bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of microsatellites for individual assignment: the North Atlantic redfish (genusSebastes) species complex as a case study
Authors: Roques Severine , Duchesne Pierre , Bernatchez Louis 
Published: March 2003

AbstractWe used the four redfish taxa (genusSebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.
Macrogeographical population differentiation in oceanic environments: a case study of European hake (Merluccius merluccius), a commercially important fish
Authors: Lundy Caroline J. , Moran Paloma , Rico Ciro , Milner Richard S. , Hewitt Godfrey M. 
Published: March 2003

AbstractPolymorphism at six microsatellite loci was used to study genetic variability and population structure in six geographically distant natural populations of European hake (Merluccius merluccius L.). Four hundred and eighty‐three individuals were sampled from Trondheimsfjord in Norway, the Celtic Sea, the southern Bay of Biscay, Faro off Portugal, the Mediterranean Sea north of the coast of Tunisia and the Adriatic Sea. Population subdivision was found between Mediterranean and Atlantic samples, θ = 0.029 (P < 0.001). No substructuring was found between samples within the Mediterranean Sea, θ = 0.003 and RST = 0.007 (P > 0.05). The Atlantic population structure appears to be more complex than previously suggested by the placement of stock boundaries by the International Council for the Exploration of the Seas (ICES). Analyses based on various models of microsatellite evolution all suggest that differentiation exists between Bay of Biscay and Portugese samples, θ = 0.013 (P < 0.001), RST = 0.036 (P < 0.001) which are currently managed as one stock. By contrast, fixation indices indicated no differentiation between southern Bay of Biscay samples and Celtic Sea samples, θ = 0.003 (P = 0.02), φST = 0.007 (P = 0.10) which are managed as separate stocks. These results suggest that if the observed trends are stable through time, current management policy of European hake may need revision.
Mitochondrial sequence analysis of Salamandra taxa suggests old splits of major lineages and postglacial recolonizations of Central Europe from distinct source populations of Salamandra salamandra
Authors: Steinfartz Sebastian , Veith Michael , Tautz Diethard 
Published: March 2003

AbstractRepresentatives of the genus Salamandra occur in Europe, Northern Africa and the Near East. Many local variants are known but species and subspecies status of these is still a matter of dispute. We have analysed samples from locations covering the whole expansion range of Salamandra by sequence analysis of mitochondrial D‐loop regions. In addition, we have calibrated the rate of divergence of the D‐loop on the basis of geologically dated splits of the closely related genus Euproctus. Phylogenetic analysis of the sequences suggests that six major monophyletic groups exist (S. salamandra, S. algira, S. infraimmaculata, S. corsica, S. atra and S. lanzai) which have split between 5 and 13 million years ago (Ma). We find that each of the Salamandra species occupies a distinct geographical area, with the exception of S. salamandra. This species occurs all over Europe from Spain to Greece, suggesting that it was the only species that has recolonized Central Europe after the last glaciation. The occurrence of specific east and west European haplotypes, as well as allozyme alleles in the S. salamandra populations suggests that this recolonization has started from at least two source populations, possibly originating in the Iberian peninsula and the Balkans. Two subpopulations of S. salamandra were found that are genetically very distinct from the other populations. One lives in northern Spain (S. s. bernardezi) and one in southern Italy (S. s. gigliolii). Surprisingly, the mitochondrial lineages of these subpopulations group closer together than the remainder S. salamandra lineages. We suggest that these populations are remnants of a large homogeneous population that had colonized Central Europe in a previous interglacial period, approximately 500 000 years ago. Animals from these populations were apparently not successful in later recolonizations. Still, they have maintained their separate genetic identity in their areas, although they are not separated by geographical barriers from very closely related neighbouring populations.
Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post‐Pleistocene recolonization of northern Europe
Authors: Weiss S. , Antunes A. , Schlötterer C. , Alexandrino P. 
Published: March 2003

AbstractMitochondrial haplotype diversity in seven Portuguese populations of brown trout, Salmo trutta L., was investigated by sequencing the 5′ end of the mitochondrial DNA (mtDNA) control region. Five new haplotypes were described for this species, each two to three mutational steps distant from the common north Atlantic haplotype. Significant population subdivision of mtDNA haplotypes was also apparent. Based on these results, as well as on published data describing the distribution of both mtDNA haplotypes and allozyme alleles throughout Europe, the postglacial recolonization of northern Europe was re‐evaluated. It is argued that the available data do not support the contribution of two major glacial refugia (southwest Atlantic and Ponto‐Caspian Basin) to this postglacial recolonization, as proposed in a recently published model. The unique genetic architecture of Portuguese brown trout within the Atlantic‐basin clade of this species represents a highly valuable genetic resource that should be protected from introgression with nonendemic strains of hatchery fish.
The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS‐1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR)
Authors: Hess J. , Kadereit J. W. , Vargas P. 
Published: March 2003

AbstractPhylogenetic relationships in the Olea europaea complex and the phylogeography of 24 populations of the Macaronesian olive (O. europaea ssp. cerasiformis) were assessed by using three molecular markers: nuclear ribosomal internal transcribed spacer 1 (ITS‐1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR). Parsimony analysis of the ITS‐1 sequences and Neighbour‐joining (NJ) analyses of RAPD and ISSR banding variation revealed four major lineages in the O. europaea complex: (1) ssp. cuspidata; (2) ssp. cerasiformis from Madeira; (3) ssp. laperrinei; and (4) ssp. cerasiformis from the Canary Islands plus ssp. europaea. These results provide unequivocal support for two independent dispersal events of Olea to the Madeira and Canary Islands. Molecular and morphological evidence led to recognition of two separate olive taxa in Macaronesia, to date included in ssp. cerasiformis. NJ analyses of the combined RAPD and ISSR data suggest that the colonization of the Canaries by O. europaea may have followed an east to west stepping‐stone model. An interisland dispersal sequence can be recognized, starting from the continent to Fuerteventura, Gran Canaria, Tenerife, La Gomera, and finally La Palma. High dispersal activity of the lipid‐rich Olea fruits by birds in the Mediterranean region is congruent with multiple dispersal of olives to Macaronesia and successive colonization of the archipelagos. The observation of strong genetic isolation between populations of different islands of the Canary Islands suggests, however, that subsequent interisland dispersal and establishment has been very rare or may not have occurred at all.
Do earthworms help to sustain the slug predatorPterostichus melanarius(Coleoptera: Carabidae) within crops? Investigations using monoclonal antibodies
Authors: Symondson W. O. C. , Glen D. M. , Erickson M. L. , Liddell J. E. , Langdon C. J. 
Published: March 2003

AbstractEarthworms provide a major potential source of alternative food for polyphagous predators, such as carabid beetles, that are natural enemies of slugs, aphids and other agricultural pests. Non‐pest prey may foster larger numbers of natural enemies, which then help to control pests, or alternatively may help to divert the predators away from pest control. An earthworm‐specific monoclonal antibody was developed to study carabid–earthworm interactions in the field and assess the role of earthworms as alternative prey. The antibody could identify as little at 7 ng of earthworm protein in an ELISA, and could detect earthworm remains in the foregut of the carabid beetlePterostichus melanariusfor 64 h after consumption. Thirty‐six per cent of field‐collected beetles contained earthworm remains. Quantities of earthworm proteins in the beetle foreguts were negatively related to total foregut biomass, suggesting that earthworm consumption increased as total prey availability declined. There was also a negative relationship between foregut biomass and beetle numbers, but both quantities and concentrations of earthworm proteins in beetle foreguts were positively related to beetle numbers. This suggests that as beetle activity–density increased, total prey availability declined, or, as prey availability declined, beetles spent more time searching. In these circumstances, beetles fed to a greater extent on earthworms, an acceptable but nonpreferred food item. Earthworms may, therefore, provide an ideal alternative prey forP. melanarius, helping to sustain it when pest numbers are low but allowing it to perform a ‘lying‐in‐wait’ strategy, ready to switch back to feeding on pests when they become available.
Genetic diversity and heavy metal tolerance in populations ofSilene paradoxaL. (Caryophyllaceae): a random amplified polymorphic DNA analysis
Authors: Mengoni A. , Gonnelli C. , Galardi F. , Gabbrielli R. , Bazzicalupo M. 
Published: March 2003

AbstractMetal‐contaminated sites can occur naturally in serpentine outcrops or as consequence of anthropogenic activities, such as mining deposits, aerial fallout from smelters and industrial processes. Serpentine outcrops are characterized by high levels of nickel, cobalt and chromium and present a typical vegetation which includes endemisms and plants which also live in uncontaminated soils. These latter metal‐tolerant populations provide the opportunity to investigate the first steps in the differentiation of plant populations under severe selection pressure and to select plants to be used in the phytoremediation of industrially contaminated soils. In this report eight populations ofSilene paradoxaL. (Caryophyllaceae) growing in copper mine deposits, in serpentine outcrops or in noncontaminated soil in central Italy, were analysed using random amplified polymorphic DNA (RAPD) markers to investigate the pattern of genetic variation. The genetic diversity observed in populations at copper mine deposits was found to be at least as high as that of the neighbouring serpentine populations. Analysis of molecular variance (amova) of the RAPD markers gave high statistical significance to the groupings of populations according: (i) with their geographical location; and (ii) with the metals present in the soil of origin (copper vs. nickel), indicating that RAPD markers detected a polymorphism related to the soil contamination by copper. Finally, two RAPD bands exclusive to copper‐tolerant populations were identified.
Genetic structure of avian populations — allozymes revisited
Authors: Crochet P.‐A. 
Published: March 2003

AbstractSelection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci.
Fragmented forests, evolving flies: molecular variation in African populations of Drosophila teissieri
Authors: Cobb Matthew , Huet Michèle , Lachaise Daniel , Veuille Michel 
Published: March 2003

AbstractMicrosatellite variation from eight loci was studied in five populations of Drosophila teissieri, a fruit‐fly found only in the rain forests of sub‐Saharan Africa. Five noncontiguous rain forest sites (from Tanzania, Gabon and Ivory Coast) were sampled to measure the effects of historical forest fragmentation on population structure in an obligatory forest‐dwelling species. The Ivory Coast and Gabon populations showed a wider range of alleles, different modal alleles and had a higher genetic diversity than the three East African populations. As could be expected, genetic differentiation (FST) was significantly correlated with physical distance, but the westernmost population (Ivory Coast) showed values that were intermediate between the central (Gabon) and Eastern (Tanzania) populations. A migration‐drift equilibrium in a stable continuum of populations did not appear adequate to describe the observed distribution. It seems probable that the species has undergone abrupt changes involving isolation, merging and migration of populations, as a consequence of repeated waves of forest fragmentation and coalescence.
Large sequence divergence of mitochondrial DNA genotypes of the control region within populations of the African antelope, kob (Kobus kob)
Authors: Birungi J. , Arctander P. 
Published: March 2003

AbstractThe genetic differentiation among kob populations (Kobus kob) representing two recognized subspecies was examined using mitochondrial control region sequences. Two distinct lineages (estimated sequence divergence of 9.8%) exhibited different geographical distributions and do not coincide with previously recognized ranges of subspecies. The presence of the two lineages was further supported with sequences of mitochondrial cytochrome b gene. One lineage was predominant in the west and southern ranges of the populations studied and the other was commonly found in a more northern distribution (Murchison populations) in Uganda. Murchison and the geographically intermediate Toro populations (Uganda) represented the area of overlap. The existence of the two lineages in the area of overlap is hypothesized to have resulted from a range expansion and secondary contact of the two lineages of kob that evolved in allopatry. The existence of the kob during the Pleistocene offers a plausible explanation for the observed biogeographic pattern. Our mitochondrial data reveal two examples of discordance between a gene tree and presumed species tree as: (i) the two lineages co‐occur in the kob subspecies, Kobus kob thomasi (Uganda kob); and (ii) the puku, which was included in the analysis because of its controversial taxonomic status (currently recognized as a distinct species from the kob), is paraphyletic with respect to the kob. Significant degrees of heterogeneity were detected between populations. Relatively high genetic variation was observed in the populations, however, the inclusion of distinct lineages influences the population structure and nucleotide diversity of the kob populations.
Mating behaviour ofRhytidoponerasp. 12 ants inferred from microsatellite analysis
Authors: Tay W. T. , Crozier R. H. 
Published: March 2003

AbstractIn the queenless ponerine antRhytidoponerasp. 12, all workers have a spermatheca and functional ovaries and are potentially able to mate and reproduce. Within a colony gamergates may either be full sisters to each other (Type 1 colony), or they may not be full sisters but still be significantly related to each other (Type 2 colony) due to daughter gamergates reproducing in their natal colonies after mating. Despite many studies the mating behaviour ofR. sp. 12 has been poorly understood. In this study, we used microsatellite markers to investigate intracolony relatednesses of male mates to the gamergates (bmq) and between male mates (bmm), and mating frequencies and mating patterns, using gamergate DNA and sperm DNA isolated from the spermathecae of gamergates from five colonies. Averagebmmandbmqestimates for all five colonies studied were not significantly different from zero, suggesting that on average, within colonies, mating males were unrelated both to each other and to the gamergates. A low frequency (3%) of multiple mating by gamergates was detected. Multiple mating by individual males with sister gamergates within Type 1 colonies was also detected at 3% and could give rise to half‐sister nestmate workers. Polygamy inR. sp. 12 might indicate local female‐biased operational sex ratios despite the expectation of overall male biases. Our results concur with previous reports that gamergates mate within the colony or nearby, but indicate more diversity in mating patterns than previously indicated for this polygynous ponerine ant species.
Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce
Authors: Sperisen C. , Büchler U. , Gugerli F. , Mátyás G. , Geburek T. , Vendramin G. G. 
Published: March 2003

AbstractMitochondrial DNA, widely applied in studies of population differentiation in animals, is rarely used in plants because of its slow rate of sequence evolution and its complex genomic organization. We demonstrate the utility of two polymorphic mitochondrial tandem repeats located in the second intron of the nad1 gene of Norway spruce. Most of the size variants showed pronounced population differentiation and a distinct geographical distribution. A GenBank search revealed that mitochondrial tandem repeats occur in a broad range of plant species and may serve as a novel molecular marker for unravelling population processes in plants.
Population genetic structure of the lemon shark (Negaprion brevirostris) in the western Atlantic: DNA microsatellite variation
Authors: Feldheim K. A. , Gruber S. H. , Ashley M. V. 
Published: March 2003

AbstractDNA microsatellite markers were used to characterize the population genetic structure of the lemon shark, Negaprion brevirostris, in the western Atlantic. This study demonstrates for the first time the usefulness of microsatellites to study population genetic structure and mating systems in the Chondricthyes. Lemon sharks (mostly juveniles) were sampled non‐destructively from four locations, Gullivan Bay and Marquesas Key in Florida, Bimini, Bahamas, and Atol das Rocas, Brazil. At least 545 individuals were genotyped at each of four dinucleotide loci. The number of alleles per locus ranged from 19 to 43, and expected heterozygosities ranged from 0.69 to 0.90. Relatively little genetic structure was found in the western Atlantic, with small but significant values for estimators of FST and RST among populations, θ (0.016) and ρ (0.026), respectively. No sharp discontinuities were found between the Caribbean sites and Brazil, and most alleles were found at all four sites, indicating that gene flow occurs throughout the western Atlantic with no evidence for distinct stocks.
Surprising similarity of sneaking rates and genetic mating patterns in two populations of sand goby experiencing disparate sexual selection regimes
Authors: Jones Adam G. , Walker Deette , Lindström Kai , Kvarnemo Charlotta , Avise John C. 
Published: March 2003

AbstractMolecular markers have proved extremely useful in resolving mating patterns within individual populations of a number of species, but little is known about how genetic mating systems might vary geographically within a species. Here we use microsatellite markers to compare patterns of sneaked fertilization and mating success in two populations of sand goby (Pomatoschistus minutus) that differ dramatically with respect to nest‐site density and the documented nature and intensity of sexual selection. At the Tvärminne site in the Baltic Sea, the microsatellite genotypes of 17 nest‐tending males and mean samples of more than 50 progeny per nest indicated that approximately 35% of the nests contained eggs that had been fertilized by sneaker males. Successful nest holders mated with an average of 3.0 females, and the distribution of mate numbers for these males did not differ significantly from the Poisson expectation. These genetically deduced mating‐system parameters in the Tvärminne population are remarkably similar to those in sand gobies at a distant site adjoining the North Sea. Thus, pronounced differences in the ecological setting and sexual selection regimes in these two populations have not translated into evident differences in cuckoldry rates or other monitored patterns of male mating success. In this case, the ecological setting appears not to be predictive of alternative male mating strategies, a finding of relevance to sexual selection theory.