History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants

Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.     

Environmental change as a driver of diversification in temporary aquatic habitats: does the genetic structure of extant fairy shrimp populations reflect historic aridification?

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Will the genetic individualization of disease force a new paradigm?

Disease, through the ages, has been considered as a 'visitation' from afar to the body or as 'disequilibrium' of an internal order. In practical terms, these two concepts of disease have generated a nosology, that is a classification of disease states. Genetics, in its dazzling recent advances, has opened another conceptual framework: disease is an individual event, inasmuch as our growing understanding of the genetic 'terrain' makes all subjects true individuals. Hence, it is time to abandon the old conceptual dichotomy for a Hegelian synthesis: there are no diseases (either as visitation or disequilibrium) only diseased individuals.     

Host manipulation by Ligula intestinalis: a cause or consequence of parasite aggregation?

Previous investigations suggest that the infection of the cyprinid roach, Rutilus rutilus, with the larval plerocercoid forms of the cestode, Ligula intestinalis, creates behavioural and morphological changes in the fish host, potentially of adaptive significance to the parasite in promoting transmission to definitive avian hosts. Here we consider whether these behavioural changes are important in shaping the distribution of parasite individuals across the fish population. An examination of field data illustrates that fish infected with a single parasite were more scarce than expected under the negative binomial distribution, and in many months were more scarce than burdens of two, three or more, leading to a bimodal distribution of worm counts (peaks at 0 and >1). This scarcity of single-larval worm infections could be accounted for a priori by a predominance of multiple infection. However, experimental infections of roach gave no evidence for the establishment of multiple worms, even when the host was challenged with multiple intermediate crustacean hosts, each multiply infected. A second hypothesis assumes that host manipulation following an initial single infection leads to an increased probability of subsequent infection (thus creating a contagious distribution). If manipulated fish are more likely to encounter infected first-intermediate hosts (through microhabitat change, increased ingestion, or both), then host manipulation could act as a powerful cause of aggregation. A number of scenarios based on contagious distribution models of aggregation are explored, contrasted with alternative compound Poisson models, and compared with the empirical data on L. intestinalis aggregation in their roach intermediate hosts. Our results indicate that parasite-induced host manipulation in this system can function simultaneously as both a consequence and a cause of parasite aggregation. This mutual interaction between host manipulation and parasite aggregation points to a set of ecological interactions that are easily missed in most experimental studies of either phenomenon.     

Host–parasite interactions: a litmus test for ocean acidification?

The effects of ocean acidification (OA) on marine species and ecosystems have received significant scientific attention in the past 10 years. However, to date, the effects of OA on host-parasite interactions have been largely ignored. As parasites play a multidimensional role in the regulation of marine population, community, and ecosystem dynamics, this knowledge gap may result in an incomplete understanding of the consequences of OA. In addition, the impact of stressors associated with OA on host-parasite interactions may serve as an indicator of future changes to the biodiversity of marine systems. This opinion article discusses the potential effects of OA on host and parasite species and proposes the use of parasites as bioindicators of OA disturbance.     

Fine-scale genetic structure in a salamander with two reproductive modes: Does reproductive mode affect dispersal?

Reproduction is intimately linked with dispersal, but the effects of changes in reproductive strategies on dispersal have received little attention. Such changes have occurred in many taxonomic groups, resulting in profound alterations in life-history. In amphibians, many species shifted from oviparous/larviparous aquatic reproduction (deposition of eggs or pre-metamorphic larvae in water) to pueriparous terrestrial reproduction (parturition of terrestrial juveniles). The latter provides greater independence from water by skipping the aquatic larval stage; however, the eco-evolutionary implications of this evolutionary step have been underexplored, largely because reproductive modes rarely vary at the intraspecific level, preventing meaningful comparisons. We studied the effects of a transition to pueriparity on dispersal and fine-scale genetic structure in the fire salamander (Salamandra salamandra), a species exhibiting two co-occurring reproductive modes: larviparity and pueriparity. We performed genetic analyses (parentage and genetic spatial autocorrelation) using 11 microsatellite loci to compare dispersal and fine-scale genetic structure in three larviparous and three pueriparous populations (354 individuals in total). We did not find significant differences between reproductive modes, but in some larviparous populations movement patterns may be influenced by site-specific features (type of water bodies), possibly due to passive water-borne dispersal of larvae along streams. Additionally, females (especially larviparous ones) appeared to be more philopatric, while males showed greater variation in dispersal distances. This study also points to future avenues of research to better understand the eco-evolutionary implications of changes in reproductive modes in amphibians.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal:a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes.We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure(SGS) will be higher in more peripheral populations because of lower population density.The study was performed on the predominantly selfing Avena sterilis and included:(1) direct measurement of dispersal in a controlled environment;and(2) analyses of SGS in three natural populations,sampled in linear transects at fixed increasing inter-plant distances.We found that in A.sterilis major seed dispersal is by gravity in close(less than 2 m) vicinity of the mother plant,with a minor additional effect of wind.Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1 m only in the most peripheral desert population,while in the two core populations with Mediterranean conditions,no genetic structure was found.Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within-population gene flow related to low plant density.Our findings also show that predominant self-pollination and highly localized seed dispersal lead to SGS at a very fine scale,but only if plant density is not too high.     

Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: a rule or exception?

Gene flow at a fine scale is still poorly understood despite its recognized importance for plant population demographic and genetic processes. We tested the hypothesis that intensity of gene flow will be lower and strength of spatial genetic structure (SGS) will be higher in more peripheral populations because of lower population density. The study was performed on the predominantly selfing Avena sterilis and included: (1) direct measurement of dispersal in a controlled environment; and (2) analyses of SGS in three natural populations, sampled in linear transects at fixed increasing inter plant distances. We found that in A.sterilis major seed dispersal is by gravity in close (less than 2m) vicinity of the mother plant, with a minor additional effect of wind. Analysis of SGS with six nuclear SSRs revealed a significant autocorrelation for the distance class of 1m only in the most peripheral desert population, while in the two core populations with Mediterranean conditions, no genetic structure was found. Our results support the hypothesis that intensity of SGS increases from the species core to periphery as a result of decreased within population gene flow related to low plant density. Our findings also show that predominant self pollination and highly localized seed dispersal lead to SGS at a very fine scale, but only if plant density is not too high.     

Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures

Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. Despite differences in the community composition, no indications were found for functional differences in the bacterial metagenomes predicted to be associated with algae in the salinities tested, suggesting functional redundancy in the associated bacterial community. Our study provides an example of how microbial communities may impact the acclimation and physiological response of algae to different environments, and thus possibly act as facilitators of speciation. It paves the way for functional examinations of the underlying host–microbe interactions, both in controlled laboratory and natural conditions.     

Host genetics as a cause of overdispersion of parasites among hosts: how general a phenomenon?

In the white-footed mouse, Peromyscus leucopus, the tapeworm Hymenolepis citelli occurs at low (2-3%) prevalence in the field. We found that mature infections (i.e., with egg production) developed in up to 100% of hosts. In the laboratory, a majority of hosts lost their infection by 28 days postintubation. In wild mice infected in the laboratory and returned to the field, infections were more prolonged, with half of the mice still infected at 100 days postintubation. A majority of previously infected hosts resisted challenge infection. Our introduction of laboratory-infected mice into a natural population of hosts appeared to cause infections among previously uninfected mice, leading to an increase in the prevalence of tapeworm infection among mice not intubated. Although genetically based expulsion of tapeworms before maturity is important in causing low prevalence in a similar host-parasite system, such resistance cannot explain low prevalence in the present system. It appears that both heterogeneous distribution and rarity of intermediate hosts as well as short parasite lifespan contribute to low prevalence and overdispersion. Host-parasite dynamics of 2 very similar systems appear to differ markedly.     

Estimating fitness consequences of dispersal: a road to 'know-where'? Non-random dispersal and the underestimation of dispersers' fitness

1. Many studies investigating fitness correlates of dispersal in vertebrates report dispersers to have lower fitness than philopatric individuals. However, if dispersers are more likely to produce dispersing young or are more likely to disperse again in the next year(s) than philopatric individuals, there is a risk that fitness estimates based on local adult survival and local recruitment will be underestimated for dispersers. 2. We review the available empirical evidence on parent-offspring resemblance and individual lifelong consistency in dispersal behaviour, and relate these studies to recent studies of fitness correlates of dispersal in vertebrates. 3. Of the 12 studies testing directly for parent-offspring resemblance in dispersal propensity, five report a significant resemblance. The average effect size (r) of parent-offspring resemblance in dispersal was 0.15 [95% confidence interval (CI) = 0.07-0.22], with no difference between the sexes (average weighted effect size of 0.12 (0.08-0.16) and 0.16 (0.11-0.20) for females and males, respectively). Only three studies report data on within-individual consistency in dispersal propensity, of which two suggest dispersers to be more likely to disperse again. 4. To assess the magnitude of fitness underestimation expected for dispersing individuals depending on the heritability of dispersal distance and study area size, we used a simulation approach. Even when study area size is 10 times the mean dispersal distance, local recruitment per breeding event may be underestimated by 4-10%, generating a potential difference of 4-60% in average lifetime production of recruits between dispersing and philopatric individuals, with larger differences in long-lived species. 5. Estimates of both fitness correlates of dispersal and parent-offspring resemblance or within-individual consistency in dispersal behaviour have been reported for 11 species. Although some comparisons suggest genuine differences in fitness components between philopatric and dispersing individuals, others, based on adult and juvenile survival, are open to the alternative explanation of biased fitness estimates. 6. We list three potential ways of reducing the risk of making wrong inferences on biased fitness estimates due to such non-random dispersal behaviour between dispersing and philopatric individuals: (a) diagnosing effects of non-random dispersal, (b) reducing the effects of spatially limited study area and (c) performing controlled experiments.     

Gondwanan break-up: legacies of a lost world?

Fierce debate surrounds the history of organisms in the southern hemisphere; did Gondwanan break-up produce ocean barriers that imposed distribution patterns on phylogenies (vicariance)? Or have organisms modified their distributions through trans-oceanic dispersal? Recent advances in biogeographical theory suggest that the current focus on vicariance versus dispersal is too narrow because it ignores 'geodispersal' (i.e. expansion of species into areas when geographical barriers disappear), extinction and sampling errors. Geodispersal produces multiple, conflicting vicariance patterns, and extinction and sampling errors destroy vicariance patterns. This perspective suggests that it is more difficult to detect vicariance than trans-oceanic dispersal and that specialized methods must be applied if an unbiased understanding of southern hemisphere biogeography is to be achieved.     

Microarrays: lost in a storm of data?

Microarray expression profiling is instrumental to our understanding of the function of the genome. Resolution of functionally relevant expression patterns will require the analysis of large data sets compiled from multiple investigators. For this and other reasons, I argue that it is crucial for array data to be publicly shared in a format as close to the 'raw data' as possible. Issues such as protection of intellectual property, ensuring quality of the data, and the format and timing for sharing array data are also discussed.     

Introduction of Alien Host–parasite Complexes in a Natural Environment and the Symbiota Concept

When a species is introduced in a new territory its parasites may also follow, thus forming a sort of biotic unit. We propose the term symbiota to indicate this host–parasite complex. This concept is at the basis of the present research in which 11 species of alien and native freshwater fish were collected by electrofishing in the Po river area (Northern Italy). The alien host fish Ictalurus melas and Silurus glanis were parasitized by only one monogenean species each. Lepomis gibbosus, of North American origin, hosted four monogeneans and Carassius carassius three. All these parasites should be considered as alien species, except those collected from C. carassius that should be considered in part natives and in part aliens.     

Evolution of the genetic machinery of the visual cycle: a novelty of the vertebrate eye?

The discovery in invertebrates of ciliary photoreceptor cells and ciliary (c)-opsins established that at least two of the three elements that characterize the vertebrate photoreceptor system were already present before vertebrate evolution. However, the origin of the third element, a series of biochemical reactions known as the "retinoid cycle," remained uncertain. To understand the evolution of the retinoid cycle, I have searched for the genetic machinery of the cycle in invertebrate genomes, with special emphasis on the cephalochordate amphioxus. Amphioxus is closely related to vertebrates, has a fairly prototypical genome, and possesses ciliary photoreceptor cells and c-opsins. Phylogenetic and structural analyses of the amphioxus sequences related with the vertebrate machinery do not support a function of amphioxus proteins in chromophore regeneration but suggest that the genetic machinery of the retinoid cycle arose in vertebrates due to duplications of ancestral nonvisual genes. These results favor the hypothesis that the retinoid cycle machinery was a functional innovation of the primitive vertebrate eye.     

Identifying ‘firebreaks’ to fragment dispersal networks of a marine parasite

Marine ecosystems are beset by disease outbreaks, and efficient strategies to control dispersal of pathogens are scarce. We tested whether introducing no-farming areas or ‘firebreaks’ could disconnect dispersal networks of a parasitic disease affecting the world’s largest marine fish farming industry (～1000 farms). Larval salmon lice (Lepeophtheirus salmonis) are released from and transported among salmon farms by ocean currents, creating inter-farm networks of louse dispersal. We used a state-of-the-art biophysical model to predict louse movement along the Norwegian coastline and network analysis to identify firebreaks to dispersal. At least one firebreak that fragmented the network into two large unconnected groups of farms was identified for all seasons. During spring, when wild salmon migrate out into the ocean, and louse levels per fish at farms must be minimised, two effective firebreaks were created by removing 13 and 21 farms (1.3% and 2.2% of all farms in the system) at ～61°N and 67°N, respectively. We have demonstrated that dispersal models coupled with network analysis can identify no-farming zones that fragment dispersal networks. Reduced dispersal pathways should lower infection pressure at farms, slow the evolution of resistance to parasite control measures, and alleviate infection pressure on wild salmon populations.     

Specialized and generalized dispersal systems: where does ‘the paradigm’ stand?

I explore the specialization versus generalization paradigm in frugivory and seed dispersal. This view predicts that some tropical trees produce nutritious fruits adapted for use by a small coterie of specialized frugivores that provide reliable seed dissemination. Other tree species are expected to offer superabundant fruits of lower nutritional reward, relying instead on common opportunistic frugivores that are individually less reliable, but collectively disperse seeds effectively. Though widely referenced, many aspects of the paradigm are untested with tropical trees and avian frugivores, primarily because plant ecologists rarely determine whether specialist or generalist foragers are responsible for different patterns of seed distribution, while students of foraging behavior rarely determine the effects seed dispersal by different animals for survival of seeds or seedlings of specialist or generalist trees.Ecological paradigms provide alternative hypotheses, without evolutionary arguments. Keystone species have ecological effects disproportionate to their abundance; it is important for management considerations to know whether fruiting trees or frugivores serve as keystone mutualists in tropical forests. Alternatively, the extent to which vertebrate seed dispersers influence density-dependent seed, seedling, sapling, or adult mortality may have important consequences for spatial dispersion and population dynamics of tree species in tropical forests.