bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in clonal diversity in glasshouse infestations of the aphid, Aphis gossypii Glover in southern France
Authors: Fuller S. J. , Chavigny P. , Lapchin L. , Vanlerberghe‐Masutti F.
Published: March 2003

Aphis gossypii is an aphid species that is found throughout the world and is extremely polyphagous. It is considered a major pest of cotton and cucurbit species. In Europe, A. gossypii is assumed to reproduce exclusively by apomictic parthenogenesis. The present study investigates the genetic diversity of A. gossypii in a microgeographic, fragmented habitat consisting of eight glasshouses of cucurbit crops. This analysis, which was based on the results from seven microsatellite loci, has confirmed that A. gossypii populations in southern France are primarily asexual, as only 12 nonrecombinant genotypic classes (clones) were identified from 694 aphids. Moreover, a high proportion of the aphids (87%) had one of three common genotypes. No significant correlation was found between genotypic class and host plant species. Within a glasshouse population of A. gossypii, a significant reduction in clonal diversity was observed as the spring/summer season progressed. The final predominance of a clone could result from interclonal competition. At the microgeographic level (i.e. glasshouses within a 500‐m radius), significant genetic subdivision was detected and could be attributed to founder effects and the limitation of gene flow imposed by the enclosed nature of the glasshouse structure. Finally, the three common clones of A. gossypii detected in 1996 reappeared in spring 1997 following the winter extinction, together with rare clones that had not previously been seen. The probability that A. gossypii overwinters within refuges at a microgeographic scale from which populations are renewed each spring is discussed.
Species‐specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae)
Authors: Blomster J. , Hoey E. M. , Maggs C. A. , Stanhope M. J.
Published: March 2003

The green seaweeds Enteromorpha intestinalis and E. compressa are important fouling organisms commonly found in polluted and nutrient‐enriched marine and brackish water habitats, where they are used in environmental monitoring. Discrimination of the two species is extremely difficult because of overlapping morphological characters. In this study a quick molecular method for species identification was developed based on the nuclear rDNA ITS2 sequence data of 54 E. intestinalis samples and 20 E. compressa samples from a wide geographical range. Oligonucleotide probes were designed for species‐specific hybridization to dot‐blots of the PCR‐amplified ITS1, 5.8S gene and ITS2 fragment of both E. intestinalis and E. compressa. Specificity of the oligonucleotide probes was confirmed by tests with taxonomically diverse species that could morphologically be confused with E. intestinalis or E. compressa. This is the first use of species‐specific probes for macroalgae. The restriction endonuclease NruI digested specifically the amplified PCR product from E. compressa into two fragments detectable on agarose gels, but no suitable restriction sites were identifiable in the PCR product of E. intestinalis.
Molecular tracking of mountain lions in the Yosemite Valley region in California: genetic analysis using microsatellites and faecal DNA
Authors: Ernest H. B. , Penedo M. C. T. , May B. P. , Syvanen M. , Boyce W. M.
Published: March 2003

Twelve microsatellite loci were characterized in California mountain lions (Puma concolor) and sufficient polymorphism was found to uniquely genotype 62 animals sampled at necropsy. Microsatellite genotypes obtained using mountain lion faecal DNA matched those from muscle for all of 15 individuals examined. DNA from potential prey species and animals whose faeces could be misidentified as mountain lion faeces were reliably distinguished from mountain lions using this microsatellite panel. In a field application of this technique, 32 faecal samples were collected from hiking trails in the Yosemite Valley region where seven mountain lions previously had been captured, sampled, and released. Twelve samples yielded characteristic mountain lion genotypes, three displayed bobcat‐type genotypes, and 17 did not amplify. The genotype of one of the 12 mountain lion faecal samples was identical to one of the mountain lions that previously had been captured. Three of the 12 faecal samples yielded identical genotypes, and eight new genotypes were detected in the remaining samples. This analysis provided a minimum estimate of 16 mountain lions (seven identified by capture and nine identified by faecal DNA) living in or travelling through Yosemite Valley from March 1997 to August 1998. Match probabilities (probabilities that identical DNA genotypes would be drawn at random a second time from the population) indicated that the samples with identical genotypes probably came from the same mountain lion. Our results demonstrate that faecal DNA analysis is an effective method for detecting and identifying individual mountain lions.
Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I
Authors: García‐Martínez J. , Rodríguez‐Valera F.
Published: March 2003

The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S–23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro‐organisms. In terms of community structure, our results show that although depth‐related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface‐associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well‐defined taxonomic units.
Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting
Authors: Hansson B. , Bensch S. , Hasselquist D. , Lillandt B.‐G. , Wennerberg L. , Von Schantz T.
Published: March 2003

Genetic similarity within pairs of individuals was examined using both 10 polymorphic microsatellite loci and multi‐locus DNA fingerprinting profiles in a semi‐isolated population of great reed warblers at Lake Kvismaren, south Central Sweden, in 1987–1993. The population was founded by a few individuals in 1978, followed by a gradual increase in numbers until 1988, since when the population has remained relatively stable with about 60 breeding birds. We have previously found that high genetic similarity between pair‐mates in the population during the early part of the study period reduced egg hatching success, and hence reproductive success. The measures of pairwise genetic similarity, microsatellite allele sharing and DNA fingerprinting band sharing, were highly correlated with pedigree‐based relatedness. Both microsatellite and DNA fingerprinting similarities between pair‐mates declined significantly over the study period, and the pattern was most pronounced in the DNA fingerprinting data. Analyses restricted to the microsatellite data showed that the average annual microsatellite similarity between pairwise combinations of individuals, as well as individual homozygosity in males, declined significantly over the study period, and that several immigrants carrying novel alleles entered the population during the study. Hence, the temporal decline in genetic similarity of mates in the population is probably a consequence of increased immigration, facilitated by the recent expansion of the species in the region. These results suggest that the population has now recovered genetically, or is in the process of recovering, from a recent founder event.
The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris
Authors: Giannasi Nicholas , Thorpe Roger S. , Malhotra Anita
Published: March 2003

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.
Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling
Authors: James Timothy Y. , Vilgalys Rytas
Published: March 2003

Selective spore trapping and molecular genotyping methods were employed to examine potential long‐distance gene flow among Caribbean populations of the common mushroom Schizophyllum commune. Spore‐trap samples from five locations were analysed using restriction fragment polymorphisms of five enzymatically amplified gene regions. Successful trappings suggested S. commune spores to be abundant in the air, with an estimated sedimentation rate of ≈ 18 spores/m2/h. High levels of genetic diversity characterized the spore‐trap samples, with as many as 12 alleles observed at a single locus (chitin synthase) over all samples. In addition, spore‐trap samples showed significant among sample heterogeneity including geographical population substructure. The ribosomal DNA (rDNA) intergenic spacer displayed the greatest allele frequency differences among samples, clearly separating the samples into those possessing only a South American‐type allele and those segregating for both North and South American‐type alleles. The molecular variation provided no clear evidence for dispersal over large, aquatic barriers within the Caribbean region, and instead suggested that spore‐trapping experiments are primarily reflective of the local, established population.
Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spiderAptostichus simus
Authors: Bond J. E. , Hedin M. C. , Ramirez M. G. , Opell B. D.
Published: March 2003

Aptostichus simusis a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6–12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations ofA. simusdepends upon the species concept utilized. If a time‐limited genealogical perspective is employed,A. simuswould be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.
Diamondback moth compensatory consumption of protease inhibitor‐transformed plants
Authors: Winterer Juliette , Bergelson Joy
Published: March 2003

Prior study of the effect of protease inhibitors (PIs) on diamondback moths suggests that moths are resistant to them, so PIs represent an ineffective defence against moths. However, our data suggest that diamondback moths do suffer lower growth rates when they consume plants transformed with potato protease inhibitor (PI2), but that effect is hidden by compensatory consumption. Plants, instead of gaining an advantage by lowering the insect growth rate, suffer a disadvantage as moths consume more tissue to mitigate the effect. Furthermore, PI2, when used in conjunction with another transgenic pesticidal protein, Bt (from Bacillus thuringiensis) counteracts the effectiveness of Bt at protecting plant tissue. Thus, transgenic PIs are not only less effective than previously thought in protecting Brassica plants from diamondback moths, they may actually lead to increased plant damage by the moths.
Genetic characterization of hybridization and introgression between anadromous rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki)
Authors: Young William P. , Ostberg Carl O. , Keim Paul , Thorgaard Gary H.
Published: March 2003

Interspecific hybridization represents a dynamic evolutionary phenomenon and major conservation problem in salmonid fishes. In this study we used amplified fragment length polymorphisms (AFLP) and mitochondrial DNA (mtDNA) markers to describe the extent and characterize the pattern of hybridization and introgression between coastal rainbow trout (Oncorhynchus mykiss irideus) and coastal cutthroat trout (O. clarki clarki). Hybrid individuals were initially identified using principle coordinate analysis of 133 polymorphic AFLP markers. Subsequent analysis using 23 diagnostic AFLP markers revealed the presence of F1, rainbow trout backcross, cutthroat trout backcross and later‐generation hybrids. mtDNA analysis demonstrated equal numbers of F1 hybrids with rainbow and cutthroat trout mtDNA indicating reciprocal mating of the parental types. In contrast, rainbow and cutthroat trout backcross hybrids always exhibited the mtDNA from the recurrent parent, indicating a male hybrid mating with a pure female. This study illustrates the usefulness of the AFLP technique for generating large numbers of species diagnostic markers. The pattern of hybridization raises many questions concerning the existence and action of reproductive isolating mechanisms between these two species. Our findings are consistent with the hypothesis that introgression between anadromous populations of coastal rainbow and coastal cutthroat trout is limited by an environment‐dependent reduction in hybrid fitness.
Microsatellite variation and fine‐scale population structure in the wood frog (Rana sylvatica)
Authors: Newman Robert A. , Squire Tina
Published: March 2003

We investigated genetic population structure in wood frogs (Rana sylvatica) from a series of Prairie Pothole wetlands in the northern Great Plains. Amphibians are often thought to exist in demographic metapopulations, which require some movement between populations, yet genetic studies have revealed strong subdivision among populations, even at relatively fine scales (several km). Wood frogs are highly philopatric and studies of dispersal suggest that they may exhibit subdivision on a scale of ≈ 1–2 km. We used microsatellites to examine population structure among 11 breeding assemblages separated by as little as 50 m up to ≈ 5.5 km, plus one population separated from the others by 20 km. We found evidence for differentiation at the largest distances we examined and among a few neighbouring ponds, but most populations were strikingly similar in allele frequencies, suggesting high gene flow among all but the most distant populations. We hypothesize that the few significant differences among neighbouring populations at the finest scale may be a transient effect of extinction–recolonization founder events, driven by periodic drying of wetlands in this hydrologically dynamic landscape.
Microsatellite variation in naturalDrosophila melanogasterpopulations from New South Wales (Australia) and Tasmania
Authors: Agis M. , Schlötterer C.
Published: March 2003

Microsatellite variation was studied at 48 microsatellite loci in 10Drosophila melanogasterpopulations to investigate the population structure on the Australian east coast. Low, but statistically significant population differentiation was observed among most populations. The populations on the Australian mainland did not show evidence for isolation by distance. We conclude that the population structure ofD. melanogasteron the Australian mainland is probably the result of a shared history (recent colonization). The observed differences between localD. melanogasterpopulations probably reflect variation in effective population sizes rather than patterns of gene flow. Two populations from Tasmania were more differentiated from the Australian mainland than a population from Israel, raising the question whether they are derived from the Australian mainland or colonized from a different source population.
Hierarchical genetic structure of the introduced wasp Vespula germanica in Australia
Authors: Goodisman Michael A. D. , Matthews Robert W. , Crozier Ross H.
Published: March 2003

The wasp Vespula germanica is a highly successful invasive pest. This study examined the population genetic structure of V. germanica in its introduced range in Australia. We sampled 1320 workers and 376 males from 141 nests obtained from three widely separated geographical areas on the Australian mainland and one on the island of Tasmania. The genotypes of all wasps were assayed at three polymorphic DNA microsatellite markers. Our analyses uncovered significant allelic differentiation among all four V. germanica populations. Pairwise estimates of genetic divergence between populations agreed with the results of a model‐based clustering algorithm which indicated that the Tasmanian population was particularly distinct from the other populations. Within‐population analyses revealed that genetic similarity declined with spatial distance, indicating that wasps from nests separated by more than ~25 km belonged to separate mating pools. We suggest that the observed genetic patterns resulted from frequent bottlenecks experienced by the V. germanica populations during their colonization of Australia.
Geographical and genetic distances among zooplankton populations in a set of interconnected ponds: a plea for using GIS modelling of the effective geographical distance
Authors: Michels E. , Cottenie K. , Neys L. , De Gelas K. , Coppin P. , De Meester L.
Published: March 2003

In systems of interconnected ponds or lakes, the dispersal of zooplankton may be mediated by the active population component, with rivulets and overflows functioning as dispersal pathways. Using a landscape‐based approach, we modelled the effective geographical distance among a set of interconnected ponds (De Maten, Genk, Belgium) in a Geographic Information System (GIS) environment. The first model (the Landscape Model; LM) corrects for the presence of direct connections among ponds and was based on the existing landscape structure (i.e. network of connecting elements among ponds, travelling distance and direction of the current). A second model (the Flow Rate Model; FRM) also incorporated field data on flow rates in the connecting elements as the driving force for the passive dispersal of the active zooplankton population component. Finally, the third model (the Dispersal Rate Model; DRM) incorporated field data on zooplankton dispersal rates. An analysis of the pattern of genetic differentiation among Daphnia ambigua populations inhabiting 10 ponds in the pond complex reveals that the effective geographical distance as modelled by the flow rate and the dispersal rate model provide a better approximation of the true rates of genetic exchange among populations than mere Euclidean geographical distances or the landscape model that takes into account solely the presence of physical connections.
Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences
Authors: Barber P. H. , Palumbi S. R. , Erdmann M. V. , Moosa M. K.
Published: March 2003

To help stem the precipitous decline of coral reef ecosystems world‐wide, conservation efforts are focused on establishing interconnected reserve networks to protect threatened populations. Because many coral reef organisms have a planktonic or pelagic larval dispersal phase, it is critical to understand the patterns of ecological connectivity between reserve populations that result from larval dispersal. We used genetics to infer dispersal patterns among 24 Indo‐West Pacific populations of the mantis shrimp, Haptosquilla pulchella. Contrary to predictions of high dispersal facilitated by the strong currents of the Indonesian throughflow, mitochondrial DNA sequences from 393 individuals displayed striking patterns of regional genetic differentiation concordant with ocean basins isolated during periods of lowered sea level. Patterns of genetic structuring indicate that although dispersal within geographical regions with semicontiguous coastlines spanning thousands of kilometres may be common, ecologically meaningful connections can be rare among populations separated by as little as 300 km of open ocean. Strong genetic mosaics in a species with high dispersal potential highlight the utility of genetics for identifying regional patterns of genetic connectivity between marine populations and show that the assumption that ocean currents will provide ecological connectivity among marine populations must be empirically tested in the design of marine reserve networks.
Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard
Authors: Paulo Octávio S. , Jordan William C. , Bruford Michael W. , Nichols Richard A.
Published: March 2003

The distribution of the lizard Lacerta schreiberi is likely to have been severely affected by the climatic cycles that have influenced the Iberian Peninsula. Information about the species ecology and Iberian physiogeography was used to generate specific hypotheses about episodes of colonization and subsequent population persistence. These hypotheses generated predictions about the distribution of genetic variation, which were tested using nested clade analysis (NCA) supplemented by analysis of molecular variance (amova). Two predictions were confirmed by NCA; that is those that specified multiple and allopatric refugia. However, the remaining three predictions were not corroborated by the analyses. Firstly, a simple analysis of the distribution of genetic variability failed to detect an expected difference in the pattern of colonization between the inland mountain system and the coastal region. Moreover, while NCA did detect the expected genetic pattern in southern coastal populations, it was explained in terms of long‐distance migration, which seems implausible because of the extent of unsuitable habitat. A more likely cause of the pattern is population fragmentation and a reduction in population size caused during the Holocene. Finally, NCA also failed to detect a northwestern population expansion, which is supported by other evidence. We conclude that NCA has a limited ability to detect range expansion led by individuals with more ancestral (interior) haplotypes.
Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster
Authors: Schlötterer Christian , Harr Bettina
Published: March 2003

Single nucleotide polymorphisms (SNPs) are about to become one of the most popular genetic markers for genetic model organisms. To test the usefulness of SNPs for estimating genetic diversity, we surveyed three genomic regions in two Drosophila melanogaster populations, one from Africa and one European, collected in Austria. Diversity estimates based on the full SNP set indicated higher levels of variability in the African than in the European flies. When the analysis was based on the European SNP set, European and African flies had similar levels of variability. Interestingly, this bias was not observed for diversity estimates using SNPs derived from the ancestral African population. This result suggests that diversity estimates based on SNPs from ancestral populations could provide a general strategy to avoid biased SNP diversity estimates. Finally, the potential of SNPs for nonmodel organisms is discussed.
Mesobuthus gibbosus (Scorpiones: Buthidae) on the island of Rhodes — hybridization between Ulysses’ stowaways and native scorpions?
Authors: Gantenbein B. , Largiadèr C. R.
Published: March 2003

Allozyme data suggest that the Rhodes population of Mesobuthus gibbosus is a hybrid population of recent origin. Namely, it is a mixture between an autochthonous population and an artificially introduced population probably from the Greek mainland. All samples were mainly composed of F1 hybrid genotypes and genotypes either fixed for autochthonous or introduced alleles. Back‐cross hybrid genotypes were very rare. Mitochondrial DNA analysis, in contrast, revealed only one group of closely related haplotypes that are unique for the Rhodes populations, thus suggesting asymmetric introgression of the two marker classes.
Microsatellite diversity and genetic structure of fragmented populations of the rare, fire‐dependent shrubGrevillea macleayana
Authors: England Phillip R. , Usher Annette V. , Whelan Robert J. , Ayre David J.
Published: March 2003

Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self‐compatible and have limited seed dispersal. However, long‐lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species,Grevillea macleayana(Proteaceae), that occurs in many small populations, is self‐compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long‐lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found thatG. macleayanamay have relatively low within‐population diversity (3.2–4.2 alleles/locus;Hexp= 0.420–0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation‐drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire‐shaped distribution, may have restricted long‐distance gene flow in the past.
Genetic structure and phylogeography of European catfish (Silurus glanis) populations
Authors: Triantafyllidis A. , Krieg F. , Cottin C. , Abatzopoulos T. J. , Triantaphyllidis C. , Guyomard R.
Published: March 2003

The genetic structure of Silurus glanis (Europe’s largest freshwater fish species) across most of its natural distribution was investigated using 10 microsatellite loci. The revealed levels of genetic diversity were much higher than previous allozyme and restriction fragment length polymorphism mitochondrial DNA analyses had shown; relative levels of variability among populations were however, in good agreement with the previous studies. Populations from large basins (Volga and Danube rivers) were the most polymorphic, while samples from the smaller Greek rivers, which are more prone to genetic bottleneck, exhibited the lowest levels of genetic diversity. Microsatellite multilocus genotyping permitted the assignment of individual fish to their population of origin with a score as high as 98.3%. Despite the great genetic differentiation of S. glanis populations, no consistent pattern of geographical structuring was revealed, in contrast to previous studies of European freshwater fish species. A model of isolation by distance seems more probable and a hypothesis of recent dispersion from only one glacial refugium is proposed. The discovery of the highest levels of microsatellite and mitochondrial diversity in the Volga sample and the presence of river connections, during the Pleistocene, between this area and all major areas of the present catfish distribution, place this refugium around the Ponto‐Caspian region. Combining these data with those from previous studies, a number of markers are now available to monitor wild and hatchery populations even at the individual level.
Land barriers and open oceans: effects on gene diversity and population structure in Avicennia germinans L. (Avicenniaceae)
Authors: Dodd R. S. , Afzal‐Rafii Z. , Kashani N. , Budrick J.
Published: March 2003

Avicennia germinans L. is a widespread mangrove species occupying the west coast of Africa and the Atlantic and Pacific coasts of the Americas from the Bahamas to Brazil and Baja California to Peru. An amplified fragment length polymorphism (AFLP) molecular analysis was carried out to assess genetic architecture within this species and to evaluate the effects of the Atlantic Ocean and the Central American Isthmus (CAI) on population and regional genetic diversity and differentiation. In total, 349 polymorphic AFLP fragments were identified among 144 individuals from 14 populations from the east Atlantic, west Atlantic and east Pacific. Levels of genetic diversity varied considerably among populations, but were generally higher in populations from the east Atlantic. Regional differentiation between the Pacific coast and Atlantic populations was greater than between east and west Atlantic populations, suggesting that the CAI has had an important influence on population genetic structure in this species. The lower level of divergence of east Atlantic from west Atlantic populations suggests some dispersal across the Atlantic Ocean, although migration rates are probably low; Nm from GST equal to 0.41 and accumulation of private and rare alleles in the east Atlantic. Population differentiation did not appear to follow an isolation by distance model and has probably resulted from complex patterns of population bottlenecks, and founder events due to landscape changes during the Pleistocene, particularly in the west Atlantic. The molecular data provide no support for the treatment of east Atlantic populations as a separate species A. africana.
Locating the sources of an invasive pest, grape phylloxera, using a mitochondrial DNA gene genealogy
Authors: Downie D. A.
Published: March 2003

Range expansions through human introductions have increased with global commerce and have led to the extinction of native species, alterations in community structure and pest status of the invasive species. Inferring the evolutionary history of invasive species can help to build a firmer footing for management tactics. This study used mitochondrial DNA (mtDNA) sequence comparisons of samples collected from the native and introduced ranges of a pest herbivore of cultivated grapes, grape phylloxera (Daktulosphaira vitifoliae Fitch, Phylloxeridae) to infer the sources and pattern of introductions into worldwide viticulture. Introductions into viticulture from its native North American range first occurred in the mid‐19th century. The pattern of spread has suggested a focus of introduction into France, but independent introductions may have occurred elsewhere. The results show that the introduced population represents a limited subsample of the native genetic diversity. The data suggest that most grape phylloxera in viticulture, including all European, have originated in the northeastern USA where the grape species Vitis riparia dominates. There was evidence for independent introductions into South Africa and California. Most California haplotypes were most closely related to native grape phylloxera from the Atlantic Coast on V. vulpina. It is likely that subsequent spread from California into Australia, New Zealand and Peru has occurred.
Trans‐specific evolution of opsin alleles and the maintenance of trichromatic colour vision in Callitrichine primates
Authors: Surridge Alison K. , Mundy Nicholas I.
Published: March 2003

Many New World (NW) primates possess a remarkable polymorphism in an X‐linked locus, which encodes for the visual pigments (opsins) used for colour vision. Females that are heterozygous for opsin alleles of different spectral sensitivity at this locus have trichromatic colour vision, whereas homozygous females and males are dichromatic, with poor colour discrimination in the red–green range. Here we describe an extensive survey of allelic variation in both exons and introns at this locus within and among species of the Callitrichines (marmosets and tamarins). All five genera of Callitrichines have the X‐linked polymorphism, and only the three functional allelic classes described previously (with maximum wavelength sensitivities at about 543 nm, 556 nm and 563 nm) were found among the 16 species and 233 or more X‐chromosomes sampled. In spite of the homogenizing effects of gene conversion, phylogenetic analyses provide direct evidence for trans‐specific evolution of alleles over time periods of at least 5–6 million years, and up to 14 million years (estimated from independent phylogenies). These conclusions are supported by the distribution of insertions and deletions in introns. The maintenance of polymorphism over these time periods requires an adaptive explanation, which must involve a heterozygote advantage for trichromats. The lack of detection of alleles that are recombinant for spectral sensitivity suggests that such alleles are suboptimal. The two main hypotheses for the selective advantage of trichromacy in primates are frugivory for ripe fruits and folivory for young leaves. The latter can be discounted in Callitrichines, as they are not folivorous.
Microsatellite analysis reveals remating by wild Mediterranean fruit fly females, Ceratitis capitata
Authors: Bonizzoni M. , Katsoyannos B. I. , Marguerie R. , Guglielmino C. R. , Gasperi G. , Malacrida A. , Chapman T.
Published: March 2003

Accurate estimates of remating in wild female insects are required for an understanding of the causes of variation in remating between individuals, populations and species. Such estimates are also of profound importance for major economic fruit pests such as the Mediterranean fruit fly (Ceratitis capitata). A major method for the suppression of this pest is the sterile insect technique (SIT), which relies on matings between mass‐reared, sterilized males and wild females. Remating by wild females will thus impact negatively on the success of SIT. We used microsatellite markers to determine the level of remating in wild (field‐collected) Mediterranean fruit fly females from the Greek Island of Chios. We compared the four locus microsatellite genotypes of these females and their offspring. Our data showed 7.1% of wild females remated. Skewed paternity among progeny arrays provided further evidence for double matings. Our lowest estimate of remating was 3.8% and the highest was 21%.
Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation
Authors: Collevatti Rosane G. , Grattapaglia Dario , Hay JOHN. D.
Published: March 2003

In this work we report on the phylogeography of the endangered tree species Caryocar brasiliense based on variability in two classes of maternally inherited chloroplast DNA sequences with different rates of molecular evolution. Eleven sequence haplotypes of a noncoding region between the genes trnT and trnF and 21 distinct 10‐locus microsatellite haplotypes could be identified in a total of 160 individuals, collected in 10 widespread populations of C. brasiliense. An amova indicated that most of the variation can be attributed to differences among populations, both for DNA sequence (87.51%) and microsatellites (84.38%). Phylogeography based on a median‐joining network analysis of the noncoding region showed a sharp difference from the analysis of microsatellite haplotypes. Nevertheless, both analyses indicated that multiple lineages may have contributed to the origin of C. brasiliense populations in Brazilian Cerrado. Incongruences in the microsatellite haplotypes network suggest that homoplasy, which emerged from recurrent and independent mutations, greatly influenced the evolution of the C. brasiliense chloroplast genome. We hypothesize that our results may show the outcome of the restriction of ancient relic populations to moist refugias during extended droughts coinciding with glaciation in the northern hemisphere. The subsequent spread to favourable areas throughout Central Brazil may have caused contact between different lineages during the interglacial periods. The extinction of megafauna dispersers in the last glaciation may have caused a restriction in seed movement and currently, gene flow has been occurring mainly by pollen movement.
Divergent selection maintains adaptive differentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordaxMitchill)
Authors: Saint‐Laurent Robert , Legault Michel , Bernatchez Louis
Published: March 2003

In this study, we investigate the relative role of historical factors and evolutionary forces in promoting population differentiation in a new case of sympatric dwarf and normal ecotypes of the rainbow smelt (Osmerus mordaxMitchill) in Lac Saint‐Jean (Québec, Canada). Our first objective was to test the hypothesis that the evolution of sympatric smelt ecotypes in Lac Saint‐Jean has been contingent upon the secondary contact between two evolutionary lineages in postglacial times. Secondly, theQSTmethod was applied to test the null hypothesis that the extent of phenotypic differences relative to that of neutral marker variation would be similar in comparisons involving populations within and among ecotypes. Thirdly, we applied a quantitative‐genetic method as an exploratory assessment as to whether the amount of gene flow observed between populations could affect divergence in adaptive traits under specific conditions. This study revealed a unique situation of dwarf and normal smelt ecotypes that are, respectively, characterized by selmiparous and iteroparous life histories and the occurrence in each of two genetically distinct populations that synchronously use the same spawning habitat in two tributaries. Historical contingency has apparently played little role in the origin of these populations. In contrast, an important role of divergent natural selection in driving their phenotypic divergence was suggested. While divergent selection has apparently been strong enough to maintain phenotypic differentiation in the face of migration, this study suggests that gene flow has been sufficiently important to modulate the extent of adaptive differentiation being achieved between ecotypes, unless the extent of stabilizing selection acting on smelt ecotypes is much more pronounced than usually reported in natural populations.
Fine‐scale genetic structure in a free‐living ungulate population
Authors: Coltman D. W. , Pilkington J. G. , Pemberton J. M.
Published: March 2003

The fine‐scale genetic structure of wild animal populations has rarely been analysed, yet is potentially important as a confounding factor in quantitative genetic and allelic association studies, as well as having implications for population dynamics, inbreeding and kin selection. In this study, we examined the extent to which the three spatial subunits, or hefts, of the Village Bay population of Soay sheep (Ovis aries) on St Kilda, Scotland, are genetically structured using data from 20 microsatellite and protein loci. Allele frequencies differed significantly among three hefts in all the study years we considered (1987–2000 inclusive). Small but significantly positive FST and negative FIS values were observed in most years, indicating that the hefts are genetically differentiated, and that within each heft there is more observed heterozygosity than would be expected if each were an isolated breeding population. Males showed less fidelity to their natal heft, and as a consequence higher levels of relatedness within hefts were observed among females than among males. There was a significant negative relationship between geographical proximity and relatedness in pairwise comparisons involving females, and on average pairs of females located within 50 m of each other were related at the equivalent level of second cousins. Structure is therefore largely driven by incomplete postnatal dispersal by females. Mating appears to be random with respect to the spatial‐genetic substructure of the hefts, and therefore genetic structure does not contribute to the overall rate of inbreeding in the population. However, genetic substructure can lead to allelic associations and generate environmental effects within lineages that have the potential to confound heritability analyses and allelic association studies.
Patterns of linkage disequilibrium in mitochondrial DNA of 16 ruminant populations
Authors: Slate J. , Phua S. H.
Published: March 2003

Mitochondrial DNA (mtDNA) is a widely employed molecular tool in phylogeography, in the inference of human evolutionary history, in dating the domestication of livestock and in forensic science. In humans and other vertebrates the popularity of mtDNA can be partially attributed to an assumption of strict maternal inheritance, such that there is no recombination between mitochondrial lineages. The recent demonstration that linkage disequilibrium (LD) declines as a function of distance between polymorphic sites in hominid mitochondrial genomes has been interpreted as evidence of recombination between mtDNA haplotypes, and hence nonclonal inheritance. However, critics of mtDNA recombination have suggested that this association is an artefact of an inappropriate measure of LD or of sequencing error, and subsequent studies of other populations have failed to replicate the initial finding. Here we report the analysis of 16 ruminant populations and present evidence that LD significantly declines with distance in five of them. A meta‐analysis of the data indicates a nonsignificant trend of LD declining with distance. Most of the earlier criticisms of patterns between LD and distance in hominid mtDNA are not applicable to this data set. Our results suggest that either ruminant mtDNA is not strictly clonal or that compensatory selection has influenced patterns of variation at closely linked sites within the mitochondrial control region. The potential impact of these processes should be considered when using mtDNA as a tool in vertebrate population genetic, phylogenetic and forensic studies.
Historical demography and genetic structure of sister species: deermice (Peromyscus) in the North American temperate rain forest
Authors: Zheng Xiaoguang , Arbogast Brian S. , Kenagy G. J.
Published: March 2003

To investigate the evolutionary and biogeographical history ofPeromyscus keeniandP. maniculatuswithin the coastal forest ecosystem of the Pacific Northwest of North America, we sampled 128 individuals from 43 localities from southeastern Alaska through Oregon. We analysed mitochondrial DNA variation using DNA sequence data from the mitochondrial cytochrome‐b(cyt‐b) gene and control region, and we found two distinct clades consistent with the morphological designation of the two species. The sequence divergence between the two clades was 0.0484 substitutions per site for cyt‐band 0.0396 for the control region, suggesting that divergence of the two clades occurred during the middle to late Pleistocene. We also examined the historical demography of the two clades using stepwise and exponential expansion models, both of which indicated recent rapid population growth. Furthermore, using the programmigratewe found evidence of migration from populations north of the Fraser River (British Columbia) to the south in both clades. This study demonstrates the utility of these model‐based demographic methods in illuminating the evolutionary and biogegographic history of natural systems.
A new approach to study dispersal: immigration of novel alleles reveals female‐biased dispersal in great reed warblers
Authors: Hansson Bengt , Bensch Staffan , Hasselquist Dennis
Published: March 2003

We use the assignment technique and a new approach, the ‘novel allele technique’, to detect sex‐biased dispersal in great reed warblersAcrocephalus arundinaceus. The data set consisted of immigrants and philopatric birds in a semi‐isolated population in Sweden scored at 21 microsatellite loci. Fourteen cohorts were represented of which the four earliest were used to define a reference population. Female immigrants had lower assignment probability than males (i.e. were less likely to have been sampled in the reference population), and carried the majority of ‘novel alleles’ (i.e. alleles observed in the population for the first time). The difference in number of novel alleles between sexes was caused by a strong over‐representation of females among the few individuals that carried several novel alleles, and there was a tendency for a corresponding female bias among individuals with low assignment probabilities. Immigrant males had similar or lower reproductive success than females. These results lead us to conclude that important interregional gene flow in great reed warblers depends on relatively few dispersing females, and that the novel allele technique may be a useful complement to the assignment technique when evaluating dispersal patterns from temporally structured data.