bluuebunny/crossref_metadata_2025 huggingface dataset:
A mechanism for the activation of the Na/H exchanger NHE‐1 by cytoplasmic acidification and mitogens
Authors: Lacroix Jérôme , Poët Mallorie , Maehrel Céline , Counillon Laurent
Published: January 2004

Eukaryotic cells constantly have to fight against internal acidification. In mammals, this task is mainly performed by the ubiquitously expressed electroneutral Na+/H+ exchanger NHE‐1, which activates in a cooperative manner when cells become acidic. Despite its biological importance, the mechanism of this activation is still poorly understood, the most commonly accepted hypothesis being the existence of a proton‐sensor site on the internal face of the transporter. This work uncovers mutations that lead to a nonallosteric form of the exchanger and demonstrates that NHE‐1 activation is best described by a Monod–Wyman–Changeux concerted mechanism for a dimeric transporter. During intracellular acidification, a low‐affinity form of NHE‐1 is converted into a form possessing a higher affinity for intracellular protons, with no requirement for an additional proton‐sensor site on the protein. This new mechanism also explains the activation of the exchanger by growth signals, which shift the equilibrium towards the high‐affinity form.
Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution
Authors: Castellano Sergi , Novoselov Sergey V , Kryukov Gregory V , Lescure Alain , Blanco Enrique , Krol Alain , Gladyshev Vadim N , Guigó Roderic
Published: January 2004

While the genome sequence and gene content are available for an increasing number of organisms, eukaryotic selenoproteins remain poorly characterized. The dual role of the UGA codon confounds the identification of novel selenoprotein genes. Here, we describe a comparative genomics approach that relies on the genome‐wide prediction of genes with in‐frame TGA codons, and the subsequent comparison of predictions from different genomes, wherein conservation in regions flanking the TGA codon suggests selenocysteine coding function. Application of this method to human and fugu genomes identified a novel selenoprotein family, named SelU, in the puffer fish. The selenocysteine‐containing form also occurred in other fish, chicken, sea urchin, green algae and diatoms. In contrast, mammals, worms and land plants contained cysteine homologues. We demonstrated selenium incorporation into chicken SelU and characterized the SelU expression pattern in zebrafish embryos. Our data indicate a scattered evolutionary distribution of selenoproteins in eukaryotes, and suggest that, contrary to the picture emerging from data available so far, other taxa‐specific selenoproteins probably exist.
MlaA, a hexameric ATPase linked to the Mre11 complex in archaeal genomes
Authors: Manzan Angelo , Pfeiffer Günter , Hefferin Melissa L , Lang Cara E , Carney James P , Hopfner Karl‐Peter
Published: January 2004

We identify and characterize MlaA, a novel protein, which is found in a conserved operon with Mre11 and Rad50 in archaeal genomes. MlaA is fused with Mre11 in Methanobacter thermoautotrophicus, suggesting the MlaA is functionally linked to the Mre11 complex. MlaA preferentially and cooperatively binds double‐stranded and secondary structure containing DNA and has double‐stranded but not single‐stranded DNA‐stimulated ATPase activity. Electron microscopy reveals that MlaA forms a 360‐kDa hexameric ring structure with a central hole. Our data suggest that the archaeal Mre11 complex is associated with a novel hexameric ATPase that could be required for the processing of DNA double‐stranded breaks and recombination intermediates.
Involvement of the intermediate filament protein cytokeratin‐18 in actin pedestal formation during EPEC infection
Authors: Batchelor Miranda , Guignot Julie , Patel Amit , Cummings Nicola , Cleary Jennifer , Knutton Stuart , Holden David W , Connerton Ian , Frankel Gad
Published: January 2004

While remaining extracellular, enteropathogenic Escherichia coli (EPEC) establish direct links with the cytoskeleton of the target epithelial cell leading to the formation of actin‐rich pedestals underneath attached bacteria. The translocated adaptor protein Tir forms the transmembrane bridge between the cytoskeleton and the bacterium; the extracellular domain of Tir functions as a receptor for the bacterial adhesin intimin, while the intracellular amino and carboxy termini interact with a number of focal adhesion and other cytoskeletal proteins; and recruitment of some is dependent on phosphorylation of Tyr 474. Using Tir as bait and HeLa cell cDNA library as prey in a yeast two‐hybrid screen, we identified cytokeratin 18 as a novel Tir partner protein. Cytokeratin 18 is recruited to the EPEC‐induced pedestal and has a direct role in actin accretion and cytoskeleton reorganization. This study is the first to implicate intermediate filaments in microfilament reorganization following EPEC infection.
Molecular evidence indicating that the yeast PAF complex is required for transcription elongation
Authors: Rondón Ana G , Gallardo Mercedes , García‐Rubio María , Aguilera Andrés
Published: January 2004

PAF is a five‐subunit protein complex composed of Paf1, Cdc73, Leo1, Rtf1 and Ctr9, which was purified from yeast in association with RNA polymerase II and which is believed to function in transcription elongation. However, no direct proof exists for this yet. To assay whether PAF is required in elongation, we determined the in vitro transcription‐elongation efficiencies of mutant cell extracts using a DNA template containing two G‐less cassettes. paf1Δ or cdc73Δ cell extracts showed reduced transcription‐elongation efficiencies (16–18% of the wild‐type levels), whereas leo1Δ and rtf1Δ showed wild‐type levels. In vivo transcription efficiency was diminished in the four mutants analysed, as determined by their abilities to transcribe lacZ. Our work provides molecular evidence that PAF has a positive role in transcription elongation and is composed of at least two functionally different types of subunits (Paf1‐Cdc73 and Leo1‐Rtf1).
Cyclin B degradation leads to NuMA release from dynein/dynactin and from spindle poles
Authors: Gehmlich Katja , Haren Laurence , Merdes Andreas
Published: January 2004

The protein NuMA localizes to mitotic spindle poles where it contributes to the organization of microtubules. In this study, we demonstrate that NuMA loses its stable association with the spindle poles after anaphase onset. Using extracts from Xenopus laevis eggs, we show that NuMA is dephosphorylated in anaphase and released from dynein and dynactin. In the presence of a nondegradable form of cyclin B (Δ90), NuMA remains phosphorylated and associated with dynein and dynactin, and remains localized to stable spindle poles that fail to disassemble at the end of mitosis. Inhibition of NuMA or dynein allows completion of mitosis, despite inducing spindle pole abnormalities. We propose that NuMA functions early in mitosis during the formation of spindle poles, but is released from the spindle after anaphase, to allow spindle disassembly and remodelling of the microtubule network.
Vegfc is required for vascular development and endoderm morphogenesis in zebrafish
Authors: Ober Elke A , Olofsson Birgitta , Mäkinen Taija , Jin Suk‐Won , Shoji Wataru , Koh Gou Young , Alitalo Kari , Stainier Didier Y R
Published: January 2004

During embryogenesis, complex morphogenetic events lead endodermal cells to coalesce at the midline and form the primitive gut tube and associated organs. While several genes have recently been implicated in endoderm differentiation, we know little about the genes that regulate endodermal morphogenesis. Here, we show that vascular endothelial growth factor C (Vegfc), an angiogenic as well as a lymphangiogenic factor, is unexpectedly involved in this process in zebrafish. Reducing Vegfc levels using morpholino antisense oligonucleotides, or through overexpression of a soluble form of the VEGFC receptor, VEGFR‐3, affects the coalescence of endodermal cells in the anterior midline, leading to the formation of a forked gut tube and the duplication of the liver and pancreatic buds. Further analyses indicate that Vegfc is additionally required for the initial formation of the dorsal endoderm. We also demonstrate that Vegfc is required for vasculogenesis as well as angiogenesis in the zebrafish embryo. These data argue for a requirement of Vegfc in the developing vasculature and, more surprisingly, implicate Vegfc signalling in two distinct steps during endoderm development, first during the initial differentiation of the dorsal endoderm, and second in the coalescence of the anterior endoderm to the midline.
D4476, a cell‐permeant inhibitor of CK1, suppresses the site‐specific phosphorylation and nuclear exclusion of FOXO1a
Authors: Rena Graham , Bain Jenny , Elliott Matthew , Cohen Philip
Published: January 2004

The protein kinase CK1 phosphorylates serine residues that are located close to another phosphoserine in the consensus pSer‐Xaa‐Xaa‐Ser. This specificity generates regions in its target proteins containing two or more neighbouring phosphoserine residues, termed here multisite phosphorylation domains (MPDs). In this paper, we demonstrate that D4476 is a potent and rather selective inhibitor of CK1 in vitro and in cells. In H4IIE hepatoma cells, D4476 specifically inhibits the phosphorylation of endogenous forkhead box transcription factor O1a (FOXO1a) on Ser322 and Ser325 within its MPD, without affecting the phosphorylation of other sites. Our results indicate that these residues are targeted by CK1 in vivo and that the CK1‐mediated phosphorylation of the MPD is required for accelerated nuclear exclusion of FOXO1a in response to IGF‐1 and insulin. D4476 is much more potent and specific than IC261 or CKI‐7, and is therefore the most useful CK1 inhibitor currently available for identifying physiological substrates of CK1.
Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering
Authors: Tehei Moeava , Franzetti Bruno , Madern Dominique , Ginzburg Margaret , Ginzburg Ben Z , Giudici‐Orticoni Marie‐Thérèse , Bruschi Mireille , Zaccai Giuseppe
Published: January 2004

Mean macromolecular dynamics was quantified in vivo by neutron scattering in psychrophile, mesophile, thermophile and hyperthermophile bacteria. Root mean square atomic fluctuation amplitudes determining macromolecular flexibility were found to be similar for each organism at its physiological temperature (∼1 Å in the 0.1 ns timescale). Effective force constants determining the mean macromolecular resilience were found to increase with physiological temperature from 0.2 N/m for the psychrophiles, which grow at 4°C, to 0.6 N/m for the hyperthermophiles (85°C), indicating that the increase in stabilization free energy is dominated by enthalpic rather than entropic terms. Larger resilience allows macromolecular stability at high temperatures, while maintaining flexibility within acceptable limits for biological activity.
A test of the CoHR motif associated with meiotic double‐strand breaks in Saccharomyces cerevisiae
Authors: Haring Stuart J , Lautner Lucas J , Comeron Josep M , Malone Robert E
Published: January 2004

Meiotic recombination is not random along chromosomes; rather, there are preferred regions for initiation called hotspots. Although the general properties of meiotic hotspots are known, the requirements at the DNA sequence level for the determination of hotspot activity are still unclear. The sequence of six known hotspots in Saccharomyces cerevisiae was compared to identify a common homology region (CoHR). They reported that the locations of CoHR sequences correspond to mapped double‐strand break (DSB) sites along three chromosomes (I, III, VI). We report here that a deletion of CoHR at HIS2, a hotspot used to identify the motif, has no significant effect on recombination. In the absence of CoHR, DSB formation occurs at a high frequency and at the same sequences as in wild‐type strains. In cases where the deletion of sequences containing the CoHR motif has been shown to reduce recombination, we propose that it may be a reflection of the location of the deletion, rather than the loss of CoHR, per se.
Chemotaxis: signalling modules join hands at front and tail
Authors: Postma Marten , Bosgraaf Leonard , Loovers Harriët M , Van Haastert Peter J M
Published: January 2004

Chemotaxis is the result of a refined interplay among various intracellular molecules that process spatial and temporal information. Here we present a modular scheme of the complex interactions between the front and the back of cells that allows them to navigate. First, at the front of the cell, activated Rho‐type GTPases induce actin polymerization and pseudopod formation. Second, phosphatidylinositol‐3,4,5‐trisphosphate (PtdIns(3,4,5)P3) is produced in a patch at the leading edge, where it binds pleckstrin‐homology‐domain‐containing proteins, which enhance actin polymerization and translocation of the pseudopod. Third, in Dictyostelium amoebae, a cyclic‐GMP‐signalling cascade has been identified that regulates myosin filament formation in the posterior of the cell, thereby inhibiting the formation of lateral pseudopodia that could misdirect the cell.
Roles of G‐protein‐coupled receptor dimerization
Authors: Terrillon Sonia , Bouvier Michel
Published: January 2004

The classical idea that G‐protein‐coupled receptors (GPCRs) function as monomeric entities has been unsettled by the emerging concept of GPCR dimerization. Recent findings have indicated not only that many GPCRs exist as homodimers and heterodimers, but also that their oligomeric assembly could have important functional roles. Several studies have shown that dimerization occurs early after biosynthesis, suggesting that it has a primary role in receptor maturation. G‐protein coupling, downstream signalling and regulatory processes such as internalization have also been shown to be influenced by the dimeric nature of the receptors. In addition to raising fundamental questions about GPCR function, the concept of dimerization could be important in the development and screening of drugs that act through this receptor class. In particular, the changes in ligand‐binding and signalling properties that accompany heterodimerization could give rise to an unexpected pharmacological diversity that would need to be considered.
Distinct molecular phenotypes in bovine prion diseases
Authors: Biacabe Anne‐Gaëlle , Laplanche Jean‐Louis , Ryder Stephen , Baron Thierry
Published: January 2004

Bovine spongiform encephalopathy (BSE) in cattle, the most likely cause of variant Creutzfeldt–Jakob disease in humans, is thought to be caused by a unique infectious agent, with stable features, even when transmitted to other species. Here, we show the existence of an atypical molecular phenotype among cattle diagnosed with BSE in France. Following western blot analysis, three cases showed unusual features of the electrophoretic profiles of the protease‐resistant prion protein (PrPres) accumulating in the brain. The PrPres patterns were similar in these three atypical cases, showing a higher molecular mass of unglycosylated PrPres and strong labelling by P4 monoclonal antibody compared to 55 typical BSE cases. This finding suggests either some phenotypic modifications of PrPres following infection by the BSE agent or the existence of alternative origins of such diseases in cattle.
Genetic diversity and structure of urban populations ofPierisbutterflies assessed using amplified fragment length polymorphism
Authors: Takami Yasuoki , Koshio Chiharu , Ishii Minoru , Fujii Hisashi , Hidaka Toshitaka , Shimizu Isamu
Published: January 2004

Conservation programs in urban ecosystems need to determine the genetic background in populations of urban dwellers. We examined the genetic diversity and structure ofPieris rapaeandP.meleteusing AFLP markers, and compared them between species and between urban and rural environments. As a result: (i) in both species, there was no reduction in genetic diversity within urban populations by direct comparison of diversity measurements, although the analysis of molecular variance suggested significant reductions in the variance within seasonal subpopulations in urban populations; (ii)P.rapaeretained greater genetic diversity within species and populations; (iii) populations of both species showed significant genetic differentiation, andP.meletewas more strongly subdivided; (iv) in both species, geographically close populations did not cluster with one another in theupgmaanalysis; (v) there was no genetic isolation due to geographical distance in either species; (vi) the genetic composition of seasonal subpopulations differed in urban populations of both species, and the genetic distances among subpopulations were correlated with seasonal differences inP.rapaeand with temporal differences inP.melete. These results indicate that the genetic diversity in urban populations of both species was reduced at times, but was maintained by dispersal from genetically differentiated populations. Differences in the ability and mode of dispersal in the two species may be reflected in the degree of population subdivision and patterns of seasonal change in the genetic composition.
Effective size of two feral domestic cat populations (Felis catusL.): effect of the mating system
Authors: Kaeuffer R. , Pontier D. , Devillard S. , Perrin N.
Published: January 2004

A variety of behavioural traits have substantial effects on the gene dynamics and genetic structure of local populations. The mating system is a plastic trait that varies with environmental conditions in the domestic cat (Felis catus) allowing an intraspecific comparison of the impact of this feature on genetic characteristics of the population. To assess the potential effect of the heterogenity of males’ contribution to the next generation on variance effective size, we applied the ecological approach of Nunney & Elam (1994) based upon a demographic and behavioural study, and the genetic ‘temporal methods’ of Waples (1989) and Berthieret al. (2002) using microsatellite markers. The two cat populations studied were nearly closed, similar in size and survival parameters, but differed in their mating system. Immigration appeared extremely restricted in both cases due to environmental and social constraints. As expected, the ratio of effective size to census number (Ne/N) was higher in the promiscuous cat population (harmonic mean = 42%) than in the polygynous one (33%), whenNewas calculated from the ecological method. Only the genetic results based on Waples’ estimator were consistent with the ecological results, but failed to evidence an effect of the mating system. Results based on the estimation of Berthieret al. (2002) were extremely variable, withNesometimes exceeding census size. Such low reliability in the genetic results should retain attention for conservation purposes.
Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae
Authors: Sumner Joanna , Jessop Tim , Paetkau David , Moritz Craig
Published: January 2004

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50–80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.
Historical data refute recent range contraction as cause of low genetic diversity in isolated frog populations
Authors: Hoffman Eric A. , Blouin Michael S.
Published: January 2004

This study tested whether low genetic diversity in remnant populations of a declining amphibian is best explained by recent bottlenecks or by a history of being peripheral. We compared diversity from eight microsatellite loci in historical and extant populations from the interior and former periphery of the species’ range. We found that historic peripheral populations already had reduced levels of genetic variation before the range contraction. Therefore, low diversity in remnants could not be ascribed to recent range contractions. This study shows that a common conservation strategy for rescuing genetically depauperate populations, artificial gene flow, may often be unwarranted and detrimental to evolutionarily important peripheral populations.
Fine‐scale diversity and specificity in the most prevalent lineage of symbiotic dinoflagellates (Symbiodinium, Dinophyceae) of the Caribbean
Authors: Santos S. R. , Shearer T. L. , Hannes A. R. , Coffroth M. A.
Published: January 2004

The success of coral reefs is due to obligate mutualistic symbioses involving invertebrates and photosynthetic dinoflagellate symbionts belonging to the genus Symbiodinium. In the Caribbean, the vast majority of octocorals and other invertebrate hosts associate with Symbiodinium clade B, and more selectively, with a single lineage of this clade, Symbiodinium B1/B184. Although B1/B184 represents the most prevalent Symbiodinium in the Caribbean, there is little evidence supporting fine‐scale diversity and host–alga specificity within this lineage. We explored simultaneously the questions of diversity and specificity in Symbiodinium B1/B184 by sequencing the flanking regions of two polymorphic microsatellites from a series of Symbiodinium clade B cultures along with Symbiodinium B1/B184 populations of the octocorals Pseudopterogorgia elisabethae, P. bipinnata and Gorgonia ventalina. Seven unique sequence variants were identified based on concatenation of the two loci. Phylogenetic analyses of these variants, which we refer to as phylotypes, recognized five as belonging to B1/B184, thus providing the first evidence of distinct taxa within this Symbiodinium lineage. Furthermore, sympatric P. elisabethae and P. bipinnata at San Salvador in the Bahamas were found to harbour distinct Symbiodinium B1/B184 phylotypes, demonstrating unequivocally the existence of fine‐scale specificity between Caribbean octocorals and these algae. Taken together, this study exemplifies the complex nature of Symbiodinium biodiversity and specificity.
Inbreeding avoidance in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat
Authors: Stow A. J. , Sunnucks P.
Published: January 2004

Habitat fragmentation/alteration has been proposed as a distinct process threatening the viability of populations of many organisms. One expression of its impact may be the disruption of core population processes such as inbreeding avoidance. Using the experimental design outlined in our companion paper, we report on the impact of habitat alteration (deforestation) on inbreeding in the rock‐dwelling Australian lizard Egernia cunninghami. Ten microsatellite loci were used to calculate relatedness coefficients of potential and actual breeding pairs, and to examine mate‐choice and heterozygosity. Despite significantly less dispersal and higher within‐group relatedness between potential mates in deforested than in natural habitats, this did not result in significantly more inbred matings. Average relatedness amongst breeding pairs was low, with no significant difference between natural and fragmented populations in relatedness between breeding pairs, or individual heterozygosity. Active avoidance of close kin as mates was indicated by the substantially and significantly lower relatedness in actual breeding pairs than potential ones. These facts, and heterozygote excesses in all groups of immature lizards from both habitats, show that E. cunninghami maintained outbreeding in the face of increased accumulation of relatives.
High mate and site fidelity in Cunningham's skinks (Egernia cunninghami) in natural and fragmented habitat
Authors: Stow A. J. , Sunnucks P.
Published: January 2004

While habitat alteration has considerable potential to disrupt important within‐population processes, such as mating and kin structure, via changed patterns of dispersal, this has rarely been tested. We are investigating the impact of anthropogenic habitat alteration on the population biology of the rock‐dwelling Australian lizard Egernia cunninghami on the Central Tablelands of New South Wales, Australia, by comparing deforested and adjacent naturally vegetated areas. The novel analyses in this paper, and its companion, build on previous work by adding a new replicate site, more loci and more individuals. The additional microsatellite loci yield sufficient power for parentage analysis and the sociobiological inferences that flow from it. Genetic and capture–mark–recapture techniques were used to investigate mate and site fidelity and associated kin structure. Analyses of the mating system and philopatry using 10 microsatellite loci showed high levels of site fidelity by parents and their offspring in natural and deforested habitats. Parentage assignment revealed few individuals with multiple breeding partners within seasons and fidelity of pairs across two or more breeding seasons was typical. Despite reduced dispersal, increased group sizes and significant, dramatic increases in relatedness among individuals within rock outcrops in deforested areas, no significant differences between deforested and natural areas were evident in the degree of multiple mating or philopatry of breeding partners within and across seasons. With the exception that there was a significantly higher proportion of unmated males in the deforested area, the social and mating structure of this species has so far been surprisingly robust to substantial perturbation of dispersal and relatedness structure. Nonetheless, approximately 10‐fold elevation of mean pairwise relatedness in the deforested areas has great potential to increase inbred matings, which is investigated in the companion paper.
Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. × divaricarpa, and A. holboellii (Brassicaceae)
Authors: Dobeš C. H. , Mitchell‐Olds T. , Koch M. A.
Published: January 2004

Arabis drummondii, A. holboellii and their hybrid A. × divaricarpa are widespread perennials of open habitats in North America. A phylogenetic analysis based on noncoding chloroplast DNA sequences (trnL intron and trnL/F intergenic spacer) resolved A. drummondii as a monophyletic taxon, but found A. holboellii to bear chloroplast haplotypes from highly diverged evolutionary lineages. This raised the question of a possible polyphyletic origin of A. holboellii. Arabis × divaricarpa was found to be of recent and polytopic origin, a result consistent with its presumed hybrid origin. One hundred and three chloroplast haplotypes were detected within 719 Arabis accessions investigated. The majority of chloroplast‐types were estimated to have arisen prior to the Wisconsin glaciation. Phylogeographical analysis using nested clade analysis, suggested for A. holboellii (i) past fragmentation events, partitioning genetic variation in several instances between the Sierra Nevada, the Southern Rocky Mountains and the Colorado Plateau on the one hand and the Central to Northern Rockies of the United States and adjacent Cascades on the other; and for both parental species (ii) recolonization of major areas formerly covered by the Wisconsin glaciation by three haplotypes; and (iii) restricted gene flow indicating isolation by distance in areas south of the last glacial maximum. Arabis × divaricarpa is closely codistributed with its parental species and resampled their haplotypes. The highest genetic diversity was found in the Rocky Mountains from Idaho and Montana south to Utah and Colorado. This area was further hypothesized to have played a major role in the origin of both parental species and probably represented an important glacial refugium. However, evidence for glacial refugia was also found in arctic and boreal regions of Alaska and near the Great Lakes. In comparison to nuclear ribosomal internal transcribed spacer data, chloroplast DNA divergence was very high and evidently predated the origin of A. drummondii and possibly A. holboellii. Divergence of major chloroplast lineages dates back to the middle of the Pleistocene at least. Extensive hybridization is the most likely evolutionary factor working on A. holboellii to explain the revealed discrepancy in nuclear DNA and chloroplast DNA diversification.
Genetic structure among closely spaced leks in a peripheral population of lesser prairie‐chickens
Authors: Bouzat Juan L. , Johnson Kristine
Published: January 2004

We evaluated the genetic structure of birds from four closely spaced leks in a peripheral population of lesser prairie‐chickens (Tympanuchus pallidicinctus). Analyses of molecular variance revealed significant genetic structuring among birds from different leks for six microsatellite loci (FST = 0.036; P = 0.002), but we found no genetic differentiation at the mtDNA control region. Significant deviations from Hardy–Weinberg revealed an excess of homozygote genotypes within each of the leks studied (FIS = 0.190–0.307), indicative of increased inbreeding. Estimates of relatedness using microsatellite data suggest that the genetic structuring among lesser prairie‐chicken leks occurs in part because of a lek mating system in which males at some leks are related. Structuring may also be caused by stochastic effects associated with a historical decline in population size leading to small, semi‐isolated leks and high site fidelity by reproductive males. Results from this study suggest that microspatial genetic structuring may occur in lek‐mating bird species with low levels of dispersal.
Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes
Authors: Thalmann O. , Hebler J. , Poinar H. N. , Pääbo S. , Vigilant L.
Published: January 2004

Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic ‘barcode’ for an objective species classification scheme. However, there are technical pitfalls associated with the acquisition of mtDNA data. One problem is the presence of translocated pieces of mtDNA in the nuclear genome of many taxa that may be mistaken for authentic organellar mtDNA. We assessed the extent to which such ‘numt’ sequences may pose an overlooked problem in analyses of mtDNA from humans and apes. Using long‐range polymerase chain reaction (PCR), we generated necessarily authentic mtDNA sequences for comparison with sequences obtained using typical methods for a segment of the mtDNA control region in humans, chimpanzees, bonobos, gorillas and orangutans. Results revealed that gorillas are notable for having such a variety of numt sequences bearing high similarity to authentic mtDNA that any analysis of mtDNA using standard approaches is rendered impossible. Studies on humans, chimpanzees, bonobos or orangutans are apparently less problematic. One implication is that explicit measures need to be taken to authenticate mtDNA sequences in newly studied taxa or when any irregularities arise. Furthermore, some taxa may not be amenable to analysis of mtDNA variation at all.
Behavioural structuring of relatedness in the spotted hyena (Crocuta crocuta) suggests direct fitness benefits of clan‐level cooperation
Authors: Van Horn Russell C. , Engh Anne L. , Scribner Kim T. , Funk Stephan M. , Holekamp Kay E.
Published: January 2004

Spotted hyenas (Crocuta crocuta) are gregarious carnivores that live in multigenerational social groups, called clans, containing one to several matrilines. Members of multiple matrilines within a clan cooperate during dangerous interactions with inter‐ and intraspecific competitors. The evolution of cooperation may be influenced by relatedness between individuals, which in turn is influenced by reproductive skew and mate choice, dispersal and territorial behaviours. Behavioural data exist for spotted hyenas, but corresponding data on patterns of relatedness are unavailable; this lack of data makes it difficult to assess the relative importance of selection pressures favouring cooperative behaviour within and among groups. Therefore we conducted a longitudinal analysis of relatedness within a single large clan of spotted hyenas, as well as a cross‐sectional analysis of relatedness among hyenas from multiple clans. Within a clan, patterns of relatedness reflected known pedigree relationships, and relatedness was higher within than among matrilines, even across generations. Although mean within‐matriline relatedness varied among matrilines, it did not decline with matriline rank. On average, clan members were not related closely, due to high levels of male‐mediated gene flow among clans, and relatedness declined very slightly across clan borders. Low mean relatedness within clans suggests that spotted hyenas cooperate with unrelated clan‐mates against close paternal kin in other clans. Our data also suggest that spotted hyenas must derive large net direct fitness benefits from group living and cooperation.
Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L.) as revealed by mitochondrial DNA
Authors: Godoy José A. , Negro Juan J. , Hiraldo Fernando , Donázar José A.
Published: January 2004

Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East–West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo‐types in eastern populations are recently derived, as revealed by their peripheral location in median‐joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among‐population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re‐sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.
Postglacial colonization shows evidence for sympatric population splitting of Eurasian perch (Perca fluviatilis L.) in Lake Constance
Authors: Behrmann‐Godel J. , Gerlach G. , Eckmann R.
Published: January 2004

Previous microsatellite analysis showed that two subpopulations of perch (Perca fluviatilis L.) exist in Lake Constance. This raises questions of whether (i) Lake Constance was colonized by two populations that diverged in allopatry, or (ii) the two subpopulations diverged in sympatry. Sequence analysis of a 365 bp mtDNA fragment (5′‐end of the D‐loop) of perch from Lake Constance and adjacent waters revealed 10 haplotypes. We suggest colonization via the Danube river, based on the frequency and dispersion of haplotypes, and knowledge of the lake's palaeohydrological development. Pairwise FST‐values using mitochondrial DNA sequences showed no significant population subdivision. Our study provides strong evidence that subpopulations of perch in Lake Constance have diverged in sympatry.
The population genetics of a biological control introduction: mitochondrial DNA and microsatellie variation in native and introduced populations ofAphidus ervi, a parisitoid wasp
Authors: Hufbauer R. A. , Bogdanowicz S. M. , Harrison R. G.
Published: January 2004

Introductions of biological control agents may cause bottlenecks in population size despite efforts to avoid them. We examined the population genetics of Aphidius ervi (Hymenoptera: Braconidae), a parasitoid that was introduced to North America from Western Europe in 1959 to control pea aphids. To explore the phylogeographical relationships of A. ervi we sequenced 1249 bp of mitochondrial DNA (mtDNA) from 27 individuals from the native range and 51 individuals from the introduced range. Most individuals from Western Europe, the Middle East and North America shared one of two common haplotypes, consistent with the known history of the introduction. However, some A. ervi from the Pacific Northwest have a haplotype that is most similar to haplotypes found in Japan, raising the possibility of a second accidental introduction. To examine population structure and assess whether a bottleneck occurred upon introduction to North America, we assayed variation at 5 microsatellite loci in 62 individuals from 2 native populations and 230 individuals from 6 introduced populations. Introduced samples had fewer rare alleles than native samples (F1,34 = 13.5, P = 0.0008), but heterozygosity did not differ significantly. These results suggest that a mild bottleneck occurred in spite of the introduction of over 1000 individuals. Using a hierarchical Bayesian approach, the founding population size was estimated to be 245 individuals. amova showed significant genetic differentiation between the European and North American samples, and a Bayesian assignment approach clustered individuals into four groups, with most European individuals in one group and most North American individuals in the other three. These results highlight that genetic changes are associated with founder events in rapidly growing natural populations, even when the founding population size is relatively large.
Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae)
Authors: Wong B. B. M. , Keogh J. S. , McGlashan D. J.
Published: January 2004

Dispersal can play an important role in the genetic structuring of natural populations. In this regard, freshwater fishes often exhibit extensive population genetic subdivision and are ideal subjects for investigating current and historical patterns of connection and dissociation between drainages. We set out to generate a comprehensive molecular phylogeny for a widespread freshwater fish from eastern Australia, the Pacific blue‐eye Pseudomugil signifer. Although movement via flood events may be important in the southern end of the species’ range, genetic structuring revealed the importance of historical drainage connections and dissociations in mediating or disrupting dispersal. A dominant feature of our phylogeny is a split between northern and southern populations, which appears to be congruent with a biogeographical barrier recently implicated as important for the connectivity of freshwater organisms in eastern Australia. The extent of the split also has taxonomic implications consistent with suggestions that the Pacific blue‐eye may represent more than a single species.
Phylogeography of the common goby, Pomatoschistus microps, with particular emphasis on the colonization of the Mediterranean and the North Sea
Authors: Gysels E. S. , Hellemans B. , Pampoulie C. , Volckaert F. A. M.
Published: January 2004

The phylogeographical patterns of a small marine fish, the common goby, Pomatoschistus microps, were assessed at 12 sites along the northeastern Atlantic coasts and the western Mediterranean Sea. A combination of two genetic markers was employed: cellulose acetate allozyme electrophoresis (CAGE) and sequence analysis of a 289 bp fragment of the mitochondrial locus cytochrome b. Both markers were congruent in revealing significant differences between samples (global FST = 0.247 for the allozymes and ΦST = 0.437 for the mitochondrial DNA data) and a pattern of isolation‐by‐distance. Phylogeographical analyses yielded a shallow branching structure with four groups. Three of those were confined to the Atlantic basin and showed a star‐like pattern. The fourth group contained a central haplotype occurring at the edges of the species’ distribution, accompanied by a few more rare variants, which were restricted to the Mediterranean Sea. A genetic break was observed around the British Isles, with distinct haplotypes dominating at either side of the English Channel. A significantly negative correlation between the degree of genetic diversity and latitude was recorded both for mitochondrial DNA (mtDNA) and allozymes in the Atlantic basin. Gene flow analysis suggested that recolonization of the North Sea and the coasts of western Scotland and Ireland may have taken place from a glacial refugium in the Southern Bight of the North Sea. These results are discussed in the perspective of possible postglacial migration routes of marine fish along the northeastern Atlantic coasts.
Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska
Authors: Ramstad K. M. , Woody C. A. , Sage G. K. , Allendorf F. W.
Published: January 2004

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six‐mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six‐mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six‐mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six‐mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.
Colony genetic organization and colony fusion in the termiteReticulitermes flavipesas revealed by foraging patterns over time and space
Authors: Deheer Christopher J. , Vargo Edward L.
Published: January 2004

Temporal and spatial analyses are seldom utilized in the study of colony genetic structure, but they are potentially powerful methods which can yield novel insights into the mechanisms underlying variation in breeding systems. Here we present the results of a study which incorporated both of these dimensions in an examination of genetic structure of subterranean termites in the genusReticulitermes (primarilyR. flavipes). Most colonies of this species (70%) were simple families apparently headed by outbred primary reproductives, while most of the remaining (27% of the total) colonies contained low effective numbers of moderately inbred reproductives. Mapping the spatial distribution of colony foraging sites over time revealed that despite the high colony density, the absolute foraging boundaries of mostR. flavipescolonies were persistent and exclusive of other conspecific colonies, which suggests that this species is more territorial than has been implied by laboratory studies of intraspecific aggression. Nevertheless, we found a single colony (3% of all colonies) which contained the offspring of more than two unrelated reproductives. Although other studies have also described subterranean termite colonies with a similarly complex genetic composition, we demonstrate here that such colonies can form under natural conditions via the fusion of whole colonies. This study underscores how repeated sampling from individual colonies over time and space can yield information about colony spatial and genetic structure that cannot be obtained from conventional analyses or sampling methods.