bluuebunny/crossref_metadata_2025 huggingface dataset:
Translation, Value, and Space: Theorizing an Ethnographic and Engaged Environmental Anthropology
Authors: WEST PAIGE
Published: December 2005

In this article, I argue for placing the politics of translation and theories of value and spatial production at the center of environmental anthropology. For the past ten years, the Gimi‐speaking peoples living in Maimafu village, Papua New Guinea, have taken part in an integrated conservation and development project attempting to foster a local system of valuing “nature” by tying biological diversity to economic markets through the creation of “eco‐enterprises.” However, the project fails to consider how Gimi produce, theorize, transmit, and express knowledge. Using ethnographic material concerned with hunting and song composition, I show that Gimi understand their forests to be part of a series of transactive dialectical relationships that work to produce identity and space. I also demonstrate that, as part of this project, Gimi social relations with their forests have been translated in ways that fit their beliefs into generic and easily understandable categories. This has been detrimental to the conservation project and it is politically problematic for an engaged environmental anthropology.
Emplacement and Millennial Expectations in an Era of Development and Globalization: Heaven and the Appeal of Christianity for the Ipili
Authors: JACKA JERRY K.
Published: December 2005

Non‐Western Christianity engages with capitalist development and ideas of modernization from multiple and competing perspectives. In this article, I argue that as researchers we can weave together disparate theoretical strands attempting to explain the appeal of Christianity—particularly its Pentecostal and charismatic forms—by examining indigenous notions of “salvation” that have often been overlooked in the literature. To illustrate, I examine millennial Christianity among the Ipili of Papua New Guinea, demonstrating how their understandings of “heaven” and their desire for the Second Coming articulate with a concern regarding how social relations are spatialized through engagement with capitalist mining development, evangelical Christianity, and traditional spirits responsible for maintaining the world's integrity.
The Obvious Aspects of Ecological Underprivilege in Ankarana, Northern Madagascar
Authors: WALSH ANDREW
Published: December 2005

On the basis of research conducted in the Ankarana region of northern Madagascar, I discuss the speculating that Malagasy participants in the local sapphire trade do about foreign ecotourists who come to this region. Although some have been promoting international ecotourism in the region as a viable means to a sustainable future for local people and ecosystems, others, including many of the observers discussed here, see the rise of the ecotourist trade and the increasing presence of its clients in Ankarana as signs of foreigners' long‐standing interests in Malagasy resources. I argue that to understand the perspectives of these critical observers, it is necessary to appreciate what they take to be obvious about ecotourism and the conservation projects with which they are commonly associated.
The Organization of Male and Female Labor in Foraging Societies: Implications for Early Paleoindian Archaeology
Authors: WAGUESPACK NICOLE M.
Published: December 2005

I use cross‐cultural ethnographic data to explore the relationship between male and female subsistence labor among hunter‐gatherer populations by examining data regarding resource procurement, time allocation, and task differentiation between the sexes relative to dependence on hunted foods. The findings indicate that female foragers generally perform a variety of nonsubsistence collection activities and preferentially procure high‐return resources in hunting‐based economies. I develop ideas about predictable relationships concerning the amount of time female foragers expend on subsistence and technological tasks relative to the dietary contribution of meat. I then use ethnographic trends to evaluate archaeological assumptions regarding the sexual division of labor in prehistoric foraging contexts, focusing on the dichotomous views of Clovis labor organization. I argue that archaeological interpretations of prehistoric labor roles in hunting‐based foraging societies are commonly polarized between stereotypical views of male and female subsistence behaviors. I develop an interpretation of Early Paleoindian labor organization, emphasizing female labor in the production of material goods and the procurement of low‐risk plant and animal resources based on global economic trends among foragers.
Anthropology as a Subversive Art: A Review of Through These Eyes
Authors: RUBY JAY
Published: December 2005

This is a review of the film Through These Eyes, by Charles Laird. The film explores the historical moment during the Cold War in which the National Science Foundation funded educational curricula and programs to advance education in the sciences. Through These Eyes focuses on the history of one course of study as a part of these programs, a year‐long course called “Man, a Course of Study” that presented fifth‐grade students with materials designed to have them explore what it means to be a human being, by combining biology, primatology, and some anthropology.
Updating Images of South Sudan
Authors: SHANDY DIANNA J.
Published: December 2005

In this essay, I compare and contrast two recent films that update the anthropological record on what has become of Nuer and Dinka people of southern Sudan by documenting their resettlement in the United States as refugees. Lost Boys of Sudan and A Great Wonder: Lost Children of Sudan Resettling in America trace the displacement of Sudanese youth by the civil war and their adaptation to U.S. life. Both films provide an alternative way of viewing these youth that challenges the “uprooted” and “denuded” refugee stereotype. By examining Nuer and Dinka within a refugee migration framework, these films engage broader theoretical questions about the tension between refugees as victims of larger structural events beyond their control and their adaptive strategies in negotiating complex and shifting circumstances.
Critical Investigations of Age and Aging in the United States
Authors: LAMB SARAH E.
Published: December 2005

Aged by Culture. Margaret Morganroth Gullette. Chicago: University of Chicago Press, 2004. 267 pp.

Breaking the Watch: The Meanings of Retirement in America. Joel S. Savishinsky. Ithaca, NY: Cornell University Press, 2000. 281 pp.

My Mother's Hip: Lessons from the World of Eldercare. Luisa Margolies. Philadelphia: Temple University Press, 2004. 339 pp.
Indigenous Peoples, State‐Sanctioned Knowledge, and the Politics of Recognition
Authors: RANCO DARREN J.
Published: December 2005

Invisible Indigenes: The Politics of Nonrecognition. Bruce G. Miller. Lincoln: University of Nebraska Press, 2003. 248 pp.

Forgotten Tribes: Unrecognized Indians and the Federal Acknowledgement Process. Mark Edwin Miller. Lincoln: University of Nebraska Press, 2004. 355 pp.

Gambling and Survival in Native North America. Paul Pasquaretta. Tucson: University of Arizona Press, 2003. 202 pp.
Culture on Tour: Ethnographies of Travel
Authors: KAHN MIRIAM
Published: December 2005

Culture on Tour: Ethnographies of Travel. Edward M. Bruner. Chicago: University of Chicago Press, 2005. 308 pp.
After Kinship
Authors: BARLOW KATHLEEN
Published: December 2005

After Kinship. Janet Carsten. Cambridge: Cambridge University Press, 2004. 216 pp.
Ruth Landes: A Life in Anthropology
Authors: SILVERSTEIN LENI M.
Published: December 2005

Ruth Landes:. Life in Anthropology. Sally Cole. Lincoln: University of Nebraska Press, 2004. 299 pp.
Anthropology in the Margins of the State
Authors: HAYDEN ROBERT M.
Published: December 2005

Anthropology in the Margins of the State. Veena Das and Deborah Poole, eds. Santa Fe: School of American Research Press, 2004. 330 pp.
The Gift in Sixteenth‐Century France
Authors: OHNUKI‐TIERNEY EMIKO
Published: December 2005

The Gift in Sixteenth‐Century France. Natalie Zemon Davis. Madison: University of Wisconsin Press. 2000. 196 pp.
Stitches on Time: Colonial Textures and Postcolonial Tangles
Authors: LUDDEN DAVID
Published: December 2005

Stitches on Time: Colonial Textures and Postcolonial Tangles. Saurabh Dube. Durham, NC: Duke University Press, 2004. 259 pp.
The Curious Feminist: Searching for Women in a New Age of Empire
Authors: HANGEN SUSAN
Published: December 2005

The Curious Feminist: Searching for Women in. New Age of Empire. Cynthia Enloe. Berkeley: University of California Press, 2004. 367 pp.
Making Place: State Projects, Globalisation and Local Responses in China
Authors: JACKA TAMARA
Published: December 2005

Making Place: State Projects, Globalisation and Local Responses in China. Stephan Feuchtwang, ed. London: University College London Press, 2004. 214 pp.
The Spectacular City: Violence and Performance in Urban Bolivia
Authors: GOODALE MARK
Published: December 2005

The Spectacular City: Violence and Performance in Urban Bolivia. Daniel M. Goldstein. Durham, NC: Duke University Press, 2004. 275 pp.
Reckoning with Homelessness
Authors: BERISS DAVID I.
Published: December 2005

Reckoning with Homelessness. Kim Hopper. Ithaca, NY: Cornell University Press, 2003. 271 pp.
Casta Painting
Authors: DELPLATO JOAN
Published: December 2005

Casta Painting. Ilona Katzew. New Haven, CT: Yale University Press, 2004. 256 pp.
Words and Stones: The Politics of Language and Identity in Israel
Authors: STEIN REBECCA L.
Published: December 2005

Words and Stones: The Politics of Language and Identity in Israel. Daniel Lefkowitz. New York: Oxford University Press, 2004. 316 pp.
Cattle Bring Us to Our Enemies: Turkana Ecology, Politics, and Raiding in a Disequilibrium System
Authors: LESOROGOL CAROLYN K.
Published: December 2005

Cattle Bring Us to Our Enemies: Turkana Ecology, Politics, and Raiding in. Disequilibrium System. J. Terrence McCabe. Ann Arbor: University of Michigan Press, 2004. 299 pp.
Global Prescriptions: Gendering Health and Human Rights
Authors: FINKLER KAJA
Published: December 2005

Global Prescriptions: Gendering Health and Human Rights. Rosalind Pollack Petchesky. London: Zed Books, 2003. 306 pp.
Working Images: Visual Research and Representation in Ethnography
Authors: BIRD S. ELIZABETH
Published: December 2005

Working Images: Visual Research and Representation in Ethnography. Sarah Pink, László Kürti, and Ana Isabel Afonso. New York: Routledge, 2004. 224 pp.
Colormute: Race Talk Dilemmas in an American School
Authors: PAGE ENOCH H.
Published: December 2005

Colormute: Race Talk Dilemmas in an American School. Mica Pollock. Princeton, NJ: Princeton University Press, 2004. 268 pp.
Household Decisions, Gender and Development: A Synthesis of Recent Research
Authors: CHANT SYLVIA
Published: December 2005

Household Decisions, Gender and Development:. Synthesis of Recent Research. Agnes R. Quisumbing, ed. Washington, DC: International Food Policy Research Institute, 2003. 274 pp.
Culture and Public Action
Authors: HARRISON ELIZABETH
Published: December 2005

Culture and Public Action. Vijayendra Rao and Michael Walton, eds. Stanford: Stanford University Press, 2004. 442 pp.
Kahnawa:ke: Factionalism, Traditionalism, and Nationalism in a Mohawk Community
Authors: BONVILLAIN NANCY
Published: December 2005

Kahnawa:ke: Factionalism, Traditionalism, and Nationalism in. Mohawk Community. Gerald F. Reid. Lincoln: University of Nebraska Press, 2004. 235 pp.
Governing China's Multiethnic Frontiers
Authors: CULAS CHRISTIAN
Published: December 2005

Governing China's Multiethnic Frontiers. Morris Rossabi, ed. Seattle: University of Washington Press, 2004. 296 pp.
Threatening Others: Nicaraguans and the Formation of National Identities in Costa Rica
Authors: BASOK TANYA
Published: December 2005

Threatening Others: Nicaraguans and the Formation of National Identities in Costa Rica. Carlos Sandoval‐García. Athens: Ohio University Press, 2004. 263 pp.
The Political Landscape: Constellations of Authority in Early Complex Polities
Authors: STEINBERG JOHN M.
Published: December 2005

The Political Landscape: Constellations of Authority in Early Complex Polities. Adam T. Smith. Berkeley: University of California Press, 2003. 346 pp.
Biological Anthropology and Ethics: From Repatriation to Genetic Identity
Authors: DELGADO ROBERTO
Published: December 2005

Biological Anthropology and Ethics: From Repatriation to Genetic Identity. Trudy R. Turner, ed. Albany: State University of New York Press, 2004. 327 pp.
The Intimate Economies of Bangkok: Tomboys, Tycoons, and Avon Ladies in the Global City
Authors: SCHEIN LOUISA
Published: December 2005

The Intimate Economies of Bangkok: Tomboys, Tycoons, and Avon Ladies in the Global City. Ara Wilson. Berkeley: University of California Press, 2004. 272 pp.
Culture and the Question of Rights: Forests, Coasts, and Seas in Southeast Asia
Authors: LOWE CELIA
Published: December 2005

Culture and the Question of Rights: Forests, Coasts, and Seas in Southeast Asia. Charles Zerner, ed. Durham, NC: Duke University Press, 2003. 289 pp.
Music and Late Elizabethan Politics: The Identities of Oriana and Diana
Authors: SMITH JEREMY L.
Published: December 2005

This essay challenges the current assessment that Thomas Morley's collection, The Triumphes of Oriana, was an uncomplicated musical tribute to Queen Elizabeth I, who was represented allegorically by Oriana, heroine of the romance Amadis de Gaule. It takes into account both the political context surrounding the Essex Revolt, the Elizabethan succession question, and the Catholic issue and the ideas reflected in the poetry that was set to music, as well as some of the music itself. It can be shown that both Morley and his mentor William Byrd were strongly linked to the Sidney/Essex complex of ideals that had a special appeal to Catholics who hoped for a more tolerant regime and who looked to Essex and a Jamesian succession as possible vehicles of salvation. Demonstrating the unsuitability of the Oriana characterization for Elizabeth, I propose a different allegorical identity not only for “Oriana” (James's wife Anna) but also for the character “Diana” (Essex's sister Penelope Rich), who appears in key works by Byrd and in all the Oriana madrigals as well. Certain songs by Byrd promoted the ideas of Sidney and his circle as well as Essex's image as the “heir to Sir Philip Sidney.” Morley's project for the Triumphes began originally, evidence shows, as a musical offering pleasing to the Essex camp and supportive of James's succession. A marked shift in political circumstances between 1600 and 1601 made it incumbent upon Morley and his collaborators to pay tribute to Elizabeth instead, but not all traces of the original intent were effaced. The ambivalence in the meaning of the Oriana and Diana allegories continued into the post-Elizabethan era.
The Beloved's Image: Handel's Admeto and the Statue of Alcestis
Authors: HELLER WENDY
Published: December 2005

This essay offers a new interpretation of Handel's Admeto (1727) in the context of its literary and operatic antecedents. Focusing on the erotic triangle between the lover, the beloved, and the image of the beloved—a “fundamental story” expressed in its paradigmatic form in Euripides' play Alcestis—the essay demonstrates the unexpected ways in which Handel's opera—and its Venetian and Hannoverian predecessors—absorbed the residue of the Euripidean tradition, reconciling fundamental truths about lovers and their beloveds with early modern customs and ways of thinking about art, theater, and life. It takes account of the special importance that this libretto had for the Hannoverian dynasty (in particular Electress Sophia, consort of Ernst August, the father of George I), exploring as well how one of opera's most ubiquitous props—the portrait—reflected an early modern fascination with the power of simulacra to substitute for living beings. In this context, the oft-criticized conventions of Venetian opera that were retained by Handel—including not only the use of the portrait, but transvestism and a double-woman plot—emerge as part of a seicento sensibility that was not only embraced by the Venetians and the Hannoverians, but was integral to the dramatic vision expressed in Admeto. In so doing, the essay provides not only a new account of Admeto's rapport with the ancients, but also a more nuanced account of Handel's debt to the Venetian legacy.
A Minstrel in a World without Minstrels: Adorno and the Case of Schreker
Authors: LEE SHERRY D.
Published: December 2005

Franz Schreker (1878–1934) was widely regarded during the height of his career as a daringly modern and controversial composer. The tremendous initial popularity of his operas gave no forewarning of the virtual oblivion to which their composer would be consigned by history. Theodor W. Adorno's 1959 essay on Schreker recalls the composer's importance on the early modernist scene, but criticizes him for producing sensually alluring yet technically defi- cient works that sought to escape rather than authentically express the crisis of the modernist human condition. This article takes Adorno's essay as a starting point for a reexamination of Schreker's Der ferne Klang (1912) and defends the critical quality of Schreker's artistic conception. Adorno focuses on Schreker's idea of musical sound: Klang as a harmonic-timbral entity that draws attention to itself as sensuous sonority, evocative of pleasurable fantasy. However, the opera's text, which Schreker wrote himself, demonstrates a critical awareness of the problems confronting the modern artist, whose expressive needs collide with society's limitations. While the musical dimension evokes the ineffable qualities of the artist's vision of expressive freedom, the realm of narrative embodies, in sometimes strikingly realistic terms, the all-too-present social realities he cannot escape. Rehearing Der ferne Klang after a close reading of the narrative reveals a dialectical dimension between music and text that problematizes Adorno's critique.
Modeling Haplotype Block Variation Using Markov Chains
Authors: Greenspan G , Geiger D
Published: December 2005

Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model that groups SNPs into haplotype blocks and represents the dependencies between blocks by a Markov chain. We develop an error measure to compare the performance of this model against the common model that assumes that blocks are independent. By examining data from the International Haplotype Mapping project, we show how the Markov model over haplotype blocks is most accurate when representing blocks in strong linkage disequilibrium. This contrasts with the independent model, which is rendered less accurate by linkage disequilibrium. We provide a theoretical explanation for this surprising property of the Markov model and relate its behavior to allele diversity.
Optimal Design and Analysis of Genetic Studies on Gene Expression
Authors: Fu Jingyuan , Jansen Ritsert C
Published: December 2005

Whole-genome profiling of gene expression in a segregating population has the potential to identify the regulatory consequences of natural allelic variation. Costs of such studies are high and require that resources—microarrays and population—are used as efficiently as possible. We show that current studies can be improved significantly by a new design for two-color microarrays. Our “distant pair design” profiles twice as many individuals as there are arrays, cohybridizes individuals with dissimilar genomes, gives more weight to known regulatory loci if wished, and therewith maximizes the power for decomposing expression variation into regulatory factors. It can also exploit a large population (larger than twice the number of available microarrays) as a useful resource to select the most dissimilar pairs of individuals from. Our approach identifies more regulatory factors than alternative strategies do in computer simulations for realistic genome sizes, and similar promising results are obtained in an application on Arabidopsis thaliana. Our results will aid the design and analysis of future studies on gene expression and will help to shed more light on gene regulatory networks.
Efficient Inference of Haplotypes From Genotypes on a Large Animal Pedigree
Authors: Baruch Eyal , Weller Joel Ira , Cohen-Zinder Miri , Ron Micha , Seroussi Eyal
Published: December 2005

We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes. The rate of haplotype resolution for the simulated data was >91% with a standard deviation of 2%. With 20% missing data, the rate of haplotype resolution was 67.5% with a standard deviation of 1.3%. In both cases all recovered haplotypes were correct. In the real data, allele origin was resolved for 22% of the heterozygous genotypes, even though 70% of the genotypes were missing. Haplotypes were resolved for 36% of the males. Computing time was insignificant for both data sets. Despite the intricacy of large-scale real pedigree genotypes, the proposed algorithm provides a practical rule-based solution for resolving haplotypes for small chromosomal segments in commercial animal populations.
Evolutionary Rates and Expression Level in Chlamydomonas
Authors: Popescu Cristina E , Borza Tudor , Bielawski Joseph P , Lee Robert W
Published: December 2005

In many biological systems, especially bacteria and unicellular eukaryotes, rates of synonymous and nonsynonymous nucleotide divergence are negatively correlated with the level of gene expression, a phenomenon that has been attributed to natural selection. Surprisingly, this relationship has not been examined in many important groups, including the unicellular model organism Chlamydomonas reinhardtii. Prior to this study, comparative data on protein-coding sequences from C. reinhardtii and its close noninterfertile relative C. incerta were very limited. We compiled and analyzed protein-coding sequences for 67 nuclear genes from these taxa; the sequences were mostly obtained from the C. reinhardtii EST database and our C. incerta EST data. Compositional and synonymous codon usage biases varied among genes within each species but were highly correlated between the orthologous genes of the two species. Relative rates of synonymous and nonsynonymous substitution across genes varied widely and showed a strong negative correlation with the level of gene expression estimated by the codon adaptation index. Our comparative analysis of substitution rates in introns of lowly and highly expressed genes suggests that natural selection has a larger contribution than mutation to the observed correlation between evolutionary rates and gene expression level in Chlamydomonas.
Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula)
Authors: Ingvarsson Pär K , García M Victoria , Hall David , Luquez Virginia , Jansson Stefan
Published: December 2005

The initiation of growth cessation and dormancy represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees. The most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset of these trees in a growth chamber experiment. Buds set showed significant clinal variation with latitude, explaining ∼90% of the population variation in bud set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of an adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions with excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation can be useful for identifying sites putatively involved in local adaptation.
Allele Frequency Distribution Under Recurrent Selective Sweeps
Authors: Kim Yuseob
Published: December 2005

The allele frequency of a neutral variant in a population is pushed either upward or downward by directional selection on a linked beneficial mutation (“selective sweeps”). DNA sequences sampled after the fixation of the beneficial allele thus contain an excess of rare neutral alleles. This study investigates the allele frequency distribution under selective sweep models using analytic approximation and simulation. First, given a single selective sweep at a fixed time, I derive an expression for the sampling probabilities of neutral mutants. This solution can be used to estimate the time of the fixation of a beneficial allele from sequence data. Next, I obtain an approximation to mean allele frequencies under recurrent selective sweeps. Under recurrent sweeps, the frequency spectrum is skewed toward rare alleles. However, the excess of high-frequency derived alleles, previously shown to be a signature of single selective sweeps, disappears with recurrent sweeps. It is shown that, using this approximation and multilocus polymorphism data, genomewide parameters of directional selection can be estimated.
The Concordance of Gene Trees and Species Trees at Two Linked Loci
Authors: Slatkin Montgomery , Pollack Joshua L
Published: December 2005

The gene genealogies of two linked loci in three species are analyzed using a series of Markov chain models. We calculate the probability that the gene tree of one locus is concordant with the species tree, given that the gene tree of the other locus is concordant. We define a threshold value of the recombination rate, r*, to be the rate for which the difference between the conditional probability of concordance and its asymptotic value is reduced to 5% of the initial difference. We find that, although r* depends in a complicated way on the times of speciation and effective population sizes, it is always relatively small, <10/N4, where N4 is the effective size of the species represented by the internal branch of the species tree. Consequently, the concordance of gene trees of neutral loci with the species tree is expected to be on roughly the same length scale on the chromosome as the extent of significant linkage disequilibrium within species unless the effective size of contemporary populations is very different from the effective sizes of their ancestral populations. Both balancing selection and selective sweeps can result in much longer genomic regions having concordant gene trees.
Variable Pleiotropic Effects From Mutations at the Same Locus Hamper Prediction of Fitness From a Fitness Component
Authors: Pepin Kim M , Samuel Melanie A , Wichman Holly A
Published: December 2005

The relationship of genotype, fitness components, and fitness can be complicated by genetic effects such as pleiotropy and epistasis and by heterogeneous environments. However, because it is often difficult to measure genotype and fitness directly, fitness components are commonly used to estimate fitness without regard to genetic architecture. The small bacteriophage ϕX174 enables direct evaluation of genetic and environmental effects on fitness components and fitness. We used 15 mutants to study mutation effects on attachment rate and fitness in six hosts. The mutants differed from our lab strain of ϕX174 by only one or two amino acids in the major capsid protein (gpF, sites 101 and 102). The sites are variable in natural and experimentally evolved ϕX174 populations and affect phage attachment rate. Within the limits of detection of our assays, all mutations were neutral or deleterious relative to the wild type; 11 mutants had decreased host range. While fitness was predictable from attachment rate in most cases, 3 mutants had rapid attachment but low fitness on most hosts. Thus, some mutations had a pleiotropic effect on a fitness component other than attachment rate. In addition, on one host most mutants had high attachment rate but decreased fitness, suggesting that pleiotropic effects also depended on host. The data highlight that even in this simple, well-characterized system, prediction of fitness from a fitness component depends on genetic architecture and environment.
Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags
Authors: Begun David J , Lindfors Heather A , Thompson Melissa E , Holloway Alisha K
Published: December 2005

The fraction of the genome associated with male reproduction in Drosophila may be unusually dynamic. For example, male reproduction-related genes show higher-than-average rates of protein divergence and gene expression evolution compared to most Drosophila genes. Drosophila male reproduction may also be enriched for novel genetic functions. Our earlier work, based on accessory gland protein genes (Acp's) in D. simulans and D. melanogaster, suggested that the melanogaster subgroup Acp's may be lost and/or gained on a relatively rapid timescale. Here we investigate this possibility more thoroughly through description of the accessory gland transcriptome in two melanogaster subgroup species, D. yakuba and D. erecta. A genomic analysis of previously unknown genes isolated from cDNA libraries of these species revealed several cases of genes present in one or both species, yet absent from ingroup and outgroup species. We found no evidence that these novel genes are attributable primarily to duplication and divergence, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA.
Chromosome Segment Duplications in Neurospora crassa and Their Effects on Repeat-Induced Point Mutation and Meiotic Silencing by Unpaired DNA
Authors: Vyas Meenal , Ravindran C , Kasbekar Durgadas P
Published: December 2005

The size and extent of four Neurospora crassa duplications, Dp(AR17), Dp(IBj5), Dp(OY329), and Dp(B362i), was determined by testing the coverage of RFLP markers. The first three duplications were all >∼350 kb and have been shown in earlier studies to act as dominant suppressors of repeat-induced point mutation (RIP) in gene-sized duplications, possibly via titration of the RIP machinery. Dp(B362i), which is only ∼117 kb long, failed to suppress RIP. RIP suppression in gene-sized duplications by large duplications was demonstrated using another test gene, dow, and supposedly applies generally. Crosses homozygous for Dp(AR17) or Dp(IBj5) were as barren as heterozygous crosses. Barrenness of the heterozygous but not the homozygous crosses was suppressible by Sad-1, a semidominant suppressor of RNAi-dependent meiotic silencing by unpaired DNA. A model is proposed in which large duplications recessively suppress semidominant Sad-1 mutations. The wild-isolated Sugartown strain is hypothesized to contain a duplication that confers not only dominant suppression of RIP but also a barren phenotype, which is linked (9%) to supercontig 7.118 in LG VII.
New Arabidopsis Recombinant Inbred Line Populations Genotyped Using SNPWave and Their Use for Mapping Flowering-Time Quantitative Trait Loci
Authors: El-Lithy Mohamed E , Bentsink Leónie , Hanhart Corrie J , Ruys Gerda J , Rovito Daniela , Broekhof José L M , van der Poel Hein J A , van Eijk Michiel J T , Vreugdenhil Dick , Koornneef Maarten
Published: December 2005

The SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Ler as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Ler has an allele different from one, two, or three of the other accessions.
Gene Action of New Mutations in Arabidopsis thaliana
Authors: Shaw Ruth G , Chang Shu-Mei
Published: December 2005

For a newly arising mutation affecting a trait under selection, its degree of dominance relative to the preexisting allele(s) strongly influences its evolutionary impact. We have estimated dominance parameters for spontaneous mutations in a subset of lines derived from a highly inbred founder of Arabidopsis thaliana by at least 17 generations of mutation accumulation (MA). The labor-intensive nature of the crosses and the anticipated subtlety of effects limited the number of MA lines included in this study to 8. Each MA line was selfed and reciprocally crossed to plants representing the founder genotype, and progeny were assayed in the greenhouse. Significant mutational effects on reproductive fitness included a recessive fitness-enhancing effect in one line and fitness-reducing effects, one additive and the other slightly recessive. Mutations conferring earlier phenology or smaller leaves were significantly recessive. For effects increasing leaf number and reducing height at flowering, additive gene action accounted for the expression of the traits. The sole example of a significantly dominant mutational effect delayed phenology. Our findings of recessive action of a fitness-enhancing mutational effect and additive action of a deleterious effect counter a common expectation of (partial) dominance of alleles that increase fitness, but the frequency of occurrence of such mutations is unknown.
Pleiotropic Quantitative Trait Loci Contribute to Population Divergence in Traits Associated With Life-History Variation in Mimulus guttatus
Authors: Hall Megan C , Basten Christopher J , Willis John H
Published: December 2005

Evolutionary biologists seek to understand the genetic basis for multivariate phenotypic divergence. We constructed an F2 mapping population (N = 539) between two distinct populations of Mimulus guttatus. We measured 20 floral, vegetative, and life-history characters on parents and F1 and F2 hybrids in a common garden experiment. We employed multitrait composite interval mapping to determine the number, effect, and degree of pleiotropy in quantitative trait loci (QTL) affecting divergence in floral, vegetative, and life-history characters. We detected 16 QTL affecting floral traits; 7 affecting vegetative traits; and 5 affecting selected floral, vegetative, and life-history traits. Floral and vegetative traits are clearly polygenic. We detected a few major QTL, with all remaining QTL of small effect. Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained. We also compared the genetic architecture controlling floral trait divergence both within (our intraspecific study) and between species, on the basis of a previously published analysis of M. guttatus and M. nasutus. Eleven of our 16 floral QTL map to approximately the same location in the interspecific map based on shared, collinear markers, implying that there may be a shared genetic basis for floral divergence within and among species of Mimulus.
Chromosome-Level Homeology in Paleopolyploid Soybean (Glycine max) Revealed Through Integration of Genetic and Chromosome Maps
Authors: Walling Jason G , Shoemaker Randy , Young Nevin , Mudge Joann , Jackson Scott
Published: December 2005

Soybean has 20 chromosome pairs that are derived from at least two rounds of genomewide duplication or polyploidy events although, cytogenetically, soybean behaves like a diploid and has disomic inheritance for most loci. Genetically anchored genomic clones were used as probes for fluorescence in situ hybridization (FISH) to determine the level of postpolyploid chromosomal rearrangements and to integrate the genetic and physical maps to (1) assign linkage groups to specific chromosomes, (2) assess chromosomal structure, and (3) determine the distribution of recombination along the length of a chromosome. FISH mapping of seven putatively gene-rich BACs from linkage group L (chromosome 19) revealed that most of the genetic map correlates to the highly euchromatic long arm and that there is extensive homeology with another chromosome pair, although colinearity of some loci does appear to be disrupted. Moreover, mapping of BACs containing high-copy sequences revealed sequestration of high-copy repeats to the pericentromeric regions of this chromosome. Taken together, these data present a model of chromosome structure in a highly duplicated but diploidized eukaryote, soybean.
Fold Recognition of the Human Immunodeficiency Virus Type 1 V3 Loop and Flexibility of Its Crown Structure During the Course of Adaptation to a Host
Authors: Watabe Teruaki , Kishino Hirohisa , Okuhara Yoshiyasu , Kitazoe Yasuhiro
Published: December 2005

The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of the virus, which is an important determinant of HIV pathogenesis. Hence, the information about preferred conformations of the V3-loop region and its flexibility could be a crucial tool for understanding the mechanisms of progression from an initial infection to AIDS. Taking into account the uncertainty of the loop structure, we predicted the structural flexibility, diversity, and sequence fitness to the V3-loop structure for each of the sequences serially sampled during an asymptomatic period. Structural diversity correlated with sequence diversity. The predicted crown structure usage implied that structural flexibility depended on the patient and that the antigenic character of the virus might be almost uniform in a patient whose immune system is strong. Furthermore, the predicted structural ensemble suggested that toward the end of the asymptomatic period there was a change in the V3-loop structure or in the environment surrounding the V3 loop, possibly because of its proximity to the gp120 core.
Glc7–Reg1 Phosphatase Signals to Yck1,2 Casein Kinase 1 to Regulate Transport Activity and Glucose-Induced Inactivation of Saccharomyces Maltose Permease
Authors: Gadura Nidhi , Robinson Lucy C , Michels Corinne A
Published: December 2005

The Saccharomyces casein kinase 1 isoforms encoded by the essential gene pair YCK1 and YCK2 control cell growth and morphogenesis and are linked to the endocytosis of several membrane proteins. Here we define roles for the Yck1,2 kinases in Mal61p maltose permease activation and trafficking, using a yck1Δ yck2-2ts (yckts) strain with conditional Yck activity. Moreover, we provide evidence that Glc7–Reg1 phosphatase acts as an upstream activator of Yck1,2 kinases in a novel signaling pathway that modulates kinase activity in response to carbon source availability. The yckts strain exhibits significantly reduced maltose transport activity despite apparently normal levels and cell surface localization of maltose permease protein. Glucose-induced internalization and rapid loss of maltose transport activity of Mal61/HAp-GFP are not observed in the yckts strain and maltose permease proteolysis is blocked. We show that a reg1Δ mutant exhibits a phenotype remarkably similar to that conferred by yckts. The reg1Δ phenotype is not enhanced in the yckts reg1Δ double mutant and is suppressed by increased Yck1,2p dosage. Further, although Yck2p localization and abundance do not change in the reg1Δ mutant, Yck1,2 kinase activity, as assayed by glucose-induced HXT1 expression and Mth1 repressor stability, is substantially reduced in the reg1Δ strain.
The Integral Membrane Protein Pom34p Functionally Links Nucleoporin Subcomplexes
Authors: Miao Mi , Ryan Kathryn J , Wente Susan R
Published: December 2005

Here we have examined the function of Pom34p, a novel membrane protein in Saccharomyces cerevisiae, localized to nuclear pore complexes (NPCs). Membrane topology analysis revealed that Pom34p is a double-pass transmembrane protein with both the amino (N) and carboxy (C) termini positioned on the cytosolic/pore face. The network of genetic interactions between POM34 and genes encoding other nucleoporins was established and showed specific links between Pom34p function and Nup170p, Nup188p, Nup59p, Gle2p, Nup159p, and Nup82p. The transmembrane domains of Pom34p in addition to either the N- or C-terminal region were necessary for its function in different double mutants. We further characterized the pom34ΔN nup188Δ mutant and found it to be perturbed in both NPC structure and function. Mislocalization of a subset of nucleoporins harboring phenylalanine–glycine repeats was observed, and nuclear import capacity for the Kap104p and Kap121p pathways was inhibited. In contrast, the pom34Δ pom152Δ double mutant was viable at all temperatures and showed no such defects. Interestingly, POM152 overexpression suppressed the synthetic lethality of pom34Δ nup170Δ and pom34Δ nup59Δ mutants. We speculate that multiple integral membrane proteins, either within the nuclear pore domain or in the nuclear envelope, execute coordinated roles in NPC structure and function.
Analysis of Pyrimidine Catabolism inDrosophila melanogasterUsing Epistatic Interactions With Mutations of Pyrimidine Biosynthesis and β-Alanine Metabolism
Authors: Rawls John M
Published: December 2005

The biochemical pathway for pyrimidine catabolism links the pathways for pyrimidine biosynthesis and salvage with β-alanine metabolism, providing an array of epistatic interactions with which to analyze mutations of these pathways. Loss-of-function mutations have been identified and characterized for each of the enzymes for pyrimidine catabolism: dihydropyrimidine dehydrogenase (DPD), su(r) mutants; dihydropyrimidinase (DHP), CRMP mutants; β-alanine synthase (βAS), pyd3 mutants. For all three genes, mutants are viable and fertile and manifest no obvious phenotypes, aside from a variety of epistatic interactions. Mutations of all three genes disrupt suppression by the rudimentary gain-of-function mutation (rSu(b)) of the dark cuticle phenotype of black mutants in which β-alanine pools are diminished; these results confirm that pyrimidines are the major source of β-alanine in cuticle pigmentation. The truncated wing phenotype of rudimentary mutants is suppressed completely by su(r) mutations and partially by CRMP mutations; however, no suppression is exhibited by pyd3 mutations. Similarly, su(r) mutants are hypersensitive to dietary 5-fluorouracil, CRMP mutants are less sensitive, and pyd3 mutants exhibit wild-type sensitivity. These results are discussed in the context of similar consequences of 5-fluoropyrimidine toxicity and pyrimidine catabolism mutations in humans.
Genomewide Screen Reveals a Wide Regulatory Network for Di/Tripeptide Utilization inSaccharomyces cerevisiae
Authors: Cai Houjian , Kauffman Sarah , Naider Fred , Becker Jeffrey M
Published: December 2005

Small peptides of two to six residues serve as important sources of amino acids and nitrogen required for growth by a variety of organisms. In the yeast Saccharomyces cerevisiae, the membrane transport protein Ptr2p, encoded by PTR2, mediates the uptake of di/tripeptides. To identify genes involved in regulation of dipeptide utilization, we performed a systematic, functional examination of this process in a haploid, nonessential, single-gene deletion mutant library. We have identified 103 candidate genes: 57 genes whose deletion decreased dipeptide utilization and 46 genes whose deletion enhanced dipeptide utilization. On the basis of Ptr2p-GFP expression studies, together with PTR2 expression analysis and dipeptide uptake assays, 42 genes were ascribed to the regulation of PTR2 expression, 37 genes were involved in Ptr2p localization, and 24 genes did not apparently affect Ptr2p-GFP expression or localization. The 103 genes regulating dipeptide utilization were distributed among most of the Gene Ontology functional categories, indicating a very wide regulatory network involved in transport and utilization of dipeptides in yeast. It is anticipated that further characterization of how these genes affect peptide utilization should add new insights into the global mechanisms of regulation of transport systems in general and peptide utilization in particular.
Goldfish Hematopoietic Necrosis Herpesvirus (Cyprinid Herpesvirus 2) in the USA: Molecular Confirmation of Isolates from Diseased Fish
Authors: Goodwin A. E. , Khoo L. , LaPatra S. E. , Bonar C. , Key D. W. , Garner M. , Lee M. V. , Hanson L.
Published: December 2005

Moribund goldfish Carassius auratus from private collections and breeding facilities were tested for hematopoietic necrosis herpesvirus 2 (also known as cyprinid herpesvirus 2 (CyHV-2)) by degenerate polymerase chain reaction (PCR) of the viral polymerase gene followed by sequencing. The degenerate PCR method produced a fragment with a DNA sequence that was more than 99% identical to the sequence of CyHV-2. Histology and electron microscopy showed that the moribund fish had severe necrosis in the hematopoietic tissues of the kidney and spleen and that herpesvirus particles were present. In the three cases studied, the presence of the virus was associated with high mortality (up to 80%) that could not be attributed to any other cause. The CyHV-2 is very difficult to isolate in cell culture, but our PCR and case studies demonstrate that this virus has a wide geographic distribution in the United States and that goldfish hematopoietic necrosis herpesvirus disease is likely to be an important, but rarely detected, disease of goldfish.