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Population Genetics (population + genetics)
Terms modified by Population Genetics Selected AbstractsDO RECENT FINDINGS IN PLANT MITOCHONDRIAL MOLECULAR AND POPULATION GENETICS HAVE IMPLICATIONS FOR THE STUDY OF GYNODIOECY AND CYTONUCLEAR CONFLICT?EVOLUTION, Issue 5 2008David E. McCauley The coexistence of females and hermaphrodites in plant populations, or gynodioecy, is a puzzle recognized by Darwin. Correns identified cytoplasmic inheritance of one component of sex expression, now known as cytoplasmic male sterility (CMS). Lewis established cytonuclear inheritance of gynodioecy as an example of genetic conflict. Although biologists have since developed an understanding of the mechanisms allowing the joint maintenance of CMS and nuclear male fertility restorer genes, puzzles remain concerning the inheritance of sex expression and mechanisms governing the origination of CMS. Much of the theory of gynodioecy rests on the assumption of maternal inheritance of the mitochondrial genome. Here we review recent studies of the genetics of plant mitochondria, and their implications for the evolution and transmission of CMS. New studies of intragenomic recombination provide a plausible origin for the chimeric ORFs that characterize CMS. Moreover, evidence suggests that nonmaternal inheritance of mitochondria may be more common than once believed. These findings may have consequences for the maintenance of cytonuclear polymorphism, mitochondrial recombination, generation of gynomonoecious phenotypes, and interpretation of experimental crosses. Finally we point out that CMS can alter the nature of the cytonuclear conflict that may have originally selected for uniparental inheritance. [source] ANTHROPOGENIC EFFECTS ON POPULATION GENETICS OF PHYTOPHAGOUS INSECTS ASSOCIATED WITH DOMESTICATED PLANTSEVOLUTION, Issue 12 2007Nadir Alvarez The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (P < 10,4), no IBD was found when pairs of beetle populations on domesticated beans were examined (P= 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides. [source] THE POPULATION GENETICS OF ADAPTATION ON CORRELATED FITNESS LANDSCAPES: THE BLOCK MODELEVOLUTION, Issue 6 2006H. Allen Orr Abstract Several recent theoretical studies of the genetics of adaptation have focused on the mutational landscape model, which considers evolution on rugged fitness landscapes (i.e., ones having many local optima). Adaptation in this model is characterized by several simple results. Here I ask whether these results also hold on correlated fitness landscapes, which are smoother than those considered in the mutational landscape model. In particular, I study the genetics of adaptation in the block model, a tunably rugged model of fitness landscapes. Considering the scenario in which adaptation begins from a high fitness wild-type DNA sequence, I use extreme value theory and computer simulations to study both single adaptive steps and entire adaptive walks. I show that all previous results characterizing single steps in adaptation in the mutational landscape model hold at least approximately on correlated landscapes in the block model; many entire-walk results, however, do not. [source] THE POPULATION GENETICS OF SPOROPHYTIC SELF-INCOMPABILITY IN SENECIO SQUALIDUS L. (ASTERACEAE): THE NUMBER, FREQUENCY, AND DOMINANCE INTERACTIONS OF S ALLELES ACROSS ITS BRITISH RANGEEVOLUTION, Issue 2 2006Adrian C. Brennan Abstract Sporophytic self-incompatibility (SSI) was studied in 11 British Senecio squalidus populations to quantify mating system variation and determine how its recent colonization of the United Kingdom has influenced its mating behavior. S allele number, frequency, and dominance interactions in populations were assessed using full diallels of controlled pollinations. A mean of 5.1 S alleles per population was observed, and no population contained more than six S alleles. Numbers of S alleles within populations of S. squalidus declined with increasing distance from the center of its introduction (Oxford). Cross-classification of S alleles allowed an estimate of approximately seven and no more than 11 S alleles for the entire British S. squalidus population. The low number of S alleles observed in British S. squalidus compared to other SI species is consistent with the population bottleneck associated with S. squalidus introduction to the Oxford Botanic Garden and subsequent colonization of Britain. Extensive S allele dominance interactions were observed to be a feature of the S. squalidus SSI system and may represent an adaptive response to improve limited mate availability imposed by the presence of so few S alleles. Multilocus allozyme genotypes were also identified for individuals in all populations and geographic patterns of S locus and allozyme loci variation investigated. Less interpopulation structure was observed for the S locus than for allozyme diversity-a finding indicative of the effects of negative frequency-dependent selection at the S locus maintaining equal S phenotypes within populations and enhancing effective migration between populations [source] THE POPULATION GENETICS OF ADAPTATION: THE ADAPTATION OF DNA SEQUENCESEVOLUTION, Issue 7 2002H. Allen Orr Abstract I describe several patterns characterizing the genetics of adaptation at the DNA level. Following Gillespie (1983, 1984, 1991), I consider a population presently fixed for the ith best allele at a locus and study the sequential substitution of favorable mutations that results in fixation of the fittest DNA sequence locally available. Given a wild type sequence that is less than optimal, I derive the fitness rank of the next allele typically fixed by natural selection as well as the mean and variance of the jump in fitness that results when natural selection drives a substitution. Looking over the whole series of substitutions required to reach the best allele, I show that the mean fitness jumps occurring throughout an adaptive walk are constrained to a twofold window of values, assuming only that adaptation begins from a reasonably fit allele. I also show that the first substitution and the substitution of largest effect account for a large share of the total fitness increase during adaptation. I further show that the distribution of selection coefficients fixed throughout such an adaptive walk is exponential (ignoring mutations of small effect), a finding reminiscent of that seen in Fisher's geometric model of adaptation. Last, I show that adaptation by natural selection behaves in several respects as the average of two idealized forms of adaptation, perfect and random. [source] HARTL, D. L.: A Primer of Population Genetics.JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2001Inc. Publishers, Sinauer Associates, Sunderland [source] Does Species Range and Rarity Affect Population Genetics?BIOTROPICA, Issue 4 2007A Case Study of Four Graptophyllum Species from Queensland, Australia ABSTRACT There are four species of Graptophyllum (Acanthaceae) in Australia which span a gradient in rarity and conservation status from the most endangered, Graptophyllum reticulatum (endangered), to G. ilicifolium (vulnerable), to G. excelsum (rare), to the least endangered G. spinigerum (widespread). Graptophyllum reticulatum and G. ilicifolium are each only known from three locations. All species were found to have quite high levels of genetic diversity (He, A, Ap, P) and there was no significant difference among species in genetic diversity (P > 0.05), thus, genetic diversity was unrelated to conservation status or species geographic range. All species had high allelic fixation values (F ), indicating that populations were effectively inbred regardless of conservation status and geographic range. The genetic diversity among populations (FST) was not related to rarity and contrasted among the most restricted species, where diversity among populations was twice as high among G. reticulatum populations (FST, 0.22) compared with among G. ilicifolium populations (FST, 0.11). [source] Population genetics of the European trout (Salmo trutta L.) migration system in the river Rhine: recolonisation by sea troutECOLOGY OF FRESHWATER FISH, Issue 1 2005A. Schreiber Abstract , Allozyme genetics (34 loci) is studied in up to 1010 European trout (Salmo trutta) from the Rhine, Meuse, Weser, Elbe and Danube river systems in Central Europe. Population samples from single collection sites, chiefly small streams (GCG = 0.2126), rather than the divergence of the trout from Atlantic and Danubian drainages (GSG = 0.0711), contributed to the overall gene diversity of GST = 0.2824. Sea trout (n = 164) and brown trout (n = 767) in Atlantic rivers adhere to the same biogeographical stock, but anadromous trout from the Rhine and the Elbe display more genetic cohesion than resident brown trout from the Rhine system alone. Strayers from the Elbe could have founded the recently re-established sea trout population of the Rhine, after a few decades of absence or precarious rarity. Migrants may even connect the Rhine and Elbe stocks by ongoing gene flow. A release,recapture study confirms that all trout in the Rhine belong to one partly migratory population network: Six of 2400 juvenile sea trout released into a tributary of the Rhine were later recorded as emigrants to the Rhine delta, against three of 1600 released brown trout. One migrant had entered the open North Sea, but the other dispersers were recorded in fresh waters of the Rhine delta (Ijsselmeer, Amstelmeer). Stocking presumably elevated both heterozygosity and fixation indices of brown trout, but this effect is subtle within the range of the Atlantic population group. Improved sea trout management in the Rhine, and modifications to brown trout stocking in the upper Danubian area are recommended. [source] Population genetics of Escherichia coli in a natural population of native Australian ratsENVIRONMENTAL MICROBIOLOGY, Issue 6 2000Gulietta M. Pupo Escherichia coli, a normal inhabitant of the intestinal tract of mammals and birds, is a diverse species. Most studies on E. coli populations involve organisms from humans or human-associated animals. In this study, we undertook a survey of E. coli from native Australian mammals, predominantly Rattus tunneyi, living in a relatively pristine environment in the Bundjalung National Park. The genetic diversity was assessed and compared by multilocus enzyme electrophoresis (MLEE), sequence analysis of the mdh (malate dehydrogenase) gene and biotyping using seven sugars. Ninety-nine electrophoretic types were identified from the 242 isolates analysed by MLEE and 15 sequences from the mdh genes sequenced from 21 representative strains. The Bundjalung isolates extend the diversity represented by the E. coli reference (ECOR) set, with new MLEE alleles found in six out of 10 loci. Many of the Bundjalung isolates fell into a discrete group in MLEE. Other Bundjalung strains fell into the recognized E. coli ECOR set groups, but tended to be at the base of both the MLEE and mdh gene trees, implying that these strains are derived independently from ancestral forms of the ECOR groups and that ECOR strains represent only a subset of E. coli adapted to humans and human-associated animals. Linkage disequilibrium analysis showed that the Bundjalung population has an ,epidemic' population structure. The Bundjalung isolates were able to utilize more sugars than the ECOR strains, suggesting that diet plays a prominent role in adaptation of E. coli. [source] Frequencies of the -330 (T , G) IL-2 and -590 (T , C) IL-4 gene polymorphisms in a population from south-eastern BrazilINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 4 2002R. M. Scarel-Caminaga Summary Polymorphisms in the promoter regions of cytokine genes may affect their transcription. A T/G substitution at position ,330 of the interleukin-2 (IL-2) gene and a T/C substitution at position ,590 of the interleukin-4 (IL-4) gene have been described previously. The ,590 (T , C) IL-4 gene polymorphism was associated with asthma and atopy in US and Japanese populations. Population genetics is a useful tool for determination of the biological significance of genetic polymorphisms. The aim of this study was to investigate the frequencies of polymorphisms in the promoter regions of the IL-2 and IL-4 genes in a population from south-eastern Brazil and to compare them with those published for other populations. Allele frequencies were estimated in 114 unrelated individuals from São Paulo State. These subjects had an average age of 41.2 years (± 12.4 years) and the ethnic composition of the sample was: 78.07% Caucasian, 11.4% Black and 10.53% Mulatto. DNA from subjects was extracted from epithelial buccal cells, and the PCR-RFLP technique was employed to investigate the ,330 (T , G) IL-2 and ,590 (T , C) IL-4 gene polymorphisms. The allele frequency of the IL-2 gene polymorphism obtained in our study was similar to that found in UK Caucasoid groups. The T allele frequency of the IL-4 gene polymorphism observed in the Caucasian Brazilian group was similar to that found in UK and Australian populations, while the frequency observed for the Black Brazilian group was similar to that found in Japanese and Kuwaiti Arab populations. The results for the ,330 (T , G) IL-2 and ,590 (T , C) IL-4 polymorphisms are consistent with the high contribution of European lineages to the population in south-eastern Brazil. [source] Polymorphism of LMP2, TAP1, LMP7 and TAP2 in Brazilian Amerindians and Caucasoids: implications for the evolution of allelic and haplotypic diversityINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2000F. Rueda Faucz In the class II region of the major histocompatibility complex (MHC), four genes implicated in processing of MHC class I-presented antigens have been described. Two of these (TAP1 and TAP2) code for endoplasmic reticulum membrane transporter proteins and the other two (LMP2 and LMP7) for proteasome subunits. These genes are polymorphic, although much less so than classical MHC class I and II genes. There is controversy concerning the possible functional implications of this variation. Population genetics is one of the means of investigating the evolutionary and functional significance of genetic polymorphisms; however, few populations have been analysed with respect to TAP and LMP diversity. We present here the polymorphism of TAP1, TAP2, LMP2 and LMP7 genes in the Kaingang and Guarani Amerindian tribes, and in the Caucasoid population of the Brazilian State of Paraná. Allele frequencies found in the Caucasoids were close to those described for similar populations. Amerindians had a somewhat more restricted polymorphism, and allele and haplotype frequencies differed greatly between the two tribes. Overall linkage disequilibrium (LD) between the four genes was low in the Caucasoids, but high in the Amerindians, for which significant LD was seen for all informative pairs of loci. Comparing results of this and previous studies we observed that, whenever significant LD occurs in non-Amerindians, it tends to be similar in the different ethnic groups. While this might be interpreted as evidence of co-evolution of genes in the TAP-LMP region, the high haplotypic diversity in all populations and low LD in non-Amerindians indicate absence of co-evolution of the different genes. Distributions of allele and genotype frequencies are consistent with the hypothesis of selective neutrality. We conclude that genetic polymorphism of the human TAP and LMP genes and haplotypes is of little, if any, functional significance. [source] Population genetics suggests effectiveness of habitat connectivity measures for the European tree frog in SwitzerlandJOURNAL OF APPLIED ECOLOGY, Issue 4 2009Sonia Angelone Summary 1.,Governmental authorities in many countries financially support the implementation of habitat connectivity measures to enhance the exchange of individuals among fragmented populations. The evaluation of the effectiveness of such measures is crucial for future management directions and can be accomplished by using genetic methods. 2.,We retraced the population history of the European tree frog in two Swiss river valleys (Reuss and Thur), performed comprehensive population sampling to infer the genetic structure at 11 microsatellite markers, and used first-generation migrant assignment tests to evaluate the contemporary exchange of individuals. 3.,Compared with the Thur valley, the Reuss valley has lost almost double the number of breeding sites and exhibited a more pronounced genetic grouping. However, similar numbers of contemporary migrants were detected in both valleys. In the Reuss valley, 81% of the migration events occurred within the identified genetic groups, whereas in the Thur valley migration patterns were diffuse. 4.,Our results show that the connectivity measures implemented in the Reuss valley facilitated effective tree frog migration among breeding sites within distances up to 4 km. Nevertheless, the Reuss valley exhibited high genetic differentiation, which reflected the impact of barriers to tree frog movement such as the River Reuss. By contrast in the Thur valley, a larger number of breeding sites have been preserved and high admixture indicated exchange of individuals at distances up to 16 km. 5.,Synthesis and applications. We show that genetic methods can substantiate the effectiveness of connectivity measures taken in conservation management at the landscape scale. We urge responsible authorities from both river valleys to continue implementing connectivity measures and to create a dense network of breeding sites, as spatial gaps of 8 km are rarely traversed by tree frogs. [source] Population genetics and breeding system of Tupistra pingbianensis (Liliaceae), a naturally rare plant endemic to SW ChinaJOURNAL OF SYSTEMATICS EVOLUTION, Issue 1 2010Qin QIAO Abstract The levels and partitioning of genetic diversity and inbreeding depression were investigated in Tupistra pingbianensis, a narrow endemic of southeast Yunnan, China, characterized by a naturally fragmented distribution due to extreme specialization on a rare habitat type. Here genetic diversity and patterns of genetic variation within and among 11 populations were analyzed using amplified fragment length polymorphism markers with 97 individuals across its whole geographical range. High levels of genetic variation were revealed both at the species level (P99= 96.012%; Ht= 0.302) and at the population level (P99= 51.41%; Hs= 0.224). Strong genetic differentiation among populations was also detected (FST= 0.2961; ,II= 0.281), which corresponded to results reported for typical animal-pollinated, mixed selfing, and outcrossing plant species. This result was consistent with mating patterns detected by our pollination experiments. The indirect estimate of gene flow based on ,II was low (Nm= 0.64). Special habitat and its life history traits might play an important role in shaping the genetic diversity and the genetic structure of this species. A pollination experiment also failed to detect significant inbreeding depression upon F1 fruit set, seed weight, and germinate rate fitness-traits. As a naturally rare species, T. pingbianensis is not seriously genetically impoverished and likely to have adapted to tolerating a high level of inbreeding early in its history, we propose this species need only periodic monitoring to ensure their continued persistence, but not intervention to remain viable. [source] Population genetics of the endangered limpet Patella ferruginea (Gastropoda: Patellidae): taxonomic, conservation and evolutionary considerationsJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2006F. Espinosa Abstract The limpet Patella ferruginea is the most endangered marine invertebrate in the western Mediterranean rocky shores, whereas Patella caerulea is the most common Mediterranean limpet. From Pleistocene to historic age, P. ferruginea was distributed around the whole Mediterranean basin, since the shells of this species are a characteristic feature of Palaeolithic and Neolithic deposits in this area. However, its Mediterranean range has progressively contracted to a few restricted areas. The ancient origin of the species (18 Ma) and the present geographical isolation among relic populations could have led to a great genetic difference among populations, taking into account the supposedly low dispersal ability of the species. However, we have observed a few genetic differences among populations and a ,star phylogeny' of COI haplotypes from the 41 individuals of P. ferruginea analysed; a similar pattern has also been observed for the seven individuals of P. caerulea studied. Genetic evidences show a possible bottleneck event on late Pleistocene that affected the two species. The results have an important implication on the future management of this endangered species. Additionally, two different morphological types of P. ferruginea have been described by Payraudeau in 1826: lamarcki and rouxi forms. Clear morphological differences occur between these two types and some authors pointed out the hypothesis about the existence of two different species. The results of the present study conclude that the two different forms of P. ferruginea are ecotypes, rather than different species or subspecies, and intermediate steps are an ecological range instead of hybridization events among different species. Resumen Patella ferruginea es el invertebrado marino más amenazado de las costas del Mediterráneo occidental, mientras que Patella caerulea es una especie muy común. Desde el Pleistoceno hasta épocas históricas, P. ferruginea estuvo distribuída alrededor de toda la cuenca mediterránea, ya que su concha es característica de depósitos paleolíticos y neolíticos en esta área. Sin embargo, su rango de distribución se ha visto reducido a unas pocas áreas restringidas. Su orígen primitivo (18 Ma) y el presente aislamiento geográfico entre las poblaciones podría haber generado importantes diferencias genéticas inter-poblacionales, teniendo en cuenta la supuesta baja capacidad de dispersión de la especie. Sin embargo, se han observado pocas diferencias genéticas inter-poblacionales y una ,,filogenia en estrella'' de los haplotipos de la COI procedentes de los 41 individuos de P. ferruginea analizados, un patrón similar ha sido también observado para los 7 individuos de P. caerulea estudiados. Las evidencias genéticas sugieren un posible cuello de botella a finales del Pleistoceno que afectó a las dos especies. Estos resultados tienen gran importancia en la futura gestión de esta especie amenazada. Adicionalmente, Payraudeau en 1826 describió dos tipo morfológicos de P. ferruginea: formas rouxi y lamarcki. Importantes diferencias morfológicas aparecen entre las dos formas y algunos autores han señalado la hipótesis de que podrían ser dos especies distintas. Los resultados del presente estudio concluyen que las dos formas de P. ferruginea son ecotipos en lugar de especies o subespecies distintas, y que las formas intermedias serían parte de un rango ecológico en lugar de ser fenómenos de hibridación entre especies diferentes. [source] Population genetics of Galápagos land iguana (genus Conolophus) remnant populationsMOLECULAR ECOLOGY, Issue 23 2008ATHANASIA C. TZIKA Abstract The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive-bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species-specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile. [source] Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limitsMOLECULAR ECOLOGY, Issue 24 2007CURTIS E. LIND Abstract Intraspecific genetic diversity governs the potential of species to prevail in the face of environmental or ecological challenges; therefore, its protection is critical. The Indo-Australian Archipelago (IAA) is a significant reservoir of the world's marine biodiversity and a region of high conservation priority. Yet, despite indications that the IAA may harbour greater intraspecific variation, multiple-locus genetic diversity data are limited. We investigated microsatellite DNA variation in Pinctada maxima populations from the IAA to elucidate potential factors influencing levels of genetic diversity in the region. Results indicate that genetic diversity decreases as the geographical distance away from central Indonesia increases, and that populations located towards the centre of P. maxima's range are more genetically diverse than those located peripherally (P < 0.01). Significant partitioning of genetic variation was identified (FST = 0.027; RST = 0.023, P < 0.001) and indicates that historical biogeographical episodes or oceanographic factors have shaped present population genetic structure. We propose that the genetic diversity peak in P. maxima populations may be due to (i) an abundance of suitable habitat within the IAA, meaning larger, more temporally stable populations can be maintained and are less likely to encounter genetic bottlenecks; and/or (ii) the close proximity of biogeographical barriers around central Indonesia results in increased genetic diversity in the region because of admixture of genetically divergent populations. We encourage further genetic diversity studies of IAA marine biota to confirm whether this region has a significant role in maintaining intraspecific diversity, which will greatly assist the planning and efficacy of future conservation efforts. [source] Population genetics of the endangered Knysna seahorse, Hippocampus capensisMOLECULAR ECOLOGY, Issue 7 2003P. R. Teske Abstract The evolutionary history of the endangered Knysna seahorse, Hippocampus capensis, and the extent of gene flow among its three known populations, were investigated using 138 mitochondrial DNA control region sequences. Similarly high levels of genetic diversity were found in two of the populations (Knysna and Keurbooms Estuaries), whereas diversity in the third population (Swartvlei Estuary) was lower. Although most haplotypes are shared between at least two populations, based on the haplotype frequency distributions the three assemblages constitute distinct management units. The extant population structure of H. capensis suggests that the Knysna seahorse originated in the large Knysna Estuary. The presence of seahorses in the two smaller estuaries is either the result of a vicariance event at the beginning of the present interglacial period, colonization of the estuaries via the sea, or a combination of the two. [source] Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequencesMOLECULAR ECOLOGY, Issue 10 2002C. Grunwald Abstract Shortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 101 to 104, but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty-nine mtDNA nucleotide-substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2,5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide-substitution haplotypes and length-variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once-glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five-region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units. [source] Population genetics of the black ant Formica lemani (Hymenoptera: Formicidae)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2009PERTTU SEPPÄ Colony kin structure and spatial population structure were studied in multiple populations of the ant Formica lemani, using allozymes and DNA microsatellites. Average genetic relatedness between nestmate workers varied little between populations (r = 0.51,0.76), indicating that the average colony kin structure was relatively simple. Worker genotypes could not be explained with a single breeding pair in all nests, however, and the distribution of relatedness estimates across nests was bimodal, suggesting that single- and multi-queen colonies co-occur. We studied spatial population structure in a successional boreal forest system, which is a mixture of different aged habitats. Newly clear-cut open habitat patches are quickly colonized by F. lemani, where it is able to persist for a limited number of generations. Newly-founded populations showed signs of a founder effect and spatial substructuring, whereas older populations were more homogenous. This suggests that new populations are founded by a limited number of colonizers arriving from more than one source. Genetic differentiation among local populations was minor, indicating strong migration between them. There were, however, indications of both isolation by distance and populations becoming more isolated as habitat patches grew older. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 247,258. [source] Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studiesECOGRAPHY, Issue 6 2008Melanie A. Murphy Landscape genetics, an emerging field integrating landscape ecology and population genetics, has great potential to influence our understanding of habitat connectivity and distribution of organisms. Whereas typical population genetics studies summarize gene flow as pairwise measures between sampling localities, landscape characteristics that influence population genetic connectivity are often continuously distributed in space. Thus, there are currently gaps in both the ability to analyze genotypic data in a continuous spatial context and our knowledge of expected of landscape genetic structure under varying conditions. We present a framework for generating continuous "genetic surfaces", evaluate their statistical properties, and quantify statistical behavior of landscape genetic structure in a simple landscape. We simulated microsatellite genotypes under varying parameters (time since vicariance, migration, effective population size) and used ancestry (q) values from STRUCTURE to interpolate a genetic surface. Using a spatially adjusted Pearson's correlation coefficient to test the significance of landscape variable(s) on genetic structure we were able to detect landscape genetic structure on a contemporary time scale (,5 generations post vicariance, migration probability ,0.10) even when population differentiation was minimal (FST,0.00015). We show that genetic variation can be significantly correlated with geographic distance even when genetic structure is due to landscape variable(s), demonstrating the importance of testing landscape influence on genetic structure. Finally, we apply genetic surfacing to analyze an empirical dataset of black bears from northern Idaho USA. We find black bear genetic variation is a function of distance (autocorrelation) and habitat patch (spatial dependency), consistent with previous results indicating genetic variation was influenced by landscape by resistance. These results suggest genetic surfaces can be used to test competing hypotheses of the influence of landscape characteristics on genetic structure without delineation of categorical groups. [source] Connections between species diversity and genetic diversityECOLOGY LETTERS, Issue 7 2005Mark Vellend Abstract Species diversity and genetic diversity remain the nearly exclusive domains of community ecology and population genetics, respectively, despite repeated recognition in the literature over the past 30 years of close parallels between these two levels of diversity. Species diversity within communities and genetic diversity within populations are hypothesized to co-vary in space or time because of locality characteristics that influence the two levels of diversity via parallel processes, or because of direct effects of one level of diversity on the other via several different mechanisms. Here, we draw on a wide range of studies in ecology and evolution to examine the theoretical underpinnings of these hypotheses, review relevant empirical literature, and outline an agenda for future research. The plausibility of species diversity,genetic diversity relationships is supported by a variety of theoretical and empirical studies, and several recent studies provide direct, though preliminary support. Focusing on potential connections between species diversity and genetic diversity complements other approaches to synthesis at the ecology,evolution interface, and should contribute to conceptual unification of biodiversity research at the levels of genes and species. [source] "Paterniplex", a highly discriminative decaplex STR multiplex tailored for investigating special problems in paternity testingELECTROPHORESIS, Issue 21 2007Thomas Betz Abstract The goal of the study was to develop a STR multiplex ("Paterniplex") that is , as supplement to commercially available multiplex kits like the Identifiler® kit (Applied Biosystems, Foster City, CA) , suitable for solving complex paternity cases such as deficiency cases or cases with mutations. The Paterniplex comprises the nine highly polymorphic STRs D8S1132, D7S1517, D10S2325, D12S391, Se33, D17S976, Penta E, Penta D and FGA in addition to Amelogenin as sex determination marker. The loci were selected because of their high degree of polymorphism (higher than that of the widely used TH01 marker). Only one locus, FGA, is shared with the Identifiler kit to avoid sample mix up. The study further gives details on the population genetics of the loci in a German Caucasian population (allelic distribution, Hardy,Weinberg Equilibrium and forensic efficiency markers such as the Discriminating Power) and three examples for cases that could not be solved using commercially available kits alone, but using the Paterniplex in addition to a commercial kit. [source] SNPlexing the human Y-chromosome: A single-assay system for major haplogroup screeningELECTROPHORESIS, Issue 18 2007Gemma Berniell-Lee Abstract SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup. [source] Multiplex primer extension analysis for rapid detection of major European mitochondrial haplogroupsELECTROPHORESIS, Issue 19 2006Martina Wiesbauer Abstract The evolution of the human mitochondrial genome is reflected in the existence of ethnically distinct lineages or haplogroups. Alterations of mitochondrial DNA (mtDNA) have been instrumental in studies of human phylogeny, in population genetics, and in molecular medicine to link pathological mutations to a variety of human diseases of complex etiology. For each of these applications, rapid and cost effective assays for mtDNA haplogrouping are invaluable. Here we describe a hierarchical system for mtDNA haplogrouping that combines multiplex PCR amplifications, multiplex single-base primer extensions, and CE for analyzing ten haplogroup-diagnostic mitochondrial single nucleotide polymorphisms. Using this rapid and cost-effective mtDNA genotyping method, we were able to show that within a large, randomly selected cohort of healthy Austrians (n,=,1172), mtDNAs could be assigned to all nine major European haplogroups. Forty-four percent belonged to haplogroup H, the most frequent haplogroup in European Caucasian populations. The other major haplogroups identified were U (15.4%), J (11.8%), T (8.2%) and K (5.1%). The frequencies of haplogroups in Austria is within the range observed for other European countries. Our method may be suitable for mitochondrial genotyping of samples from large-scale epidemiology studies and for identifying markers of genetic susceptibility. [source] Microbial diversity , insights from population geneticsENVIRONMENTAL MICROBIOLOGY, Issue 1 2008Ted H. M. Mes Summary Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, Ne, is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 103 and 107 suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what Ne of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities. [source] Approaches to prokaryotic biodiversity: a population genetics perspectiveENVIRONMENTAL MICROBIOLOGY, Issue 11 2002Francisco Rodríguez-Valera Summary The study of prokaryotic diversity has blossomed during the last 10,15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution. [source] Genetic diversity of Clethrionomys glareolus populations from highly contaminated sites in the Chornobyl region, UkraineENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 8 2000Cole W. Matson Abstract At radioactive sites, at least two mechanisms may affect the genetic diversity of populations of a given species. Increased mutation rates due to radiation exposure may increase the amount of genetic diversity in a population. Alternatively, population bottlenecks exacerbated by environmental degradation may lead to a reduction of diversity. The relationship between these two contradictory forces is complex. To explore this relationship, long-term monitoring of a genetic marker within a population is needed. To provide baseline data on the population genetics of the bank vole (Clethrionomys glareolus) living in the most contaminated regions at Chornobyl, Ukraine, we have sequenced 291 base pairs of the mitochondrial DNA control region. Bank voles were chosen as a model system because they have the highest levels of internal dose of cesium-134, cesium-137, and strontium-90 within the Chornobyl exclusion zone. We sampled three geographic sites, which were Oranoe, a reference site with virtually no radioactive contamination (<2 Ci/km2), and two highly contaminated sites, Glyboke Lake and the Red Forest (both 1,000 Ci/km2). Genetic diversity in the population from Red Forest (0.722 ± 0.024) was significantly greater than at the Oranoe reference site (0.615 ± 0.039), while genetic diversity at Glyboke Lake (0.677 ± 0.068) was intermediate. It is concluded that long-term studies of historical and demographic characteristics for experimental and reference populations are required in order to employ population genetics to understand the biological impact of environmental contaminants on the genetics of natural populations. [source] IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?EVOLUTION, Issue 1 2009Scott V. Edwards The advent and maturation of algorithms for estimating species trees,phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes,represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions. [source] THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?EVOLUTION, Issue 9 2008David L. Stern Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis -regulatory, rather than the coding, regions of developmental genes. This "cis -regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis -regulatory hypothesis. We then test the empirical support for the cis -regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis -regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis -regulatory changes published annually is rapidly increasing. Above the species level, cis -regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis -regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis -regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics. [source] ADAPTIVE EVOLUTION OF ASEXUAL POPULATIONS UNDER MULLER'S RATCHETEVOLUTION, Issue 7 2004Doris Bachtrog Abstract We study the population genetics of adaptation in nonequilibrium haploid asexual populations. We find that the accumulation of deleterious mutations, due to the operation of Muller's ratchet, can considerably reduce the rate of fixation of advantageous alleles. Such reduction can be approximated reasonably well by a reduction in the effective population size. In the absence of Muller's ratchet, a beneficial mutation can only become fixed if it creates the best possible genotype; if Muller's ratchet operates, however, mutations initially arising in a nonoptimal genotype can also become fixed in the population, since the loss of the least-loaded class implies that an initially nonoptimal background can become optimal. We show that, while the rate at which adaptive mutations become fixed is reduced, the rate of fixation of deleterious mutations due to the ratchet is not changed by the presence of beneficial mutations as long as the rate of their occurrence is low and the deleterious effects of mutations (sd) are higher than the beneficial effects (sa). When sa>sd, the advantage of a beneficial mutation can outweigh the deleterious effects of associated mutations. Under these conditions, a beneficial allele can drag to fixation deleterious mutations initially associated with it at a higher rate than in the absence of advantageous alleles. We propose analytical approximations for the rates of accumulation of deleterious and beneficial mutations. Furthermore, when allowing for the possible occurrence of interference between beneficial alleles, we find that the presence of deleterious mutations of either very weak or very strong effect can marginally increase the rate of accumulation of beneficial mutations over that observed in the absence of such deleterious mutations. [source] | |||||||||||||||||||||||||||||||||||||||||||