Phylogenetic diversity and conservation

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Phylogenetic diversity and conservation

Phononic crystals

direction _ _ [ ) of incident i

positive refraction

(b)

(a)

Fig. 2. Phenomenon of negative refraction. (a) Comparison of positive ~nd negative. refraction at an interface. 8; angle of incidence; 8, angle of refraction. {b) Negat1ve refraction of ultrasonic waves emerging from a 20 phononic crystal prism. The directions of the group velocity, v9 , and of the wave vector, ken inside the crystal, and of the wave vector in the water, kwah are shown by arrows.

=

=

band structure, calculated using multiple scattering theory, for a three-dimensional phononic crystal of 0.8-mm-diameter tungsten carbide beads immersed in water. The band structure can be investigated experimentally by measuring the ultrasonic phase velocity as a function of frequency; representative data are shown in Fig. 1a. This phononic crystal has a complete band gap near 1 MHz, at which frequency

4

-4

(a)

(b)

Fig. 3. Focusing by negative refraction. (a) Ray diagram showing how a point source may be focused by negative refraction in a phononic crystal. (b) Demonstration of focusing by negative refraction in a 30 phononic crystal; this picture shows the focal spot obtained when a diverging beam from a small-diameter transducer is imaged by the crystal. The height of the surface maps the sound intensity across the neighborhood of the focal point. (After S. Yang et al., Focusing of sound in a 3D phononic crystal, Phys. Rev. Lett., 93:024301:1-4, 2004)

the spacing between adjacent planes of beads is ap. proximately half the ultrasonic wavelength in water. For the frequencies in the band gap, the transmission coefficient or fraction of the incident wave ampu. tude that is transmitted through the crystal exhibits a deep minimum (Fig. 1b). However, in a band gap the transmitted signal is not zero, although there are no propagating modes. The origin of this signal is explained by the tunneling of ultrasound, an effect that is completely analogous to the tunneling of a quantum-mechanical particle through a potential barrier. As a result, the transmission coefficient decreases exponentially with crystal thickness in a band gap, and is thus very small even for thin crystals. A remarkable signature of the tunneling mechanism is that the velocity of a pulse transmitted through the crystal (the group velocity) can be larger that in any of the constituent materials, and increases with the crystal thickness. This unusual effect has been observed experimentally using ultrasonic waves, in good agreement with theoretical predictions. Application to noise suppression. Because of the ability of phononic crystals to effectively block sound waves over a range of frequencies , they can be used as acoustic filters, suppressing noise in places where a vibrationless or noise-free environment is desired. Consequently, it is of the great importance to determine and optimize the factors that influence the width of the band gap. 1n general, for two phononic crystals having the same crystal structure, the one with the greater density and sound velocity mismatch between constituent materials will have the wider band gap . Other factors that control the w idth of the band gap are the shapes of the scattering elements, the symmetry of the crystal lattice, and the filling fraction, w hich is the ratio of the volume occupied by the scatterers to the total volume. One practical example that has been proposed for block· ing traffic noise along the edges of a highway is a 2D phononic crystal fence made from an array of solid cylinders in air. Another is the use of locally resonant microstructures to construct compact crystals with band gaps in the audible range. By exploiting the low-frequency resonance of heavy spherical scatterers coated with a weak elastic material and embedded in a stiffer matrix material, band gaps can be obtained in phononic crystals with interscatterer separations that are 1/100th the wavelength in air. Such compact structures have considerable potential for noise-proof devices. Applications of defects. Another promising field with numerous potential applications takes advantage of defects to modify wave transport in phononic crystals. Defects may be any objects breaking the symmetry in the otherwise perfect crystal. For example, in case of a two-dimensional phononic crystal, the defect can be a single rod that differs in its acoustic properties from the rest of the rods (for example, the defect rod may be hollow, of different shape, or made of different material) or simply a missing rod. It has been shown both theoretically and eXperimentally that, as a result of such modifications,

the transmission spectrum of the phononic crystal with the defect exhibits a narrow peak at a particular frequency inside the band gap. By changing the different characteristics of the defect (for example, changing the itmer or outer diameters of a hollow rod or filling the rod with various fluids) , the frequency of the transmitted peak can be controlled . Thus, phononic crystals w ith defects may be used as tunable acoustic filters to select waves of a certait1 frequency. By removing an entire row of rods, a line defect inside a 2D phononic crystal can be created . If the crystal has a complete band gap, waves entering the line defect will be confined inside it, creating a waveguide for acoustic waves. The waveguide also can be made tunable to transmit waves of a selected frequency or frequencies. To this end, the line defect can be created by using rods different from the rest of the rods in the phononic crystal rather than removing the rods completely. These applications of defects in 2D crystals can be readily extended to 3D phononic crystals, even though their implementation may be more difficult to engineer. Negative refraction and sound focusing. Another unusual phenomenon exhibited by phononic crystals is negative refraction. At some frequencies , ultrasonic waves entering or leaving a phononic crystal may bend in a direction that is opposite to the norm for uniform materials, so that the effective angle of refraction at the interface is negative (Fig. 2a). This effect can occur when the group velocity, v8 , which determitles the direction in which energy is transported through the crystal (and hence the ray direction), points in a different direction than the wave vector, k , which describes the direction of travel of the phase oscillations in the wave. In the sin1plest case of negative refraction, v8 and k are anti parallel. Figure 2b shows an example of negative refraction fo r ultrasonic waves emerging from a prism-shaped phononic crystal of steel rods in water. The waves are incident from the upper right side of the figure. The directions of the group velocity, v8 , and of the wave vector inside the crystal, k c,., are shown by arrows. 1n this frequency range, which corresponds to the second pass band of the crystal, the frequencies of the modes decrease as the wave vector increases (sitnilar to the branches of the 3D band structure shown in Fig. 1a for frequencies above 1.2 MHz); hence the group velocity v8 , which is given by the derivative of frequency w with respect to wave vector, has the opposite sign to the wave vector. Since the wave can be transported across the crystal only when the group velocity is positive, the wave vector k c,. points backward, as indicated. (ln general, the relationship between the direction of the group velocity and the wave vector can be found by determining the equifrequency or slowness surface, Which displays the magnitude of the wave vector as a function of its direction for waves of a sit1gle frequency. SitlCe v8 = \1 kw(k) , v8 is perpendicular to this surface; it points it1 the opposite direction to k if the equifrequency surface is circular and if the surface shrinks in size as frequency it1creases, as is the

case here.) Consequently, Snell's law, which states that the component of the wave vector parallel to the interface should be the same on both sides of the boundary, predicts that a negatively refracted wave will emerge from the prism crystal as shown. These experimental results are in excellent agreement with predictions based on multiple scattering theory for the magnitudes and directions of the wave vector and the group velocity for this 2D crystal. The ability of phononic crystals to refract sound waves negatively allows them to be used as lenses for focusing smmd. When an initially diverging beam from a source point is incident on the crystal, the rays are bent back by negative refraction toward the axis of the lens, so that when they emerge of the far side of the crystal, where they travel it1 their original directions, they are brought to a focus (Fig. 3a). The focusing of sound by a flat 3D phononic crystal has been demonstrated experimentally (Fig. 3b). A potential advantage of this novel type of focusing is improved resolution compared with traditional lenses, and theoretical predictions of image of a point source as small as one-seventh the wavelength have been made. For background information see ACOUSTIC NOISE; BAND THEORY OF SOLIDS; COMPOSITE MATERIAL; CRYSTAL DEFECTS; GROUP VELOCITY; REFRACTION OF WAVES; SOLID-STATE PHYSICS ; TUNNELING IN SOLIDS

in the McGraw-Hill Encyclopedia of Science & Technology. Alexey Sukhovich; John H. Page Bibliography. Z. Liu et a!. , Locally resonant sonic materials, Science, 289:1734-1 736, 2000;]. H. Page et a!. , Phononic crystals, Phys. Stat. Sol. (b) , 241:3454- 3462 , 2004; Y. Permec eta!. , 1\mable filtering and demultiplexing in phononic crystals with hollow cylinders. Phys. Rev. E, 69:046608:1 - 6, 2004; I. E. Psarobas (ed.), Phononic crystals: Sonic bandgap materials, a special issue of Zeitschrift fur Kr·istallographie, vol. 220, iss. 9-10, 2005 ; S. Yang et a!. , Focusing of sound in a 3D phononic crystal, Phys. Rev. Lett., 93:024301: 1-4, 2004; S. Yang eta!. , Ultrasound tunneling through 3D phononic crystals, Phys. Rev. Lett., 88:1 04301 :1-4, 2002.

Phylogenetic diversity and conservation "Biodiversity" refers to the variety of life on the planet-extending in scale from genes to species to ecosystems. Our understandit1g of biodiversity conservation, however, faces a twofold knowledge gap. First, we have no complete list of the components of biodiversity at the different levels, and second, it is difficult to judge what their values might be in the future . Therefore a core strategy for biodiversity conservation is to estimate patterns of variation, and then try to conserve as much of that variation as possible, so as to retain the full range of possible future values. Phylogeny, the evolutionary "tree of life," can play an important role in estimating biodiversity patterns. A phylogenetic pattern for a taxonomic group displays evolutionary relationships among species, or

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Phylogenetic diversity and conservation other taxa, in two ways. It reflects the process of cladogenesis, where one lineage splits into two, and it also reflects the process of anagenesis, where evolutionary changes in genetic, morphological, or other features occur along a given lineage. Such a summary of the complex evolutionary history of a group is never revealed to us as the definitive "true" phylogeny. Instead, the discipline of phylogenetic inference uses genetic or other features of organisms to evaluate competing hypotheses about the true phylogenetic pattern. Phylogeny-based strategies for biodiversity estimation reverse this discovery process. The corresponding biodiversity inference process uses inferred phylogenetic patterns to make a predictive link from the taxon level to general patterns of variation at the lower level of genes or other features. Conservation priorities may then be based on assessment of the potential losses in feature diversity from different scenarios of taxon extinction. Theoretical arguments, based on the simple idea that shared ancestry should account for shared features, suggest that any subset of taxa that has greater phylogenetic diversity will represent greater genetic or feature diversity. A measure of phylogenetic diversity (PD) is defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the tree (see illustration). Larger PD values imply greater expected feature diversity. The total PD represented by different-sized sets of taxa defines a "features/taxa" curve. It is analogous to the well-known species/area curve, which illustrates the linear relationship between log transformations of number of species and total area. Using PD, the increase in represented feature diversity is initially rapid as we add taxa to a set. As the size of the set grows larger, the rate of gain in features becomes progressively lower.

Phylogenetic tree for taxa a-h. The branching pattern reflects splitting of lineages and the length of the branches reflects character change along lineages. The total PO of the set of taxa {a, b, f, g, h} is represented by the sum of the lengths of the thick branches. Extinction of taxon a implies a PO loss of x units. However, if taxon b is extinct, then loss of a implies a PO loss of an additional y unit represented by the deeper branch. Taxa are restricted in distribution (endemic) to individual places, p1-p4. Phylogenetic clumping of taxa in p1 implies that loss of that place corresponds to loss also of the deeper branch, z. Historical relationships among places imply that phylogenetic patterns for other groups may be concordant, supporting general PO-endemism, for example, of p1.

Phylogenetic diversity and conservation It has been argued that conservation actions that maximize species/taxon diversity automatically maximize conservation of PD. However, because species are not equal in factors such as extinction vulnerability and branch length contributions, actual gains and losses in PD often are not predicted well by species counts. PD gains and losses. Tn practice, PD is typically used to assess marginal gains and losses, such as those implied by the loss of a single species, or other taxon, that is "pruned" by extinction from the phylogenetic tree (see illustration). Similarly, gains may be recorded as additional taxa that are represented in new conservation areas. Unlike traditional metrics using species diversity, PD focuses on the overall number of features that might be lost from a given community with the loss of a particular species. This shift in focus also presents a potential advantage of PD-based assessments, namely that PD sidesteps conventional difficulties in deciding exactly what is, or is not, a "species." Conservation scenarios therefore can be evaluated in terms of gains in feature diversity, ignoring species counts. The PD loss corresponding to loss of a given taxon is not a fixed value. It depends on which other taxa are extant (not extinct). For example, in the illustration, the PD Joss implied by the loss of taxon a will be greater if taxon b already has been lost. The loss of both taxa does not imply a PD Joss simply equal to the sum of the individual losses. Instead, losing both taxa means we also lose the PD contribution from the branch or lineage linking those two taxa. Such phylogenetic "clumping" of losses, and consequent inflation of PD loss, has been documented in some studies. A recent assessment of Indonesian fauna showed that the vulnerability of these species to extinction is phylogenetically clumped. Therefore the amount of PD at risk in Indonesia is significantly greater than it would be for the loss of the same number of species selected at random. Global-scale studies of both birds and carnivores suggest that many extinct and currently threatened species are phylagenetically clumped. Other global-scale studies, such as one for Felids (the "cat" family), suggest that extinction vulnerability of species is distributed more or less randomly across the phylogeny of the group. Other forms of extinction bias also may inflate the loss of PD. For example, greater extinction vulnerability for taxa at the ends of long branches will increase potential PD Joss. Also, greater vulnerability of species with few close relatives will place more PD at risk, because there is a greater chance that deeper branches will not retain any extant representation. Both of these factors have . been implicated in extinction patterns for Australian marsupials. The nonrandom geographic distribution of taxa is a major factor in determining potential PD losses. Often the units for conservation planning are geographic places, and PD assessment reflects possible gains and losses for whole collections of taxa, potentially from many taxonomic groups. The loss of

a place may imply taxon loss that is phylogenetical!Y clumped or dispersed depending on the environment (see illustration). Both scenarios may flag conservation opportunities. Numerous places that individually capture high phylogenetic diversity provide flexibility in conservation planning for representative protected areas, and individual places recognized as having a phylogenetic concentration of taxa attract higher conversation priority based on the potential high loss of PD. PD endemism. PD contributions may be restricted (endemic) to a particular place. While endemism conventionally refers to counts of the species restricted to a place, PD endemism reflects the presence of unique amounts of phylogenetic diversity, and indicates the feature diversity inevitably lost if that place is lost (see illustration). For example, PD endemism based on an estimated phylogeny of amphipods has highlighted the unique biodiversity value of forests in northwestern Tasmania that were not apparent from corresponding species counts. Global hotspots are regions where high species endemism currently overlaps with a high overall threat to biodiversity. A recent study used estimated phylogenetic trees for carnivores and for primates to argue that the 25 named global hotspots are critical for conservation, as they contain large amounts of PD found nowhere else. The high PD endemism is reflected in the fact that a remarkable one-third of the total PD of primates and carnivores is contained only in these hotspots. Collectively, they correspond to the scenario in the illustration, where the endemic taxa are phylogenetically clumped . Tf we lost the hotspots, the amount of PD lost would be significantly greater than for a loss of a random selection of the same number of species in other areas. At the continental scale, an Australian hotspots study revealed that the places having high PD endemism often differ from places of high species endemism. While that comparison was based on limited phylogenetic information, PD endemism patterns for one phylogenetic group may predict more general PD endemism. One factor promoting general predictions is co-evolution, for example, of hosts and parasites. Similarly, phylogenetic patterns for different taxonomic groups may reflect shared historical relationships among areas (see illustration), so that a single area may have PD endemism for many different groups. Phylogenetic clumping and PD endemism are important at other scales of variation as well. For example, a recent study showed that the phylogenetic diversity of a little known group of bacteria, occurring widely in anaerobic enviroll111ents, displayed strong phylogenetic clumping linked to different animal hosts (for example, termites and birds). The gut of each animal species corresponds to a phylogenetic radiation , resulting in PD endemism at that scale. The Phylogenetic clumping seen there, analogous to that for global hotspots, means that loss of a gut fauna would imply a disproportionate loss in bacterial PD.

Consideration of fine-scale variation extends to applications of PD within species. Here, phylogenetic patterns describe relationships among populations and genetic variants. For example, mitochondrial DNA phylogenies for different vertebrate species from Queensland rainforests show congruent patterns for the PD contributions of different areas. Another recent snicly has argued that within-species variation generally can be expected to be distributed unevenly among populations. Global samples of Pseudomonas bacteria revealed that a disproportionate fraction of the phylogenetically structured diversity was clumped in small subpopulations. Conservation priority for these places could avoid inflated PD loss associated with deep branches (see illustration). Prospects. The utility of PD for conservation will depend on phylogenetic information being readily available in contexts where biodiversity is under threat. Prospects for tllis were highlighted in a recent study of the freshwater invertebrate taxa found in headwaters of streams in N.S.W Australia, which are under threat from mining and new dams. The phylogenetic and distribution patterns for these groups suggested repeated cases of PD endemism ancl location-based phylogenetic clumping. For example, the "spiny crayfish" had one lineage restricted to a location that could be lost to mining impacts. This suggests a higher conservation priority for another threatened location, uniquely holding a sister lineage, because the combination of losses would imply a large PD loss (see illustration). Phylogenetic inference for that study was based on a mitochondrial gene called cytochrome-c-oxidase subunit I (CO/) . The sequence of this gene can potentially distinguish between closely related species across a broad range of biodiversity, and rapid CO/ assessment is seen as providing a general "barcoding" approach for assignment of unidentified individuals to particular species. As suggested by the CO/ phylogenetic/spatial patterns for freshwater organisms, future rapid conservation assessments could side-step the associated difficulties in distinguishing species and apply PD to phylogenetic patterns based in part on CO/. A global bar-coding program integrating PD assessment could provide more rapid identification of places of high PD endenlism. See DNA BARCODING .

For background information see BIODIVERSITY; CONSERVATION OF RESOURCES; EXTINCTION (BIOLOGY) ; ORGANIC EVOLUTION; PHYLOGENY; ZOOGEO-

GRAPHY in t11e McGraw-Hill Encyclopedia of Science Daniel P. Faith; Kristen J. Williams and Technology. Bibliography. D. P Faith, Conservation evaluation and phylogenetic diversity, Bioi. Conserv. , 61:1-10 , 1992; G. M. Mace et a!. , Preserving the tree of life, Science, 300:1 707 -1 709 , 2003; D. P Faith, Biodiversity, in E. N. Zalta (ed .) , The Stanf.ord Encyclopedia ofPhilosophy , 2003 ; W Sechrest et al. , Hotspots and the conservation of evolutionary history, PNAS, 99(4):2067 -207 1, 2002.

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Articles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-349

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Paleozoic bivalve borings A. A. Ekdale Permian-Triassic mass extinction Margaret L. Fraiser Pharmaceutical residues in the environment Diana S. Aga Phononic crystals Alexey Suld1ovich; John H. Page Phylogenetic diversity and conservation Daniel P. Faith; Kristen J. Williams Phytoremediation Melinda A. Klein; Ashot Papoyan; Leon V. Kochian Plant cell walls Breeanna Rae Urbanowicz; Sarah Nell Davidson; Jocelyn Kenneth Campbell Rose Plume imagery Guust Nolet Polymer stereochemistry and properties Yoshio Okamoto Polymers for microelectronics C. W Bielawsld; C. G. Willson Post-perovskite Thorne Lay Primate communication Charles T. Snowdon Primate origins Christophe Soligo Printing on demand Harold Henke Process improvement methodologies Donna H. Rhodes Proteomics Megan S. Lim; Kojo S. J. Elenitoba-Johnson Proximal probe molecular analysis S. S. Sheiko Psychopathology and the Human Genome Project Sarah Cohen; Peter McGuffin Pterosaur Matthew T. Wilkinson Quantum chaos in a three-body system Alfred S. Schlachter Queuing theory (health care) John Blake Radar meteorology Jon Eastment Reactive oxygen species Marcus S. Cooke; Mark D. Evans Regional climate modeling Wen-Yili Sun Risk analysis (homeland security) Vicki M. Bier Salmon farming James R. A. Butler Sedna John Stansberry Self-recognition Alain Morin Size effect on strength (civil engineering) Milan Jirasek

Geochronology Donald W Davis Global biogeochemical cycles Ame Winguth Graph-based intelligence analysis Thayne Coffman Herbicide resistance Lyle F. Friesen; Rene C. Van Acker; Chris Willenborg Heuristics in judgment and decision making Rolf Reber Homo floresiensis Terry Harrison Human papillomaviruses John P. Harley Hydrogen-powered flight Timothy D. Smith Infectious disease and human evolution Donald J. Ortner Infrasonic monitoring Michael A. H. Redlin Insect flight Z.JaneWang Intelligent vehicles and infrastructure Christopher K. Wilson Interaction of photons with ionized matter Ronald A. Phaneuf Internet communications Daniel Heer; Michael Rauchwerk Invasive forest species Barbara L. Illman Jet boring (mining) Barry W Schmitke Life-cycle analysis of civil structures Dan M. Frangopol; Min Liu Liver X receptor (LXR) Christopher J. Fielding Mangrove forests and tsunami protection F. Dahdouh-Guebas Mars Rovers Eric T. Baumgartner Metagenomics J. Handelsman Microbial dechlorination Claudia K. Gunsch Microbial forensics Randall S. Murch Mineralogy of Mars Jim Bell Nanometer magnets Denis Koltsov Nitrogen deposition and forest degradation Timothy H. Tear Nobel prizes Yearbook Editors Noncoalescence of droplets Pasquale Dell'Aversana Nonconventional aircraft designs N. Qin Ontology (information technology) Ruben Prieto-Diaz X

3D inkjet printing Alexandra Pekamvicova; Jan Pekamvic Tissue and organ printing Gabor Forgacs; Vladimir Mironov Transgressive segregation (plant breeding) Nolan C. Kane; Briana L. Gmss; Loren H. Rieseberg Trapped-ion optical clocks Hugh Klein Vehicle-highway automation systems Steven E. Shladover Vernalization Richard Atnasino Very small flying machines Robert C. Michelson Whale-fall worms G. W Rouse World Wide Web search engines Brian D. Davison

Space flight Jesco von Puttkamer Space probe communications Charles D. Edwards Spider silk Nitin Kumar; Gareth H. McKinley Steel construction Reidar Bjorhovde sumatra-Andaman earthquake Jeffrey J. Park sum-frequency vibrational spectroscopy John C. Conboy Superconductor wires M. Parans Paranthaman Telerobotics (mining) Gregory R. Baiden Tetrapod origins Jennifer A. Clack

xi