bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle
Authors: OVENDEN JENNIFER R. , SALINI JOHN , O'CONNOR SALLY , STREET RAEWYN 
Published: December 2004

AbstractThe East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long‐lived, fecund snapper species that is distributed throughout the East Indies and Indo‐Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67–0.82), as was intraspecific sequence divergence (range 0–5.8%). FST between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; FST was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.
Reproductive effects and geographical distributions of twoWolbachiastrains infecting the Neotropical beetle,Chelymorpha alternansBoh. (Chrysomelidae, Cassidinae)
Authors: KELLER G. P. , WINDSOR D. M. , SAUCEDO J. M. , WERREN J. H. 
Published: December 2004

AbstractWolbachiaare maternally inherited endocellular bacteria known to alter insect host reproduction to facilitate their own transmission. MultipleWolbachiainfections are more common in tropical than temperate insects but few studies have investigated their dynamics in field populations. The beetle,Chelymorpha alternans, found throughout the Isthmus of Panama, is infected with two strains ofWolbachia,wCalt1 (99.2% of beetles) andwCalt2 (53%). Populations infected solely by thewCalt1 strain were limited to western Pacific Panama, whereas populations outside this region were either polymorphic for single (wCalt1) and double infections (wCalt1 +wCalt2) or consisted entirely of double infections. ThewCalt2 strain was not found as a single infection in the wild. Both strains caused cytoplasmic incompatibility (CI). ThewCalt1 strain caused weak CI (∼20%) and the double infection induced moderate CI (∼70–90%) in crosses with uninfected beetles. ThewCalt1 strain rescued about 75% of eggs fertilized by sperm fromwCalt2 males. Based on the relationships of beetle mtDNA and infection status, maternal transmission, and repeated population sampling we determined that the double infection invadedC.alternanspopulations about 100 000 years ago and that thewCalt2 strain appears to be declining in some populations, possibly due to environmental factors. This may be the first study to demonstrate an association between widespread strain loss and environmental factors in the field.
Differences in mycorrhizal preferences between two tropical orchids
Authors: OTERO J. TUPAC , ACKERMAN JAMES D. , BAYMAN PAUL 
Published: December 2004

AbstractOrchids parasitize their mycorrhizal fungi and are dependent on them for seed germination. Controversy reigns over how specific the mycorrhizal association is in tropical species. Although there is little experimental evidence to support any viewpoint, some variation is known to exist. We compared mycorrhizal specificity and performance in two phylogenetically related epiphytic orchids from Puerto Rico, Tolumnia variegata and Ionopsis utricularioides (Oncidiinae) by integrating two techniques: phylogenetic analysis of mycorrhizal fungi based on nuclear ribosomal internal transcribed spacer (ITS) sequences, and symbiotic seed germination experiments. Most of the mycorrhizal isolates from T. variegata fell into four different clades of Ceratobasidium, while most of those from I. utricularioides were restricted to a single clade of the same genus. Seeds of T. variegata germinated equally well with fungi from both T. variegata and I. utricularioides, but seeds of I. utricularioides germinated significantly better with its own isolates. Seeds of I. utricularioides germinated and developed faster than those of T. variegata. Both the molecular phylogeny and the seed germination experiments showed that T. variegata is a generalist in its association with fungal symbionts. In contrast, I. utricularioides is more specialized and more effective at exploiting a specific fungal clade. Our data are consistent with the theoretical trade‐offs between specialized and generalized interactions.
Phylogeographical patterns in the American Pacific Northwest: lessons from the arionid slugProphysaon coeruleum
Authors: WILKE T. , DUNCAN N. 
Published: December 2004

AbstractSome of the earliest studies of phylogenetic concordance involve native plants from the Pacific Northwest where many taxa showed clear genetic breaks between southern and northern populations. To test whether similar breaks also occur in invertebrate species with low dispersal capacities, genetic data from two mitochondrial genes are assembled for individuals of the arionid slugProphysaon coeruleumthroughout the species’ range. Bayesian inference revealed three major clades and a total of eight subclades. It is argued that the demographic and genealogical past ofP. coeruleumhas resulted in a deep and shallow phylogeographical structure. The deep structure is at least 2.6–5.9 million years old and therefore clearly predates the Pleistocene period. Superimposed on this structure is a shallow structure that is most likely less than 2 million years old and probably the result of Pleistocene perturbations. Molecular analyses revealed that the three known colour traits inP. coeruleumdo not represent monophyletic groups and that they do not match the patterns of genetic structure found. It is argued that the colour traits are perhaps a response to different levels of UV‐radiation. The study adds to the increasing evidence that the phylogeographical structure of some taxa is more complex than previously thought. Moreover, it shows that genealogical concordance should not be deduced from phylogeographical patterns alone but should be based on an understanding of timing and causes of historical processes that lead to those patterns.
Nest architecture and genetic differentiation in a species complex of Australian stingless bees
Authors: FRANCK P. , CAMERON E. , GOOD G. , RASPLUS J.‐Y. , OLDROYD B. P. 
Published: December 2004

AbstractWe investigated the taxonomic significance of nest shape and its putative role in speciation inTrigona(Heterotrigona)carbonariaandT.(H.)hockingsi, two sibling species of stingless bee species from eastern Australia. These species are primarily distinguished by their nest architecture, as in all other respects they are nearly identical. We genotyped 130 colonies from six locations in Queensland at 13 microsatellite loci together with 106 additional colonies from six other Indo‐PacificTrigonaspecies. Whether they were present in allopatry or in sympatry, colonies that displayed theT. carbonariaor theT. hockingsinest architecture could be unambiguously differentiated at the genetic level. However,T. hockingsicolonies were classifiable into two highly differentiated paraphyletic and geographically separate populations, one in northern and one in southern Queensland. These two populations probably belong to two distinct species,T. hockingsiandT. davenportinov. sp. Our results suggest that nest architecture characters are relevant but not sufficient criteria to identify species in this group. Consequently, modifications of nest architecture are probably not of prime importance in the speciation process of Australian stingless bees, although nest architecture differences probably result from relatively simple mechanisms. The rare interspecific hybrid colonies detected did not display a nest with an intermediate form betweenT. hockingsiandT. carbonaria.
Quantitative trait loci affecting knockdown resistance to high temperature in Drosophila melanogaster
Authors: NORRY F. M. , DAHLGAARD J. , LOESCHCKE V. 
Published: December 2004

AbstractKnockdown resistance to high temperature is an ecologically important trait in small insects. A composite interval mapping was performed on the two major autosomes of Drosophila melanogaster to search for quantitative trait loci (QTL) affecting knockdown resistance to high temperature (KRHT). Two dramatically divergent lines from geographically different thermal environments were artificially selected on KRHT. These lines were crossed to produce two backcross (BC) populations. Each BC was analysed for 200 males with 18 marker loci on chromosomes 2 and 3. Three X‐linked markers were used to test for X‐linked QTL in an exploratory way. The largest estimate of autosome additive effects was found in the pericentromeric region of chromosome 2, accounting for 19.26% (BC to the low line) and 29.15% (BC to the high line) of the phenotypic variance in BC populations, but it could represent multiple closely linked QTL. Complete dominance was apparent for three QTL on chromosome 3, where heat‐shock genes are concentrated. Exploratory analysis of chromosome X indicated a substantial contribution of this chromosome to KRHT. The results show that a large‐effect QTL with dominant gene action maps on the right arm of chromosome 3. Further, the results confirm that QTL for heat resistance are not limited to chromosome 3.
Population structure of the large Japanese field mouse,Apodemus speciosus(Rodentia: Muridae), in suburban landscape, based on mitochondrial D‐loop sequences
Authors: HIROTA TADAO , HIROHATA TETSUO , MASHIMA HIROSHI , SATOH TOSHIYUKI , OBARA YOSHIAKI 
Published: December 2004

AbstractGenetic structure of the large Japanese field mouse populations in suburban landscape of West Tokyo, Japan was determined using mitochondrial DNA control region sequence. Samples were collected from six habitats linked by forests and green tract along the Tama River, and from two forests segregated by urban areas from those continuous habitats. Thirty‐five haplotypes were detected in 221 animals. Four to eight haplotypes were found within each local population belonging to the continuous landscape. Some haplotypes were shared by two or three adjacent local populations. On the other hand, two isolated habitats were occupied by one or two indigenous haplotypes. Significant genetic differentiation between all pairs of local populations, except for one pair in the continuous habitats, was found by analysis of molecular variance (amova). The geographical distance between habitats did not explain the large variance of pairwiseFST‐values among local populations.FST‐values between local populations segregated by urban areas were higher than those between local populations in the continuous habitat, regardless of geographical distance. The results of this study demonstrated quantitatively that urban areas inhibit the migration ofApodemus speciosus, whereas a linear green tract along a river functions as a corridor. Moreover, it preserves the metapopulation structure ofA. speciosusas well as the corridors in suburban landscape.
Estimation of genetically effective breeding numbers using a rejection algorithm approach
Authors: RAMAKRISHNAN UMA , STORZ JAY F. , TAYLOR BARBARA L. , LANDE RUSSELL 
Published: December 2004

AbstractPolygynous mating results in nonrandom sampling of the adult male gamete pool in each generation, thereby increasing the rate of genetic drift. In principle, genetic paternity analysis can be used to infer the effective number of breeding males (Nebm). However, this requires genetic data from an exhaustive sample of candidate males. Here we describe a new approach to estimate Nebm using a rejection algorithm in association with three statistics: Euclidean distance between the frequency distributions of maternally and paternally inherited alleles, average number of paternally inherited alleles and average gene diversity of paternally inherited alleles. We quantify the relationship between these statistics and Nebm using an individual‐based simulation model in which the male mating system varied continuously between random mating and extreme polygyny. We evaluate this method using genetic data from a natural population of highly polygynous fruit bats (Cynopterous sphinx). Using data in the form of mother–offspring genotypes, we demonstrate that estimates of Nebm are very similar to independent estimates based on a direct paternity analysis that included data on candidate males. Our method also permits an evaluation of uncertainty in estimates of Nebm and thus facilitates inferences about the mating system from genetic data. Finally, we investigate the sensitivity of our method to sample size, model assumptions, adult population size and the mating system. These analyses demonstrate that the rejection algorithm provides accurate estimates of Nebm across a broad range of demographic scenarios, except when the true Nebm is high.
Molecular markers reveal extensive intraspecific below‐ground overlap of silver fir fine roots
Authors: BRUNNER I. , RUF M. , LÜSCHER P. , SPERISEN C. 
Published: December 2004

AbstractFine roots are expected to be important determinants of plant competition, but very little is known about the extent of root system overlap. Here, we describe the application of two highly variable plastide microsatellites to study the fine root distribution of tree individuals in a silver fir forest. We demonstrate that the spread of fine roots exceeds the width of above‐ground parts, and that fine root overlaps among neighbouring trees are extensive both laterally and in depth. This approach will help to improve models of below‐ground competition and will facilitate estimations of fine root biomass and thus of below‐ground C pools.
Neutral genetic variation among wild North American populations of the weedy plant Arabidopsis thaliana is not geographically structured
Authors: JØRGENSEN S. , MAURICIO R. 
Published: December 2004

AbstractWe investigated neutral genetic variation within and among 53 wild‐collected populations of the weedy annual plant, Arabidopsis thaliana, in North America, using amplified fragment length polymorphism (AFLP) markers. A. thaliana is thought to have been introduced to North America from Eurasia by humans; such an introduction might be expected to leave a clear geographical signal in the genetic data. To detect such patterns, we sampled populations at several hierarchical geographical levels. We collected individuals from populations in two areas of the Southeast and one in the Midwest, as well as individuals from populations in the Pacific Northwest and Northeast. To estimate within‐population variation, we sampled eight individuals from each of six populations in the Southeast and Midwest. Among all 95 individuals analysed, we detected 131 polymorphic AFLP fragments. We found no evidence for continental or regional diversification. Individuals sampled from Midwestern and Southeastern populations intermingled in a neighbour‐joining tree, and Mantel tests conducted within the Midwestern and Southeastern regions as well as the full data set failed to detect any significant relationship between geographical and genetic distance. These results mirror those found for most global surveys of neutral genetic variability in A. thaliana. Surprisingly, we detected substantial amounts of neutral genetic variability within populations. The levels of genetic variation within populations, coupled with the nongeographical nature of divergence among populations, are consistent with contemporary gene flow and point to a complex and dynamic population history of A. thaliana in North America.
Prey selection by linyphiid spiders: molecular tracking of the effects of alternative prey on rates of aphid consumption in the field
Authors: HARWOOD JAMES D. , SUNDERLAND KEITH D. , SYMONDSON WILLIAM O. C. 
Published: December 2004

AbstractA molecular approach, using aphid‐specific monoclonal antibodies, was used to test the hypothesis that alternative prey can affect predation on aphids by linyphiid spiders. These spiders locate their webs in cereal crops within microsites where prey density is high. Previous work demonstrated that of two subfamilies of Linyphiidae, one, the Linyphiinae, is web‐dependent and makes its webs at sites where they were more likely to intercept flying insects plus those (principally aphids) falling from the crop above. The other, the Erigoninae, is less web‐dependent, making its webs at ground level at sites with higher densities of ground‐living detritivores, especially Collembola. The guts of the spiders were analysed to detect aphid proteins using enzyme‐linked immunosorbent assay (ELISA). Female spiders were consuming more aphid than males of both subfamilies and female Linyphiinae were, as predicted, eating more aphid than female Erigoninae. Rates of predation on aphids by Linyphiinae were related to aphid density and were not affected by the availability of alternative prey. However, predation by the Erigoninae on aphids was significantly affected by Collembola density. Itinerant Linyphiinae, caught away from their webs, contained the same concentration of aphid in their guts as web‐owners. However, nonweb‐owning Erigoninae, living away from Collembola aggregations at web‐sites, contained significantly higher concentrations of aphid. For both subfamilies there was evidence of a disproportionate increase in predation on aphids once Collembola populations had declined. It was concluded that nonaphid prey, by helping to maintain spiders in the field, can significantly affect predation on aphids.
Spatial and population genetic structure of microsatellites in white pine
Authors: MARQUARDT PAULA E. , EPPERSON BRYAN K. 
Published: December 2004

AbstractWe evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120–122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity was high and inbreeding low. When comparing these populations, there is a significant, but small (less than 1%), genetic divergence between populations. Spatial distance between populations or timber harvest at the second growth site were reasonable explanations for the observed minor differences in allele frequencies between populations. Spatial autocorrelation analysis suggested that, for the old growth population, weak positive structuring at 15 m fits the isolation by distance model for a neighbourhood size of about 100 individuals. In comparison, genotypes were randomly distributed in the second growth population. Thus, logging may have decreased spatial structuring at the second growth site, suggesting that management practices may be used to alter natural spatial patterns. In addition, the amount of autocorrelation in the old growth population appears to be lower for some of the microsatellites, suggesting higher numbers of rare alleles and that higher mutation rates may have directly affected spatial statistics by reducing structure.
Chloroplast DNA variation in the Quercus affinis–Q. laurina complex in Mexico: geographical structure and associations with nuclear and morphological variation
Authors: GONZÁLEZ‐RODRÍGUEZ A. , BAIN J. F. , GOLDEN J. L. , OYAMA K. 
Published: December 2004

AbstractThe geographical distribution of chloroplast DNA (cpDNA) variation in 39 populations of two hybridizing Mexican red oaks, Quercus affinis and Q. laurina, was investigated using polymerase chain reaction‐restriction fragment length polymorphism (PCR–RFLP). Six haplotypes were identified. Of these, two (H1 and H4), separated by four mutations, had high frequencies (58 and 23% of the individuals, respectively) and were present across the whole geographical range of both species, often co occurring in the same populations. The other four haplotypes were rare, geographically restricted, and are probably derived from the two frequent haplotypes. Latitudinal or other clinal patterns in diversity levels or haplotype composition of populations were not apparent. The pattern of haplotype distribution was characterized by some mosaicism, with contrasting populations often situated in proximity. Average within‐population diversity (hS = 0.299) and population differentiation (GST = 0.499) were, respectively, higher and lower than values reported in previous studies of oak species. There was evidence for phylogeographical structure, as indicated by NST (0.566) being significantly higher than GST. Haplotypic variation was largely species‐independent, although some very weak associations were detected between haplotypes H1 and H4 and morphological and nuclear molecular variation correspondingly characterizing Q. affinis and Q. laurina. These oaks probably did not experience a marked restriction to one or a few particular subregions of their present range during the last glacial cycle. It is more likely that substantial populations persisted throughout several episodes of climatic change, but experienced recurrent latitudinal and altitudinal migrations which may have caused the widespread distribution of haplotypes H1 and H4 and frequent intermixing of populations.
Strong fungal specificity and selectivity for algal symbionts in Florida scrubCladonialichens
Authors: YAHR REBECCA , VILGALYS RYTAS , DEPRIEST PAULA T. 
Published: December 2004

AbstractSymbiosis is a major theme in the history of life and can be an important force driving evolution. However, across symbioses, it is difficult to tease apart the mechanisms that structure the interactions among potential partners. We used genetic similarity and frequency‐based methods to qualitatively and quantitatively examine the patterns of association among several co‐occurringCladonialichen fungi and their algal photobionts in six disjunct Florida scrub sites. The patterns of association were described by the degree of specificity, i.e. the phylogenetic range of associated partners, and of selectivity, i.e. the frequency of association among partners. Six fungal species associated with only one algal internal transcribed spacer clade, with the remaining two fungi being associated with two algal clades. In all cases, the fungi associated in unequal frequencies with the observed algal photobiont genotypes within those clades — suggesting that both specificity and selectivity were higher than expected. Fungal species can be grouped into three significantly different specificity classes: photobiont specialists, intermediates and generalists. In contrast to the pronounced specificity for photobionts among fungal species, the different Florida scrub sites do not harbour distinct photobiont pools, and differential photobiont availability cannot explain the patterning of lichen associations at this spatial scale. Therefore, we conclude that fungal specificity and selectivity for algal photobionts are major factors in determining the local composition of symbiotic partnerships.