bluuebunny/crossref_metadata_2025 huggingface dataset:
Culture‐based fisheries in non‐perennial reservoirs in Sri Lanka: production and relative performance of stocked species
Authors: WIJENAYAKE W. M. H. K. , JAYASINGHE U. A. D. , AMARASINGHE U. S. , ATHULA J. A. , PUSHPALATHA K. B. C. , DE SILVA S. S.
Published: July 2005

Abstract  In Sri Lanka, there is a great potential for the development of culture‐based fisheries because of the availability of around 12 000 non‐perennial reservoirs in the dry zone (<187 cm annual rainfall) of the island. These reservoirs fill during the north‐east monsoonal period in October to December and almost completely dry up during August to October. As these non‐perennial reservoirs are highly productive, hatchery‐reared fish fingerlings can be stocked to develop culture‐based fisheries during the water retention period of 7–9 months. The present study was conducted in 32 non‐perennial reservoirs in five administrative districts in Sri Lanka. These reservoirs were stocked with fingerlings of Indian (catla Catla catla Hamilton and rohu Labeo rohita Hamilton) and Chinese (bighead carp Aristichthys nobilis Richardson) major carps, common carp Cyprinus carpio L., genetically improved farmed tilapia (GIFT) strain of Nile tilapia, Oreochromis niloticus (L.) and post‐larvae of giant freshwater prawn, Macrobrachium rosenbergii De Man, at three different species combinations and overall stocking densities (SD) ranging from 218 to 3902 fingerlings ha−1, during the 2002–2003 culture cycle. Of the 32 reservoirs stocked, reliable data on harvest were obtained from 25 reservoirs. Fish yield ranged from 53 to 1801 kg ha−1 and the yields of non‐perennial reservoirs in southern region were significantly (P < 0.05) higher than those in the northern region. Naturally‐recruited snakehead species contributed the catches in northern reservoirs. Fish yield was curvilinearly related to reservoir area (P < 0.05), and a negative second order relationship was evident between SD and yield (P < 0.05). Chlorophyll‐a and fish yield exhibited a positive second order relationship (P < 0.01). Bighead carp yield impacted positively on the total yield (P < 0.05), whereas snakehead yield impact was negative. Bighead carp, common carp and rohu appear suitable for poly‐culture in non‐perennial reservoirs. GIFT strain O. niloticus had the lowest specific growth rate among stocked species and freshwater prawn had a low return.
Fisheries and trade of seahorses, Hippocampus spp., in southern India
Authors: SALIN K. R. , YOHANNAN T. M. , MOHANAKUMARAN NAIR C.
Published: July 2005

Abstract  Seahorses (Hippocampus spp.) are a major commodity fished from the shallow coastal seas of the south coast of India where there is an abundance of sea grasses, sponges and corals. They are in great demand for export as traditional medicines, curios and aquarium fish. Organised fishing and trade of seahorses exists in India along the Palk Bay and Gulf of Mannar coasts. At the Palk Bay coast, seahorses are targeted by divers along with sea cucumbers (Holothuria spp.) and gastropods (e.g. Murex spp.,Xancus pyrum Hornell). In the Gulf of Mannar, most of the seahorses are landed as bycatch of shrimp trawling. Seahorses are also fished from Kerala as a bycatch of trawling, although no organised fishery and trade exists. Five species of seahorses were identified from the Palk Bay coast, whereas only two species were obtained from Kerala. Most seahorses from India are exported to Singapore, Hong Kong, Malaysia and the United Arab Emirates. The volume of dried seahorse trade from India was estimated to be 9.75 t as derived from catch data in 2001, which was much higher than official statistics of 4.34 t during 2001–2002, suggesting the major part of the exports might be through non‐conventional means and goes undeclared. Some aspects of the impact of large‐scale fishing and trade on conservation of these seahorses are discussed.
Genetic characterisation of the Rhodanian twaite shad,Alosa fallax rhodanensis
Authors: LE CORRE M. , ALEXANDRINO P. , SABATIE M. R. , APRAHAMIAN M. W. , BAGLINIÈRE J. L.
Published: July 2005

Abstract Data on the genetic characteristics of the rhodanian shad,Alosa fallax rhodanensisRoule, using three Mediterranean populations (rivers Rhône, Aude and Hérault) and seven protein markers are presented. Allelic frequency distribution, and absolute and relative genetic diversity show a genetically homogeneous structure in the Mediterranean populations. Results when compared with allis (Alosa alosaLinné) and twaite (Alosa fallax fallaxLacépède) shad Atlantic populations confirm that the Rhodanian shad belongs to theAlosa fallaxRoule species. Furthermore, genetic characteristics of the twaite shad Mediterranean group were quite different from Atlantic populations but remained close to the most southern Atlantic population in the Oued Sebou (Morocco). These findings suggest that Rhodanian shad should be considered a well identified homogeneous group withinAlosa fallaxrather than a subspecies because of the low genetic distance and some relatively different biological characteristics between the Atlantic and Mediterranean twaite shad groups.
Identification and molecular characterization of defensin gene from the ant Formica aquilonia
Authors: Viljakainen L. , Pamilo P.
Published: July 2005

The effectors of the insect immune system are antimicrobial peptides. With the aim of studying the evolution of immune system genes, we identified a gene encoding the antimicrobial peptide defensin from a social insect, the wood ant Formica aquilonia. In this article we report the identification and characterization of this gene. We also compare the ant defensin gene structure to that previously obtained from two other hymenopteran species, the honeybee, Apis mellifera, and the bumblebee, Bombus ignitus. The ant defensin gene structure differs from both of these bee defensins with respect to the number and length of introns and exons.
Partial deletions of the W chromosome due to reciprocal translocation in the silkworm Bombyx mori
Authors: Abe H. , Seki M. , Ohbayashi F. , Tanaka N. , Yamashita J. , Fujii T. , Yokoyama T. , Takahashi M. , Banno Y. , Sahara K. , Yoshido A. , Ihara J. , Yasukochi Y. , Mita K. , Ajimura M. , Suzuki M. G. , Oshiki T. , Shimada T.
Published: July 2005

In the silkworm, Bombyx mori (female, ZW; male, ZZ), femaleness is determined by the presence of a single W chromosome, irrespective of the number of autosomes or Z chromosomes. The W chromosome is devoid of functional genes, except the putative female‐determining gene (Fem). However, there are strains in which chromosomal fragments containing autosomal markers have been translocated on to W. In this study, we analysed the W chromosomal regions of the Zebra‐W strain (T(W;3)Ze chromosome) and the Black‐egg‐W strain (T(W;10)+w−2 chromosome) at the molecular level. Initially, we undertook a project to identify W‐specific RAPD markers, in addition to the three already established W‐specific RAPD markers (W‐Kabuki, W‐Samurai and W‐Kamikaze). Following the screening of 3648 arbitrary 10‐mer primers, we obtained nine W‐specific RAPD marker sequences (W‐Bonsai, W‐Mikan, W‐Musashi, W‐Rikishi, W‐Sakura, W‐Sasuke, W‐Yukemuri‐L, W‐Yukemuri‐S and BMC1‐Kabuki), almost all of which contained the border regions of retrotransposons, namely portions of nested retrotransposons. We confirmed the presence of eleven out of twelve W‐specific RAPD markers in the normal W chromosomes of twenty‐five silkworm strains maintained in Japan. These results indicate that the W chromosomes of the strains in Japan are almost identical in type. The Zebra‐W strain (T(W;3)Ze chromosome) lacked the W‐Samurai and W‐Mikan RAPD markers and the Black‐egg‐W strain (T(W;10)+w−2 chromosome) lacked the W‐Mikan RAPD marker. These results strongly indicate that the regions containing the W‐Samurai and W‐Mikan RAPD markers or the W‐Mikan RAPD marker were deleted in the T(W;3)Ze and T(W;10)+w−2 chromosomes, respectively, due to reciprocal translocation between the W chromosome and the autosome. This deletion apparently does not affect the expression of Fem; therefore, this deleted region of the W chromosome does not contain the putative Fem gene.
SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms
Authors: Barnes M. J. , Lobo N. F. , Coulibaly M. B. , Sagnon N′F. , Costantini C. , Besansky N. J.
Published: July 2005

Polymorphic SINE insertions can be useful markers for assessing population structure and differentiation. Maque is a family of SINE elements which, based on bioinformatic analysis, was suggested to have been active recently in Anopheles gambiae, the major vector of malaria. Here, we report the development of polymorphic Maque insertions as population genetic markers in A. gambiae, and the use of these markers to better characterize divergence on the X chromosome between A. gambiae M and S molecular forms in populations from Burkina Faso and Mali. Our data are consistent with the recent activity of Maque. Phylogenetic analysis suggests that at least two recently active lineages may have a role in mediating genome evolution. We found differences in element insertion frequency and sequence between the M and S populations analysed. Significant differentiation was observed between these two groups across a 6 Mb region at the proximal (centromeric) end of the X chromosome. Locus‐specific FST values ranged from 0.14 to 1.00 in this region, yet were not significantly different from zero in more distal locations on the X chromosome; the trend was consistent in populations from both geographical locales suggesting that differentiation is not due to local adaptation. Strong differentiation between M and S at the proximal end of the X chromosome, but not outside this region, suggests the action of selection counteracting limited gene flow between these taxa and supports their characterization as incipient species.
Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae
Authors: Marinotti O. , Nguyen Q. K. , Calvo E. , James A. A. , Ribeiro J. M. C.
Published: July 2005

A microarray analysis of 14 900 genes of the malaria vector mosquito, Anopheles gambiae, shows that as many as 33% (4924) of their corresponding transcription products vary in abundance within 24 h after a blood meal. Approximately half (2388) of these products increase in their accumulation and the remainder (2536) decrease. Expression dynamics of 80% of the genes analysed by expressed sequence tag (EST) projects reported previously are consistent with the observations from this microarray analysis. Furthermore, the microarray analysis is more sensitive in detecting variation in abundance of gene products expressed at low levels and is more sensitive overall in that a greater number of regulated genes are detected. Major changes in transcript abundance were seen in genes encoding proteins involved in digestion, oogenesis and locomotion. The microarray data and an electronic hyperlinked version of all tables are available to the research community at http://www.angagepuci.bio.uci.edu/1/.
Molecular cloning, characterization and regulation of the cockroach vitellogenin receptor during oogenesis
Authors: Tufail M. , Takeda M.
Published: July 2005

The vitellogenin receptor (VgR) belongs to the low density lipoprotein receptor (LDLR) superfamily, and mediates the uptake of vitellogenin (Vg) into developing oocytes of all oviparous species. We cloned and characterized a VgR from previtellogenic ovaries of the cockroach, Periplaneta americana (Pa). This is the first report on a VgR from a hemimetabolous insect. The cDNA, comprising 5722 bp, encoded a 1790‐residue mature protein with a predicted molecular mass of 200.5 kDa. We next characterized the ovarian expression pattern, developmental regulation and cellular distribution of the VgR mRNA and protein. Northern blot analysis confirmed that a ∼7.2 kb transcript was specifically expressed in ovarian tissues at high levels throughout ovarian development, especially in previtellogenic ovaries and in ovaries before adult emergence. RNA in situ hybridization and immunocytochemistry localized the VgR mRNA and protein to germ‐line derived cells, the oocytes, and revealed that VgR gene transcription and translation begin very early during oocyte differentiation in the germarium. Immunoblot analysis detected an ovary‐specific VgR protein of ∼210 kDa that was present in previtellogenic ovaries on the day of female emergence. The VgR protein signal strengthened every day and was intense after initiation of vitellogenesis and onset of Vg uptake. The immunoblotting of vitellins demonstrated that Vg uptake occurred on day 5, one day after Vg first appeared in the haemolymph, indicating that the receptor‐endocytotic machinery starts functioning soon after the ligand becomes available.
Identification of candidate sialome components expressed in ixodid tick salivary glands using secretion signal complementation in mammalian cells
Authors: Lambson B. , Nene V. , Obura M. , Shah T. , Pandit P. , Ole‐MoiYoi O. , Delroux K. , Welburn S. , Skilton R. , De Villiers E. , Bishop R.
Published: July 2005

Ixodid ticks manipulate mammalian host pathways by secreting molecules from salivary glands. Novel cDNAs containing functional secretion signals were isolated from ixodid tick salivary glands using a signal sequence trap. Only 15/61Rhipicephalus appendiculatusand 1/7Amblyomma variegatumcDNAs had significant identity (< 1e‐15) to previously identified sequences. Polypeptides that may interact with host pathways included a kinase inhibitor. Two proteins encoded homologues of the yolk protein vitellogenin and seventeen contained glycine‐rich motifs. Four proteins without sequence matches had conserved structural folds, identified using a Threading algorithm. Predicted secretion signals were between fifteen and fifty‐seven amino acids long. Four homologous polymorphic proteins contained conserved (26/27 residues) signal peptides. Ten functional tick secretion signals could not be unambiguously identified using predictive algorithms.
Quantitative real‐time RT‐PCR analysis in desert locusts reveals phase dependent differences in neuroparsin transcript levels
Authors: Claeys I. , Simonet G. , Breugelmans B. , Van Soest S. , Franssens V. , Sas F. , De Loof A. , Vanden Broeck J.
Published: July 2005

In different parts of the world, locust swarms cause severe ecological and economic damage. However, the physiological mechanisms underlying this gregarization process remain elusive. In this study, we present a detailed quantitative analysis of two neuroparsin precursor (Scg‐NPP1 and Scg‐NPP2) transcripts in the brain, fat body, gut, gonads and accessory glands of male and female, gregarious and solitarious desert locusts (Schistocerca gregaria). These transcripts are generally more abundant in solitarious than in gregarious animals. In contrast to their gregarious congeners, solitarious locusts contain detectable Scg‐NPP1 and Scg‐NPP2 transcript levels in the fat body. Moreover, our data reveal temporal changes of neuroparsin mRNA levels in the brains and fat bodies of adult isolated‐reared locusts. This paper provides the first scientific evidence for phase‐dependent transcriptional regulation of neuropeptide hormone encoding genes.
Gene structure and expression profile of Manduca sexta prophenoloxidase‐activating proteinase‐3 (PAP‐3), an immune protein containing two clip domains
Authors: Zou Z. , Jiang H.
Published: July 2005

Prophenoloxidase‐activating proteinase‐3 (PAP‐3) is a component of the defence system in Manduca sexta. We have isolated genomic clones and elucidated the organization of this gene. The 3′ end of exon 2, the entire exon 3 and the 5′ end of exon 4 encode the two amino‐terminal clip domains. Southern blot analysis suggested a single copy of the PAP‐3 gene in the genome. We identified several putative immune‐responsive elements in the upstream region. The PAP‐3 gene is not highly expressed in the fat body during larval development until the wandering stage begins. The mRNA level is high in the epithelium, fat body and haemocytes. Tissue‐specific alternative splicing occurs in the fat body and trachea. A bacterial injection markedly induced the gene expression in the fat body and haemocytes.
Fertility, segregation at a herbicide‐resistance locus, and genome structure in BC1 hybrids from two important weedy Amaranthus species
Authors: TRUCCO F. , TATUM T. , RAYBURN A. L. , TRANEL P. J.
Published: July 2005

Field studies have established high potential for hybridization between two important and often coexisting weedy species, Amaranthus hybridus and Amaranthus tuberculatus. Prezygotic reproductive barriers between these species are believed to be limited to pollen competition and availability. A greenhouse study showed that a herbicide‐resistance gene (ALS) from A. hybridus could be introgressed into an advanced A. tuberculatus background (BC2). However, evidence is lacking in support of such transfer in nature. Postzygotic reproductive barriers may minimize, if not preclude, natural introgression. Indeed, A. hybridus ×A. tuberculatus hybrids are characterized by reduced fertility and even floral neuterism. The purpose of this study was to assess hybrid fertility in the BC1 generation and its relationship with genome structure and segregation at ALS. Fertility was assessed by measuring seed output and by pollen evaluation, and segregation at ALS was determined via a molecular marker system. The two parental species have the same ploidy (2n = 32) but differ in DNA content (2C) values, with A. tuberculatus chromosomes being on average 29% greater than those of A. hybridus. Given that most (98%) BC1s were homoploid, 2C values were used as indicators of relative genomic constitution. Fertility in the BC1 generation was greater than that of F1s, and 3% of BC1s had seed output similar to that of the parental species. Fertility in the BC1 did not correlate (in a strict way) with reconstitution of parental genomes. Hybrid sterility appeared to be controlled by relatively few loci. Heterozygosity at ALS was negatively correlated with fertility. Also, the A. tuberculatus ALS allele was not observed in the A. hybridus sexual condition, monoecism. Linkage of ALS to a locus associated (directly or via epistasis) with hybrid sterility may explain the fertility penalty observed with ALS introgression. Moreover, this linkage might explain why sequenced herbicide‐resistance ALS alleles from sympatric A. tuberculatus and A. hybridus populations show independent evolution.
Genomic tools and cDNA derived markers for butterflies
Authors: PAPANICOLAOU ALEXIE , JORON MATHIEU , MCMILLAN W. OWEN , BLAXTER MARK L. , JIGGINS CHRIS D.
Published: July 2005

The Lepidoptera have long been used as examples in the study of evolution, but some questions remain difficult to resolve due to a lack of molecular genetic data. However, as technology improves, genomic tools are becoming increasingly available to tackle unanswered evolutionary questions. Here we have used expressed sequence tags (ESTs) to develop genetic markers for two Müllerian mimic species,Heliconius melpomeneandHeliconius erato. In total 1363 ESTs were generated, representing 330 gene objects inH. melpomeneand 431 inH. erato. User‐friendly bioinformatic tools were used to construct a nonredundant database of these putative genes (available athttp://www.heliconius.org), and annotate them withblastsimilarity searches, InterPro matches and Gene Ontology terms. This database will be continually updated with EST sequences for the Papilionideae as they become publicly available, providing a tool for gene finding in the butterflies. Alignments of theHeliconiussequences with putative homologues derived fromBombyx morior other public data sets were used to identify conserved PCR priming sites, and develop 55 markers that can be amplified from genomic DNA in bothH. eratoandH. melpomene. These markers will be used for comparative linkage mapping inHeliconiusand will have applications in other phylogenetic and genomic studies in the Lepidoptera.
Recombination and speciation
Authors: BUTLIN ROGER K.
Published: July 2005

Speciation can be viewed as the evolution of restrictions on the freedom of genetic recombination: new combinations of alleles can be generated within species, but alleles from different species cannot be brought together. Recently, there has been increasing realization that the role of chromosomal rearrangements in speciation might be primarily a result of their influence on recombination. I argue that ideas about the role of recombination in speciation should be considered in the context of the variability of recombination rates and patterns more generally and that genic as well as chromosomal causes of restricted recombination should be considered. I review patterns of variation in recombination rates and theoretical progress in understanding the conditions that favour increased or decreased rates. Although progress has been made in understanding conditions that alter overall rates of recombination, widespread variation in patterns of recombination remains largely unexplained. I consider three models for the role of locally restricted recombination in speciation and the evidence currently supporting them.
How do misassigned paternities affect the estimation of heritability in the wild?
Authors: CHARMANTIER ANNE , RÉALE DENIS
Published: July 2005

Studies of birds have recently played an important role in the increasing success of quantitative genetics applied to natural populations. However, these studies mostly base their pedigree relationships on social information, despite the known widespread genetic polygamy in avian species. Here, we study the influence of misassigned paternities, combined with the effect of pedigree size and depth, on the estimation of heritability. First, we compute simulations of a polygenic trait for two levels of heritability (0.1 and 0.4), several extra‐pair paternity rates (ranging from 5% to 40%), and varying sample sizes (20, 50 and 100 broods) or pedigree depth (2 or 4 generations). We compare heritability estimates from the social and the genetic pedigree, running a restricted maximum‐likelihood ‘animal model’. Social pedigree underestimates heritability by an average of 0–17% for 5–20% extra‐pair paternities and by up to 18% for 40% extra‐pair paternities and a heritability of 0.4. Second, we identifyied extra‐pair offspring using microsatellite loci in two populations of blue tits (Parus caeruleus) showing high levels of extra‐pair paternities (15% and 25% of extra‐pair offspring). We compare heritabilities of tarsus length and body mass estimated with pedigrees of increasing accuracy. These analyses suggest that the bias induced by misassigned paternities on heritability estimation depends on the level of heritability and the rate of paternity error. Typical rates of extra‐pair paternities in birds (around 20% of offspring) should result in an underestimation of heritability of less than 15% when estimated over a minimum of 100 broods.
Kin interactions and changing social structure during a population outbreak of feral house mice
Authors: SUTHERLAND DUNCAN R. , SPENCER PETER B. S. , SINGLETON GRANT R. , TAYLOR ANDREA C.
Published: July 2005

Populations of feral house mice (Mus domesticus L.) in Australia undergo multiannual fluctuations in density, and these outbreaks may be partly driven by some change in behavioural self‐regulation. In other vertebrate populations with multiannual fluctuations, changes in kin structure have been proposed as a causal mechanism for changes in spacing behaviour, which consequently result in density fluctuations. We tested the predictions of two alternative conceptual models based on kin selection in a population of house mice during such an outbreak. Both published models (Charnov & Finerty 1980; Lambin & Krebs 1991) propose that the level of relatedness between interacting individuals affects their behavioural response and that this changes with population density, though the nature of this relationship differs between the two models. Neither of the models was consistent with all observed changes in relatedness between interacting female mice; however, our results suggested that changes in kin structure still have potential for explaining why mouse outbreaks begin. Therefore, we have developed a variant of one of these conceptual models suggesting that the maintenance of female kin groups through the preceding winter significantly improves recruitment during the subsequent breeding season, and is therefore necessary for mouse outbreaks. We provide six testable predictions to falsify this hypothesis.
Phylogeography of sexualHeteronotia binoei(Gekkonidae) in the Australian arid zone: climatic cycling and repetitive hybridization
Authors: STRASBURG JARED L. , KEARNEY MICHAEL
Published: July 2005

The biota of much of continental Australia have evolved within the context of gradual aridification of the region over several million years, and more recently of climatic cycling between relatively dry and humid conditions. We performed a phylogeographical study of three sexual chromosome races of theHeteronotia binoeicomplex of geckos found throughout the Australian arid zone. Two of these three races were involved in two separate hybridization events leading to parthenogenetic lineages (alsoH. binoei), and the third is widespread and broadly sympatric with the parthenogens. Based on our analyses, the three sexual races diversified approximately 6 million years ago in eastern Australia, during a period of aridification, then each moved west through northern, southern, and central dispersal corridors to occupy their current ranges. In each case, the timing of major phylogeographical inferences corresponds to inferred palaeoclimatic changes in continental Australia. This scenario provides a simple explanation for diversification, secondary contact, and hybridization between the races. However, data presented elsewhere indicate that formation of the parthenogens was considerably more recent than the westward expansion of the hybridizing races, and that multiple hybridization events were geographically and temporally distinct. We suggest that cyclical climate changes may have led to regional range changes that facilitated hybridization between the races, which are not currently known to be in sympatry.
Phylogeny and historical biogeography of African ground squirrels: the role of climate change in the evolution of Xerus
Authors: HERRON M. D. , WATERMAN J. M. , PARKINSON C. L.
Published: July 2005

We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum‐parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an ‘arid corridor’ from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well‐supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio–Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.
Comparative host–parasite population structures: disentangling prospecting and dispersal in the black‐legged kittiwakeRissa tridactyla
Authors: McCOY KAREN D. , BOULINIER THIERRY , TIRARD CLAIRE
Published: July 2005

Although much insight is to be gained through the comparison of the population genetic structures of parasites and hosts, there are, at present, few studies that take advantage of the information on vertebrate life histories available through the consideration of their parasites. Here, we examined the genetic structure of a colonial seabird, the black‐legged kittiwake (Rissa tridactyla) using seven polymorphic microsatellite markers to make inferences about population functioning and intercolony dispersal. We sampled kittiwakes from 22 colonies across the species’ range and, at the same time, collected individuals of one of its common ectoparasites, the tickIxodes uriae. Parasites were genotyped at eight microsatellite markers and the population genetic structure of host and parasite were compared. Kittiwake populations are only genetically structured at large spatial scales and show weak patterns of isolation by distance. This may be due to long‐distance dispersal events that erase local patterns of population subdivision. However, important additional information is gained by comparing results with those of the parasite. In particular, tick populations are strongly structured at regional scales and show a stepping‐stone pattern of gene flow. Due to the parasite's life history, its population structure is directly linked to the frequency and spatial extent of within‐breeding season movements of kittiwakes. The comparison of host and parasite gene flow therefore helps us to disentangle the intercolony movements of birds from that of true dispersal events (movement followed by reproduction). In addition, such data can provide essential elements for predicting the outcome of local co‐evolutionary interactions.
Phylogeographical disjunction in abundant high‐dispersal littoral gastropods
Authors: WATERS J. M. , KING T. M. , O'LOUGHLIN P. M. , SPENCER H. G.
Published: July 2005

Phylogeographical disjunctions in high‐dispersal marine taxa are variously ascribed to palaeogeographical conditions or contemporary ecological factors. Associated biogeographical studies, however, seldom incorporate the sampling design required to confidently discriminate among such competing hypotheses. In the current study, over 7800 gastropod specimens were examined for operculum colour, and 129 specimens genetically, to test ecological and historical biogeographical hypotheses relating to biogeographical disjunction in the Southern Hemisphere, and to southern Australia in particular. Mitochondrial DNA sequence analysis of the high‐dispersal intertidal gastropod Nerita atramentosa in southern Australia (88 specimens; 18 localities) revealed an east–west phylogeographical split involving two highly divergent clades (26.0 ± 1.9%) exhibiting minimal geographical overlap in the southeast. The eastern clade of Nerita atramentosa is also widespread in northern New Zealand (43 specimens, 10 localities), but no significant genetic differentiation is explained by the Tasman Sea, a 2000‐km‐wide oceanic barrier. Spatial genetic structure was not detected within either clade, consistent with the species’ dispersive planktotrophic phase lasting for 5–6 months. Digital analysis of operculum colouration revealed substantial differences between eastern (tan) and western (black) specimens. Genetic analysis and visual inspection of 88 Australian specimens revealed a completely nonrandom association between mtDNA data and operculum colouration. Independent examination of a further 7822 specimens from 14 sites in southern Australia revealed both colour morphs at all localities, but reinforced the phylogeographical data by indicating a marked turnover in colour morph abundance associated with a palaeogeographical barrier: Wilsons Promontory. This sharp biogeographical disjunction is in marked contrast to the species’ high dispersal abilities. The genetic similarity of Nerita morio (Easter Island) and the eastern Australian + New Zealand lineage (1.1 ± 0.3%) provides further evidence of long‐distance dispersal in southern Nerita. Phylogenetic relationships of nine species (four genera) of Neritidae, an almost exclusively tropical gastropod family, are consistent with the hypothesis that southern temperate black nerites comprise a monophyletic radiation.
Variation for neutral markers is correlated with variation for quantitative traits in the plant pathogenic fungus Mycosphaerella graminicola
Authors: ZHAN J. , LINDE C. C. , JÜRGENS T. , MERZ U. , STEINEBRUNNER F. , McDONALD B. A.
Published: July 2005

We compared genetic variation and population differentiation at RFLP marker loci with seven quantitative characters including fungicide resistance, temperature sensitivity, pycnidial size, pycnidial density, colony size, percentage of leaves covered by pycnidia (PLACP) and percentage of leaves covered by lesions (PLACL) in Mycosphaerella graminicola populations sampled from four regions. Wide variation in population differentiation was found across the quantitative traits assayed. Fungicide resistance, temperature sensitivity, and PLACP displayed a significantly higher QST than GST, consistent with selection for local adaptation, while pycnidial size, pycnidial density and colony size displayed a lower or significantly lower QST than GST, consistent with constraining selection. There was not a statistical difference between QST and GST in PLACL. We also found a positive and significant correlation between genetic variation in molecular marker loci and quantitative traits at the multitrait scale, suggesting that estimates of overall genetic variation for quantitative traits in M. graminicola could be derived from analysis of the molecular genetic markers.
Ancient DNA from pollen: a genetic record of population history in Scots pine
Authors: PARDUCCI L. , SUYAMA Y. , LASCOUX M. , BENNETT K. D.
Published: July 2005

Assessments of plant population dynamics in space and time have depended on dated records of fossil pollen synthesized on a subcontinental scale. Genetic analyses of extant populations have revealed spatial relationships that are indicative of past spatial dynamics, but lack an explicit timescale. Synthesis of these data requires genetic analyses from abundant dated fossil material, and this has hitherto been lacking. Fossil pollen is the most abundant material with which to fill this data gap. Here we report genetic analyses of fossil pollen retrieved from Holtjärnen postglacial lake sediment in Sweden and show that plastid DNA is recoverable from Scots Pine and Norway spruce pollen grains that are 100 and 10 000 years old. By sequencing clones from two short plastid PCR products and by using multiple controls we show that the ancient sequences were endogenous to the fossil grains. Comparison of ancient sequences and those obtained from an extant population of Scots pine establishes the first genetic link between extant and fossil samples in this species, providing genetic continuity through time. The finding of one common haplotype present in modern, 100‐year old and 10 000‐year old samples suggests that it may have persisted near Holtjärnen throughout the postglacial period. This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time.
Identification and characterization of a novel HLA‐DRB1 allele, DRB1*0830*
Authors: Hoppe B. , Heymann G.A. , Kiesewetter H. , Salama A.
Published: July 2005

Abstract:  Here, we report on the identification and characterization of a novel human leukocyte antigen (HLA) DRB1 allele, DRB1*0830. This allele was identified in a candidate for hematopoietic stem cell donation. While the DNA sequence of HLA‐DRB1*0830 most closely matches to DRB1*080202, its amino acid sequence resembles DRB1*080202 and DRB1*0813. Due to a substitution at nucleotide position 286 HLA‐typing using sequence‐specific oligonucleotide hybridization or amplification using sequence‐specific primers gave inconclusive results. Allele‐specific DNA sequencing confirmed a 286 T→A substitution resulting in Phe67Ile.
New polymorphisms for the BoLA‐DRB3 upstream regulatory region
Authors: Ripoli M.V. , Villegas‐Castagnasso E.E. , Peral‐Garcia P. , Giovambattista G.
Published: July 2005

Abstract:  Two new alleles, named BoLA‐DRB3‐P*06 and BoLA‐DRB3‐P*07, have been identified for the upstream regulatory region of the BoLA‐DRB3 gene. The 228‐bp nucleotide sequences of the promoter comprising the W, X, Y, CAAT and TATA regulatory boxes were analysed. The BoLA‐DRB3‐P*06 (AY858800) exhibits one insertion between the W and X boxes, and one transition between the X and Y boxes. On the other hand, the BoLA‐DRB3‐P*07 (AY714592) showed one insertion in the X box.
Description and characterization of two new HLA alleles, B*4051 and DRB1*1364, identified by sequence‐based typing*
Authors: Czachurski D. , Scollo A. , Skambraks A. , Perichon A.M. , Scherer S. , Tran T.H. , Opelz G. , Grappiolo I. , Mytilineos J.
Published: July 2005

Abstract:  Human leukocyte antigen (HLA)‐B and HLA‐DRB1 typing in two female individuals revealed reaction patterns that did not correspond to any known HLA‐B specificity and appeared to identify a very rare HLA‐DRB1 allele, respectively. Sequence‐based analysis of these samples revealed two new HLA alleles, one similar to B*4023 and the other to DRB1*1308. The new HLA‐B allele, which was assigned the name HLA‐B*4051, could have been generated by a double crossing over recombination between B*4001 and B*1401 or 1402, whereas DRB1*1364, the new DRB1 allele, could have been generated either by a double crossing over recombination between DRB1*1308 and DRB1*1201, 1202, or 1203 or by two independent crossing over events between DRB1*1401, DRB1*1201, 1202, or 1203 and DRB1*1301.
HLA‐DQB1 sequencing‐based typing using newly identified conserved nucleotide sequences in introns 1 and 2
Authors: Dunn P.P.J. , Day S. , Williams S. , Bendukidze N.
Published: July 2005

Abstract:  Sequencing‐based typing (SBT) human leukocyte antigen (HLA) class I and II genes should examine entire exon sequences where polymorphisms lie. Primers for the amplification of complete exons therefore anneal in introns and their design relies on accurate intron sequences being available. We decided to develop a SBT method for HLA‐DQB1 using amplification primers which anneal in introns 1 and 2, yet the amount of intron sequence data previously available in databases was sparse. Therefore, we undertook a systematic sequencing of introns 1 and 2 using DNA from cell lines homozygous for DQB1. This study confirmed an earlier report that the non‐coding regions of this gene are the most polymorphic seen in the human genome. Intron sequences within an allele group were largely identical, the exceptions being DQB1*0301 differing from other DQB1*03 allele groups and DQB1*0601 differing from all other DQB1*06 alleles. A retroviral Alu element, related to the AluYa5a2 subfamily, was identified uniquely inserted in intron 2 of DQB1*02 alleles. For the typing approach, six amplification primers were designed based on conserved allele group sequences covering all of the HLA DQB antigens, and two sequencing primers were also designed which anneal in intron 2. This method has proved to be very robust and has been used as part of a referral DNA sequencing service for a number of years.
Identification of a novel HLA‐A*02 allele, A*027401*
Authors: Piancatelli D. , Beato T.D. , Papola F. , Aureli A. , Fioroni A. , Canossi A. , Mastrangelo E. , Liberatore G. , Tessitore A. , Adorno D.
Published: July 2005

Abstract:  A novel HLA‐A*02 allele was detected in a Caucasian patient from central Italy, requiring a hematopoietic cell transplantation. Direct sequencing identified a variation in one nucleotide position, which was confirmed by cloning. The name A*027401 was officially assigned by the WHO Nomenclature Committee in November 2004 (AY796418, AY796419, AY796420, and HWS10002684). A*027401 differs from A*02010101 by a single G to A substitution at nucleotide position 595 in exon 3. The new variant would lead to a nonsynonymous nucleotide change (GGG to AGG) at codon 175, resulting in a basic Arg in the α‐helix of the α2‐domain, in place of a non‐polar Gly. The presence of an uncommon variation at a highly conserved nucleotide position could have implications in unrelated hematopoietic cell transplantation.
MHC microsatellite diversity and linkage disequilibrium among common HLA‐A, HLA‐B, DRB1 haplotypes: implications for unrelated donor hematopoietic transplantation and disease association studies
Authors: Malkki M. , Single R. , Carrington M. , Thomson G. , Petersdorf E.
Published: July 2005

Abstract: Twenty‐two human major histocompatibility complex (MHC) region microsatellite (Msat) markers were studied for diversity and linkage disequilibrium (LD) with HLA loci in hematopoietic cell transplant recipients and their HLA‐A, HLA‐B, HLA‐C, HLA‐DRB1, and HLA‐DQB1 allele‐matched unrelated donors. These Msats showed highly significant LD over much of the MHC region. The Msat diversity of five common Caucasian haplotypes (HLA‐A1‐B8‐DR3, A3‐B7‐DR15, A2‐B44‐DR4, A29‐B44‐DR7, and A2‐B7‐DR15) was examined using a new measure called ‘haplotype specific heterozygosity’ (HSH). Each of the five haplotypes had at least one Msat marker with an HSH value of zero indicating that only one Msat allele was observed for the particular HLA haplotype. In addition, the ability of Msats to predict HLA‐A‐B‐DRB1 haplotypes was studied. Over 90% prediction probability of two common haplotypes (HLA‐A1‐B8‐DR3 and HLA‐A3‐B7‐DR15) was achieved with information from three Msats (D6S265/D6S2787/D6S2894 and D6S510/D6S2810/D6S2876, respectively). We demonstrate how the HSH index can be used in the selection of informative Msats for transplantation and disease association studies. Markers with low HSH values can be used to predict specific HLA haplotypes or multilocus genotypes to supplement the screening of HLA‐matched donors for transplantation. Markers with high HSH values will be most informative in studies investigating MHC region disease‐susceptibility genes where HLA haplotypic effects are known to exist.
Growth and physiological responses to drought and elevated ultraviolet‐B in two contrasting populations of Hippophae rhamnoides
Authors: Yang Yongqing , Yao Yinan , Xu Gang , Li Chunyang
Published: July 2005

In the southeast of the Qinghai‐Tibetan Plateau of China, sea buckthorn (Hippophae rhamnoides L.), which is a thorny nitrogen‐fixing deciduously perennial shrub, has been widely used in forest restoration as the pioneer species. In our study, two contrasting populations from the low and high altitudinal regions were employed to investigate the effects of drought, ultraviolet‐B (UV‐B) and their combination on sea buckthorn. The experimental design included two watering regimes (well watered and drought stressed) and two levels of UV‐B (with and without UV‐B supplementation). Drought significantly decreased total biomass, total leaf area and specific leaf area (SLA), and increased root/shoot ratio, fine root/coarse root ratio and abscisic acid content (ABA) in both populations. However, the high altitudinal population was more responsive to drought than the low altitudinal population. On the other hand, elevated UV‐B induced increase in anthocyanins in both populations, whereas the accumulation of UV‐absorbing compounds occurred only in the low altitudinal population. The drought‐induced enhancement of ABA in the high altitudinal population was significantly suppressed in the combination of drought and elevated UV‐B. Moreover, significant drought × UV‐B interaction was detected on total biomass in both populations, total leaf area and fine root/coarse root in the low altitudinal population, and SLA in the high altitudinal population. These results demonstrated that there were different adaptive responses between two contrasting populations, the high altitudinal population exhibited higher tolerance to drought and UV‐B than the low altitudinal population.
Preparation of leaf mitochondria from Arabidopsis thaliana
Authors: Keech Olivier , Dizengremel Pierre , Gardeström Per
Published: July 2005

Arabidopsis thaliana is, perhaps, the most important model species in modern plant biology. However, the isolation of organelles from leaves of this plant has been difficult. Here, we present two different protocols for the isolation of mitochondria, yielding either highly functional crude mitochondria or highly purified mitochondria. The crude mitochondria were well coupled with the substrates tested (malate + glutamate, glycine and NADH), exhibiting respiratory control ratios of 2.1–3.9. Purified mitochondria with very low levels of chlorophyll contamination were obtained by Percoll gradient centrifugation, yielding 1.2 mg of mitochondrial protein from 50 g of leaves.
Antisense suppression of deoxyhypusine synthase by vacuum‐infiltration of Agrobacterium enhances growth and seed yield of canola
Authors: Wang Tzann‐Wei , Wu Wendy , Zhang Chun‐Guang , Nowack Linda M. , Liu Zhongda , Thompson John E.
Published: July 2005

Deoxyhypusine synthase (DHS; EC 2.5.1.46) mediates the first of two enzymatic reactions that convert inactive eukaryotic translation initiation factor‐5A (eIF‐5A) to an activated form, thought to facilitate translation. A full‐length cDNA clone encoding canola (Brassica napus cv. Westar) DHS was isolated from a cDNA‐expression library prepared from senescing leaves. Transgenic canola lines with suppressed DHS expression were obtained by introducing a transgene expressing antisense 3′‐UTR canola DHS cDNA under the regulation of the constitutive cauliflower mosaic virus 35S (CaMV‐35S) promoter. Transformed seed was obtained by vacuum infiltration of canola inflorescences using the protocol developed for Arabidopsis with modifications. The resultant transgenic plants had reduced levels of leaf DHS protein and exhibited delayed natural leaf senescence. Suppression of DHS also increased leaf size by 1.5‐ to two‐fold and resulted in increases in seed yield of up to 65%. Moreover, the enhanced performance of transgenic plants reflected increased tolerance to chronic sublethal stress. When wild‐type and transgenic plants were grown in 6‐inch pots, the increase in seed yield accruing from suppression of DHS was approximately 4.5‐fold greater than when the plants were grown in 12‐inch pots. Thus, suppression of DHS appears to ameliorate the effects of sublethal stress engendered by growth in small containers.
Manganese accumulation in leaves of Hakea prostrata (Proteaceae) and the significance of cluster roots for micronutrient uptake as dependent on phosphorus supply
Authors: Shane Michael W. , Lambers Hans
Published: July 2005

When grown at a low P supply, Hakea prostrata R.Br. (Proteaceae) develops dense clusters of determinate branch roots, termed ‘proteoid’ or ‘cluster’ roots and accumulates Mn in its leaves. The aim of this study was to vary the production of cluster roots and assess the relationship between Mn uptake and cluster‐root mass. We collected native soil from a location inhabited by H. prostrata and amended this with ‘high’ and ‘low’ amounts of insoluble or soluble P. After 14 months, we measured the impact of the treatments on cluster‐root development and the [P], [Mn], [Fe], [Zn] and [Cu] in young (expanding) and mature leaves. Dry mass and leaf area increased with increasing P availability in the soil, but growth decreased at the highest soluble [P], which caused symptoms of P toxicity. The [P] in young leaves (1.3–2.7 mg g−1 DM) exceeded that in older leaves (0.28–0.85 mg g−1 DM), except when plants were grown with soluble P (3.2–21 mg g−1 DM). Cluster‐root formation was inhibited when leaf [P] increased; [P] in young leaves, rather than that in old leaves, appeared to be the factor that determined the proportion of the root mass invested in cluster roots. Old leaves of all treatments had [Mn] from 90 to 120 µg g−1 DM, except for plants grown at high levels of soluble P, when [Mn] decreased below 30 µg g−1 DM. The [Mn] and [Zn] in old leaves and the [Cu] in young leaves were positively correlated with the fraction of roots invested in cluster roots. These findings support our hypothesis that cluster roots play a significant role in micronutrient acquisition, and also provide an explanation for Mn accumulation in leaves of H. prostrata, and presumably Proteaceae in general.