bluuebunny/crossref_metadata_2025 huggingface dataset:
Microsatellite analysis of North American wapiti (Cervus elaphus) populations
Authors: Polziehn Renee O. , Hamr Joe , Mallory Frank F. , Strobeck Curtis
Published: March 2003

Eleven populations of wapiti (Cervus elaphus) were analysed for genetic diversity using 12 microsatellite loci. Samples were taken from Vancouver Island, British Columbia; Burwash and French River herds in Ontario; Ya Ha Tinda Ranch, Alberta; and Banff, Elk Island, Jasper, Kootenay, Riding Mountain, Yellowstone and Yoho National Parks. Overall, wapiti populations have on average three to four alleles per locus and an average expected heterozygosity that ranged from 25.75 to 52.85%. The greatest genetic distances were observed between the Vancouver population and all other populations. Using the assignment test, Roosevelt wapiti (C. e. rooseveltiMerriam 1897) assigned only to the Vancouver Island population. The distance and assignment values suggest a divergence of the Roosevelt wapiti from other populations and support the subspecific status for the Vancouver Island population. No evidence was found for the existence of unique Eastern wapiti (C. e. canadensisErxleben 1777) in the Burwash or French River herds in Ontario. The overlapping distribution of genotypes from indigenous populations from Riding Mountain, Elk Island and Yellowstone National Parks suggests that wapiti were once a continuous population before settlers decimated their numbers. The lack of differentiation between these populations raises questions about the status of Manitoban (C. e.manitobensisMillais 1915) and Rocky Mountain (C. e.nelsoniBailey 1935) subspecies.
Genetic diversity in an endangered alpine plant,Eryngium alpinumL. (Apiaceae), inferred from amplified fragment length polymorphism markers
Authors: Gaudeul M. , Taberlet P. , Till‐Bottraud I.
Published: March 2003

Eryngium alpinumL. is an endangered species found across the European Alps. In order to obtain base‐line data for the conservation of this species, we investigated levels of genetic diversity within and among 14 populations from the French Alps. We used the amplified fragment length polymorphism (AFLP) technique with three primer pairs and scored a total of 62 unambiguous, polymorphic markers in 327 individuals. Because AFLP markers are dominant, within‐population genetic structure (e.g.FIS) could not be assessed. Analyses based either on the assumption of random‐mating or on complete selfing lead to very similar results. Diversity levels within populations were relatively high (mean Nei’s expected heterozygosity = 0.198; mean Shannon index = 0.283), and a positive correlation was detected between both genetic diversity measurements and population size (Spearman rank correlation:P = 0.005 andP = 0.002, respectively). Moreover,FSTvalues and exact tests of differentiation revealed high differentiation among populations (mean pairwiseFST = 0.40), which appeared to be independent of geographical distance (nonsignificant Mantel test). Founder events during postglacial colonizations and/or bottlenecks are proposed to explain this high but random genetic differentiation. By contrast, we detected a pattern of isolation by distance within populations and valleys. Predominant local gene flow by pollen or seed is probably responsible for this pattern. Concerning the management ofE. alpinum, the high genetic differentiation leads us to recommend the conservation of a maximum number of populations. This study demonstrates that AFLP markers enable a quick and reliable assessment of intraspecific genetic variability in conservation genetics.
Historical biogeography in a linear system: genetic variation of Sea Rocket (Cakile maritima) and Sea Holly (Eryngium maritimum) along European coasts
Authors: Clausing G. , Vickers K. , Kadereit J. W.
Published: March 2003

The exclusively coastal Cakile maritima and Eryngium maritimum represent a linear biogeographical system. Genetic variation among 25 individuals of C. maritima and 16 individuals of E. maritimum, from the coasts of Europe, North Africa and the Canary Islands, was analysed using random amplified polymorphic DNAs (RAPDs) and intersimple sequence repeats (ISSRs). Genetic distances (Dice) were calculated and used to investigate the correlation between genetic and geographical distances, to construct Neighbour Joining (NJ) trees, and to compare mean genetic distances between areas within and across species. Genetic distances and geographical distances measured along the coast are well correlated in Cakile and Eryngium. This implies that dispersal in both species is largely along the coast. The NJ analyses resulted in the recognition of Atlantic and Mediterranean clusters in both Cakile and Eryngium. The genetic distance between these two clusters is much larger in Eryngium (0.285) than in Cakile (0.037). Mean genetic distances are substantially higher in the Mediterranean than in the Atlantic clusters in both species, and higher in Cakile than in Eryngium particularly in the Atlantic cluster. It is argued that all similarities and differences between the two species can be explained with the presumed distribution of the two species in the Würm glacial as reconstructed from their extant temperature requirements, the distribution of ice cover, permafrost, and sea surface temperatures in that period, and indirect fossil evidence.
Microsatellite analysis of a population crash and bottleneck in the Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense(Asteraceae), and its implications for reintroduction
Authors: Friar E. A. , Ladoux T. , Roalson E. H. , Robichaux R. H.
Published: March 2003

The Mauna Kea silversword,Argyroxiphium sandwicensessp.sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.
Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe
Authors: Sharbel Timothy F. , Haubold Bernhard , Mitchell‐Olds Thomas
Published: March 2003

Arabidopsis thaliana provides a useful model system for functional, evolutionary and ecological studies in plant biology. We have analysed natural genetic variation in A. thaliana in order to infer its biogeographical and historical distribution across Eurasia. We analysed 79 amplified fragment length polymorphism (AFLP) markers in 142 accessions from the species’ native range, and found highly significant genetic isolation by distance among A. thaliana accessions from Eurasia and southern Europe. These spatial patterns of genetic variation suggest that A. thaliana colonized central and northern Europe from Asia and from Mediterranean Pleistocene refugia, a trend which has been identified in other species. Statistically significant levels of multilocus linkage disequilibrium suggest intermediate levels of disequilibrium among subsets of loci, and analysis of genetic relationships among accessions reveal a star or bush‐like dendrogram with low bootstrap support. Taken together, it appears that there has been sufficient historical recombination in the A. thaliana genome such that accessions do not conform to a tree‐like, bifurcating pattern of evolution – there is no ‘ecotype phylogeny.’ Nonetheless, significant isolation by distance provides a framework upon which studies of natural variation in A. thaliana may be designed and interpreted.
The genetic architecture of disease resistance in plants and the maintenance of recombination by parasites
Authors: Kover Paula X. , Caicedo Ana Lucia
Published: March 2003

Parasites represent strong selection on host populations because they are ubiquitous and can drastically reduce host fitness. It has been hypothesized that parasite selection could explain the widespread occurrence of recombination because it is a coevolving force that favours new genetic combinations in the host. A review of deterministic models for the maintenance of recombination reveals that for recombination to be favoured, multiple genes that interact with each other must be under selection. To evaluate whether parasite selection can explain the maintenance of recombination, we review 85 studies that investigated the genetic architecture of plant disease resistance and discuss whether they conform to the requirements that emerge from theoretical models. General characteristics of disease resistance in plants and problems in evaluating resistance experimentally are also discussed. We found strong evidence that disease resistance in plants is determined by multiple loci. Furthermore, in most cases where loci were tested for interactions, epistasis between loci that affect resistance was found. However, we found weak support for the idea that specific allelic combinations determine resistance to different host genotypes and there was little data on whether epistasis between resistance genes is negative or positive. Thus, the current data indicate that it is possible that parasite selection can favour recombination, but more studies in natural populations that specifically address the nature of the interactions between resistance genes are necessary. The data summarized here suggest that disease resistance is a complex trait and that environmental effects and fitness trade‐offs should be considered in future models of the coevolutionary dynamics of host and parasites.
Speciation, hybrid zones and phylogeography — or seeing genes in space and time
Authors: Hewitt Godfrey M.
Published: March 2003

The origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A ‘tree of trees’ summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions.
The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus)
Authors: Jehle R. , Arntzen J. W. , Burke T. , Krupa A. P. , Hödl W.
Published: March 2003

Pond‐breeding amphibians are deme‐structured organisms with a population genetic structure particularly susceptible to demographic threats. We estimated the effective number of breeding adults (Nb) and the effective population size (Ne) of the European urodele amphibians Triturus cristatus (the crested newt) and T. marmoratus (the marbled newt), using temporal shifts in microsatellite allele frequencies. Eight microsatellite loci isolated from a T. cristatus library were used, five of which proved polymorphic in T. marmoratus, albeit with high frequencies of null alleles at two loci. Three ponds in western France were sampled, situated 4–10 kilometres apart and inhabited by both species. Parent–offspring cohort comparisons were used to measure Nb; samples collected at time intervals of nine or 12 years, respectively, were used to measure Ne. The adult population census size (N) was determined by mark–recapture techniques. With one exception, genetic distances (FST) between temporal samples were lower than among populations. Nb ranged between 10.6 and 101.8 individuals, Ne ranged between 9.6 and 13.4 individuals. For the pond where both parameters were available, Nb/N (overall range: 0.10–0.19) was marginally larger than Ne/N (overall range: 0.09–0.16), which is reflected in the temporal stability of N. In line with the observed differences in reproductive life‐histories between the species, Nb/N ratios for newts were about one order of magnitude higher than for the anuran amphibian Bufo bufo. Despite of the colonization of the study area by T. cristatus only some decades ago, no significant genetic bottleneck could be detected. Our findings give rise to concerns about the long‐term demographic viability of amphibian populations in situations typical for European landscapes.
Phylogeography of the dusky shrew,Sorex monticolus(Insectivora, Soricidae): insight into deep and shallow history in northwestern North America
Authors: Demboski John R. , Cook Joseph A.
Published: March 2003

Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S.bairdi,S.bendirii,S.neomexicanus,S.ornatus,S.pacificus,S.palustris,S.sonomaeandS.vagrans) were assessed using sequences from the mitochondrial cytochromebgene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi,S.neomexicanusandS.pacificus) were poorly differentiated.SorexornatusandS.vagransrepresented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containingS.monticolus(Arizona to Alaska, includingS.neomexicanus); (ii) a Coastal clade containingS.monticolus(Oregon to south‐east Alaska, includingS.bairdiandS.pacificus); (iii) the semiaquatic species (S. bendiriiandS.palustris); and (iv)S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5–6.2%), which exceeds many interspecific comparisons within this species complex and within the genusSorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also thatS. monticolusis not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America.
The extent of clonality and genetic diversity in lingonberry (Vaccinium vitis‐idaea L.) revealed by RAPDs and leaf‐shape analysis
Authors: Persson H. A. , Gustavsson B. A.
Published: March 2003

Numerous plant species reproduce mainly by clonal growth, implying that levels of genetic variation may be comparatively low. In this study we describe the genetic and genotypic diversity within and between four Swedish populations of the clonal shrub lingonberry, Vaccinium vitis‐idaea L. Two approaches were used to assess the amount and partitioning of variation: automated image analysis of leaf shape and random amplified polymorphic DNA (RAPD) analysis. Morphometric analyses, using moment invariants and elliptic Fourier coefficients, revealed that most of the variation could be attributed to within‐population variation. With the use of 43 polymorphic RAPD markers, we were able to identify 29 different genotypes (i.e. putative clones) among 129 plants from two populations. The genotypic diversity (D: mean 0.84) and evenness (E: mean 0.81) were higher than the average for clonal plant species. Within‐population gene diversity was similar to values reported in nonclonal plants, suggesting that sexual reproduction has played a significant role in these populations despite low levels of seedling recruitment in present‐day populations. An analysis of molecular variance revealed that most of the variation (89.2%) resided within populations. Comparisons between the different suites of characters indicated a congruent pattern of partitions of diversity, particularly when comparing moment invariants and RAPDs. When comparing the ability of the two descriptor suites to assign the plants to the RAPD‐defined clones, elliptic Fourier coefficients yielded the best result; a classification test correctly reassigned 96.9% and 98.1% of the plant material in the two respective populations.
A comparison of microsatellite‐based pairwise relatedness estimators
Authors: Van De Casteele T. , Galbusera P. , Matthysen E.
Published: March 2003

Studies of inbreeding depression or kin selection require knowledge of relatedness between individuals. If pedigree information is lacking, one has to rely on genotypic information to infer relatedness. In this study we investigated the performance (absolute and relative) of 10 marker‐based relatedness estimators using allele frequencies at microsatellite loci obtained from natural populations of two bird species and one mammal species. Using Monte Carlo simulations we show that many factors affect the performance of estimators and that different sets of loci promote the use of different estimators: in general, there is no single best‐performing estimator. The use of locus‐specific weights turns out to greatly improve the performance of estimators when marker loci are used that differ strongly in allele frequency distribution. Microsatellite‐based estimates are expected to explain between 25 and 79% of variation in true relatedness depending on the microsatellite dataset and on the population composition (i.e. the frequency distribution of relationship in the population). We recommend performing Monte Carlo simulations to decide which estimator to use in studies of pairwise relatedness.
Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR–RFLP analyses of plastid DNA
Authors: Brunner I. , Brodbeck S. , BÜchler U. , Sperisen C.
Published: March 2003

Fine roots of trees are intensively used as indicators to assess soil alterations, e.g. those owing to atmospheric inputs of acidifying substances, but their identification to species with morphological criteria is difficult. In this study, we established molecular techniques in order to identify fine roots of the 30 most common tree species of the Alps. We developed a protocol for efficient isolation of DNA from fine roots with extraction of DNA in the presence of polyvinylpyrrolidone (PVP) and polyvinylpolypyrrolidone (PVPP). The trnL (UAA) intron of plastid DNA was used as a marker for fine root identification. We amplified and sequenced this intron with plant universal primers. The size of the sequences ranged from 444 to 672 bp. A synoptic key for species identification was designed on the basis of restriction fragment patterns predicted from sequence data. Using the restriction enzyme TaqI as key enzyme, and where necessary HinfI, RsaI and CfoI, 16 taxa, including Picea abies, Larix decidua, Abies alba, and Fagus sylvatica, the dominant tree species of the Alpine region could be identified by agarose gel electrophoresis of restriction fragments. Fourteen taxa could be identified to the genus level, among them Quercus, Salix and Populus species. In a field study, conducted in a 20 × 30 m plot of a mixed forest with five tree species, fine roots of 43 out of 46 samples were identified and their distributions were mapped. These results demonstrate the utility of our DNA extraction method and of the trnL intron for the identification of fine tree roots.
Postglacial colonization of Northern Europe by distinct phylogeographic lineages of the bullhead, Cottus gobio
Authors: Kontula Tytti , VÄinölä Risto
Published: March 2003

Three major phylogeographic lineages of the cottid fish Cottus gobio (bullhead) were identified in northern Europe from mitochondrial DNA sequences and allozyme data. The largely separate freshwater distributions of the lineages demonstrate distinct postglacial colonization histories. West of the Baltic Sea, Swedish lakes were invaded from the southwest (Germany). Another, eastern lineage has colonized the inland waters northeast and east of the Baltic, from refugia in northwest Russia; this lineage comprises a distinct subgroup found only from Estonia. The third lineage, found south and southeast of the Baltic, probably descended from rivers draining to the Black Sea from the north (e.g. Dnepr). In coastal waters of the Baltic Sea, and in near‐coast inland waters, the lineages are now found intermixed in various combinations. The alternating fresh‐ and saltwater phases of the Baltic basin have variously enabled and disabled the use of coastal waters as colonization routes. Hypotheses on the chronology of dispersal and lineage mixing can be based on the distribution of the marker genes and the palæohydrographical record. The diversity of the Fennoscandian bullhead thus comprises anciently diverged (probably mid‐Pleistocene) refugial lineages that in their freshwater range constitute distinct evolutionarily significant units. The thorough mixing of the various genomic origins in and around the Baltic, however, refutes the controversial view of distinct species status for the western and eastern (‘Cottus koshewnikowi’) bullheads. The postglacial contact of the lineages has created new diversity that cannot be interpreted in a conventional hierarchical framework of taxonomic or conservation units.
Species‐specific detection ofLobaria pulmonaria(lichenized ascomycete) diaspores in litter samples trapped in snow cover
Authors: Walser J.‐C. , Zoller S. , Büchler U. , Scheidegger C.
Published: March 2003

The foliose lichenLobaria pulmonariahas suffered a substantial decline in central and northern Europe during the twentieth century and is now considered to be critically endangered in many European lowland regions. Based on demographic studies, it has been proposed that under the present environmental conditions and forest management regimes, dispersal of diaspores and subsequent establishment of new thalli are insufficient to maintain the remnant small lowland populations. Chances of long‐term survival may therefore be reduced. The data and analytical power of these demographic studies are limited. Since lichen diaspores show very few species‐specific morphological characteristics, and are therefore almost indistinguishable, the accurate assessment of diaspore flux would be a fundamental first step in better understanding the life cycle ofL. pulmonaria. Here we present a new molecular approach to investigate the dispersal ofL. pulmonariadiaspores in its natural environment by specifically identifying small amounts of DNA in snow litter samples at varying distances from known sources. We used a species‐specific polymerase chain reaction (PCR) primer pair to amplify the ribosomal internal transcribed spacer region (ITS rDNA) and a sensitive automated PCR product detection system using fluorescent labelled primers. We detected considerable amounts of naturally dispersed diaspores, deposited as far as 50 m away from the closest potential source. Diaspores were only found in the direction of the prevailing wind. Diaspore deposition varied from 1.2 diaspores per m2per day at 50 m distance from the source to 15 diaspores per m2per day at 1 m distance. The method described in this paper opens up perspectives for studies of population dynamics and dispersal ecology mainly in lichenized ascomycetes but also in other organisms with small, wind‐dispersed diaspores.
Intraspecific phylogeography of Percina evides (Percidae: Etheostomatinae): an additional test of the Central Highlands pre‐Pleistocene vicariance hypothesis
Authors: Near Thomas J. , Page Lawrence M. , Mayden Richard L.
Published: March 2003

North America exhibits the most diverse freshwater fish fauna among temperate regions of the world. Species diversity is concentrated in the Central Highlands, drained by the Mississippi, Gulf Slope and Atlantic Slope river systems. Previous investigations of Central Highlands biogeography have led to conflicting hypotheses involving dispersal and vicariance to explain the diversity and distribution of the freshwater fish fauna. In this investigation predictions of the Central Highlands pre‐Pleistocene vicariance hypothesis are tested with a phylogeographic analysis of the percid species Percina evides, which is widely distributed in several disjunct areas of the Central Highlands. Phylogenetic analysis of complete gene sequences of mitochondrially encoded cytochrome b recover three phylogroups, with very low levels of sequence polymorphism within groups. The two western phylogroups are monophyletic with respect to the eastern phylogroup. The recovery of two monophyletic lineages with an eastern and western distribution in the disjunct highland areas is a pattern expected from vicariance, but is not predicted by the Central Highlands pre‐Pleistocene vicariance hypothesis. The recovery of very limited mitochondrial DNA polymorphism and lack of phylogeographic structuring across the entire range of the eastern clade, very shallow polymorphism between the disjunct Missouri River and upper Mississippi River populations, and lack of sequence polymorphism in the upper Mississippi River populations, support a hypothesis of dispersal during or following the Pleistocene. The present distribution of P. evides is best explained by both vicariant and dispersal events.
The contribution of haploids, diploids and clones to fine‐scale population structure in the seaweedCladophoropsis membranacea(Chlorophyta)
Authors: Van Der Strate H. J. , Van De Zande L. , Stam W.T. , Olsen J. L.
Published: March 2003

Local populations ofCladophoropsis membranaceaexist as mats of coalesced thalli composed of free‐living haploid and diploid plants including clonally reproduced plants of either phase. None of the phases are morphologically distinguishable. We used eight microsatellite loci to explore clonality and fine‐scale patch structure inC. membranaceaat six sites on the Canary Islands. Mats were always composites of many individuals; not single, large clones. Haploids outnumbered diploids at all sites (from 2:1 to 10:1). In both haploid and diploid plants, genetic diversity was high and there was no significant difference in allele frequencies. Significant heterozygote deficiencies were found in the diploid plants at five out of six sites and linkage disequilibrium was associated with the haploid phase at all sites. Short dispersal distances of gametes/spores and small effective population sizes associated with clonality probably contribute to inbreeding. Spatial autocorrelation analysis revealed that most clones were found within a radius of ≈ 60 cm and rarely further than 5 m. Dominance of the haploid phase may reflect seasonal shifts in the relative frequencies of haploids and diploids, but may alternatively reflect superiority of locally adapted and competitively dominant, haploid clones; a strategy that is theoretically favoured in disturbed environments. Although sexual reproduction may be infrequent inC. membranacea, it is sufficient to maintain both life history phases and supports theoretical modelling studies that show that haploid–diploid life histories are an evolutionarily stable strategy.
Mitochondrial DNA variation in a species with two mitochondrial genomes: the case of Mytilus galloprovincialis from the Atlantic, the Mediterranean and the Black Sea
Authors: Ladoukakis E.D. , Saavedra C. , Magoulas A. , Zouros E.
Published: March 2003

We have examined mitochondrial DNA (mtDNA) variation in samples of the mussel Mytilus galloprovincialis from the Black Sea, the Mediterranean and the Spanish Atlantic coast by scoring for presence or absence of cleavage at 20 restriction sites of a fragment of the COIII gene and at four restriction sites of the 16S RNA gene. This species contains two types of mtDNA genomes, one that is transmitted maternally (the F type) and one that is transmitted paternally (the M type). The M genome evolves at a higher rate than the F genome. Normally, females are homoplasmic for an F type and males are heteroplasmic for an F and an M type. Occasionally molecules from the F lineage invade the paternal transmission route, resulting in males that carry two F‐type mtDNA genomes. These features of the mussel mtDNA system give rise to a new set of questions when using mtDNA variation in population studies and phylogeny. We show here that the two mtDNA types provide different information with regard to amounts of variation and genetic distances among populations. The F genome exhibits higher degrees of diversity within populations, while the M genome produces higher degrees of differentiation among populations. There is a strong differentiation between the Atlantic and the Black Sea. The Mediterranean samples have intermediate haplotype frequencies, yet are much closer to the Black Sea than to the Atlantic. We conclude that in this species gene flow among the three Seas is restricted and not enough to erase the combined effect of mutation and random drift. In one sample, that from the Black Sea, the majority of males did not contain an M mtDNA type. This suggests that a molecule of the maternal lineage has recently invaded the paternal route and has increased its frequency in the population to the point that the present pool of paternally transmitted mtDNA molecules is highly heterogeneous and cannot be used to read the population’s history. This liability of the paternal route means that in species with doubly uniparental inheritance, the maternal lineage provides more reliable information for population and phylogenetic studies.
Reconstructing recent divergence: evaluating nonequilibrium population structure in New Zealand chinook salmon
Authors: Kinnison M. T. , Bentzen P. , Unwin M. J. , Quinn T. P.
Published: March 2003

Newly established or perturbed populations are often the focus of conservation concerns but they pose special challenges for population genetics because drift−migration equilibrium is unlikely. To advance our understanding of the evolution of such populations, we investigated structure and gene flow among populations of chinook salmon that formed via natural straying following introduction to New Zealand in the early 1900s. We examined 11 microsatellite loci from samples collected in several sites and years to address two questions: (i) what population differentiation has arisen in the ≈ 30 generations since salmon were introduced to New Zealand, relative to temporal variation within populations; and (ii) what are the approximate effective population sizes and amounts of gene flow in these populations? These questions are routinely addressed in studies of indigenous populations, but less often in the case of new populations and rarely with consideration of equilibrium assumptions. We show that despite the recent introduction, continued gene flow and high temporal variability among samples, detectable population structure has arisen among the New Zealand populations, consistent with their colonization pattern and isolation by geographical distance. Furthermore, we use simple individual‐based simulations and estimates of effective population sizes to estimate the effective gene flow among drainages under likely nonequilibrium conditions. Similar methodology may be broadly applicable to other studies of population structure and phenotypic evolution under similar nonequilibrium, high gene flow conditions.
Tests for sex‐biased dispersal using bi‐parentally inherited genetic markers
Authors: Goudet Jérôme , Perrin Nicolas , Waser Peter
Published: March 2003

Understanding why dispersal is sex‐biased in many taxa is still a major concern in evolutionary ecology. Dispersal tends to be male‐biased in mammals and female‐biased in birds, but counter‐examples exist and little is known about sex bias in other taxa. Obtaining accurate measures of dispersal in the field remains a problem. Here we describe and compare several methods for detecting sex‐biased dispersal using bi‐parentally inherited, codominant genetic markers. If gene flow is restricted among populations, then the genotype of an individual tells something about its origin. Provided that dispersal occurs at the juvenile stage and that sampling is carried out on adults, genotypes sampled from the dispersing sex should on average be less likely (compared to genotypes from the philopatric sex) in the population in which they were sampled. The dispersing sex should be less genetically structured and should present a larger heterozygote deficit. In this study we use computer simulations and a permutation test on four statistics to investigate the conditions under which sex‐biased dispersal can be detected. Two tests emerge as fairly powerful. We present results concerning the optimal sampling strategy (varying number of samples, individuals, loci per individual and level of polymorphism) under different amounts of dispersal for each sex. These tests for biases in dispersal are also appropriate for any attribute (e.g. size, colour, status) suspected to influence the probability of dispersal. A windows program carrying out these tests can be freely downloaded from http://www.unil.ch/izea/softwares/fstat.html
New insights into the distribution of polyploid Daphnia: the Holarctic revisited and Argentina explored
Authors: Adamowicz Sarah J. , Gregory T. Ryan , Marinone María Cristina , Hebert Paul D. N.
Published: March 2003

It has long been known that polyploid organisms are more prevalent in arctic than in temperate environments. Past explanations for this geographical trend have focused on the role of glacial cycles in generating polyploids and the influence of abiotic factors in favouring polyploidy in the north. In combination, these mechanisms probably suffice to explain the observed geographical cline in ploidy levels in members of the Daphnia pulex complex in the Holarctic. While only diploid members of the D. pulex complex are found in the temperate regions of North America and Europe, allozyme and DNA quantification analyses indicate that the southern Argentine pulex‐complex fauna is dominated by polyploids. Indeed, the present study is the first to document the presence of polyploid members of the D. pulex complex in any temperate climate. The results of phylogeographic analyses suggest that this difference in polyploid distribution between the northern and southern hemispheres is based more on ecological and historical contingencies than direct selection for polyploidy. Specifically, competition with diploid relatives probably limits the lower latitudinal range of polyploids in the north, but appears not to have occurred in Argentina. Because of these differences, the present study provides important insights into the diverse factors that determine the distributions and evolutionary fates of polyploid organisms.
Historical biogeography and molecular systematics of the Indo‐Pacific genus Dascyllus (Teleostei: Pomacentridae)
Authors: McCafferty S. , Bermingham E. , Quenouille B. , Planes S. , Hoelzer G. , Asoh K.
Published: March 2003

The phylogeographical and systematic relationships among species in the tropical marine fish genus Dascyllus were inferred using mitochondrial DNA (mtDNA) sequence data. Although our results were generally consistent with previously published phylogenies based on both morphological and mitochondrial data, our broad taxonomic and geographical sampling design revealed novel insights into the phylogenetic history of Dascyllus that had escaped previous notice. These results include: (a) the polyphyletic nature of D. reticulatus mtDNAs, representing two divergent and geographically separated lineages, one shared with D. flavicaudus and the second forming the sister lineage of D. carneus; (b) the paraphyly of D. trimaculatus relative to the closely related D. abisella; and (c) phylogeographical structure within the widespread taxa D. aruanus and D. trimaculatus. Application of a molecular clock permits us to posit a causative role for tectonic and oceanic changes regarding some Dascyllus speciation events. Finally, we mapped body size and the presence or absence of protogynous sex change on the mtDNA tree, and tested published hypotheses regarding determinants of the evolution of mating system and protogyny in the genus. Our data rejected a model based on body size but not one based on phylogenetic inertia. The ability to change sex arose once in the ancestor to the entire genus, and was lost once in the ancestor of the D. trimaculatus complex. For taxa that are as geographically widespread as many Indo‐Pacific genera, this study highlights the importance of adequate geographical sampling when inferring patterns of species diversification and life history evolution.
Hybrid status of kuwini, Mangifera odorata Griff. (Anacardiaceae) verified by amplified fragment length polymorphism
Authors: Teo L. L. , Kiew R. , Set O. , Lee S. K. , Gan Y. Y.
Published: March 2003

Mangifera odorata Griff. (Anacardiaceae), was suggested to be a hybrid between M. indica L. and M. foetida Lour. due to morphological intermediacy. Results from this study show that M. indica and M. foetida produced unique amplified fragment length polymorphism (AFLP) profiles. Mangifera odorata did not produce any unique bands. All the M. odorata samples additively inherit bands specific to M. indica and M. foetida, which strongly suggested the hybrid origin. Three major clusters were produced in the phenogram. All samples of M. indica, M. foetida and M. odorata segregated distinctly. Mangifera odorata was closer to M. foetida than to M. indica, indicating that backcrossing with M. foetida might have taken place. AFLP analysis therefore verified the hybrid status of M. odorata.
Late glacial history of the cold‐adapted freshwater fish Cottus gobio, revealed by microsatellites
Authors: Hänfling B. , Hellemans B. , Volckaert F. A. M. , Carvalho G. R.
Published: March 2003

The distribution of genetic diversity at 10 highly polymorphic microsatellite loci within the European freshwater fish, Cottus gobio, L. was examined. The sampling range comprised a large geographical scale including lineages known to be highly divergent at both mitochondrial DNA (mtDNA) and allozymes. An analysis of genetic variability within populations showed that expected heterozygosity and allelic richness could be explained largely by current effective population sizes. Evidence was found, however, that historical processes predating the last major glaciation affected allelic richness. In addition to confirming the large‐scale patterns from earlier studies, the microsatellite data revealed new insights into recent processes by analysing genetic structure within ancient lineages defined by mtDNA data. Stepwise mutation model (SMM) and nonSMM‐based methods demonstrated a clear genetic structuring within the Northwestern European lineage comprising populations from Britain and Belgium, and within the Central European lineage populations from the rivers Danube, Elbe and Main. Supported by an analysis of genetic variability within populations these results showed that the bullhead populations most probably persisted throughout the last major glaciation within the British Isles and within the drainages of the rivers Elbe and Main. Such observations provide the first genetic evidence for a glacial refugium in such close proximity to the European glacial margins.
Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis
Authors: Estoup Arnaud , Jarne Philippe , Cornuet Jean‐Marie
Published: March 2003

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.
Mitochondrial pseudo‐control region in old world eagles (genus Aquila)
Authors: Väli Ü.
Published: March 2003

The mitochondrial pseudo‐control region was analysed in five species of Aquila eagles. Indels caused great length differences in the nonrepetitive part of the region, whereas tandem repeat units were highly conserved among the genus. In a reconstructed phylogenetic tree, the clade formed by A. clanga and A. pomarina showed approximately the same distance to A. chrysaetos as did the clade A. heliaca/nipalensis. In Estonian subpopulations, 12 haplotypes were found among 51 A. pomarina individuals and 7 haplotypes among 8 A. clanga individuals. Nucleotide diversity in A. clanga was greater, and may be caused by decreased breeding density or by gene flow from other subpopulations.
A genetic method to resolve gender complements investigations on sex ratios in Rumex acetosa
Authors: Korpelainen Helena
Published: March 2003

The perennial dioecious weed, Rumex acetosa, possesses sex chromosomes (XX in females, XY1Y2 in males). Yet, the operational sex ratios are female‐biased. Until now, sex ratio studies in R. acetosa, as in most plants, have relied on data obtained at sexual maturity. To resolve gender among the seeds and nonflowering plants of R. acetosa, a genetic method involving a DNA marker located on both Y chromosomes has now been developed and applied. The results suggest that the sex ratios are about 1 : 1 in the whole seed pool, but that a significant female bias develops by the time of flowering. Since the age of sexually mature plants is two years or more, the time frame during which the female bias present at sexual maturity develops can be several years. It appears that male seeds germinate at a lower rate and males suffer from a greater mortality during the years‐long lifespan of R. acetosa. However, there are no considerable sex‐related differences in vegetative vigour.
Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages
Authors: Stehlik I. , Blattner F. R. , Holderegger R. , Bachmann K.
Published: March 2003

Polymerase chain reaction–restriction fragment length polymorphisms (PCR‐RFLPs) and sequence analysis of noncoding regions of chloroplast DNA were used to investigate 37 populations of Eritrichium nanum covering its total distribution area, the European Alps. There was no haplotypic variation within the populations, and most haplotypes were restricted to single sites or to neighbouring populations, suggesting low levels of long distance gene flow via seeds. The present geographical distribution of haplotypes probably reflects an ancient geographical pattern within two regions in the intensely glaciated western and eastern central Alps identified as genetic hotspot areas. These two regions contained seven of the total of 11 haplotypes, including many of the most derived ones. The divergent haplotypes formed closely related groups, which supported a separate evolution of these haplotypes in these two regions and, more importantly, gave strong evidence for the in situ survival of these populations on nunataks within the western and eastern central Alps during Pleistocene glaciation. This result is in concordance with a previous study on E. nanum using nuclear markers. Only one haplotype was common and widespread throughout the distributional range of E. nanum. At the same time, it was the evolutionarily basal‐most and all other haplotypes were best described as its descendants. This haplotype is hypothesized to be genetically identical to a Tertiary Alpine colonizing ancestor, whose distribution was secondarily fragmented and infiltrated by derived haplotypes originating through local mutations.
Long‐term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations
Authors: Hansen Michael M. , Ruzzante Daniel E. , Nielsen Einar E. , Bekkevold Dorte , Mensberg Karen‐Lise D.
Published: March 2003

We examined the long‐term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo truttaL) collected from five anadromous populations in Denmark to assess the long‐term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise θSTestimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates ofNe, using a likelihood‐based implementation of the temporal method, revealedNe ≥ 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showedNe ≥ 300. Assuming a stepping‐stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations.Neappears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.