Although clonal species are dominant in many habitats, from unicellular organisms to plants and animals, ecological and particularly evolutionary studies on clonal species have been strongly limited by the difficulty in assessing the number, size and longevity of genetic individuals within a population. The development of molecular markers has allowed progress in this area, and although allozymes remain of limited use due to their typically low level of polymorphism, more polymorphic markers have been discovered during the last decades, supplying powerful tools to overcome the problem of clonality assessment. However, population genetics studies on clonal organisms lack a standardized framework to assess clonality, and to adapt conventional data analyses to account for the potential bias due to the possible replication of the same individuals in the sampling. Moreover, existing studies used a variety of indices to describe clonal diversity and structure such that comparison among studies is difficult at best. We emphasize the need for standardizing studies on clonal organisms, and particularly on clonal plants, in order to clarify the way clonality is taken into account in sampling designs and data analysis, and to allow further comparison of results reported in distinct studies. In order to provide a first step towards a standardized framework to address clonality in population studies, we review, on the basis of a thorough revision of the literature on population structure of clonal plants and of a complementary revision on other clonal organisms, the indices and statistics used so far to estimate genotypic or clonal diversity and to describe clonal structure in plants. We examine their advantages and weaknesses as well as various conceptual issues associated with statistical analyses of population genetics data on clonal organisms. We do so by testing them on results from simulations, as well as on two empirical data sets of microsatellites of the seagrasses Posidonia oceanica and Cymodocea nodosa. Finally, we also propose a selection of new indices and methods to estimate clonal diversity and describe clonal structure in a way that should facilitate comparison between future studies on clonal plants, most of which may be of interest for clonal organisms in general.

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system by using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and from the usual underlying hypotheses required for the interpretation of classical analyses, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial.conservation biology ͉ gene flow ͉ networks ͉ population genetics U nderstanding the connectivity between components of a metapopulation system and their role as weak or strong links remains a major challenge of population ecology (1-3). Advances in molecular biology fostered the use of indirect approaches to understand metapopulation structure, based on describing the distribution of gene variants (alleles) in space within the theoretical framework of population genetics (4-7). Yet, the premises of the classical Wright-Fisher model (4, 6), such as ''migration-drift'' and ''mutation-drift'' equilibrium (8), ''equal population sizes'' or symmetrical rate migration among populations, are often violated in real metapopulation systems. Threatened or pathogen species, for example, are precisely studied for their state of demographic disequilibrium due to decline and local extinctions in the first case, or to their complex dynamics of local decline and sudden pandemic burst in the second. Furthermore, the underlying hypotheses of equal population size and symmetrical migration rates hamper the identification of putative population ''hubs'' centralizing migration pathways or acting as sources in a metapopulation system, which is a central issue in ecology in general, and in conservation biology or epidemiology in particular. Finally, complementary methods of genetic structure analyses, such as hierarchical AMOVA and coalescent methods rely on a priori information (or priors) as to the clustering or demographic state of populations, requiring either subjective assumptions or the availability of reliable demographic, historical or ecological information that are seldom available.Network theory is emerging as a powerful tool to un...

Sequences of the internal transcribed spacer region (ITS-1, 5.8S, and ITS-2) of nuclear ribosomal DNA were obtained from 16 species representing all six genera of Fucaceae (Ascophyllum, Fucus, Hesperophycus, Pelvetia, Pelvetiopsis, and Xiphophora) plus one outgroup (Hormosira). Parsimony analysis indicated that the family Fucaceae is monophyletic and that the northern hemisphere taxa are highly divergent from the only southern hemisphere genus, Xiphophora. The genus Pelvetia is not monophyletic because the European P. canaliculata is more closely related to Fucus, Hesperophycus, and Pelvetiopsis than to other Pelvetia species. We establish Silvetia, gen. nov. and transfer the 3 Pacific species of Pelvetia to the new genus. Fucus is monophyletic and not ancestral in the Fucaceae. The ITS sequences identified two strongly supported lineages within Fucus, one with F. serratus sister to the clade containing F. gardneri, F. distichus, and F. evanescens and a second including F. vesiculosus, F. spiralis, F. ceranoides, and F. virsoides. The ITS was not useful for resolving relationships within each of these clusters and between populations of F. vesiculosus. Within-individual variation in ITS sequences is high in Fucus, a derived genus, compared to Ascophyllum, a more ancestral genus. Mapping of the two characters that form the basis of Powell's model for speciation in the Fucaceae showed that 1) number of eggs per oogonium has not followed a gradual reduction and that 2) monoecy/dioecy has changed several times during evolution of this family.

SynopsisIn the marine environment, both external fertilization and settlement are critical processes linking adult and early juvenile life-history phases. The success of both processes can be tightly linked in organisms lacking a larval dispersive phase. This review focuses on synchronous gamete release (¼ spawning) in fucoid algae. These brown macroalgae are important components of temperate intertidal ecosystems in many parts of the world, and achieve synchronous gamete release by integrating various environmental signals. Photosynthesis-dependent sensing of boundary-layer inorganic carbon fluxes, as well as blue light and green light signals, possibly perceived via a chloroplast-located photoreceptor(s), are integrated into pathways that restrict gamete release to periods of low water motion. Avoidance of turbulent and/or high flow conditions in the intertidal zone allows high levels of fertilization success in this group. Temporal patterns and synchrony of spawning in natural populations are reviewed. Most species/populations have a more or less semilunar periodicity, although phase differences occur both between and within species at different geographical locations, raising the possibility that tidal and diurnal cues are more important than semilunar cues in entraining the response. The ecological and evolutionary role(s) of synchronous spawning in the intertidal zone are considered, particularly with regard to hybridization/reproductive isolation in species complexes, and reproductive versus recruitment assurance in the intertidal zone, where synchronous spawning during calm periods may be important for recruitment assurance in addition to fertilization success. Ways in which the roles of spawning synchrony could be tested in closely related species with contrasting mating systems (outcrossing versus selfing) are discussed. IntroductionBroadcast spawning and external fertilization are common in many groups of marine organisms, despite the pitfalls of ensuring reproductive success in the sea. Perhaps the single most important factor favoring successful syngamy is the synchronous release of gametes from reproductive individuals. Indeed, the literature contains many striking examples of spawning synchrony, from the Palolo worm in the south Pacific (see Caspers 1984) to the mass spawning of many species of corals (Harrison and others 1984; Babcock and others 1986). In these and other examples, organisms respond to 1 or more cues from multiple environmental cycles, including daily (light-dark), tidal, semilunar, lunar, and seasonal, to synchronize gamete release (Morgan and Christy 1994;Yamahira 2004; Skov and others 2005). Tight control over the timing of gamete release, and therefore sensitivity to environmental cues, is very important for reproductive assurance in externally fertilizing species. Until recently, the prevailing paradigm has been that sperm limitation is widespread in the sea (reviewed by Levitan and Petersen 1995; but also see Yund 2000). This conclusion is mainly based on experimental stu...

Abstract. The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.