The dynamic clonal genome and its adaptive potential

Populations of clonal organisms are often represented as being evolutionary inert with persistent genetic fidelity. The advent of molecular methods and the corresponding increased genetic resolution of clonal populations forces a reconsideration of this viewpoint. We review molecular data from viruses, prokaryotes and eukaryotes to support the argument that clones possess a highly dynamic and adaptive genome.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 193–208.     

Genetic changes within an aphid clone: homogenization of rDNA intergenic spacers after insecticide selection

A single asexual maternal lineage (i.e. clone) of the greenbug aphid, Schizaphis graminum (Rondani) was repeatedly selected with the insecticide disulfoton ( O , O -diethyl S- [2-(ethylthio)ethyl] phosphorodioate). A parallel colony of the non-selected clone was also maintained. After approximately 200 generations (4 years) of continuous selection, both the selected and non-selected clones were assayed for changes in intergenic spacer (IGS) length variants of the rRNA cistron. No changes in sets of IGS variants were detected in the non-selected clone. However, the selected clone was found to have lost three variants present in the non-selected clone. This probably occurred by unequal cross-over between sister chromatids, whereby the cistron became homogenized by an increase of frequency of two smaller variants. This documents a large-scale genetic change occurring within the rRNA cistron in a parthenogenetically reproducing aphid.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 101–105.     

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.     

Female-biased natal and breeding dispersal in an alpine lizard, Niveoscincus microlepidotus

We measured two aspects of dispersal in the alpine Australian scincid lizard, Niveoscincus micolepidotus : (1) natal dispersal, i.e. shift in home range over the lizard's first year of life, and (2) breeding dispersal, i.e. shifts of home ranges between breeding attempts as adults. On average, displacements were surprisingly small. Female neonates dispersed about twice as far as did males in the same cohort (means of 12 m vs. 6 m). A female's natal dispersal distance was not correlated with her body size or our estimate of physiological performance (sprint speed). However, larger, faster-running male neonates dispersed further than did smaller, slower males. As was the case for neonates, adult females moved significantly further between breeding seasons than did adult males (14.2 m vs. 9.6 m). Because of a female's long gestation period (more than 1 year), two groups of females occur simultaneously in the population, non-ovulated (i.e. with yolking folicles) and pregnant females (i.e. approaching parturition). Females that were not yet ovulated showed a markedly stronger dispersal in response to high reproductive effort (i.e. clutch size in relation to body condition) than did pregnant females. In adult males, body size was negatively correlated with dispersal distance, suggesting that although males have overlapping territories, they exhibit an increasing level of site tenacity with age and/or size. Thus, selection for the relatively more pronounced site tenacity in adult males may have resulted in the more marked philopatric behaviour compared to females also as neonates.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 277–283.     

Chimerism following fusion in a clonal ascidian (Urochordata)

Many marine invertebrates bud vegetatively to produce a modular colony of individuals derived from a single zygote. Fusion of different colonies to produce a genetically composite entity (a chimera) is known from experiments on sponges, hydroids, corals, bryozoans and ascidians – groups which together dominate sessile faunas on marine hard substrates. Random amplified polymorphic DNA–polymerase chain reaction (RAPD–PCR) analysis was applied to individual modules (zooids) dissected from colonies of a colonial ascidian, Diplosoma listerianum (Milne Edwards), to investigate the presence and extent of chimerism. The technique revealed chimerism in wild material. In total, 288 colonies from eight different natural populations were analysed. Chimeric colonies were present in all populations, at frequencies of up to 61%, with up to six different genotypes present in some colonies. Zooids of different genetic origin often intermingled within a chimeric colony to produce a zooidal mosaic. Although fusion of colonies has been observed directly in the laboratory, an unknown proportion of the chimerism detected in wild populations might have arisen through somatic mutation. To assess this possibility, tissue of 12 clones in culture was sampled repeatedly over a period of 3 years and subjected to RAPD–PCR analysis. RAPD banding patterns were generally very stable; the changes noted mostly involved minor bands that would not, on their own, have been taken as evidence for chimerism under the conservative criteria adopted for the study of wild populations. It was concluded that a large proportion of natural chimerism is attributable to colony fusion.  © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 183–192.     

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.     

Can a sponge feeder be a herbivore? Tylodina perversa (Gastropoda) feeding on Aplysina aerophoba (Demospongiae)

Feeding biology in mollusks has important biological, ecological and evolutionary implications because many of the characteristics we observe in mollusks arise from their co-evolution with diet organisms. We investigated the relationship between the opisthobranch Tylodina perversa and the sponges Aplysina aerophoba and Aplysina cavernicola in order to ascertain the trophic interactions between them. The opisthobranch preferred specimens of Aplysina aerophoba inhabiting shallow overdeep waters, ectosome of Aplysina aerophoba over choanosome, and showed no preference for Aplysina cavernicola . The sponge Aplysina cavernicola lacks the cyanobacteria abundant in the ectosome of Aplysina aerophoba . Our study shows that the opisthobranch Tylodina perversa actively selects for sponges or sponge zones with high concentration of cyanobacteria, i.e. only a fraction of the ingested material is of animal origin. Addition of cyanobacteria to symbiont-free sponge material induced a shift in mollusk preference. Our results cast doubt over the widely recognized qualification of Tylodina perversa as a carnivorous sponge feeder and show evidence that cyanobacteria determine the opisthobranch food selection. Whether this is an isolated example of how symbionts may determine trophic interactions between hosts and predators or it is widespread in benthic organisms remains an open question that requires further investigation.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 429–438.     

The Deschampsia cespitosa complex (Poaceae: Aveneae) with special reference to Russia

The Deschampsia cespitosa complex in Russia is revised. Related taxa common to Russia and adjacent regions (i.e. northern Europe, Arctic America and Japan) are also considered. Deschampsia cespitosa s.l. is characterized by open to less commonly rather contracted panicles, spikelets (1) 2 (3)-flowered, 4-toothed lemmas with the lateral teeth larger, and awns straight or bent, inserted from the base to the top of the lemmas. Due to extensive overlapping in diagnostic characters, it is not possible to accept the specific status for D. borealis (Traut.) Roshev., D. brevifolia R.Br., D. macrothyrsa Tatew. et Ohwi and D. obensis Roshev; instead, they are treated as subspecies of D. cespitosa (L.) Beauv. Morphological differences are insufficient for a clear differentiation among subspecies, and geographical distributions also need to be considered. A total of 14 subspecies is accepted. Observations on ecology, problems of specific and subspecific delimitation, a distribution map, and considerations of evolution of the complex are provided. One new combination is made, Deschampsia cespitosa ssp. sukatschewii (Popl.) Chiapella & Prob.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 142 , 213–228.     

The brine shrimp's tale: a topsy turvy evolutionary fable

It has been suggested that: (1) the brine shrimp, Artemia (Branchiopoda: Anostraca), which habitually swims inverted, has 'only recently turned over'; (2) if this habit were to persist for tens of millions of years, original dorsal–ventral homologies would become obliterated; (3) it would become necessary to re-define the concept of dorsal and ventral because so many details would have changed over evolutionary time; and (4) if modern brine shrimps were to maintain the habit of swimming upside down for 100 Myr into the future, they might give rise to a whole new subkingdom whose descendants would be defined as having a dorsal nerve cord. However, brine shrimps and their allies have not recently turned over. All the nearly 300 extant anostracans swim inverted, and members of the order have clearly done so for more than 400 Myr, yet their anatomical arrangements are the same as in crustaceans that live dorsal side up. Nor do crustaceans that swim inverted and even hang from the surface film depart from the standard arrangement. The claim that inverted swimming became a genetically determined attribute of brine shrimps via the operation of the so-called Baldwin effect is rejected, as is the concept itself.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 377–382.     

The marginal band, a new structural component of the developing angiosperm leaf

The marginal band, a newly described structure of the dicot leaf, plays an essential role in the formation of this organ. It arises along the two edges of a leaf as several files of adaxial epidermal cells during the peg stage of ontogeny. Functionally, it appears to serve as the prepattern for a number of secondary features including (i) the marginal growth meristem present in all leaves as seen in mountain laurel, (ii) rows of lobes and spines as in Salvia and Ilex , (iii) pigmentation as in some cultivars of Hydrangea , (iv) propagation as in the plantlets of Kalanchoe pinnata , (v) marginal ridges for support in a few varieties of Viburnum and Ilex , and (vi) marginal necrosis as in Strelitzia for blade partitioning.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 21–28.     

Some remarks on the genus Astragalus sect. Incani in Iran

New findings are given for the Astragalus sect. Incani , which occurs within the area covered by the Flora of Iran. Astragalus wojciechowskianus Ranjbar is described as a new species. A. procerus Boiss. & Hausskn . , A. cottonianus Aitch. & Baker, A. achundovii Grossh., A. orduabadensis Grossh. and A. glaucophyllus Bunge are reported as new records for the flora of Iran .   © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 443–447.     

A new species of Silene (Caryophyllaceae) from South Anatolia, Turkey

Silene doganii A.Duran & Y.Menemen sp. nov. from the Amanos Mountains (C6: Osmaniye-Turkey) is described and illustrated. It is closely related to S. caramanica Boiss. & Heldr., from which it differs mainly in its habit, hairiness, leaf and floral features.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 109−113.     

A new diploid Hieracium (Asteraceae: Lactuceae) from Bulgaria

Hieracium kittanae Vladimirov, a new diploid (2 n  = 18) species restricted to a few gorges in the Central Rhodope Mountains, south Bulgaria, is described and illustrated. It occurs in crevices of limestone rock in shady to sunny places with high atmospheric humidity. Morphologically, it to some extent resembles taxa from the H. glaucinum and H. schmidtii groups, but is otherwise very distinct, without close relatives in the Rhodope and neighbouring mountains.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003 , 143 , 213−218.     

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.     

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.     

The adaptive significance of coloration in lagomorphs

Lagomorph pelage coloration was matched to habitat type, geographical region, altitude and behaviour to explore the adaptive significance of coloration patterns in this little-studied order of mammals. Analyses were conducted with and without taking phylogeny into account. The former analyses were based on a weighted, phylogenetic supertree for all extant species of lagomorphs that we constructed using morphological and molecular data from 146 papers in the literature. Although our analyses represent an initial, somewhat crude investigation, several clear trends are evident. First, overall body coloration across lagomorphs tends to match the background as shown for pale and red coloration and perhaps seasonal pelage change. The case for countershading being a method of concealment is far less strong. Second, ear tips appear to have a communicative role since they are conspicuous in many different habitats. Third, hypotheses for tail tips having a communicative role, for extremities being dark for physiological reasons, and for Gloger's rule received only partial support.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 309–328.     

The effectiveness of some mechanisms of reproductive isolation in Arum maculatum and A. italicum (Araceae)

Mechanisms of reproductive isolation were studied in two species of Arum , A. italicum and A. maculatum , growing in England and the south of France. The study focused on three potential mechanisms for reproductive isolation: the effectiveness of dichogamy as a barrier to autogamy; the ability of self and outcrossed pollen to germinate on stigmas at different stages of anthesis and to effect pollination; and postzygotic barriers to selfing. Dichogamy was found to provide a very effective barrier to within-inflorescence selfing in these species, as no seeds were produced by spontaneous self-pollination (i.e. autogamy) in any population of either species. However, the study found that geitonogamy (cross-pollination between inflorescences of a same individual or clone) was possible, as genotypes frequently produced several inflorescences and stigmas were found to be receptive to pollen from before anthesis until their contraction at the end of the female phase of flowering. Hand pollination with self pollen from clone inflorescences produced as numerous and heavy seeds as outcross pollination. In addition, the germination and growth of geitonogamously produced seed was similar to that of outcrossed seed, suggesting that this potential postzygotic barrier is absent or weak. These findings suggest that geitonogamous seed production may be unrestricted by significant pre- or postzygotic barriers. The possible advantages of geitonogamy in Arum are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 323–328.