Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus

Genetic bottlenecks may occur in virus populations when only a few individuals are transferred horizontally from one host to another, or when a viral population moves systemically from the infection site. Genetic bottlenecks during the systemic movement of an RNA plant virus population were reported previously (H. Li and M. J. Roossinck, J. Virol. 78:10582-10587, 2004). In this study we mechanically inoculated an artificial population consisting of 12 restriction enzyme marker mutants of Cucumber mosaic virus (CMV) onto young leaves of squash plants and used two aphid species, Aphis gossypii and Myzus persicae, to transmit the virus populations from infected source plants to healthy squash plants. Horizontal transmission by aphids constituted a significant bottleneck, as the population in the aphid-inoculated plants contained far fewer mutants than the original inoculum source. Additional experiments demonstrated that genetic variation in the artificial population of CMV is not reduced during the acquisition of the virus but is significantly reduced during the inoculation period.     

Conservation genetics of population bottlenecks: the role of chance,selection, and history

Conservation genetics studies of populations bottlenecks are commonly framed under the detrimental paradigm of inbreeding depression. This conceptual paradigm presupposes a direct and unambiguous relationship between population size, genetic diversity, fitness, and extinction. Here, I review a series of studies that emphasize the role of chance, selection, and history in determining the genetic consequences of population bottlenecks. The variable responses of bottlenecks to fitness, phenotypic variation, and heritable variation emphasize the necessity to explore the relationship between molecular genetic diversity, fitness, adaptive genetic diversity, and extinction beyond the detrimental paradigm of inbreeding depression. Implications for conservation and management are presented as guidelines and testable predictions regarding the potential effects of bottlenecks on population viability and extinction.     

Host population bottlenecks drive parasite extinction during antagonistic coevolution

Host–parasite interactions are often characterized by large fluctuations in host population size, and we investigated how such host bottlenecks affected coevolution between a bacterium and a virus. Previous theory suggests that host bottlenecks should provide parasites with an evolutionary advantage, but instead we found that phages were rapidly driven to extinction when coevolving with hosts exposed to large genetic bottlenecks. This was caused by the stochastic loss of sensitive bacteria, which are required for phage persistence and infectivity evolution. Our findings emphasize the importance of feedbacks between ecological and coevolutionary dynamics, and how this feedback can qualitatively alter coevolutionary dynamics.     

Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers.

Population bottlenecks are often invoked to explain low levels of genetic variation in natural populations, yet few studies have documented the direct genetic consequences of known bottlenecks in the wild. Empirical studies of natural population bottlenecks are therefore needed, because key assumptions of theoretical and laboratory studies of bottlenecks may not hold in the wild. Here we present microsatellite data from a severe bottleneck (95% mortality) in an insular population of song sparrows (Melospiza melodia). The major findings of our study are as follows: (i) The bottleneck reduced heterozygosity and allelic diversity nearly to neutral expectations, despite non-random survival of birds with respect to inbreeding and wing length. (ii) All measures of genetic diversity regained pre-bottleneck levels within two to three years of the crash. This rapid recovery was due to low levels of immigration. (iii) The rapid recovery occurred despite a coincident, strong increase in average inbreeding. These results show that immigration at levels that are hard to measure in most field studies can lead to qualitatively very different genetic outcomes from those expected from mutations only. We suggest that future theoretical and empirical work on bottlenecks and metapopulations should address the impact of immigration.     

Bottlenecks and rescue effects in a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis)

Mammal species characterized by highly fluctuating populations often maintain genetic diversity in response to frequent demographic bottlenecks, suggesting the ameliorating influence of life history and behavioral factors. Immigration in particular is expected to promote genetic recovery and is hypothesized to be the most likely process maintaining genetic diversity in fluctuating mammal populations. Most demographic bottlenecks have been inferred retrospectively, and direct analysis of a natural population before, during, and after a bottleneck is rare. Using a continuous 10-year dataset detailing the complete demographic and genetic history of a fluctuating population of golden-mantled ground squirrels (Spermophilus lateralis), we analyzed the genetic consequences of a 4-year demographic bottleneck that reduced the population to seven adult squirrels, and we evaluated the potential “rescue effect” of immigration. Analysis of six microsatellite loci revealed that, while a decline in allelic richness was observed during the bottleneck, there was no observed excess of heterozygosity, a characteristic bottleneck signature, and no evidence for heterozygote deficiency during the recovery phase. In addition, we found no evidence for inbreeding depression during or after the bottleneck. By identifying immigrants and analyzing their demographic and genetic contributions, we found that immigration promoted demographic recovery and countered the genetic effects of the bottleneck, especially the loss of allelic richness. Within 3 years both population size and genetic variation had recovered to pre-bottleneck levels, supporting the role of immigration in maintaining genetic variation during bottleneck events in fluctuating populations. Our analyses revealed considerable variation among analytical techniques in their ability to detect genetic bottlenecks, suggesting that caution is warranted when evaluating bottleneck events based on one technique.     

Estimation of population bottlenecks during systemic movement of tobacco mosaic virus in tobacco plants

More often than not, analyses of virus evolution have considered that virus populations are so large that evolution can be explained by purely deterministic models. However, virus populations could have much smaller effective numbers than the huge reported census numbers, and random genetic drift could be important in virus evolution. A reason for this would be population bottlenecks during the virus life cycle. Here we report a quantitative estimate of population bottlenecks during the systemic colonization of tobacco leaves by Tobacco mosaic virus (TMV). Our analysis is based on the experimental estimation of the frequency of different genotypes of TMV in the inoculated leaf, and in systemically infected leaves, of tobacco plants coinoculated with two TMV genotypes. A simple model, based on the probability that a leaf in coinoculated plants is infected by just one genotype and on the frequency of each genotype in the source, was used to estimate the effective number of founders for the populations in each leaf. Results from the analysis of three leaves per plant in plants inoculated with different combinations of three TMV genotypes yielded highly consistent estimates. Founder numbers for each leaf were small, in the order of units. This would result in effective population numbers much smaller than the census numbers and indicates that random effects due to genetic drift should be considered for understanding virus evolution within an infected plant.     

Serial population bottlenecks and genetic variation: Translocated populations of the New Zealand Saddleback (<Emphasis Type="Italic">Philesturnus carunculatus rufusater</Emphasis>)

The genetic effects of population bottlenecks have been well studied theoretically, in laboratory studies, and to some extent, in natural situations. The effects of serial population bottlenecks (SPBs), however, are less well understood. This is significant because recurrent population bottlenecks are likely to be a common feature of the life history of many species. The lack of understanding of SPBs in natural populations has certainly been hampered by a lack of good examples where it can be studied. We report the results of a study into island populations of North Island Saddleback (Philesturnus carunculatus rufusater) that have undergone 13 translocations since 1964, all but one of these has been deliberate and for which detailed records are available. We have examined nine island populations of this passerine bird, from the source population, three first-order bottlenecked and five second-order bottlenecked populations. We examine variation in these nine populations using multilocus minisatellite DNA markers, together with Mendelian loci comprising six microsatellite DNA loci and a variable isozyme locus. Despite the generally low level of genetic variation in the Saddleback source population, we were able to detect a pattern of significant changes in both the mean number of minisatellite DNA bands per individual and the frequency of alleles at the Mendelian loci, with increasing population bottlenecks. This study generally shows that in a natural population, SPBs result in more pronounced genetic changes than do single population bottlenecks by themselves, thereby highlighting their importance for the conservation of rare and endangered species.     

Evidence for recent population bottlenecks in northern spotted owls (<Emphasis Type="Italic">Strix occidentalis caurina</Emphasis>)

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the US Endangered Species Act. Despite protection of its remaining forest habitat, recent field studies show continued declines of northern spotted owls. One potential threat to northern spotted owls which has not yet been shown is loss of genetic variation from population bottlenecks. Bottlenecks can increase the probability of mating among related individuals, potentially causing inbreeding depression, and can decrease adaptive potential. Here we report evidence for recent bottlenecks in northern spotted owls using a large genetic dataset (352 individuals and 10 microsatellite loci). The signature of bottlenecks was strongest in the Washington Cascade Mountains, in agreement with field data. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies’ persistence. Reduced effective population size (N _e) shown here in addition to field evidence for demographic decline highlights the increasing vulnerability of this bird to extinction.     

No evidence for loss of genetic variation following sequential translocations in extant populations of a genetically depauperate species

Repeated population bottlenecks can lead to loss of genetic variation and normally should be avoided in threatened species to preserve evolutionary potential. We examined the effect of repeated bottlenecks, in the form of sequential translocations, on loss of genetic variation in a threatened passerine, the saddleback (Philesturnus carunculatus carunculatus), a species that has recovered from a remnant population with historically low levels of genetic variation. Although a slight but nonsignificant loss of alleles may have occurred between the first-order translocation and the extirpated source population, first-, second-, and third-order translocated populations had very similar levels of genetic variation to each other. The most obvious difference among the seven island populations appeared to lie in allele frequencies with little or no loss of alleles among extant populations. Although sequential translocations are known to cause loss of variation in genetically diverse species, our study indicates that genetically depauperate species may be less sensitive to loss of genetic variation through founder events presumably because the few remaining alleles are well represented in founding individuals. These results show that ancient bottlenecks may have a long-term effect on genetic variation, to the extent that contemporary population bottlenecks may leave no appreciable genetic signature. Our results suggest that subjecting genetically depauperate endangered species to sequential translocations could be used to rapidly establish new populations without further eroding genetic variation.     

Genetic structure in an expanding cervid population after population reduction

The Norwegian red deer population (Cervus elaphus) was from the mid eighteenth to the early twentieth century drastically reduced in size and distribution but has the last century expanded both demographically and spatially. We have investigated genetic variation, differentiation and admixture in this spatially expanding ungulate population, using 14 microsatellites. The present genetic structure is moderate to strong with an average F _ST = 0.08. Low M-ratios indicate loss of genetic variation in all localities and signals of a recent bottleneck was identified in 14 of 15 localities. Genetic distances between the localities indicate two main routes of dispersal during expansion, from the north–west and south–west, respectively. Bayesian assignment tests verify a break of the dataset in two, and demonstrate 99.9% probability for the existence of five sub-populations, which coincide well with five relict populations described by historic records. Computer simulations suggest that the observed genetic differentiation is recent rather than ancient, and that it may be explained by models of fragmentation or of founder events and subsequent merging rather than by models of recent bottlenecks in some particular demes within an ancient genetic structure.     

Estimation of the effective number of founders that initiate an infection after aphid transmission of a multipartite plant virus

The fecundity of RNA viruses can be very high. Thus, it is often assumed that viruses have large populations, and RNA virus evolution has been mostly explained using purely deterministic models. However, population bottlenecks during the virus life cycle could result in effective population numbers being much smaller than reported censuses, and random genetic drift could be important in virus evolution. A step at which population bottlenecks may be severe is host-to-host transmission. We report here an estimate of the size of the population that starts a new infection when Cucumber mosaic virus (CMV) is transmitted by the aphid Aphis gossypii, based on the segregation of two CMV genotypes in plants infected by aphids that acquired the virus from plants infected by both genotypes. Results show very small effective numbers of founders, between one and two, both in experiments in which the three-partite genome of CMV was aphid transmitted and in experiments in which a fourth RNA, CMV satellite RNA, was also transmitted. These numbers are very similar to those published for Potato virus Y, which has a monopartite genome and is transmitted by aphids according to a different mechanism than CMV. Thus, the number of genomic segments seems not to be a major determinant of the effective number of founders. Also, our results suggest that the occurrence of severe bottlenecks during horizontal transmission is general for viruses nonpersistently transmitted by aphids, indicating that random genetic drift should be considered when modeling virus evolution.     

Reliability of genetic bottleneck tests for detecting recent population declines

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.     

Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence

Increasing habitat fragmentation poses an immediate threat to population viability, as gene flow patterns are changed in these altered landscapes. Patterns of genetic divergence can potentially reveal the impact of these shifts in landscape connectivity. However, divergence patterns not only carry the signature of altered contemporary landscapes, but also historical ones. When considered separately, both recent and historical landscape structure appear to significantly affect connectivity among 51 wood frog ( Rana sylvatica ) populations. However, by controlling for correlations among landscape structure from multiple time periods, we show that patterns of genetic divergence reflect recent landscape structure as opposed to landscape structure prior to European settlement of the region (before 1850s). At the same time, within-population genetic diversities remain high and a genetic signature of population bottlenecks is lacking. Together, these results suggest that metapopulation processes – not drift-induced divergence associated with strong demographic bottlenecks following habitat loss – underlie the strikingly rapid consequences of temporally shifting landscape structure on these amphibians. We discuss the implications of these results in the context of understanding the role of population demography in the adaptive variation observed in wood frog populations.     

Trait variation in yeast is defined by population history

A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific genetic variants. Key to such an understanding is the detailed mapping of the natural genomic and phenomic space and a bridging of the gap that separates these worlds. Here we chart a high-resolution map of natural trait variation in one of the most important genetic model organisms, the budding yeast Saccharomyces cerevisiae, and its closest wild relatives and trace the genetic basis and timing of major phenotype changing events in its recent history. We show that natural trait variation in S. cerevisiae exceeds that of its relatives, despite limited genetic variation, and follows the population history rather than the source environment. In particular, the West African population is phenotypically unique, with an extreme abundance of low-performance alleles, notably a premature translational termination signal in GAL3 that cause inability to utilize galactose. Our observations suggest that many S. cerevisiae traits may be the consequence of genetic drift rather than selection, in line with the assumption that natural yeast lineages are remnants of recent population bottlenecks. Disconcertingly, the universal type strain S288C was found to be highly atypical, highlighting the danger of extrapolating gene-trait connections obtained in mosaic, lab-domesticated lineages to the species as a whole. Overall, this study represents a step towards an in-depth understanding of the causal relationship between co-variation in ecology, selection pressure, natural traits, molecular mechanism, and alleles in a key model organism.     

Genetic diversity and conservation in a small endangered horse population

The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy–Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population.     

Selection maintains MHC diversity through a natural population bottleneck

A perceived consequence of a population bottleneck is the erosion of genetic diversity and concomitant reduction in individual fitness and evolutionary potential. Although reduced genetic variation associated with demographic perturbation has been amply demonstrated for neutral molecular markers, the effective management of genetic resources in natural populations is hindered by a lack of understanding of how adaptive genetic variation will respond to population fluctuations, given these are affected by selection as well as drift. Here, we demonstrate that selection counters drift to maintain polymorphism at a major histocompatibility complex (MHC) locus through a population bottleneck in an inbred island population of water voles. Before and after the bottleneck, MHC allele frequencies were close to balancing selection equilibrium but became skewed by drift when the population size was critically low. MHC heterozygosity generally conformed to Hardy-Weinberg expectations except in one generation during the population recovery where there was a significant excess of heterozygous genotypes, which simulations ascribed to strong differential MHC-dependent survival. Low allelic diversity and highly skewed frequency distributions at microsatellite loci indicated potent genetic drift due to a strong founder affect and/or previous population bottlenecks. This study is a real-time examination of the predictions of fundamental evolutionary theory in low genetic diversity situations. The findings highlight that conservation efforts to maintain the genetic health and evolutionary potential of natural populations should consider the genetic basis for fitness-related traits, and how such adaptive genetic diversity will vary in response to both the demographic fluctuations and the effects of selection.     

Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of the northern elephant seal

This paper reviews some of the important factors related to the impact of population bottlenecks, using the northern elephant seal (Mirounga angustirostrus) as a case study for illustration. The northern elephant seal was hunted extensively in the 19th century and forced through a bottleneck of approximately 10–20 seals. All measures of molecular genetic variation show current levels for the northern elephant seal to be low. Levels of genetic variation were compared with expectations based on a simulation model that recapitulates demographic growth, based on age-specific data on reproduction and mortality. Predictions from the simulation model are then presented to illustrate the importance of differences in life-history strategy and skewed reproductive success. Either high reproductive skew (e.g. polygyny) or a low growth rate in a population can increase the impact of a bottleneck on molecular variation. Severe population bottlenecks can also disrupt aspects of developmental stability and thereby increase the fluctuating asymmetry and variability of quantitative traits. A comparison of skulls collected before and after the bottleneck showed this to have occurred for some elephant seal quantitative characters.     

West Nile virus genetic diversity is maintained during transmission by Culex pipiens quinquefasciatus mosquitoes

Due to error-prone replication, RNA viruses exist within hosts as a heterogeneous population of non-identical, but related viral variants. These populations may undergo bottlenecks during transmission that stochastically reduce variability leading to fitness declines. Such bottlenecks have been documented for several single-host RNA viruses, but their role in the population biology of obligate two-host viruses such as arthropod-borne viruses (arboviruses) in vivo is unclear, but of central importance in understanding arbovirus persistence and emergence. Therefore, we tracked the composition of West Nile virus (WNV; Flaviviridae, Flavivirus) populations during infection of the vector mosquito, Culex pipiens quinquefasciatus to determine whether WNV populations undergo bottlenecks during transmission by this host. Quantitative, qualitative and phylogenetic analyses of WNV sequences in mosquito midguts, hemolymph and saliva failed to document reductions in genetic diversity during mosquito infection. Further, migration analysis of individual viral variants revealed that while there was some evidence of compartmentalization, anatomical barriers do not impose genetic bottlenecks on WNV populations. Together, these data suggest that the complexity of WNV populations are not significantly diminished during the extrinsic incubation period of mosquitoes.     

Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness.

Genetic bottlenecks are important events in the genetic diversification of organisms and colonization of new ecological niches. Repeated bottlenecking of RNA viruses often leads to fitness losses due to the operation of Muller's ratchet. Herein we use vesicular stomatitis virus to determine the transmission population size which leads to fitness decreases of virus populations. Remarkably, the effective size of a genetic bottleneck associated with fitness loss is greater when the fitness of the parental population increases. For example, for starting virus populations with low fitness, population transfers of five-clone-to-five-clone passages resulted in a fitness increase. However, when a parental population with high fitness was transferred, 30-clone-to-30-clone passages were required simply to maintain fitness values.     

Fine-scale genetic structure in Ethiopian wolves imposed by sociality,migration, and population bottlenecks

We used demographic, spatial, and microsatellite data to assess fine-scale genetic structure in Ethiopian wolves found in the Bale Mountains and evaluated the impact of historical versus recent demographic processes on genetic variation. We applied several analytical methods, assuming equilibrium and nonequilibrium conditions, to assess demography and genetic structure. Genetic variation (H _E = 0.584–0.607, allelic richness = 4.2–4.3) was higher than previously reported for this species and genetic structure was influenced by geography and social structure. Statistically significant F _ST values (0.06–0.08) implied differentiation among subpopulations. STRUCTURE analyses showed that neighbouring packs often have shared co-ancestry and spatial autocorrelation showed higher genetic similarity between individuals within packs and between individuals in neighbouring packs compared to random pairs of individuals. Recent effective population sizes were lower than 2n (where n is the number of packs) and lower than the number of breeding individuals with N _e /N ratios near 0.20. All subpopulations have experienced bottlenecks, one occurring due to a rabies outbreak in 2003. Nevertheless, differentiation among these subpopulations is consistent with long-term migration rates and fragmentation at the end of the Pleistocene. Enhanced drift due to population bottlenecks may be countered by higher migration into disease-affected subpopulations. Contemporary factors such as social structure and population bottlenecks are clearly influencing the level and distribution of genetic variation in this population, which has implications for its conservation.