Random Genetic Drift

Generalized Polya urn models have been used to model the establishment dynamics of a small founding population consisting of k different genotypes or strategies. As population sizes get large, these population processes are well-approximated by a mean limit ordinary differential equation whose state space is the k simplex. We prove that if this mean limit ODE has an attractor at which the temporal averages of the population growth rate is positive, then there is a positive probability of the population not going extinct (i.e. growing without bound) and its distribution converging to the attractor. Conversely, when the temporal averages of the population growth rate is negative along this attractor, the population distribution does not converge to the attractor. For the stochastic analog of the replicator equations which can exhibit non-equilibrium dynamics, we show that verifying the conditions for convergence and non-convergence reduces to a simple algebraic problem. We also apply these results to selection-mutation dynamics to illustrate convergence to periodic solutions of these population genetics models with positive probability.

Bombus and 2 Psithyrus bumble bee species from North America. The mean expected heterozygosity (H) for the Bombus species was 0.008 + 0.006 (95% confidence limits) and that for the Psithyrus was O. 007 +_ O. 007. These levels" are significantly lower than found in other Hymenoptera but are comparable to those found in previous studies of bumble bees based on far fewer loci. Neutral mutation and random genetic drift can account for the observed variation, but this implies a very small effective population size for species of bumble bees.

Lycoris sanguinea Maxim. var. koreana (Nakai) Koyama (Amaryllidaceae), a sexually and clonally reproducing herbaceous perennial, is distributed in a few localities in the southern Korea and Japan (Kyushu and Tsushima Island). Seven Korean populations of the variety were analyzed by starch gel electrophoresis to measure genetic variation at 19 allozyme loci. Populations of L. sanguinea var. koreana maintain similar levels of allozyme diversity (percent of polymorphic loci, P = 15% and mean expected heterozygosity, H e = 0.052) to values for its widespread congener L. chinensis Traub. Genetic divergence among populations of the variety was low (mean G ST = 0.092). This might be due to recent divergence of populations in Korea. As nearly all genetic diversity in the variety is contained within populations, conserving on one Korean population of the variety would maintain most of the genetic diversity in the Korean populations as a whole.

Evolutionary explanations for the origin of modularity in genetic and developmental pathways generally assume that modularity confers a selective advantage. However, our results suggest that even in the absence of any direct selective advantage, genotypic modularity may increase through the formation of new subfunctions under near-neutral processes. Two subfunctions may be formed from a single ancestral subfunction by the process of fission. Subfunction fission occurs when multiple functions under unified genetic control become subdivided into more restricted functions under independent genetic control. Provided that population size is sufficiently small, random genetic drift and mutation can conspire to produce changes in the number of subfunctions in the genome of a species without necessarily altering the phenotype. Extensive genotypic modularity may then accrue in a near-neutral fashion in permissive population-genetic environments, potentially opening novel pathways to morpholo...

Background: The E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a Cterminal domain (CT) comprising two segments, a pre-anchor and a trans-membrane (TM) region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1. Results: Two computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method applied to FP and CT primary structures, respectively. In spite of the relatively low random genetic drift between genotypes, co-evolution analysis of sequences from five HCV genotypes revealed a greater correlation between the FP and CT domains than respect to a control HCV sequence from Core protein, so giving a clear, albeit still inconclusive, support to the physical interaction hypothesis. The second approach relies upon a non-linear signal analysis method widely used in protein science called Recurrence Quantification Analysis (RQA). This method allows for a direct comparison of domains for the presence of common hydrophobicity patterns, on which the physical interaction is based upon. RQA greatly strengthened the reliability of the hypothesis by the scoring of a lot of cross-recurrences between FP and CT peptides hydrophobicity patterning largely outnumbering chance expectations and pointing to putative interaction sites. Intriguingly, mutations in the CT region of E1, reducing the fusion process in vitro, strongly reduced the amount of cross-recurrence further supporting interaction between this region and FP.

Philosophers of science sometimes seem to imply that there are evolutionary models in which a counterfactual infinite population of organisms plays a crucial role. As is sometimes noted, this idea is incoherent if "infinite population" is understood literally. This paper uses case studies of modeling in evolutionary biology to examine roles that "infinite population", and assumptions about random drift, play in modeling practices. Sometimes various effects of the absence of drift are understood as having to do with limits as population size goes toward infinity; in other cases these effects are conceptualized as having to do with large population sizes. Some models make assumptions about population size and effects of drift that might seem inconsistent: in some cases drift is included in part of a model, but excluded in another, or excluded even though population size is treated as finite. Because of such facts, I argue that there is no fixed set of assumptions associated with drift or its absence, and that there is no clear meaning for "infinite population" and similar terms. Rather "infinite population" is figurative language that is merely associated with various assumptions about the absence of drift.

Populations that encounter a novel environment can lose genetic diversity. Intense, directional selection can affect reproduction and lead to a gene pool dominated by relatively few genotypes. A loss of haplotype diversity (h) in the mitochondrial genome in populations of meiobenthic, harpacticoid copepods around offshore oil platforms has been linked to lethal and sublethal responses to factors proximal to offshore oil platforms. However, it was not possible to determine if the effects were related directly to increased concentrations of contaminants produced by drilling at the platforms. An experiment was designed to test whether populations of Nitocra lacustris Schmankevitsch (Copepoda: Harpacticoida) would lose haplotype diversity over 3 generations following exposure to sediment-associated hydrocarbons. Haplotype diversity was estimated by comparing restriction fragment length polymorphisms generated from mitochondrial DNA amplified from individual copepods. An additional component of the study was to determine the effects of population size on estimates of diversity. Haplotype diversity could be underestimated by using too few individuals, because random genetic drift in very small populations could cause lower diversity even in the absence of strong selection. The relationship between sample size and h was determined by randomly sub-sampling, at different sample sizes, a large data set collected for two copepod species. Cultures treated with phenanthrene, a polycyclic aromatic hydrocarbon, experienced lower adult survival, fewer surviving offspring per female, and lower haplotype diversity relative to control cultures. After the first generation, mortality declined, but larval survival and haplotype diversity did not change in subsequent generations. Diversity was slightly underestimated due to assaying too small a number of individuals, but could not account for all of the differences between treatments. Despite mortality, populations in culture were not reduced to the point where random drift seemed to have a significant effect. These results support the hypothesis that loss of mtDNA diversity in naturally occurring populations of Harpacticoida may serve as a marker for negative effects of exposure to xenobiotic contaminants.

This article challenges Speakman's hypothesis that the modern genetic predisposition to obesity has arisen through random genetic drift in the two million years following predation release. We present evidence in support of the hypothesis that a mixture of famines and seasonal food shortages in the post-agricultural era have exerted natural selection in favour of fat storage; an effect most likely mediated through fertility, rather than viability, selection. We conclude that, far from being time to call off the search, recently developed genetic and bio-informatic methods will soon provide a definitive resolution to this longstanding 'thrifty gene' controversy.

This paper studies a class of non Markovian and non homogeneous stochastic processes on a finite state space. It provides an unified approach to simulated annealing type processes, certain vertex reinforced random walks and certain models of learning in games including Markovian fictitious play.

Cedrus libani of Lebanon is a valuable natural resource and the dominant species in its natural ecosystem. Intense and diverse anthropogenic pressures over historical times raised concerns about its genetic vigor and continued survival. Our investigation of the genetic diversity included samples from all remnant natural populations. Assessment of the genetic diversity using random amplified polymorphic DNA markers revealed the persistence of considerable variation distributed within populations with low population differentiation corroborated by Bayesian and analysis of molecular variance estimates (G ST =0.07, Φ ST = 0.09). Individual assignment tests were carried out to investigate measures of gene flow. Inferences concluded that this natural heritage is not currently threatened by inbreeding or by random genetic drift. Correlation studies investigated possible effects of spatial distribution and environmental conditions on genetic structure. A climatic trend corresponding to a temperature-humidity gradient correlated significantly with the level of genetic diversity, while the edaphic variation did not.

Spatial autocorrelation statistics are used for description of geographic variation of gene frequencies, but the relationship of these indices with the parameters describing the genetic structure of populations is not established. A simple relation is derived here between kinship coefficient and a measure of spatial autocorrelation, Moran's I. The autocorrelation coefficient of gene frequencies at a given distance is a direct function of the kinship at that distance, and an inverse function of the standardized gene frequency variance, Fst. Under isolation by distance, the expected values of Moran's I for any allele may be calculated by means of Malkcot-Morton function, which predicts an exponential decline of genetic similarity in space. This allows comparison of observed gene frequency patterns with the patterns that should be caused by interaction of short range migration and random genetic drift.

The alcohol dehydrogenase (Adh) region of Drosophila pseudoobscura, which includes the two genes Adh and Adh-Dup, was used to examine the pattern and organization of linkage disequilibrium among pairs of segregating nucleotide sites. A collection of 99 strains from the geographic range of D. pseudoobscura were nucleotide-sequenced with polymerase chain reaction-mediated techniques. All pairs of the 359 polymorphic sites in the 3.5-kb Adh region were tested for significant linkage disequilibrium with Fisher's exact test. Of the 74,278 pairwise comparisons of segregating sites, 127 were in significant linkage disequilibrium at the 5% level. The distribution of five linkage disequilibrium estimators D,, D2, r,j, ? and Dij were compared to theoretical distributions. The observed distributions of D,, D2, r, and ? were consistent with the theoretical distribution given an infinite sites model. The observed distribution of Dij differed from the theoretical distribution because of an excess of values at-1 and 1. N o spatial pattern was observed in the linkage disequilibrium pattern in the Adh region except for two clusters of sites nonrandomly associated in the adult intron and intron 2 of Adh. The magnitude of linkage disequilibrium decreases significantly as nucleotide distance increases, or a distance effect. Adh-Dup had a larger estimate of the recombination parameter, 4Nc, than Adh, where N is the effective population size and c is the recombination rate. A comparison of the mutation and recombination parameters shows that 7-17 recombination events occur for each mutation event. The heterogeneous estimates of the recombination parameter and the inverse relationship between linkage disequilibrium and nucleotide distance are no longer significant when the two clusters of Adh intron sites are excluded from analyses. The most likely explanation for the two clusters of linkage disequilibria is epistatic selection between sites in the cluster to maintain pre-mRNA secondary structure. The observation of significant linkage disequilibrium that is consistent between populations is a very sensitive detector of natural selection (LEWONTIN 1974).

Amino acid sequences of the first half of MSEL-and VLDV-neurophysins from goose and chicken have been determined. Identical substitutions in positions 17, 18, 35, 36 and 41 of both neurophysins of a given species when compared with their mammalian counterparts suggest a gene conversion between vasotocin-MSEL-neurophysin and mesotocin-VLDV-neurophysin genes. This event, which has already been observed for three mammalian species, seems recurrent and would link the evolution of the two neurohypophysial hormone precursors.

Neurohypophysial hormones are nonapeptides derived from precursors containing two or three domains, namely the hormonal moiety, a small protein, neurophysin (93/95 residues) and occasionally a glycopeptide, copeptin (39 residues). Enzymic processing of the precursors is very fast and separate domains are usually found in neurohypophysis. These fragments can be used on one hand to trace two phylogenetic lineages in vertebrates, on the other hand to follow expression of the precursor genes during the early stages of development. Regarding the hormonal domains, whereas mammalian species possess virtually always vasopressin and oxytocin, nonmammalian tetrapods have vasotocin ([Ile 3]-vasopressin) and mesotocin ([Ile 8]-oxytocin). Concerning the neurophysin domains, the two types MSEL-neurophysin (vasopressin-associated) and VLDV-neurophysin (oxytocin

The major histocompatibility complex (MHC) plays an important role in infectious disease resistance. The presence of certain MHC alleles and functionally similar groups of MHC alleles (i.e., supertypes) has been associated with resistance to particular parasite species. Farmed and domesticated fish stocks are often depleted in their MHC alleles and supertype diversity, possibly as a consequence of artificial selection for desirable traits, inbreeding (loss of heterozygosity), genetic drift (loss of allelic diversity) and/or reduced parasite biodiversity. Here we quantify the effects of depletion of MHC class II genotype and supertype variation on resistance to the parasite Gyrodactylus turnbulli in guppies (Poecilia reticulata). Compared to the descendants of wild‐caught guppies, ornamental fish had a significantly reduced MHC variation (i.e., the numbers of MHC alleles and supertypes per individual, and per population). In addition, ornamental fish were significantly more susceptib...

As the CCi-FEAST conference organisers have pointed out, an emerging, knowledgebased society creates demand for evolutionary economics that consider outputs, inputs and social networks wherein peoples' choices are dependent upon, and valuated by, the choices of others. How individuals behave within these contexts is fundamental to the nature of growth of creative industries, in whether they proceed in predictable directions, or drift upon the tides of fashion. It is useful to model elements of creative industries as being positioned along a highly simplified spectrum, between ideas that are copied randomly among people as fashions, and ideas that are selected for inherent qualities. Characterizing innovation along this fashion-selection spectrum gives crucial insight to the dynamics of how certain behaviours increase or decline. As the spectrum becomes broadly defined, the approach can be made incrementally more complex through incorporating additional model parameters tested against industry-supplied empirical data (1). Conceptualised this way, the study of creative industries can take advantage of sophisticated tools from epidemiology (2), population genetics (3) and other culture evolution models in all their variety (4). For the 'selection' end of the spectrum, we have a wealth of models of independent decision-makers who weigh the costs and benefits of their options, while subject to various biases of influence (5). This applies well to behaviours that serve some adaptive purpose, i.e., that matter to human values, or the spread of a useful idea (6). Even a display of fashion, if it carries some meaningful signal (e.g. mating potential), can be seen as subject to cost/benefit decisions (7). At the other end of the spectrum are behaviours that do not inherently 'matter', in terms of human survival, and for which there is often a large variety of optionsdecorative designs, musical motifs, and word forms, for example. In analogy to population genetics, these choices can be considered 'neutral' traits, in that what is chosen has no inherent value relative to other options (8,9). The neutral model would assume that whether a mother names her girl "Jane" or "Jamelia" depends on who, and how many, already have the name, rather than any qualities of the name itself. This is formalised as the random copying or neutral model, akin to the neutral-trait model of population genetics, for popular culture change (3). Practically speaking, the random copying model does not require that people make choices without any reasons at all, but rather that the statistics of all their idiosyncratic choices, at the population level, are comparable to random copying. The model simply allows us to ask, what if everyone simply copied each other, with occasional innovation? Against this background 'canvas', more interesting phenomena become visible. In one study, we used the expectations under random copying as the background on which to fit data on dog breed popularity in the 20 th century. The rapid rise and fall of Dalmatians was then clearly visible just after 1984 (10). The reason for the spike in Dalmatian popularity was surely the re-release of the Disney movie 101 Damatians during this year. However, not all movies have this 'celebrity

As the CCi-FEAST conference organisers have pointed out, an emerging, knowledgebased society creates demand for evolutionary economics that consider outputs, inputs and social networks wherein peoples' choices are dependent upon, and valuated by, the choices of others. How individuals behave within these contexts is fundamental to the nature of growth of creative industries, in whether they proceed in predictable directions, or drift upon the tides of fashion. It is useful to model elements of creative industries as being positioned along a highly simplified spectrum, between ideas that are copied randomly among people as fashions, and ideas that are selected for inherent qualities. Characterizing innovation along this fashion-selection spectrum gives crucial insight to the dynamics of how certain behaviours increase or decline. As the spectrum becomes broadly defined, the approach can be made incrementally more complex through incorporating additional model parameters tested against industry-supplied empirical data (1). Conceptualised this way, the study of creative industries can take advantage of sophisticated tools from epidemiology (2), population genetics (3) and other culture evolution models in all their variety (4). For the 'selection' end of the spectrum, we have a wealth of models of independent decision-makers who weigh the costs and benefits of their options, while subject to various biases of influence (5). This applies well to behaviours that serve some adaptive purpose, i.e., that matter to human values, or the spread of a useful idea (6). Even a display of fashion, if it carries some meaningful signal (e.g. mating potential), can be seen as subject to cost/benefit decisions (7). At the other end of the spectrum are behaviours that do not inherently 'matter', in terms of human survival, and for which there is often a large variety of optionsdecorative designs, musical motifs, and word forms, for example. In analogy to population genetics, these choices can be considered 'neutral' traits, in that what is chosen has no inherent value relative to other options (8,9). The neutral model would assume that whether a mother names her girl "Jane" or "Jamelia" depends on who, and how many, already have the name, rather than any qualities of the name itself. This is formalised as the random copying or neutral model, akin to the neutral-trait model of population genetics, for popular culture change (3). Practically speaking, the random copying model does not require that people make choices without any reasons at all, but rather that the statistics of all their idiosyncratic choices, at the population level, are comparable to random copying. The model simply allows us to ask, what if everyone simply copied each other, with occasional innovation? Against this background 'canvas', more interesting phenomena become visible. In one study, we used the expectations under random copying as the background on which to fit data on dog breed popularity in the 20 th century. The rapid rise and fall of Dalmatians was then clearly visible just after 1984 (10). The reason for the spike in Dalmatian popularity was surely the re-release of the Disney movie 101 Damatians during this year. However, not all movies have this 'celebrity

We investigated allozyme variation in 16 populations of the rare monotypic fern Mankyua chejuense and 11 populations of a closely related, widespread fern Botrychium ternatum. Genetic diversity was extremely low in the critically endangered M. chejuense (%P s ¼ 10%, A s ¼ 1.13, and H es ¼ 0.007) relative to that found in B. ternatum (%P s ¼ 22.7%, A s ¼ 1.23, and H es ¼ 0.026). We detected homozygous genotypes for alternative alleles at a few loci, which suggests occurrence of intragametophytic self-fertilization. High degrees of population differentiation were found in both M. chejuense (F ST ¼ 0.245) and B. ternatum (F ST ¼ 0.414).The extremely low levels of genetic diversity in M. chejuense would be attributable to inbreeding coupled with random genetic drift and rarity. In situ protection of habitats of standing populations and ex situ preservation of several populations are suggested for the development of conservation strategies for M. chejuense.

We describe a primer pair that amplifies a 203 base pair fragment containing 4 single nucleotide polymorphisms (SNPs) within the cytochrome b region of the mitochondrial DNA that, when sequenced, conclusively distinguishes Washington state gray wolves from domestic dogs. The method is more efficient and cost-effective than other established methods for genetically distinguishing domestic dogs from gray wolves when using potentially degraded scat samples. Further testing may find that the SNP panel is also applicable to studies in Oregon, Idaho, Montana, and Wyoming, as these wolves belong to the same distinct population segment as Washington state gray wolves.

Determining the molecular basis of parasite adaptation to its host is an important component in understanding host-parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short-and long-term adaptive evolution in the eukaryotic parasite, Gyrodactylus bullatarudis, infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analyzing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G-protein and serine proteases genes, which are likely important in host-parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the notion that recombination between divergent genomes can result in particularly successful parasites.

The major histocompatibility complex (MHC) is crucial to the adaptive immune response of vertebrates and is among the most polymorphic gene families known. Its high diversity is usually attributed to selection imposed by fast-evolving pathogens. Pathogens are thought to evolve to escape recognition by common immune alleles, and, hence, novel MHC alleles, introduced through mutation, recombination, or gene flow, are predicted to give hosts superior resistance. Although this theoretical prediction underpins host-pathogen "Red Queen" coevolution, it has not been demonstrated in the context of natural MHC diversity. Here, we experimentally tested whether novel MHC variants (both alleles and functional "supertypes") increased resistance of guppies () to a common ectoparasite (). We used exposure-controlled infection trials with wild-sourced parasites, and -naïve host fish that were F descendants of crossed wild populations. Hosts carrying MHC variants (alleles or supe...

Arginine vasotocin (AVT) and AVT C-tcrminally extended with glycine (AVT-Gly) were isolated from the neurointermediate lobes of the bullfrog. Rana catesbeiana, using C ls SEP-PAK cartridges, and Sephadex G-50 and reverse-phase HPLC columns. These peptides exhibited marked aldosterone-releasing activity when injected into Xenopus juveniles. AVT-Gly (0.1-5//g) as well as AVT (0.01-5 jug) injected subcutaneously into Xenopus juveniles (8 g body weight) stimulated the discharge of a secretory material presumably from the granulated glands in the skin, AVT-Gly being less potent than AVT. Both peptides also induced defecation in the animals, the incidence of defecation increasing with higher dosage.

Background The E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a C-terminal domain (CT) comprising two segments, a pre-anchor and a trans-membrane (TM) region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1. Results Two computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method app...

Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the cont...

Spatially resolved genetic data is increasingly used to reconstruct the migrational history of species. To assist such inference, we study, by means of simulations and analytical methods, the dynamics of neutral gene frequencies in a population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds C.A., Lillie A.S. & Cavalli-Sforza L.L. ( ) Proc Natl Acad Sci USA 101: 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in pushed waves than in pulled waves, and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics.

Competition between random genetic drift and natural selection play a central role in evolution: Whereas nonbeneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well mixed populations of two fluorescently labeled strains of Escherichia coli develop well defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies ( Saccharomyces cerevisiae ) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions.

Adaptation in spatially extended populations entails the propagation of evolutionary novelties across habitat ranges. Driven by natural selection, beneficial mutations sweep through the population in a ''wave of advance''. The standard model for these traveling waves, due to R. Fisher and A. Kolmogorov, plays an important role in many scientific areas besides evolution, such as ecology, epidemiology, chemical kinetics, and recently even in particle physics. Here, we extend the Fisher-Kolmogorov model to account for mutations that confer an increase in the density of the population, for instance as a result of an improved metabolic efficiency. We show that these mutations invade by the action of random genetic drift, even if the mutations are slightly deleterious. The ensuing class of noise-driven waves are characterized by a wave speed that decreases with increasing population sizes, contrary to conventional Fisher-Kolmogorov waves. When a trade-off exists between density and growth rate, an evolutionary optimal population density can be predicted. Our simulations and analytical results show that genetic drift in conjunction with spatial structure promotes the economical use of limited resources. The simplicity of our model, which lacks any complex interactions between individuals, suggests that noiseinduced pattern formation may arise in many complex biological systems including evolution.

A classical view of speciation is that reproductive isolation arises as a by-product of genetic divergence. Here, individual-based simulations are used to evaluate whether the mechanisms implied by this view may result in rapid speciation if the only source of genetic divergence are mutation and random genetic drift. Distinctive features of the simulations are the consideration of the complete process of speciation (from initiation until completion), and of a large number of loci, which was only one order of magnitude smaller than that of bacteria. It is demonstrated that rapid speciation on the timescale of hundreds of generations is plausible without the need for extreme founder events, complete geographic isolation, the existence of distinct adaptive peaks or selection for local adaptation. The plausibility of speciation is enhanced by population subdivision. Simultaneous emergence of more than two new species from a subdivided population is highly probable. Numerical examples relevant to the theory of centrifugal speciation and to the conjectures about the fate of`ring species' and`sexual continuums' are presented.

Habitat alteration, fragmentation and destruction as a consequence of human impact are a global phenomenon. Here we document changes in genetic variation in the marsh orchid Anacamptis palustris as a consequence of such habitat changes. We examined historical specimens that were collected during the nineteenth and early twentieth centuries, prior to the most recent massive habitat changes affecting this species. Sequences of a hypervariable region in the plastid DNA, located in the tRNA LEU intron, from herbarium vouchers were compared with those from a near-exhaustive survey of the extant A. palustris populations on the Italian peninsula. It was found that private haplotypes and alleles found in small, extant populations were once widespread and more common in historic populations and that alleles, once present in historic populations, have gone extinct. In addition, genetic differentiation among populations has increased over time and haplotype frequencies significantly differ among historic and extant populations. These results document that human induced habitat changes have reduced genetic diversity and increased the importance of random genetic drift in this species. It is concluded that the analysis of herbarium specimens may provide important insights into changes of genetic diversity over time and may be critical for correct inference of the evolutionary history of rare and endangered species.

Determining the molecular basis of parasite adaptation to its host is an important component in understanding host-parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short-and long-term adaptive evolution in the eukaryotic parasite, Gyrodactylus bullatarudis, infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analyzing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G-protein and serine proteases genes, which are likely important in host-parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the notion that recombination between divergent genomes can result in particularly successful parasites.

The results from empirical studies on the impact of habitat fragmentation on genetic variation of populations are controversial, ranging from negative to positive effects. This contradiction has been attributed to either species characteristics (e.g. plant life history) or environmental components (e.g. the scale of habitat fragmentation). To examine the role of DNA marker types on these effects, we carried out a comparative study of seven populations of Capparis spinosa L. (caper, Capparaceae) using ISSR markers and compared these results with those obtained previously using RAPD markers. Although both ISSR and RAPD markers showed high consistency and indicated that genetic variation in populations was not correlated with either geographical distance (P ≥ 0.47, P ≥ 0.83; for ISSR and RAPD, respectively) or altitude (P ≥ 0.535, P ≥ 0.419; for ISSR and RAPD respectively), the levels of variation were related to population size. ISSR analysis showed that genetic variation did not sign...

The main Korean mountain range (the so-called "Baekdudaegan"), which stretches from north to south across most of the country, has been thought to harbor glacial refugia for boreal plant species, where they likely found relatively stable habitats and maintained large population sizes. Under this scenario, high levels of genetic variation and low or moderate degree of differentiation among populations within these species were expected. To test this hypothesis, we examined levels of allozyme diversity (14 loci) in eight populations of the boreal herb Lilium cernuum, which in Korea occurs largely along the Baekdudaegan and, as a reference, in eight populations of its congener Lilium amabile, a temperate species that is distributed on lower hillsides in peripheral regions of the Baekdudaegan. L. cernuum harbored higher levels of genetic variation within populations than L. amabile (%P ¼ 49.1 vs. 25.0, A ¼ 1.71 vs. 1.34, and H e ¼ 0.159 vs. 0.048). Genetic differentiation among populations was low for both species (F ST ¼ 0.119 and 0.014 for L. cernuum and L. amabile, respectively). A series of historical and ecological factors may explain the contrasting levels of genetic diversity between L. cernuum and L. amabile: occurrence within the main ranges of the Baekdudaegan (enduring the glacial periods in macrorefugia) vs. low elevation peripheral areas (in microrefugia) and shade-tolerant vs. shade-intolerant. This study, as well as previous population genetics studies, strongly suggests that the Baekdudaegan merits high priority for conservation given its proposed role as glacial refugia for montane species.

The q-Pólya urn is a q-analog of the Pólya urn and is a model of ball extraction from an urn with balls of two colors, A and B. Balls of color B have priority to be picked over those of color A. We prove that, in an infinite sequence of extractions, almost surely, the number of balls of color A that are picked has a finite limit and we identify its distribution. Then we prove functional limit theorems for the number of balls of color A extracted. The limit is either a pure birth process or a diffusion, depending on the initial composition of the urn. Finally, we discuss basic results for the q-Pólya urn with more than two colors.

Aliozyme frequencies of Anolis grahami from Bermuda were compared to those from Jamaica. These lizards were introduced into Bermuda from Jamaica in 1905. The magnitude of the genetic changes were consistent with the hypothesis that these changes were produced by random genetic drift. The changes for the separate alleles were, however, more heterogeneous than expected if caused by random drift alone. It is concluded that not all the alleles examined have been selectively neutral.

Melanistic garter snakes (77umnophi.s Sirialir) are unusually common near Lake Erie, apparently because selection for thermoregulatory ability in cool lake-shore habitats (which favours melanistic morphs) outweighs selection for crypsis (which favours striped morphs). However, morph frequencies are highly variable among sites, suggesting that random genetic drift also influences colour pattern. In an effort to better understand the evolutionary processes influencing garter snake colour patterns, we estimated F,, and Nm (the number of migrants per generation) among island and mainland populations from patterns of allozymic variation detected using electrophoresis. Estimates of Nm were high, ranging from 2.7 to 37.6 between pairs of study sites and making it unlikely that differences in morph frequencies among sites were solely the result of random genetic drift. Furthermore, differences in F,, estimates between colour pattern (a one-locus two-allele trait) and allozyme loci suggest that colour pattern alleles are not in Hardy-Weinberg equilibrium, most likely as a result of natural selection. Comparison of allozymic data from Lake Erie with those from more distant sites suggests that gene flow occurs over long distances in T. sirtalis. 01996 The Linnean Society of London ADDITIONAL KEY WORDS-Thnmnophis SirialiCnatural selectionrandom genetic driftallozymescolour pattern.

Neutral evolution is a frequently used model to analyse changes in frequencies of cultural variants over time. Variants are chosen to be copied according to their relative frequency and new variants are introduced by a process of random mutation. Here we present a non-equilibrium neutral model which accounts for temporally varying population sizes and mutation rates and makes it possible to analyse the cultural system under consideration at any point in time. This framework gives an indication whether observed changes in the frequency distributions of a set of cultural variants between two time points are consistent with the random copying hypothesis. We find that the likelihood of the existence of the observed assemblage at the end of the considered time period (expressed by the probability of the observed number of cultural variants present in the population during the whole period under neutral evolution) is a powerful indicator of departures from neutrality. Further, we study the effects of frequency-dependent selection on the evolutionary trajectories and present a case study of change in the decoration of pottery in early Neolithic Central Europe. Based on the framework developed we show that neutral evolution is not an adequate description of the observed changes in frequency.

There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development resolving long standing questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and by inference, transfer of trait and disease alleles among dog breeds.

Cedrus libani of Lebanon is a valuable natural resource and the dominant species in its natural ecosystem. Intense and diverse anthropogenic pressures over historical times raised concerns about its genetic vigor and continued survival. Our investigation of the genetic diversity included samples from all remnant natural populations. Assessment of the genetic diversity using random amplified polymorphic DNA markers revealed the persistence of considerable variation distributed within populations with low population differentiation corroborated by Bayesian and analysis of molecular variance estimates (G ST =0.07, Φ ST = 0.09). Individual assignment tests were carried out to investigate measures of gene flow. Inferences concluded that this natural heritage is not currently threatened by inbreeding or by random genetic drift. Correlation studies investigated possible effects of spatial distribution and environmental conditions on genetic structure. A climatic trend corresponding to a temperature-humidity gradient correlated significantly with the level of genetic diversity, while the edaphic variation did not.

A field experiment was conducted in 2010 to identify canola traits suited to the new and expanding high rainfall cropping region of south-eastern Australia. Winter and spring cultivars from Europe were assessed to test the hypothesis that cultivars from other high rainfall regions of the world would make better use of the longer growing season and therefore produce greater yields than cultivars currently available to farmers. The grain yield, yield components and level of blackleg infection of four canola cultivars from Europe (3 winter types and 1 spring type) were compared to a high yielding Australian spring type. Crops were grown +/spring irrigation and +/plant growth regulator (PGR). The European types produced approximately 20% more grain than the Australian control with grain yields as high as 8.0 t ha -1 under irrigation. The application of 45 mm of irrigation in spring resulted in approximately 1 t ha -1 more grain than the rain fed treatment. The PGR caused a significant h...

A field experiment was conducted in 2010 to identify canola traits suited to the new and expanding high rainfall cropping region of south-eastern Australia. Winter and spring cultivars from Europe were assessed to test the hypothesis that cultivars from other high rainfall regions of the world would make better use of the longer growing season and therefore produce greater yields than cultivars currently available to farmers. The grain yield, yield components and level of blackleg infection of four canola cultivars from Europe (3 winter types and 1 spring type) were compared to a high yielding Australian spring type. Crops were grown +/spring irrigation and +/plant growth regulator (PGR). The European types produced approximately 20% more grain than the Australian control with grain yields as high as 8.0 t ha -1 under irrigation. The application of 45 mm of irrigation in spring resulted in approximately 1 t ha -1 more grain than the rain fed treatment. The PGR caused a significant h...

Effective population size (N e) influences the degree to which random genetic drift changes allele frequencies, increases inbreeding, and decreases genetic diversity, and thus is a parameter of direct relevance to the conservation of rare species. Few empirical data are available, however, concerning the effects of clonal structure on N e in plant species reproducing both sexually and asexually. Using genetic markers and spatial autocorrelation analysis, we quantified the statistical significance and spatial scale of clonal spread of six populations of the rare terrestrial orchid Cremastra appendiculata (D. Don) Makino in a large (180 ha), undisturbed landscape on Oenaro Island, located off of the southeastern coast of South Korea. We used this information to calculate three demographic estimators of N e : the number of ramets within a population, the number of genets, and an estimator that incorporates information on both the number of genets and variation in the number of ramets per genet. Taking clonal structure into account results in up to a fivefold decrease in estimates of N e relative to the ecologically apparent number of individuals within populations. Levels of standing genetic variation are in fact greater than expected given our estimates of N e , leading us to consider historical factors resulting in N e being greater in the past than in present-day populations. Like C. appendiculata, many terrestrial orchids occur in relatively small, spatially isolated populations and are of special concern for conservation. Our results indicate that efforts aimed at the long-term preservation of these species should be based on a sound understanding of the potential for clonal structure and its implications for the sensitivity of populations to losses of genetic diversity and fitness via random genetic drift.

Recent morphological, physiological, and molecular studies that shed light on the functional significance of the neurohypophysial peptide arginine vasotocin (AVT) in the reptilian kidney are reviewed. Several structural features of the reptilian nephron are highlighted, including the presence of an incipient juxta-glomerular apparatus, aglomerular nephrons, and the thin, very short intermediate segment (IS) joining proximal and distal convoluted tubules. Although the V 2-like AVT receptor and its gene have yet to be sequenced in any reptile, AVT receptors have been located in both the IS and the branched collecting duct system in the agamid lizard Ctenophorus ornatus. These findings suggest that AVT may have a dual effect in the reptilian kidney, first diluting the urinary fluid in the thin-intermediate segment, prior to its entering the collecting duct system, and then facilitating water reabsorption along an osmotic gradient as the urine passes through the final segments of the nephron. The IS may thus prove to be the evolutionary homologue of the thin-ascending limb of the loop of Henle in the mammalian kidney.

a n , Ja c e k 2 0 2 0. G e n e d u plic a tio n s, div e r g e n c e a n d r e c o m bi n a tio n s h a p e a d a p tiv e e v ol u tio n of t h e fis h e c t o p a r a si t e Gy ro d a c tylu s b ull a t a r u di s. M ol e c ul a r E c olo gy 2 9 (8) , p p. 1 4 9 4-1 5 0 7. 1 0. 1 1 1 1/ m e c. 1 5 4 2 1 file Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite, Gyrodactylus bullatarudis

Mathematical studies are conducted on three problems that arise in molecular population genetics. (1) The time required for a particular allele to become extinct in a population under the effects of mutation, selection, and random genetic drift is studied. In the absence of selection, the mean extinction time of an allele with an initial frequency close to 1 is of the order of the reciprocal of the mutation rate when 4Nv << 1, where N is the effective population size and v is the mutation rate per generation. Advantageous mutations reduce the extinction time considerably, whereas deleterious mutations increase it tremendously even if the effect on fitness is very slight. (2) Mathematical formulae are derived for the distribution and the moments of extinction time of a particular allele from one or both of two related populations or species under the assumption of no selection. When 4Nv << 1, the mean extinction time is about half that for a single population, if the two ...