Showing papers on "Genetic drift published in 2004"

Mapping the Antigenic and Genetic Evolution of Influenza Virus

Abstract: The antigenic evolution of influenza A (H3N2) virus was quantified and visualized from its introduction into humans in 1968 to 2003. Although there was remarkable correspondence between antigenic and genetic evolution, significant differences were observed: Antigenic evolution was more punctuated than genetic evolution, and genetic change sometimes had a disproportionately large antigenic effect. The method readily allows monitoring of antigenic differences among vaccine and circulating strains and thus estimation of the effects of vaccination. Further, this approach offers a route to predicting the relative success of emerging strains, which could be achieved by quantifying the combined effects of population level immune escape and viral fitness on strain evolution.

Genetic variation increases during biological invasion by a Cuban lizard

Abstract: A genetic paradox1,2 exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction1,3,4. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs5,6. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed7.

Variation in sexual reproduction in orchids and its evolutionary consequences: a spasmodic journey to diversification

Abstract: The great taxonomic diversity of the Orchidaceae is often attributed to adaptive radiation for specific pollinators driven by selection for outcrossing. However, when one looks beyond the product to the process, the evidence for selection is less than overwhelming. We explore this problem by discussing relevant aspects of orchid biology and asking which aspects of reproduction explain the intricate pollination mechanisms and diversification of this family. We reaffirm that orchids are primarily pollination limited, the severity of which is affected by resource constraints. Fruit set is higher in temperate than in tropical species, and in species which offer pollinator rewards than those that do not. Reproductive success is skewed towards few individuals in a population and effective population sizes are often small. Population structure, reproductive success and gene flow among populations suggest that in many situations genetic drift may be as important as selection in fostering genetic and morphological variation in this family. Although there is some evidence for a gradualist model of evolutionary change, we believe that the great diversity in this family is largely a consequence of sequential and rapid interplay between drift and natural selection. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 1–54.

Genetic variation, classification and 'race'.

Abstract: New genetic data has enabled scientists to re-examine the relationship between human genetic variation and 'race'. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now yields reasonably accurate estimates of genetic similarity among individuals, rather than populations. Clustering of individuals is correlated with geographic origin or ancestry. These clusters are also correlated with some traditional concepts of race, but the correlations are imperfect because genetic variation tends to be distributed in a continuous, overlapping fashion among populations. Therefore, ancestry, or even race, may in some cases prove useful in the biomedical setting, but direct assessment of disease-related genetic variation will ultimately yield more accurate and beneficial information.

Implications of biogeography of human populations for 'race' and medicine.

Abstract: In this review, we focus on the biogeographical distribution of genetic variation and address whether or not populations cluster according to the popular concept of 'race'. We show that racial classifications are inadequate descriptors of the distribution of genetic variation in our species. Although populations do cluster by broad geographic regions, which generally correspond to socially recognized races, the distribution of genetic variation is quasicontinuous in clinal patterns related to geography. The broad global pattern reflects the accumulation of genetic drift associated with a recent African origin of modern humans, followed by expansion out of Africa and across the rest of the globe. Because disease genes may be geographically restricted due to mutation, genetic drift, migration and natural selection, knowledge of individual ancestry will be important for biomedical studies. Identifiers based on race will often be insufficient.

The Population Genetic Theory of Hidden Variation and Genetic Robustness

Abstract: One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been considered as evidence that the wild type has evolved robustness against genetic variation, i.e., genetic canalization. In this article we present a general model for the interaction of a major mutation or a novel environment with the additive genetic basis of a quantitative character under stabilizing selection. We introduce an approximation to the genetic variance in mutation-selection-drift balance that includes the previously used stochastic Gaussian and house-of-cards approximations as limiting cases. We then show that the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction, regardless of whether the wild-type genotype is canalized or not. As a consequence, the additive genetic variance increases upon a change in the environment or the genetic background even if the mutant character state is as robust as the wild-type character. Estimates show that this predicted increase can be considerable, in particular in large populations and if there are conditionally neutral alleles at the loci underlying the trait. A brief review of the relevant literature suggests that the assumptions of this model are likely to be generic for polygenic traits. We conclude that the release of hidden genetic variance due to a major mutation or environmental stress does not demonstrate canalization of the wild-type genotype.

Aquaculture and Fisheries Biotechnology: Genetic Approaches

Abstract: 1. History of Biotechnology, Genetics and Selective Breeding in Aquaculture and Fisheries 2. Phenotypic Variation and Environmental Effects 3. Basic Genetics, Qualitative Traits and Selection for Qualitative Traits 4. Strain Evaluation, Domestication and Strain Selection 5. Population Size, Inbreeding, Random Genetic Drift and Maintenance of Genetic Quality 6. Gynogenesis, Androgenesis, Cloned Populations and Nuclear Transplantation 7. Intraspecific Crossbreeding 8. Interspecific Hybridization 9. Selection and Correlated Responses to Selection 10. Polyploidy and Xenogenesis 11. Sex Reversal and Breeding 12. Biochemical and Molecular Markers 13. Population Genetics and Interactions of Hatchery and Wild Fish 14. Genomics, Gene Mapping, Quantitative Trait Locus Mapping and Marker-assisted Selection 15. Gene Expression 16. Gene-transfer Technology 17. Combining Genetic Enhancement Programmes 18. Genotype-Environment Interactions 19. Commercial Application of Fish Biotechnology 20. Environmental Risk of Aquatic Organisms from Genetic Biotechnology 21. Food Safety of Transgenic Aquatic Organisms 22. A Case Example: Safety of Consumption of Transgenic Salmon Potentially Containing Elevated Levels of Growth Hormone and Insulin-like Growth Factor 23. Government Regulation of Transgenic Fish and Biotechnology Products 24. Strategies for Genetic Conservation, Gene Banking and Maintaining Genetic Quality 25. Ethics 26. Constraints and Limitations of Genetic Biotechnology.

Genetic Bottlenecks Reduce Population Variation in an Experimental RNA Virus Population

Abstract: Genetic bottlenecks are stochastic events that limit genetic variation in a population and result in founding populations that can lead to genetic drift. Evidence of past genetic bottlenecks in numerous biological systems, from mammals to viruses, has been described. In this study, we used an artificial population of Cucumber mosaic virus consisting of 12 restriction enzyme marker-bearing mutants. This population was inoculated onto young leaves of tobacco plants and monitored throughout the course of systemic infection. We show here that the genetic variation in a defined population of an RNA virus is significantly, stochastically, and reproducibly reduced during the systemic infection process, providing clear evidence of a genetic bottleneck.

Detecting genetic drift versus selection in human evolution.

Abstract: Recent paleoanthropological discoveries reveal a diverse, potentially speciose human fossil record. Such extensive morphological diversity results from the action of divergent evolutionary forces on an evolving lineage. Here, we apply quantitative evolutionary theory to test whether random evolutionary processes alone can explain the morphological diversity seen among fossil australopith and early Homo crania from the Plio–Pleistocene. We show that although selection may have played an important role in diversifying hominin facial morphology in the late Pliocene, this is not the case during the early evolution of the genus Homo, where genetic drift was probably the primary force responsible for facial diversification.

Genetic Effects of a Persistent Bottleneck on a Natural Population of Ornate Box Turtles (Terrapene ornata)

Abstract: Human activities in the past few hundred years have caused enormous impacts on many ecosystems, greatly accelerating the rate of population decline and extinction. In addition to habitat alteration and destruction, the loss of genetic diversity due to reduced population size has become a major conservation issue for many imperiled species. However, the genetic effects of persistent population bottlenecks can be very different for long-lived and short-lived species when considering the time scale of centuries. To investigate the genetic effects of persistent population bottlenecks on long-lived species, we use microsatellite markers to assess the level of genetic diversity of a small ornate box turtle population that has experienced a persistent bottleneck in the past century, and compare it to a large relatively undisturbed population. The genetic signature of a recent bottleneck is detected by examining the deviation from mutation-drift equilibrium in the small population, but the bottleneck had little effect on its level of genetic diversity. Computer simulations combined with information on population structure suggest that an effective population size of 300, which results in a census population size of 700, would be required for the small population to maintain 90% of the average number of alleles per locus in the next 200 years. The life history of long-lived species could mask the accelerated rate of genetic drift, making population recovery a relatively slow process. Statistical analysis of genetic data and empirical-based computer simulations can be important tools to facilitate conservation planning.

Rapid evolution of a sexually selected trait following population establishment in a novel habitat.

Abstract: Colonization of novel environments creates new selection pressures. Sexually selected traits are affected by the physical and social environment and should be especially susceptible to change, but this has rarely been studied. In southern California, dark-eyed juncos, (Junco hyemalis) naturally breed in mixed-coniferous temperate forests, typically from 1500 m to 3000 m in elevation. In the early 1980s, a small population became established in a coastal habitat, the University of California, San Diego campus, which has a mild, Mediterranean climate. I show that a sexually and socially selected signaling trait-the amount of white in the tail-has declined by approximately 22% as compared to mountain juncos. I address three main factors that could explain the difference between mountain and coastal juncos: phenotypic plasticity, genetic drift, and selection. Results indicate that the first two can be ruled out as the sole cause of the plumage change, which implies that selection contributed to the genetic differentiation from the mountain population. The estimated rate of evolution is about 0.2 haldanes, comparable with rates of change in systems where individuals have been artificially introduced into new environments (e.g., guppies and Drosophila). This is the first study to demonstrate evolution of a sexually selected trait after only several generations resulting from a natural invasion into a novel environment.

The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination

Abstract: Summary The catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide substitution (G1510A; Glu487Lys) in exon 12 of the ALDH2 locus. This SNP, and four non-coding SNPs, including one in the promoter, span 40 kb of ALDH2; these and one downstream STRP have been tested in 37 worldwide populations. Only four major SNP-defined haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the functional variant and is only found in East Asians. Though the SNPs showed virtually no historic recombination, LD values are quite variable because of varying haplotype frequencies, demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome, and is not a function solely of recombination. Among populations, different sets of tagging SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus, solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs globally applicable. The Fst values of the promoter region SNP and the functional SNP were about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers. These high Fst values may indicate selection has operated at these or very tightly linked sites.

Variation of female and male lineages in Sub-Saharan populations: The importance of sociocultural factors

Abstract: In this paper, we present a study of genetic variation in sub-Saharan Africa, which is based on published and unpublished data on fast-evolving (hypervariable region 1 of mitochondrial DNA and six microsatellites of Y chromosome) and slow-evolving (haplogroup frequencies) polymorphisms of mtDNA and Y chromosome. Our study reveals a striking difference in the genetic structure of food-producer (Bantu and Sudanic speakers) and hunter-gatherer populations (Pygmies, Kung, and Hadza). In fact, the ratio of mtDNA to Y-chromosome Nupsilon is substantially higher in food producers than in hunter-gatherers as determined by fast-evolving polymorphisms (1.76 versus 0.11). This finding indicates that the two population groups differ substantially in female and male migration rate and/or effective size. The difference also persists when linguistically homogeneous populations are used and outlier populations are eliminated (1.78 vs 0.19) or when the jacknife procedure is applied to a paired population data set (1.32 to 7.84 versus 0.14 to 0.66). The higher ratio of mtDNA to Y-chromosome Nnu in food producers than in hunter-gatherers is further confirmed by the use of slow-evolving polymorphisms (1.59 to 7.91 versus 0.12 to 0.35). To explain these results, we propose a model that integrates demographic and genetic aspects and incorporates ethnographic knowledge. In such a model, the asymmetric gene flow, polyginy, and patrilocality play an important role in differentiating the genetic structure of sub-Saharan populations. The existence of an asymmetric gene flow is supported by the phylogeographic features of mtDNA and Y-chromosome haplogroups found in the two population groups. The role of polyginy and patrilocality is sustained by the evidence of a differential pressure of genetic drift and gene flow on maternal and paternal lineages of food producers and hunter-gatherers that is revealed through the analysis of mitochondrial and Y-chromosomal intrapopulational variation.

A new hypothesis to explain geographic parthenogenesis

Abstract: In many plants and animal species, asexuals are more common in marginal habitats such as high latitudes or altitudes than their closely related sexual counterparts. Here we propose a new hypothesis to explain this patterncalled "geographic parthenogenesis". In marginal habitats, populations may often exist as metapopulations with high degrees of subdivision and local extinction and recolonization, resulting in genetic bottlenecks during colonization. Our hypothesis states that such dynamics could play a key role in geographic parthenogenesis. Genetic bottlenecks and subsequent drift have stronger negative fitness consequences in sexuals than in asexuals because genetic drift leads to increased homozygosity and inbreeding depression in sexual but not in asexual populations. Migration, leading to inter-population hybridisation, may induce temporary fitness recovery in sexuals. Asexuals arising from such hybrids have an increased likelihood of invading sexual populations because they keep their high fitness, whereas the fitness of sexuals is doomed to decrease due to subsequent inbreeding and inbreeding depression. Therefore, asexuals may replace sexuals in subdivided habitats with local extinction and recolonization while they would not succeed in unstructured habitats without local turnover dynamics.

Opposing natural selection from herbivores and pathogens may maintain floral-color variation in Claytonia virginica (Portulacaceae).

Abstract: The maintenance of floral-color variation within natural populations is enigmatic because directional selection through pollinator preferences combined with random genetic drift should lead to the rapid loss of such variation. Fluctuating, balancing, and negative frequency-dependent selection mediated through pollinators have been identified as factors that may contribute to the maintenance of floral-color variation, and recently it has been suggested that indirect responses to selection on correlated characters through agents of selection other than pollinators may substantially shape the evolution of floral traits. Here, I provide empirical support for this latter view in Claytonia virginica (Portulacaceae) through a multiseason field study, a pollen supplementation study, and an artificial herbivory experiment. These studies show that most individuals fall into one of four discrete color classes, and suggest pollinator-mediated selection for increased floral redness in concurrent years. Floral color is also an indirect target of opposing directional selection via herbivores and pathogens that fluctuates through time. Taken together, these data suggest a novel mechanism by which floral-color variation may be maintained, and illustrate the importance of an inclusive, pluralistic view of selection when investigating the evolution of complex phenotypes.

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA.

Abstract: Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East–West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.

Did Natural Selection or Genetic Drift Produce the Cranial Diversification of Neotropical Monkeys

Abstract: A central controversy among biologists is the relative importance of natural selection and genetic drift as creative forces shaping biological diversification (Fisher 1930; Wright 1931). Historically, this controversy has been an effective engine powering several evolutionary research programs during the last century (Provine 1989). While all biologists agree that both processes operate in nature to produce evolutionary change, there is a diversity of opinion about which process dominates at any particular organizational level (from DNA and proteins to complex morphologies). To address this last level, we did a broadscale analysis of cranial diversification among all living New World monkeys. Quantitative genetic models yield specific predictions about the relationship between variation patterns within and between populations that may be used to test the hypothesis that genetic drift is a sufficient explanation for morphological diversification. Diversity at several levels in a hierarchy of taxo...

Gene flow in forest trees: how far do genes really travel? 1

Abstract: Gene flow is one of the most important factors shaping the genetic structure of populations. In recent decades, a number of studies have addressed issues of contemporary gene flow in forest trees, including pollen and seed dispersal, and gene immigration into natural and breeding populations (primarily seed orchards). Gene flow might be considered either beneficial or deleterious from the point of view of a conservation geneticist or a tree breeder. Extensive gene dispersal within local populations promotes panmixis and reduces family structuring in natural regeneration, thus reducing the potential for inbreeding. However, gene flow may reduce fitness of offspring if genes come from populations maladapted to the habitat of offspring establishment. Furthermore, substantial gene flow limits divergence among populations that might otherwise occur because of genetic drift and directional selection, and may enhance genetic diversity within populations. The robustness and discriminatory power of parentage analysis have been significantly improved in recent years due to advances in molecular marker technology and analytical techniques. However, knowledge of gene flow in forest trees is still unsatisfactory due to continued shortcomings of available markers, inherent limitations of statistical models, and the anecdotal nature of many gene flow studies, which are typically limited in scope. Another limitation is that pollen gene flow is usually estimated by sampling seeds from a number of mother trees. Restricting sampling to seeds seems adequate when evaluating gene flow in seed collections to be used for artificial reforestation. However, in naturally regenerating populations, the most important parameter is the proportion of immigrant alleles in established seedlings. If natural selection favours local genotypes, this should be reflected in the difference between potential gene flow measured at the seed stage and realized gene flow measured in established seedlings. Realized gene flow is a complex phenomenon that depends on a large number of deterministic and stochastic variables. Profound understanding of effective gene flow observed at the landscape level may require joint efforts in population genetics, ecology, advanced multivariate statistics, and spatial simulation modelling.

MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population.

Abstract: The relative roles of natural selection and accentuated genetic drift as explanations for the high frequency of more than 20 Ashkenazi Jewish disease alleles remain controversial. To test for the effects of a maternal bottleneck on the Ashkenazi Jewish population, we performed an extensive analysis of mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) sequence and restriction site polymorphisms in 565 Ashkenazi Jews from different parts of Europe. These patterns of variation were compared with those of five Near Eastern (n ¼ 327) and 10 host European (n ¼ 849) non-Jewish populations. Only four mtDNA haplogroups (Hgs) (defined on the basis of diagnostic coding region RFLPs and HVS-1 sequence variants) account for B70% of Ashkenazi mtDNA variation. While several Ashkenazi Jewish mtDNA Hgs appear to derive from the Near East, there is also evidence for a low level of introgression from host European non-Jewish populations. HVS-1 sequence analysis revealed increased frequencies of Ashkenazi Jewish haplotypes that are rare or absent in other populations, and a reduced number of singletons in the Ashkenazi Jewish sample. These diversity patterns provide evidence for a prolonged period of low effective size in the history of the Ashkenazi population. The data best fit a model of an early bottleneck (B100 generations ago), perhaps corresponding to initial migrations of ancestral Ashkenazim in the Near East or to Europe. A genetic bottleneck followed by the recent phenomenon of rapid population growth are likely to have produced the conditions that led to the high frequency of many genetic disease alleles in the Ashkenazi population.

Temporal changes in allele frequencies and low effective population size in greater prairie‐chickens

Abstract: The number of greater prairie-chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo-likelihood approach that accounted for migration, estimates of Ne (15-32 prairie-chickens within each management area) were 10 times lower than census numbers from booming-ground counts. These low estimates of Ne are consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reduced Ne, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie-chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.

Molecular population divergence and sexual selection on morphology in the banded demoiselle (Calopteryx splendens)

Abstract: The importance of sexual selection in population divergence is of much interest, mainly because it is thought to cause reproductive isolation and hence could lead to speciation. Sexually selected traits have been hypothesized to diverge faster between populations than other traits, presumably because of differences in the strength, mechanism or dynamics of selection. We investigated this by quantifying population divergence in eight morphological characters in 12 south Swedish populations of a sexually dimorphic damselfly, the banded demoiselle (Calopteryx splendens). The morphological characters included a secondary sexual character, the male melanized wing spot, which has an important function in both inter- and intrasexual selection. In addition, we investigated molecular population divergence, revealed by amplified fragment length polymorphism (AFLP) analysis. Molecular population divergence was highly significant among these Northern European populations (overall Fst=0.054; pairwise population Fst's ranged from ∼0 to 0.13). We found evidence for isolation-by-distance (r=0.70) for the molecular markers and a significant correlation between molecular and phenotypic population divergence (r=0.39). One interpretation is that population divergence for the AFLP loci are affected by genetic drift, but is also indirectly influenced by selection, due to linkage with loci for the phenotypic traits. Field estimates of sexual and natural selection from two of the populations revealed fairly strong sexual selection on wing spot length, indicating that this trait has the potential to rapidly diverge, provided that variation is heritable and the observed selection is chronic.

Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations

Abstract: The molecular basis of more than 25 genetic diseases has been described in Ashkenazi Jewish populations. Most of these diseases are characterized by one or two major founder mutations that are present in the Ashkenazi population at elevated frequencies. One explanation for this preponderance of recessive diseases is accentuated genetic drift resulting from a series of dispersals to and within Europe, endogamy, and/or recent rapid population growth. However, a clear picture of the manner in which neutral genetic variation has been affected by such a demographic history has not yet emerged. We have examined a set of 32 binary markers (single nucleotide polymorphisms; SNPs) and 10 microsatellites on the non-recombining portion of the Y chromosome (NRY) to investigate the ways in which patterns of variation differ between Ashkenazi Jewish and their non-Jewish host populations in Europe. This set of SNPs defines a total of 20 NRY haplogroups in these populations, at least four of which are likely to have been part of the ancestral Ashkenazi gene pool in the Near East, and at least three of which may have introgressed to some degree into Ashkenazi populations after their dispersal to Europe. It is striking that whereas Ashkenazi populations are genetically more diverse at both the SNP and STR level compared with their European non-Jewish counterparts, they have greatly reduced within-haplogroup STR variability, especially in those founder haplogroups that migrated from the Near East. This contrasting pattern of diversity in Ashkenazi populations is evidence for a reduction in male effective population size, possibly resulting from a series of founder events and high rates of endogamy within Europe. This reduced effective population size may explain the high incidence of founder disease mutations despite overall high levels of NRY diversity.

Genetic and morphological evolution following a founder event in the dark-eyed junco, Junco hyemalis thurberi.

Abstract: An isolated population of dark-eyed juncos, Junco hyemalis, became established on the campus of the University of California at San Diego (UCSD), probably in the early 1980s. It now numbers about 70 breeding pairs. Populations across the entire natural range of the subspecies J. h. thurberi are weakly differentiated from each other at five microsatellite loci ( F ST = 0.01). The UCSD population is significantly different from these populations, the closest of which is 70 km away. It has 88% of the genetic heterozygosity and 63% of the allelic richness of populations in the montane range of the subspecies, consistent with a harmonic mean effective population size of 32 (but with 95% confidence limits from four to > 70) over the eight generations since founding. Results suggest a moderate bottleneck in the early establishment phase but with more than seven effective founders. Individuals in the UCSD population have shorter wings and tails than those in the nearby mountains and a common garden experiment indicates that the morphological differences are genetically based. The moderate effective population size is not sufficient for the observed morphological differences to have evolved as a consequence of genetic drift, indicating a major role for selection subsequent to the founding of the UCSD population.

Identifying species from pieces of faeces

Abstract: This thesis investigates how changes in population size and spatial movements of individuals have shaped the distribution and abundance of neutral genetic variation in the arctic fox. This is done through mitochondrial and microsatellite DNA analyses on samples covering most of the species’ distribution, but with special emphasis on Scandinavia. On the species level, nucleotide diversity was relatively low, which indicated a historical expansion in population size in connection with the onset of the last Ice Age. It is thus possible that the glacial cycles have affected the arctic fox, and other cold-adapted species, in a way opposite to their effect on temperate species. Gene flow seemed to be high among arctic fox populations on a circumpolar scale, especially between populations where lemmings are the main food source, which could be explained by the spatial synchrony in lemming fluctuations. In Scandinavia, the arctic fox went through a severe demographic bottleneck in the beginning of the 20th century. Although some genetic variation was lost during this bottleneck, the loss was much smaller than expected, probably due to post-bottleneck gene flow from Russia. The arctic fox in Scandinavia is divided into four relatively isolated populations. Within each population, dispersal seemed to be high despite the high availability of empty territories close to natal dens, which supported the hypothesis that lemming fluctuations influence arctic fox dispersal. Genetic analyses on samples collected between 1989 and 2004 indicated an ongoing genetic drift and inbreeding within the Scandinavian populations. Furthermore, individual genetic variation was negatively associated with fitness, which could be attributed to an ongoing inbreeding depression. Analyses on faecal samples suggested that arctic foxes move higher up in the mountains and farther from the tree-line during summer compared to winter. This seasonal shift in distribution is probably caused by interspecific competition from the red fox, which is likely to be higher during summer due to red fox predation on arctic fox cubs. The results presented in this thesis have several implications for the conservation of the Scandinavian arctic fox. The finding of four isolated populations within Scandinavia and an ongoing inbreeding depression suggests that the risk of extinction is higher than previously thought. Conservation actions need to be taken in all populations to be effective, and could include genetic restoration through translocation.

Phylogeography of a parasitoid wasp (Diaeretiella rapae): no evidence of host-associated lineages.

Abstract: The exceptional diversity of insects is often attributed to the effects of specialized relationships between insects and their hosts. Parasite–host interactions are influenced by current natural selection and dispersal, in addition to historical effects that may include past selection, vicariance, and random genetic drift. Both current and historical events can lead to reduced fitness on some hosts. If trade-offs in fitness on alternate hosts are common, adaptation to one host can prevent adaptation to another, giving rise to genetic differentiation among host-associated lineages. Previous studies of Diaeretiella rapae (Hymenoptera: Aphidiidae), a parasitoid of aphids, have revealed additive genetic differences in performance between populations that parasitize different aphid host species. To determine whether D. rapae populations collected from different aphid hosts have diverged into genetically independent lineages, we constructed a haplotype network based on sequence variation in mitochondrial DNA (mtDNA). We used single strand conformation polymorphism (SSCP) analysis to examine 2041 base pairs of mtDNA and to identify nucleotide sequences of 42 unique SSCP haplotypes. We found no association between mtDNA haplotypes and host species in either the ancestral range (Europe, Mediterranean region, Middle East, Asia) or part of the introduced range (western North America). Haplotypes likely to be ancestral were geographically widespread and found on both hosts, suggesting that the ability to use both hosts evolved prior to the diversification of the mtDNA. Ongoing gene flow appears to prevent the formation of host races.

Consanguinity, inbreeding, and genetic drift in Italy

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Ecological and life history characteristics predict population genetic divergence of two salmonids in the same landscape

Abstract: Ecological and life history characteristics such as population size, dispersal pattern, and mating system mediate the influence of genetic drift and gene flow on population subdivision. Bull trout (Salvelinus confluentus) and mountain whitefish (Prosopium williamsoni) differ markedly in spawning location, population size and mating system. Based on these differences, we predicted that bull trout would have reduced genetic variation within and greater differentiation among populations compared with mountain whitefish. To test this hypothesis, we used microsatellite markers to determine patterns of genetic divergence for each species in the Clark Fork River, Montana, USA. As predicted, bull trout had a much greater proportion of genetic variation partitioned among populations than mountain whitefish. Among all sites, FST was seven times greater for bull trout (FST = 0.304 for bull trout, 0.042 for mountain whitefish. After removing genetically differentiated high mountain lake sites for each species FST, was 10 times greater for bull trout (FST = 0.176 for bull trout; FST = 0.018 for mountain whitefish). The same characteristics that affect dispersal patterns in these species also lead to predictions about the amount and scale of adaptive divergence among populations. We provide a theoretical framework that incorporates variation in ecological and life history factors, neutral divergence, and adaptive divergence to interpret how neutral and adaptive divergence might be correlates of ecological and life history factors.