bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex mutations in a high proportion of microsatellite loci from the protozoan parasite Plasmodium falciparum
Authors: Anderson Timothy J. C. , Su Xin‐Zhuan , Roddam AndreW. , Day Karen P.
Published: March 2003

Microsatellite loci are generally assumed to evolve via a stepwise mutational process and a battery of statistical techniques has been developed in recent years based on this or related mutation models. It is therefore important to investigate the appropriateness of these models in a wide variety of taxa. We used two approaches to examine mutation patterns in the malaria parasite Plasmodium falciparum: (i) we examined sequence variation at 12 tri‐nucleotide repeat loci; and (ii) we analysed patterns of repeat structure and heterozygosity at 114 loci using data from 12 laboratory parasite lines. The sequencing study revealed complex patterns of mutation in five of the 12 loci studied. Alleles at two loci contain indels of 24 bp and 57 bp in flanking regions, while in the other three loci, blocks of imperfect microsatellites appear to be duplicated or inserted; these loci essentially consist of minisatellite repeats, with each repeat unit containing four to eight microsatellites. The survey of heterozygosity revealed a positive relationship between repeat number and microsatellite variability for both di‐ and trinucleotides, indicating a higher mutation rate in loci with longer repeat arrays. Comparisons of levels of variation in different repeat types indicate that the mutation rate of dinucleotide‐bearing loci is 1.6–2.1 times faster than trinucleotides, consistent with the lower mean number of repeats in trinucleotide‐bearing loci. However, despite the evidence that microsatellite arrays themselves are evolving in a manner consistent with stepwise mutation model in P. falciparum, the high frequency of complex mutations precludes the use of analytical tools based on this mutation model for many microsatellite‐bearing loci in this protozoan. The results call into question the generality of models based on stepwise mutation for analysing microsatellite data, but also demonstrate the ease with which loci that violate model assumptions can be detected using minimal sequencing effort.
World‐wide genetic differentiation of Eubalaena: questioning the number of right whale species
Authors: Rosenbaum H. C. , Brownell R. L. , Brown M. W. , Schaeff C. , Portway V. , White B. N. , Malik S. , Pastene L. A. , Patenaude N. J. , Baker C. S. , Goto M. , Best P. B. , Clapham P. J. , Hamilton P. , Moore M. , Payne R. , Rowntree V. , Tynan C. T. , Bannister J. L. , Desalle R.
Published: March 2003

Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world‐wide.
Markers derived from amplified fragment length polymorphism gels for plant ecology and evolution studies
Authors: Mclenachan P. A. , Stöckler K. , Winkworth R. C. , Mcbreen K. , Zauner S. , Lockhart P. J.
Published: March 2003

We describe the types of polymerase chain reaction (PCR) markers that we have isolated using amplified fragment length polymorphisms (AFLP) in closely related taxa from diverse plant genera. With these markers, both inter‐ and intraspecific differences have been identified. The characterization of the nucleotide sequences and fragment length polymorphisms of such AFLP‐derived PCR markers is promising for investigating the ecology and evolution of closely related plant taxa.
Patterns of genetic variation inGymnadenia conopsea, the fragrant orchid
Authors: Gustafsson S.
Published: March 2003

Gymnadenia conopsea (L.) R. Br., or the fragrant orchid, is one of many plant species negatively influenced by new practices in agriculture and forestry during the last decades. This study describes the level of microsatellite variation within and among 10 Swedish populations of this species. It was not possible to detect strong effects of small population size or fragmentation. In general, the species had high genetic variation within and low genetic divergence among populations, although the correlation between population size and number of alleles was close to significance at the 95% level. Also, a significant isolation by distance effect was observed, indicating the presence of modest restrictions in gene dispersal between the investigated populations.
Juxtaposed microsatellite systems as diagnostic markers for admixture: an empirical evaluation with brown trout (Salmo trutta) as model organism
Authors: Estoup A. , Largiadèr C. R. , Cornuet J.‐M. , Gharbi K. , Presa P. , Guyomard R.
Published: March 2003

A juxtaposed microsatellite system (JMS) is composed of two microsatellite repeat arrays separated by a sequence of less than 200 bp and more than 20 bp. This paper presents the first empirical evaluation of JMSs for the study of genetic admixture induced by man, with brown trout (Salmo trutta) as model organism. Two distinct admixture situations were studied: native populations from streams of the Atlantic basin and of the Mediterranean basin, respectively, all stocked with domestic strains originating from the Atlantic basin. For these two situations, we first evaluated by simulation the ability of JMSs to differentiate between alien alleles and naturally shared homoplasious or ancestral alleles, and thus to behave as diagnostic markers for admixture. Simulations indicated that JMSs are expected to be reliable diagnostic markers in most divergent (i.e. Mediterranean) populations and nonreliable diagnostic markers in most closely related (i.e. Atlantic) populations. Three JMSs were genotyped in domestic strains as well as in nonstocked and stocked populations of brown trout sampled in different rivers of the Mediterranean and Atlantic basins. The observed distributions of JMS haplotypes were consistent with simulation predictions confirming that JMSs were reliable diagnostic markers only over a given proportion of the species range, i.e. in substantially divergent populations. JMSs also reinforced the diagnostic character of three microsatellite sites for the studied Mediterranean populations. This last result is consistent with our simulation results which showed that, although much less frequently than at JMSs, diagnostic markers are likely to be found at single site microsatellites provided that the native Mediterranean population has a sufficiently small effective population size. For each population of the Mediterranean basin admixture coefficients did not differ significantly across JMSs and mean admixture coefficients sometimes differ among populations. The interpretation of the origin of JMS haplotypes based on the allele length variants was supported by nucleotide sequence analysis.
The genetic mating system of spotted sunfish (Lepomis punctatus): mate numbers and the influence of male reproductive parasites
Authors: Dewoody J. A. , Fletcher D. E. , Mackiewicz M. , Wilkins S. D. , Avise J. C.
Published: March 2003

In nest‐building fish species, mature males often exhibit one of two alternative reproductive behaviours. Bourgeois males build nests, court females, and guard their eggs. Parasitic cuckolders attempt to steal fertilizations from bourgeois males and do not invest in parental care. Previous evidence from the bluegill sunfish (Lepomis macrochirus) suggests that adult males are morphologically specialized for these two tactics. Here, we used microsatellite markers to determine genetic parentage in a natural population of the spotted sunfish (L. punctatus) that also displayed both bourgeois and parasitic male morphs. As gauged by relative investments in gonadal vs. somatic tissues, between 5 and 15% of the mature adult males were parasites. Multi‐locus genotypes were generated for more than 1400 embryos in 30 nests, their nest‐guardian males, and for other adults in the population. Progeny in approximately 57% of the nests were sired exclusively by the guardian male, but the remaining nests contained embryos resulting from cuckoldry as well. Overall, the frequency of offspring resulting from stolen fertilizations was only 1.3%, indicating that the great majority of paternity is by bourgeois nesting males. With regard to maternity, 87% of the nests had at least three dams, and computer simulations estimate that about 7.2 dams spawned per nest.
Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area
Authors: Nilsson J. , Gross R. , Asplund T. , Dove O. , Jansson H. , Kelloniemi J. , Kohlmann K. , LÖytynoja A. , Nielsen E. E. , Paaver T. , Primmer C. R. , Titov S. , VasemÄgi A. , Veselov A. , Öst T. , Lumme J.
Published: March 2003

Sixty‐four samples from 46 salmon populations totalling 2369 specimens were used for polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of the mitochondrial ND1 region. The final analyses included 3095 specimens from 60 populations in Northern Europe. A subsample was analysed by RFLP of ND3/4/5/6. Representative RFLP haplotypes from different parts of the distribution area were sequenced and the phylogeny of European haplotypes and their relations to the North American lineage was described. The four common European haplotypes derive from the ancestral ND1‐BBBA (rooting the European clade to the North American) by one‐step substitutions: AAAA < AABA < BBBA > BBBB. The Swedish west‐coast populations differ from the geographically close southern Baltic, indicating absence of inward and limited outward gene flow through the Danish straits during the last 8000 years. Within the Baltic Sea, only three ND1 haplotypes were detected and there was no variation for ND3/4/5/6. In the whole southern Baltic and in lakes Vänern, Ladoga and Onega the haplotype AABA dominated. Proposed postglacial colonization routes to the Baltic Sea are discussed in relation to the haplotype distribution pattern.
Resistance or emigration: response of the high‐alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps
Authors: Stehlik I. , Schneller J. J. , Bachmann K.
Published: March 2003

Two main possibilities regarding glacial survival of the mountain flora of the Alps during the Quaternary have been discussed: the tabula rasa and the nunatak hypotheses. Eritrichium nanum (L.) Gaudin (Boraginaceae) is a perennial cushion plant, occurring at high elevations of the Central Alps and having a preference for extreme habitats. It belongs to a group of high‐alpine plants, for which in situ glacial survival on nunataks is ecologically possible. By investigating 20 populations of E. nanum of potential nunatak and peripheral refugial regions using amplified fragment length polymorphism, considerable genetic differences between populations from the Central Alps and populations from peripheral refugia were detected; hence, the latter probably did not serve as potential sources for the re‐colonization of the Central Alps after glaciation. Genetic variation was hierarchically structured (

amova), and three genetically distinct regions could be identified in the Central Alps. Two of these, the Penninic and Rhaetic Alps, correspond to nunatak regions proposed in the biogeographic literature. Populations from the Lepontic Alps formed a third genetic group. Genetic correlation (Mantel statistics) was highest within populations, with a modest decline among populations within specific nunatak regions and a negative correlation outside the genetic influence of specific nunatak regions. In situ glacial survival in E. nanum could be a model for the Quaternary history of other alpine plants, especially those that also occur at high elevations and in similar habitats.
The contribution of epistasis to species differences in annual sunflowers
Authors: Kim Seung‐Chul , Rieseberg Loren H.
Published: March 2003

The contribution of epistasis to 15 morphological traits differentiating two annual sunflowers (Helianthus annuus and H. debilis ssp. cucumerifolius) and to hybrid pollen sterility was estimated in a first generation backcross (BC1) mapping population. Analysis of digenic interactions among quantitative trait loci (QTLs) with significant main effects revealed significant interaction effects for six of the 15 morphological traits and for pollen sterility. Likewise, a genome‐wide scan of all possible two‐locus combinations detected additional significant interactions for three of the traits with significant epistasis in the original analysis: stem pigmentation, phyllary pubescence, and pollen viability. However, these were the only traits of the 16 examined in which detected interactions explained more than 5% of phenotypic variance. The implications of these findings for adaptive evolution and for the introgression of advantageous morphological QTLs across a natural hybrid zone between these taxa are discussed.
Differential success in northwards range expansion between ecotypes of the marble gallwasp Andricuskollari: a tale of two lifecycles
Authors: Stone Graham , Atkinson Rachel , Rokas Antonis , Csóka György , Nieves‐Aldrey José‐Luis
Published: March 2003

The Marble gallwasp Andricus kollari has a native range divided into two geographically separated lifecycles. In Eastern Europe and Turkey, the lifecycle involves a sexual generation on Turkey oak, Quercus cerris, while in Iberia and North Africa the sexual generation host is cork oak, Q. suber. Over the last 500 years, A. kollari has expanded its range into northern Europe, following human planting of Q. cerris from Italy and the Balkans. We ask: (i) what is the genetic relationship between eastern and western distributions of Andricus kollari? Can we determine which lifecycle is ancestral, and how long ago they diverged? (ii) To what extent have eastern and western native ranges contributed to northwards range expansion? (iii) Is there any evidence for hybridization between the two life cycle types? We present analyses of allozyme data for 13 polymorphic loci and of sequence variation for a 433 bp fragment of the mitochondrial cytochrome b gene. These show: (i) that four haplotype lineages (one in Spain, two in Hungary/Italy and one in Turkey) diverged more or less simultaneously between 1 and 2 million years ago, suggesting the existence of at least four refuges through recent ice age cycles. Our data cannot resolve which lifecycle type is ancestral. (ii) Populations north of putative refuges are divided into two sets. Populations in south‐west France are allied to Spain, while all remaining populations in northern Europe have been colonized from Italy and the Balkans. (iii) The transition from one race to another in south‐west France is marked by abrupt transitions in the frequency of refuge‐specific private alleles and corresponds closely to the northern limit of the distribution of cork oak. Although hybrids were detected in north‐west France, none were detected where the two lifecycles meet in south‐western France. The biology of oak gallwasps predicts that any hybrid zone will be narrow, and limited to regions where Q. cerris and Q. suber meet. Our data suggest that eastern and western A. kollari are effectively separate species.
Intimately linked or hardly speaking? The relationship between genotype and environmental gradients in a Louisiana Iris hybrid population
Authors: Johnston Jill A. , Wesselingh Renate A. , Bouck Amy C. , Donovan Lisa A. , Arnold Michael L.
Published: March 2003

Several models of hybrid zone evolution predict the same spatial patterns of genotypic distribution whether or not structuring is due to environment‐dependent or ‐independent selection. In this study, we tested for evidence of environment‐dependent selection in anIris fulva×Iris brevicaulishybrid population by examining the distribution of genotypes in relation to environmental gradients. We selected 201 Louisiana Iris plants from within a known hybrid population (80 m × 80 m) and placed them in four different genotypic classes (I. fulva, I. fulva‐like hybrid,I. brevicaulis‐like hybrid andI. brevicaulis) based on seven species‐specific random amplified polymorphic DNA (RAPD) markers and two chloroplast DNA haplotypes. Environmental variables were then measured. These variables included percentage cover by tree canopy, elevation from the high water mark, soil pH and percentage soil organic matter. Each variable was sampled for all 201 plants. Canonical discriminant analysis (CDA) was used to infer the environmental factors most strongly associated with the different genotypic groups. Slight differences in elevation (−0.5 m to +0.4 m) were important for distinguishing habitat distributions described by CDA, even though there were no statistical differences between mean elevations alone.I. brevicaulisoccurred in a broad range of habitats, whileI. fulvahad a narrower distribution. Of all the possible combinations,I. fulva‐like hybrids andI. brevicaulis‐like hybrids occurred in the most distinct habitat types relative to one another. Each hybrid class was not significantly different from its closest parent with regard to habitat occupied, but was statistically unique from its more distant parental species. Within the hybrid genotypes, most, but not all, RAPD loci were individually correlated with environmental variables. This study suggests that, at a very fine spatial scale, environment‐dependent selection contributed to the genetic structuring of this hybrid zone.
Genetic structure of North American wolverine (Gulo gulo) populations
Authors: Kyle C. J. , Strobeck C.
Published: March 2003

Wolverines (Gulo gulo) are found in low densities throughout their circumpolar distribution. They are also potentially susceptible to human‐caused population fragmentation (development, recreation and fur harvesting). The combination of these factors has contributed to this species being listed as having either vulnerable or endangered status across much of its current range. The effects of inherently low densities and anthropogenic pressures on the genetic structure and variation of wolverine populations are, as yet, unknown. In this study, 461 individuals were typed at 12 microsatellite loci to investigate the population genetic structure of wolverines from north‐western Alaska to eastern Manitoba. Levels of gene flow and population differentiation among the sampled regions were estimated via a genotype assignment test, pairwise FST, and two genetic distance measures. Our results suggest that wolverine populations from southernmost regions, in which anthropogenic factors are strongest, revealed more genetic structuring than did northern populations. Furthermore, these results suggest that reductions in this species’ range may have led to population fragmentation in the extreme reaches of its southern distribution. The continued reduction of suitable habitat for this species may lead to more populations becoming isolated remnants of a larger distribution of northern wolverines, as documented in other North American carnivore species.
Population structure of Atlantic salmon (Salmo salar L.): a range‐wide perspective from microsatellite DNA variation
Authors: King T. L. , Kalinowski S. T. , Schill W. B. , Spidle A. P. , Lubinski B. A.
Published: March 2003

Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south‐central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5–37/locus) range‐wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum‐likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.
A comparison of nuclear and mitochondrial cline shapes in a hybrid zone in theSceloporus grammicuscomplex (Squamata; Phrynosomatidae)
Authors: Marshall Jonathon C. , Sites Jack W.
Published: March 2003

The F5 and FM2 chromosome races of theSceloporus grammicuscomplex form a hybrid zone in the Mexican state of Hidalgo. Previous studies of this zone have assessed genetic structure by averaging estimates of shape and width across three diagnostic chromosome markers. This approach is likely to mask subtle differences in cline shape among loci (e.g. selected vs. neutral), and obscure any displacement of cline centres (if present). Here we use maximum likelihood methods to construct the best fitting individual clines for three chromosomal markers, and also add two new markers; the mitochondrial DNA (mtDNA) locus, and the nuclear ribosomal DNA (rDNA) repeat. For each locus, hybrid zone models were fitted by cline shape and width, and the position and number of segments describing the centre of the zone. Pairwise comparisons between all clines revealed concordance between chromosomes 2 and 6, but significant discordance in cline structure among all other paired combinations. The concordance of chromosomes 2 and 6 suggests that these clines are maintained by genome‐wide forces. The discordance of the chromosome 1 cline suggests an influence of asymmetric introgression, while the mtDNA cline is probably influenced by selection and drift. The rDNA locus reveals a pattern best explained by either extreme asymmetric introgression or gene conversion. The structure of zone indicates that genome‐wide processes and locus specific selective forces as well as drift, are operating to different degrees on different loci. The locus‐by‐locus approach used here permits a finer discrimination among possible mechanisms responsible for the maintenance of the individual clines.
Allozymic evidence of parapatric differentiation of brown trout (Salmo trutta L.) within an Atlantic river basin of the Iberian Peninsula
Authors: Bouza C. , Castro J. , Sánchez L. , Martínez P.
Published: March 2003

The genetic variation of brown trout from Duero, one of the main Atlantic Iberian river basins, was assessed at 34 enzymatic loci in 62 native populations. A strong intrabasin differentiation was detected (GST = 0.46; range D: 0–0.066), mainly attributable to the existence of two divergent groups of populations within Duero: southern and northern groups. This divergence was mainly a consequence of the unequal distribution of *75 and *100 alleles at sMDH‐B1,2* isoloci, which were correlated with substantial differences in genetic diversity among regions. The Lower Course region (nearly fixed for the *100 allele) and Pisuerga River (nearly fixed for the *75 allele) showed lower heterozygosities (H ≈ 0.8%) in contrast with adjacent areas, which evidenced intermediate frequencies for both alleles and higher heterozygosities (H: 2.2–3.1%). Vicariance appeared as the more probable explanation for the significant positive correlation detected between genetic and geographical distances in Duero Basin. Genetic relationships with adjacent Iberian drainages indicate a close similarity between the southern group and Cantabric trout, whereas the northern group constitutes an ancient form from this basin. This study confirmed complex genetic relationships in brown trout from northwest Iberia, reasserting the existence of clines at several loci and for genetic diversity. The interaction between Cantabric and Duero trout, as well as the location of the limit of the anadromous form around the 42° N parallel, are both required to understand the genetic characteristics of brown trout from this area.
Phylogeography of Cape Verde Island skinks (Mabuya)
Authors: Brown R. P. , Suarez N. M. , Smith A. , Pestano J.
Published: March 2003

The Cape Verde Islands are of volcanic origin with most having appeared between the early Miocene and mid‐Pleistocene. They contain six known species of Mabuya skinks. Phylogeographical relationships within and among the relatively widespread taxa M. stangeri, M. spinalis and M. delalandii were inferred, based on ≈ 1 kbp of the cytochrome b gene (mitochondrial DNA). Reciprocal monophyly of M. spinalis and M. stangeri was established, which may have arisen from an early Pliocene/late Miocene cladogenetic event. Considerable between‐island sequence divergence was detected among M. spinalis, which appears to have colonized the older islands (Sal and Boavista) first. Much lower sequence divergence was found in M. delalandii, indicating a more recent range expansion. Here, evidence points to colonization of the younger islands of Brava and Fogo soon after appearance. There are similarities between some of the described patterns and those seen in lizards from the Canary Islands.
Gene flow, dispersal, and nested clade analysis among populations of the stonefly Peltoperla tarteri in the southern Appalachians
Authors: Schultheis A. S. , Weigt L. A. , Hendricks A. C.
Published: March 2003

We examined the genetic structure and phylogeography of populations of the stonefly Peltoperla tarteri in the Southern Appalachians to determine the extent and likely mechanism for dispersal of this stream insect. A 454‐base‐pair (bp) portion of the mitochondrial control region was sequenced from a minimum of 20 individuals from eight populations. Pairwise FST and exact tests showed high levels of differentiation among almost all populations except those on the same stream. amova analysis detected significant genetic differentiation between streams within drainages (φSD = 0.14, P < 0.001), and there was a slight positive correlation between aquatic distance and genetic distance (r = 0.295, P = 0.03). According to nested clade analysis, the present day pattern of genetic variation in P. tarteri is the result of a historical range expansion coupled with restricted gene flow with isolation by distance. Together, these analyses suggest that adult dispersal is limited and that movement by larvae is the primary dispersal mechanism for P. tarteri.
Intensive genetic assessment of the mating system and reproductive success in a semi‐closed population of the mottled sculpin, Cottus bairdi
Authors: Fiumera Anthony C. , Porter Brady A. , Grossman Gary D. , Avise John C.
Published: March 2003

Most genetic surveys of parentage in nature sample only a small fraction of the breeding population. Here we apply microsatellite markers to deduce the genetic mating system and assess the reproductive success of females and males in an extensively collected, semi‐closed stream population of the mottled sculpin fish, Cottus bairdi. In this species, males guard nest rocks where females deposit the eggs for fertilization. The potential exists for both males and females to mate with multiple partners and for males to provide parental care to genetically unrelated offspring. Four hundred and fifty‐five adults and subadults, as well as 1259 offspring from 23 nests, were genotyped at five polymorphic microsatellite loci. Multilocus maternal genotypes, deduced via genetic analyses of embryos, were reconstructed for more than 90% of the analysed nests, thus allowing both male and female reproductive success to be estimated accurately. There was no genetic evidence for cuckoldry, but one nest probably represents a takeover event. Successful males spawned with a mean of 2.8 partners, whereas each female apparently deposited her entire clutch of eggs in a single nest (mean fecundity = 66 eggs/female). On average, genetically deduced sires and dams were captured 1.6 and 9.3 metres from their respective nests, indicating little movement by breeders during the spawning season. Based on a ‘genetic mark–recapture’ estimate, the total number of potentially breeding adults (c. 570) was an order‐of‐magnitude larger than genetically based estimates of the effective number of breeders (c. 54). In addition, significantly fewer eggs per female were deposited in single than in multidam nests. Not only were perceived high‐quality males spawning with multiple partners, but they were receiving more eggs from each female.
Population differentiation of Potamogeton pectinatus in the Baltic Sea with reference to waterfowl dispersal
Authors: King R. A. , Gornall R. J. , Preston C. D. , Croft J. M.
Published: March 2003

Forty populations of Potamogeton pectinatus L. were sampled from around the Baltic Sea basin. Analysis of 62 ISSR ‘loci’ showed that the number of clones per population is very variable but shows a tendency to decrease with latitude. Analysis of molecular variance revealed that, overall, just over half the variability is stored within populations and just under half between them (φST 0.496). In pairwise comparisons, most populations are significantly differentiated. Genetic distance between populations, as measured by φST, increases with geographical distance. Levels of population differentiation, however, are lower on the southeastern Swedish coast than elsewhere, a reduction correlated with the importance of this area as a staging post for the massive migrations of waterfowl from arctic Russia and western Siberia. Cumulative plots of φST against geographical distance along this coast suggest that, although it does not prevent significant population differentiation, bird traffic reduces it over distances of 150–200 km.
The Baltic Sea as a model system for studying postglacial colonization and ecological differentiation, exemplified by the red alga Ceramium tenuicorne
Authors: Gabrielsen T. M. , Brochmann C. , Rueness J.
Published: March 2003

The Baltic Sea provides a unique model system for studying genetic effects of postglacial colonization and ecological differentiation, because all marine organisms must have immigrated after the opening of the Danish Straits 8000 years ago and responded to the development of the steep Skagerrak‐Baltic salinity gradient. The red alga Ceramium tenuicorne shows conspicuous variation in growth and reproduction along this gradient. Herein we obtained reproductive data coupled with two types of molecular markers, one organellar (cox2–3 spacer sequences of mitochondrial DNA; mtDNA) and one mainly nuclear (random amplified polymorphic DNAs; RAPDs). Nine main populations were sampled in a nested spatial hierarchy including three salinity regions (Oslofjorden, Kattegat, and the Baltic Sea), and nine additional populations were sampled for the mtDNA analysis. Asexuality was frequent at low (Baltic) and medium (Kattegat) salinities but virtually absent at the highest salinity (Oslofjorden). Five mtDNA haplotypes were observed, of which two highly divergent ones were common. One was restricted to and fixed in Oslofjorden, and the other, which was closely related to the three rare haplotypes, was found from southernmost Norway via Kattegat into the Baltic. The RAPD data revealed, on the other hand, a continuous cline corresponding to the salinity gradient, with 27.4% divergence among salinity regions and most of the variation stored at the smallest spatial scale analysed (64.2%; within 1 m2 subpopulations). The combined data suggest colonization from a diverse Atlantic glacial gene pool followed by (1) lineage sorting of ancestral mtDNA polymorphisms and (2) strong differential selection among nuclear genotypes along the salinity gradient, including selection for nonrecombinant multiplication of those best fit to the marginal low‐salinity habitats.
Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx
Authors: Palomares F. , Godoy J. A. , Piriz A. , O'Brien S. J. , W. E. Johnson
Published: March 2003

Noninvasive methods using genetic markers have been suggested as ways to overcome difficulties associated with documenting the presence of elusive species. We present and assess a novel, reliable and effective molecular genetic technique for the unequivocal genetic identification of faeces from the endangered Iberian lynx (Lynx pardinus). From mitochondrial DNA (mtDNA) cytochrome bandD‐loop region sequences, we designed four species‐specific primers (for products 130–161 bp long) that were considered to be likely to amplify degraded DNA. We compared two DNA extraction methods, various DNA amplification conditions and the robustness and specificity of the primer pairs with 87 lynx samples from 5 potentially different lynx populations and with 328 samples of other carnivore species. The utility of the identification technique was tested with faeces of different ages, with faeces from controlled field experiments, and with faeces collected from locales with possible lynx populations from throughout the state of Andalusia, Spain (8052 km2). Faecal mtDNA extraction was more efficient using PBS wash of the faeces instead of a faeces homogenate. Our assay increased from 92.6 to 99% efficiency with a second amplification and a reduction in template concentration to overcome polymerase chain reaction (PCR) inhibition. Our assay never produced false positives, and correctly identified all lynx faeces. Of 252 faeces samples of unknown species collected throughout Andalusia, 26.6% (from three different areas) were classified as Iberian lynx, 1.4% showed evidence of PCR inhibition and 1.2% were of uncertain origin. This method has proven to be a reliable technique that can be incorporated into large‐scale surveys of Iberian lynx populations and exemplifies an approach that can easily be extended to other species.
Genetic differences among three colour morphotypes of the black rockfish, Sebastes inermis, inferred from mtDNA and AFLP analyses
Authors: Kai Yoshiaki , Nakayama Kouji , Nakabo Tetsuji
Published: March 2003

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.
The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): A microsatellite analysis
Authors: Vernesi C. , Crestanello B. , Pecchioli E. , Tartari D. , Caramelli D. , Hauffe H. , Bertorelle G.
Published: March 2003

The reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well‐understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but ≈ 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.
The city‐fox phenomenon: genetic consequences of a recent colonization of urban habitat
Authors: Wandeler P. , Funk S. M. , Largiadèr C. R. , Gloor S. , Breitenmoser U.
Published: March 2003

The red fox (Vulpes vulpes) is one of the best‐documented examples of a species that has successfully occupied cities and their suburbs during the last century. The city of Zurich (Switzerland) was colonized by red foxes 15 years ago and the number of recorded individuals has increased steadily since then. Here, we assessed the hypothesis that the fox population within the city of Zurich is isolated from adjacent rural fox populations against the alternative hypothesis that urban habitat acts as a constant sink for rural dispersers. We examined 11 microsatellite loci in 128 foxes from two urban areas, separated by the main river crossing the city, and three adjacent rural areas from the region of Zurich. Mean observed heterozygosity across individuals and the number of detected alleles were lower for foxes collected within the city as compared with their rural conspecifics. Genetic differentiation was significantly lower between rural than between rural and urban populations, and highest value of pairwise FST was recorded between the two urban areas. Our results indicate that the two urban areas were independently founded by a small number of individuals from adjacent rural areas resulting in genetic drift and genetic differentiation between rural and urban fox populations. Population admixture and immigration analysis revealed that urban–rural gene flow was higher than expected from FST statistics. In the five to seven generations since colonization, fox density has dramatically increased. Currently observed levels of migration between urban and rural populations will probably erode genetic differentiation over time.
Bacterial preprotein translocase: mechanism and conformational dynamics of a processive enzyme
Authors: Economou Anastassios
Published: March 2003

Preprotein translocase, the membrane transporter for secretory proteins, is a processive enzyme. It comprises the membrane proteins SecYEG(DFYajC) and the peripheral ATPase SecA, which acts as a motor subunit. Translocase subunits form dynamic complexes in the lipid bilayer and build an aqueous conduit through which preprotein substrates are transported at the expense of energy. Preproteins bind to translocase and trigger cycles of ATP binding and hydrolysis that drive a transition of SecA between two distinct conformational states. These changes are transmitted to SecG and lead to inversion of its membrane topology. SecA conformational changes promote directed migration of the polymeric substrate through the translocase, in steps of 20–30 aminoacyl residues. Translocase dissociates from the substrate only after the whole preprotein chain length has been transported to the trans side of the membrane, where it is fully released.
A pathway‐specific transcriptional activator regulates late steps of clavulanic acid biosynthesis in Streptomyces clavuligerus
Authors: Paradkar Ashish S. , Aidoo Kwamena A. , Jensen Susan E.
Published: March 2003

A Streptomyces clavuligerus gene (designated claR ) located downstream from the gene encoding clavaminate synthase in the clavulanic acid biosynthetic gene cluster is involved in regulation of the late steps in clavulanic acid biosynthesis. Nucleotide sequence analysis and database searching of ClaR identified a significant similarity to the helix–turn–helix motif (HTH) region of LysR transcriptional regulators. A gene replacement mutant disrupted in claR was unable to produce clavulanic acid, suggesting that claR is essential for clavulanic acid biosynthesis. Furthermore, the accumulation of clavaminic acid in the claR mutant suggested that ClaR regulates the late steps in the clavulanic acid pathway, i.e. those involved in the conversion of clavaminic acid to clavulanic acid. Transcriptional analysis using RNA isolated from the wild type and the claR mutant showed that the expression of the putative late genes, but not the early genes, was regulated by ClaR. High‐resolution S1 nuclease analysis of claR suggested that it is expressed as a monocistronic transcript and also as a bicistronic transcript along with the late gene orf‐9. The transcription start site of the monocistronic claR transcript was identified as a C residue 155 nucleotides upstream from the claR start codon.
Membrane targeting of RecA during genetic transformation
Authors: Masure H. Robert , Pearce Barbara J. , Shio Helen , Spellerberg Barbara
Published: March 2003

Recombination in prokaryotes and eukaryotes is mediated by the RecA family of proteins. Although the interactions between RecA and DNA are well studied, the cellular location of these interactions is not known. Using genetic transformation of Streptococcus pneumoniae as a model system, there was increased expression of a protein, colligrin, and RecA, products of the rec locus during genetic transfer. These proteins formed a complex and were found associated with the membranes of genetically competent cells. With immunoelectron microscopy and subcellular fractionation, we showed that the induction of competence led to the translocation of RecA and colligrin to the membrane and to the formation of clusters of RecA in a colligrin‐dependent step. Based on the behaviour of colligrin and RecA during genetic exchange and the numerous proteins in prokaryotes and eukaryotes with domains similar to colligrin, we suggest that there may exist a family of proteins, which gathers macromolecules at specific sites in biological membranes.
Cytochrome c biogenesis is involved in the transposon Tn5‐mediated bleomycin resistance and the associated fitness effect in Escherichia coli
Authors: Adam Eric , Volkert Michael R. , Blot Michel
Published: March 2003

The transposon Tn5 ble gene and the Escherichia coli alkylation‐inducible aidC locus are co‐operatively involved in the resistance to the anti‐cancer drug and DNA‐cleaving agent bleomycin and enhance fitness of bacteria in the absence of the drug. In this report, we demonstrate that the aidC locus is identical to nrfGthe last gene of the nrf operon involved in the periplasmic formate‐dependent nitrite reduction. In the presence of Ble, NrfG expression is specifically induced and restores both bleomycin resistance and its associated beneficial growth effect in an aidC− strain. In vitro DNA protection assays reveal that purified Ble prevents bleomycin‐mediated DNA breakage, as do bleomycin‐binding proteins. Similarities between haems of the cytochrome c biogenesis nrf pathway and iron bleomycin suggest a DNA repair‐independent molecular mechanism for both bleomycin resistance and increased viability. The Ble protein binds bleomycin and prevents DNA breakage. It also induces the nrf locus that may assimilate bleomycin into haem for extracellular transport or inactivate bleomycin. Inactivation of potent DNA oxidants confers a better fitness to the bacterium carrying the transposon, suggesting a symbiotic relationship between host and transposon.
Mechanisms involved in the intrinsic isoniazid resistance of Mycobacterium avium
Authors: Mdluli Khisimuzi , Swanson John , Fischer Elizabeth , Lee Richard E. , Barry Iii Clifton E.
Published: March 2003

Isoniazid (INH), which acts by inhibiting mycolic acid biosynthesis, is very potent against the tuberculous mycobacteria. It is about 100‐fold less effective against Mycobacterium avium. This difference has often been attributed to a decreased permeability of the cell wall. We measured the rate of conversion of radiolabelled INH to 4‐pyridylmethanol by whole cells and cell‐free extracts and estimated the permeability barrier imposed by the cell wall to INH influx in Mycobacterium tuberculosis and M. avium. There was no significant difference in the relative permeability to INH between these two species. However, the total conversion rate in M. tuberculosis was found to be four times greater. Examination of in vitro‐generated mutants revealed that the major resistance mechanism for both species is loss of the catalase‐peroxidase KatG. Analysis of lipid and protein biosynthetic profiles demonstrated that the molecular target of activated INH was identical for both species. M. avium, however, formed colonies at INH concentrations inhibitory for mycolic acid biosynthesis. These mycolate‐deficient M. avium exhibited altered colony morphologies, modified cell wall ultrastructure and were 10‐fold more sensitive to treatment with hydrophobic antibiotics, such as rifampin. These findings may significantly impact the design of new therapeutic regimens for the treatment of infections with atypical mycobacteria.