Severe Bottleneck Research Articles

An experimentally induced host shift in a seed beetle

AbstractMany insects use a fairly well‐defined set of host plants, but are occasionally observed on an atypical host. The seed beetle Callosobruchus maculatus (F.) (Coleoptera: Chrysomelidae: Bruchinae) has rarely been reported to attack lentil, which is distantly related to its usual legume hosts. An initial assay of an Asian beetle population revealed that none of the 100 larvae entering lentil seeds survived to adult emergence. Nevertheless, three attempts at mass selection, in which more than 2 000 adults were added to lentil seeds, eventually yielded self‐sustaining populations. In each case, a severe bottleneck was followed by a rapid increase in survival, which exceeded 65% after only five generations and surpassed 85% in <20 generations. Subsequent large‐scale experiments indicated that survival in lentil is initially <2% and that most larvae die before they have completely entered a seed. The only potential trade‐off associated with rapid adaptation to lentil was a modest increase in the time required to develop in the ancestral host, mung bean. Reciprocal crosses between a lentil‐adapted line (F10) and a mung‐bean line produced offspring with intermediate survival, very long development times, and small size. Although the Asian population has been kept under uniform laboratory conditions for more than 200 generations, it appears to maintain rare alleles that permit the colonization of an extremely poor host. Such standing genetic variation can account for the sporadic appearance of unusual ‘biotypes’ among herbivorous insects.

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

The brown bear has proved a useful model for studying Late Quaternary mammalian phylogeography. However, information is lacking from northern continental Eurasia, which constitutes a large part of the species' current distribution. We analysed mitochondrial DNA sequences (totalling 1943 bp) from 205 bears from northeast Europe and Russia in order to characterize the maternal phylogeography of bears in this region. We also estimated the formation times of the sampled brown bear lineages and those of its extinct relative, the cave bear. Four closely related haplogroups belonging to a single mitochondrial subclade were identified in northern continental Eurasia. Several haplotypes were found throughout the whole study area, while one haplogroup was restricted to Kamchatka. The haplotype network, estimated divergence times and various statistical tests indicated that bears in northern continental Eurasia recently underwent a sudden expansion, preceded by a severe bottleneck. This brown bear population was therefore most likely founded by a small number of bears that were restricted to a single refuge area during the last glacial maximum. This pattern has been described previously for other mammal species and as such may represent one general model for the phylogeography of Eurasian mammals. Bayesian divergence time estimates are presented for different brown and cave bear clades. Moreover, our results demonstrate the extent of substitution rate variation occurring throughout the phylogenetic tree, highlighting the need for appropriate calibration when estimating divergence times.

Comparative genetic analyses of historical and contemporary collections highlight contrasting demographic histories for the bumble beesBombus pensylvanicusandB.impatiensin Illinois

Direct comparison of genetic patterns between museum specimens and contemporary collections can be a powerful approach for detecting recent demographic changes. Using microsatellite markers, we examined historical and contemporary genetic variation from an apparently declining bumble bee species, Bombus pensylvanicus, and from a stable species, Bombus impatiens, in central Illinois. For each species, we genotyped specimens from the Illinois Natural History Survey collected from three populations between 1969-1972 and from a resurvey of the same areas conducted in 2008. Population structure in B. pensylvanicus increased markedly over the last four decades (from theta(ST) = 0.001 to 0.027) while no structure was detected in B. impatiens for either time period (theta(ST) = -0.006 to -0.003). Changes in genetic diversity were not significant for either species, although small reductions were observed for B. pensylvanicus in all three populations. Coalescent simulations incorporating both contemporary and historical samples suggest that this small change is not surprising for recent population declines, as large reductions in genetic diversity were only apparent under the most severe bottleneck scenarios. These results demonstrate how comparisons of genetic patterns between temporal periods and species can help elucidate potential threats to population health and suggest several strategies that might be useful in the conservation of B. pensylvanicus in the Midwestern USA.

Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity

Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.

High microsatellite genetic variability of the stone loach, Barbatula barbatula, in anthropogenically disturbed watercourses

Abstract Genetic variation within and among stone loach, Barbatula barbatula L., populations inhabiting anthropogenically degraded watercourses in Flanders (northern part of Belgium) was assessed using five microsatellite markers. High levels of genetic diversity were observed at all sampling sites, (MNA: 6.2–11.2; HO: 0.64–0.75; HE: 0.67–0.85). Estimates of the effective population size varied between 1535 and 3021 individuals and there were no indications of recent severe bottlenecks. Significant genetic differentiation was observed among sites belonging to different river systems and drainage basins. These results suggest human activities, such as pollution and river engineering, have not impacted significantly on genetic variability in the stone loach populations investigated. It is possible that this lack of genetic erosion may be attributed to species‐specific characteristics such as pollution tolerance and ecological flexibility.

Experimental evidence for density‐dependent reproduction in a cooperatively breeding passerine

Temporal variation in survival, fecundity, and dispersal rates is associated with density-dependent and density-independent processes. Stable natural populations are expected to be regulated by density-dependent factors. However, detecting this by investigating natural variation in density is difficult because density-dependent and independent factors affecting population dynamics may covary. Therefore, experiments are needed to assess the density dependence of demographic rates. In this study, we investigate the effect of density on demographic rates of the Seychelles Warbler (Acrocephalus sechellensis). This species, endemic to a few islands in the Indian Ocean, went through a severe population bottleneck in the middle of the last century, with only approximately 30 individuals left on one small island, but has since recovered. Our monitoring shows that since reaching the island's carrying capacity, population density has remained stable. However, we detected neither density-dependent reproduction nor survival on the basis of natural density variation during this stable period. For conservation reasons, new populations have been established by transferring birds to nearby suitable islands. Using the change of numbers during the process of saturation as a natural experiment, we investigated whether we can detect regulation of numbers via density-dependent survival and reproduction within these new populations. We found that populations were mainly regulated by density-dependent reproduction, and not survival. Variation in density between islands can be explained by food abundance, measured as insect density. Islands with the highest insect densities also had the highest bird densities and the largest breeding groups. Consequently, we suggest that the density-dependent effect on reproduction is caused by competition for food.

The phylogeographical history of the Iberian steppe plant Ferula loscosii (Apiaceae): a test of the abundant‐centre hypothesis

The geology and climate of the western Mediterranean area were strongly modified during the Late Tertiary and the Quaternary. These geological and climatic events are thought to have induced changes in the population histories of plants in the Iberian Peninsula. However, fine-scale genetic spatial architecture across western Mediterranean steppe plant refugia has rarely been investigated. A population genetic analysis of amplified fragment length polymorphism variation was conducted on present-day, relict populations of Ferula loscosii (Apiaceae). This species exhibits high individual/population numbers in the middle Ebro river valley and, according to the hypothesis of an abundant-centre distribution, these northern populations might represent a long-standing/ancestral distribution centre. However, our results suggest that the decimated southern and central Iberian populations are more variable and structured than the northeastern ones, representing the likely vestiges of an ancestral distribution centre of the species. Phylogeographical analysis suggests that F. loscosii likely originated in southern Spain and then migrated towards the central and northeastern ranges, further supporting a Late Miocene southern-bound Mediterranean migratory way for its oriental steppe ancestors. In addition, different glacial-induced conditions affected the southern and northern steppe Iberian refugia during the Quaternary. The contrasting genetic homogeneity of the Ebro valley range populations compared to the southern Iberian ones possibly reflects more severe bottlenecks and subsequent genetic drift experienced by populations of the northern Iberia refugium during the Pleistocene, followed by successful postglacial expansion from only a few founder plants.

Is the winter period a severe bottleneck of anadromous riverine Arctic charr parr?

Abstract – Winter growth and survival of wild individually tagged juvenile Arctic charr (1+ age) from a riverine anadromous stock, were studied in a small ice‐covered (∼6 months) ground water brook (temperature ∼1 °C) connected to Skibotnelva in subarctic northern Norway. The overall winter survival was estimated to be 68% from late October 2005 to early May 2006. The recaptured charr were not significantly different in initial length or weight compared with the nonrecaptured fish suggesting low size‐dependent mortality. The majority (98%) of the recaptured charr showed significant increase in size, with a mean increment of 62% from their initial bodyweight and 12% of the charr parr had more than doubled their weight. The mean specific growth rate was calculated to be slightly lower (0.27) than estimated values from a growth model (∼0.35). In addition, the condition factor increased significantly during the field experiment. These results are the first individual growth data on riverine anadromous Arctic charr parr under natural winter conditions, and indicate that charr can grow relatively fast during periods with low temperature and also that ground water brooks can be good over‐wintering habitat for juvenile Arctic charr. These results suggest that the winter period is perhaps a less severe bottleneck than previously recognised for the cold‐adapted Arctic charr.

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

The HIV-1 epidemic in sub-Saharan Africa is driven largely by heterosexual transmission of non-subtype B viruses, of which subtypes C and A are predominant. Previous studies of subtype B and subtype C transmission pairs have suggested that a single variant from the chronically infected partner can establish infection in their newly infected partner. However, in subtype A infected individuals from a sex worker cohort and subtype B individuals from STD clinics, infection was frequently established by multiple variants. This study examined over 1750 single-genome amplified viral sequences derived from epidemiologically linked subtype C and subtype A transmission pairs very early after infection. In 90% (18/20) of the pairs, HIV-1 infection is initiated by a single viral variant that is derived from the quasispecies of the transmitting partner. In addition, the virus initiating infection in individuals who were infected by someone other than their spouse was characterized to determine if genital infections mitigated the severe genetic bottleneck observed in a majority of epidemiologically linked heterosexual HIV-1 transmission events. In nearly 50% (3/7) of individuals infected by someone other than their spouse, multiple genetic variants from a single individual established infection. A statistically significant association was observed between infection by multiple genetic variants and an inflammatory genital infection in the newly infected individual. Thus, in the vast majority of HIV-1 transmission events in cohabiting heterosexual couples, a single genetic variant establishes infection. Nevertheless, this severe genetic bottleneck can be mitigated by the presence of inflammatory genital infections in the at risk partner, suggesting that this restriction on genetic diversity is imposed in large part by the mucosal barrier.

Molecular species identification of historical whale remains from South Georgia

The island of South Georgia is located at the southern extreme of the South Atlantic Ocean, on the edge of the Southern Ocean that surrounds Antarctica. Intensive commercial whaling at South Georgia began in 1904, when the first land-based whaling station was built in Grytviken (54°17′S, 36°30′W). Five other shore stations were eventually built: Ocean Harbour (54°20′S, 36°16′W), Leith Harbour (54°08′S, 36°41′W), Husvik Harbour (54°18′S, 36°71′W), Stromness Harbour (54°90′S, 36°41′W), and Prince Olav Harbour (54°40′S, 36°90′W). Another site, Godthul (54°17′S, 36°17′W), was used as a protected anchorage for floating factories. By 1965, when shore-based whaling activity ceased, over 175,000 whales had been processed on the island (Moore et al. 1999). The once abundant stocks of baleen whales in the Antarctic had at that time been reduced to about a third of their former sizes (Laws 1977). When considering blue (Balaenoptera musculus), fin (B. physalus), sei (B. borealis), and humpback (Megaptera novaeangliae) whales together, the average population size was reduced to ca. 18% (Laws 1977). Humpback and blue whales experienced the most severe bottlenecks, having been reduced to about 3% and 5% of the estimated initial populations, respectively. According to more recent estimates, even 80%–95% of the pristine populations of humpback, blue, and fin whales have been killed (Baker and Clapham 2002). For the blue whales depletion to even less than 1% of the pre-exploitation population size has been reported (Branch et al. 2004, 2007). Currently, knowledge about the recovery from the bottlenecks and current population sizes, structures, and migration patterns are important issues in the conservation of Southern Hemisphere baleen whales. In this context, insight into historical population structures would be of great value.

Peripatric differentiation among adjacent marine lake and lagoon populations of a coastal fish, Sphaeramia orbicularis (Apogonidae, Perciformes, Teleostei)

The effect of geographical isolation on speciation, particularly within short geographical ranges, is poorly understood among marine organisms. Focusing on marine lakes of the Palau Islands, we investigated the effect of geographical isolation on Sphaeramia orbicularis, a coastal fish inhabiting marine lakes and lagoons. We collected a total of 157 individuals from three meromictic marine lakes and three lagoon sites, and analyzed the genetic diversity and differentiation of the populations based on complete sequences of the mitochondrial control region (824 bp). The analyses show that the genetic diversity of marine lake populations is much lower than that of lagoon populations. Moreover, a mismatch distribution analysis suggests that marine lake populations have experienced a decrease followed by a rapid expansion of their population size. These results reveal that marine lake populations have experienced severe founder and/or bottleneck events during the last thousand to tens of thousand years. Pairwise Phi(ST )values ranged from 0.531 to 0.848 between marine lake and lagoon populations and from 0.429 to 0.870 among marine lake populations, indicating a high degree of genetic differentiation. We speculate that such peripatric differentiation between marine lake and lagoon populations was caused by a small number of individuals colonizing the lakes from the lagoon (founder event) followed by repetitive bottleneck events, such as those generated by the El Niño-Southern Oscillation (ENSO). So far, such high genetic divergences in extremely short geographical ranges (approximately 150-250 m) have scarcely been reported for marine organisms. We suggest that the marine lake is one of the good model of geographical isolation in marine organisms and each marine lake population is in the early stages of speciation.

Post‐bottleneck mtDNA diversity in a free‐living population of European bison: implications for conservation

AbstractA free‐living population of European bison Bison bonasus in the Białowieża Primeval Forest originated from only seven founder animals after a severe bottleneck that occurred at the beginning of the 20th century. Consequently, the contemporary population of the species is characterized by low genetic diversity. We studied a total of 195 individuals (127 males and 68 females). A 1429 bp fragment of mitochondrial DNA (mtDNA) including the D‐loop region was analyzed in 87 individuals and revealed only three distinct haplotypes. Nucleotide (π) and haplotype (Hd) diversity values were estimated for the European bison and were compared with π and Hd estimated from three individuals of American bison Bison bison. Very low diversity values were found in the European bison in comparison with the diversity values found in the American bison. The low mtDNA variability in the European bison is in concordance with theoretical expectations for a species that has undergone a severe and recent bottleneck. A management strategy for the preservation of the rare and very rare haplotypes present in the Białowieża population of the European bison is discussed. Furthermore, all 195 individuals were investigated for heteroplasmy involving these three haplotypes, in order to detect a possible association between heteroplasmy and the incidence of males affected by posthitis, a disease that affects the male reproductive organs, leading to necrotic lesions. Heteroplasmy was found in 15 females, in 17 males affected by posthitis and in 11 non‐affected males, and no significant association was found.

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata).

BackgroundAquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great importance for aquaculture.ResultsA public data base was constructed, consisting of 19,734 unique clusters (3,563 contigs and 16,171 singletons). Functional annotation was obtained for 8,021 clusters. Over 4,000 sequences were also associated with a GO entry. Two 60mer probes were designed for each gene and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Platform reproducibility and accuracy were assessed on two early stages of sea bream development (one-day and four days old larvae). Correlation between technical replicates was always > 0.99, with strong positive correlation between paired probes. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. Functional analysis suggested that down-regulated transcripts (407) in older larvae are mostly essential/housekeeping genes, whereas tissue-specific genes are up-regulated in parallel with the formation of key organs (eye, digestive system). Cross-validation of microarray data was carried out using quantitative qRT-PCR on 11 target genes, selected to reflect the whole range of fold-change and both up-regulated and down-regulated genes. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates. Good concordance between qRT-PCR and microarray data was observed between 2- and 7-fold change, while fold-change compression in the microarray was present for differences greater than 10-fold in the qRT-PCR.ConclusionA highly reliable oligo-microarray platform was developed and validated for the gilthead sea bream despite the presently limited knowledge of the species transcriptome. Because of the flexible design this array will be able to accommodate additional probes as soon as novel unique transcripts are available.

Past demography in forest trees: what can we learn from nuclear DNA sequences that we do not already know?

Acquiring nuclear DNA sequences in forest tree species is becoming easier as molecular tools are developing rapidly and we now have at our disposal an array of theoretical methods to carry out statistical inferences from multilocus sequence variation. In the present article we use results from two recent studies of nuclear DNA sequence polymorphism in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) to illustrate what additional insights to each species' history can be gained compared with classical phylogeographic studies based on chloroplast or mitochondrial DNA. The sampling schemes and statistical analyses used in these two studies were similar facilitating a comparison between them. In both cases we inferred the presence of a rather severe bottleneck predating the Last Glacial Maximum (∼18,000 years ago). This result is discussed in relation to recent reassessments of the fossil pollen record and to its implication for our understanding of adaptation. Finally we briefly outline some suggestions for future research.

Patterns of genetic variation in US federal bison herds

Like many wide-ranging mammals, American bison (Bison bison) have experienced significant range contraction over the past two centuries and are maintained in artificially isolated populations. A basic understanding of the distribution of genetic variation among populations is necessary to facilitate long-term germplasm preservation and species conservation. The 11 herds maintained within the US federal system are a critically important source of germplasm for bison conservation, as they include many of the oldest herds in the USA and have served as a primary resource for the establishment of private and public herds worldwide. In this study, we used a panel of 51 nuclear markers to investigate patterns of neutral genetic variation among these herds. Most of these herds have maintained remarkably high levels of variation despite the severe bottleneck suffered in the late 1800s. However, differences were noted in the patterns of variation and levels of differentiation among herds, which were compared with historical records of establishment, supplementation, herd size, and culling practices. Although some lineages have been replicated across multiple herds within the US federal system, other lineages with high levels of genetic variation exist in isolated herds and should be considered targets for the establishment of satellite herds. From this and other studies, it is clear that the genetic variation represented in the US federal system is unevenly distributed among National Park Service and Fish and Wildlife Service herds, and that these resources must be carefully managed to ensure long-term species conservation.

Population fragmentation leads to isolation by distance but not genetic impoverishment in the philopatric Lesser Kestrel: a comparison with the widespread and sympatric Eurasian Kestrel

Population fragmentation is a widespread phenomenon usually associated with human activity. As a result of habitat transformation, the philopatric and steppe-specialist Lesser Kestrel Falco naumanni underwent a severe population decline during the last century that increased population fragmentation throughout its breeding range. In contrast, the ubiquitous Eurasian Kestrel Falco tinnunculus did not suffer such adverse effects, its breeding range still remaining rather continuous. Using microsatellites, we tested the effects of population fragmentation on large-scale spatial patterns of genetic differentiation and diversity by comparing these two sympatric and phylogenetically related species. Our results suggest that habitat fragmentation has increased genetic differentiation between Lesser Kestrel populations, following an isolation-by-distance pattern, while the population of Eurasian Kestrels is panmictic. Contrary to expectations, we did not detect significant evidence of reduced genetic variation or increased inbreeding in Lesser Kestrels. Although this study reports genetic differentiation in a species that has potential for long-distance dispersal but philopatry-limited gene flow, large enough effective population sizes and migration may have been sufficient to mitigate genetic depauperation. A serious reduction of genetic diversity in Lesser Kestrels would, therefore, only be expected after severe population bottlenecks following extreme geographic isolation.

Genetic diversity and structure of the invasive tree Miconia calvescens in Pacific islands

ABSTRACTAim This study investigates the amount and distribution of genetic variation within and among populations of the highly invasive tree, Miconia calvescens (Melastomataceae; hereafter miconia), in tropical island habitats that are differently impacted (distribution and spread) by this weed.Location Invasive populations were included from northern and southern Pacific islands including the Hawaiian Islands (Hawaii, Kauai and Maui), Marquesas Islands (Nuku Hiva), Society Islands (Tahiti, Tahaa, Moorea, Raiatea) and New Caledonia.Methods We used 9 codominant microsatellite and 77 highly variable dominant intersimple sequence repeat markers (ISSRs) to characterize and compare genetic diversity among and within invasive miconia populations. For the codominant microsatellite data we calculated standard population genetic estimates (heterozygosity, number of alleles, inbreeding coefficients, etc.) and described population genetic structure using AMOVA, Mantel tests (to test for isolation by distance), unweighted pair‐group method with arithmetic averages (UPGMA) cluster analysis and principal components analysis (PCA). We also tested for the presence of a population bottleneck and used a Bayesian analysis of population structure in combination with individual assignment tests. For the dominant ISSR data we used AMOVA, PCA, upgma and a Bayesian approach to investigate population genetic structure.Results Both markers types showed little to no genetic differentiation among miconia populations from northern and southern Pacific hemispheres (AMOVA: microsatellite, 3%; ISSR, 0%). Bayesian and frequency‐based analysis also failed to support geographical genetic structure, confirming considerable low genetic differentiation throughout the Pacific. Molecular data furthermore showed that highly successful miconia populations throughout the Pacific are currently undergoing severe bottlenecks and high levels of inbreeding (f = 0.91, ISSR; FIS = 0.27, microsatellite).Main conclusions The lack of population genetic structure is indicative of similar geographical sources for both hemispheres and small founding populations. Differences in invasive spread and distribution among Pacific islands are most likely the result of differences in introduction dates to different islands and their accompanying lag phases. Miconia has been introduced to relatively few tropical islands in the Pacific, and the accidental introduction of a few or even a single seed into favourable habitats could lead to high invasive success.

Strong genetic impoverishment from the centre of distribution in southern Europe to peripheral Baltic and isolated Scandinavian populations of the pearly heath butterfly

AbstractAim Climatic changes and fluctuations in the past have strongly influenced the distribution of animal and plant species. Such fluctuations are also reflected in the patterns of genetic diversity on both local and global scales. The genetic pattern of the pearly heath butterfly,Coenonympha arcania, was used to evaluate the genetic differentiation of isolated (in north‐western Europe), peripheral (in north‐eastern Europe) and central (in southern Europe) populations in the context of post‐glacial distributional changes of the species.Location Europe (Sweden, Germany, the Baltic states, Italy, Slovenia, Hungary, Romania, Bulgaria). Thus, samples were collected from large parts of the species’ distribution representing the three categories mentioned above.Methods We analysed 18 loci of 569 individuals from 28 populations by allozyme electrophoresis. We used both individual‐based and population‐based analyses, includingF‐statistics, various clustering methods and Markov chain Monte Carlo simulations.Results All loci, exceptFum, were polymorphic. The meanFSTfor all samples was 0.18. The mean genetic distance among populations was 0.046. Two major genetic lineages were distinguished. Populations from the centre of the distributional range in southern Europe and the northern periphery of the distributional range differed significantly in their level of genetic variability. The central populations of south‐eastern Europe showed high levels of genetic diversity and no differentiation among populations.Main conclusions Most probably the two major genetic lineages evolved during glacial isolation in two disjunct Mediterranean refugia. The lack of genetic differentiation across south‐eastern Europe implies a continuous Würm ice age distribution in this area, thus supporting the functional existence of steppe forests throughout this region. The peripheral‐isolated populations in Sweden seem to have suffered from one or more severe bottlenecks, resulting in substantial genetic impoverishment. The peripheral‐connected eastern Baltic populations, on the other hand, are affected by post‐glacial and possibly recurrent gene flow from more central parts of the distribution.

Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization.

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Despite their high mutation rate and rapid evolution, this parameter is poorly documented experimentally in viruses, particularly plant viruses. All available studies, however, have demonstrated the existence of huge within-host demographic fluctuations, drastically reducing Ne upon systemic invasion of different organs and tissues. Notably, extreme bottlenecks have been detected at the stage of systemic leaf colonization in all plant viral species investigated so far, sustaining the general idea that some unknown obstacle(s) imposes a barrier on the development of all plant viruses. This idea has important implications, as it appoints genetic drift as a constant major force in plant virus evolution. By co-inoculating several genetic variants of Cauliflower mosaic virus into a large number of replicate host plants, and by monitoring their relative frequency within the viral population over the course of the host systemic infection, only minute stochastic variations were detected. This allowed the estimation of the CaMV Ne during colonization of successive leaves at several hundreds of viral genomes, a value about 100-fold higher than that reported for any other plant virus investigated so far, and indicated the very limited role played by genetic drift during plant systemic infection by this virus. These results suggest that the barriers that generate bottlenecks in some plant virus species might well not exist, or can be surmounted by other viruses, implying that severe bottlenecks during host colonization do not necessarily apply to all plant-infecting viruses.

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.