Intraclonal variation in RNA viruses: generation, maintenance and consequences

This paper explores the evolutionary implications of the enormous variability that characterizes populations of RNA viruses and retroviruses. It begins by examining the magnitude of genetic variation in both natural and experimental populations. In natural populations, differences arise even within individual infected patients, with the per-site nucleotide diversity at this level ranging from < 1% to 6%. In laboratory populations, two viruses sampled from the same clone differed by ∼0.7% in their fitness. Three different mechanisms that may be important in maintaining viral genetic variability were tested: (1) Fisher's fundamental theorem, to compare the observed rate of fitness change with the extent of fitness-related variation within the same experimental populations; (2) magnitude of genomic mutation rate, to assess whether it correlated with fitness-related variation, as predicted by the mutation-selection balance hypothesis; (3) frequency-dependent selection, which affords rare genotypes an advantage. The paper concludes with a discussion of two evolutionary consequences of variability: the fixation of deleterious mutations by drift in small populations and the role of clonal interference in large ones.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 17–26.     

Transposable elements in clonal lineages: lethal hangover from sex

Long-term coevolution of transposable elements (TEs) in sexual hosts leads to evolution of extremely active and dangerous mutagens kept in tenuous check by host-derived mechanisms and via natural selection against TE-rich genomes. To the extent that sexual reproduction and recombination are important in maintaining a stable TE copy number and a tolerable mutation load, the switch to clonality from sexual reproduction can be extremely damaging and, generally, should lead to clonal lineage extinction. Surprisingly however, the loss of powerful selective mechanisms constraining TEs can be beneficial in the short-term by immediately eliminating selective load and possibly promoting the early success of clonal lineages. The clonal lineages that do survive in the long-term must find a way to eliminate or domesticate TEs. Indeed bdelloid rotifers, which are ancient asexuals, do appear to have lost most of the otherwise wide-spread TEs and might have domesticated others. The path to this TE-free haven is anything but clear at the moment. We have considered a novel scenario of instantaneous inactivation of TEs by starting off with a genome carrying repressive host alleles for all TEs in the genome. We show that such a scenario appears plausible and provide some limited empirical evidence in its support.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 33–41.     

Genetic diversity and population structure of Pichia guilliermondii over 400 generations of experimental microevolution

An in vitro evolution model was used to study changes in the genetic diversity of 24 strains of Pichia guilliermondii isolated from the midgut of bark beetles of the genus Dendroctonus . The genetic diversity of P. guilliermondii strains over 400 generations was analysed using multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) markers. Resemblance relationships among strains were observed by cluster analysis. From the MLEE and RAPD markers, it was shown that the effective number of alleles, polymorphism and expected heterozygosity varied over the generations. The average heterozygosity among generations was statistically significant. Both the genetic diversity and the average heterozygosity were statistically significant among generations. The reduction in the population size from 10⁹ to 10⁵ yeast mL⁻¹ associated with each transfer in P. guilliermondii strains and the clonal population structure observed along 400 generations suggest that genetic diversity changes and the observed replacement of genotypes are a consequence of a genetic drift process and not of the reproductive mode.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 475–486.     

Arbuscular mycorrhizal fungi: genetics of multigenomic, clonal networks and its ecological consequences

Arbuscular mycorrhizal fungi are thought to have remained asexual for 400 million years, although recent studies have suggested that considerable genetic and phenotypic variation could potentially exist in populations. A brief discussion of these multigenomic organisms is presented.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 59–60.     

Phylogeography of five Polytrichum species within Europe

Using allozymes and microsatellites we have analysed the genetic structure among European populations for several Polytrichum species to infer relevant factors, such as historical events or gene flow, that have shaped their genetic structure. As we observed low levels of genetic differentiation among populations, and no decreasing levels of genetic variation with increasing latitude within most of the examined species, no genetic evidence was obtained for a step-wise recolonization of Europe from southern refugia after the latest glacial period for P. commune , P. uliginosum , P. formosum and P. piliferum . The near absence of population substructuring within these species does indicate that extensive spore dispersal is the most important factor determining the genetic structure among European Polytrichum populations. Gene flow levels have apparently been sufficient to prevent genetic differentiation among populations caused by genetic drift, and to wipe out any genetic structure caused by the postglacial recolonization process. On the other hand, increased genetic differentiation of alpine P. formosum populations suggests that mountain ranges might restrict gene flow significantly among Polytrichum populations. In contrast to most examined Polytrichum species, P. juniperinum showed high levels of genetic differentiation and a profound genetic structure. Assuming that gene flow is not more restricted in P. juniperinum , these findings suggest that this species has recolonized Europe after the latest glacial period from two different refugia, one possibly being the British Isles.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 203–213.     

Disjunctions in relict alpine plants: phylogeography of Androsace brevis and A. wulfeniana (Primulaceae)

Amplified Fragment Length Polymorphism (AFLP) was used to clarify the glacial history of the rare, disjunctly distributed, alpine cushion plant Androsace wulfeniana , which is endemic to the Eastern Alps (Austria and Italy). Disjunct populations in the Dolomites are genetically very distinct from those in the main distributional area. It is hypothesized that they are descendants of long-term isolated glacial survivors and are not a result of recent long-­distance dispersal. Within the main distributional area of the species in the central Eastern Alps, two groups of ­populations can be distinguished, which are congruent with hotspots of rare relictual vascular plant taxa. In the ­taxonomically closely related A. brevis growing in the Southern Alps (Italy, Switzerland), no genetic-geographical structure was found. Genetic variation is extremely low in disjunct populations of A. wulfeniana in the Dolomites and in A. brevis . In contrast, in the main distributional area of A. wulfeniana , genetic variation is similar to that of the colonizing widespread congener A. alpina .  © 2003 The Linnean Society of London, Botanical Journal of the ­Linnean Society , 2003, 141 , 437–446.     

High levels of genetic diversity in populations of Iris aphylla L. (Iridaceae), an endangered species in Poland

We used RAPDs (Random Amplified Polymorphic DNAs) to investigate genetic diversity and its partition within and between three populations of Iris aphylla in Poland. Analysis of Molecular Variance (AMOVA) of 84 distinct RAPD multiband genotypes revealed higher variation within populations (77.2%) than genetic differentiation between them (22.8%, P  < 0.002). Values of genetic diversity indices ( H ) were similar in all three sites (0.21–0.24). The differentiation of the populations corresponded to low average gene flow ( Nm  = 0.81). Our results indicated that genetic diversity was independent of population size. We concluded that although sexual reproduction and gene flow between populations of I. aphylla were very limited, they preserved high levels of genetic diversity. Relatively large number of seeds, which migrated in the past to populations, as well as patterns of reproduction and life history of I. aphylla may explain this situation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 65–72.     

Non-metric morphological divergence in the western house mouse, Mus musculus domesticus, from the Barcelona chromosomal hybrid zone

The effect of hybridization on morphological variation was investigated in 120 western house mice, Mus musculus domesticus , from the hybrid zone between the Barcelona and standard chromosomal races. The incidence of 37 non-metric cranial traits was calculated for standard mice (2 n  = 40) and Barcelona-standard hybrids (2 n  = 27–39). Subsequent analyses were conducted on several karyological subgroups, established by grouping the animals according to either their diploid number or their degree of chromosomal heterozygosity. Results revealed no significant difference by sex, asymmetry, or geographical distance. Significant phenetic divergences were found between the karyotypes studied in relation to several variants. Differences were especially substantial between the standard race and hybrid mice, even with respect to those hybrids with karyotypes close to that of the standard race. Within the hybrids, the maximum divergence corresponded to the 28-chromosome homozygotes, chromosomally close to the Barcelona race, and to the heterozygotes with more than two fusions. Since differences in non-metric trait frequencies are generally considered a measure of genetic divergence, the results suggest the occurrence of a barrier to gene flow in the Barcelona hybrid zone. The decrease of genetic exchange between the chromosomally differentiated mice might be due to reduced fertility in hybrids, associated with chromosomal heterozygosity.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 313–322.     

Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea)

Margaritifera margaritifera and M. auricularia are among the most endangered freshwater mussels in the world, and the only species of the genus found in Europe. Our genetic study explores allozymic variability (27 loci) and differentiation at the mitochondrial sequence level (partial COI and 16S rRNA gene sequences). The Spanish M. auricularia population showed genetic parameters of variation that were of the same order as those of other freshwater molluscs (though at the lower end of the range), probably permitting its potential recovery. The difference between this species and M. margaritifera was clearly established (ten diagnostic allozymic loci, Nei = 0.462, and mean nucleotide divergence around 9.4%). The M. margaritifera populations analysed showed a certain degree of population genetic structure (according to allozyme data) that was not, however, related to a geographical cline. Nevertheless, two mitochondrial lineages (albeit very closely related) were identified: a northern lineage extending from Ireland to the Kola Peninsula including the western Atlantic coast, and a second cluster distributed from Ireland to the Iberian Peninsula. The phylogenetic relationships between these two species and other related taxa were established. The putative M. m. durrovensis could be considered an 'ecophenotype'. Palaeobiogeographical scenarios are presented and indicate unexpected 'recent' gene flow between M. margaritifera populations that were theoretically isolated in the early Tertiary.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 235–252.     

Genetic structure of the critically endangered endemic Cochlearia polonica (Brassicaceae): efficiency of the last-chance transplantation

Cochlearia polonica , a narrow endemic of southern Poland, is one of the rarest and most endangered species of the European flora. All natural populations are extinct and the species has survived in only one transplanted population derived from 14 original individuals. Using AFLPs, the genetic variation and spatial structure of this population were analysed approximately 30 years after transplantation. The incidence of polymorphic AFLP bands (30.46%) is low compared with data from a natural population of another Cochlearia species, C. tatrae . Principal co-ordinates and spatial autocorrelation analyses demonstrated the presence of significant genetic structure. It is recommended that conservation efforts on C. polonica should preserve the complete population area, because local extinctions may lead to a loss of genetic information. The presence of genetic structure should also be taken into account during the sampling of material (plants or seeds) for ex situ conservation measures.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 527–532.     

The effect of ploidy level on fitness in parthenogenetic flatworms

Although polyploidy plays an important role in speciation, its impact on fitness is still debated. One problem is that its adaptive significance can only be inferred by comparing forms with different ploidy that are identical in all other traits. This situation is uncommon, presumably because ploidy types often differ in reproduction mode, genetic background or habitat. Here we compare fitness in a system of triploid and tetraploid karyotypes of the planarian flatworm Schmidtea polychroa . Both types have the same type of sperm-dependent parthenogenesis and share the same genetic background and habitat. Hence, fitness differences, if any, can be attributed to different ploidy levels only. Contrary to the general assumption of a positive correlation between fitness and ploidy level, we showed that triploids produced 58% more offspring than tetraploids. Within each ploidy type, we identified groups of highly related clones using microsatellites. Significant variation among clonal groups in body size, offspring and cocoon number and hatching time indicated a genetic basis for variance in these traits. A small model shows that despite low fitness of tetraploids, stable coexistence of triploids and tetraploids can be explained by the recurrent origin of triploids from tetraploids and vice versa.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 191–198.     

A new species of Valantia (Rubiaceae) from Spain

A new species of Valantia , V. lainzii Devesa & Ortega-Olivencia, endemic to the coastal zone of Granada (southern Spain) is described. The species recalls V. muralis L. in its general aspect, and V. deltoidea Brullo in the type of fructiferous body.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 331–335.     

Rapid changes in clonal lines: the death of a 'sacred cow'

It is well established that asexually reproducing viruses and prokaryotes mutate rapidly. In contrast, the eukaryotic clone is often still treated as if it is genetically homogeneous within and between populations, i.e. that it is assumed to show genetic fidelity. However, such fidelity has rarely been tested empirically using the range of high-resolution molecular markers now available, culminating with direct sequencing of the DNA. If such a biological entity as a 'clone' really did exist, it would be a fantastic entity, differing from everything else known in biology, i.e. it would possess a population mean but no variance for any particular trait. It would not be amenable to selection and adaptive variation and would thus be unchanging in time and space. In this paper, we argue that the general acceptance of clonal fidelity is a scientific convenience, since the rate of asexual reproduction of eukaryotes is not as fast as that of bacteria and hence it is easier to accept fidelity as a 'fact' rather than test for it. We propose that part of the acceptance of fidelity may have a cultural basis and thereby is a kind of 'pre-Darwinian relic'. Instead, a clonal genotype is perhaps largely a function of marker resolution, i.e. dependent on the number and type of markers employed. If this is so and were enough of the genome explored, perhaps each individual within a clone would be found to differ genetically at particular regions of the chromosomes. The question of what constitutes a clone is not just a semantic one and impacts directly on recent attempts to understand and produce 'artificial' clones, especially of mammals. New research is already confirming that mutations and epigenetic influences play a crucial role in the success of cloning attempts.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79 , 3–16.     

Patterns of genetic diversity in related taxa of Antirrhinum L. assessed using allozymes

Allozyme diversity was studied within and among populations of five related taxa of Antirrhinum L. endemic to the Iberian Peninsula ( A. graniticum Rothm. ssp. graniticum , ssp. brachycalyx Sutton and ssp. ambiguum (Lange) Mateu & Segarra, A. boissieri Rothm. and A. onubensis (Fdez. Casas) Fdez. Casas). All of the studied taxa are obligate outcrossing endemic perennial herbs which form isolated populations. However, the taxa vary in range and population sizes, and are found on different soil types. The level and distribution of allozyme diversity differed widely between taxa: A. graniticum ssp. brachycalyx had the lowest level of allozyme diversity (H_T = 0.09), whilst the highest level was detected in A. boissieri (H_T = 0.25). Total variation was partitioned into within- and among-population variation. The proportion attributable to variation within populations varied from about 67% up to 84.3% and 89.5% in A. graniticum ssp. brachycalyx and A. graniticum ssp. ambiguum , respectively. Both these subspecies also showed little population divergence (G_ST = 0.10 and 0.09, respectively) and had high levels of estimated gene flow (Nm = 2.18 and 2.62, respectively). These results are discussed in relation to geographical proximity of populations and habitat continuity. Isolation by distance was not detected in any of the studied taxa. This result suggests that divergence among populations is due to random genetic drift.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 79 , 299–307.     

Contrasting levels of genetic diversity between the common, self-compatible Liparis kumokiri and rare, self-incompatible Liparis makinoana (Orchidaceae) in South Korea

Levels of allozyme variation and intrapopulation spatial genetic structure of the two terrestrial clonal orchids Liparis kumokiri , a self-compatible relatively common species, and L. makinoana , a self-incompatible rare species, were examined for 17 ( N  = 1875) and four ( N  = 425) populations, respectively, in South Korea. Populations of L. makinoana harboured high levels of genetic variation ( H _e = 0.319) across 15 loci. In contrast, L. kumokiri exhibited a complete lack of allozyme variation ( H _e = 0.000). Considering the lack of genetic variability, it is suggested that current populations of L. kumokiri in South Korea originated from a genetically depauperate ancestral population. For L. makinoana , a significant deficit of heterozygosity (mean F _IS = 0.198) was found in population samples excluding clonal ramets, suggesting that pollen dispersal is localized, generating biparental inbreeding. The significant fine-scale genetic structuring (≤ 2 m) found in a previous study, in addition to the moderate levels of population differentiation ( F _ST = 0.107) and the significant relationship between genetic and geographical distances ( r  = 0.680) found here, suggests a leptokurtic distribution of seed dispersal for L. makinoana . Although populations of L. makinoana harbour high levels of genetic variation, they are affected by a recent genetic bottleneck. This information suggests that genetic drift and limited gene flow could be the main evolutionary forces for speciation of a species-rich genus such as Liparis .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 41–48.     

High variability of genetic pattern in giant clam (Tridacna maxima) populations within French Polynesia

Nine populations of giant clams, Tridacna maxima, from six islands of French Polynesia were screened for allozyme variation at ten polymorphic loci. The genetic structure of populations of T. maxima were studied at different spatial scales: within an island, between islands of the same archipelago and between archipelagos. Significant genetic differences were observed only between populations from different archipelagos, and genetic differentiation was correlated with geographical separation. However, these results were only supported by a single locus, PEP * and all other loci were homogeneous between studied populations. According to Lewontin & Krakauer's model, the genetic structure can be explained by selection. The selective factors most likely depend on the respective habitat of each archipelago. We also studied genotype–phenotype correlation using the colour of the clam mantle, and did not find any relationship between the mantle colour and the genetic structure of the individuals.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 221–231.     

Astragalus neo-assadianus (Fabaceae), a new species in sect. Alopecuroidei from Iran

Astragalus neo-assadianus (Fabaceae), a new species endemic to Iran, is described and illustrated. This species belongs to A. sect . Alopecuroidei and is distinct and interesting among the Iranian species. It is confined to the north-eastern part of Iran (Khorasan Province) and only known from a single collection close to the Turkmenistan frontier.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 197–200.