junction area. The width of the main channel was fixed at 3.2m while the branch had a changeable value of 0.8m, 1.6m and 2.4m, respectively. Up to 295 university students took part in the experiments and all trajectories were extracted using the mean-shift algorithm. Lane formation was found downstream in the main channel and the increasing amplitude of the lane width formed by the branch flow became weaker with the increasing width of the branch channel. The saturated flow was approximately 4.9ped/s (1.5ped/m/s) and when the branch channel was 2.4m, the main and branch channel became mutual bottlenecks to each other. Moreover, microscopic characteristics of pedestrian interaction were analyzed. Velocity-position relationships with the 1.6m and 2.4m branch widths showed the velocity in the main channel decreased when pedestrians got close to the merging area and the velocity in the branch channel was suppressed significantly compared to that with the 0.8m branch. Density in the corner increased when the branch width increased and reached about 6ped/m2 when the branch width was 2.4m. What's more, pedestrian flow in the branch became jammed in this situation. The results can be used to calibrate pedestrian simulation models and improve public infrastructure design.

A radicle solution: morphology and biomechanics of the Eucalyptocrinites ‘root’ system

Eucalyptocrinites is one the most common and familiar mid-Palaeozoic crinoids and is the exemplar of a form with dendritic radicular holdfasts. American museums have hundreds of specimens of Eucalyptocrinites holdfasts from the Silurian Waldron Shale of Indiana and Kentucky, USA. The radix (‘root’) system of Eucalyptocrinites can be described as comprised of links (branches) that meet at nodes. Measured values include the x- and y-coordinates of the nodes, the distances of the nodes from the stem, the angles between branches, branch length and branch width. Rose diagrams show clearly that the root systems are not isotropic but have preferred orientations. Branch angles are highly variable, but cluster around 60 degrees. Branch lengths and distal branch widths are relatively constant, but branch width increases variably towards the column. The branching pattern can be modelled as a self-similar (‘fractal’) structure. Several specimens labelled as Eucalyptocrinites show a distinct fivefold symmetry without branching and very likely represent a different taxon. The Eucalyptocrinites radix system, along with the probably stiff dististele, most likely functioned as a rigid plate that resisted rotational forces due to currents acting on the crown. Upstream radicles experienced tension, whereas downstream roots were compressed. This force distribution may explain the observed anisotropies in radix morphology. The ‘roots’ of Eucalyptocrinites and other crinoids have long been compared with the root systems of plants. Although there are superficial similarities, there are fundamental differences.

Microelectrode bioimpedance analysis distinguishes basal and claudin-low subtypes of triple negative breast cancer cells.

Triple negative breast cancer (TNBC) is highly aggressive and has a poor prognosis when compared to other molecular subtypes. In particular, the claudin-low subtype of TNBC exhibits tumor-initiating/cancer stem cell like properties. Here, we seek to find new biomarkers to discriminate different forms of TNBC by characterizing their bioimpedance. A customized bioimpedance sensor with four identical branched microelectrodes with branch widths adjusted to accommodate spreading of individual cells was fabricated on silicon and pyrex/glass substrates. Cell analyses were performed on the silicon devices which showed somewhat improved inter-electrode and intra-device reliability. We performed detailed analysis of the bioimpedance spectra of four TNBC cell lines, comparing the peak magnitude, peak frequency and peak phase angle between claudin-low TNBC subtype represented by MDA-MB-231 and Hs578T with that of two basal cells types, the TNBC MDA-MB-468, and an immortalized non-malignant basal breast cell line, MCF-10A. The claudin-low TNBC cell lines showed significantly higher peak frequencies and peak phase angles than the properties might be useful in distinguishing the clinically significant claudin-low subtype of TNBC.

The Ediacaran macroalga Zhongbaodaophyton Chen et al. from South China

Wang, Y., Wang, Y., Du, W. & Xang, X., 13.2.2015. The Ediacaran macroalga Zhongbaodaophyton Chen et al. from South China. Alcheringa 39, xxx–xxx. ISSN 0311-5518Zhongbaodaophyton Chen et al. (including two species Z. crassa Chen et al. and Z. robustus Wang et al.) is an Ediacaran macroscopic genus in the Wenghui biota from black shales of the upper Doushantuo Formation (ca 551–593 Ma) in northeastern Guizhou, South China. Zhongbaodaophyton has an unequally dichotomous thallus and a robust holdfast, resembling phaeophytes in morphology; however, its cytological features are not determinable from the carbonaceous compression fossils. Its thallus bears at least nine photosynthetic branches, and its holdfast consists of a globose tuberous rhizome with many unbranched or dichotomous filamentous rhizoids. In addition, these Ediacaran macroalgal species bear pith in the stipe and tuberous rhizome, which is a key feature of phaeophytes. Based on the measurements of 129 Z. robustus specimens, the degree of branching is closely related to the thallus length, the stipe width, and the width ratio of two primary branches; and the stipe width is correlated with the thallus length, the two primary branch widths, and the first branching angle. The thallus grew primarily upward to enhance its competitiveness for sunlight and/or nutrient uptake in the Ediacaran marine ecosystem. A turning point toward reduced growth rates may have occurred in the life history of Z. robustus individuals (at the fourth or fifth axial bifurcation).Yue Wang [gzyuewang@126.com], School of Resources and Environments, Guizhou University, Guiyang 550003, PR China; Ye Wang [gboywangye@126.com] and Xunlian Wang [wxl@cugb.edu.cn], School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China; Wei Du [duwei@ea.c.u-tokyo.ac.jp], Department of Earth Science and Astronomy, The University of Tokyo, Tokyo 153-8902, Japan.

Unsorted homology within locus and species trees.

The concept of homology lies at the root of evolutionary biology. Since the seminal work of Fitch (1970), three main categories of homology relationships have been defined at the molecular level: orthology, paralogy, and xenology. In brief, if two gene copies arose by duplication they are paralogs, whereas if they arose through speciation they are orthologs. If one of them was transferred from a contemporaneous species, we call them xenologs (Supplementary Fig. S1 in Supplementary Material online, available at http://dx.doi.org/10.5061/dryad.87k57; see Gray and Fitch (1983); Fitch (2000)). Indeed, these terms were coined under a phylogenetic framework in which species were represented by single individuals, and as such they have remained very much intact during the last four decades—although particular cases within these categories have received specific names (Mindell and Meyer 2001). However, advances in sequencing technology have changed the field, and it is now very common to collect data sets containing multiple gene loci and/or multiple individuals per species. In general, such genome-wide data sets not only have unveiled extensive phylogenomic incongruence (Jeffroy et al. 2006; Salichos and Rokas 2013) but have brought back to the spotlight the consideration of how ancestral polymorphisms sort within populations (Edwards 2009). Altogether, phylogenomic data make imperative the explicit distinction between organismal and gene histories. Let us consider phylogenetic relationships at three different levels: species, loci, and gene copies (Fig. 1). The distinction between species/population trees and gene trees has been known for decades (Goodman et al. 1979; Pamilo and Nei 1988; Takahata 1989), whereas the introduction of locus trees into these models is very recent (Rasmussen and Kellis 2012). In brief, a species tree depicts the evolutionary history of the sampled organisms. In this case, the nodes represent speciation events, connected by branches that reflect the population history along these periods, and where their widths represent effective population size (Ne) and their lengths represent time (usually in years or number of generations). Apart from speciations, only evolutionary processes that affect species as a whole are represented at this level, like hybridization. Note that species trees are equivalent to population trees when the organismal units of interest are conspecific populations. In this case, the nodes of the population trees represent isolation events. In general, we will refer to “species” as any diverging, interbreeding group of individuals regardless of its taxonomic rank. On the other hand, a locus tree represents the evolutionary history of the sampled loci for a given gene family (see Rasmussen and Kellis 2012). Since the loci exist inside individuals evolving as part of a population, the locus tree is embedded within the species tree. In a locus tree, the nodes depict either genetic divergence due to speciation in the embedding species tree or locus-level events such as duplication, losses, or horizontal gene transfers, whereas the branch lengths and widths represent time and Ne, respectively. Here, we assume that the locuslevel events get immediately fixed in the population, so these Ne are equivalent to those in the species tree and are the same for every locus. Finally, a gene tree represents the evolutionary history of the sampled gene copies that evolve inside the locus tree. Gene tree nodes indicate coalescent events, which looking forward in time correspond to the process of DNA replication and divergence, and that can occur around the speciation time, well before (deep coalescence) or afterwards (migration in population trees). The branches of the gene tree usually represent amount of substitutions per site, and can also represent number of generations or other measures of time. Importantly, these three historical layers do not necessarily coincide. True species/population trees can differ from true locus trees due to gene duplications, losses, and/or horizontal gene transfers, whereas true gene trees can differ from their embedding locus and species trees if there is incomplete lineage sorting (ILS) (Maddison 1997; Page and Charleston 1997) (and migration in the case of population trees). In this regard,

Vibration reduction using biologically inspired topology optimization method: optimal stiffeners distribution on an acoustically excited plate

This paper presents the development of a biologically inspired method for topology optimization and its application to a vibration suppression problem. The proposed method is based on modeling the structure topology (distribution of stiffening ribs) by replicating the natural growth of dendritic structures, which are ramified branches as those e.g. in leaves or in insect wings. The test case is a plate excited by acoustic pressure. The multi-objectives topology optimization aims to reduce both the vibration amplitude and mass of the plate. Experimental tests are performed for baseline plate model validation and identification of acoustic excitation distribution. A set of solutions are designed by the proposed method and numerically compared with traditional optimization approaches, showing improved performances. Finally, in order to evaluate industrial applicability, the robustness of the solutions to uncertainty in branch widths is demonstrated.

Theoretical morphology of colonial meshworks in the Fenestrata (Bryozoa): modelling hydraulic-resistance constraints and minimum fenestrule widths

Ancient fenestrate bryozoans (Fenestellidae, Polyporidae) exhibit a range of fenestrule widths that can be investigated to gain insights about constraints on meshwork morphology. Theoretical morphospace analyses of branch width and spacing reveal that there is a minimum fenestrule width common to both groups. We propose that the minimum fenestrule width observed in fenestrate colonies was constrained by hydraulic resistance (the hydraulic-resistance-constraint hypothesis). Modelling that considers both the viscous and inertial components of fluid-flow resistance through hypothetical fenestrate meshworks corroborates this hypothesis for the smaller fenestrate meshworks of the biserial fenestellids and for polyporids with branch widths less than about 0.6 mm. However, the geometry of the polyporid meshworks in species with branches wider than 0.6 mm does not appear to have been determined by a hydraulic-resistance constraint. Instead, maximum branch densities in the larger-branched polyserial polyporid colonies appear to have been constrained by a limit on the number of zooid rows that these colonies could develop on their branches (the zooid-row-limit hypothesis). The observed decrease in the minimum fenestrule width in these colonies is the indirect geometric result of the inability of the larger polyserial polyporid colonies to develop meshworks with high branch densities.

Hybrid Self‐Assembly, Crystal, and Fractal Behavior of a Carboxy‐Ended Hyperbranched Polyester/Copper Complex

AbstractThe novel hybrid self‐assembly of a carboxy‐ended hyperbranched polyester/copper complex on glass substrates is presented. Ordered, tree‐like self‐assemblies with sizes of about 400–900 μm and branch widths of about 1 μm are obtained, which demonstrate an intriguing crystalline and fractal structure by XRD, DSC, and SEM techniques. The fractal dimension (Df) of 1.67 suggests a perfect supramolecular structure. Factors affecting the morphology of self‐assembly, including self‐assembly time, relative humidity, and concentration of the complex, are investigated and the hybrid self‐assembly is attributed to the synergistic action of cupric ion coordination induction, micelle formation, and diffusion‐limited aggregation of micelles.

Leaf-cutting ants as road engineers: the width of trails at branching points in Atta cephalotes

We used a simple engineering principle, which suggests that the width of a road needed for a smooth traffic flow is proportional to the peak traffic volume (“engineering hypothesis”), to analyze the adaptive significance of trail width at branching points in the leaf-cutting ant Atta cephalotes. Since the flow of outgoing ants splits at trail bifurcations and merges when ants return to the nest through the same paths, the sum of branch widths should equal the width of the trail section upstream of the bifurcation. We measured the width of branches and their preceding trail section and also performed field measurements and manipulations to analyze ant flow, number of collisions, and ant speed in different trail sectors. Contrary to the prediction of the “engineering hypothesis”, the sum of branch widths was larger than the width of the trail immediately before the bifurcation. Our data contradict the “trail addition hypothesis” and support the “border effect hypothesis” to explain this pattern. First, the width of the widest branch was smaller than the width of the trail upstream of the bifurcation, an unexpected result if one branch is merely the continuation of the basal trail. Second, ants collided with obstacles more often in the margin than in the central portion of the trail, relocated ants from central to margin trail sectors reduced their speed, and ant flow was higher in the central sections of the trail. Since the delaying effect of trail margins increases as the trail width decreases, ants may build branches wider than expected to reduce the border effect. The delaying effect of trail margins should be included in the analysis of costs and benefits to fully understand the adaptive value of the design of ant trail networks.

Dissolution driven crack branching in polycarbonate

Stress corrosion, in the form of chemically assisted crack growth, in polycarbonate is examined with focus on crack branching characteristics. Cracks with finite width are observed; this is to be expected for dissolution driven cracking. The cracks branched repeatedly and crack widths before and after branching are measured. Both symmetric and asymmetric branching is found. The dissolution rate is assumed to be a linear function of the strain along the crack surface. In the literature, it is proposed that the crack width is proportional to the square of the mode I stress intensity factor. Energy considerations lead to that the sum of branch widths must equal the width of the unbranched crack. The results from this study correspond fairly well with this assumption. The branching angle is found to be 32°± 12°, which is in line with results for sharp cracks reported in the literature. The mean growth direction of the branches is found to deviate slightly from the expected straight. No significant correlation between angles and crack widths is found. The scatter in results is mainly addressed to the inherent perturbation sensitivity of stress corrosion cracking. Also numerically simulations of crack branching is performed. These results show promising agreement with the experiments.

Self-gating in an electron Y-branch switch at room temperature

The authors have observed a self-gating effect in electron Y-branch switches at room temperature. The devices, with geometrical branch widths smaller than 50nm, were fabricated by electron beam lithography and shallow wet chemical etching from a modulation doped GaAs∕AlGaAs heterostructure with a two-dimensional electron gas approximately 30nm below the surface. The side-gate operation is enhanced by the self-gating effect between the branches. In particular, the differential voltage gain of the Y-branch switch increases approximately quadratically with the bias voltage.

Asymmetry of Retinal Arteriolar Branch Widths at Junctions Affects Ability of Formulae to Predict Trunk Arteriolar Widths

To describe a revised formula for the estimation of retinal trunk arteriole widths from their respective arteriolar branch widths that improves the summarizing of retinal arteriolar diameters. A group of young, healthy individuals underwent retinal photography and arteriolar and venular branching points were identified. Vessel widths of the vessel trunks and their branches were determined. The relationship between the branching coefficient (BC; quotient of the area of the branch and trunk vessels) and the asymmetry index (AI) of the vessel branches was explored. The result was used to formulate a new BC. To test the new BC, a second group of young, healthy individuals also underwent retinal photography. Arteriolar branching points were identified, and the trunk and branch arteriolar widths were recorded. This "revised" BC was compared against the gold standard of the BC as a constant value (1.28), as well as a theoretical formula for the BC that includes the angle between the two vessel branches. The BC of arterioles (but not venules) related to the AI (R = 0.275, P = 0.0001; BC arterioles = 0.78 +/- 0.63 . AI). In the second group, the mean arteriolar trunk diameter was 15.56 pixels. The linear regression model for the arteriolar BC was superior to the BC constant of 1.28 (mean difference between estimated and calculated trunk vessel width was 2.16 vs. 2.23 pixels, respectively). The model based on the angle between the branch arterioles was the least accurate (3.43 pixels). A revised formula has been devised for the arteriolar BC using a linear regression model that incorporates its relationship to the AI. Further studies using this refined formula to calculate the BC are needed to determine whether it improves the ability to detect smaller associations between the retinal vascular network and cardiovascular disease.

Gene Trees in Species Trees

Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and ex- tinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relation- ships. Each of the processes of discord could yield a different parsimony criterion for reconstruct- ing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the prob- ability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of inter- breeding. (Biogeography; coalescence; coevolution; evolution; gene duplication; gene genealogy; gene trees; horizontal transfer; hybridization; lineage sorting; parsimony; phylogeny; species con- cepts; species trees; tree reconciliation.)