bluuebunny/crossref_metadata_2025 huggingface dataset:
Reciprocal hybrid formation ofSpartinain San Francisco Bay
Authors: Anttila C. K. , King R. A. , Ferris C. , Ayres D. R. , Strong D. R.
Published: March 2003

Diversity in the tRNALEU1intron of the chloroplast genome ofSpartinawas used to study hybridization of native California cordgrass,Spartina foliosa, withS. alterniflora, introduced to San Francisco Bay ≈ 25 years ago. We sequenced 544 bases of the tRNALEU1intron and found three polymorphic sites, a pyrimidine transition at site 126 and transversions at sites 382 and 430.Spartinafrom outside of San Francisco Bay, where hybridization between these species is impossible, gave cpDNA genotypes of the parental species.S. foliosahad a single chloroplast haplotype, CCT, and this was unique to California cordgrass.S. alterniflorafrom the native range along the Atlantic coast of North America had three chloroplast haplotypes, CAT, TAA, and TAT. Hybrids were discriminated by random amplified polymorphic DNA (RAPD) phenotypes developed in a previous study. We found one hybrid that contained a cpDNA haplotype unknown in either parental species (TCT). The most significant finding was that hybridization proceeds in both directions, assuming maternal inheritance of cpDNA; 26 of the 36 hybridSpartinaplants from San Francisco Bay contained theS. foliosahaplotype, nine contained haplotypes of the invadingS. alterniflora, and one had the cpDNA of unknown origin. Furthermore, cpDNA of both parental species was distributed throughout the broad range of RAPD phenotypes, suggesting ongoing contributions to the hybrid swarm from both. The preponderance ofS. foliosacpDNA has entered the hybrid swarm indirectly, we propose, from F1s that backcross toS. foliosa. Flowering of the native precedes by several weeks that of the invading species, with little overlap between the two. Thus, F1 hybrids would be rare and sired by the lastS. foliosapollen upon the firstS. alterniflorastigmas. The native species produces little pollen and this has low viability. An intermediate flowering time of hybrids as well as pollen that is more vigourous and abundant than that of the native species would predispose F1s to high fitness in a vast sea of native ovules. Thus, spread of hybrids to otherS. foliosamarshes could be an even greater threat to the native species than introductions of alienS. alterniflora.
Dynamics of genotypic structure in clonal Rhododendron ferrugineum (Ericaceae) populations
Authors: Pornon A. , Escaravage N. , Thomas P. , Taberlet P.
Published: March 2003

Two populations of Rhododendron ferrugineum growing at subalpine level in the Pyrenees (France) were studied in two sites (Bethmale and Mourtis). Identification and delimitation of genets were inferred from amplified fragment length polymorphism (AFLP) markers, along a closure gradient (from meadow to more closed heath) in each site. Surface and age of genets, genotypic diversity (Simpson’s index D), ‘proportion distinguishable’ genotypes and genetic relationships between genets were then estimated. Amplification of the 312 DNA samples with three selective primer pairs gave a mean of 98 detectable peaks (i.e. bands) per sample, with size ranging from 60 to 300 bp. In total 60% (Bethmale) and 70% (Mourtis) of the peaks were polymorphic, and a total of 31 and 23 multilocus genotypes were identified, in Bethmale and Mourtis, respectively. We inferred that pioneer genotypes began arriving 110 years ago mainly over a 40‐year period in the Mourtis meadow, and began about 130 years ago over a 100‐year period in the Bethmale meadow. After this pioneer stage, populations extended vegetatively. Two different patterns of genotypic dynamics can be identified. At Bethmale, population closure could have led to a dramatic loss of genets and to the selection of highly genetically related genotypes. In contrast, at Mourtis, genotypic diversity and genet density did not change fundamentally along the closure gradient. However the range of genetic diversity diminished from the open to the closed situation, suggesting that thinning could have occurred in the past.
Offspring sex ratios in tree swallows: females in better condition produce more sons
Authors: Whittingham Linda A. , Dunn Peter O.
Published: March 2003

Organisms are expected to adjust the sex ratio of their offspring in relation to the relative fitness benefits of sons and daughters. We used a molecular sexing technique that amplifies an intron of the CHD1 gene in birds to examine the sex ratio at egg‐laying in socially monogamous tree swallows (Tachycineta bicolor). We examined all individuals in 40 broods (210 young), including all unhatched eggs and nestlings. Thus, the sex ratio we measured was the same as the sex ratio at laying. Overall, the mean sex ratio per brood (± SD) was biased significantly towards males (57 ± 2% male). Within broods, male‐biased sex ratios were associated with females in better body condition, and these females were more likely to produce sons in better condition. Tree swallows have one of the highest known levels of extra‐pair paternity in birds (38–76% extra‐pair young), and, as a consequence, variance in male reproductive success is greater than that of females. Thus, in tree swallows, investment in sons has the potential for higher fitness returns than investment in daughters, assuming that sons in better condition have greater reproductive success.
Genetic variation and population structure in the endangered greater horseshoe bat Rhinolophus ferrumequinum
Authors: Rossiter Stephen J. , Jones Gareth , Ransome Roger D. , Barratt Elizabeth M.
Published: March 2003

Following a dramatic decline last century, the British population of the endangered greater horseshoe bat Rhinolophus ferrumequinum is highly fragmented. To examine the consequences of fragmentation and limited dispersal on patterns of genetic structure and variation, we used microsatellite markers to screen bats from around 50% of the known maternity colonies in Britain, and two areas from continental Europe. Analyses revealed that Welsh and English colonies were genetically isolated. This, and lower variability in Britain than north France, may result from either genetic drift, or the species’ colonization history. Gene flow among most neighbouring colonies was not generally restricted, with one exception. These findings have important implications for the ongoing conservation management of this species.
Absence of evidence for isolation by distance in an expanding cane toad (Bufo marinus) population: an individual‐based analysis of microsatellite genotypes
Authors: Leblois Raphael , Rousset François , Tikel Dani , Moritz Craig , Estoup Arnaud
Published: March 2003

The cane toad (Bufo marinus) was introduced in 1935 in Australia, where it spread rapidly. We have tested for isolation by distance by analysing at a local geographical scale a continuous population using seven microsatellite markers and an individual‐based method. The matrix of pairwise individual differentiation was not significantly correlated with that of geographical distance. Regression analyses gave a low positive slope of 0.00072 (all individuals) or a negative slope of 0.0017 (individuals with a distance higher than the previously estimated mean dispersal distance). The absence of evidence for isolation by distance favours the hypothesis that the substantial differentiation and autocorrelation previously observed at enzyme loci, mainly results from discontinuities in the colonization process with founder effects occurring at the time of the establishment of new populations.
Identifying key cereal aphid predators by molecular gut analysis
Authors: Chen Y. , Giles K. L. , Payton M. E. , Greenstone M. H.
Published: March 2003

We describe polymerase chain reaction (PCR) primers for gut analysis of aphid predators. The primers amplify aphid mitochondrial COII fragments ranging in size from 77 to 386 bp. Using these primers, we were able to distinguish six species of US Great Plains cereal aphids, including two congeners,Rhopalosiphum maidis(Fitch) andR. padi(L.), and to detect them in extracts of coccinellid and chrysopid predators. We devised a protocol for deriving half‐lives of detectability for the DNA of a single aphid consumed by predators maintained under simulated field dietary and temperature conditions. Using this protocol and primers that amplify a 198‐bp fragment, we determined statistically different half‐lives of detectability for a singleR. maidisof 3.95 h inChrysoperla plorabunda(Fitch) and 8.78 h inHippodamia convergensGuerin. The detectability half‐life for a 339‐bpR. maidisfragment was statistically longer inC. plorabundabut not inH. convergens. The sensitivity of the assay for the 198‐bp fragment is 10−7aphid equivalents. For species‐specific predator gut analysis, PCR is superior to monoclonal antibody technology, giving comparable detectability half‐lives with lower expense, much shorter development times, and greater certainty of a successful outcome.
Morphological and molecular differentiation of invasive freshwater species of the genus Corbicula (Bivalvia,Corbiculidea) suggest the presence of three taxa in French rivers
Authors: Renard E. , Bachmann V. , Cariou M. L. , Moreteau J. C.
Published: March 2003

Asiatic Clams are common in brackish and fresh water in Asia, and they were introduced into North America in 1924 and have now spread throughout the continent. During the last two decades they have been reported in Europe, but the number of species here is uncertain. Populations of Corbicula from France and the Netherlands were analysed morphologically and genetically to quantify the degree of species and/or population differentiation. The morphological and genetic data, based on allozymes and mitochondrial sequences, were in full agreement. They indicate that there are two distinct species, identified as C. fluminalis and C. fluminea, in the two countries. Analyses of the mitochondrial COI gene revealed an unexpected divergent population of Corbicula in the Rhône. All these individuals were morphologically identified as C. fluminea, but had a COI sequence different from the two previous species. This population may, therefore, be a more ancient population, or a distinct species introduced via a different colonization route.
Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests
Authors: Kõljalg U. , Dahlberg A. , Taylor A. F. S. , Larsson E. , Hallenberg N. , Stenlid J. , Larsson K.‐H. , Fransson P. M. , Kårén O. , Jonsson L.
Published: March 2003

Resupinate thelephoroid fungi (hereafter called tomentelloid fungi) have a world‐wide distribution and comprise ≈70 basidiomycete species with inconspicuous, resupinate sporocarps. It is only recently that their ability to form ectomycorrhizas (EM) has been realized, so their distribution, abundance and significance as mycobionts in forest ecosystems is still largely unexplored. In order to provide baseline data for future ecological studies of tomentelloid fungi, we explored their presence and abundance in nine Swedish boreal forests in which the EM communities had been analysed. Phylogenetic analyses were used to compare the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) sequence data obtained from mycobionts on single ectomycorrhizal tips with that obtained from sporocarps of identified tomentelloid fungi. Five species of Tomentella and one species of Pseudotomentella were identified as ectomycorrhizal fungi. The symbiotic nature of Tomentella bryophila, T. stuposa, T. badia and T. atramentaria is demonstrated for the first time. T. stuposa and Pseudotomentellatristis were the most commonly encountered tomentelloid fungi, with the other species, including T. sublilacina, only being recorded from single stands. Overall, tomentelloid fungi were found in five of the studies, colonizing between 1 and 8% of the mycorrhizal root tips. Two of the five sites supported several tomentelloid species. Tomentelloid fungi appear to be relatively common ectomycorrhizal symbionts with a wide distribution in Swedish coniferous forests. The results are in accordance with accumulating data that fungal species which lack conspicuous sporocarps may be of considerable importance in EM communities.
Genetic (RAPD) diversity inPeromyscus maniculatuspopulations in a naturally fragmented landscape
Authors: Vucetich L. M. , Vucetich J. A. , Joshi C. P. , Waite T. A. , Peterson R. O.
Published: March 2003

We assessed the effects of long‐term habitat fragmentation on genetic (random amplified polymorphic DNA) diversity in 11Peromyscus maniculatuspopulations in the Lake Superior watershed. We analysed genetic structure at two spatial scales and the effect of island size and isolation on genetic diversity. At the regional scale, island populations differed from mainland populations (FST = 0.36), but mainland populations did not differ from each other (FST = 0.01). At the local scale, populations of the main island of Isle Royale differed from adjacent islet populations (P < 0.001; Monte Carlo approximation of Fisher’s exact test), but not from each other (combinedP = 0.63). Although geographical distance and genetic distance were positively correlated (P < 0.01; Mantel test), cluster analysis revealed some inconsistencies. Finally, genetic diversity was inversely related to isolation (P = 0.01), but had an unexpectedly negative relationship with island area (P = 0.03). The genetic structure ofP. maniculatuspopulations in portions of the Lake Superior watershed appears to have been affected by long‐term habitat fragmentation.
The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species‐level phylogenies
Authors: Ribera I. , Barraclough T. G. , Vogler A. P.
Published: March 2003

Most aquatic beetles in the family Dytiscidae are tightly associated either with running (lotic) or stagnant (lentic) water bodies. The range size of lotic species is known to be, on average, much smaller than that of lentic species, presumably as a result of differences in dispersal strategies in each habitat type. We explored possible effects of these differences on clade evolution and speciation rates by comparing species‐level phylogenies based on cytochrome oxidase I (COI) and 16S rRNA mitochondrial genes for two genera, the lenticIlybiusand the loticDeronectes. The expectation that species turnover is higher in lotic lineages due to their lower dispersal propensity compared to lentic species was not strongly supported.Deronectesdisplays a higher frequency of recent splits thanIlybius, consistent with the hypothesis, but the difference was not significant compared to expected patterns under a constant speciation rate null model. Similarly, when the degree of sympatry was plotted against relative node age, more allopatric splits were evident in the lenticDeronectes, suggesting a slower rate of range movement since speciation, but the differences were not significant. We discuss two explanations for our failure to detect differences between the two clades. First, current methods for analysing species‐level phylogenies may be sensitive to taxonomic and sampling artefacts. Second, lentic and lotic clades may indeed display similar levels of species turnover despite occupying very different habitats at different spatial scales. More work is needed to investigate the effects of population level processes and spatial scale on macroevolutionary dynamics.
Comparative allozyme and microsatellite population structure in a narrow endemic plant species,Centaurea corymbosaPourret (Asteraceae)
Authors: Freville H. , Justy F. , Olivieri I.
Published: March 2003

Centaurea corymbosaPourret (Asteraceae) is a narrow endemic species known only from six populations located in a 3‐km2area in the south of France. Earlier field experiments have suggested that pollen and seed dispersal were highly restricted within and among populations. Consistent with the field results, populations were highly differentiated for five allozyme loci and among‐population variation fitted an isolation‐by‐distance model. In the present study, we investigated the genetic structure ofC. corymbosausing six microsatellite loci. As with allozymes, microsatellites revealed no within‐population structure and a large differentiation among populations. However, allozyme loci were less powerful than microsatellites in detecting the extent of gene flow assessed by assignment tests. The patterns of structuration greatly varied among loci for both types of marker; we suggest that differences in single‐locus pattern could mainly be an effect of stochastic variation for allozymes and an effect of variation in mutation rate for microsatellites. In contrast to the multilocus results, the two most polymorphic microsatellite loci did not show any isolation‐by‐distance pattern. Our results suggest that highly variable loci might not always be the best suited markers to quantify levels of gene flow among populations.
Microsatellites reveal high levels of gene flow among populations of the California squid Loligo opalescens
Authors: Reichow D. , Smith M. J.
Published: March 2003

Information on the extent of genetic differentiation among populations of the squid Loligo opalescens is crucial for the conservation of this commercially utilized species. We analysed six highly variable microsatellite loci in 11 collections of L. opalescens from different locations and spawning seasons to estimate the relative influence of two major evolutionary forces, gene flow and genetic drift. Microsatellite allele frequency patterns suggest that gene flow prevents population differentiation in L. opalescens. Tests for genetic differentiation showed homogeneity of the samples with an overall FST/RST of 0.0028/−0.0013. Genetic uniformity among samples from different year classes indicates that allele frequency patterns in L. opalescens are relatively stable over time. However, a more complete and detailed picture of fine‐scale allele frequency shifts in this species will require a systematic microsatellite analysis of local populations over consecutive spawning cycles.
Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow
Authors: Hedrick P. W. , Parker K. M. , Lee R. N.
Published: March 2003

Highly variable loci can provide insight into the recognition of species, evolutionarily significant units (ESUs) and management units (MUs). In general, the ESU and MU categories are thought to be reflective of adaptive differences between them. Here we examine this premise by presenting a comprehensive examination of genetic variation for both microsatellite loci and a major histocompatibility complex (MHC) locus, thought to be of adaptive significance, in the endangered Sonoran topminnow. The extent of variation for the microsatellite loci and the MHC gene within the 13 populations of the Gila topminnow is highly correlated, suggesting that nonselective factors have played an important role in influencing variation within and between populations for the MHC locus. Therefore, using all of these loci, we found that the eight natural populations of the Gila topminnow fell into two different ESUs, one of which had four different MUs. The source of the Boyce Thompson sample, a population that was used extensively for restocking, appeared to be Monkey Spring. The source of the Watson Wash population also appeared to be Monkey Spring (or Boyce Thompson). The newly colonized Santa Cruz River population, which had the most genetic variation of any Gila topminnow population, appeared to descend primarily from Sonoita Creek populations. The Yaqui topminnow, presently considered another subspecies of the Sonoran topminnow, was very distinct for both microsatellite (only two of 25 alleles found in the Yaqui were in any of the Gila topminnow samples) and MHC alleles (nonoverlapping sets of alleles for the two groups). As a result, it appeared that the taxonomic status of the two subspecies should be re‐evaluated and that full species status for Gila and Yaqui topminnows was appropriate. There was evidence for the importance of long‐term selection at the MHC locus in the higher rate of nonsynonymous than synonymous substitution. In addition, there appeared to have been a duplication of the MHC locus that was present in most of the fish in six of the natural populations of the Gila topminnow.
Assessment of concordance among genealogical reconstructions from various mtDNA segments in three species of Pacific salmon (genus Oncorhynchus)
Authors: Churikov D. , Matsuoka M. , Luan X. , Gray A. K. , Brykov VL. A. , Gharrett A. J.
Published: March 2003

Seven segments of mitochondrial DNA (mtDNA), comprising 97% of the mitochondrial genome, were amplified by polymerase chain reaction (PCR) and examined for restriction site variation using 13 restriction endonucleases in three species of Pacific salmon: pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon. The distribution of variability across the seven mtDNA segments differed substantially among species. Little similarity in the distribution of variable restriction sites was found even between the mitochondrial genomes of the even‐ and odd‐year broodlines of pink salmon. Significantly different levels of nucleotide diversity were detected among three groups of genes: six NADH‐dehydrogenase genes had the highest; two rRNA genes had the lowest; and a group that included genes for ATPase and cytochrome oxidase subunits, the cytochrome b gene, and the control region had intermediate levels of nucleotide diversity. Genealogies of mtDNA haplotypes were reconstructed for each species, based on the variation in all mtDNA segments. The contributions of variation within different segments to resolution of the genealogical trees were compared within each species. With the exception of sockeye salmon, restriction site data from different genome segments tended to produce rather different trees (and hence rather different genealogies). In the majority of cases, genealogical information in different segments of mitochondrial genome was additive rather than congruent. This finding has a relevance to phylogeographic studies of other organisms and emphasizes the importance of not relying on a limited segment of the mtDNA genome to derive a phylogeographic structure.
Phylogeography of the Alpine salamander,Salamandra atra(Salamandridae) and the influence of the Pleistocene climatic oscillations on population divergence
Authors: Riberon A. , Miaud C. , Grossenbacher K. , Taberlet P.
Published: March 2003

Fifty individuals of the endemic Alpine salamander,Salamandra atra, representing 13 populations throughout the range of the two currently recognized subspecies,atraandaurorae, were examined for sequence variation in a large portion (1050 bp) of the mitochondrial cytochromebgene. We revealed a large number of mitochondrial DNA (mtDNA) haplotypes (10). Interpopulation sequence divergence was very low, ranging from 0 to 3.1%. The relationships among haplotypes were poorly resolved. The divergence time estimate between several mtDNA haplotypes suggested a pre‐Pleistocene differentiation approximately 3 million years ago. Moreover, the impact of the Pleistocene glaciations on the phylogeographical patterns appears to have been secondary, although a somewhat reduced genetic variability was found in populations living in areas that were directly affected by the glaciation.
Late Quaternary distributional stasis in the submediterranean mountain plant Anthyllis montana L. (Fabaceae) inferred from ITS sequences and amplified fragment length polymorphism markers
Authors: Kropf Matthias , Kadereit Joachim W. , Comes Hans Peter
Published: March 2003

Anthyllis montana is a submediterranean, herbaceous plant of the southern and central European mountains. The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from multiple accessions of the species and several closely related taxa. In addition, amplified fragment length polymorphism (AFLP) was analysed from 71 individuals of A. montana collected in 20 localities, mainly in the Pyrenees, Alps, Italian Peninsula and Balkans. Our ITS phylogeny showed a sequential branching pattern in A. montana, implying a western Mediterranean origin followed by an eastward migration. ITS clock calibrations suggest that speciation of A. montana took place at the Pliocene–Pleistocene boundary, while intraspecific divergence dates to Late Quaternary times (i.e. 0.7 million years ago). The AFLP analyses revealed a major genetic (west/east) subdivision within A. montana, probably caused by the massive glaciation of the Alps during this latter time period. The present‐day absence of A. montana from vast parts of the Alps, which appear ecologically suitable for the species, together with the finding of evenly distributed AFLP variability within each of the two western and eastern lineages identified, is taken as evidence for a largely static Late Quaternary history without large‐scale migration. High levels of AFLP variation observed among populations, together with weak or absent patterns of isolation by distance, seem to be in accord with long‐term population insularization and distributional stasis. However, recent small‐scale migration and a narrow hybrid zone between western and eastern lineages need to be postulated to explain the intermediate genetic composition of individuals from the Maritime Alps, a well‐known suture‐zone for other plant and animal species.
Genetic diversity and differentiation of Kermode bear populations
Authors: Marshall H. D. , Ritland K.
Published: March 2003

The Kermode bear is a white phase of the North American black bear that occurs in low to moderate frequency on British Columbia’s mid‐coast. To investigate the genetic uniqueness of populations containing the white phase, and to ascertain levels of gene flow among populations, we surveyed 10 highly polymorphic microsatellite loci, assayed from trapped bear hairs. A total of 216 unique bear genotypes, 18 of which were white, was sampled among 12 localities. Island populations, where Kermodes are most frequent, show ≈ 4% less diversity than mainland populations, and the island richest in white bears (Gribbell) exhibited substantial genetic isolation, with a mean pairwise FST of 0.14 with other localities. Among all localities, FST for the molecular variant underlying the coat‐colour difference (A893G) was 0.223, which falls into the 95th percentile of the distribution of FST values among microsatellite alleles, suggestive of greater differentiation for coat colour than expected under neutrality. Control‐region sequences confirm that Kermode bears are part of a coastal or western lineage of black bears whose existence predates the Wisconsin glaciation, but microsatellite variation gave no evidence of past population expansion. We conclude that Kermodism was established and is maintained in populations by a combination of genetic isolation and somewhat reduced population sizes in insular habitat, with the possible contribution of selective pressure and/or nonrandom mating.
Reproductive success in reindeer males in a herd with varying sex ratio
Authors: Røed Knut H. , Holand Øystein , Smith Martin E. , Gjøstein Hallvard , Kumpula Jouko , Nieminen Mauri
Published: March 2003

In polygynous species, male reproductive success is often correlated with dominance status of individual males and sex ratio in the population. Reindeer,Rangifer tarandus, is a polygynous species, and here we compared the variation in male reproductive success and dominance status during two successive years in a herd with a male:female sex ratio of 1:7 and 1:3. Copulations were recorded, together with data on male dominance hierarchy and size of mating groups. Male reproductive success was estimated by paternity analysis of calves using microsatellite DNA markers. The distribution of reproductive success among the males was highly skewed for both years with the most dominant male also being the most successful. The largest mating group was established in the herd with the least skew in sex ratio. In this herd some of the adult males present were less reproductively successful than some of the more subordinate younger males. Estimates of the mating group size of males, correcting for dominance status when more than one male is present in the groups, gave good prediction of individual males’ reproductive success.
Temporal change in the genetic structure between and within cohorts of a marine fish, Diplodus sargus, induced by a large variance in individual reproductive success
Authors: Planes S. , Lenfant P.
Published: March 2003

Temporal changes at 16 allozyme loci in the Diplodus sargus population of Banyuls‐sur‐Mer (Mediterranean Sea, France) were monitored. Temporal genetic variation within a single population was examined over two temporal scales: (i) among three year‐classes sampled at the same age, and (ii) within a single year‐class sampled three times over a two‐year period. We observed a significant change in the genotypic structure within the same cohort during the first two years following settlement and before recruitment into the adult population. In addition, comparison of year‐classes showed that cohorts differed significantly one year after settlement, whereas they became similar later on before recruitment into the adult population. The observed changes in the genetic structure within and between year‐classes may be the result of complex selective processes or genetic drift. Linkage disequilibrium and genetic relatedness data suggest that these changes are due to large variation in reproductive success, followed by homogenization through adult movement. Overall, these results demonstrated a rapid genetic change within a population.
Genetic diversity in natural and anthropogenic inland populations of salt‐tolerant plants: random amplified polymorphic DNA analyses of Aster tripolium L. (Compositae) and Salicornia ramosissima Woods (Chenopodiaceae)
Authors: Krüger A. M. , Hellwig F. H. , Oberprieler C.
Published: March 2003

Eight populations of Aster tripolium (Compositae) and six of Salicornia ramosissima (Chenopodiaceae) from inland, naturally salt‐contaminated habitats and anthropogenic salt‐polluted sites in central Germany (Thuringia, Anhalt‐Saxony) were analysed using random amplified polymorphic DNA (RAPD) markers to investigate the patterns of genetic variation. In both species, the genetic diversity observed in the younger, anthropogenic sites caused by potash mines during the last century was found to be not significantly lower than in the older, naturally salt‐contaminated habitats. Therefore, it is speculated that the loss of genetic diversity caused by founder effects on the anthropogenic habitats was balanced by successive colonization events, actual gene flow between populations, or the rapid growth of populations on the secondary habitats after colonization. Analyses of molecular variance (amova) of the RAPD markers, neighbour‐joining clustering of populations based on Reynolds’ co‐ancestry distances, and Mantel tests indicate that: (i) anthropogenic habitats were colonized independently; (ii) genetic differentiation among populations of S. ramosissima is more pronounced than in A. tripolium, which is considered to be mainly due to biological differences between the two species; and (iii) the geographical pattern of genetic diversity was considerably modulated by historical events and/or population genetic effects.
Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces
Authors: Janzen Fredric J. , Krenz James G. , Haselkorn Tamara S. , Brodie Edmund D. , Edmund D. Brodie III
Published: March 2003

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well‐supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.
Genetic parentage assessment in the crayfish Orconectes placidus, a high‐fecundity invertebrate with extended maternal brood care
Authors: Walker D. , Porter B. A. , Avise J. C.
Published: March 2003

Microsatellite data have recently been introduced in the context of genetic maternity and paternity assignments in high‐fecundity fish species with single‐parent‐tended broods. Here we extend such analyses to an aquatic invertebrate, the crayfish Orconectes placidus, in which gravid females carry large numbers of offspring. Genetic parentage analyses of more than 900 progeny from 15 wild crayfish broods revealed that gravid females were invariably the exclusive dams of the offspring they tended (i.e. there was no allomaternal care), and that most of the females had mated with multiple (usually two) males who contributed sometimes highly skewed numbers of offspring to a brood. Within any multiply sired brood, the unhatched eggs (or the hatched juveniles) from different fathers were randomly distributed across the mother's brood space. All of these genetic findings are discussed in the light of observations on the mating behaviours and reproductive biology of crayfishes.
Taxonomic complexity and breeding system transitions: conservation genetics of theEpipactis leptochilacomplex (Orchidaceae)
Authors: Squirrell J. , Hollingsworth P. M. , Bateman R. M. , Tebbitt M. C. , Hollingsworth M. L.
Published: March 2003

The genusEpipactiscontains a problematical complex of autogamous taxa among which species limits are difficult to define. Different authors have treated these plants in different ways, some recognizing the different taxa as distinct species, others considering them as minor intraspecific variants. These contrasting treatments have a direct impact on the conservation resources and status such plants command; ‘endemic orchid species’ are perceived as having high conservation value, ‘localized minor variants’ are not. We used allozyme and chloroplast restriction fragment length polymorphism (RFLP) and sequencing analyses to investigate patterns of population genetic structure underlying the taxonomic complexity in this group. Populations ofE. dunensis,E. leptochilaandE. muelleriwere homozygous and uniform for all loci studied here. There were, however, fixed genetic differences among these taxa. Comparisons with published data from the putative progenitor species for the autogamous taxa (the widespread, allogamousE. helleborine) suggest iterative origins of autogamy, rather than the self‐pollinating taxa all being merely mutational variants of a single autogamous lineage.
Estimating allelic richness: Effects of sample size and bottlenecks
Authors: Leberg P. L.
Published: March 2003

Although differences in sampling intensity can bias comparisons of allelic richness (A) among populations, investigators often fail to correct estimates ofAfor differences in sample size. Methods that standardizeAon the basis of the size of the smallest number of samples in a comparison are preferable to other approaches. Rarefaction and repeated random subsampling provide unbiased estimates ofAwith the greatest precision and thus provide greatest statistical power to detect differences in variation. Less promising approaches, in terms of bias or precision, include single random subsampling, eliminating very small samples, using sample size as a covariate or extrapolating estimates obtained from small samples to a larger number of individuals.
Phylogeography of field voles (Microtus agrestis) in Eurasia inferred from mitochondrial DNA sequences
Authors: Jaarola Maarit , Searle Jeremy B.
Published: March 2003

In a distribution‐wide phylogeographic survey of the field vole (Microtus agrestis), 75 specimens from 56 localities across Eurasia were examined for DNA sequence variation along the whole 1140 base pair (bp) mitochondrial (mt) cytochrome b gene. The species is subdivided into three main mtDNA phylogeographic groups — western, eastern and southern — with largely allopatric distributions. The western phylogeographical group is found in west and central Europe and spread most probably from a glacial refugium in the Carpathians. The eastern group covers a large range from Lithuania to central Asia, and probably originated from a southeast European source (e.g. the southern Urals or the Caucasus). The southern group occupies an area from Portugal to Hungary, with division into two distinct mtDNA sublineages that presumably derive from separate glacial refugia in the Iberian Peninsula. Molecular clock estimates suggest that the western and eastern field vole populations separated during the last glaciation, whereas the southern population dates back 0.5–0.9 Myr. High levels of mtDNA variation indicate relatively large population sizes and subdivisions within phylogeographic groups during the last glaciation. We report a possible new suture zone in east Europe.
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review
Authors: Li You‐Chun , Korol Abraham B. , Fahima Tzion , Beiles Avigdor , Nevo Eviatar
Published: March 2003

Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.
Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites
Authors: Llewellyn K. S. , Loxdale H. D. , Harrington R. , Brookes C. P. , Clark S. J. , Sunnucks P.
Published: March 2003

Genetic structuring of populations reflects the interaction of genetic drift, mutation, migration and selection, with influences from life history. Aphids are interesting in this regard as they have the potential for unusually high levels of dispersal and natural selection, which typically counter each other. In the present study, winged grain aphidsSitobion avenae(F.) were collected in four 12.2‐m high suction traps along a north–south transect in Britain in order to eliminate sampling bias from plant hosts (cereals and grasses; Poaceae), it being known that these insects show host adaptation demonstrable using molecular markers. Samples were analysed at four polymorphic microsatellite loci over two consecutive years. Population allele frequencies were similar nationally during the two years, although clonal diversity varied greatly between sites and years. In the first sampling year following a harsh winter, diversity was found to display a latitudinal clinal trend: the proportion of unique clones (genotypes) increased with latitude. However, this pattern was less apparent the following year, after a milder winter. Nonetheless, overallFSTanalysis showed that there was little spatial genetic structuring in either sampling year. These data support the view that the insect is highly migratory and also support a theoretical model and previous data suggesting that the reproductive mode is clinal inS. avenae. This appears to be because natural selection (reduced reproductive success of asexual genotypes under cold conditions) is sufficiently powerful to overcome the homogenizing effects of strong migration. There was no clear evidence for isolation by distance for the genetic data obtained. The data are compared with similar data from other aphid species and other insects. Only by the collection of such data sets can an accurate picture be built up relating genetic variability to flight behaviour, including migratory ambit in this group of insects since, due to their small size and rapid dilution in the air, other marking approaches are impracticable over large geographical distances.
Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout
Authors: Ardren William R. , Kapuscinski Anne R.
Published: March 2003

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.
Habitat differentiation vs. isolation‐by‐distance: the genetic population structure of Elymus athericus in European salt marshes
Authors: Bockelmann A.‐C. , Reusch T. B. H. , Bijlsma R. , Bakker J. P.
Published: March 2003

We investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt‐marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt‐marsh species, we were interested in population differentiation through isolation‐by‐distance, and among strongly divergent habitats (low and high marsh) in this wind‐ and water‐dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross‐species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation‐by‐distance was present only on larger scales (60–443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation‐by‐distance) effects among six sites 2.5–443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection‐mediated restrictions to gene flow simultaneously.
Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle
Authors: Perlman Steve J. , Spicer Greg S. , Shoemaker D. Dewayne , Jaenike John
Published: March 2003

Little is known about what determines patterns of host association of horizontally transmitted parasites over evolutionary timescales. We examine the evolution of associations between mushroom‐feeding Drosophila flies (Diptera: Drosophilidae), particularly in the quinaria and testacea species groups, and their horizontally transmitted Howardula nematode parasites (Tylenchida: Allantonematidae). Howardula species were identified by molecular characterization of nematodes collected from wild‐caught flies. In addition, DNA sequence data is used to infer the phylogenetic relationships of both host Drosophila (mtDNA: COI, II, III) and their Howardula parasites (rDNA: 18S, ITS1; mtDNA: COI). Host and parasite phylogenies are not congruent, with patterns of host association resulting from frequent and sometimes rapid host colonizations. Drosophila‐parasitic Howardula are not monophyletic, and host switches have occurred between Drosophila and distantly related mycophagous sphaerocerid flies. There is evidence for some phylogenetic association between parasites and hosts, with some nematode clades associated with certain host lineages. Overall, these host associations are highly dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared breeding sites and large potential host ranges of the nematodes.