bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial DNA diversity in an apomictic Daphnia complex from the Canadian High Arctic
Authors: van RAAY T.J. , CREASE T. J.
Published: April 2008

Cyclic parthenogenesis is the ancestral mode of reproduction in the cladoceran crustacean, Daphnia pulex, but some populations have made the transition to obligate parthenogenesis and this is the only mode of reproduction known to occur in arctic populations. Melanism and polyploidy are also common in arctic populations of this species. Prior allozyme studies of arctic D. pulex revealed substantial levels of clonal diversity on a regional scale. Clonal groupings based on cluster analysis of allozyme genotypes do not conform to groupings based on the presence/absence of melanin or on ploidy level. In order to further elucidate genetic relationships among arctic D. pulex clones, mitochondrial DNA (mtDNA) variation was examined in 31 populations from two Canadian high‐arctic sites. The data were also compared to a previous study of mtDNA variation in populations from a Canadian low‐arctic site. Cladistic analysis of restriction site variation of the entire mitochondrial genome and nucleotide sequence variation of the mitochondrial control region was used to construct genetic relationships among mitochondrial genotypes. Three distinct mitochondrial lineages were detected. One lineage was associated with diploid, nonmelanic clones and is the same as the lineage that is found in temperate populations of D. pulex. The other two lineages (A & B) were associated with polyploid, melanic clones. Sequence divergence between the A and B lineages was 2.4%. Sequence divergence between D. pulex and either of these two lineages exceeded 3%. It is suggested that the melanic, polyploid clones are hybrids between males of D. pulex (and/or a closely related congener, D. pulicaria) and females of either of two ancestral melanic species that have mitochondrial lineages A and B. Geographic patterns of mitochondrial diversity in ‘melanic’ lineage B support the hypothesis of an high‐arctic refuge for the ancestral species during the last glacial period.
Introgression of Luxilus cornutus mtDNA into allopatric populations of Luxilus chrysocephalus (Teleostei: Cyprinidae) in Missouri and Arkansas
Authors: DUVERNELL D. D. , ASPINWALL N.
Published: April 2008

The cyprinid fishes Luxilus cornutus and Luxilus chrysocephalus hybridize extensively in a zone extending through the Great Lakes region with extensive introgression of L. cornutus mtDNA occurring in populations of L. chrysocephalus south of the present hybrid zone in Ohio. Western populations of these two species occur adjacent to one another in Missouri but hybridization has never been observed. In order to determine if hybridization has occurred historically in Missouri, allopatric populations of L. chrysocephalus were analysed for mtDNA introgression. Extensive introgression of L. ***cornutus mtDNA was observed in most populations of L. chrysocephalus in Missouri resulting in the elimination of L. chrysocephalus mtDNA in many populations. Luxilus cornutus mtDNA in L. chrysocephalus is found approximately 300 km south of extant L. cornutus populations in Missouri. Luxilus chrysocephalus mtDNA was replaced by four unique L. cornutus mtDNA haplotypes, with one particular haplotype becoming fixed in several L. chrysocephalus populations. The pattern of introgression suggests that historically L. cornutus occupied a more southern distribution in Missouri bringing it into contact with western populations of L. chrysocephalus and resulting in a hybrid zone.
Relative genetic structure of a population of Rhizobium meliloti isolated directly from soil and from nodules of alfalfa (Medicago sativa) and sweet clover (Melilotus alba)
Authors: BROMFIELD E. S. P. , BARRAN L. R. , WHEATCROFT R.
Published: April 2008

Insertion sequence (IS) hybridization was used to define the structure of a population of Rhizobium meliloti isolated directly from soil and from nodules of Medicago sativa (alfalfa) and Melilotus alba (sweet clover) grown under controlled conditions and inoculated with a suspension of the same soil. The detection of R. meliloti isolated from soil on agar plates was facilitated by use of a highly species specific DNA probe derived from ISRm5. All R. meliloti obtained directly from soil proved to be symbiotic (i.e. nodulated and fixed nitrogen with alfalfa). Analysis of 293 R. meliloti isolates revealed a total of 17 distinct IS genotypes of which 9, 9 and 15 were from soil, M. alba and M. sativa, respectively; 8 genotypes were common to soil and both plant species. The frequency of R. meliloti genotypes from soil differed markedly from that sampled from nodules of both legume species: 5 genotypes represented about 90% of the isolates from soil whereas a single genotype predominated among isolates from nodules accounting for more than 55% of the total. The distribution of genotypes differed between M. sativa and M. alba indicating species variation in nodulation preferences for indigenous R. meliloti. The data are discussed in the context of competition for nodulation of the host plant and the selection of Rhizobium strains for use in legume inoculants. This study has ecological implications and suggests that the composition of R. meliloti populations sampled by the traditionally used host legume may not be representative of that actually present in soil.
Recombinant and wild‐type Pseudomonas aureofaciens strains introduced into soil microcosms: effect on decomposition of cellulose and straw
Authors: ENGLAND L. S. , LEE HUNG , TREVORS J. T.
Published: April 2008

The effect of a genetically engineered Pseudomonas aureofaciens (Ps3732RNL11) strain (GEM) and the parental wild‐type (Ps3732RN) on decomposition of cellulose paper, straw and calico cloth was assessed after 18 weeks incubation in laboratory soil microcosms. Effect(s) of inoculum density (103, 105, and 108 cells/ g dry soil) and single versus multiple bacterial inoculations were also investigated. Cellulose paper was completely decomposed after 18 weeks in all treatments. There were no significant differences (95% level), between treatments, in percentage decomposition of either straw or calico cloth. Recovery of the GEM at 18 weeks, using viable plating, was limited to treatments originally receiving 108 cells/g dry soil. Log 1.8 CFU/g dry soil were recovered from the single dose treatment while log 4.2 CFU/g dry soil were recovered from the multiple dose treatment Biolog metabolic tests were used to determine if the GEM or parental wild‐type had any effect on overall carbon utilization in soil. Results suggested they did not. Detection of the recombinant lacZY gene sequence in soil using PCR suggested the possibility of viable but nonculturable cells and/or persistence of chromosomal DNA.
Microsatellites reveal high genetic diversity within colonies of Camponotus ants
Authors: GERTSCH P. , PAMILO P. , VARVIO S. L.
Published: April 2008

In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR‐products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats.
DNA fingerprinting provides evidence of discriminate suckling and non‐random mating in little brown bats Myotis lucifugus
Authors: WATT E. M. , FENTON M. BROCK
Published: April 2008

Recent advances in DNA extraction and fingerprinting techniques allowed examination of genetic similarity of groups of Myotis lucifugus at maternity roosts. Mean percentage band‐sharing between young was significantly higher than between mothers, suggesting fertilization success skewed for individual males or male lineages. Mean percentage band‐sharing between presumed mothers and young was significantly higher than band‐sharing between all other groups, suggesting that Myotis lucifugus preferentially suckle their own young.
Multilocus DNA fingerprinting and RAPD reveal similar genetic relationships between strains of Oreochromis niloticus (Pisces: Cichlidae)
Authors: NAISH K. A. , WARREN M. , BARDAKCI F. , SKIBINSKI D. O. F. , CARVALHO G. R. , MAIR G. C.
Published: April 2008

Two molecular techniques which reveal highly variable DNA polymorphisms, RAPD and multilocus DNA fingerprinting, were used to evaluate genetic diversity between six aquacultural strains of Oreochromis niloticus (tilapia) from the Philippines. The results using both techniques were in close agreement Within‐strain heterozygosity values were similar and were correlated between the two data sets, but statistical errors associated with the RAPD data set were lower. Although genetic distances between strains were greater using DNA fingerprinting, the distances measured using both methods were significantly correlated. Both methods were useful in estimating variation between strains, but they offered different advantages. RAPD was technically easier to perform and produced results with low statistical error, whereas DNA fingerprinting detected greater genetic differentiation between strains. The theoretical basis for using RAPD and multilocus minisatellite markers for population studies is discussed.
Intraspecies differentiation in the powdery mildew Erysiphe cichoracearum determined with rDNA RFLPs
Authors: ZELLER K. A. , LEVY M.
Published: April 2008

The powdery mildew species Erysiphe cichoracearum has a described host range of over 300 plant species from among several families. Host‐range testing indicates host‐specialized subdivision within this taxonomic species. However, the extent of subdivision remains largely undetermined among host‐limited forms. We have characterized diversity among field collections of E. cichoracearum from a variety of hosts, and from other powdery mildew species, with RFLPs from a PCR amplified ribosomal DNA (rDNA) segment The E. cichoracearum samples expressed six distinct RFLP haplotypes. Each haplotype was specific to either a single host or to a set of related host species. These haplotypes formed a continuum of divergence ranging from about 18–35% average pairwise distance from one another, while those from other mildew species clustered at consistently higher average pairwise distances from E. cichoracearum and from each other. Our findings support earlier suggestions, based on host‐range and morphological characterizations, that E. cichoracearum is a complex of morphologically similar, but host‐limited forms. Also, comparisons of rDNA haplotype distance between E. cichoracearum and Blumeria (Erysiphe) graminis were consistently greater than between E. cichoracearum and Sphaerotheca fulginea. This result supports earlier questions concerning the monophyletic nature of Erysiphe.
Genetic diversity of trout (genus Salmo) from its most eastern native range based on mitochondrial DNA and nuclear gene variation
Authors: BERNATCHEZ L. , OSINOV A.
Published: April 2008

Russia and western Asia harbour trout populations that have been classified as distinct species and subspecies, most often on the basis of morphological and ecological variation. In order to assess their origins and to verify whether traditional taxonomy reflects their evolutionary distinctiveness, we documented their genetic relationships on the basis of mitochondrial DNA (mtDNA) RFLP, mtDNA sequence analysis, and allozyme variation. Both mtDNA and nuclear gene variation defined two ancient phylogenetic assemblages of populations distributed among northern (Baltic, White, Barents), and southern (Black, Caspian, Aral) sea basins, between which gene flow has been possible but limited in postglacial times. These results supported the traditional taxonomic differentiation between populations of these two regions. They provided weak support for the taxonomic distinction of southern brown trout (Salmo trutta) populations based on their basin of origin. They also refuted the hypothesis that L. Sevan trout (Salmo ischchan) diverged from a primitive brown trout ancestor. Nevertheless, all trout populations from southern sea basins possessed private alleles or mtDNA genotypes and were genetically distinct Therefore, they represent unique gene pools that warrant individual recognition for conservation and management.
Population subdivision and gene flow in Danish house mice
Authors: DALLAS J. F. , DOD B. , BOURSO P. , PRAGER E. M. , BONHOMME F.
Published: April 2008

Genetic subdivision in local populations of the European house mice, Mus musculus domesticus and M. m. musculus, was analysed to study patterns of gene flow. The data consisted of frequencies of microsatellite alleles in 16 samples (250 individuals) from a total of 11 sites in Jutland, which included successive samples from three sites. Sequences of the control region of mitochondrial DNA in three successive samples from one site were also analysed. Microsatellite genotype frequencies within samples were close to Hardy‐Weinberg expectations. Levels of microsatellite differentiation among samples (θ= 0.05–0.21) corresponded to limited gene flow at migration‐drift equilibrium (Nm= 1–5). Weak isolation by distance for microsatellites in M. m. musculus suggested that gene flow tends to occur among neighbouring sites. Estimates of effective population size over a few generations were much lower than those corresponding to the long periods needed for arrival at mutation‐drift equilibrium. This suggested that subpopulations had been influenced by gene flow since formation, or had originated recently from genetically diverse founders.
Microsatellite analysis of population structure in Canadian polar bears
Authors: PAETKAU D. , CALVERT W. , STIRLING I. , STROBECK C.
Published: April 2008

Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait ‐ Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long‐distance seasonal movements undertaken by polar bears.
One hundred years of Spartina altemiflora (Poaceae) in Willapa Bay, Washington: random amplified polymorphic DNA analysis of an invasive population
Authors: STILLER J. W. , DENTON A. L.
Published: April 2008

Spartina altemiflora (smooth cordgrass) has invaded Willapa Bay, Washington, covering bare mud flats and seagrass beds. At current expansion rates it threatens to occupy most of the intertidal habitat in the bay within 40 years. Although a major mitigation effort is underway, nothing is known about the genetic structure of the Willapa Bay S. altemiflora population or the underlying causes for the dramatic increase in seed set that has occurred in the last 15 years. Random amplified polymorphic DNA (RAPD) analysis was assessed as a method of DNA fingerprinting to analyse the genetic history and current structure of the Willapa population. The results suggest that all S. alterniflora clones in Willapa Bay are descended from a single genet. Given the limited genetic variability expected in a clonally founded population, we discuss the utility of RAPDs as genetic markers to explore the large morphological and reproductive differences reported among Willapa clones. Cluster analysis of RAPD fragments was used to show relatedness among S. alteniflora genets and may be helpful in locating the most prolific clones for mitigation efforts. Overall, RAPDs show great potential in genetic analysis of S. altemiflora, particularly in invasive populations where isozyme variability is low or nonexistent.
Geographic and microgeographic genetic differentiation in two aphid species over southern England using the multilocus (GATA)4 probe
Authors: de BARRO P. J. , SHERRATT T. N. , CARVALHO G.R. , NICOL D. , IYENGAR A. , MACLEAN N.
Published: April 2008

Samples of the grain aphid Sitobion avenue (F.) and the rose‐grain aphid Metopolophium dirhodum (Walker) were collected in late March from wheat fields and adjacent road‐side grasses at a number of locations in southern England. Unparasitized aphids were DNA fingerprinted using the multilocus (GATA)4 probe. Over all locations, the fingerprints of individual S. avenue caught in wheat had lower overall average distances of band migration (ADBM) and shared a higher proportion of bands, than fingerprints of individuals caught in adjacent road‐side grasses. The ADBM of fingerprints of S. avenue collected on road‐side grasses altered significantly with geographical location, while the ADBM of fingerprints of S. avenue caught on wheat did not. A comparison of the fingerprints of individual M. dirhodum caught in wheat and neighbouring road‐side grasses did not reveal any genetic differentiation. Fingerprints of M. dirhodum that were caught in the same host type did however, show significant variation in ADBM between different locations. With both S. avenue and M. dirhodum, spatial autocorrelation revealed that locations that were close together were no more likely to have individuals with similar ADBM than locations mat were far apart Our results suggest that (i) particular clones of S. avenue prefer to colonize wheat; and/or that (ii) particular clones of S. avenae perform better on wheat man other clones. It is unclear why M. dirhodum did not show any genetic structuring according to host type, but this species appears to engage in sexual reproduction much more frequently than S. avenae in southern England. M. dirhodum is likely to have displayed genetic heterogeneity between locations either because of founder effects, or because of genetic drift.
Species identification of Cecidophyopsis mites (Acari: Eriophyidae) from different Ribes species and countries using molecular genetics
Authors: FENTON B. , MALLOCH G. , JONES A. T. , AMRINE J. W. , GORDON S. C. , A'HARA S. , MCGAVIN W. J. , BIRCH A. N. E.
Published: April 2008

Cecidophyopsis mites were studied by PCR amplification of parts of their ribosomal DNA, followed by restriction enzyme analysis. Mite specimens on Ribes nigrum (black currant) from six countries gave the same digestion pattern, which was distinct from the pattern for mites found on R. rubrum from Poland and Finland and for R. grossularia from the USA. This suggests that each Ribes species is host to a different mite species: C. ribis, C. selachodon and C. grossulariae, respectively. Two other mite samples from R. alpinum and R. aureum were identical but were distinct from each of the other species.
A single‐locus minisatellite discriminates chinook salmon (Oncorhynchus tshawytscha) populations
Authors: HEATH D. D. , BERNIERM N. J. , MOUSSEAU T. A.
Published: April 2008

A knowledge of genetic structure in natural populations is often necessary for conservation and management purposes, especially in declining Pacific salmon populations. To test for genetic differentiation between nine populations of chinook salmon, Oncorhynchus tshawytscha, from south‐western British Columbia, Canada, DNA was extracted from 603 fish and hybridized with a single‐locus minisatellite probe. Multivariate statistical analyses of the resulting allele size data permitted successful overall population identification of 52% (individual population range: 24–78%; P < 0.005), indicating a high level of genetic differentiation among the nine populations. Two of the nine populations were further analysed using data from a second minisatellite locus. The discrimination success rate improved from 81.1% (one‐locus analyses) to 90.0% (two‐locus analyses), indicating the potential for greatly increased resolution gained by the addition of more loci. These results indicate that variation at minisatellite loci can be used for assessing population‐level genetic structure, even with artificial gene flow.
PCR amplification of intergenic spacers in the ribosomal DNA of Drosophila melanogaster reveals high levels of turnover in length and copy‐number of spacers in geographically separated populations
Authors: BOWEN T. , DOVER G. A.
Published: April 2008

A recently described PCR‐based method for the analysis of intergenic spacer (IGS) length variation in the ribosomal (r) DNA of Drosophila melanogaster was used to analyse the distribution of IGS length variants in the rDNA of a number of recently collected D. melanogaster populations. One group of populations, from Europe and North Africa, was shown to have low intrapopulation IGS length variation following maintenance of massed populations in the laboratory for an extended period. However, a greater degree of IGS profile variability was detected at a number of levels in the majority of laboratory‐maintained isofemale lines from two of these populations plus a second group of populations which were collected more recently from the eastern coast of Australia; all of which were immediately divided into isofemale lines following collection. Interestingly, PCR analysis of pooled DNA extracts from 30 individuals of either sex showed almost identical PCR profiles from each of the Australian populations. These preliminary results are discussed with regard to the possible combinations of forces (natural selection, neutral drift and genomic molecular drive) on the patterns of IGS length variation.
Mitochondrial DNA products among RAPD profiles are frequent and strongly differentiated between races of Douglas‐fir
Authors: AAGAARD J. E. , VOLLMER S. S. , SORENSEN F. C. , STRAUSS S. H.
Published: April 2008

Racial differentiation and genetic variability were studied between and within the coastal, north interior, and south interior races of Douglas‐fir using RAPD and allozyme markers. Nearly half of all RAPD bands scored (13:45%) were found to be amplified from mitochondrial DNA. They exhibited maternal inheritance among hybrids and back‐crosses between the races, and were much more highly differentiated (GST= 0.62 for haplotype frequencies) than were allozymes (GST= 0.26). No evidence of hybridization or introgression was detected where the coastal and interior races come into proximity in central Oregon.
Patterns of covert infection by invertebrate pathogens: iridescent viruses of blackflies
Authors: WILLIAMS T.
Published: April 2008

Recently, it has been recognized that blackfly populations may host two forms of infection by iridescent viruses (IVs); a covert (inapparent, nonlethal) form which was common in springtime populations in the River Ystwyth, Wales, and a patent (obvious, lethal) form which was rare. This study aimed to investigate the changes in frequency of the two types of infection in blackfly populations over the reproductive period of the flies, April‐September 1992. Blackfly larvae sampled from three different sites along the river were bioassayed for the presence of covert IV infection. Of 870 larvae assayed, 17 were found to be infected. All the infected larvae appeared to be Simnulium variegatum, the dominant species during the sampling period. IV infections were common in the spring (17–37% depending on site) but appeared absent in the S. variegatum population for most of the summer months, reappearing again in the autumn (0–20% infected). These fluctuations were concurrent with biotic and abiotic factors: elevated levels of covert infection occurred at low population densities, high water flow rates, low temperatures (and presumably slower growth rates), although it is not clear if any cause‐and‐effect relationship exists. Patent infections occurred immediately after the peak of covert infection in the spring, and again in the autumn. Virus characterization of isolates from covertly infected larvae showed that three distinct groups of isolates were present in the blackfly population. Isolates from the springtime populations were mostly variants of an isolate found in patently infected blackfly larvae in the 1970s (Aberystwyth IV). Isolates from the autumn populations were mostly variants of an isolate from a patently infected larva found in September the previous year. A third group comprised a single novel isolate which was detected in a covertly infected larva. The mechanisms by which IVs persist in blackfly populations remain unknown, although the role of alternative hosts is a possibility which needs to be studied.
RAPD assessment of California phylloxera diversity
Authors: FONG G. , WALKER M. A. , GRANETT J.
Published: April 2008

Grape phylloxera, Daktulosphaira vitifoliae Fitch, is a parthenogenetic, aphid‐like pest which attacks the roots and leaves of many Vitis L. species. Feeding on the roots of V. vinifera L. cultivars leads to decreased plant productivity and eventual death. Isolates of phylloxera have been grouped into ‘biotypes’ based on the aggressiveness of their feeding behaviour, relative reproductive rates, and abilities to cause decline on V. vinifera and the grape rootstock AXR1. The goal of our research was to determine whether these bio‐type definitions were reflected in the genetic diversity among laboratory‐cultured colonies of Californian phylloxera. Thirteen phylloxera isolates, encompassing biotypes A, B and non‐A or ‐B types based on their feeding and reproduction, were analysed using the RAPD‐PCR method. Results indicate that there were genetic differences among isolates and that there was as much polymorphism within biotypes as among biotypes. This is surprising in a parthenogenetic organism and leads us to suggest that there have been multiple introductions of phylloxera into California, that phylloxera are not obligately parthenogenetic, or that there are other mechanisms whereby phylloxera may evolve relatively rapidly.
Mitochondrial DNA variation in Moroccan and Spanish honey bee populations
Authors: GARNERY L. , MOSSHINE E. H. , OLDROYD B. P. , CORNUET J. M.
Published: April 2008

The mitochondrial DNAs of 192 Moroccan and 173 Spanish honey bee colonies were characterized by a rapid test involving the restriction by DraI of a PCR‐fragment of the COI‐COII region. In Morocco, we found eight haplotypes, all characteristic of the African (A) lineage, suggesting that most if not all the maternal lineages of the colonies repeatedly imported from Europe over the last 150 years have not contributed mitochondrial genomes to the local population. Using two new genetic distances analogous to the shared allele distance defined for nuclear genes, we showed that Morocco was most probably colonized by two sublineages, one from the north‐east and the other one from the south of the country and that the contact zone between them extends along both sides of the Atlas range. In Spain, we found eight haplotypes characteristic of lineage A (six in common with Morocco) and four of lineage M (the West European lineage). The distribution of haplotypes of both lineages forms a gradient with c. 10% of lineage M in the south of Spain (Seville) and up to 100% in the north (San Sebastian). Three hypotheses are presented to explain the large differences of haplotype frequencies between Moroccan and lineage A Spanish colonies: a non‐Moroccan origin of lineage A in Spain, an ancient Moroccan origin or a recent Moroccan origin with a rapid shift of haplotype frequencies due to a founder effect.
Marked mitochondrial DNA differences between Mediterranean and Atlantic populations of the swordfish, Xiphias gladius
Authors: KOTOULAS G. , MAGOULAS A. , TSIMENIDES N. , ZOUROS E.
Published: April 2008

Restriction analysis of mitochondrial DNA (mtDNA) from 204 individuals of swordfish (Xiphias gladius) revealed no differentiation among samples from three sites in the Mediterranean Sea (Greece, Italy, Spain), but a high degree of differentiation between Mediterranean samples and a sample from the Gulf of Guinea. A fifth sample from the Atlantic side of the Straits of Gibraltar (Tarifa) consisted mostly of mitotypes that are common in the Mediterranean, but contained several of mtDNA types of the Guinea sample not found in the Mediterranean. We conclude that, in spite of free migration of swordfish across the Straits of Gibraltar, little genetic exchange occurs between the populations inhabiting the Mediterranean Sea and the tropical Atlantic ocean. This is the first evidence of genetic differentiation among geographic populations of this highly mobile species that supports a world‐wide fishery.
Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallowHirundo rustica
Authors: PRIMMER C. R. , MØLLER A. P. , ELLEGREN H.
Published: April 2008

Eight polymorphic microsatellite markers from the swallow were isolated and characterized. Extraordinary variability was revealed at theHrU6locus with 45 different alleles scored among 46 unrelated individuals. The probability that the same genotype combination would occur in two random and unrelated individuals at six selected loci was as low as 1.3 × 10‐8and the combined exclusion probability was 0.9996. Stable Mendelian inheritance was observed in about 1000 meioses. No significant linkage was revealed and for almost all combinations of marker‐pairs, linkage closer than 5 cM could be excluded. At two loci, null (nonamplifying) alleles were encountered. Thirteen (30%) extra‐pair offspring were identified in 5 (56%) broods when applying the marker set on a nearly complete swallow colony. We were able to identify a single male from the other families in the colony as the most likely father for nine of the 13 extra‐pair offspring.
Multiple paternity in the red‐eyed treefrog Agalychnis callidryas (Cope)
Authors: D'ORGEIX C. A. , TURNER B. J.
Published: April 2008

DNA fingerprinting of tadpoles from two different ‘one female‐two male’ matings of the red‐eyed treefrog, Agalychnis callidryas, revealed multiple paternity of offspring. Offspring were assigned paternity based on bands shared with the putative father, but not shared between putative fathers or with the mother. Paternity was split 44/56% and 36/64% in two matings. These results do not support a hypothesis of sperm priority in access to unfertilized eggs by primary males. Multiple paternity may be commonplace in species of anurans with matings by multiple males.
PCR‐based identification of wheat genomes
Authors: SALLARES R. , ALLABY R. G. , BROWN T. A.
Published: April 2008

We describe a PCR system that distinguishes the A, B and D genomes in wheat DNA extracts. PCRs were directed at the ‘non‐transcribed spacer’ regions of the rDNA loci. The spacers within the D genome locus have a 71‐bp insertion that is absent from the corresponding A and B loci PCR product sizes therefore enable D‐ and D+ genomes to be distinguished. The A and B genomes can be differentiated by PCR with an internal primer which does not anneal to A genome sequences. This work is relevant to the ancient ecology of wheat, as it is often difficult to determine ploidy level from morphological examination of archaeobotanical remains.
Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus)
Authors: GERLOFF U. , SCHLÖTTERER C. , RASSMANN K. , RAMBOLD I. , HOHMANN G. , FRUTH B. , TAUTZ D.
Published: April 2008

We show that nuclear DNA extracted from faeces of free living bonobos (Pan paniscus) can be used to amplify hypervariable simple sequence repeats, which can be used for paternity analysis and kinship studies. Of 130 DNA extractions of samples from 33 different animals, about two‐thirds yielded PCR products at the first attempt. For several samples only a second extraction resulted in positive amplifications. Consistency tests revealed that in some cases only one of the two alleles was amplified. Presumably this is due to a very limited amount of bonobo DNA in the sample and we suggest therefore that a sample found to be homozygous at a given locus should be typed repeatedly for verification.
The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed
Authors: NAKATSU C. H. , FULTHORPE R. R. , HOLLAND B. A. , PEEL M. C. , WYNDHAM R. C.
Published: April 2008

Horizontal gene transfer in the Bacteria has been demonstrated to occur under natural conditions. The ecological impact of gene transfer events depends on the new genetic material being expressed in recipient organisms, and on natural selection processes operating on these recipients. The phylogenetic distribution of cbaAB genes for chlorobenzoate 3,4‐(4,5)‐dioxygenase, which are carried within Tn5271 on the IncPβ plas‐mid pBRC60, was investigated using isolates from freshwater microcosms and from the Niagara River watershed. The latter included isolates from surface water, groundwater and bioremediation reactor samples. The cbaAB genes have become integrated, through interspecific transfer, primarily into species of the β Proteobacteria (44/48 isolates). Only four isolates, identified as Pseudomonas fluorescens (3/48) and Xanthomonas maltophilia (1/48), belonged to the Γ Proteobacteria, despite the observation that pBRC60 was capable of mobilizing these genes into a wide range of β and Γ Proteobacteria in the laboratory. The natural host range correlated with the distribution of the meta‐ring‐fission pathway for metabolism of protocatechuates formed when the cbaAB genes were expressed (45/48 isolates). We proposed the hypothesis that natural selection has favoured recipients that successfully integrate the activity of the transferred dioxygenase with the conserved meta ring‐fission pathway. The hypothesis was tested by transferring a plasmid construct containing the cbaAB genes into type strains representative of the β and γ Proteobacteria. The concept of applying mobile catabolic genes to probe the phylogenetic distribution of compatible degradative pathways is discussed.
Microbial community structure and biogeochemistry of Miocene subsurface sediments: implications for long‐term microbial survival
Authors: FREDRICKSON J. K. , MCKINLEY J. P. , NIERZWICKI‐BAUER S. A. , WHITE D. C. , RINGELBERG D. B. , RAWSON S. A. , LI SHU‐MEI , BROCKMAN F. J. , BJORNSTAD B. N.
Published: April 2008

Thirty closely spaced cores were obtained from Miocene‐aged fluvial, lacustrine and palaeosol subsurface sediments ranging in depth from 173 to 197 m at a site in south‐central Washington to investigate the size and composition of the microbial community in relation to sediment geochemical and geophysical properties. Total phospholipid fatty acid (PLFA) analysis indicated that the greatest concentrations of microbial bio‐mass were in low‐permeability lacustrine sediments that also contained high concentrations of organic carbon. Community structure, based on lipid analyses and on in situ hybridization of bacterial cells with 16S RNA‐directed DNA probes, also revealed the presence of metabolically active bacteria that respire sulphate and/or Fe(III) in the lacustrine sediments. Concentrations of pore water sulphate were low (4–8 mg/L) and HCI‐extractable Fe was predominantly Fe(II) in the same samples where total biomass and organic carbon were highest. The low hydraulic conductivity (10‐6 to < 10‐9 cm/s) of these sediments has likely contributed to the long term maintenance of both bacteria and organic carbon by limiting the supply of soluble electron acceptors for microbial respiration. These results suggest that the current subsurface microbial population was derived from organisms that were present during lake sedimentation = 6–8 million years ago.
DNA‐based monitoring of total bacterial community structure in environmental samples
Authors: HOLBEN W. E. , HARRIS D.
Published: April 2008

Determining the structure of bacterial communities and their response to stimuli is key to understanding community function and the interactions that occur between microorganisms and the environment. However, bacterial communities often comprise complex assemblages of large numbers of different bacterial populations. An approach is presented which allows bacterial community structure to be determined by fractionation of the complex mixture of total bacterial community DNA using the DNA‐binding dye bisbenzimidazole which imposes G + C‐dependent changes in the buoyant density of DNA. Bacterial community structure presented as percentage of total DNA vs. percentage G + C content of DNA is an indication of the relative abundance of phylogenetic groups of bacteria. Changes in the composition of a soil bacterial community in response to perturbations in the form of carbon amendment and altered water status were monitored.
Molecules are more than markers: new directions in molecular microbial ecology
Authors: LENSKI R. E.
Published: April 2008

Macromolecules such as DNA, RNA, and proteins are widely used to quantify diversity in natural communities, to monitor the dispersal of organisms and their genes, and to trace phylogenetic relationships among organisms. With such widespread use of molecules as markers, it is easy to forget that they perform functions that are integral to the survival of organisms. The structural and functional properties of macromolecules have been intensively studied in genetics, biochemistry, and physiology. These fields, however, have not generally focused on the ecological significance of molecular variation, but instead have used defective variants as tools for identifying structure and function. Understanding the significance of molecular variation for organismal success or failure is a central problem in ecology, one whose solution will require the integration of diverse approaches and perspectives from ecology, molecular biology, genetics, physiology, and evolutionary biology. I review several studies of bacterial populations evolving in simple environments that have begun to integrate these approaches and perspectives in order to examine the consequences of molecular variation for ecological performance.
A phylogeographic survey of brook charr (Salvelinus fontinalis) in Algonquin Park, Ontario based upon mitochondrial DNA variation
Authors: DANZMANN R. G. , IHSSEN P. E.
Published: April 2008

Forty‐nine populations of brook charr (Salvelinus fontinalis) from Algonquin Park lakes and rivers were analysed for mitochondrial DNA variation. Haplotypic distributions of wild fish in the Algonquin Park region of Ontario, Canada, predominantly reflect postglacial dispersal patterns into the region in spite of substantial hatchery plantings. Two major refugial groupings colonized this region. Northern and eastern watersheds (Amable du Fond, Bonnechere, and northern Petawawa), were colonized primarily by haplotype 1 fish (B1 phylogenetic assemblage), while Oxtongue River, southern Petawawa, and York River populations were colonized predominately by fish from the B2 and A mtDNA phylogenetic assemblages. Fish with haplotypes in the A and B2 phylogenetic assemblages are common in the Lake Huron drainage. All watersheds in the Park drain into the Ottawa River, except the Oxtongue drainage (part of the Lake Huron watershed). This suggests that early glacial outflows south of the Algonquin Park region (Kirkfield‐Trent) may have been colonized by fish that initially invaded ‘Ontario island’ (south‐western Ontario), while fish which invaded northern Algonquin Park were derived from a different refugial grouping(s) which may have involved colonization both up the Ottawa River drainage, and/or from a more westerly (Mississippian) refugial grouping. A majority of the populations in Algonquin Park have been planted with hatchery reared brook charr since the 1940s. The Hills Lake or ‘Domestic’ strain was used almost exclusively for these plantings. Comparisons of mtDNA haplotypic distributions in hatchery and wild fish suggests that hatchery females had minimal spawning success and/or their progeny had poor survivorship in the wild.
Dynamics ofMhcevolution in birds and crocodilians: amplification of class II genes with degenerate primers
Authors: EDWARDS S. V. , GRAHN M. , POTTS W. K.
Published: April 2008

Genes of the major histocompatibility complex (Mhc) are the most polymorphic functional loci in mammalian populations, but little is known ofMhcvariability in natural populations of nonmammalian vertebrates. To help extend such studies to birds and relatives, we present a pair of degenerate primers that amplify polymorphic segments of one chain (the β chain) of the class II genes from the major histocompatibility complex (Mhc) of archosaurs (birds + crocodilians). The primers target two conserved regions lying within portions of the antigen‐binding site (ABS) encoded by the second exon and amplify multiple genes from both genomic DNA and cDNA. The pattern of nucleotide substitution in ABS codons of 51 sequences amplified and cloned from five species of passerine birds and an alligator (Alligator mississippiensis) indicates that archosaurian class II β genes are subject to selective forces similar to those operating in mammalian populations. Hybridization of a genomic clone generated by the primers revealed highly polymorphic bands in a sample of Florida scrub jays (Aphelocoma coerulescens coerulescens). Because the primers amplify only part of the ABS from multiple class II genes, they will be useful primarily for generating species specific clones, thereby providing a critical inroad to more detailed structural and evolutionary studies.
Mitochondrial DNA variation in Atlantic capelin, Mallotus villosus: a comparison of restriction and sequence analyses
Authors: BIRT T. P. , FRIESEN V. L. , BIRT R. D. , GREEN J. M. , DAVIDSON W. S.
Published: April 2008

Divergence estimates were calculated using restriction analysis and cytochrome‐b sequences for capelin Mallotus villosus mitochondrial genomes sampled from Newfoundland and Norwegian populations. On average, pairwise divergence values based on cytochrome‐b sequences were 2.7 times greater than those based on restriction data. Since the rate of evolution in the cytochrome‐b gene is low, it appears that restriction analysis underestimated divergence values, possibly due to limited sensitivity of this method when variable nucleotide positions are not randomly distributed. Mitochondrial genotypes were not shared among the two populations.
Distribution and abundance of trypanosome (subgenus Nannomonas) infections of the tsetse fly Glossina pallidipes in southern Africa
Authors: WOOLHOUSE M. E. J. , MCNAMARA J. J. , HARGROVE J. W. , BEALBY K. A.
Published: April 2008

Over 10000 Glossina pallidipes tsetse flies were collected during two field studies in the Zambezi Valley, Zimbabwe and one in the Luangwa Valley, Zambia. These were screened for mature trypanosome infections and 234 dot‐blot preparations were made of infected midguts, which were screened using DNA probes or PCR with primers specific to different species or types of the trypanosome subgenus Nannomonas. Over 70% of midgut infections were successfully identified as either Trypanosoma godfreyi, T. simiae or three types of T. congolense, savannah, riverine‐forest and Kilifi. The relative abundance of species and types did not vary significantly between study locations, habitat, season or tsetse age or sex, although there were differences between DNA probe and PCR results. Mixed species and/or mixed type infections were common and were more often detected using PCR. The distribution of infections among flies was highly aggregated, but there was no tendency for multiple infections to accumulate in older flies, implying that sequential superinfection may be uncommon. Possible explanations for these patterns are discussed.
Genetic differentiation of continental and island populations of Bombus terrestris (Hymenoptera: Apidae) in Europe
Authors: ESTOUP A. , SOLIGNAC M. , CORNUET J. M. , GOUDET J. , SCHOLL A.
Published: April 2008

Ten microsatellite loci and a partial sequence of the COII mitochondrial gene were used to investigate genetic differentiation in B. terrestris, a bumble bee of interest for its high‐value crop pollination. The analysis included eight populations from the European continent, five from Mediterranean islands (six subspecies altogether) and one from Tenerife (initially described as a colour form of B. terrestris but recently considered as a separate species, B. canariensis). Eight of the 10 microsatellite loci displayed high levels of polymorphism in most populations. In B. terrestris populations, the total number of alleles detected per polymorphic locus ranged from 3 to 16, with observed allelic diversity from 3.8 ± 0.5 to 6.5 ± 1.4 and average calculated heterozygosities from 0.41 ± 0.09 to 0.65 ± 0.07. B. canariensis showed a significantly lower average calculated heterozygosity (0.12 ± 0.08) and observed allelic diversity (1.5 ± 0.04) as compared to both continental and island populations of B. terrestris. No significant differentiation was found among populations of B. terrestris from the European continent. In contrast, island populations were all significantly and most of them strongly differentiated from continental populations. B. terrestris mitochondrial DNA is characterized by a low nucleotide diversity: 0.18%± 0.07%, 0.20%± 0.04% and 0.27%± 0.04% for the continental populations, the island populations and all populations together, respectively. The only haplotype found in the Tenerife population differs by a single nucleotide substitution from the most common continental haplotype of B. terrestris. This situation, identical to that of Tyrrhenian islands populations and quite different from that of B. lucorum (15 substitutions between terrestris and lucorum mtDNA) casts doubts on the species status of B. canariensis. The large genetic distance between the Tenerife and B. terrestris populations estimated from microsatellite data result, most probably, from a severe bottleneck in the Canary island population. Microsatellite and mitochondrial DNA data call for the protection of the island populations of B. terrestris against importation of bumble bees of foreign origin which are used as crop pollinators.