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Population Bottlenecks (population + bottleneck)
Kinds of Population Bottlenecks Selected AbstractsTHE EFFECT OF EPISTASIS ON THE EXCESS OF THE ADDITIVE AND NONADDITIVE VARIANCES AFTER POPULATION BOTTLENECKSEVOLUTION, Issue 5 2002Carlos López-Fanjul Abstract The effect of population bottlenecks on the components of the genetic variance generated by two neutral independent epistatic loci has been studied theoretically (VA, additive; VD, dominant; VAA, additive × additive; VAD, additive × dominant; VDD; dominant × dominant components of variance). Nonoverdominance and overdominance models were considered, covering all possible types of marginal gene action at the single locus level. The variance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of allele frequencies and effects at each locus and the corresponding epistatic value. An excess of VA after bottlenecks can be assigned to two sources: (1) the spatiotemporal changes in the marginal average effects of gene substitution ai, which are equal to zero only for additive gene action within and between loci; and (2) the covariance between a2i and the heterozygosity at the loci involved, which is generated by dominance, with or without epistasis. Numerical examples were analyzed, indicating that an increase in VA after bottlenecks will only occur if its ancestral value is minimal or very small. For the nonoverdominance model with weak reinforcing epistasis, that increase has been detected only for extreme frequencies of the negative allele at one or both loci. With strong epistasis, however, this result can be extended to a broad range of intermediate frequencies. With no epistasis, the same qualitative results were found, indicating that dominance can be considered as the primary cause of an increase in VA following bottlenecks. In parallel, the derived total nonadditive variance exceeded its ancestral value (VNA= VD+ VAA+VAD+ VDD) for a range of combinations of allele frequencies covering those for an excess of VA and for very large frequencies of the negative allele at both loci. For the overdominance model, an increase in VA and VNA was respectively observed for equilibrium (intermediate) frequencies at one or both loci or for extreme frequencies at both loci. For all models, the magnitude of the change of VA and VNA was inversely related to N and t. At low levels of inbreeding, the between-line variance was not affected by the type of gene action. For the models considered, the results indicate that it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived VA over its ancestral value. [source] A Comparison of the Variability Spectra of Two Genomic Loci in a European Group of Individuals Reveals Fundamental Differences Pointing to Selection or a Population BottleneckANNALS OF HUMAN GENETICS, Issue 3 2007C. Schmegner Summary Knowledge about the variability spectra of neutrally evolving sequences in a population is a prerequisite for the identification of genes, which may have been under positive selection during recent human evolution. Here, we report the results of a re-sequencing project of a presumably neutrally evolving chromosome 22 locus with a severely reduced recombination frequency in a group of 24 individuals of German origin. The comparison of these data with the results of a similar analysis of a chromosome 17 locus revealed striking differences, although the same group of individuals was used. For the chromosome 17 locus two well-separated groups of sequences, a positive value of Tajima's D and a TMRCA of 700 000 years were observed. In contrast, the sequences from the chromosome 22 locus were found to be relatively homogeneous, with no deep splits between subgroups; the obtained value for Tajima's D was negative and the TMRCA was only 260 000 years. These discrepancies may be explained by selection or demographic processes. Regarding demography, the most plausible explanation is the assumption of a severe bottleneck in the history of the European population: in the case of the chromosome 17 locus two ancient lineages passed this bottleneck; for the chromosome 22 locus it was only one ancient lineage. [source] Detecting past population bottlenecks using temporal genetic dataMOLECULAR ECOLOGY, Issue 10 2005UMA RAMAKRISHNAN Abstract Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations. [source] A developmental bottleneck in dispersing larvae: implications for spatial population dynamicsECOLOGY LETTERS, Issue 4 2003Daniel W. Schneider Abstract We found evidence for a critical population bottleneck at a developmental-stage transition in larvae of the zebra mussel Dreissena polymorpha Pallas from field estimates of mortality. Identification of this critical period in the field was made possible by closely tracking cohorts of larvae over 5 days of development as they dispersed 128 km in a river system. The presence of a survival bottleneck during development was confirmed in laboratory studies of zebra mussel larvae. Development-specific mortality has important implications for spatial population dynamics of the zebra mussel in particular, and all species with indirect development in general. Marine reserves that do not take development-specific mortality into account may dramatically underestimate reserve size needed to protect rare and/or exploited marine populations. Conversely, for the zebra mussel, the lower contribution of dispersing individuals to population growth downstream of reserves can lead to more feasible control through the blocking of dispersal. [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] EFFECTS OF GENETIC DRIFT ON VARIANCE COMPONENTS UNDER A GENERAL MODEL OF EPISTASISEVOLUTION, Issue 10 2004N.H. Barton Abstract We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(,z,) =where n is the number of loci contributing to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*A), is closely related to var(,z,); (V*A) (1 ,F)Thus, epistasis inflates the expected additive variance above VA(1 ,F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)). This is not true in general with diploidy, because dominance alone can reduce (V*A) below VA(1 ,F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(,z,)==1 (2F) kVA(k) and (V*A) = (1 ,F)k(2F)k-1VA(k) With dominance (and even without epistasis), var(,z,)and (V*A) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*A)(1 ,F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms describing covariances between additive effects and dominance and additive × dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase VA, we question the evolutionary importance of such increases. [source] Reduced genetic variation in Norwegian Peregrine Falcons Falco peregrinus indicated by minisatellite DNA fingerprintingIBIS, Issue 1 2002Jan T. Lifjeld The Scandinavian Peregrine Falcon Falco peregrinus population went through a severe population bottleneck during the second half of the twentieth century, and was almost extinct during the 1970s. This event may have reduced the amount of genetic variation in the population. With this background, a comparative study, using multilocus, minisatellite DNA fingerprinting, was carried out on broods of the Peregrine Falcon, the Merlin Falco columbarius and the Eurasian Hobby Falco subbuteo from south-east Norway. Band-sharing analysis of DNA fingerprints was used to test whether broods of Peregrine Falcons showed a greater between-nest similarity in their fingerprint profiles than did broods of the two congeneric species breeding in the same region, which have not undergone any recent population bottlenecks. The results show that broods of Peregrine Falcons were significantly more similar to each other genetically than were broods of either Merlins or Eurasian Hobbies. Furthermore, there was a positive correlation between the similarity in minisatellite DNA and the similarity in a set of 11 microsatellite loci analysed for a subset of the Peregrine Falcon samples. The correlation supports the assumption that minisatellite fingerprints provide a reliable indicator of overall genetic similarity, i.e. relatedness, between breeding pairs in the population. Hence we can conclude that broods of Peregrine Falcons were genetically more related to each other than were broods of the other two species. The high similarity in minisatellite DNA between broods indicates a loss of genetic variation in the Peregrine Falcon population caused by the bottleneck, but this explanation can only be verified through a comparative genetic study of individuals sampled before and after the bottleneck event. [source] Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversityMOLECULAR ECOLOGY, Issue 8 2009ROSS BARNETT Abstract Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions. [source] Phylogeography and the geographic cline in the armament of a seed-predatory weevil: effects of historical events vs. natural selection from the host plantMOLECULAR ECOLOGY, Issue 13 2006HIROKAZU TOJU Abstract Japanese camellia (Camellia japonica) and its seed predator, the camellia weevil (Curculio camelliae), provide a notable example of a geographic mosaic of coevolution. In the species interaction, the offensive trait of the weevil (rostrum length) and the defensive trait of the plant (pericarp thickness) are involved in a geographically-structured arms race, and these traits and selective pressures acting on the plant defence vary greatly across a geographical landscape. To further explore the geographical structure of this interspecific interaction, we tested whether the geographical variation in the weevil rostrum over an 800-km range along latitude is attributed to local natural selection or constrained by historical (phylogeographical) events of local populations. Phylogeographical analyses of the mitochondrial DNA sequences of the camellia weevil revealed that this species has experienced differentiation into two regions, with a population bottleneck and subsequent range and/or population expansion within each region. Although these phylogeographical factors have affected the variation in rostrum length, analyses of competing factors for the geographical variation revealed that this pattern is primarily determined by the defensive trait of the host plant rather than by the effects of historical events of populations and a climatic factor (annual mean temperature). Thus, our study suggests the overwhelming strength of coevolutionary selection against the effect of historical events, which may have limited local adaptation. [source] Population histories of right whales (Cetacea: Eubalaena) inferred from mitochondrial sequence diversities and divergences of their whale lice (Amphipoda: Cyamus)MOLECULAR ECOLOGY, Issue 11 2005ZOFIA A. KALISZEWSKA Abstract Right whales carry large populations of three ,whale lice' (Cyamus ovalis, Cyamus gracilis, Cyamus erraticus) that have no other hosts. We used sequence variation in the mitochondrial COI gene to ask (i) whether cyamid population structures might reveal associations among right whale individuals and subpopulations, (ii) whether the divergences of the three nominally conspecific cyamid species on North Atlantic, North Pacific, and southern right whales (Eubalaena glacialis, Eubalaena japonica, Eubalaena australis) might indicate their times of separation, and (iii) whether the shapes of cyamid gene trees might contain information about changes in the population sizes of right whales. We found high levels of nucleotide diversity but almost no population structure within oceans, indicating large effective population sizes and high rates of transfer between whales and subpopulations. North Atlantic and Southern Ocean populations of all three species are reciprocally monophyletic, and North Pacific C. erraticus is well separated from North Atlantic and southern C. erraticus. Mitochondrial clock calibrations suggest that these divergences occurred around 6 million years ago (Ma), and that the Eubalaena mitochondrial clock is very slow. North Pacific C. ovalis forms a clade inside the southern C. ovalis gene tree, implying that at least one right whale has crossed the equator in the Pacific Ocean within the last 1,2 million years (Myr). Low-frequency polymorphisms are more common than expected under neutrality for populations of constant size, but there is no obvious signal of rapid, interspecifically congruent expansion of the kind that would be expected if North Atlantic or southern right whales had experienced a prolonged population bottleneck within the last 0.5 Myr. [source] Microsatellite variation and population structure in a declining Australian Hylid Litoria aureaMOLECULAR ECOLOGY, Issue 7 2004Emma L. Burns Abstract The green and golden bell frog (Litoria aurea) was once a common Australian Hylid. Today, many populations are small and fragmented as a result of dramatic declines in distribution and abundance. We undertook a large-scale assessment of genetic structure and diversity in L. aurea using four species-specific microsatellite markers. Twenty-one locations were sampled from throughout the species range covering 1000 km of the east coast of Australia. Levels of allelic diversity and heterozygosity were high (uncorrected mean alleles/locus and HE were 4.8,8.8 and 0.43,0.8, respectively) compared to other amphibian species and significant differences among sampled sites were recorded. Despite recent population declines, no sites displayed a genetic signature indicative of a population bottleneck. Significant genetic structuring (overall FST 0.172) was detected throughout the species range, but was relatively low compared to previous amphibian studies employing microsatellites. In addition we found that some areas sampled within continuous habitat showed evidence of weak genetic structuring (data subset FST 0.034). We conclude that maintaining areas of continuous habitat is critical to the conservation of the species and argue that population recovery and/or persistence in all areas sampled is possible if appropriate protection and management are afforded. [source] Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath henMOLECULAR ECOLOGY, Issue 7 2004Eric P. Palkovacs Abstract Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens. [source] X-chromosome lineages and the settlement of the AmericasAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Stephane Bourgeois Abstract Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y-chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X-chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8-kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X-chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s). Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source] Patterns of isozyme variation as indicators of biogeographic history in Pilgerodendron uviferum (D. Don) FlorínDIVERSITY AND DISTRIBUTIONS, Issue 2 2002A. C. Premoli Abstract. The effects of Pleistocene glaciations on the genetic characteristics of the most austral conifer in the world, Pilgerodendron uviferum, were analysed with specific reference to the hypothesis that the species persisted locally in ice-free areas in temperate South America. It was expected that genetic variation would decrease with latitude, given that ice fields were larger in southern Patagonia and thus refugia were probably located towards the northern distributional limit of the species as suggested by the fossil record. In addition, an increase in among-population genetic divergence was expected with increasing distance to putative glacial refugia. We examined the relationship between location and within-population variability indices of 20 Pilgerodendron populations derived from isozyme analyses. We analysed possible refugia hypotheses by the distribution of allele frequencies using multivariate discriminant analysis. The degree of genetic differentiation with geographical distance between all population pairs was investigated by Mantel tests. Results indicated that Pilgerodendron populations are highly monomorphic, probably reflecting past population bottlenecks and reduced gene flow. Southernmost populations tend to be the least genetically variable and were therefore probably more affected by glacial activity than northern ones. Populations located outside ice limits seem to have been isolated during the glacial period. The presence of centres of genetic diversity, together with the lack of a significant correlation between genetic and geographical distances and the absence of geographical patterns of allelic frequencies at most analysed alleles, may indicate that Pilgerodendron did not advance southward after the last glaciation from a unique northern refugium, but spread from several surviving populations in ice-free areas in Patagonia instead. [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] EFFECTS OF GENETIC DRIFT ON VARIANCE COMPONENTS UNDER A GENERAL MODEL OF EPISTASISEVOLUTION, Issue 10 2004N.H. Barton Abstract We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(,z,) =where n is the number of loci contributing to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*A), is closely related to var(,z,); (V*A) (1 ,F)Thus, epistasis inflates the expected additive variance above VA(1 ,F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)). This is not true in general with diploidy, because dominance alone can reduce (V*A) below VA(1 ,F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(,z,)==1 (2F) kVA(k) and (V*A) = (1 ,F)k(2F)k-1VA(k) With dominance (and even without epistasis), var(,z,)and (V*A) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*A)(1 ,F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms describing covariances between additive effects and dominance and additive × dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase VA, we question the evolutionary importance of such increases. [source] EPISTASIS AND THE TEMPORAL CHANGE IN THE ADDITIVE VARIANCE-COVARIANCE MATRIX INDUCED BY DRIFTEVOLUTION, Issue 8 2004Carlos López-Fanjul Abstract The effect of population bottlenecks on the components of the genetic covariance generated by two neutral independent epistatic loci has been studied theoretically (additive, covA; dominance, covD; additive-by-additive, covAA; additive-by-dominance, covAD; and dominance-by-dominance, covDD). The additive-by-additive model and a more general model covering all possible types of marginal gene action at the single-locus level (additive/dominance epistatic model) were considered. The covariance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium over replicates randomly derived from the base population, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of the allele frequencies and effects at each locus, the corresponding epistatic effects and the inbreeding coefficient Ft. These expressions show that the contribution of nonadditive loci to the derived additive covariance (covAt) does not linearly decrease with inbreeding, as in the pure additive case, and may initially increase or even change sign in specific situations. Numerical examples were also analyzed, restricted for simplicity to the case of all covariance components being positive. For additive-by-additive epistasis, the condition covAt > covA only holds for high frequencies of the allele decreasing the metric traits at each locus (negative allele) if epistasis is weak, or for intermediate allele frequencies if it is strong. For the additive/dominance epistatic model, however, covAt > covA applies for low frequencies of the negative alleles at one or both loci and mild epistasis, but this result can be progressively extended to intermediate frequencies as epistasis becomes stronger. Without epistasis the same qualitative results were found, indicating that marginal dominance induced by epistasis can be considered as the primary cause of an increase of the additive covariance after bottlenecks. For all models, the magnitude of the ratio covAt/covA was inversely related to N and t. [source] THE ADDITIVE GENETIC VARIANCE AFTER BOTTLENECKS IS AFFECTED BY THE NUMBER OF LOCI INVOLVED IN EPISTATIC INTERACTIONSEVOLUTION, Issue 4 2003Yamama Naciri-Graven Abstract We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of "pure" epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distributions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks. [source] THE EFFECT OF EPISTASIS ON THE EXCESS OF THE ADDITIVE AND NONADDITIVE VARIANCES AFTER POPULATION BOTTLENECKSEVOLUTION, Issue 5 2002Carlos López-Fanjul Abstract The effect of population bottlenecks on the components of the genetic variance generated by two neutral independent epistatic loci has been studied theoretically (VA, additive; VD, dominant; VAA, additive × additive; VAD, additive × dominant; VDD; dominant × dominant components of variance). Nonoverdominance and overdominance models were considered, covering all possible types of marginal gene action at the single locus level. The variance components in an infinitely large panmictic population (ancestral components) were compared with their expected values at equilibrium, after t consecutive bottlenecks of equal size N (derived components). Formulae were obtained in terms of allele frequencies and effects at each locus and the corresponding epistatic value. An excess of VA after bottlenecks can be assigned to two sources: (1) the spatiotemporal changes in the marginal average effects of gene substitution ai, which are equal to zero only for additive gene action within and between loci; and (2) the covariance between a2i and the heterozygosity at the loci involved, which is generated by dominance, with or without epistasis. Numerical examples were analyzed, indicating that an increase in VA after bottlenecks will only occur if its ancestral value is minimal or very small. For the nonoverdominance model with weak reinforcing epistasis, that increase has been detected only for extreme frequencies of the negative allele at one or both loci. With strong epistasis, however, this result can be extended to a broad range of intermediate frequencies. With no epistasis, the same qualitative results were found, indicating that dominance can be considered as the primary cause of an increase in VA following bottlenecks. In parallel, the derived total nonadditive variance exceeded its ancestral value (VNA= VD+ VAA+VAD+ VDD) for a range of combinations of allele frequencies covering those for an excess of VA and for very large frequencies of the negative allele at both loci. For the overdominance model, an increase in VA and VNA was respectively observed for equilibrium (intermediate) frequencies at one or both loci or for extreme frequencies at both loci. For all models, the magnitude of the change of VA and VNA was inversely related to N and t. At low levels of inbreeding, the between-line variance was not affected by the type of gene action. For the models considered, the results indicate that it is unlikely that the rate of evolution may be accelerated after population bottlenecks, in spite of occasional increments of the derived VA over its ancestral value. [source] DIVERGENCE WITH GENE FLOW IN THE ROCK-DWELLING CICHLIDS OF LAKE MALAWIEVOLUTION, Issue 5 2000Patrick D. Danley Abstract Within the past two million years, more than 450 species of haplochromine cichlids have diverged from a single common ancestor in Lake Malawi. Several factors have been implicated in the diversification of this monophyletic clade, including changes in lake level and low levels of gene flow across limited geographic scales. The objectives of this study were to determine the effect of recent lake-level fluctuations on patterns of allelic diversity in the genus Metriaclima, to describe the patterns of population structure within this genus, and to identify barriers to migration. This was accomplished through an analysis of allele frequencies at four microsatellite loci. Twelve populations spanning four species within Metriaclima were surveyed. The effect of lake-level fluctuations can be seen in the reduced genetic diversity of the most recently colonized sites; however, genetic diversity is not depressed at the species level. Low levels of population structure exist among populations, yet some gene flow persists across long stretches of inhospitable habitat. No general barrier to migration was identified. The results of this study are interpreted with respect to several speciation models. Divergence via population bottlenecks is unlikely due to the large allelic diversity observed within each species. Genetic drift and microallopatric divergence are also rejected because some gene flow does occur between adjacent populations. However, the reduced levels of gene flow between populations does suggest that minor changes in the selective environment could cause the divergence of populations. [source] Reduced genetic variation in Norwegian Peregrine Falcons Falco peregrinus indicated by minisatellite DNA fingerprintingIBIS, Issue 1 2002Jan T. Lifjeld The Scandinavian Peregrine Falcon Falco peregrinus population went through a severe population bottleneck during the second half of the twentieth century, and was almost extinct during the 1970s. This event may have reduced the amount of genetic variation in the population. With this background, a comparative study, using multilocus, minisatellite DNA fingerprinting, was carried out on broods of the Peregrine Falcon, the Merlin Falco columbarius and the Eurasian Hobby Falco subbuteo from south-east Norway. Band-sharing analysis of DNA fingerprints was used to test whether broods of Peregrine Falcons showed a greater between-nest similarity in their fingerprint profiles than did broods of the two congeneric species breeding in the same region, which have not undergone any recent population bottlenecks. The results show that broods of Peregrine Falcons were significantly more similar to each other genetically than were broods of either Merlins or Eurasian Hobbies. Furthermore, there was a positive correlation between the similarity in minisatellite DNA and the similarity in a set of 11 microsatellite loci analysed for a subset of the Peregrine Falcon samples. The correlation supports the assumption that minisatellite fingerprints provide a reliable indicator of overall genetic similarity, i.e. relatedness, between breeding pairs in the population. Hence we can conclude that broods of Peregrine Falcons were genetically more related to each other than were broods of the other two species. The high similarity in minisatellite DNA between broods indicates a loss of genetic variation in the Peregrine Falcon population caused by the bottleneck, but this explanation can only be verified through a comparative genetic study of individuals sampled before and after the bottleneck event. [source] Implications of mitochondrial DNA polyphyly in two ecologically undifferentiated but morphologically distinct migratory birds, the masked and white-browed woodswallows Artamus spp. of inland AustraliaJOURNAL OF AVIAN BIOLOGY, Issue 6 2006Leo Joseph The white-browed woodswallow Artamus superciliosus and masked woodswallow A. personatus (Passeriformes: Artamidae) are members of Australia's diverse arid- and semi-arid zone avifauna. Widely sympatric and among Australia's relatively few obligate long-distance temperate-tropical migrants, the two are well differentiated morphologically but not ecologically and vocally. They are pair breeders unlike other Artamus species, which are at least facultative cooperative breeders. For these reasons they are an excellent case in which to use molecular data in integrative study of their evolution from ecological and biogeographical perspectives. We used mitochondrial DNA (mtDNA) to test whether they are each other's closest relatives, whether they evolved migration independently, whether they have molecular signatures of population expansions like some other Australian arid zone birds, and to estimate the timing of any inferred population expansions. Their mtDNAs are monophyletic with respect to other species of Artamus but polyphyletic with respect to each other. The two species appear not to have evolved migration independently of each other but their morphological and mtDNA evolution have been strongly decoupled. Some level of hybridization and introgression cannot be dismissed outright as being involved in their mtDNA polyphyly but incomplete sorting of their most recent common ancestor's mtDNA is a simpler explanation consistent with their ecology. Bayesian phylogenetic inference and analyses of diversity within the two species (n=77) with conventional diversity statistics, statistical parsimony, and tests for population expansion vs stability (Tajima's D, Fu's Fs and Ramos-Onsin and Rozas's R2) all favour recent population increases. However, a non-starlike network suggests expansion(s) relatively early in the Pleistocene. Repeated population bottlenecks corresponding with multiple peaks of Pleistocene aridity could explain our findings, which add a new dimension to accruing data on the effects of Pleistocene aridity on the Australian biota. [source] High resolution analysis of mating systems: inbreeding in natural populations of Pinus radiataJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2002C. Vogl Pinus radiata has a history of population bottlenecks and is currently restricted to five relatively small populations, three in mainland California, and two on islands off the coast of Baja California. Using highly polymorphic microsatellite markers and a newly developed statistical approach, we were able to estimate individual inbreeding coefficients and can thus analyse the mating system with high resolution. We find a bimodal distribution of inbreeding coefficients: most individuals result from selfing whereas few (in the mainland populations) to a modest number (in the island populations) are likely selfed. In most other pine species and presumably in the ancestral P. radiata population, occurrence of mature selfed individuals would be impossible because of the high genetic load. We therefore conclude that inbreeding depression has been purged in P. radiata and that the mating system has changed as a consequence. [source] Population genetic structure of the round stingray Urobatis halleri (Elasmobranchii: Rajiformes) in southern California and the Gulf of CaliforniaJOURNAL OF FISH BIOLOGY, Issue 2 2010S. M. Plank The round stingray, Urobatis halleri, is a viviparous elasmobranch that inhabits inshore, benthic habitats ranging from the western U.S.A. to Panama. The population genetic structure of this species was inferred with seven polymorphic microsatellite loci in samples collected at three sites in coastal southern California, one near Santa Catalina Island, California and one in the eastern Gulf of California. Urobatis halleri is relatively common, but little is known of its movement patterns or population structure. Small FST values (,0·0017 to 0·0005) suggested little structure among coastal populations of southern and Baja California. The population sampled at Santa Catalina Island, which is separated by a deep-water channel from the coastal sites, however, was significantly divergent (large FST, 0·0251) from the other populations, suggesting low connectivity with coastal populations. The Santa Catalina Island population also had the lowest allele richness and lowest average heterozygosity, suggesting recent population bottlenecks in size. [source] Oviposition preference and larval performance of the sweet potato butterfly Acraea acerata on Ipomoea species in EthiopiaAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 2 2010Ferdu Azerefegne 1The sweet potato butterfly Acraea acerata is an indigenous species in Ethiopia that has become a major pest on the introduced sweet potato Ipomoea batatas. To assess the role of wild Ethiopian Ipomoea species as host plants, the presence of larvae on wild ipomoeas was studied, and female oviposition choice and larval performance were tested on five wild ipomoeas, as well as on sweet potato. 2In laboratory tests, oviposition and larval development were successful on two wild ipomoeas (Ipomoea tenuirostris and Ipomoea cairica) but no oviposition occurred on the remaining three species. Of the latter, larvae did not feed on Ipomoea hochstetteri and Ipomoea indica, and survival rates were extremely low on Ipomoea purpurea. 3Sweet potato was a better host plant than I. tenuirostris and I. cairica in terms of oviposition preference, larval survival and pupal size; pupae were larger, resulting in more fecund female butterflies. 4In the wild butterfly populations were abundant on I. tenuirostris but absent on I. cairica. Females also tended to prefer I. tenuirostris to I. cairica in oviposition choice experiments. However, no significant differences in performance were found between larvae raised on I. tenuirostris and I. cairica in the laboratory. 5Wild populations of A. acerata also existed on Ipomoea obscura, a plant not investigated in the present study. 6The abundance of A. acerata on wild ipomoeas is too low to likely affect butterfly population densities on sweet potato. However, wild populations may act as reservoirs subsequent to butterfly population bottlenecks on sweet potato. [source] Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickensMOLECULAR ECOLOGY, Issue 11 2007JEFF A. JOHNSON Abstract Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and mdiv). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (,), population divergence time (t), and time to the most recent common ancestor (TMRCA) from mdiv were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history. [source] Contrasting patterns in genetic diversity following multiple invasions of fresh and brackish watersMOLECULAR ECOLOGY, Issue 12 2006DAVID W. KELLY Abstract Biological invasions may combine the genetic effects of population bottlenecks and selection and thus provide valuable insight into the role of such processes during novel environmental colonizations. However, these processes are also influenced by multiple invasions, the number of individuals introduced and the degree of similarity between source and receiving habitats. The amphipod Gammarus tigrinus provides a useful model to assess these factors, as its invasion history has involved major environmental transitions. This species is native to the northwest Atlantic Ocean, although it invaded both brackish and freshwater habitats in the British Isles after introduction more than 65 years ago. It has also spread to similar habitats in Western Europe and, most recently, to Eastern Europe, the Baltic Sea, and the Laurentian Great Lakes. To examine sources of invasion and patterns of genetic change, we sampled populations from 13 native estuaries and 19 invaded sites and sequenced 542 bp of the mitochondrial COI gene. Strong native phylogeographical structure allowed us to unambiguously identify three allopatrically evolved clades (2.3,3.1% divergent) in invading populations, indicative of multiple introductions. The most divergent clades occurred in the British Isles and mainland Europe and were sourced from the St Lawrence and Chesapeake/Delaware Bay estuaries. A third clade was found in the Great Lakes and sourced to the Hudson River estuary. Despite extensive sampling, G. tigrinus did not occur in freshwater at putative source sites. Some European populations showed reduced genetic diversity consistent with bottlenecks, although selection effects cannot be excluded. The habitat distribution of clades in Europe was congruent with the known invasion history of secondary spread from the British Isles. Differences in salinity tolerance among lineages were suggested by patterns of habitat colonization by different native COI clades. Populations consisting of admixtures of the two invading clades were found principally at recently invaded fresh and brackish water sites in Eastern Europe, and were characterized by higher genetic diversity than putative source populations. Further studies are required to determine if these represent novel genotypes. Our results confirm that biological invasions need not result in diminished genetic diversity, particularly if multiple source populations, each with distinctive genetic composition, contribute to the founding populations. [source] Molecular ecology of zebra mussel invasionsMOLECULAR ECOLOGY, Issue 4 2006GEMMA E. MAY Abstract The invasion of the zebra mussel, Dreissena polymorpha, into North American waters has resulted in profound ecological disturbances and large monetary losses. This study examined the invasion history and patterns of genetic diversity among endemic and invading populations of zebra mussels using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. Patterns of haplotype frequency indicate that all invasive populations of zebra mussels from North America and Europe originated from the Ponto-Caspian Sea region. The distribution of haplotypes was consistent with invasive populations arising from the Black Sea drainage, but could not exclude the possibility of an origin from the Caspian Sea drainage. Similar haplotype frequencies among North American populations of D. polymorpha suggest colonization by a single founding population. There was no evidence of invasive populations arising from tectonic lakes in Turkey, while lakes in Greece and Macedonia contained only Dreissena stankovici. Populations in Turkey might be members of a sibling species complex of D. polymorpha. Ponto-Caspian derived populations of D. polymorpha (, = 0.0011) and Dreissena bugensis (one haplotype) exhibited low levels of genetic diversity at the COI gene, perhaps as a result of repeated population bottlenecks. In contrast, geographically isolated tectonic lake populations exhibited relatively high levels of genetic diversity (, = 0.0032 to 0.0134). It is possible that the fluctuating environment of the Ponto-Caspian basin facilitated the colonizing habit of invasive populations of D. polymorpha and D. bugensis. Our findings were concordant with the general trend of destructive freshwater invaders in the Great Lakes arising from the Ponto-Caspian Sea basin. [source] Phylogeography and systematics of zebra mussels and related speciesMOLECULAR ECOLOGY, Issue 4 2006GREGORY W. GELEMBIUK Abstract The genus Dreissena includes two widespread and aggressive aquatic invaders, the zebra mussel, Dreissena polymorpha, and the quagga mussel, Dreissena bugensis. This genus evolved in the Ponto-Caspian Sea basin, characterized by dynamic instability over multiple timescales and a unique evolutionary environment that may predispose to invasiveness. The objectives of this study were to gain insights into the demographic history of Dreissena species in their endemic range, to reconstruct intraspecific phylogeographic relationships among populations, and to clarify systematics of the genus, using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. We found four deeply diverged clades within this genus, with a basal split that approximately coincided with the Cretaceous,Tertiary boundary. Divergence events within the four base clades were much more recent, corresponding to geographically disjunct sets of populations, which might represent species complexes. Across all taxa, populations of Dreissena shared a common pattern of genetic signatures indicating historical population bottlenecks and expansions. Haplotype diversity was relatively low in Ponto-Caspian drainages relative to more stable tectonic lakes in Greece, Macedonia, and Turkey. The phylogeographic and demographic patterns in the endemic range of Dreissena might have resulted from vicariance events, habitat instability, and the high fecundity and passive dispersal of these organisms. [source] Detecting past population bottlenecks using temporal genetic dataMOLECULAR ECOLOGY, Issue 10 2005UMA RAMAKRISHNAN Abstract Population bottlenecks wield a powerful influence on the evolution of species and populations by reducing the repertoire of responses available for stochastic environmental events. Although modern contractions of wild populations due to human-related impacts have been documented globally, discerning historic bottlenecks for all but the most recent and severe events remains a serious challenge. Genetic samples dating to different points in time may provide a solution in some cases. We conducted serial coalescent simulations to assess the extent to which temporal genetic data are informative regarding population bottlenecks. These simulations demonstrated that the power to reject a constant population size hypothesis using both ancient and modern genetic data is almost always higher than that based solely on modern data. The difference in power between the modern and temporal DNA approaches depends significantly on effective population size and bottleneck intensity and less significantly on sample size. The temporal approach provides more power in cases of genetic recovery (via migration) from a bottleneck than in cases of demographic recovery (via population growth). Choice of genetic region is critical, as mutation rate heavily influences the extent to which temporal sampling yields novel information regarding the demographic history of populations. [source] | ||||||||||||||||||||||||||||