bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the population genetic structure of Gleditsia triacanthos L.: seed dispersal and variation in female reproductive success
Authors: SCHNABEL A. , NASON J. D. , HAMRICK J. L.
Published: March 2003

Fine‐scale genetic structuring is influenced by a variety of ecological factors and can directly affect the evolutionary dynamics of plant populations by influencing effective population size and patterns of viability selection. In many plant species, genetic structuring within populations may result from highly localized patterns of seed dispersal around maternal plants or by the correlated dispersal and recruitment of siblings from the same fruit. This fine‐scale genetic structuring may be enhanced if female parents vary significantly in their reproductive success. To test these hypotheses, we used genetic data from 17 allozyme loci and a maximum‐likelihood, ‘maternity‐analysis’ model to estimate individual female fertilities for maternal trees across a large number of naturally established seedlings and saplings in two populations of Gleditsia triacanthos L. (Leguminosae). Maximum‐likelihood fertility estimates showed that the three highest fertility females accounted for 58% of the 313 progeny at the first site and 46% of the 651 progeny at the second site, whereas 18 of 35 and 16 of 34 females, respectively, had fertility estimates that did not exceed 1%. Additional analyses of the second site found individual female fertility to vary significantly both within and among juvenile age classes. Female fertility at the first site was weakly correlated with maternal tree size and spatial location relative to the open, old‐field portions of the population, where the great majority of seedlings and saplings were growing, but no such correlations were found at the second site. Estimates of realized seed dispersal distances indicated that dispersal was highly localized at the first site, but was nearly random at the second site, possibly reflecting differences between the two sites in the behaviour of animal dispersers. The combined estimates of seed dispersal patterns and fertility variation are sufficient to explain previously described patterns of significant fine‐scale spatial genetic structure in these two populations. In general, our results demonstrate that effective seed dispersal distributions may vary significantly from population to population of a species due to the unpredictable behaviour of secondary dispersers. Consequently, the effects of seed dispersal on realized fine‐scale genetic structure may also be relatively unpredictable.
Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change
Authors: LUIKART G. , SHERWIN W. B. , STEELE B. M. , ALLENDORF F. W.
Published: March 2003

It is important to detect population bottlenecks in threatened and managed species because bottlenecks can increase the risk of population extinction. Early detection is critical and can be facilitated by statistically powerful monitoring programs for detecting bottleneck‐induced genetic change. We used Monte Carlo computer simulations to evaluate the power of the following tests for detecting genetic changes caused by a severe reduction in a population's effective size (Ne): a test for loss of heterozygosity, two tests for loss of alleles, two tests for change in the distribution of allele frequencies, and a test for smallNebased on variance in allele frequencies (the ‘variance test’). The variance test was most powerful; it provided an 85% probability of detecting a bottleneck of sizeNe= 10 when monitoring five microsatellite loci and sampling 30 individuals both before and one generation after the bottleneck. The variance test was almost 10‐times more powerful than a commonly used test for loss of heterozygosity, and it allowed for detection of bottlenecks before 5% of a population's heterozygosity had been lost. The second most powerful tests were generally the tests for loss of alleles. However, these tests had reduced power for detecting genetic bottlenecks caused by skewed sex ratios. We provide guidelines for the number of loci and individuals needed to achieve high‐power tests when monitoring via the variance test. We also illustrate how the variance test performs when monitoring loci that have widely different allele frequency distributions as observed in five wild populations of mountain sheep (Ovis canadensis).
Genetic diversity and population structure in two species of sea cucumber: differing patterns according to mode of development
Authors: ARNDT A. , SMITH M. J.
Published: March 2003

The population structure of two species of sea cucumber was examined based on mitochondrial DNA sequence analysis. Cucumaria miniata, a species with pelagic nonfeeding larvae lasting less than 2 weeks, and C. pseudocurata, a brooding species lacking a pelagic phase, both occur over similar wide ranges of the northeastern Pacific between Alaska and California. No significant genetic structuring was observed among C. miniata samples with 95% of the observed nucleotide variance attributable to that within population samples. Conversely, only 3.4% of the observed variance was attributed to that within C. pseudocurata population samples, with sampling sites typically greater than 100 km apart. At a finer scale, two C. pseudocurata population samples taken 5 km apart were not statistically different. A significant genetic disjunction was observed among populations of the brooding species, but not in species with pelagic larvae, north of Vancouver Island, Canada, corresponding to the splitting of the California and Alaska currents. Given the observed high levels of genetic diversity in northern samples, this genetic break indicates survival in northern, as well as southern, Pleistocene refugia. These results clearly demonstrate the effects that changes in life‐history patterns can have on dispersal, population structure, and the potential for speciation events.
Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers
Authors: COOK L. M. , SOLTIS P. S. , BRUNSFELD S. J. , SOLTIS D. E.
Published: March 2003

Polyploidy is widely recognized as a significant force leading to the formation of new plant species. Estimates of the number of angiosperm species with polyploid origins are as high as ≈ 50%; however, in spite of this prevalence, many aspects of polyploid evolution remain poorly understood. Recent studies have suggested that recurrent origins of polyploid species are the rule rather than the exception. The present study is one of only a few designed to quantify the number of independent origins of a polyploid species. The two tetraploid species Tragopogon mirus and T. miscellus (Asteraceae) arose within the past 50 years in the Palouse region of eastern Washington and adjacent northern Idaho. Previous work using morphology, cpDNA and rDNA restriction site analyses, allozymes, cytology, and flavonoid chemistry established that T. mirus had arisen at least five times, and T. miscellus at least twice, on the Palouse. To assess the frequency of multiple origins of these species more rigorously, seven populations of T. mirus and three populations of T. miscellus that were indistinguishable based on previous markers were surveyed using random amplified polymorphic DNA (RAPD) markers; populations of the diploid progenitor species from the same sites were also analysed. Each tetraploid population had a unique RAPD marker profile, suggesting that each population surveyed originated independently of the other populations in the region. Only two of the tetraploid populations combined the RAPD marker profiles of the diploid progenitors occurring at the same site. Both polyploid species, whose ranges and numbers have greatly increased since their formation in the early part of the twentieth century, have formed repeatedly on a local geographical scale and during a short time frame. Furthermore, each tetraploid species is spreading not primarily by dispersal of propagules from a single population of origin, but through repeated, independent polyploidization events that recreate the polyploid taxa.
Wolbachia in two insect host–parasitoid communities
Authors: WEST S. A. , COOK J. M. , WERREN J. H. , GODFRAY H. C. J.
Published: March 2003

Wolbachia form a group of intracellular bacteria that alter reproduction in their arthropod hosts. Two major phylogenetic subdivisions (A and B) of Wolbachia occur. Using a polymerase chain reaction assay we surveyed for the A and B group Wolbachia in 82 insect species from two temperate host–parasitoid communities (food webs) and a general collection of Lepidoptera caught at a light trap. One host–parasitoid community was based around leaf‐mining Lepidoptera, and the other around Aphids. We found that: (i) 22.0% of insects sampled were infected with Wolbachia; and (ii) the prevalence and type (A or B) of Wolbachia infection differed significantly between communities and taxonomic groups. We obtained DNA sequences from the ftsZ gene for the group B Wolbachia found in six leaf‐mining species and one of their parasitoids, as well as four of the Lepidoptera caught by a light trap. Taken together, the results of our survey and phylogenetic analyses of the sequence data suggest that host–parasitoid transfer of Wolbachia is not the major route through which the species we have examined become infected. In addition, the Wolbachia strains observed in five leaf‐mining species from the same genus were not closely related, indicating that transfer between species has not occurred due to a shared feeding niche or cospeciation.
Environmental calcium and mitochondrial DNA polymorphism among local populations of Gammarus fossarum (Crustacea, Amphipoda)
Authors: MEYRAN J. C. , GIELLY L. , TABERLET P.
Published: March 2003

Mitochondrial DNA sequence analysis was used to investigate genetic diversity and phylogeographic population structure among geographically isolated alpine populations of the amphipod Gammarus fossarum. This study was performed across a region with an important glacial history and substantial geographical variations in calcium levels, in order to evaluate the relative impact on the genetic diversity of the population history and this environmental factor known to be associated with local adaptation and population growth. Analysis of the nucleotide sequences for a 376‐bp segment of the cytochrome c oxidase I gene in 84 specimens from seven different populations revealed 20 different haplotypes distributed into five major lineages that are not geographically structured. Analysis of molecular variance indicates that the populations from the crystalline massif are less diverse than those living on limestone, suggesting a global correlation between genetic diversity and calcium concentration of the water. However, the role of this environmental factor appears to be indirect, with smaller population size leading to lower genetic diversity.
Postglacial recolonization patterns and genetic relationships among whitefish (Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers
Authors: HANSEN M. M. , MENSBERG K.‐L. D. , BERG S.
Published: March 2003

The genetic relationships among morphologically and geographically divergent populations of whitefish (genus: Coregonus) from Denmark and the Baltic Sea region were studied by analysis of microsatellites and polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis of mitochondrial DNA (mtDNA) segments. The endangered North Sea houting (classified as C. oxyrhynchus) differs morphologically and physiologically from other Danish whitefish (C. lavaretus). However, limited divergence of North Sea houting was observed both at the level of mtDNA and microsatellites. The implications of these results for the conservation status of North Sea houting are discussed in the light of current definitions of evolutionary significant units. Both mtDNA and microsatellite data indicated that postglacial recolonization by C. lavaretus in Denmark was less likely to have taken place from the Baltic Sea. Instead, the data suggested a recent common origin of all Danish whitefish populations, including North Sea houting, probably by recolonization via the postglacial Elbe River system. Estimates of genetic differentiation among populations based on mtDNA and microsatellites were qualitatively different. In addition, for both classes of markers analyses of genetic differentiation yielded different results, depending on whether molecular distances between alleles or haplotypes were included.
Subtle population structuring within a highly vagile marine invertebrate, the veined squid Loligo forbesi, demonstrated with microsatellite DNA markers
Authors: SHAW P. W. , PIERCE G. J. , BOYLE P. R.
Published: March 2003

Microsatellite DNA markers were applied for the first time in a population genetic study of a cephalopod and compared with previous estimates of genetic differentiation obtained using allozyme and mitochondrial DNA (mtDNA) markers. Levels of genetic variation detected with microsatellites were much higher than found with previous markers (mean number of alleles per locus=10.6, mean expected heterozygosity (HE)=0.79; allozyme HE=0.08; mtDNA restriction fragment length polymorphism (RFLP) HE=0.16). In agreement with previous studies, microsatellites demonstrated genetic uniformity across the population occupying the European shelf seas of the North East Atlantic, and extreme genetic differentiation of the Azores population (RST/FST=0.252/0.245; allozyme FST=0.536; mtDNA FST=0.789). In contrast to other markers, microsatellites detected more subtle, and significant, levels of differentiation between the populations of the North East Atlantic offshore banks (Rockall and Faroes) and the shelf population (RST=0.048 and 0.057). Breakdown of extensive gene flow among these populations is indicated, with hydrographic (water depth) and hydrodynamic (isolating current regimes) factors suggested as possible barriers to migration. The demonstration of genetic subdivision in an abundant, highly mobile marine invertebrate has implications for the interpretation of dispersal and population dynamics, and consequent management, of such a commercially exploited species. Relative levels of differentiation indicated by the three different marker systems, and the use of measures of differentiation (assuming different mutation models), are discussed.
Genetic diversity of rhizobia from Leucaena leucocephala nodules in Mexican soils
Authors: Wang En Tao , Martínez‐Romero Julio , Martínez‐Romero Esperanza
Published: March 2003

Leucaena species are leguminous plants native to Mexico. Using two L. leucocephala cultivars grown in different soils, we obtained 150 isolates from the nodules. Twelve rDNA types were identified which clustered into groups corresponding to Mesorhizobium, Rhizobium, and Sinorhizobium by restriction fragment length polymorphism (RFLP) of amplified 16S rRNA genes. Types 2, 4, 5, 6, 10, 11, and 12 were distinct from all the defined species. Others had patterns indistinguishable from some recognized species. Most of the isolates corresponded to Sinorhizobium. Forty‐one electrophoretic types (ETs) were identified among the isolates based on the different combinations of electrophoretic patterns of 13 metabolic enzymes. ETs were clustered into groups in general agreement with the rDNA types. Diverse plasmid patterns were obtained among the isolates, but common plasmids were observed among most isolates within rDNA types 5, 10, and 11. The symbiotic plasmids were identified among most of the isolates, except for the Mesorhizobium isolates. The affinities of host cultivars for different rhizobial groups and the impact of soil cultivation on the soil populations of rhizobia were analysed from the estimation of isolation frequencies and diversity. The results showed differences in rhizobial populations in cultivated and uncultivated soils and also differences in rhizobia trapped by L. leucocephala cv. Cunningham or Peruvian.
Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae)
Authors: Jackson  , Steane  , Potts  , Vaillancourt
Published: March 2003

Four highly differentiated chloroplast DNA (cpDNA) lineages were identified in the forest tree species Eucalyptus globulus Labill. (Myrtaceae) in Australia using restriction site polymorphisms from Southern analysis. The cpDNA variation did not conform with ssp. boundaries, yet there was a strong geographical pattern to the distribution of the lineages. One lineage (C) was geographically central and widespread, whereas the other three lineages were found in peripheral populations: Western (W), Northern (N) and Southern (S). Thirteen haplotypes were detected in E. globulus, seven of which belonged to clade C. At least three of the cpDNA lineages (C, N and S) were shared extensively with other species. On the east coast of the island of Tasmania, there was a major north–south difference in cpDNA in the virtually continuous distribution of E. globulus. Northern populations harboured haplotypes from clade C while southeastern populations harboured a single haplotype from clade S. This difference was also reflected in several co‐occurring endemic species. It is argued that the extensive cpDNA differentiation within E. globulus is likely to originate from interspecific hybridization and ‘chloroplast capture’ from different species in different parts of its range. Superficially, this hybridization is not evident in taxonomic traits; however, large‐scale common garden experiments have revealed a steep cline in quantitative genetic variation that coincides with the haplotype transition in Tasmania. Our cpDNA results provide the strongest evidence to date that hybridization has had a widespread impact on a eucalypt species and indicate that reticulate evolution may be occurring on an unappreciated scale in Eucalyptus.
Pollen dispersal inferred from paternity analysis in a mixed oak stand of Quercus robur L. and Q. petraea (Matt.) Liebl.
Authors: Streiff  , Ducousso  , Lexer  , Steinkellner  , Gloessl  , Kremer
Published: March 2003

Paternity analysis was used to determine the spatial distribution of male parents of 984 offspring collected from 13 identified mother trees in a natural stand of 5.76 ha and comprising 296 adult trees of Quercus petraea and Q. robur. For seven of the 13 maternal progeny arrays sampled, we found an excess of nearby matings and a preferential direction of pollination. For the remaining progeny arrays, no departure from random distribution of male parents was detected. A common trend among all families was a high percentage (averaging 65% for Q. robur and 69% for Q. petraea) of offspring that were pollinated by male parents from outside the study site. By pooling the data over all families, the average pollen dispersal curve within the stand was inferred and fitted to a negative exponential distribution. This model extrapolated for distances over the spatial scale of the study stand was insufficient to explain the high level of gene flow detected by the paternity analysis, suggesting a substantial level of long‐distance pollination events. The genetic composition of the pollen pools received by each maternal tree was compared and showed significant differentiation that could be attributed to differences in male reproductive success. By contrast, no significant differentiation between the pollen clouds from outside and inside the study stand was detected, suggesting genetic homogeneity between the surrounding forest and the study stand.
Genetic structure of harbour porpoisePhocoena phocoenapopulations in the northwest Atlantic based on mitochondrial and nuclear markers
Authors: Rosel P. E. , France S. C. , Wang J. Y. , Kocher T. D.
Published: March 2003

The harbour porpoise,Phocoena phocoena, experiences high levels of nonnatural mortality owing to interactions with commercial fisheries throughout its range. To accurately evaluate the significance of this bycatch, information on population structure is required. We have examined the population structure of this species in the northwest Atlantic Ocean using mitochondrial DNA (mtDNA) sequence and nuclear microsatellite data. Samples from four previously proposed summer breeding populations—the Gulf of Maine, eastern Newfoundland, the Gulf of St Lawrence and West Greenland—were analysed. Control‐region sequences revealed a significant partitioning of genetic variation among most of these summer populations, indicating that northwest Atlantic harbour porpoises should not be considered one panmictic population. Analysis of females alone yielded the highest levels of population subdivision, suggesting that females are more philopatric than males. At least three management units may be defined for harbour porpoises in the northwest Atlantic based on these data. Analysis of six microsatellite loci failed to detect significant population subdivision. Male‐mediated gene flow may maintain homogeneity among nuclear loci, while female philopatry is sufficient to produce a signal of population subdivision in the maternally inherited mtDNA genome. mtDNA analyses also indicate that winter aggregations of harbour porpoises along the US mid‐Atlantic states comprise animals from more than one summer breeding population.
Can multiple‐copy sequences of prey DNA be detected amongst the gut contents of invertebrate predators?
Authors: Zaidi R. H. , Jaal Z. , Hawkes N. J. , Hemingway J. , Symondson W. O. C.
Published: March 2003

The first experiments to clearly demonstrate that DNA techniques might be used to detect predator–prey interactions between arthropods are reported. The accurate modelling of such interactions has depended until now upon a mixture of laboratory experiments, population monitoring and biochemical tests. The latter involve gut‐content analyses, and have most recently depended upon the development of prey‐specific monoclonal antibodies. Although these are excellent for detecting predation on a target prey, they are impractical for analysing the prey range of a particular predator. Molecular detection depends upon the ability of DNA to resist digestion in the predator gut and of the polymerase chain reaction (PCR) to amplify prey‐specific DNA from semidigested material. As a first step, experiments using carabid beetles, Pterostichus cupreus L., as predators and mosquitoes as prey are reported. The target sequences were fully characterized multiple‐copy esterase genes from two laboratory strains of Culex quinquefasciatus Say. Although DNA was extracted from homogenates of whole beetles (minus appendages), a 146 bp product could be amplified from both mosquito strains digested in the beetle gut for 28 h. The larger, 263 bp product was detectable for 28 h in one mosquito strain, but could not be amplified after 5 h from the other. Whether the beetles had eaten one mosquito or six, digested for zero or 28 h, the prey were equally detectable. Having demonstrated that shorter, multiple‐copy sequences survive digestion for a considerable period in the gut of a predator, the opportunity exists to develop new detection systems for studying predation in the field.
Extra‐pair paternity in relation to male age in Bullock’s orioles
Authors: Richardson D. S. , Burke T.
Published: March 2003

Single‐locus minisatellite DNA profiling was used to assign paternity in a population of Bullock’s orioles,Icterus galbula bullockii, and to determine the contribution of age to a male’s success in obtaining extra‐pair paternity. There was a very low rate of intraspecific brood parasitism (2/202 = 1.0% of chicks). Older adult males lost less within‐pair paternity and gained more extra‐pair fertilizations than did yearling subadult males. This resulted in adult males benefiting from an annual reproductive success more than double that of subadult males. Behavioural observations, used to determine the role of female choice in extra‐pair copulations (EPCs), indicated that females actively participate in EPCs and that they prefer to obtain them from older males. While it was possible that females obtained EPCs as an insurance against the possible infertility of their social mate, the results of this study fit best with the hypothesis that females were attempting to obtain better‐quality genes for their offspring by obtaining EPCs with older, better‐quality males.
Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus)
Authors: Fowler E. V. , Houlden B. A. , Hoeben P. , Timms P.
Published: March 2003

Habitat fragmentation and destruction associated with the rapid urban and rural development of southeast Queensland presents an immediate threat to the survival of koala populations within this region. A sensitive method combining heteroduplex analysis (HDA) with temperature gradient gel electrophoresis (TGGE) was optimized to detect within‐species variation in a  mitochondrial DNA (mtDNA) control‐region fragment, ≈ 670 bp in length, from the koala. Eight different haplotypes were characterized in koalas, of which four were novel. Analysis of mtDNA diversity in 96 koalas from five populations in southeast Queensland revealed that the number of haplotypes in a single population ranged from one to five, with an average within‐population haplotype diversity of 0.379 ± 0.016, and nucleotide diversity of 0.22 ± 0.001%. Nucleotide divergence between populations averaged 0.09 ± 0.001% and ranged from 0.00 to 0.14%. Significant genetic heterogeneity was observed among most populations, suggesting that koala populations may be spatially structured along matrilines, although this may not be universal. The limited distribution of the central phylogenetic haplotype suggested the possibility of historical population bottlenecks north of the Gold Coast, while the presence of two highly divergent haplotypes at the Moreton site may indicate the occurrence of one or more undocumented translocation events into this area.
Patterns of paternal relatedness in British grey seal colonies
Authors: Wilmer J. Worthington , Overall A. J. , Pomeroy P. P. , Twiss S. D. , Amos W.
Published: March 2003

Previous studies of breeding behaviour in the grey seal, Halichoerus grypus, have painted conflicting pictures. Behavioural observations suggest a classical polygynous system with a small number of dominant males fathering most of the offspring. However, genetic analysis suggests that many potential fathers spend little time ashore, that some pairs of seals show partner fidelity and that the dominant males are not as successful as their behaviour would suggest. Here we used paternal relatedness between pups with known mothers, sampled over an 11‐year period, to show that behavioural dominance leading to enhanced fitness is a feature of only a handful of males located near the centre of the breeding colony. The vast majority of pups are fathered by any of a large number of males who all share approximately equal success, including virtually all those males who have previously escaped our best sampling efforts. As expected, the frequency of full‐sibs is reduced in this longer time series relative to the original study. However, absolute estimates of the frequency of full‐sibs seem to be confounded by a tendency for females who produce paternally unrelated pups to have conceived to males who are more genetically dissimilar from each other than expected by chance alone. Together, these elements of breeding behaviour would help to maintain maximum genetic diversity and to minimize the effects of inbreeding.
Molecular ecology and biological control: the mating system of a marsupial pest
Authors: Sarre S. D. , Aitken N. , Clout M. N. , Ji W. , Robins J. , Lambert D. M.
Published: March 2003

Many studies in molecular ecology have focused on the use of repeat DNA markers to determine the nature of mating systems in a wide variety of animal species. Whilst these studies typically have focused on important issues such as the evolutionary consequences of fitness variation among males, genetic studies of mating systems are potentially also important because they can generate information of significance to wider issues in wildlife management. For example, genetically modified, sexually transmitted viral diseases have been suggested as potential agents for the control of vertebrate pest species. An understanding of the epidemiology of such agents requires an intimate knowledge of the sexual contact rates between individuals of the target species. Here, we report the use of minisatellite DNA profiling to reveal the mating system in two New Zealand populations of the introduced Australian brushtail possum. The brushtail possum is New Zealand’s most important mammalian pest and a species for which control by a sexually transmitted immunocontraceptive has been proposed. Encouragingly, we report considerable variation in the reproductive success of males at both study sites, with one male siring offspring from four females in one year (mean no. of offspring/reproductively successful male/year at the two sites is 1.95–2.15), while many sired none. This bias in the pattern of reproductive success among males will probably facilitate the spread of an immunocontraceptive agent and thereby increase the power of this approach to biological control.
Microsatellite variation in Daphnia pulex from both sides of the Baltic Sea
Authors: Pálsson Snæbjörn
Published: March 2003

Despite large genetic differentiation among neighbouring populations of many freshwater zooplankton species, a macrogeographical homogeneity of allozyme variation is generally observed. A study on breeding systems in Scandinavian populations of Daphnia pulex suggested a latitudinally related cline in breeding system with both diploid cyclic parthenogens and diploid obligate parthenogens at the latitude of 60–61°N. Variation at neutral markers may be more affected by selection at linked loci in such species than in strictly sexual species. In this paper I present a study of variation at five microsatellite loci in a total of 34 populations from small ponds and rockpools on both sides of the Baltic Sea at 60–61°N. Two major groups, which may represent different species of the D. pulex complex, are defined with the microsatellites. Neighbouring populations show both similar and well differentiated genetic composition. Populations separated by larger geographical distances show only a large differentiation and a macrogeographic pattern. The large differentiation observed at small distances can be explained with small effective population size: variation at the microsatellite loci has been shaped by population bottlenecks followed with expansion in size, and possibly by selection. No conclusive evidence is found for obligative parthenogenesis.
Chloroplast DNA haplotype variation and population differentiation in Sorbus aucuparia L. (Rosaceae: Maloideae)
Authors: Raspé O. , Saumitou‐Laprade P. , Cuguen J. , Jacquemart A.‐L.
Published: March 2003

Intra‐specific chloroplast DNA (cpDNA) variation was studied in Sorbus aucuparia L., an entomophilous, mid‐or early successional tree producing fleshy fruits. Eight PCR‐amplified fragments of the chloroplast genome were screened for restriction fragment length polymorphisms, using one or two 4 bp‐cutter restriction endonucleases. cpDNA variation was investigated on two geographical scales: (1) among four regions in France and Belgium; and (2) within the Belgian region. A total of 150 individuals from six populations were analysed. Fourteen polymorphisms were detected in six of the cpDNA fragments. All polymorphisms probably resulted from insertions or deletions, and allowed the identification of 12 haplotypes. The level of genetic differentiation computed on the basis of haplotype frequencies was similar on the two geographical scales considered (GSTc = 0.286 among regions, GSTc = 0.259 among populations within the Belgian region). These values are much lower than those obtained in nine previously studied temperate tree species, which are all wind‐pollinated, late‐successional species producing dry fruits. These results might primarily be accounted for by the contrasting life history traits of S. aucuparia. In order to obtain insights into the relative contribution of pollen and seeds to gene flow, GSTc was also compared with previously obtained GST estimates based on allozyme data.
Genetic analysis and conservation of 31 surviving individuals of a rare New Zealand tree, Metrosideros bartlettii (Myrtaceae)
Authors: Drummond R. S. M. , Keeling D. J. , Richardson T. E. , Gardner R. C. , Wright S. D.
Published: March 2003

Metrosideros bartlettii (Myrtaceae) is a distinctive and extremely rare tree, endemic to New Zealand, first discovered in 1975. Prior to this study, a total of 19 adult individuals of the species had been reported; these are located in three small forest remnants in the far north of the North Island of New Zealand. Here we describe a total of 31 adult M. bartlettii at the three sites, including 12 individuals newly discovered by us. We analyse the genetic diversity of the species, using microsatellites to examine the chloroplast genome and amplified fragment length polymorphisms (AFLPs) to monitor nuclear variation. The results clearly demonstrate that M. bartlettii is a unique species, distinct from its two closest relatives M. robusta and M. excelsa. Analysis of genetic diversity within the 31 remaining individuals of M. bartlettii showed an average heterozygosity (< H >) of 0.18 and a proportion of polymorphic genes (< P >) of 0.44. Population structure, as shown by 286 AFLP loci, varied between the three geographical sites; the site with fewest individuals, containing two trees, showed some separation from the populations at the other two locations. These two latter sites, by contrast, had highly overlapping AFLP population diversity profiles. The implications of these results for conservation of the species are discussed.
Evolutionary genetics of metamorphic failure using wild‐caught vs. laboratory axolotls (Ambystoma mexicanum)
Authors: Voss S. R. , Shaffer H. B.
Published: March 2003

In many organisms metamorphosis allows for an ecologically important habitat‐shift from water to land. However, in some salamanders an adaptive life cycle mode has evolved that is characterized by metamorphic failure (paedomorphosis); these species remain in the aquatic habitat throughout the life cycle. Perhaps the most famous example of metamorphic failure is the Mexican axolotl (Ambystoma mexicanum), which has become a focal species for developmental biology since it was introduced into laboratory culture in the 1800s. Our previous genetic linkage mapping analysis, using an interspecific crossing design, demonstrated that a major gene effect underlies the expression of metamorphic failure in laboratory stocks of the Mexican axolotl. Here, we repeated this experiment using A. mexicanum that were sampled directly from their natural habitat at Lake Xochimilco, Mexico. We found no significant association between the major gene and metamorphic failure when wild‐caught axolotls were used in the experimental design, although there is evidence of a smaller genetic effect. Thus, there appears to be genetic variation among Mexican axolotls (and possibly A. tigrinum tigrinum) at loci that contribute to metamorphic failure. This result suggests a role for more than one mutation and possibly artificial selection in the evolution of the major gene effect in the laboratory Mexican axolotl.
Across the Southern Alps by river capture? Freshwater fish phylogeography in South Island, New Zealand
Authors: Waters Jonathan M. , Wallis Graham P.
Published: March 2003

We used DNA analysis of galaxiid fish to test a hypothesis of localized headwater capture in South Island, New Zealand. The restricted western, but widespread eastern, distributions of three nonmigratory freshwater fish species suggest that part of the east‐flowing Waiau River has been captured by the west‐flowing Buller River. However, mitochondrial control region (Kimura 2‐parameter distance = 4.1–5.4%) and microsatellite flanking sequences do not support a relationship between Waiau (N = 4 fish sequences) and western populations (N = 8) of Galaxias vulgaris. Instead, the point of capture is probably to the north‐east, perhaps the Nelson lakes region. Phylogenetic analysis indicates that western populations, along with populations in the north‐east (N = 18), represent a previously unidentified monophyletic Evolutionarily Significant Unit, possibly a cryptic species. We suggest a general caveat for zoogeographic conclusions based on distributional data alone.
Variation of haplotype distributions of two genomic regions of Citrus tristeza virus populations from eastern Spain
Authors: D’Urso F. , Sambade A. , Moya A. , Guerri J. , Moreno P.
Published: March 2003

Genetic variation in natural populations of Citrus tristeza virus (CTV) was studied using haplotypes detected by single‐strand conformation polymorphism (SSCP) analysis of two genomic regions (p20 gene and segment A, located in ORF1a). Analysis of 254 samples from 125 trees, collected at 12 different sites, yielded 8 different haplotypes for p20 and 5 for segment A. The most frequent haplotype of p20 was predominant at all sites, but several sites differed in the predominance of segment A haplotypes. At most sites, the homozygosity observed for the p20 gene tended to be higher than expected in a neutral evolution, whereas the opposite was true for segment A. Comparison of the populations at different sites showed that 44 of the 66 possible population pairs were genetically distinct for segment A, but only six pairs differed for the p20 gene. Analysis of molecular variance grouping trees by site, scion variety, rootstock or age, showed that variation in segment A was significantly affected by site, tree age and rootstock, and that variation between trees in each group and within trees was even more important. In contrast, variation in p20 was affected only by site and rootstock, each factor contributing to < 2% of the variation. The data suggest that sequence variations in segment A must be functionally less important and that it has less evolutionary constraints than p20. Detection of different haplotypes in neighbour trees or in samples from the same tree may help explain part of the variability observed in CTV symptom expression.
Tripartite genetic subdivisions in the ornate shrew (Sorex ornatus)
Authors: Maldonado Jesus E. , VilÀ Carles , Wayne Robert K.
Published: March 2003

We examined cytochromebsequence variation in 251 ornate shrews (Sorex ornatus) from 20 localities distributed throughout their geographical range. Additionally, vagrant (S. vagrans) and montane (S. monticolus) shrews from four localities were used as outgroups. We found 24 haplotypes in ornate shrews from California (USA) and Baja California (Mexico) that differed by 1–31 substitutions in 392 bp of mitochondrial DNA (mtDNA) sequence. In a subset of individuals, we sequenced 699 bp of cytochromebto better resolve the phylogeographic relationships of populations. The ornate shrew is phylogeographically structured into three haplotype clades representing southern, central and northern localities. Analysis of allozyme variation reveals a similar pattern of variation. Several other small California vertebrates have a similar tripartite pattern of genetic subdivision. We suggest that topographic barriers and expansion and contraction of wetland habitats in the central valley during Pleistocene glacial cycles account for these patterns of genetic variation. Remarkably, the northern ornate shrew clade is phylogenetically clustered with another species of shrew suggesting that it may be a unique lowland form of the vagrant shrew that evolved in parallel to their southern California counterparts.
Divergence betweenDrosophila santomeaand allopatric or sympatric populations ofD. yakubausing paralogous amylase genes and migration scenarios along the Cameroon volcanic line
Authors: Cariou M.‐L. , Silvain J.‐F. , Daubin V. , Da Lage J.‐L. , Lachaise D.
Published: March 2003

We have used two paralogous genes (AmyrelandAmy) of the amylase multigene family to reconstruct the phylogeny of the nineDrosophila melanogastersubgroup sister species, includingD. santomea, the newly discovered endemic from São Tomé island. The evolutionary divergence of these genes is of special interest as it is suspected to result from physiological evolution via gene duplication. This paper describes the relationship between the geographical origin of the various strains and the patterns of mating and phylogeny, focusing on the evolution ofD. santomeaand its relationship to other species and their niches. TheAmyrelandAmydata indicate that, contrary to expectations, the sympatric insularD. yakubapopulation is less closely related toD. santomeathan allopatric mainland ones, suggesting that the extant insularD. yakubapopulation on São Tomé results from a recent secondary colonization. Data for sympatric and allopatricD. yakubasuggest thatD. santomeaarose from a mainlandD. yakubaparental stock when montane habitats of the Cameroon volcanic line extended to lower altitudes during colder and less humid periods. Despite their different modes of evolution and different functions, theAmyrelandAmygenes provide remarkably consistent topologies and hence reflect the same history, that of the species.
Genetic variation and clonal diversity in four clonal sedges (Carex) along the Arctic coast of Eurasia
Authors: Stenström Anna , Jonsson B. Olle , Jónsdóttir Ingibjörg S. , Fagerström Torbjörn , Augner Magnus
Published: March 2003

We studied the structure of genetic variation (at both ramet‐ and genet‐level) and clonal diversity within and among populations in the four closely related arctic clonal sedges Carex bigelowii, C. ensifolia, C. lugens and C. stans by use of allozyme markers. Compared to other sedges and arctic plants, the studied taxa all had high levels of genetic variation, both within populations and taxa. These taxa contained most of the total gene diversity (HT) within populations and a small part of the diversity among populations (GST ranged 0.05–0.43). Carex bigelowii had genetic variation (HS = 0.173, mean for populations) at a comparable level to other outbreeding arctic plants and to other widespread, rhizomatous and mainly outbreeding Carex species. In contrast, C. ensifolia (HS = 0.335), C. lugens (HS = 0.339) and C. stans (HS = 0.294) had within‐population variations that were higher than in most other studied Carex species and for arctic plants in general. Genetic variation was not related to any tested environmental variable, but it was lower in areas deglaciated only 10 000 years

bp compared to areas deglaciated 60 000 years

bp or not glaciated at all during the Weichselian. All the populations were multiclonal, except for two populations of C. stans that were monoclonal. In contrast to genetic variation, clonal diversity decreased with latitude and did not differ between areas with different times of deglaciation. In accordance with previous studies, C. bigelowii and C. lugens were found to be outbreeding, while C. ensifolia and C. stans had mixed mating systems.
Correspondence between genet diversity and spatial distribution of above‐ and below‐ground populations of the ectomycorrhizal fungus Hebeloma cylindrosporum
Authors: Guidot A. , Debaud J.‐C. , Marmeisse R.
Published: March 2003

Population studies of ectomycorrhizal fungal species have largely relied upon fruit body (the reproductive organ) sampling. Analysis of the fruit bodies alone supposes that they reflect the present and spatial organization of all below‐ground genets (mycorrhizas and extramatrical mycelia). The relation between fruit bodies and ectomycorrhizas was investigated for the basidiomycete agaric Hebeloma cylindrosporum in four Pinus pinaster stands in south‐west France. Genet identification was based on the comparison of polymorphisms within a hypervariable segment of the ribosomal intergenic spacer amplified by polymerase chain reaction (PCR) using a H. cylindrosporum species‐specific primer. Mycorrhizas were sorted from soil samples collected underneath patches of fruit bodies or patches where fruit bodies had or had not been observed during the years prior to mycorrhiza collection. On average 65% of the 1026 mycorrhizas collected underneath fruit bodies were formed by H. cylindrosporum, whereas only 2% of the 954 collected in places from where fruit bodies were absent were formed by this species. All genotypes identified above ground were also identified below ground. In patches where one genotype formed all or more than 90% of the fruit bodies, the same genotype formed all or a large majority of the mycorrhizas. In patches occupied by several different fruiting genotypes, additional nonfruiting ones could be present on the root systems. In all cases, the mycorrhizas of one genotype were found no more than 10–20 cm away from its corresponding fruit bodies, and fruit body disappearance at a given place was associated with the disappearance of the corresponding mycorrhizas within 1 year. Although there was not a strict coincidence between the total numbers of genets present below ground and of those forming fruit bodies, fruit body analysis for H. cylindrosporum appears to reflect both the genetic diversity and the spatial structure of its below‐ground populations. The results obtained also illustrate the rapid turnover of ectomycorrhizal fungal species on the root systems in the absence of any obvious major disturbance of the ecosystem.
Conservation genetics of peripheral populations of the mygalomorph spider Atypus affinis (Atypidae) in northern Europe
Authors: Pedersen A. AA. , Loeschcke V.
Published: March 2003

Genetic diversity and differentiation were studied in peripheral populations of the recently rediscovered purse‐web spider Atypus affinis in Denmark and Sweden using allozyme electrophoresis. Because of the very narrow environmental niche exploited by this species, only a limited number of potential habitats are available. Furthermore, fragmentation has reduced the number and size of potential habitats within the last century. The level of genetic diversity in A. affinis was intermediate compared with other nonsocial spiders, but low compared with invertebrates in general. Significant genetic differentiation was found within distances of only 1–10 km with FST estimates ranging from 0.020 to 0.075. Within distances of 30–60 km FST ranged from 0.081 to 0.312. Hierarchical FST revealed that genetic variability was partitioned at 89.8% within populations, 9.5% among populations within regions and only 0.7% among the four main regions in Denmark and Sweden. Comparing the result of the genetic analysis with the life history of A. affinis, it is concluded that the level of successful dispersal is low, and that the species has not recently reinvaded northern Europe but prevailed undiscovered for several decades. Finally, it is suggested that the genetic scenario found for A. affinis might represent that for a wide range of other arthropods with similar life history characteristics.