bluuebunny/crossref_metadata_2025 huggingface dataset:
Limited polymorphism at major histocompatibility complex (MHC) loci in the Swedish moose A. alces
Authors: ELLEGREN H. , MIKK S. , WALLIN K. , ANDERSSON L.
Published: April 2008

The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Both methods revealed limited amounts of polymorphism. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. DNA fingerprinting was used to determine if the unusual pattern of low MHC variability could be explained by a low degree of genome‐wide genetic diversity. Hybridizations with two minisatellite probes gave similarity indices somewhat higher than the average for other natural population, but the data suggest that the low MHC variability cannot be explained by a recent population bottleneck. However, since minisatellite sequences evolve more rapidly than MHC sequences, the low levels of MHC diversity may be attributed to a bottleneck of more ancient origin. The selection pressure for MHC variability in moose may also be reduced and we discuss the possibility that its solitary life style may reduce lateral transmission of pathogens in the population.
Associations between physical isolation and geographical variation within three species of Neotropical birds
Authors: BRAWN J. D. , COLLINS T. M. , MEDINA M. , BERMINGHAM E.
Published: April 2008

We studied effects of physical isolation on geographical variation in mtDNA RFLP polymorphisms and a suite of morphological characters within three species of neotropical forest birds; the crimson‐backed tanager Ramphocelus dimidiatus, the blue‐gray tanager Thraupis episcopus, and the streaked saltator Saltator albicollis. Variation among populations within continuous habitat on the Isthmus of Panama was compared with that among island populations isolated for about 10000 years. Putative barriers to dispersal were influential, but apparent isolation effects varied by species, geographical scale, and whether molecular or morphological traits were being assessed. We found no geographical structuring among the contiguous, mainland sampling sites. Migration rates among the islands appeared sufficient to maintain homogeneity in mtDNA haplotype frequencies. In contrast, variation in external morphology among islands was significant within two of three species. For all species, we found significant variation in genetic and morphological traits between the island (collectively) and mainland populations. Interspecific variation in the effects of isolation was likely related to differential vagility. These data generally corroborate other studies reporting relatively great geographical structuring within tropical birds over short distances. Behaviourally based traits ‐ low vagility and high ‘sensitivity’ to geographical barriers ‐ may underlie extensive diversification within neotropical forest birds, but more extensive ecological and phylogeographic information are needed on a diverse sample of species.
Microsatellite differentiation between Phillip Island and mainland Australian populations of the red foxVulpes vulpes
Authors: LADE J. A. , MURRAY N. D. , MARKS C. A. , ROBINSON N. A.
Published: April 2008

Predation by the red foxVulpes vulpesis believed to be threatening the little penguinEudyptula minoron Phillip Island in Victoria. Polymorphism at seven microsatellite loci was examined to estimate the extent of differentiation between Phillip Island and mainland populations ofV. vulpes. Loss of alleles has occurred on Phillip Island where foxes first appeared = 88 years ago compared with mainland populations. Genetic differentiation between the Phillip Island and mainland populations was high. The relatively high differentiation found between the two populations could be due to either low migration rates, the effect of the composition of founder animals or both effects. Further ecological and historical information about the populations is needed to explore the likely significance of these effects.
Detection and pattern of interspecific hybridization between Gliricidia sepium and G. maculata in Meso‐America revealed by PCR‐based assays
Authors: DAWSON I. K. , SIMONS A. J. , WAUGH R. , POWELL W.
Published: April 2008

Gliricidia sepium provides a variety of products important for rural communities in tropical countries. Native populations in Meso‐America currently form an important source of seed for distribution to farmers, but concerns centre on mechanisms which may lead to their genetic erosion, including anthropogenic dispersal and subsequent introgression from the related species, G. maculata.

Populations of Gliricidia were examined genetically using approaches based on the polymerase chain reaction to test for interspecific hybridization and introgression between G. sepium and G. maculata. Analysis involved 13 RAPD and two RFLP‐PCR markers which were identified to have species‐diagnostic distributions. Data from both approaches corresponded and indicated three locations where multilocus genotypes were consistent with an hybrid origin. Data at one of these sites was consistent with introgression following hybridization. The hybrid origin of populations was supported by the intermediate geographical location of these sites to ‘pure’ populations of each species. Analysis of maternally inherited organellar DNA, which involved the detection of SSCPs in mitochondrial DNA amplification products, allowed further delineation of genetic structure among Gliricidia populations. Mitochondrial data indicated a high degree of organelle differentiation between sampled locations and identified G. sepium‐ and G. maculata‐diagnostic haplotypes. This data supported the interpretation of genetic structure based on RAPDs and RFLP‐PCR. In addition, cytonuclear analysis allowed the directionality of gene transfer during the formation of hybrid populations to be described. Despite evidence for the occurrence of interspecific hybridization and introgression in Gliricidia, important resource populations of G. sepium on the Pacific coast appear to have retained their genetic integrity. Implications in terms of the conservation and utilization of genetic resources within the genus are discussed.
Amplified fragment length polymorphism (AFLP) fingerprinting of symbiotic fungi cultured by the fungus‐growing ant Cyphomyrmex minutus
Authors: MUELLER U. G. , LIPARI S. E. , MILGROOM M. G.
Published: April 2008

A PCR‐based fingerprinting technique based on amplified fragment length polymorphisms (AFLP) is used to screen symbiotic fungi of the fungus‐growing ant Cyphomyrmex minutus for genetic differences. AFLP fingerprints reveal several fungal ‘types’ that (a) represent distinct clones propagated vegetatively by the ant, or (b) correspond to free‐living fungi that may be acquired by the ant. Fungal types identified by AFLP fingerprints correspond to vegetative‐compatibility groups established previously, suggesting that vegetative compatibility can be used as a crude indicator of genetic differences between fungi of C. minutus.
Microsatellite markers for the study of cetacean populations
Authors: VALSECCHI E. , AMOS W.
Published: April 2008

Microsatellites are one of the most important classes of nuclear genetic markers and offer many advantages for the study of marine mammals. Here we describe the isolation and characterization of 12 cetacean microsatellites which are then tested across 30 different cetacean species. For around half the species tested, five or more polymorphic loci were identified. Since many species were represented by only one or two specimens, this figure is likely to underestimate the usefulness of these markers. No relationship was found between microsatellite repeat length and proportion of species which gave polymorphic products.
RAPD analysis reveals low genetic variability in the endangered light‐footed clapper rail
Authors: NUSSER J. A. , GOTO R. M. , LEDIG D. B. , FLEISCHER R. C. , MILLER M. M.
Published: April 2008

Numbers of light‐footed clapper rails Rallus longirostris levipes, an endangered bird inhabiting southern California salt marshes, have substantially declined from historic levels. RAPD (randomly amplified polymorphic DNA) analysis was employed to assess the genetic variability within and among four of the largest remaining light‐footed clapper rail populations. A single, larger population of the endangered Yuma clapper rail Rallus longirostris yumanensis was used for comparison.

A total of 325 RAPD primers were tested on DNA from a subset of five clapper rails composed of a single representative for each of the four light‐footed clapper rail populations and a representative for the single Yuma clapper rail population. Of the 1338 amplified bands (loci) surveyed in these five representative birds, approximately 1% were polymorphic, indicating the level of differentiation across all loci is quite low. Nine primers yielding these 16 polymorphic bands were used to analyse 48 individuals from five populations. Five of these bands were polymorphic in both subspecies, six were polymorphic only within the light‐footed clapper rails, and five were polymorphic only within the Yuma clapper rail samples. Considering the few bands that were polymorphic among the light‐footed clapper rail populations, a surprisingly high level of population differentiation (GST=0.28) was found. This is in accord with the results of AMOVA analyses which show that a fairly high percentage of the limited variability among the rails is due to either differences between subspecies or differences between the light‐footed rail populations. Because inbreeding depression is suspected and overall genetic distances between populations are low, movement of light‐footed clapper rails from larger populations into smaller ones might be considered as a management strategy. Employing RAPDs as one of a series of assays is useful in revealing the population structure of genetically depauperate species.
Phylogeography and population structure of the Atlantic and Mediterranean green turtleChelonia mydas: a mitochondrial DNA control region sequence assessment
Authors: ENCALADA S. E. , LAHANAS P. N. , BJORNDAL K. A. , BOLTEN A. B. , MIYAMOTO M. M. , BOWEN B. W.
Published: April 2008

Mitochondrial (mt) DNA sequences were analysed to resolve the phylogeography and population genetic structure of Atlantic and Mediterranean populations of green turtles (Chelonia mydas). Analysis of sequence variation over 487 base pairs of the control (D‐loop) region identified 18 haplotypes among 147 individuals from nine nesting populations. Pairwise comparisons of haplotype frequencies distinguished most nesting colonies, indicating significant genetic differentiation among rookeries and a strong propensity for natal homing behaviour by nesting females. Comparison of control region sequence data to earlier restriction fragment length polymorphism (RFLP) data for the same individuals demonstrates approximately a sixfold higher substitution rate in the 5′ end of the control region. The sequence data provide higher resolution both in terms of the number of mtDNA genotype variants and the phylogeographic relationships detected within the Atlantic region, and reveal a gene genealogy that distinguishes two groups of haplotypes corresponding to (i) the western Caribbean and Mediterranean, and (ii) eastern Caribbean, South Atlantic and West Africa. The data suggest that phylogeographic patterns in the Atlantic Ocean may be interpreted in terms of female nest site fidelity and episodic dispersal events. The distribution of mtDNA haplotypes within the region is thus explained by the geological and climatic alternations (glacial and interglacial) over the last million years.
Genetic structure of the global population of banana black leaf streak fungus, Mycosphaerella fijiensis
Authors: CARLIER J. , LEBRUN M. H. , ZAPATER M. F. , DUBOIS C. , MOURICHON X.
Published: April 2008

The genetic structure of Mycosphaerella fijiensis populations around the world was examined using DNA restriction fragment length polymorphism (RFLP) markers. Allele frequencies at 19 nuclear RFLP loci were estimated in a sample of 136 M. fijiensis isolates from five geographical populations representative of banana‐producing areas (South‐East Asia including the Philippines and Papua New Guinea, Africa, Latin America and Pacific Islands). Within each population, gametic disequilibrium tests between the 19 nuclear RFLP loci were mainly non significant (P > 0.05), indicating that random sexual reproduction occurred in these populations. All M. fijiensis populations had a high level of genotypic and allelic diversity (H, gene diversity: 0.25–0.59). The highest levels of gene diversity were found in the two South‐East Asian populations (H: 0.57 and 0.59). Most of the alleles (> 88%) detected in Africa, Latin America and Pacific Islands populations were also detected in South‐East Asian populations. Furthermore, a high and significant (P < 0.05) level of genetic differentiation was observed among M. fijiensis geographical populations (overall estimate of Fst: 0.32). These results were consistent with the hypothesis that M. fijiensis originated in South‐East Asia and spread recently to other parts of the world. The level of allelic diversity in M. fijiensis populations from regions other than South‐East Asia was drastically reduced, indicating founder effects. The data also suggested rare occurrence of migration of M. fijiensis between continents.
Mating structure and nestmate relatedness in a communal bee,Andrena jacobi(Hymenoptera, Andrenidae), using microsatellites
Authors: PAXTON R. J. , THOREN P. A. , TENGÖ J. , ESTOUP A. , PAMILO P.
Published: April 2008

Complex eusocial insect societies are generally matrifilial, suggesting kin selection has been of importance in their development. For simpler social systems, factors favouring their existence, in particular kin selection, have rarely been studied. Communal nesting is one of these simple social organizations, and is found in a diversity of insect species. To examine whether kin selection may play a role in the evolution and maintenance of communality, we estimated genetic relatedness of nestmate females of the facultatively communal bee,Andrena jacobi. Microsatellite loci were developed for this species and used to analyse individuals from two populations. Loci were variable, they were in heterozygote deficit and showed positive inbreeding coefficients. This may arise from nonrandom mating; previous observations (Paxton & Tengö 1996) indicate that a large proportion of females mate intranidally with nestmate males in their natal nests before first emerging. Nestmate relatedness was low, no different from zero for all loci in one population and for three of four loci in the other population. The large number of nestmates sharing a common nest (up to 594) may explain the low relatedness estimates, although relatedness was also independent of the number of females sharing a nest. Lack of inclusive fitness payoffs could constrain social evolution in this communal species.
Micro‐evolution in the weevil genus Larinus: the formation of host biotypes and speciation
Authors: BRIESE D. T. , ESPIAU C. , POUCHOT‐LERMANS A.
Published: April 2008

Data are presented on allozyme variation between 15 populations of the stenophagous capitulum weevil, Larinus cynarae, and three populations of its congener, L. latus, that had been collected throughout the northern mediterranean range of these species. A phenetic analysis of these data revealed no direct relationship between genetic variation and host‐plant association within L. cynarae, but there was a strong geographical structuring of allozyme patterns. Most of the genetic variation was due to differences between geographical regions and variation within these was small. Wright's FST values showed that Italian and Greek populations of L. cynarae were most distinct from L. latus, with southern Iberian, northern Spanish and French populations increasingly less so. This pattern was associated with a cline in the frequencies of certain alleles along this geographical arc from France to Greece. A phenogram of Nei's genetic distances indicated the close genetic relationship between the two species of Larinus and separated the populations of L. cynarae into three allopatric groups. These groups have different host‐plant spectra — dominated by Cynara cardunculus in Italy and Greece, Cynara humilis/Onopordum in southern Iberia and Onopordum spp. in France/Northern Spain — and can be considered to be host biotypes of L. cynarae. L. latus, which occurs in Greece and further east is also an Onopordum specialist. An analysis of the phylogeny of this group of Larinus indicates a primary separation into eastern (L. latus) and western (L. cynarae) taxa, with further branching of the L. cynarae lineage into the putative host‐biotypes. An hypothesis for the evolution of these taxa is given, based on the evolutionary history of host‐plant taxa and geographical constraints.
Chloroplast DNA phylogeography of the argan tree of Morocco
Authors: MOUSADIK A. EL , PETIT R. J.
Published: April 2008

Polymorphisms in the chloroplast genome of the argan tree (Sapotaceae), an endemic species of south‐western Morocco, have been detected by restriction site studies of PCR‐amplified fragments. A total of 12 chloroplast DNA (cpDNA) and two mitochondrial DNA (mtDNA) fragments were amplified and digested with a single restriction enzyme (HinfI). Polymorphisms were identified in six of the cpDNA fragments, whereas no mtDNA polymorphisms were detected in a survey of 95 individuals from 19 populations encompassing most of the natural range of the species. The cpDNA polymorphisms allowed the identification of 11 haplotypes. Two lineages, one in the south‐east and the other in the north‐west, divide the range of the argan tree into two distinct areas. The level of genetic differentiation measured at the haplotype level (GSTc= 0.60) (i.e. with unordered haplotypes) was smaller than when phylogenetic relationships were taken into account (NSTc= 0.71‐0.74) (ordered haplotypes), indicating that population history must be considered in the study of the geographical distribution of cpDNA lineages in this species. If contrasted with the level of nuclear genetic differentiation measured in a previous study with isozymes (GSTn= 0.25), the results indicate a relatively high level of gene flow by seeds, or conversely a relatively low level of gene flow by pollen, as compared with other tree species. Goats and camels could have played an important role in disseminating the fruits of this tree.
Microsatellites from the beluga whaleDelphinapterus leucas
Authors: BUCHANAN F. C. , FRIESEN M. K. , LITTLEJOHN R. P. , CLAYTON J. W.
Published: April 2008

Fifteen microsatellites were isolated from a beluga whaleDelphinapterus leucas, genomic library. The microsatellites were amplified in 100 beluga obtained from two widely separated locations. An average of 8.6 alleles per locus were detected and the average heterozygosity was 0.65 with a range of 0.27–0.86. All microsatellites were polymorphic and 13 of the genotype distributions observed were in Hardy‐Weinberg equilibrium. It was possible with these microsatellites to assign correctly individual whales to their stock‐of‐origin 98% of the time. Microsatellites were amplified in 15 other cetaceans with these beluga‐derived primers.
Identification of a hybrid zone between distinctive colour variants of the alpine wetaHemideina maori(Orthoptera: Stenopelmatidae) on the Rock and Pillar range, southern New Zealand
Authors: KING T. M. , WALLIS G. P. , HAMILTON S. A. , FRASER J. R.
Published: April 2008

The wetaHemideina maorioccurs as yellow (to the north), black (to the south) and intermediate colour variants on the Rock and Pillar range in New Zealand. Isozyme electrophoresis revealed little genetic variation, whereas RFLP analysis of an amplified mtDNA sequence uncovered two haplotypes correlating completely with colour in allopatry and nearly so in sympatry. Intermediates had one or other haplotype. The observed distribution of colour variation and mtDNA genotypes is characteristic of a hybrid zone, perhaps formed by secondary contact. Work is continuing to locate nuclear DNA markers and to study the genetic interactions of the colour variants.
Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa
Authors: DOW B. D. , ASHLEY M. V.
Published: April 2008

Microsatellite analysis was used to examine parentage and spatial distributions of 62 adult bur oaks Quercus macrocarpa, and 100 saplings in a single stand. Using genotypes scored by PCR products at four microsatellite loci, we determined that 94 saplings matched at least one parent in the stand. Saplings often occur as dense clusters of half‐sibs around the presumed maternal parent, and only four adults were seed parents to a large proportion of the saplings sampled. A stump apparently was the seed parent of the largest cluster of half‐sibs, which occupied a sizeable light gap opened up by the death of their maternal tree. Approximately half of the saplings appeared to have grown from seeds that had not been removed after falling from the tree, and half from seeds that were dispersed beyond the crown of their maternal parent. Long‐distance seed dispersal may be more common than has been previously reported. Extremely high levels of long‐distance pollination were indicated, and pollen donors within the stand were generally distributed randomly around maternal trees. More than half of the saplings had paternal parents outside of the stand. This study demonstrates the utility of microsatellite analysis for studying mating systems, seed dispersal and seedling establishment in natural plant populations.
Population structure of the yellow‐footed rock‐wallaby Petrogale xanthopus (Gray, 1854) inferred from mtDNA sequences and microsatellite loci
Authors: POPE L. C. , SHARP A. , MORITZ C.
Published: April 2008

The yellow‐footed rock‐wallaby Petrogale xanthopus is considered to be potentially vulnerable to extinction. This wallaby inhabits naturally disjunct rocky outcrops which could restrict dispersal between populations, but the extent to which that occurs is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequencing and analysis of variation at four microsatellite loci among three geographically close sites in south‐west Queensland (P. x. celeris) and, for mtDNA only, samples from South Australia (P. x. xanthopus) as well. Populations from South Australia and Queensland had phylogenetically distinct mtDNA, supporting the present classification of these two groups as evolutionarily distinct entities. Within Queensland, populations separated by 70 km of unsuitable habitat differed significantly for mtDNA and at microsatellite loci. Populations separated by 10 km of apparently suitable habitat had statistically homogeneous mtDNA, but a significant difference in allele frequency at one microsatellite locus. Tests for Hardy‐Weinberg equilibrium and micro‐geographical variation at microsatellite loci did not detect any substructuring between two wallaby aggregations within a colony encircling a single rock outcrop. Although the present study was limited by small sample sizes at two of the three Queensland locations examined, the genetic results suggest that dispersal between colonies is limited, consistent with an ecological study of dispersal at one of the sites. Considering both the genetic and ecological data, we suggest that management of yellow‐footed rock‐wallabies should treat each colony as an independent unit and that conservation of the Queensland and South Australian populations as separate entities is warranted.
Stability of transformed antagonistic Fusarium oxysporum strains in vitro and in soil microcosms
Authors: MIGHELI Q. , FRIARD O. , TEDESCO D. DEL , MUSSO M. R. , GULLINO M. L.
Published: April 2008

The stability of a genetically modified strain of Fusarium oxysporum used as antagonist against phytopathogenic formae speciales of F. oxysporum was evaluated both in vitro and in microcosm assays. The Escherichia coli hygromycin B phosphotransferase gene (hph), conferring hygromycin B resistance, was introduced by genetic transformation into a recipient strain marked by benomyl resistance and a dark red pigmentation. Hybridization with the complete plasmid suggested that the integration had generally occurred in a multiple‐tandem array at multiple sites. Among nine independent transformants tested, only three of them were mitotically stable after four rounds of vegetative growth with no selective pressure, while six showed various changes in the integration pattern. One transformant had lost the ability to grow in the presence of hygromycin B. In soil microcosms all the transformants maintained the hygromycin B resistant phenotype, but six of them showed rearrangement of transforming DNA. Only one strain (coded T26.40) underwent no obvious rearrangement both after in vitro growth and after recovery from the soil microcosm. The nine transformants were used in three biological control experiments against Fusarium wilt of carnation in comparison to two untransformed reference strains and to the recipient mutant. A high degree of variability in the biocontrol activity was observed throughout the experiments and only transformant T26.40 consistently controlled the incidence of disease. The results are discussed in relation to risk assessment of the release of transgenic antagonistic fungi.
Genetic variation in natural populations of the aphid Rhopalosiphum padi as revealed by maternally inherited markers
Authors: MARTINEZ‐TORRES D. , SIMON J. C. , FERERES A. , MOYA A.
Published: April 2008

A survey on 148 clones of the aphid Rhopalosiphum padi from 11 widespread localities has been carried out to study the genetic structure of populations of this species as revealed by mitochondrial DNA restriction site and length polymorphisms as well as by restriction site analysis of a maternally inherited plasmid carried by the aphid eubacterial endosymbiont Buchnera aphidicola. Our results support the existence in the area under study of two main aphid maternal lineages strikingly coincidental with the two main reproductive categories displayed by this species. Those aphid clones possessing an incomplete life cycle that lacks the sexual phase (anholocyclic or androcyclic clones) show mitochondrial DNA (mtDNA) haplotype I and plasmid haplotype I, whereas those clones displaying the complete life cycle (holocyclic clones) posses some other distinct mtDNA haplotypes closely related to each other and plasmid haplotype II. While restriction‐site analysis of maternally inherited markers points to a relatively ancient origin of anholocycly/androcycly (between 460 000 and 1 400 000 years) followed by interrupted gene flow with respect to the ancestral holocyclic population, mtDNA size variation also suggests that historical stochastic processes have a different effect on the evolution of both main aphid lineages. Evidence of occasional nuclear gene flow between lineages and its consequences on the correspondence between maternally inherited haplotypes and life cycle are also presented and discussed.
Molecular genetic identification of whale and dolphin products from commercial markets in Korea and Japan
Authors: BAKER C. S. , CIPRIANO F. , PALUMBI S. R.
Published: April 2008

We report the methods and results of molecular genetic identification of the species and, in some cases, geographical origins of whale and dolphin products purchased from retail markets and restaurants in Japan and South Korea. As reported previously (Baker & Palumbi 1994), we used the polymerase chain reaction (PCR) and a portable laboratory to amplify, purify and later sequence a portion of the mitochondrial DNA control region from 16 commercial products purchased in Japan. This ‘spot check’ revealed a surprising variety of species for sale, including minke, fin and humpback whales and one or two species of dolphins sold as ‘kujira’ or whale. In the Korean survey, DNA amplifications were conducted by two of us (C.S.B. and F.C.) working with independent equipment and reagents. The two sets of DNA amplifications were returned to our respective laboratories and sequenced independently for cross‐validation. Among the total of 17 species‐specific sequences we found a dolphin, a beaked whale, 13 Northern Hemisphere minke whales (representing at least seven distinct individuals) and two whales which are closely related to the recognized sei and Bryde's whales but could not be identified as either using available type sequences. We suggest that these two specimens represent a currently unrecognized species or subspecies of Bryde's whale, possibly the so‐called ‘small‐form’ reported from the tropical waters of the Indo‐Pacific.

We conclude that molecular systematic analyses of DNA sequences have tremendous utility for the identification of whale and dolphin products. However, there are certain constraints on the application of these techniques for monitoring whaling or trade in whale products. First, PCR and DNA sequencing can generate misleading artefacts. These can generally be recognized or eliminated through experimental controls. Second, phylogenetic reconstructions of DNA sequences can be misinterpreted if the database of type sequences is inadequate or the taxonomy of the group is incomplete. This constraint is, at present, a more serious obstacle to molecular monitoring of whaling. Our results highlight uncertainties about the taxonomic status of oceanic populations and morphological forms of two species (or species complexes) targeted by legal and illegal hunting, the minke and Bryde's whales. Despite these uncertainties, it is difficult to reconcile some of the species available in Japanese and Korean commercial markets with recent catch records made available to the International Whaling Commission. It is particularly disturbing that two specimens of an unrecognized species or subspecies of baleen whale were for sale in a restaurant in South Korea in October, 1994, 8 years after the acceptance of an international moratorium on commercial whaling.
Molecular genetic variation following a population crash in the endangered Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae)
Authors: FRIAR E. A. , ROBICHAUX R. H. , MOUNT D. W.
Published: April 2008

The endangered Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae), has experienced a severe decline in distribution and abundance because of predation by alien ungulates. The small remnant natural population on the Mauna Kea volcano contains only 46 individuals. By contrast, the Haleakala silversword,A. sandwicensessp.macrocephalum, consists of a large, vigorous population exceeding 60 000 individuals. Molecular genetic variation in the two populations was assessed using random amplified polymorphic DNA (RAPD) loci. Despite its severe crash in size, the Mauna Kea population did not differ significantly from the Haleakala population in the number of detectably polymorphic loci or in heterozygosity. The lack of substantial reduction in genetic variation, at least as measured with RAPD loci, suggests that the Mauna Kea population may not yet have gone through multiple generations at very small size.
Estimation of genomic variation between British populations of the potato cyst nematode Globodera pallida using RAPD‐PCR
Authors: BURROWS P. R. , HALFORD P. D. , EVANS K.
Published: April 2008

Random amplified polymorphic DNA (RAPD) has been used to investigate the interrelationships of 20 populations of Globodera pallida collected originally from field soils around the UK. RAPD analysis revealed a high level of relative genomic diversity within British G. pallida but there was no general correlation of genomic similarity with geographic distribution. Two populations of pathotype Pa1 were clearly divergent from the bulk of G. pallida and might represent a distinct introduction. Two other populations, from Scotland and Wales, were also dissimilar from each other and from the rest of the G. pallida populations.
Mitochondrial cytochrome b DNA sequence variation of Atlantic cod Gadus morhua, from Norway
Authors: ARNASON E. , PÁLSSON S.
Published: April 2008

We studied sequence variation of a fragment of the mitochondrial cytochrome b gene using polymerase chain reaction (PCR) and direct sequencing among 85 Norwegian Atlantic cod Gadus morhua, from nine sampling localities representing three overall areas: arctic, coastal and middle. In the analysis we include an additional 15 cod studied by Carr & Marshall (1991a). Nine base changes were found among the 100 sequences defining 11 haplotypes which differ from each other by one to five mutations. Two sites have been hit twice. All but one mutation are at third position silent sites. The variation passes several neutral‐theory tests and is thus suitable as marker for studying population differentiation. Coefficients of coancestry or intraclass correlation coefficient are negative both at the level of individuals within localities and localities within areas. This implies greater differences among individuals within populations than between populations. Intralocality nucleotide diversity is high and masks interlocality nucleotide divergence such that the net interlocality nucleotide divergence is nil. Similarly the net interarea nucleotide divergence is nil.
Genetic and ecotypic structure of a fluorescent Pseudomonas population
Authors: HAUBOLD B. , RAINEY B.
Published: April 2008

Fluorescent pseudomonads are among the most numerous bacteria found on plant surfaces and the activity of certain isolates can affect plant growth. In 1993, 108 fluorescent Pseudomonas isolates were collected on a single sampling occasion from the leaves of sugar beet plants grown at the Oxford University Field Station, Wytham. Isolates were obtained from 54 different leaves, from nine plants, and characterized using 10 allozyme and 23 biotype markers. Statistical analysis of the combined data revealed five biotypic traits which permitted a rational classification of the sample. Analysis of the allozyme data showed that the population was in overall linkage disequilibrium. Clonality was also observed after subdivision of allozyme data along spatial and habitat levels. However, two genetically defined subgroups were in linkage equilibrium which suggests the possibility of frequent large‐scale recombination among certain isolates. A significant correlation between isolate distribution and habitat (leaf type and plot) indicates that the population has ecotypic structure.
Molecular genetic examination of the polymorphic Arctic charr Salvelinus alpinus of Thingvallavatn, Iceland
Authors: VOLPE J. P. , FERGUSON M. M.
Published: April 2008

Thingvallavatn, Iceland contains two sympatric morphotypes (benthic and limnetic) of Arctic charr Salvelinus alpinus. Each morphotype is composed of two morphs and these differ markedly in ecology, behaviour and life history. We used molecular genetic approaches to test whether (i) genetic heterogeneity exists among morphs and (ii) if morphs arose in allopatry and came into secondary contact or arose sympatrically within the lake through genetic segregation and/or phenotypic plasticity. Direct sequencing of 275 bp of the mitochondrial DNA (mtDNA) control region, mtDNA restriction fragment length polymorphisms and single locus minisatellite analyses detected insufficient variation to test our hypotheses. Analysis of multilocus minisatellite band sharing detected no significant differences between morphs within the same morphotype. However, significant differences among morphs belonging to different morphotypes suggest some genetic heterogeneity in Thingvallavatn charr. Limnetic charr from Thingvallavatn were more similar to sympatric benthic charr than to allopatric limnetics from two other Icelandic lakes. This suggests that the Thingvallavatn morphs arose sympatrically within the lake rather than in allopatry followed by secondary contact.
Population differentiation and evolution in the common guillemot Uria aalge
Authors: FRIESEN V. L. , MONTEVECCHI W. A. , BAKER A. J. , BARRETT R. T. , DAVIDSON W. S.
Published: April 2008

Common (Uria aalge) and Brünnich's guillemots (U. Iomvia) are colonial seabirds that nest in temperate to arctic oceans throughout the Northern hemisphere. They are very similar in the characteristics of ecology, demography and life history that are thought to determine the extent of differentiation among populations, yet geographic variation in morphology is notably greater in common guillemots. Despite evidence of strong natal philopatry, previous analyses of allozymes and the mitochondrial cytochrome b gene revealed little genetic differentiation among North Atlantic colonies of Brünnich's guillemots. To determine if the more extensive morphological variability in common guillemots reflects greater genetic variability, we sequenced part of the cytochrome b gene for 160 common guillemots from 10 colonies distributed throughout the Northern hemisphere. Genotype frequencies and phylogenetic relationships among genotypes both indicated that Atlantic and Pacific populations are genetically distinct. Genetic divergence among genotypes suggested that differentiation of these populations has resulted from separation by Pleistocene glaciers and the Bering Landbridge, as well as by currently unsuitable breeding habitat in the Arctic Ocean. Cytochrome b genotype frequencies also differed among Atlantic colonies, and appeared to define a cline similar to that described for morphological characters. Analyses of sequence variation suggested that this variation probably results from secondary contact between two refugial populations from the Pleistocene glaciations, rather than from isolation by distance or selection. In contrast, the Atlantic population of Brünnich's guillemots appears to have arisen through recent expansion of a single homogeneous refugial population.
Conservation genetics of the plain pigeon Columba inornata in Puerto Rico and the Dominican Republic
Authors: YOUNG D. L. , ALLARD M. W.
Published: April 2008

Genetic sequence variation in the mitochondrial D‐loop was assessed for 42 individuals of the plain pigeon Columba inornata from Puerto Rico and the Dominican Republic. While overall genetic diversity was low in these populations, five haplotypes were observed, with one unique to Puerto Rico and three haplotypes unique to the Dominican Republic sample (with haplotype diversity of hPR= 0.479 and hDR= 0.591, and nucleotide diversity of πPR= 0.2% and πDR= 0.4% where the subscripts correspond to Puerto Rico and the Dominican Republic, respectively). A G‐test of haplotype frequencies between these two populations suggest that these two subspecies (C. i. wetmorei and C. i. inornata) are genetically distinct and should be managed separately. With little apparent gene flow between these two islands (estimates of migration Nm= 1.18) it would appear that the endangered species C. i. wetmorei is endemic to the island of Puerto Rico and that these current populations were not founded by a recent extinction and recolonization event from the Dominican Republic.
The essentiality and involvement of Streptococcus intermedius histone‐like DNA‐binding protein in bacterial viability and normal growth
Authors: Liu Dali , Yumoto Hiromichi , Murakami Keiji , Hirota Katsuhiko , Ono Tsuneko , Nagamune Hideaki , Kayama Shizuo , Matsuo Takashi , Miyake Yoichiro
Published: April 2008

Streptococcus intermedius histone‐like DNA‐binding protein (Si‐HLP) is a homodimeric protein and, conserved with Escherichia coli HU, a well‐documented nucleoid‐associated protein (NAP). In E. coli, HU plays important roles as both structural and regulatory factors, but it is not essential for E. coli viability. Streptococcal HLP has been found to bind host cells and induce cytokine production, but its physiological role remains poorly defined. In the present study, using gene insertion knockout and tetracycline‐regulated antisense RNA expression techniques, we determined whether Si‐HLP is essential for bacterial viability and normal growth in S. intermedius. The Si‐HLP‐downregulated S. intermedius strain showed alterations in its morphology and surface properties. Downregulation of Si‐HLP led to an expanded nucleoid to fill the intracellular space. Transcription levels of several genes, including virulence‐associated factors, were found to be activated or repressed in the antisense Si‐hlp RNA‐expressing strain by real‐time PCR and reverse‐transcription PCR. Collectively, these data suggest that Si‐HLP serves as an essential NAP governing the nucleoid architecture and controlling the gene transcription profile in S. intermedius.
The Ustilago maydis Cys2His2‐type zinc finger transcription factor Mzr1 regulates fungal gene expression during the biotrophic growth stage
Authors: Zheng Yan , Kief Jan , Auffarth Kathrin , Farfsing Jan W. , Mahlert Michael , Nieto Fernanda , Basse Christoph W.
Published: April 2008

The smut fungus Ustilago maydis establishes a biotrophic relationship with its host plant maize to progress through sexual development. Here, we report the identification and characterization of the Cys2His2‐type zinc finger protein Mzr1 that functions as a transcriptional activator during host colonization. Expression of the U. maydis mig2 cluster genes is tightly linked to this phase. Upon conditional overexpression, Mzr1 confers induction of a subset of mig2 genes during vegetative growth and this requires the same promoter elements that confer inducible expression in planta. Furthermore, expression of the mig2‐4 and mig2‐5 genes during biotrophic growth is strongly reduced in cells deleted in mzr1. DNA‐array analysis led to the identification of additional Mzr1‐induced genes. Some of these genes show a mig2‐like plant‐specific expression pattern and Mzr1 is responsible for their high‐level expression during pathogenesis. Mzr1 function requires the b‐dependently regulated Cys2His2‐type cell cycle regulator Biz1, indicating that two stage‐specific regulators mediate gene expression during host colonization. In spite of a role as transcriptional activator during biotrophic growth, mzr1 is not essential for pathogenesis; however, conditional overexpression interfered with proliferation during vegetative growth and mating ability, caused a cell separation defect, and triggered filamentous growth. We discuss the implications of these findings.
Plasmodium falciparum Sec24 marks transitional ER that exports a model cargo via a diacidic motif
Authors: Lee Marcus C. S. , Moura Pedro A. , Miller Elizabeth A. , Fidock David A.
Published: April 2008

Exit from the endoplasmic reticulum (ER) often occurs at distinct sites of vesicle formation known as transitional ER (tER) that are enriched for COPII vesicle coat proteins. We have characterized the organization of ER export in the malaria parasite, Plasmodium falciparum, by examining the localization of two components of the COPII machinery, PfSec12 and PfSec24a. PfSec12 was found throughout the ER, whereas the COPII cargo adaptor, PfSec24a, was concentrated at distinct foci that likely correspond to tER sites. These foci were closely apposed to cis‐Golgi sites marked by PfGRASP–GFP, and upon treatment with brefeldin A they accumulated a model cargo protein via a process dependent on the presence of an intact diacidic export motif. Our data suggest that the cargo‐binding function of PfSec24a is conserved and that accumulation of cargo in discrete tER sites depends upon positive sorting signals. Furthermore, the number and position of tER sites with respect to the cis‐Golgi suggests a co‐ordinated biogenesis of these domains.
Lack of evidence in vivo for a remote effect of Escherichia coli heat stable enterotoxin on jejunal fluid absorption
Authors: Lucas M. L. , Duncan N. W. , O’reilly N. F. , Mcilvenny T. J. , Nelson Y. B.
Published: April 2008

Abstract  On contact with the mucosa, heat stable (STa) enterotoxin from Escherichia coli reduces fluid absorption in vivo in the perfused jejunum of the anaesthetized rat. The question of whether it also has a vagally mediated remote action on jejunal absorption, when instilled into the ileum, was re‐examined, given contradictory findings in the literature. A standard perfused loop preparation was used to measure luminal uptake of fluid in vivo by means of volume recovery. STa in the ileum was found to have no effect on jejunal absorption, regardless of cervical or sub‐diaphragmatic vagotomy and also regardless of the nature of the perfusate anion. The batches of toxin were shown in parallel experiments to reduce fluid absorption directly in the jejunum and also in the ileum. Similarly, vagal nerves prior to section had demonstrable in vivo physiological function. There was therefore no evidence for an indirect, vagally mediated ileal effect of STa on proximal fluid absorption.
Targets of myenteric interneurons in the guinea‐pig small intestine
Authors: Neal K. B. , Bornstein J. C.
Published: April 2008

Abstract  Polarized outputs of myenteric interneurons in guinea‐pig small intestine have been well studied. However, the variety of motility patterns exhibited suggests that some interneuron targets remain unknown. We used antisera selected to distinguish interneuron varicosities and known myenteric neuron types to investigate outputs of three interneuron classes in guinea‐pig jejunum; two classes of descending interneurons immunoreactive (IR) for somatostatin (SOM) or nitric oxide synthase (NOS)/vasoactive intestinal peptide (VIP), and one class of ascending interneurons [calretinin/enkephalin (ENK)‐IR]. Varicosities apposed to immunohistochemically identified cell bodies were quantified by confocal microscopy. Intrinsic sensory neurons (calbindin‐IR) were apposed by few varicosities. Cholinergic secretomotor neurons (neuropeptide Y‐IR) were apposed by many SOM‐IR varicosities. Longitudinal muscle excitatory motor neurons (calretinin‐IR) were apposed by some VIP‐ and ENK‐IR varicosities, but few SOM‐IR varicosities. Ascending interneurons (calretinin‐IR) were apposed by many varicosities of all types. NOS‐IR interneurons and inhibitory motor neurons were apposed by numerous VIP‐IR and SOM‐IR varicosities. NOS‐IR short inhibitory motor neurons were apposed by significantly fewer ENK‐IR varicosities than other NOS‐IR neurons. Based on the specific chemical coding of ascending (ENK) and descending (SOM) interneurons, we conclude that cholinergic secretomotor neurons and short inhibitory neurons are located in descending reflex pathways, while ascending interneurons and NOS‐IR descending interneurons are focal points at which ascending and descending pathways converge.