bluuebunny/crossref_metadata_2025 huggingface dataset:
Microsatellites identify depredated waterfowl remains from glaucous gull stomachs
Authors: SCRIBNER KIM T. , BOWMAN TIMOTHY D.
Published: March 2003

Prey remains can provide valuable sources of information regarding causes of predation and the species composition of a predator's diet. Unfortunately, the highly degraded state of many prey samples from gastrointestinal tracts often precludes unambiguous identification. We describe a procedure by which PCR amplification of taxonomically informative microsatellite loci were used to identify species of waterfowl predated by glaucous gulls (Larus hyperboreus). We found that one microsatellite locus unambiguously distinguished between species of the subfamily Anserinae (whistling ducks, geese and swans) and those of the subfamily Anatidae (all other ducks). An additional locus distinguished the remains of all geese and swan species known to nest on the Yukon–Kuskokwim delta in western Alaska. The study focused on two waterfowl species which have experienced precipitous declines in population numbers: emperor geese (Chen canagica) and spectacled eiders (Somateria fischeri). No evidence of predation on spectacled eiders was observed. Twenty‐six percent of all glaucous gull stomachs examined contained the remains of juvenile emperor geese.
African buffalo maintain high genetic diversity in the major histocompatibility complex in spite of historically known population bottlenecks
Authors: WENINK P. W. , GROEN A. F. , ROELKE‐PARKER M. E. , PRINS H. H. T.
Published: March 2003

Historical population collapses caused by rinderpest epidemics are hypothesized to have resulted in notable genetic losses in populations of the African buffalo. Polymorphism in the major histocompatibity complex (MHC) DRB3 gene was probed by means of restriction analysis of the sequence encoding the peptide‐binding region. Nucleotide substitution patterns agreed with a positive selection acting on this fitness‐relevant locus. Buffalo populations from four National Parks, situated in eastern and southern Africa, each revealed a surprisingly high allelic diversity. Current high levels of heterozygosity may be reconciled with historical bottlenecks by assuming that local extinctions were followed by fast recolonization, in accordance with the high dispersive capabilities of buffalo. The specific amplification of DRB3 alleles also enabled the assignment of individual genotypes. For each population sample a deficiency in the expected number of heterozygous animals was found. As overdominant selection on the MHC is predicted to yield an excess of heterozygous individuals, this may not be a locus‐specific effect. Several other explanations are discussed, of which increased homozygosity caused by nonrandom mating of buffalo in populations seems the most probable.
Microsatellite evidence for monogamy and sex‐biased recombination in the Western Australian seahorse Hippocampus angustus
Authors: JONES ADAM G. , KVARNEMO CHARLOTTA , MOORE GLENN I. , SIMMONS LEIGH W. , AVISE JOHN C.
Published: March 2003

Four polymorphic microsatellite loci were used to assess biological parentage of 453 offspring from 15 pregnant males from a natural population of the Western Australian seahorse Hippocampus angustus. Microsatellite genotypes in the progeny arrays were consistent with a monogamous mating system in which both females and males had a single mate during a male brooding period. Multilocus genotypes implicated four females in the adult population sample as contributors of eggs to the broods of collected males, but there was no evidence for multiple mating by females. Based on genotypic data from the progeny arrays, two loci were linked tightly and the recombination rate appeared to be ≈ 10‐fold higher in females than in males. The utility of linked loci for parentage analyses is discussed.
Population genetic structure, phylogeography and spawning philopatry in walleye (Stizostedion vitreum) from mitochondrial DNA control region sequences
Authors: STEPIEN CAROL A. , FABER JOSEPH E.
Published: March 2003

Mitochondrial (mt) DNA control region sequences were used to test the genetic and phylogeographic structure of walleye Stizostedion vitreum populations at different geographical scales: among spawning sites, lake basins, lakes, and putative glacial refugia in the Great Lakes region. Sequencing 199 walleye revealed nucleotide substitutions and tandemly repeated sequences that varied in copy number, as well as in sequence composition, in ≈ 1200 bp of the mtDNA control region. Variable numbers of copies of an 11‐bp tandem repeat showed no geographical patterning and were not used in further analyses. Substitutions in the other areas of the control region yielded 19 haplotypes, revealing phylogeographic structure and significant differences among glacial refugia, lakes, basins and some spawning sites. Differences among spawning populations were consistent with reduced gene flow, philopatry and possible natal homing. Analysis of spawning populations showed consistency of genotypic frequencies among years and between males and females, supporting philopatry in both sexes. The unglaciated plateau in southern Ohio, USA housed a very different haplotype that diverged prior to the Missouri, Mississippi and Atlantic glacial refugia types. Haplotypes from the three refugia colonized the Great Lakes after retreat of the Wisconsin glaciers, and their present distribution reflects the geography of their prior isolation and differential colonization. Populations that became associated with spawning localities appear to have diverged further due to philopatry, resulting in fine‐scale phylogeographic structuring.
Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum
Authors: PROVAN J. , RUSSELL J. R. , BOOTH A. , POWELL W.
Published: March 2003

In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum, which includes cultivated barley (H. vulgare ssp. vulgare) and its wild progenitor H. vulgare ssp. spontaneum. Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many crop species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.
Fine‐scale genetic structuring in a natural population of European wild rabbits (Oryctolagus cuniculus)
Authors: SURRIDGE A. K. , IBRAHIM K. M. , BELL D. J. , WEBB N. J. , RICO C. , HEWITT G. M.
Published: March 2003

The genetic structure of a free‐living tagged population of European wild rabbits (Oryctolagus cuniculus) was investigated for two consecutive years (1990 and 1991) using 10 polymorphic microsatellite loci. A specific social behaviour, the formation of stable breeding groups, influenced the genetic structure of the population. These breeding groups were shown to constitute genetically differentiated units with low levels of gene flow between them. The average relatedness among members of a social group was higher than within the population as a whole. As a result of female philopatry coupled with male‐biased natal dispersal, the relatedness of females was higher than that of males, both within social groups and in the whole population. Furthermore, the average relatedness of females within groups was twice the relatedness of females between groups. This study reveals marked fine‐scale, intrapopulation genetic structure, which is attributable to the social behaviour of the European wild rabbit.
The population genetic structure of a large temperate pollinator species,Bombus pascuorum(Scopoli) (Hymenoptera: Apidae)
Authors: WIDMER A. , SCHMID‐HEMPEL P.
Published: March 2003

The genetic population structure of the bumble beeBombus pascuorumwas studied using six microsatellite loci and a partial sequence of the mitochondrial gene cytochromeb. Eighteen populations from central and northern Europe were included in the analysis. Observed levels of genetic variability and heterozygosity were high. Estimates of population differentiation based onF‐ and Φ‐statistics revealed significant genetic differentiation amongB. pascuorumpopulations and suggest that two partially isolated gene pools, separated by the Alps, do exist. The distribution of mtDNA haplotypes supports this view and presents direct evidence for gene flow across the Alps. Estimates of the number of migrants exchanged among populations north of the Alps suggest that historical events may have left a strong imprint on population structure.
Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints
Authors: ISABEL NATHALIE , BEAULIEU JEAN , THÉRIAULT PHILIPPE , BOUSQUET JEAN
Published: March 2003

The relevance of using dominant random amplified polymorphic DNA (RAPD) fingerprints for estimating population differentiation was investigated when typically small population sample sizes were used. Haploid sexual tissues were first used to determine genotypes at RAPD loci for 75 eastern white pines (Pinus strobus L.) representing five populations. Dominant RAPD fingerprints were then inferred from genotypic data for each individual at each locus, and gene diversity estimates from both sources of data were compared. Genotypic information at RAPD loci indicated little or no differentiation among populations, similar to allozyme loci. However, estimates of population differentiation derived from dominant RAPD fingerprints according to various common methods of analysis were generally inflated, especially when all fragments were considered. Simulations showed that an increase in loci sampling and population sample sizes did not significantly alleviate the biases observed.
Genetic variation of Cryphonectria hypoviruses (CHV1) in Europe, assessed using restriction fragment length polymorphism (RFLP) markers
Authors: Allemann  , Hoegger  , Heiniger  , Rigling
Published: March 2003

A total of 72 hypovirus‐infected isolates of the chestnut blight fungus Cryphonectria parasitica were sampled from nine European countries between 1975 and 1997. The double‐stranded RNA of the Cryphonectria hypoviruses (CHV1) was isolated and reverse transcription (RT)–PCR products were obtained for two different regions of the viral genome (ORF A and ORF B) using primer sequences of the type species CHV1‐EP713. Both PCR products of each viral isolate were digested with four restriction endonucleases recognizing sequences of four nucleotides. The restriction fragment length polymorphism (RFLP) analysis revealed 41 genetically distinct RFLP types of CHV1 with 10 types occurring more than once. Identical RFLP types were detected nine times among viruses collected in the same location. Cluster analysis based on the RFLP banding patterns separated the viral isolates into five CHV1 clusters or subtypes. Most viral isolates (64 out of 72) grouped into one large cluster which comprised all viruses from Italy (including CHV1‐EP747), Switzerland, Crotia, Bosnia, Hungary, Greece, and the French island Corsica, as well as five out of 11 isolates from continental France. Two additional subtypes of CHV1 were found in France (one related to CHV1‐EP713) and one each in Spain and Germany. The Swiss samples collected over a period of 20 years showed that very little RFLP variation has evolved during this time. The results of this study are consistent with the hypothesis of multiple introductions of CHV1 into Europe.
Genetic detection of sex‐biased dispersal
Authors: Mossman C. A. , Waser P. M.
Published: March 2003

We investigated the application of a recently developed genetic test for sex bias in dispersal. This test determines an animal's ‘assignment index’ or the expected frequency of its genotype in the population in which it is captured. Low assignment indices indicate a low probability of being born locally. We investigated the use of this test with the white‐footed mouse, Peromyscus leucopus, in which dispersal is predominantly male‐biased, but not extreme. We found that male P. leucopus had significantly lower assignment indices than females. These data suggest that the genetic test for sex bias in dispersal has potential to be used with species that do not have extreme sex‐biased dispersal tendencies.
Genetic relationships of populations and the origins of new infestations of the Mediterranean fruit fly
Authors: He M. , Haymer D. S.
Published: March 2003

A polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach based on the variation in intron sequences of the glucose‐6‐phosphate dehydrogenase (Zw) gene was used to assess genetic variability in 26 populations and infestations of the Mediterranean fruit fly (medfly), Ceratitis capitata. Beginning with the exon‐primed intron‐crossing PCR (EPIC–PCR) method to amplify introns of this gene, five alleles were identified on the basis of DNA sequence variants. Several of these variants affect recognition sites for the restriction enzymes RsaI and TaqI. Using these enzymes in successive digestions of the EPIC‐PCR products, each of these alleles can be identified directly from individuals. From this, surveys were conducted to document genotypes and allele frequencies in these samples. The relationships of existing populations and the invasion process represented by new infestations of the medfly were analysed using a principal coordinate analysis and the amova method to quantify the distribution of genetic diversity at different levels in a hierarchical manner. From these results, a framework of genetic relationships among the populations and infestations is presented. In addition, for at least some of the infestations, populations that are probably acting as sources of origin have been identified.
Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus)
Authors: Worthington Wilmer J. , Allen P. J. , Pomeroy P. P. , Twiss S. D. , Amos W.
Published: March 2003

Microsatellites were used to conduct an extensive analysis of paternity of grey seals from two Scottish breeding colonies at North Rona (n = 1189) and the Isle of May (n = 694), spanning more than a decade. A maximum of 46% of pups at North Rona and 29% of pups at the Isle of May could be allocated a father, even though the majority of candidate males for specific study sites within each colony were believed to have been sampled. Based on the paternities which could be assigned, both colonies showed evidence of reproductive skew, apparently due to the presence of approximately five males who were exceptionally successful. Some males were assigned paternities at least 10 years before, and colleagues 10 years after, being sampled, implying a reproductive lifespan of at least 10 years, and there are indications that the real maximum lies in the range 15–20 years. Male grey seals appear to have at least two breeding strategies they can adopt. On land, some males benefit from a traditionally polygynous system. However, between 50 and 70% of grey seal pups born at a particular colony are not fathered by males who are likely to be sampled by us, implying that these males seldom venture ashore here. We conclude that aquatic mating may play a much larger role in the grey seal than has previously been thought.
Rangewide variation of the maritime pine bast scale Matsucoccus feytaudi Duc. (Homoptera: Matsucoccidae) in relation to the genetic structure of its host
Authors: Burban C. , Petit R. J. , Carcreff E. , Jactel H.
Published: March 2003

The bast scale Matsucoccus feytaudi is a specific pest of maritime pine, but the damage inflicted by the insect on the host trees is variable, ranging from no apparent effect to severe decline of the maritime pine stands. Rangewide variation of mitochondrial DNA among M. feytaudi populations was analysed by polymerase chain reaction–restriction fragment length–single‐strand conformation polymorphism (PCR–RFLP–SSCP) analysis and the results compared with the genetic information already available for its host. Three main nonoverlapping lineages can be distinguished in M. feytaudi. The phylogeography of the pest population is clearly related to the history of its host. Most local associations could result from common evolution while others must be interpreted as intraspecific host shifts. Because the distribution of cultivated tree species is greatly influenced by humans, much may be learned concerning their genetic structure from the indirect study of their specific pests.
Small effective population size in the long‐toed salamander
Authors: Funk W. Chris , Tallmon David A. , Allendorf Fred W.
Published: March 2003

The effective population sizes (Ne) of six populations of the long‐toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 ± 79); one estimate was indistinguishable from infinity. In order to infer the actual Ne of salamander populations, we compared the frequency distribution of our observed Ne estimates with distributions obtained from simulated populations of known Ne. Our observed Ne estimate distribution was consistent with distributions from simulated populations with Ne values of 10, 25, and 50, suggesting an actual Ne for each of the six salamander populations of less than 100. This Ne estimate agrees with most other Ne estimates for amphibians. We conclude by discussing the conservation implications of small Ne values in amphibians in the context of increasing isolation of populations due to habitat fragmentation.
Evolutionary transition from single to multiple mating in fungus‐growing ants
Authors: Villesen P. , Gertsch P. J. , Frydenberg J. , Mueller U. G. , Boomsma J. J.
Published: March 2003

Queens of leafcutter ants exhibit the highest known levels of multiple mating (up to 10 mates per queen) among ants. Multiple mating may have been selected to increase genetic diversity among nestmate workers, which is hypothesized to be critical in social systems with large, long‐lived colonies under severe pressure of pathogens. Advanced fungus‐growing (leafcutter) ants have large numbers (104–106workers) and long‐lived colonies, whereas basal genera in the attine tribe have small (< 200 workers) colonies with probably substantially shorter lifespans. Basal attines are therefore expected to have lower queen mating frequencies, similar to those found in most other ants. We tested this prediction by analysing queen mating frequency and colony kin structure in three basal attine species:Myrmicocrypta ednaella,Apterostigma collareandCyphomyrmex longiscapus. Microsatellite marker analyses revealed that queens in all three species were single mated, and that worker‐to‐worker relatedness in these basal attine species is very close to 0.75, the value expected under exclusively single mating. Fungus growingper sehas therefore not selected for multiple queen mating. Instead, the advanced and highly productive social structure of the higher attine ants, which is fully dependent on the rearing of an ancient clonal fungus, may have necessitated high genetic diversity among nestmate workers. This is not the case in the lower attines, which rear fungi that were more recently derived from free‐living fungal populations.
Genetic structure of brown trout, Salmo trutta L., at the southern limit of the distribution range of the anadromous form
Authors: Bouza C. , Arias J. , Castro J. , Sánchez L. , Martínez P.
Published: March 2003

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Miño, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.
Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre‐Pleistocene vicariance of an open forest species from eastern Australia
Authors: James C. H. , Moritz C.
Published: March 2003

The eastern sedge frog Litoria fallax (Anura: Hylidae) is common throughout the open forests and coastal wetlands along the eastern coast of Australia. Its range spans four biogeographical zones from northern Queensland to central New South Wales. Phylogenetic analysis of mitochondrial DNA (mtDNA) haplotypes of 87 L. fallax individuals from 22 populations identified two major mtDNA lineages, differing by 11–12% sequence divergence. The two clades of haplotypes were separated by the McPherson Range, indicating that this mesic upland area has acted as a major long‐term barrier to gene flow for this open forest species. Slight isolation by distance was observed within both the northern and southern lineages but was insufficient to explain the large sequence divergence between lineages. Within the northern lineage, additional phylogeographical structure was observed across the relatively dry Burdekin Gap which separates Atherton populations from all populations in the central and eastern Queensland biogeographical zones. There was less phylogeographical structure in the southern lineage suggesting historical gene flow across the drier portions of the Great Dividing Range. These data, together with recent observations of deep phylogeographical divergences in rainforest‐restricted Litoria suggest that the east coast hylids of Australia represent an old (Tertiary) radiation. Individual species of Litoria have been strongly affected by climatic and ecological barriers to gene flow during the Quaternary.
A population genetic analysis of migration: the case of the noctule bat (Nyctalus noctula)
Authors: Petit Eric , Mayer Frieder
Published: March 2003

Although rarely assessed, the population genetics of hibernating colonies can help to understand some aspects of population structure, even when samples from nursery or mating colonies are not available, or in studies of migration when both types of samples are available and can be compared. Here we illustrate both points in a survey of mitochondrial DNA (mtDNA) control region sequences used to study the population genetics of hibernating colonies of a migrating species, the noctule bat (Nyctalus noctula). Lacking samples from Scandinavian nursery colonies, we use a North European hibernacula to suggest that Scandinavian populations are isolated from Central and East European colonies. Then, we compare genetic diversities of nursery and hibernating colonies. We find a significantly higher haplotype diversity in hibernacula, confirming that they consist of individuals from different nursery colonies. Finally, we show that pairwise comparisons of the haplotype frequencies of nursery and hibernating colonies contain some information on the migration direction of the noctule bat.
Do hornets have zombie workers?
Authors: Foster Kevin R. , Ratnieks Francis L. W. , Raybould Alan F.
Published: March 2003

Colonies of the European hornet,Vespa crabro, are typically founded by a single queen mated to a single male.From the resulting colony relatedness pattern we predicted strong worker–queen conflict over male production where both the workers and the queen attempt to produce the colony’s males. To test for this conflict, male production was studied in 15 hornet nests using a combination of DNA microsatellite analysis (282 males), worker ovary dissections (500 workers from eight nests) and 50 h of observation (four nests). In contrast to our prediction, the data show that hornet males are queens’ sons, that workers never attempt to lay eggs, rarely have activated ovaries, and that there is no direct aggression between the queen and the workers. This contrasts with other data for vespine wasps, which support relatedness predictions.Dolichovespula arenariahas the same kin structure asV. crabroand workers produce males in many colonies. The similarity between these two species makes it difficult to explain why workers do not reproduce inV. crabro. Self‐restraint is expected if worker reproduction significantly reduces colony productivity but there is no obvious reason why this should be important toV. crabrobut not toD. arenaria. Alternatively, queen control may be important. The absence of expressed queen–worker conflict rules out physical control. Indirect pheromonal control is a possibility and is supported by the occurrence of royal courts and queen pheromone inVespabut notDolichovespula. Pheromonal queen control is considered evolutionarily unstable, but could result from a queen–worker arms race over reproductive control in which the queen is ahead. The genetic data also revealed diploid males in one colony, the first example in the vespine wasps, and two colonies with double matrilines, suggesting that occasional usurpation by spring queens occurs.
Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences
Authors: Johnson Jerald B. , Jordan Steve
Published: March 2003

We examined intra‐specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Inter‐population sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out‐group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.
Genetic compatibility, mate choice and patterns of parentage: Invited Review
Authors: Tregenza T. , Wedell N.
Published: March 2003

There is growing interest in the possibility that genetic compatibility may drive mate choice, including gamete choice, particularly from the perspective of understanding why females frequently mate with more than one male. Mate choice for compatibility differs from other forms of choice for genetic benefits (such as ‘good genes’) because individuals are expected to differ in their mate preferences, changing the evolutionary dynamics of sexual selection. Recent experiments designed to investigate genetic benefits of polyandry suggest that mate choice on the basis of genetic compatibility may be widespread. However, in most systems the mechanisms responsible for variation in compatibility are unknown. We review potential sources of variation in genetic compatibility and whether there is any evidence for mate choice driven by these factors. Selfish genetic elements appear to have the potential to drive mate compatibility mate choice, though as yet there is only one convincing example. There is abundant evidence for assortative mating between populations in hybrid zones, but very few examples where this is clearly a result of selection against mating with genetically less compatible individuals. There are also numerous cases of inbreeding avoidance, but little evidence that mate choice or differential fertilization success driven by genetic compatibility occurs between unrelated individuals. The exceptions to this are a handful of situations where both the alleles causing incompatibility and the alleles involved in mate choice are located in a chromosome region where recombination is suppressed. As yet there are only a few potential sources of genetic compatibility which have clearly been shown to drive mate choice. This may reflect limitations in the potential for the evolution of mate choice for genetic compatibility within populations, although the most promising sources of such incompatibilities have received relatively little research.
Patterns of variation at a mitochondrial sequence‐tagged‐site locus provides new insights into the postglacial history of European Pinus sylvestris populations
Authors: Soranzo N. , Alia R. , Provan J. , Powell W.
Published: March 2003

Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost ‘ideal’ tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction–restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence‐tagged‐site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (ΦST = 0.59; P ≤ 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.
Complex social organization reflects genetic structure and relatedness in the cooperatively breeding bell miner,Manorina melanophrys
Authors: Painter J. N. , Crozier R. H. , Poiani A. , Robertson R. J. , Clarke M. F.
Published: March 2003

The cooperatively breeding bell miner,Manorina melanophrys, differs from most other cooperative breeding species in the complexity of its social system, where discrete social organization occurs on at least three levels. Microsatellite markers were used to investigate the degree of genetic structure underlying the social organization ofM. melanophrysby comparing colonies, coteries and nest contingents. The genetic data confirmed behavioural observations ofM. melanophrysliving in male kin‐based groups between which females disperse short distances to breed. Estimates ofFSTrevealed restricted gene flow between eight colonies located within 30 km that was significantly associated with geographical distance when the two most distant colonies were included. Within a high density colony significant differences were found between coteries; analysis of the degree of relatedness between coterie members showed that this is due to related individuals associating preferentially with each other. Similarly, the contingent of individuals attending a nest were generally close relatives of the young they were aiding, supporting models invoking kin selection as the selective agency mediating helping.
Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern European countries
Authors: Fineschi S. , Taurchini D. , Villani F. , Vendramin G. G.
Published: March 2003

The distribution of haplotypic diversity of 38 European chestnut (Castanea sativa Mill.) populations was investigated by PCR/RFLP analysis of regions of the chloroplast and mitochondrial genomes in order to shed light on the history of this heavily managed species. The rapid expansion of chestnut starting from 3000 years ago is strongly related to human activities such as agricultural practice. This demonstrates the importance of human impact, which lasted some thousands of years, on the present‐day distribution of the species. No polymorphism was detected for the single mitochondrial analysed region, while a total of 11 different chloroplast (cp) haplotypes were scored. The distribution of the cpDNA haplotypes revealed low geographical structure of the genetic diversity. The value of population subdivision, as measured by GSTc, is strikingly lower than in the other species of the family Fagaceae investigated. The actual distribution of haplotypic diversity may be explained by the strong human impact on this species, particularly during the Roman civilization of the continent, and to the long period of cultivation experienced during the last thousand years.
A universal molecular method for identifying underground plant parts to species
Authors: Linder C. R. , Moore L. A. , Jackson R. B.
Published: March 2003

As part of a large project to determine rooting depth and resource uptake on the Edwards Plateau of central Texas, we developed a DNA‐based technique that allows the below‐ground parts of all plants to be identified to the level of genus and usually to species. Identification is achieved by comparing DNA sequences of the internal transcribed spacer (ITS) region of the 18S–26S nuclear ribosomal DNA repeat, derived from below‐ground plant material, with a reference ITS region database for plants at a site. The method works throughout plants because the plant ITS region can be PCR amplified using a set of universal primers. Congeneric species can usually be identified because the ITS region evolves relatively rapidly. In our study, all roots were easily identified to the level of genus; most congeneric species were identified solely by ITS sequence differences but some required a combination of ITS sequence data and above‐ground surveys of species at a site. In addition to showing the feasibility and efficacy of our technique, we compare it with another DNA‐based technique used to identify below‐ground plant parts. Finally, we also describe a DNA extraction and purification technique that reliably provides high‐quality DNA of sufficient quantity from roots so that PCR can be readily accomplished. Our technique should allow the below‐ground parts of plants in any system to be identified and thereby open new possibilities for the study of below‐ground plant communities.
Ericoid mycorrhizal fungi are common root associates of a Mediterranean ectomycorrhizal plant (Quercus ilex)
Authors: Bergero R. , Perotto S. , Girlanda M. , Vidano G. , Luppi A. M.
Published: March 2003

Mycorrhiza samples of neighbouring Quercus ilex and Erica arborea plants collected in a postcutting habitat were processed to see whether plants differing in mycorrhizal status harbour the same root endophytes. Three experiments were performed in parallel: (i) isolation, identification and molecular characterization of fungi from surface‐sterilized roots of both plant species; (ii) re‐inoculation of fungal isolates on axenic E. arborea and Q. ilex seedlings; (iii) direct inoculation of field‐collected Q. ilex ectomycorrhizas onto E. arborea seedlings. About 70 and 150 fungal isolates were obtained from roots of Q. ilex and E. arborea, respectively. Among them, Oidiodendron species and five cultural morphotypes of sterile isolates formed typical ericoid mycorrhizas on E. arborea in vitro. Fungi with such mycorrhizal ability were derived from both host plants. Isolates belonging to one of these morphotypes (sd9) also exhibited an unusual pattern of colonization, with an additional extracellular hyphal net. Ericoid mycorrhizas were also readily obtained by direct inoculation of E. arborea seedlings with Q. ilex ectomycorrhizal tips. Polymerase chain–restriction fragment length polymorphism and random amplified polymorphic DNA analyses of the shared sterile morphotypes demonstrate, in the case of sd9, the occurrence of the same genet on the two host plants. These results indicate that ericoid mycorrhizal fungi associate with ectomycorrhizal roots, and the ecological significance of this finding is discussed.
Multi‐locus genetic evidence for rapid ecologically based speciation in Daphnia
Authors: Pfrender M. E. , Spitze K. , Lehman N.
Published: March 2003

The process of speciation involves the divergence of two or more subpopulations of a parent species into independent evolutionary trajectories. To study this process in natural populations requires a detailed knowledge of the genetic and ecological characteristics of the parent species and an understanding of how its populations can lose evolutionary cohesion. The cosmopolitan and speciose genus Daphnia provides many of these features by existing in multiple freshwater habitat types, particularly permanent lakes and temporary ponds, each of which presents distinct ecological challenges. We assayed the genetic composition of 20 temporary pond populations of members of the Daphnia pulex species complex in north‐western Oregon and compared them to published data on related lake and pond populations. We collected molecular genetic data from 13 allozyme loci, from six microsatellite loci, and from the control region of the mitochondrial DNA. By assaying over 400 individual Daphnia for these data, we were able to compile composite genotypes not only of individual Daphnia but of each pond population as a whole. In these ponds, we discovered two distinct genotypic constellations, one which bears resemblance to the lake‐dwelling taxon D. pulicaria, and one which bears resemblance to the pond‐dwelling taxon, D. pulex. Using published genetic data from these and other species as a frame of reference, we characterized 13 of these ponds as being ‘pond‐like’, three as being ‘lake‐like’, and four as being ‘mixed’. Unlike studies performed elsewhere, however, these ponds do not exhibit high probabilities of interspecific hybridization. Over 95% of all individuals have either a lake‐like or a pond‐like genotype at all three genetic systems, suggesting the two forms do not represent hybridized vs. nonhybridized genotypes. Because both types can be found in the same ponds at the same time in gametic disequilibrium, we also discount the possibility that they are two extremes of a single species that is highly genetically subdivided. With these genetic data, and with supporting life‐history and ecological data previously gathered on these pond populations, we conclude that the most likely description of this system is of a taxon caught in the act of speciating, with new pond‐adapted populations periodically stemming from lake‐adapted sources during river flooding events.
SSCP is not so difficult: the application and utility of single‐stranded conformation polymorphism in evolutionary biology and molecular ecology
Authors: Sunnucks P. , Wilson A. C. C. , Beheregaray L. B. , Zenger K. , French J. , Taylor A. C.
Published: March 2003

All genetic markers are estimators of DNA nucleotide sequence variation. Rather than obtaining DNA sequence data, it is cheaper and faster to use techniques that estimate sequence variation, although this usually results in the loss of some information. SSCP (single‐stranded conformation polymorphism) offers a sensitive but inexpensive, rapid, and convenient method for determining which DNA samples in a set differ in sequence, so that only an informative subset need be sequenced. In short, most DNA sequence variation can be detected with relatively little sequencing. SSCP has been widely applied in medical diagnosis, yet few studies have been published in population genetics. The utility and convenience of SSCP is far from fully appreciated by molecular population biologists. We hope to help redress this by illustrating the application of a single simple SSCP protocol to mitochondrial genes, nuclear introns, microsatellites, and anonymous nuclear sequences, in a range of vertebrates and invertebrates.
Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations
Authors: Walter R. , Epperson B. K.
Published: March 2003

Genetic diversity is low in natural populations of red pine, Pinus resinosa, a species that has a vast range across north‐eastern North America. In this study, we examined 10 chloroplast microsatellite or simple sequence repeats (cpSSR) loci in 136 individuals from 10 widespread populations. Substantial variation for the cpSSR loci was observed in the study populations. The contrast with red pine’s lack of variation for other types of loci is likely to be due to the higher mutation rates typical of SSR loci. The amount of variation is lower than that generally found for cpSSR loci in other pine species. In addition, the variation exhibits a striking geographical pattern. Most of the genetic diversity is among populations, with little within populations, indicating substantial isolation of and genetic drift within many populations in the southern half of the species distribution. The greatest diversity now occurs in the north‐eastern part of New England, which is especially intriguing because this entire area was glaciated. Thus the centre of diversity cannot be the origin of postglacial populations, rather it is likely caused by admixture, most probably because of influences from two separate refugia. Furthermore, the pattern indicates that the spread of red pine since the last glaciation is rather more complex than usually described, and it likely includes more than one refugia, complex migration routes, and postglacial‐retreat isolation and genetic drift among shrinking populations in regions of the present southern range.
Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers
Authors: Sætre Glenn‐Peter , Borge Thomas , Lindell Johan , Moum Truls , Primmer Craig R. , Sheldon Ben C. , Haavie Jon , Johnsen Arild , Ellegren Hans
Published: March 2003

Evolutionary history of Muscicapidae flycatchers is inferred from nuclear and mitochondrial DNA (mtDNA) sequence comparisons and population genetic analysis of nuclear and mtDNA markers. Phylogenetic reconstruction based on sequences from the two genomes yielded similar trees with respect to the order at which the species split off. However, the genetic distances fitted a nonlinear, polynomial model reflecting diminishing divergence rate of the mtDNA sequences compared to the nuclear DNA sequences. This could be explained by Haldane’s rule because genetic isolation might evolve more rapidly on the mitochondrial rather than the nuclear genome in birds. This is because hybrid sterility of the heterogametic sex (females) would predate that of the homogametic sex (males), leading to sex biased introgression of nuclear genes. Analyses of present hybrid zones of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) may indicate a slight sexual bias in rate of introgression, but the introgression rates were too low to allow proper statistical analyses. It is suggested, however, that the observed deviation from linearity can be explained by a more rapid mutational saturation of the mtDNA sequences than of the nuclear DNA sequences, as supported by analyses of third codon position transversions at two protein coding mtDNA genes. A phylogeographic scenario for the black and white flycatcher species is suggested based on interpretation of the genetic data obtained. Four species appear to have diverged from a common ancestor relatively simultaneously during the Pleistocene. After the last glaciation period, pied and collared flycatchers expanded their breeding ranges and eventually came into secondary contact in Central and Eastern Europe and on the Baltic Isles.
Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci
Authors: Collevatti Rosane G. , Grattapaglia Dario , Hay John D.
Published: March 2003

We report the population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at 10 microsatellite loci. Additionally, we compare heterozygosity and inbreeding estimates for continuous and fragmented populations and discuss the consequences for conservation. For a total of 314 individuals over 10 populations, the number of alleles per locus ranged from 20 to 27 and expected and observed heterozygosity varied from 0.129 to 0.924 and 0.067 to 1.000, respectively. Significant values of θ and RST showed important genetic differentiation among populations. θ was much lower than RST, suggesting that identity by state and identity by descent have diverged in these populations. Although a significant amount of inbreeding was found under the identity by descent model (f = 0.11), an estimate of inbreeding for microsatellite markers based on a more adequate stepwise mutation model showed no evidence of nonrandom mating (RIS = 0.04). Differentiation (pairwise FST) was positively correlated with geographical distance, as expected under the isolation by distance model. No effect of fragmentation on heterozygosity or inbreeding could be detected. This is most likely due to the fact that Cerrado fragmentation is a relatively recent event (~60 years) compared to the species life cycle. Also, the populations surveyed from both fragmented and disturbed areas were composed mainly of adult individuals, already present prior to ecosystem fragmentation. Adequate hypothesis testing of the effect of habitat fragmentation will require the recurrent analysis of juveniles across generations in both fragmented and nonfragmented areas.