bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractMost 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

AbstractCentaurea 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

AbstractInformation 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

AbstractHighly 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

AbstractSeven 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

AbstractFifty 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

Abstract 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

AbstractThe 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

AbstractIn 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

AbstractTemporal 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

AbstractEight 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

AbstractComplete 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

AbstractMicrosatellite 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

AbstractThe 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

AbstractAlthough 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.