@article{11849,
  abstract     = {This paper describes the DIGlTAL Continuous Profiling Infrastmcture, a sampling-based profiling system designed to run continuously on production systems. The system supports multiprocessors, works on unmodified executable& and collects profiles for entire systems, including user programs, shared libraries, and the operating system kernel. Samples are collected at a high rate (over 5200 samples/secper333-MHz processor), yet with low overhead (l-3% slowdown for most workloads). Analysis tools supplied with the profiling system use the sample data to produce an accurate accounting, down to the level of pipeline stalls incurred by individual instructions, of where time is being spent. When instructions incur stalls, the tools identify possible reasons, such as cache misses, branch mispredictions, and functional unit contention. The fine-grained instruction-level analysis guides users and automated optimizers to the causes of performance
problems and provides important insights for fixing them. },
  author       = {Anderson, Jennifer M. and Berc, Lance M. and Dean, Jeffrey and Ghemawat, Sanjay and Henzinger, Monika H and Leung, Shun-Tak A. and Sites, Richard L. and Vandevoorde, Mark T. and Waldspurger, Carl A. and Weihl, William E.},
  issn         = {0163-5980},
  journal      = {ACM SIGOPS Operating Systems Review},
  number       = {5},
  pages        = {1--14},
  publisher    = {Association for Computing Machinery},
  title        = {{Continuous profiling: Where have all the cycles gone?}},
  doi          = {10.1145/269005.266637},
  volume       = {31},
  year         = {1997},
}

@article{3482,
  abstract     = {AMPA- and NMDA-type glutamate receptors (AMPARs and NMDARs) mediate excitatory synoptic transmission in the basal ganglia and may contribute to excitotoxic injury. We investigated the functional properties of AMPARs and NMDARs expressed by six main types of basal ganglia neurons in acute rat brain slices (principal neurons and cholinergic interneurons of striatum, GABAergic and dopaminergic neurons of substantia nigra, globus pallidus neurons, and subthalamic nucleus neurons) using fast application of glutamate to nucleated and outside-out membrane patches, AMPARs in different types of basal ganglia neurons were functionally distinct. Those expressed in striatal principal neurons exhibited the slowest gating (desensitization time constant τ = 11.5 msec, 1 mM glutamate, 22°C), whereas those in striatal cholinergic interneurons showed the fastest gating (desensitization time constant τ = 3.6 msec). The lowest Ca2+ permeability of AMPARs was observed in nigral dopaminergic neurons (P(CA)/P(NA) = 0.10), whereas the highest Ca2+ permeability was found in subthalamic nucleus neurons (P(Ca)/P(Na) = 1.17). NMDARs of different types of basal ganglia neurons were less variable in their functional properties; those expressed in nigral dopaminergic neurons exhibited the slowest gating (deactivation time constant of predominant fast component τ1 150 msec, 100 μM glutamate), and those of globus pallidus neurons showed the fastest gating (τ1 = 67 msec). The Mg2+ block of NMDARs was similar; the average chord conductance ratio g(+60mv)/g(+40mV) was 0.18-0.22 in 100 μM external Mg2+. Hence, AMPARs expressed in different types of basal ganglia neurons are markedly diverse, whereas NMDARs are less variable in functional properties that are relevant for excitatory synoptic transmission and neuronal vulnerability.},
  author       = {Götz, Thomas and Kraushaar, Udo and Geiger, Jörg and Lubke, Joachim and Berger, Thomas and Jonas, Peter M},
  issn         = {0270-6474},
  journal      = {Journal of Neuroscience},
  number       = {1},
  pages        = {204 -- 215},
  publisher    = {Society for Neuroscience},
  title        = {{Functional properties of AMPA and NMDA receptors expressed in identified types of basal ganglia neurons}},
  doi          = {10.1523/JNEUROSCI.17-01-00204.1997},
  volume       = {17},
  year         = {1997},
}

@article{3483,
  abstract     = {The main excitatory pathway of the hippocampal formation is controlled by a network of morphologically distinct populations of GABAergic interneurons. Here we describe a novel type of GABAergic interneuron located in the outer molecular layer (OML) of the rat dentate gyrus with a long- range forward projection from the dentate gyrus to the subiculum across the hippocampal fissure, OML interneurons were recorded in hippocampal slices by using the whole-cell patch-clamp configuration. During recording, cells were filled with biocytin for subsequent light and electron microscopic analysis. Neurons projecting to the subiculum were distributed throughout the entire OML. They had round or ovoid somata and a multipolar dendritic morphology. Two axonal domains could be distinguished: an extensive, tangential distribution within the OML and a long-range vertical and tangential projection to layer 1 and stratum pyramidale of the subiculum. Symmetric synaptic contacts were established by these interneurons on dendritic shafts in the OML and subiculum. OML interneurons were characterized physiologically by short action potential duration and marked afterhyperpolarization that followed the spike. On sustained current injection, they generated high- frequency (up to 130 Hz, 34°C) trains of action potentials with only little adaptation. In situ hybridization and single-call RT-PCR analysis for GAD67 mRNA confirmed the GABAergic nature of OML interneurons. GABAergic interneurons in the OML projecting to the subiculum connect the input and output regions of the hippocampus. Hence, they could mediate long-range feed- forward inhibition and may participate in an oscillating cross-regional interneuron network that may synchronize the activity of spatially distributed principal neurons in the dentate gyrus and the subiculum.},
  author       = {Ceranik, Katya and Bender, Roland and Geiger, Jörg and Monyer, Hannah and Jonas, Peter M and Frotscher, Michael and Lubke, Joachim},
  issn         = {0270-6474},
  journal      = {Journal of Neuroscience},
  number       = {14},
  pages        = {5380 -- 5394},
  publisher    = {Society for Neuroscience},
  title        = {{A novel type of GABAergic interneuron connecting the input and the output regions of the hippocampus.}},
  doi          = {10.1523/JNEUROSCI.17-14-05380.1997},
  volume       = {17},
  year         = {1997},
}

@article{3484,
  abstract     = {Glutamatergic transmission at a principal neuroninterneuron synapse was investigated by dual whole-cell patch-clamp recording in rat hippocampal slices combined with morphological analysis. Evoked EPSPs with rapid time course (half duration ≃ 4 ms; 34°C) were generated at multiple synaptic contacts established on the interneuron dendrites close to the soma. The underlying postsynaptic conductance change showed a submillisecond rise and decay, due to the precise timing of glutamate release and the rapid deactivation of the postsynaptic AMPA receptors. Simulations based on a compartmental model of the interneuron indicated that the rapid postsynaptic conductance change determines the shape and the somatodendritic integration of EPSPs, thus enabling interneurons to detect synchronous principal neuron activity.},
  author       = {Geiger, Jörg and Lubke, Joachim and Roth, Arnd and Frotscher, Michael and Jonas, Peter M},
  issn         = {0896-6273},
  journal      = {Neuron},
  number       = {6},
  pages        = {1009 -- 1023},
  publisher    = {Elsevier},
  title        = {{Submillisecond AMPA receptor-mediated signaling at a principal neuron-interneuron synapse}},
  doi          = {10.1016/S0896-6273(00)80339-6},
  volume       = {18},
  year         = {1997},
}

@article{3485,
  abstract     = {1. GABAergic interneurones differ from glutamatergic principal neurones in their ability to discharge high-frequency trains of action potentials without adaptation. To examine whether Na+ channel gating contributed to these differences, Na+ currents were recorded in nucleated patches from interneurones (dentate gyrus basket cells, BCs) and principal neurones (CA1 pyramidal cells, PCs) of rat hippocampal slices. 2. The voltage dependence of Na+ channel activation in BCs and PCs was similar. The slope factors of the activation curves, fitted with Boltzmann functions raised to the third power, were 11.5 and 11.8 mV, and the mid-point potentials were -25.1 and -23.9 mV, respectively. 3. Whereas the time course of Na+ channel activation (-30 to +40 mV) was similar, the deactivation kinetics (-100 to -40 mV) were faster in BCs than in PCs (tail current decay time constants, 0.13 and 0.20 ms, respectively, at -40 mV). 4. Na+ channels in BCs and PCs differed in the voltage dependence of inactivation. The slope factors of the steady-state inactivation curves fitted with Boltzmann functions were 6.7 and 10.7 mV, and the mid-point potentials were -58.3 and -62.9 mV, respectively. 5. The onset of Na+ channel inactivation at -55 mV was slower in BC's than in PCs; the inactivation time constants were 18.6 and 9.3 ms, respectively. At more positive potentials the differences in inactivation onset were smaller. 6. The time course of recovery of Na+ channels from inactivation induced by a 30 ms pulse was fast and mono-exponential (τ = 2.0 ms at -120 mV) in BCs, whereas it was slower and biexponential in PCs (τ1 = 2.0 ms and τ2 = 133 ms; amplitude contribution of the slow component, 15%). 7. We conclude that Na+ channels of BCs and PCs differ in gating properties that contribute to the characteristic action potential patterns of the two types of neurones.},
  author       = {Martina, Marco and Jonas, Peter M},
  issn         = {0022-3751},
  journal      = {Journal of Physiology},
  number       = {3},
  pages        = {593 -- 603},
  publisher    = {Wiley-Blackwell},
  title        = {{Functional differences in Na+ channel gating between fast-spiking interneurones and principal neurones in rat hippocampus}},
  doi          = {10.1111/j.1469-7793.1997.593ba.x},
  volume       = {505},
  year         = {1997},
}

@article{3486,
  abstract     = {1. Dendritic patch-clamp recordings were obtained from mitral cells in rat olfactory bulb slices, up to 350 μm from the soma. Simultaneous dendritic and somatic whole-cell recordings indicated that action potentials (APs) evoked by somatic or dendritic current injection were initiated near the soma. Both the large amplitude (100.7 ± 1.1 mV) and the short duration (1.38 ± 0.07 ms) of the AP were maintained as the AP propagated back into the primary mitral cell dendrites. 2. Outside-out patches isolated from mitral cell dendrites contained voltage-gated Na+ channels (peak conductance density, 90 pS μm-2 at -10 mV). When an AP was used as a somatic voltage-clamp command in the presence of 1 μM tetrodotoxin (TTX), the amplitude of the dendritic potential was attenuated to 48 ± 14 mV. This shows that dendritic Na+ channels support the active back-propagation of APs. 3. Dendritic patches contained voltage-gated K+ channels with high density (conductance density, 513 pS μm-2 at 30 mV. Dendritic K+ currents were reduced to 35% by 1 mM external tetraethylammonium chloride (TEACl). When an AP was used as a somatic voltage clamp command in the presence of TEACl, the dendritic potential was markedly prolonged. This indicates that dendritic K+ channels mediate the fast repolarization of dendritic APs. 4. We conclude that voltage gated Na+ and K+ channels support dendritic APs with large amplitudes and short durations that may trigger fast transmitter release at dendrodendritic synapses in the olfactory bulb.},
  author       = {Bischofberger, Joseph and Jonas, Peter M},
  issn         = {0022-3751},
  journal      = {Journal of Physiology},
  number       = {Pt 2},
  pages        = {359 -- 365},
  publisher    = {Wiley-Blackwell},
  title        = {{Action potential propagation into the presynaptic dendrites of rat mitral cells}},
  doi          = {10.1111/j.1469-7793.1997.359be.x},
  volume       = {504},
  year         = {1997},
}

@article{3630,
  abstract     = {This paper derives the long-term effective size, Ne, for a general model of population subdivision, allowing for differential deme fitness, variable emigration and immigration rates, extinction, colonization, and correlations across generations in these processes. We show that various long-term measures of Ne are equivalent. The effective size of a metapopulation can be expressed in a variety of ways. At a demographic equilibrium, Ne can be derived from the demography by combining information about the ultimate contribution of each deme to the future genetic make-up of the population and Wright's FST's. The effective size is given by Ne = 1/(1 + var (upsilon) ((1 - FST)/Nin), where n is the number of demes, theta i is the eventual contribution of individuals in deme i to the whole population (scaled such that sigma theta i = n), and < > denotes an average weighted by theta i. This formula is applied to a catastrophic extinction model (where sites are either empty or at carrying capacity) and to a metapopulation model with explicit dynamics, where extinction is caused by demographic stochasticity and by chaos. Contrary to the expectation from the standard island model, the usual effect of population subdivision is to decrease the effective size relative to a panmictic population living on the same resource.},
  author       = {Whitlock, Michael and Barton, Nicholas H},
  issn         = {0016-6731},
  journal      = {Genetics},
  number       = {1},
  pages        = {427 -- 441},
  publisher    = {Genetics Society of America},
  title        = {{The effective size of a subdivided population}},
  doi          = {10.1093/genetics/146.1.427},
  volume       = {146},
  year         = {1997},
}

@article{3631,
  abstract     = {In spatially heterogeneous environments, natural selection for maintenance of adaptation to habitats that contribute little to the population's reproduction is weak. In this paper we model a mechanism that can result in loss of fitness in such marginal habitats, and thus lead to specialisation on the main habitat. It involves accumulation of mutations that are deleterious in the marginal habitat but neutral or nearly so in the main habitat (mutations deleterious in the main habitat and neutral in the marginal habitat have a negligible influence). If the contribution of the marginal habitat to total reproduction in the absence of the mutations is less than a threshold value, selection is too weak to counter accumulation of such mutations. A positive feedback then results in loss of fitness in the marginal habitat. This mechanism does not require antagonistic pleiotropy in adaptation to different habitats, although antagonistic pleiotropy facilitates the mutational collapse of fitness in the marginal habitat. We suggest that deleterious mutations with habitat-specific expression may play a role in the evolution of ecological specialisation and promote evolutionary conservatism of ecological niches.},
  author       = {Kawecki, Tadeusz and Barton, Nicholas H and Fry, James},
  issn         = {1010-061X},
  journal      = {Journal of Evolutionary Biology},
  number       = {3},
  pages        = {407 -- 430},
  publisher    = {Wiley-Blackwell},
  title        = {{Mutational collapse of fitness in marginal habitats and the evolution of ecological specialisation}},
  doi          = {10.1046/j.1420-9101.1997.10030407.x},
  volume       = {10},
  year         = {1997},
}

@article{3632,
  abstract     = {An important but controversial class of hypotheses concerning the evolution of female preferences for extreme male mating displays involves 'indirect selection.' Even in the absence of direct fitness effects, preference for males with high overall fitness can spread via a genetic correlation that develops between preference alleles and high fitness genotypes. Here we develop a quantitative expression for the force of indirect selection that (i) applies to any female mating behavior, (ii) is relatively insensitive to the underlying genetics, and (iii) is based on measurable quantities. In conjunction with the limited data now available, it suggests that the evolutionary force generated by indirect selection on preferences is weak in absolute terms. This finding raises the possibility that direct selection on preference genes may often be more important than indirect selection, but more data on the quantities identified by our model and on direct selection are needed to decide the question.},
  author       = {Kirkpatrick, Mark and Barton, Nicholas H},
  issn         = {0027-8424},
  journal      = {PNAS},
  number       = {4},
  pages        = {1282 -- 1286},
  publisher    = {National Academy of Sciences},
  title        = {{The strength of indirect selection on female mating preferences}},
  doi          = {10.1073/pnas.94.4.1282},
  volume       = {94},
  year         = {1997},
}

@article{4021,
  abstract     = {A homeomorphism from R-2 to itself distorts metric quantities, such as distance and area. We describe an algorithm that constructs homeomorphisms with prescribed area distortion. Such homeomorphisms can be used to generate cartograms, which are geographic maps purposely distorted so their area distributions reflects a variable different from area, as for example population density. The algorithm generates the homeomorphism through a sequence of local piecewise linear homeomorphic changes. Sample results produced by the preliminary implementation of the method are included.},
  author       = {Edelsbrunner, Herbert and Waupotitsch, Roman},
  issn         = {0925-7721},
  journal      = {Computational Geometry: Theory and Applications},
  number       = {5-6},
  pages        = {343 -- 360},
  publisher    = {Elsevier},
  title        = {{A combinatorial approach to cartograms}},
  doi          = {10.1016/S0925-7721(96)00006-5},
  volume       = {7},
  year         = {1997},
}

@article{4174,
  abstract     = {The epiphysial region of the dorsal diencephalon is the first site at which neurogenesis occurs in the roof of the zebrafish forebrain. We show that the homeobox containing gene floating head (flh) is required for neurogenesis to proceed in the epiphysis. In flh(-) embryos, the first few epiphysial neurons are generated, but beyond the 18 somite stage, neuronal production ceases. In contrast, in masterblind(-) (mbl(-)) embryos, epiphysial neurons are generated throughout the dorsal forebrain. We show that mbl is required to prevent the expression of flh in dorsal forebrain cells rostral to the epiphysis. Furthermore, epiphysial neurons are not ectopically induced in mbl(-)/flh(-) embryos, demonstrating that the epiphysial phenotype of mbl(-) embryos is mediated by ectopic Flh activity. We propose a role for Flh in linking the signaling pathways that regulate regional patterning to the signaling pathways that regulate neurogenesis.},
  author       = {Masai, Ichiro and Heisenberg, Carl-Philipp J and Barth, K Anukampa and Macdonald, Rachel and Adamek, Sylwia and Wilson, Stephen},
  issn         = {0896-6273},
  journal      = {Neuron},
  number       = {1},
  pages        = {43 -- 57},
  publisher    = {Elsevier},
  title        = {{Floating head and masterblind regulate neuronal patterning in the roof of the forebrain}},
  doi          = {10.1016/S0896-6273(01)80045-3},
  volume       = {18},
  year         = {1997},
}

@article{4201,
  abstract     = {In zebrafish, as in other vertebrates, an initially singular eye held within the neural plate has to split during morphogenesis to allow the development of two separated eyes. It has been suggested that anterior progression of midline tissue within the neural plate is involved in the bilateralization of the eye held. Mutations in the recently identified silberblick (slb) gene cause an incomplete separation of the eyes. During gastrulation and early somitogenesis, the ventral midline of the central nervous system (CNS) together with the underlying axial mesendoderm is shortened and broadened in slb embryos. While in wild-type embryos the ventral CNS midline extends to the anterior limit of the neural plate at the end of gastrulation, there is a gap between the anterior tip of the ventral CNS midline and the anterior edge of the neural plate in slb. To investigate the cause for the shortening of the ventral CNS midline in slb we determined the fate of labeled ventral CNS midline cells in wild-type and slb embryos at different stages of development. In slb, anterior migration of ventral CNS midline cells is impaired, which indicates that migration of these cells is needed for elongation of the ventral CNS midline. The anterior shortening of the ventral CNS midline in slb leads to medial instead of bilateral induction of optic stalks followed by a partial fusion of the eyes at later developmental stages. The analysis of the sIb phenotype indicates that anterior migration of midline cells within the neural plate is required for proper induction and subsequent bilateralization of an initially singular eye field. These findings may therefore provide a starting point in elucidating the role of neural plate morphogenesis in positioning of the eyes. (C) 1997 Academic Press.},
  author       = {Heisenberg, Carl-Philipp J and Nüsslein Volhard, Christiane},
  issn         = {0012-1606},
  journal      = {Developmental Biology},
  number       = {1},
  pages        = {85 -- 94},
  publisher    = {Elsevier},
  title        = {{The function of silberblick in the positioning of the eye anlage in the zebrafish embryo}},
  doi          = {10.1006/dbio.1997.8511},
  volume       = {184},
  year         = {1997},
}

@article{4285,
  abstract     = {One of the oldest hypotheses for the advantage of recombination is that recombination allo rvs beneficial mutations that arise in different individuals to be placed together on the same chromosome. Unless recombination occurs, one of the beneficial alleles is doomed to extinction, slowing the rate at which adaptive mutations are incorporated within a population. We model the effects of a modifier of recombination on the fixation probability of beneficial mutations when beneficial alleles are segregating at other loci. We find that modifier alleles that increase recombination do increase the fixation probability of beneficial mutants and subsequently hitchhike along as the mutants rise in frequency. The strength of selection favoring a modifier that increases recombination is proportional to lambda(2)S delta r/r when linkage is tight and lambda(2)S(3) delta r/N when linkage is loose, where lambda is the beneficial mutation rate per genome per generation throughout a population of size N, S is the average mutant effect, r is the average recombination rate, and delta ris the amount that recombination is modified. We conclude that selection for recombination will be substantial only if there is tight linkage within the genome or if many loci are subject to directional selection as during periods of rapid evolutionary change.},
  author       = {Otto, Sarah and Barton, Nicholas H},
  issn         = {0016-6731},
  journal      = {Genetics},
  number       = {2},
  pages        = {879 -- 906},
  publisher    = {Genetics Society of America},
  title        = {{The evolution of recombination: Removing the limits to natural selection}},
  doi          = {10.1093/genetics/147.2.879},
  volume       = {147},
  year         = {1997},
}

@article{4286,
  abstract     = {A local barrier to gene flow will delay the spread of an advantageous allele. Exact calculations for the deterministic case show that an allele that is favorable when rare is delayed very little even by a strong barrier; its spread is allowed by a time proportional to log((B/σ)√2S)/S, where B is the barrier strength, σ the dispersal range, and fitnesses are 1:1 + S:1 + 2S. However, when there is selection against heterozytes, such that the allele cannot increase from low frequency, a barrier can cause a much greater delay. If gene flow is reduced below a critical value, spread is entirely prevented. Stochastic simulations show that with additive selection, random drift slows down the spread of the allele, below the deterministic speed of σ√2S. The delay to the advance of an advantageous allele caused by a strong barrier can be substantially increased by random drift and increases with B/(2Sρσ2) in a one-dimensional habitat of density ρ. However, with selection against heterozygotes, drift can facilitate the spread and can free an allele that would otherwise be trapped indefinitely by a strong barrier. We discuss the implications of these results for the evolution of chromosome rearrangements.},
  author       = {Piálek, Jaroslav and Barton, Nicholas H},
  issn         = {0016-6731},
  journal      = {Genetics},
  number       = {2},
  pages        = {493 -- 504},
  publisher    = {Genetics Society of America},
  title        = {{The spread of an advantageous allele across a barrier: the effects of random drift and selection against heterozygotes}},
  doi          = {10.1093/genetics/145.2.493},
  volume       = {145},
  year         = {1997},
}

@article{4287,
  abstract     = {We evaluate Sewall Wright's three-phase "shifting balance" theory of evolution, examining both the theoretical issues and the relevant data from nature and the laboratory. We conclude that while phases I and II of Wright's theory (the movement of populations from one "adaptive peak" to another via drift and selection) can occur under some conditions, genetic drift is often unnecessary for movement between peaks. Phase III of the shifting balance, in which adaptations spread from particular populations to the entire species, faces two major theoretical obstacles: (1) unlike adaptations favored by simple directional selection, adaptations whose fixation requires some genetic drift are often prevented from spreading by barriers to gene flow; and (2) it is difficult to assemble complex adaptations whose constituent parts arise via peak shifts in different demes. Our review of the data from nature shows that although there is some evidence for individual phases of the shifting balance process, there are few empirical observations explained better by Wright's three-phase mechanism than by simple mass selection. Similarly, artificial selection experiments fail to show that selection in subdivided populations produces greater response than does mass selection in large populations. The complexity of the shifting balance process and the difficulty of establishing that adaptive valleys have been crossed by genetic drift make it impossible to test Wright's claim that adaptations commonly originate by this process. In view of these problems, it seems unreasonable to consider the shifting balance process as an important explanation for the evolution of adaptations. },
  author       = {Coyne, Jerry and Barton, Nicholas H and Turelli, Michael},
  issn         = {0014-3820},
  journal      = {Evolution; International Journal of Organic Evolution},
  number       = {3},
  pages        = {643 -- 671},
  publisher    = {Wiley-Blackwell},
  title        = {{Perspective: A critique of Sewall Wright's shifting balance theory of evolutionight's shifting balance theory of evolution}},
  doi          = {10.1111/j.1558-5646.1997.tb03650.x},
  volume       = {51},
  year         = {1997},
}

@article{4288,
  abstract     = {We measured the heterozygous effects on net fitness of a sample of 12 wild-type third chromosomes in D. melanogaster. Effects on fitness were assessed by competing the wild-type chromosomes against balancer chromosomes, to prevent the production of recombinants. The measurements were carried out in the population cage environment in which the life history had been evolving, in an undisturbed population with overlapping generations, and replicated measurements were made on each chromosome to control for confounding effects such as mutation accumulation. We found significant variation among the wild type chromosomes in their additive genetic effect on net fitness. The system provides an opportunity to obtain an accurate estimate of the distribution of heterozygous effects on net fitness, the contribution of different fitness components including male mating success, and the role of intra-chromosomal epistasis in fitness variation.},
  author       = {Fowler, Kevin and Semple, Colin and Barton, Nicholas H and Partridge, Linda},
  issn         = {0962-8452},
  journal      = {Proceedings of the Royal Society of London Series B Biological Sciences},
  number       = {1379},
  pages        = {191 -- 199},
  publisher    = {The Royal Society},
  title        = {{Genetic variation for total fitness in Drosophila melanogaster}},
  doi          = {10.1098/rspb.1997.0027},
  volume       = {264},
  year         = {1997},
}

@article{4289,
  abstract     = {A worldwide survey of polymorphic molecular markers shows that the human population is genetically homogeneous, in close agreement with evidence from quite different genes and traits.},
  author       = {Barton, Nicholas H},
  issn         = {0960-9822},
  journal      = {Current Biology},
  number       = {12},
  pages        = {757 -- 758},
  publisher    = {Cell Press},
  title        = {{Population genetics: A new apportionment of human diversity}},
  doi          = {10.1016/S0960-9822(06)00397-6},
  volume       = {7},
  year         = {1997},
}

@article{4611,
  abstract     = {Presents a model-checking procedure and its implementation for the automatic verification of embedded systems. The system components are described as hybrid automata-communicating machines with finite control and real-valued variables that represent continuous environment parameters such as time, pressure and temperature. The system requirements are specified in a temporal logic with stop-watches, and verified by symbolic fixpoint computation. The verification procedure-implemented in the Cornell Hybrid Technology tool, HyTech-applies to hybrid automata whose continuous dynamics is governed by linear constraints on the variables and their derivatives. We illustrate the method and the tool by checking safety, liveness, time-bounded and duration requirements of digital controllers, schedulers and distributed algorithms},
  author       = {Alur, Rajeev and Henzinger, Thomas A and Ho, Pei},
  issn         = {0018-9162},
  journal      = {IEEE Transactions on Software Engineering},
  number       = {3},
  pages        = {181 -- 201},
  publisher    = {IEEE},
  title        = {{Automatic symbolic verification of embedded systems}},
  doi          = {10.1109/32.489079},
  volume       = {22},
  year         = {1996},
}

@article{6161,
  abstract     = {The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra- 1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defined several conserved regions likely to be important for tra-1 function. The phenotype differences between Ce-tra- 1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.},
  author       = {de Bono, Mario and Hodgkin, J.},
  issn         = {00166731},
  journal      = {Genetics},
  keywords     = {amino acid sequence, article, caenorhabditis elegans, evolution, genetic variability, nonhuman, priority journal, sex determination, Amino Acid Sequence, Animals, Animals, Genetically Modified, Base Sequence, Caenorhabditis, Caenorhabditis elegans, Caenorhabditis elegans Proteins, DNA, Helminth, DNA-Binding Proteins, Evolution, Molecular, Female, Helminth Proteins, Membrane Proteins, Molecular Sequence Data, Mutagenesis, RNA, Messenger, Sequence Homology, Amino Acid, Sex Determination (Analysis), Transcription Factors, Transgenes, Turner Syndrome, Animalia, Caenorhabditis, Caenorhabditis briggsae, Caenorhabditis elegans, Nematoda},
  number       = {2},
  pages        = {587--595},
  publisher    = {Genetics Society of America},
  title        = {{Evolution of sex determination in Caenorhabditis: Unusually high divergence of tra-1 and its functional consequences}},
  volume       = {144},
  year         = {1996},
}

@inproceedings{11927,
  abstract     = {We are given a set 7 = {Tl , Tz, . . . , Tk} of rooted binary trees, each Ti leaf-labeled by a subset L(x) c {1,2 )...) n}. IfT is a tree on {1,2, . . , n}, we let T]L denote the subtree of T induced by the nodes of L and all their ancestors. The consensus tree problem asks whether there exists a tree T* such that for every I, T’ IC(Ti) is homeomorphic to Ti. We present algorithms which test if a given set of trees has a consensus tree and if so, construct one. The deterministic algorithm takes time min{O(mn’/‘), O(m + n2 logn)}, where m = Ci IZl and uses linear space. The randomized algorithm takes
time O(m log3 n) and uses linear space. The previous best for this problem was an 1981 O(mn) algorithm by Aho et al. Our faster deterministic algorithm uses a new efficient algorithm for the following interesting dynamic graph problem: Given a graph G with n nodes and m edges and a sequence of b batches of one or more edge deletions, then after each batch, either find a new component that has just been created or determine that there is no such component. For this
problem, we have a simple algorithm with running time O(n2 log n + be min{ n2, m log n}), where be is the number of batches which do not result in a new component. For our particular application, bc 5 1. If all edges are deleted, then the best previously known deterministic algorithm requires time O(mJ;ii) to solve this problem. computational evolutionary biology. The first application is in the problem of inferring consensus of trees when there can be disagreement[l6]. There have, been several models suggested for this problem[2, 3, 4, 8, ?, 11, 17, 181, of which one is called the Local Consensus Tree[l5]. The local consensus tree model presumes that the user provides a local consensus rule which determines the form of the output tree on (perhaps) each triple of leaves, and the objective is to determine whether a tree exists which is consistent with each of the constraints. We will show that we can construct the local consensus tree of k trees on n species in O(kn3) time, improving on the O(lcn3 + n”) running time if we use the Aho et al algorithm. The second application is a
heuristic for constructing the maximum likelihood tree based upon combining solutions to small subproblems.
This is a simple and yet potentially significantly interesting approach to the evolutionary tree construction
problem. },
  author       = {Henzinger, Monika H and King, Valerie and Warnow, Tandy},
  booktitle    = {7th Annual ACM-SIAM Symposium on Discrete Algorithms},
  isbn         = {0898713668},
  location     = {Atlanta, GA, United States},
  pages        = {333 --340},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology}},
  year         = {1996},
}