bluuebunny/crossref_metadata_2025 huggingface dataset:
The Ontogenesis of Trust
Authors: Clément Fabrice , Koenig Melissa , Harris Paul
Published: August 2004

Abstract: Psychologists have emphasized children's acquisition of information through first‐hand observation. However, many beliefs are acquired from others’ testimony. In two experiments, most 4‐year‐olds displayed sceptical trust in testimony. Having heard informants’ accurate or inaccurate testimony, they anticipated that informants would continue to display such differential accuracy and they trusted the hitherto reliable informant. Yet they ignored the testimony of the reliable informant if it conflicted with what they themselves had seen. By contrast, three‐year‐olds were less selective in trusting a reliable informant. Thus, young children check testimony against their own experience and increasingly recognise that some informants are more trustworthy than others.
Narratives of Space, Time, and Life
Authors: Tversky Barbara
Published: August 2004

Abstract: The mind constructs narratives from what would otherwise be chaos. Narratives viewed minimally—at least two temporally ordered events—are revealed in the way people talk about space and time. Narratives replete with a voice, causality, and emotion are reflected in the stories people tell about their own lives, stories that, as acknowledged by their tellers, distort the details around 60% of the time, but, according to their tellers, distort the ‘truth’ far less often.
On Not Expecting Too Much from Narrative
Authors: Lamarque Peter
Published: August 2004

Abstract:  The paper offers a mildly deflationary account of narrative, drawing attention to the minimal, thus easily satisfied, conditions of narrativity and showing that many of the more striking claims about narrative are either poorly supported or refer to distinct classes of narrative—usually literary or fictional—which provide a misleading paradigm for narration in general. An enquiry into structural, referential, pragmatic, and value‐based features of narrative helps circumscribe the limits of narration and the test case of the narrative definition of the self is examined and shown to yield rather less that is often claimed.
Narrative and Coherence
Authors: Currie Gregory , Jureidini Jon
Published: August 2004

Abstract: We outline a theory of one puzzling aspect of human cognition: a tendency to exaggerate the degree to which agency is manifested in the world. We call this over‐coherent thinking. We use Pylyshyn's idea of cognitive penetrability to help characterize this notion. We argue that this kind of thinking is essentially narrative in form rather than theoretical. We develop a theory of the relation between the degree of narrativity in a representation and its aptness to represent, and to express, mind. We review the prospects for several theories about how over‐coherent thinking gains a purchase on motivation. We argue that progress in this difficult area may require the abandonment of a categorical belief/imagination distinction in favour of vaguely specified clusterings in a many‐dimensional cognitive space. We conclude with the idea that an error‐prone system for the retention of ideas that are low in some of the characteristics generally thought desirable in belief might emerge as a result of an arms‐race between deceivers and deceiver‐detectors.
Music as Narrative and Music as Drama
Authors: Levinson Jerrold
Published: August 2004

Abstract:  In this paper I address the issue of narrativity in music. The central question is the extent to which pure instrumental music in the classical tradition can or should be understood as narrative, that is, as narrating a story of some kind. I am interested in the varying potential and aptness for narrative construal of different sorts of instrumental music, and in what the content of such narratives might plausibly be thought to be. But ultimately I explore, at greater length, an alternative way of construing musical process, namely, as dramatic rather than narrative in nature, following the lead of two musicologists, Anthony Newcomb and Fred Maus. After a comparison of the respective merits of narrative and dramatic construals of music, the paper concludes with an illustrative reading, in dramatic mode, of part of the opening movement of Schubert's Piano Sonata in A minor, D. 845.
Shorthand, Syntactic Ellipsis, and the Pragmatic Determinants of What Is Said
Authors: Elugardo Reinaldo , Stainton Robert J.
Published: August 2004

Abstract:  Our first aim in this paper is to respond to four novel objections in Jason Stanley's ‘Context and Logical Form’. Taken together, those objections attempt to debunk our prior claims that one can perform a genuine speech act by using a sub‐sentential expression—where by ‘sub‐sentential expression’ we mean an ordinary word or phrase, not embedded in any larger syntactic structure. Our second aim is to make it plausible that, pace Stanley, there really are pragmatic determinants of the literal truth‐conditional content of speech acts. We hope to achieve this second aim precisely by defending the genuineness of sub‐sentential speech acts. Given our two aims, it is necessary to highlight briefly their connection—which we do in the first part of the Introduction. Following that, we introduce Stanley's novel objections. This is the role of the second part of the Introduction. We offer our rebuttals in Section 2 (against ‘shorthand’) and Section 3 (against syntactic ellipsis, among other things).
The Ups and Downs of State Budget Process Reform: Experience of Three Decades
Authors: Burns Robert C. , Lee Robert D.
Published: August 2004

From zero‐base budgeting to the Government Performance and Results Act, state budgeting systems have been synonymous with budgeting reform for over 30 years. This article examines the trends, both long‐term and short‐term, which have been identified through analysis of state budgeting office practices. Particular emphasis has been placed on understanding the changes in performance measurement over the period of 1970 to 2000. The findings reveal trends such as changes in the makeup of budget office personnel, a lack of budget offices in moving toward cost accounting, and trends in budget preparation and budget documents. Some budget reforms seem to have plateaued, beginning in the mid‐1990s, while other reforms have exhibited “backsliding.” It is clear that the states are not all marching in unison in reforming their budget systems. As with earlier phases of this study, the 2000 data raise many questions that will be explored in future research.
Budgetary Decision Making by Executive and Legislative Budget Analysts: The Impact of Political Cues and Analytical Information
Authors: Goodman Doug , Clynch Edward J.
Published: August 2004

We explore the extent to which attributes of individual analysts and institutional factors lead to budgetary decisions based on political cues and/or analytical information among executive and legislative budget analysts. We surveyed executive and legislative budget analysts in 13 western states to ascertain the factors that influence their budgetary decisions. The findings build on evidence from previous studies that confirms the complexity of factors affecting budget analysts' decisions, and they provide empirical support to analysts' use of a combination of information labeled “budget rationality” by Thurmaier and Willoughby. Also, we provide more conclusive evidence that both executive and legislative analysts follow similar decision‐making patterns.
Budget Stabilization Fund: Structural Features of the Enabling Legislation and Balance Levels
Authors: Hou Yilin
Published: August 2004

This article examines what leads to high balances of the budget stabilization fund (BSF) to make it a countercyclical fiscal tool. Checking state BSF laws, this article classifies BSF structural features into purposes, funding sources, balance caps, and use approval procedures. Using panel data (1979–1999) and controlling for related variables, this article tests the features' effects on BSF levels over the sample period and different phases of the economy to identify specific effects of the features in boom and lean years. The article also forwards policy recommendations for state governments to consider in designing or revising their BSF legislation.
Grant Levels and Debt Issuance: Is There a Relationship? Is There Symmetry?
Authors: Martell Christine R. , Smith Bridget M.
Published: August 2004

Although previous work on fiscal federalism and grants has focused on the effects of grants on expenditures, no published research examines the impact of decreasing grants on state financing. This research addresses how decreasing levels of federal grant money to states affect states' long‐term debt issuance, and whether the relationship is symmetric for increasing and decreasing grants. The model is tested with time series, cross‐sectional data from 1984 to 1999. The results show that grants affect debt issuance, the effect is asymmetric, and direction of the effect differs for different types of debt issuance.
The Impact of Tax Price on Spending Preferences
Authors: Robbins Mark D. , Simonsen Bill , Feldman Barry
Published: August 2004

In this article, we explore the influence of tax price information on citizen preferences for taxes and spending using mail surveys. We explore the effects on service support when varying levels of cost information. We also observe how the magnitude of service costs influences service support. While the presence of cost information corresponded with lower levels of respondent support for the most costly services, it was associated with higher levels of support for less expensive services. These effects were the same whether the tax price represented the respondent's actual household cost or the jurisdiction average household cost for each service.
To Marry or Not to Marry: Tax Is the Question
Authors: López‐Laborda Julio , Zárate‐Marco Anabel
Published: August 2004

In this article, we estimate the impact of the Spanish personal income tax, and other variables, on the decision to marry, with the study covering the period 1979 to 2001. There are three aspects that characterize this article: first, it is the first time this topic has been examined in Spain; second, we take into account the whole duration of the marriage when constructing the tax variables, not only the year of marriage; and third, we include the cost of housing among the explanatory variables, because this can play an important and statistically significant role in the marriage decision in Spain.
Modal Completion in the Poggendorff Illusion: Support for the Depth-Processing Theory
Authors: Spehar Branka , Gillam Barbara
Published: August 2004

The Poggendorff illusion is one of the most prominent geometrical-optical illusions and has attracted enduring interest for more than a hundred years. Most modern theories explain the illusion by postulating various kinds of distortion of the “test” component of the figure by the context or the inducing component. They make no reference to the importance of processes involved in three-dimensional scene perception for understanding the illusion. We measured the strength of the Poggendorff illusion in configurations containing solid inducing surfaces as opposed to the usual parallel lines. The surface, oblique-line, and background luminances were manipulated separately to create configurations consistent with modal completion of the obliques in front of the surface. The marked decrease in the size of the illusion in conditions favoring modal completion is consistent with claims that perceived spatial layout is a major determinant of the Poggendorff illusion.
Evidence of Perspective-Taking Constraints in Children's On-Line Reference Resolution
Authors: Nadig Aparna S. , Sedivy Julie C.
Published: August 2004

Young children's communication has often been characterized as egocentric. Some researchers claim that the processing of language involves an initial stage that relies on egocentric heuristics, even in adults. Such an account, combined with general developmental difficulties with late-stage processes, could provide an explanation for much of children's egocentric communication. However, the experimental data reported in this article do not support such an account: In an elicited-production task, 5- to 6-year-old children were found to be sensitive to their partner's perspective. Moreover, in an on-line comprehension task, they showed sensitivity to common-ground information from the initial stages of language processing. We propose that mutual knowledge is not distinct from other knowledge relevant for language processing, and exerts early effects on processing in proportion to its salience and reliability.
Children's Use of Landmarks: Implications for Modularity Theory
Authors: Learmonth Amy E. , Nadel Lynn , Newcombe Nora S.
Published: August 2004

Previous studies have shown that disoriented children use the geometric features of the environment to reorient, but the results have not consistently demonstrated whether children can combine such information with landmark information. Results indicating that they cannot suggest the existence of a geometric module for reorientation. However, results indicating that children can use geometric information in combination with landmark information challenge the modularity interpretation. An uncontrolled variable in the studies yielding conflicting results has been the size of the experimental space. In the present studies, which tested young children in spaces of two different sizes, the size of the space affected their ability to use available landmark information. In the small space, the children did not use the landmark to reorient, but in the large space they did. The ability of children to use landmarks in combination with geometric information raises important questions about the existence of an encapsulated geometric module.
Practicing Perfection: Piano Performance as Expert Memory
Authors: Chaffin Roger , Imreh Gabriela
Published: August 2004

A concert pianist recorded her practice as she learned the third movement, Presto, of J.S. Bach's Italian Concerto. She also described the formal structure of the piece and reported her decisions about basic features (e.g., fingering), interpretive features (e.g., phrasing), and cues to attend to during performance (performance cues). These descriptions were used to identify which locations, features, and cues she practiced most, which caused hesitations when she first played from memory, and which affected her recall 2 years later. Effects of the formal structure and performance cues on all three activities indicated that the pianist used the formal structure as a retrieval scheme and performance cues as retrieval cues. Like expert memorists in other domains, she engaged in extended retrieval practice, going to great lengths to ensure that retrieval was as rapid and automatic from conceptual (declarative) memory as from motor and auditory memory.
Seeing Your Own Touched Hands in a Mirror Modulates Cross-Modal Interactions
Authors: Maravita Angelo , Spence Charles , Sergent Claire , Driver Jon
Published: August 2004

In mirror reflections, visual stimuli in near peripersonal space (e.g., an object in the hand) can project the retinal image of far, extrapersonal stimuli “beyond” the mirror. We studied the interaction of such visual reflections with tactile stimuli in a cross-modal congruency task. We found that visual distractors produce stronger interference on tactile judgments when placed close to the stimulated hand, but observed indirectly as distant mirror reflections, than when directly observed in equivalently distant far space, even when in contact with a dummy hand or someone else's hand in the far location. The stronger visual-tactile interference for the mirror condition implies that near stimuli seen as distant reflections in a mirror view of one's own hands can activate neural networks coding peripersonal space, because these visual stimuli are coded as having a true source near to the body.
Visual Search Is Modulated by Action Intentions
Authors: Bekkering Harold , Neggers Sebastiaan F.W.
Published: August 2004

The influence of action intentions on visual selection processes was investigated in a visual search paradigm. A predefined target object with a certain orientation and color was presented among distractors, and subjects had to either look and point at the target or look at and grasp the target. Target selection processes prior to the first saccadic eye movement were modulated by the different action intentions. Specifically, fewer saccades to objects with the wrong orientation were made in the grasping condition than in the pointing condition, whereas the number of saccades to an object with the wrong color was the same in the two conditions. Saccadic latencies were similar under the different task conditions, so the results cannot be explained by a speed-accuracy trade-off. The results suggest that a specific action intention, such as grasping, can enhance visual processing of action-relevant features, such as orientation. Together, the findings support the view that visual attention can be best understood as a selection-for-action mechanism.
The development and initial validation of a questionnaire to measure craving for amphetamine
Authors: James Darren , Davies Gareth , Willner Paul
Published: August 2004

Aim  To develop and initially validate a multi‐dimensional questionnaire to measure cravings for amphetamine (speed).

Design, setting and participants  The design of the Desires for Speed Questionnaire (DSQ) was based on the Desires for Alcohol Questionnaire and was administered to 174 amphetamine users. Exploratory factor analyses were carried out on the data and relationships between questionnaire score and other variables were assessed. Further analyses were carried out to assess the sensitivity of the factor scores of the DSQ to various methods of amphetamine ingestion.

Findings  Factor analysis revealed that a four‐factor solution best described the data and that each of these factors were differentially sensitive to methods of amphetamine ingestion, with greater craving on all measures in intravenous amphetamine users. The factor structure identified from the present analysis was almost identical to that identified in recreational drinkers by Love et al. (1998).

Conclusions  The results validate and extend the findings of the work of Love et al. (1998) and provide support for a multifactorial account of amphetamine craving.
Variation in habitat preference and population structure among three species of the Lake Malawi cichlid genus Protomelas
Authors: PEREYRA RICARDO , TAYLOR MARTIN I. , TURNER GEORGE F. , RICO CIRO
Published: August 2004

Several studies have demonstrated strong population structuring over small distances in the rocky‐shore mbuna cichlid fishes from Lake Malawi, suggesting the potential for allopatric speciation. However, many endemic Lake Malawi cichlids are neither mbuna, nor confined to rocky shores. Using microsatellites, we investigated the population structure in three species of the non‐mbuna genus Protomelas. The rocky‐shore P. taeniolatus showed high levels of population structure even over distances of less than 1 km, while the sandy‐shore species P. similis showed no significant structure over distances up to 21 km. Protomelas fenestratus, which is generally found at the interface between rocks and sand, also showed low levels of population structure. Our results suggest that the model of allopatric speciation based on habitat fragmentation within the current lake basin may be equally applicable to rocky‐shore non‐mbuna as to mbuna, but that an alternative model is required to explain speciation among sandy‐shore species as well as the deep‐water and pelagic species.
Small effective population sizes in a widespread selfing species, Lymnaea truncatula (Gastropoda: Pulmonata)
Authors: MEUNIER C. , HURTREZ‐BOUSSES S. , DURAND P. , RONDELAUD D. , RENAUD F.
Published: August 2004

We present here a spatial and temporal population genetic survey of a common freshwater snail, also a predominantly selfing species, Lymnaea truncatula. The rate of genetic diversity loss was quantified by estimating the effective size (Ne) of the snail populations, using two different methods. A temporal survey allowed estimation of a variance effective size of the populations, and a spatial survey allowed the estimation of an inbreeding effective size, from two‐locus identity disequilibria estimates. Both methods were consistent and provided low Ne values. Drift due to (i) high amounts of selfing and (ii) fluctuations in population sizes because of temporary habitats, and also selection coupled to genome‐wide linkage disequilibria, could explain such reductions in Ne. The loss of genetic diversity appears to be counterbalanced only very partially by low apparent rates of gene flow.
Chloroplast haplotype variation among monoecious and dioecious populations of Sagittaria latifolia (Alismataceae) in eastern North America
Authors: DORKEN M. E. , BARRETT S. C. H.
Published: August 2004

Aquatic plants commonly have extensive geographical distributions, implying few restrictions to dispersal. Here we investigate the postglacial history of an aquatic plant with contrasting sexual systems (monoecy and dioecy), which are predicted to affect dispersal ability. We examined the distribution of cpDNA haplotypes using polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) among 76 populations (32 monoecious, 38 dioecious, two mixed and four undetermined populations) of Sagittaria latifolia sampled throughout eastern North America. We also use these data to investigate the polarity of the evolutionary transition between monoecy and dioecy. Using PCR–RFLP, we identified eight cpDNA haplotypes. All haplotypes were found in unglaciated areas of the species’ range, clustered primarily in the southeastern United States, providing evidence that glacial refugia probably occurred in this area. Genetic diversity (hT) was more than six times greater among monoecious compared to dioecious populations. All seven of the haplotypes for which the sexual system could be determined were represented among monoecious populations. In contrast, only four haplotypes were detected in dioecious populations and 94% of individuals from dioecious populations possessed a single haplotype. Monoecious populations possessing this widespread haplotype were restricted to the southern portion of the range, indicating that dioecy probably originated in this region and then spread northwards. The distribution of cpDNA haplotypes in dioecious populations represents a subset of the variation found in monoecious populations, a pattern expected if dioecy has evolved from monoecy in S. latifolia.
Population genetic structure of North American thinhorn sheep (Ovis dalli)
Authors: WORLEY K. , STROBECK C. , ARTHUR S. , CAREY J. , SCHWANTJE H. , VEITCH A. , COLTMAN D. W.
Published: August 2004

The thinhorn sheep (Ovis dalli ssp.) provides a rare example of a North American large mammal that occupies most of its native range and maintains close to ancestral population size. There are currently two recognized subspecies, Dall's sheep (O. d. dalli) and Stone's sheep (O. d. stonei), the validity of which remains uncertain. We investigated the spatial genetic structure of thinhorn sheep populations representing both subspecies by genotyping individuals (n = 919) from across the species range at 12 variable microsatellite loci. We found high levels of genetic diversity within (HE = 0.722) and significant genetic structure among the 24 sampled areas (FST = 0.160). Genetic distance measures and Bayesian clustering analyses revealed the presence of at least eight subpopulations that are delineated by mountain range topology. A strong overall pattern of isolation‐by‐distance is evident across the sampling range (r = 0.75, P < 0.001) suggesting limited dispersal and extensive philopatry. Partial Mantel tests of this relationship showed mountain range distinctions represent significant barriers to gene flow (P = 0.0001), supporting the Bayesian analyses. Genetic structure was more strongly pronounced in southern Yukon and Alaska than elsewhere. We also show evidence for genetic differences between the two currently recognized thinhorn subspecies.
Exploring population genetic structure in three species of Lesser Antillean bats
Authors: CARSTENS B. C. , SULLIVAN J. , DAVALOS L. M. , LARSEN P. A. , PEDERSEN S. C.
Published: August 2004

We explore population genetic structure in phyllostomid bats (Ardops nichollsi,Brachyphylla cavernarumandArtibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe‐induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected inArdops nichollsi(P = 0.718), but could be rejected inB. cavernarum(P < 0.001) andArtibeus jamaicensis(P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using anamovaand was rejected in each species [Ardops nichollsi(P = 0.697);B. cavernarum(P = 0.598);Artibeus jamaicensis(P = 0.763)]. InB. cavernarumandArtibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly inArtibeus jamaicensis(PW < 0.01;PSE = 0.04), but cannot be rejected inB. cavernarum(PW = 0.81;PSE = 0.79). A conservative interpretation of the molecular data is that island populations ofArtibeus jamaicensis, although isolated geographically, are not isolated genetically.
Increased selfing and correlated paternity in a small population of a predominantly outcrossing conifer, Pinus sylvestris
Authors: ROBLEDO‐ARNUNCIO J. J. , ALÍA R. , GIL L.
Published: August 2004

Outcrossing rate, the rates of ovule and seed abortion, and levels of correlated paternity were estimated in a small population of Pinus sylvestris, a predominantly outcrossing conifer, and were compared with estimates from two widely dispersed woodlands of the same species, showing a range of densities. On average, seed trees of the small population showed an eight‐fold higher selfing rate (25 vs. 3%) and a 100‐fold greater incidence of correlated paternity (19.6 vs. 0.2%) than did trees from the large populations. No evidence was found of pollen limitation within the remnant stand, as suggested by ovule abortion rates. Investigation of the mating patterns in the small population, based on the unambiguous genealogy of 778 open‐pollinated seeds, showed a large departure from random mating. Only 8% of the possible mating pairs within the stand were observed. Correlated paternity rate within a maternal sibship was negatively associated (rs = −0.398, P < 0.050) with the distance to the nearest neighbour, and shared paternity among maternal sibships was negatively correlated (rs = −0.704, P < 0.001) with the distance between seed trees. Numerical simulations, based on the estimated individual pollen dispersal kernel, suggest that restricted dispersal might have been the key factor affecting mating patterns in the small population and, together with low population density, may account for the observed mating system variation between the small and the large populations. The results of this study show that a severe size reduction may substantially affect the mating system of a wind‐pollinated, typically outcrossed plant species.
Odorant receptor gene expression changes during the parr–smolt transformation in Atlantic salmon
Authors: DUKES J. P. , DEAVILLE R. , BRUFORD M. W. , YOUNGSON A. F. , JORDAN W. C.
Published: August 2004

The ability of salmon to home accurately to their natal stream to spawn has long intrigued biologists and has important consequences for the maintenance of population structure in these species. It is known that olfaction is crucial to homing, and that the transition from the freshwater to the marine environment (the parr–smolt transformation; PST) is a period of increased olfactory sensitivity and learning, resulting in a permanent memory of natal site odours that is retained, at least in part, in peripheral sensory neurones. These odours are then used as cues by sexually maturing fish on their homeward migration. We used quantitative polymerase chain reaction techniques to demonstrate transient increases in expression of odorant receptor transcripts (of up to fifty‐fold over pre‐PST levels) coincident with PST. Both olfactory (SORB) and vomeronasal receptors (SVRA and SVRC) are involved, which suggests that the fish learn both environmental odours and semiochemicals (pheromones). Receptor expression varies between families and changes over time indicating both genetic differences in odour stimuli and multiple periods of olfactory sensitivity. We suggest that changes in OR gene expression may have a role in homing behaviour and thus the maintenance of population structure in Atlantic salmon.
Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual–based approach
Authors: COULON A. , COSSON J. F. , ANGIBAULT J. M. , CARGNELUTTI B. , GALAN M. , MORELLET N. , PETIT E. , AULAGNIER S. , HEWISON A. J. M.
Published: August 2004

Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest‐dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, interindividual genetic distances were calculated from genotypes at 12 polymorphic microsatellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape.
Quantitative trait locus analyses and the study of evolutionary process
Authors: ERICKSON DAVID L. , FENSTER CHARLES B. , STENØIEN HANS K. , PRICE DONALD
Published: August 2004

The past decade has seen a proliferation of studies that employ quantitative trait locus (QTL) approaches to diagnose the genetic basis of trait evolution. Advances in molecular techniques and analytical methods have suggested that an exact genetic description of the number and distribution of genes affecting a trait can be obtained. Although this possibility has met with some success in model systems such as Drosophila and Arabidopsis, the pursuit of an exact description of QTL effects, i.e. individual gene effect, in most cases has proven problematic. We discuss why QTL methods will have difficulty in identifying individual genes contributing to trait variation, and distinguish between the identification of QTL (or marker intervals) and the identification of individual genes or nucleotide differences within genes (QTN). This review focuses on what ecologists and evolutionary biologists working with natural populations can realistically expect to learn from QTL studies. We highlight representative issues in ecology and evolutionary biology and discuss the range of questions that can be addressed satisfactorily using QTL approaches. We specifically address developing approaches to QTL analysis in outbred populations, and discuss practical considerations of experimental (cross) design and application of different marker types. Throughout this review we attempt to provide a balanced description of the benefits of QTL methodology to studies in ecology and evolution as well as the inherent assumptions and limitations that may constrain its application.
The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis)
Authors: ADAMS RACHEL I. , BROWN KYLE M. , HAMILTON MATTHEW B.
Published: August 2004

Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical treeCorythophora altaand 11 loci in the anadromous fishMorone saxatilisby sequencing 14–23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy forM. saxatilisloci. SevenC. altaloci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy inC. altagenerally produced little or no change in single‐locus estimates ofRST, except for two loci in which some additional differentiation among populations was revealed. Twelve‐locus estimates ofRST(including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% forC. altaandM. saxatilis, respectively. Simulations showed that the increase inRSTproduced by homoplasy correction was only slightly larger than variation inRSTestimates expected to be caused by methodological errors.
Genetic structure of desert ground squirrels over a 20‐degree‐latitude transect from Oregon through the Baja California peninsula
Authors: WHORLEY JOSHUA R. , ALVAREZ‐CASTAÑEDA S. TICUL , KENAGY G. J.
Published: August 2004

The genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500‐km transect, from 43 to 22° north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome bgene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.
Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer
Authors: JARAMILLO‐CORREA JUAN P. , BEAULIEU JEAN , BOUSQUET JEAN
Published: August 2004

Range‐wide genetic variation of black spruce (Picea mariana) was studied using polymerase chain reaction‐random fragment length polymorphism markers of the mitochondrial genome. Four polymorphic mitochondrial DNA (mtDNA) loci were surveyed and two or three alleles were detected at each locus, resulting in 10 multilocus mtDNA types or mitotypes. A significant subdivision of population genetic diversity was detected (GST = 0.671; NST = 0.726), suggesting low levels of gene flow among populations. The distribution of mitotypes was not random (NST > GST; P < 0.05) and revealed four partially overlapping zones, presumably representative of different glacial populations. Comparison of the genetic structure derived from mtDNA markers and the colonization paths previously deduced from the fossil and pollen records allow us to infer at least three southern and one northeastern glacial populations for black spruce. The patterns revealed in this study suggest that black spruce shares its biogeographical history with other forest‐associated North American species.
Temporal changes in allele frequencies and low effective population size in greater prairie‐chickens
Authors: JOHNSON JEFF A. , BELLINGER M. RENEE , TOEPFER JOHN E. , DUNN PETER
Published: August 2004

The number of greater prairie‐chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo‐likelihood approach that accounted for migration, estimates ofNe(15–32 prairie‐chickens within each management area) were 10 times lower than census numbers from booming‐ground counts. These low estimates ofNeare consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reducedNe, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie‐chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.
Testing the utility of internally transcribed spacer sequences in coral phylogenetics
Authors: VOLLMER STEVEN V. , PALUMBI STEPHEN R.
Published: August 2004

Reef‐building corals often possess high levels of intraindividual and intraspecific ribosomal DNA (rDNA) variation that is largely polyphyletic between closely related species. Polyphyletic rDNA phylogenies coupled with high intraindividual rDNA variation have been taken as evidence of introgressive hybridization in corals. Interpreting the data is problematic because the rDNA cluster evolves in a complex fashion and polyphyletic lineages can be generated by a variety of processes — such as incomplete lineage sorting and slow concerted evolution — in addition to hybridization. Using the genetically characterized Caribbean Acropora hybridization system, we evaluate how well rDNA data perform in revealing patterns of recent introgressive hybridization in contrast to genetic data from four single‐copy loci. While the rDNA data are broadly consistent with the unidirectional introgression seen in other loci, we show that the phylogenetic signature of recent introgressive hybridization is obscured in the Caribbean Acropora by ancient shared rDNA lineages that predate the divergence of the species.
Ex situ population management in the absence of pedigree information
Authors: RUSSELLO M. A. , AMATO G.
Published: August 2004

For captive breeding to play a significant role in conservation, ex situ populations must be scientifically managed to meet objective goals for retaining representative genetic variation. Imperfect genealogical information requires fundamental assumptions to be made that may bias downstream measures of genetic importance, upon which management decisions are based. The impacts of such assumptions are most pronounced within breeding programmes characterized by a high proportion of individuals of unknown ancestry, as exemplified by the large captive population of the St Vincent parrot (Amazona guildingii). The degree to which microsatellite‐based estimates of relatedness may improve upon the assumptions of conventional pedigree‐based management was investigated using genotypic data collected at eight microsatellite loci and two marker‐based relatedness estimators. The measure, rxyLR, was found to explain the highest amount of variation in true relatedness. Integration of pairwise estimates of founder relatedness with studbook data transformed current understanding of the relatedness structure of the A. guildingii population from two subgroups characterized by a high and low degree of relatedness, respectively, to a situation where all 72 individuals are prioritized for breeding according to their estimated mean kinships. Furthermore, the discovery of opposing, directional bias exhibited by rxyLR and rxyQG in assigning dyads to a given relationship category suggests that an approach that utilizes a combination of pairwise relatedness estimators may provide the most genetic information for balancing the dual considerations of maximizing gene diversity and minimizing inbreeding in developing breeding recommendations.
Spatial partitioning and asymmetric hybridization among sympatric coastal steelhead trout (Oncorhynchus mykiss irideus), coastal cutthroat trout (O. clarki clarki) and interspecific hybrids
Authors: OSTBERG CARL O. , SLATTON STACEY L. , RODRIGUEZ RUSSELL J.
Published: August 2004

Hybridization between sympatric species provides unique opportunities to examine the contrast between mechanisms that promote hybridization and maintain species integrity. We surveyed hybridization between sympatric coastal steelhead (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki) from two streams in Washington State, Olsen Creek (256 individuals sampled) and Jansen Creek (431 individuals sampled), over a 3‐year period. We applied 11O. mykiss‐specific nuclear markers, 11O. c. clarki‐specific nuclear markers and a mitochondrial DNA marker to assess spatial partitioning among species and hybrids and determine the directionality of hybridization. F1and post‐F1hybrids, respectively, composed an average of 1.2% and 33.6% of the population sampled in Jansen Creek, and 5.9% and 30.4% of the population sampled in Olsen Creek. A modest level of habitat partitioning among species and hybrids was detected. Mitochondrial DNA analysis indicated that all F1hybrids (15 from Olsen Creek and five from Jansen Creek) arose from matings between steelhead females and cutthroat males implicating a sneak spawning behaviour by cutthroat males. First‐generation cutthroat backcrosses containedO. c. clarkimtDNA more often than expected suggesting natural selection against F1hybrids. More hybrids were backcrossed toward cutthroat than steelhead and our results indicate recurrent hybridization within these creeks. Age analysis demonstrated that hybrids were between 1 and 4 years old. These results suggest that within sympatric salmonid hybrid zones, exogenous processes (environmentally dependent factors) help to maintain the distinction between parental types through reduced fitness of hybrids within parental environments while divergent natural selection promotes parental types through distinct adaptive advantages of parental phenotypes.
High degree of population subdivision in a widespread amphibian
Authors: PALO JUKKA U. , SCHMELLER DIRK S. , LAURILA ANSSI , PRIMMER CRAIG R. , KUZMIN SERGIUS L. , MERILÄ JUHA
Published: August 2004

In general, amphibians are known to exhibit a higher degree of population subdivision than any other major animal taxa, but large‐scale population genetic surveys of widely distributed species are still scarce, especially in the Eurasian continent. Using microsatellite markers and mitochondrial DNA sequences, we investigated the large‐scale population genetic structure of the common frog (Rana temporaria) — one of the most widespread amphibians of the Palearctic region. Analyses of cytochrome b sequences revealed evidence for two distinct lineages inhabiting western and eastern parts of Europe. The separation of these lineages c. 700 000 years ago may have been induced by the onset of the Middle Pleistocene continental glaciations. Analyses of the variability of microsatellite loci within each of the clades revealed evidence for evolution of a high degree of population subdivision (FST ∼ 0.23) even in northern Fennoscandia, colonized less than 10 000 years ago. The high level of substructuring is puzzling in the face of an apparently high dispersal capacity, as evidenced by the rather rapid recolonization of northern Europe. This suggests that processes other than restricted dispersal capacity need to be explored as explanations for the high degree of population subdivision in amphibians. The colonization of northern Europe has been accompanied by loss of genetic variability as evidenced by decreasing levels of intrapopulational genetic variability in microsatellite loci from south to north across Europe.
Population‐structure and genetic diversity in a haplochromine fish cichlid of a satellite lake of Lake Victoria
Authors: ABILA ROMULUS , BARLUENGA MARTA , ENGELKEN JOHANNES , MEYER AXEL , SALZBURGER WALTER
Published: August 2004

The ∼500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record‐setting 100 000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed — sequences of the mitochondrial control region as well as six microsatellite loci — and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model‐based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise FST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus, a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.