Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

Dendritic connectivity shapes spatial patterns of genetic diversity: a simulation-based study

Landscape features notoriously affect spatial patterns of biodiversity. For instance, in dendritic ecological networks (such as river basins), dendritic connectivity has been proposed to create unique spatial patterns of biodiversity. Here, we compared genetic datasets simulated under a lattice-like, a dendritic and a circular landscape to test the influence of dendritic connectivity on neutral genetic diversity. The circular landscape had a level of connectivity similar to that of the dendritic landscape, so as to isolate the influence of dendricity on genetic diversity. We found that genetic diversity and differentiation varied strikingly among the three landscapes. For instance, the dendritic landscape generated higher total number of alleles and higher global Fst than the lattice-like landscape, and these indices also varied between the dendritic and the circular landscapes, suggesting an effect of dendricity. Furthermore, in the dendritic landscape, allelic richness was higher in highly connected demes (e.g. confluences in rivers) than in low-connected demes (e.g. upstream and downstream populations), which was not the case in the circular landscape, hence confirming the major role of dendricity. This led to bell-shaped distributions of allelic richness along an upstream-downstream gradient. Conversely, genetic differentiation (Fst ) was lower in highly than in low-connected demes (which was not observed in circular landscape), and significant patterns of isolation by distance (IBD) were also observed in the dendritic landscape. We conclude that in dendritic networks, the combined influence of dendricity and connectivity generates unique spatial patterns of neutral genetic diversity, which has implications for population geneticists and conservationists.

Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems

Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.

Initial retinoid requirement for early avian development coincides with retinoid receptor coexpression in the precardiac fields and induction of normal cardiovascular development

Vitamin A requirement for early embryonic development is clearly evident in the gross cardiovascular and central nervous system abnormalities and an early death of the vitamin A-deficient quail embryo. This retinoid knockout model system was used to examine the biological activity of various natural retinoids in early cardiovascular development. We demonstrate that all-trans-, 9-cis-, 4-oxo-, and didehydroretinoic acids, and didehydroretinol and all-trans-retinol induce and maintain normal cardiovascular development as well as induce expression of the retinoic acid receptor beta2 in the vitamin A-deficient quail embryo. The expression of RARbeta2 is at the same level and at the same sites where it is expressed in the normal embryo. Retinoids provided to the vitamin A-deficient embryo up to the 5-somite stage of development, but not later, completely rescue embryonic development, suggesting the 5-somite stage as a critical retinoid-sensitive time point during early avian embryogenesis. Retinoid receptors RARalpha, RARgamma, and RXRalpha are expressed in both the precardiac endoderm and mesoderm in the normal and the vitamin A-deficient quail embryo, while the expression of RXRgamma is restricted to precardiac endoderm. Vitamin A deficiency downregulates the expression of RARalpha and RARbeta. Our studies provide strong evidence for a narrow retinoid-requiring developmental window during early embryogenesis, in which the presence of bioactive retinoids and their receptors is essential for a subsequent normal embryonic development.

The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data

Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.

New questions on the hemispheric encoding/retrieval asymmetry (HERA) model assessed by divided visual-field tachistoscopy in normal subjects

According to the hemispheric encoding/retrieval asymmetry (HERA) model, based on data obtained through functional neuroimaging, the left and right prefrontal cortices are preferentially, and, respectively, involved in long-term episodic memory encoding and retrieval. In this study, the HERA model was tested from a behavioral perspective using divided visual-field tachistoscopy. A recognition paradigm with both verbal and visuospatial materials was devised to differentiate memory-related effects (encoding vs. retrieval) from effects linked to the materials. The paradigm used lists of 12 and four items to assess long-term episodic memory and short-term memory, respectively. The aim of the latter condition was to test whether the HERA model is applicable in short-term memory. For long-term episodic memory, the data obtained validated the HERA model; the direction of the hemispheric asymmetry was found to depend on the type of materials used, whereas its magnitude was determined by the type of memory process. For verbal short-term memory, the HERA model seems to be confirmed. The pre-existing representations of the material could take into account the similarity of the hemispheric asymmetry pattern between short-term memory and long-term memory. In contrast, for visuospatial short-term memory, Baddeley's working memory model seems to better explain our results insofar as the asymmetries were essentially linked to the material in encoding but not in retrieval. This latter difference between short-term memory and long-term indicates that processes involved in LTM depend on episodic processes per se, hence, lending more support for the HERA model. Accordingly, these two memory systems seem to bring into play two different modes of hemisphere specialization.

Predicting global invasion risks: a management tool to prevent future introductions

Predicting regions at risk from introductions of non-native species and the subsequent invasions is a fundamental aspect of horizon scanning activities that enable the development of more effective preventative actions and planning of management measures. The Asian cyprinid fish topmouth gudgeon Pseudorasbora parva has proved highly invasive across Europe since its introduction in the 1960s. In addition to direct negative impacts on native fish populations, P. parva has potential for further damage through transmission of an emergent infectious disease, known to cause mortality in other species. To quantify its invasion risk, in regions where it has yet to be introduced, we trained 900 ecological niche models and constructed an Ensemble Model predicting suitability, then integrated a proxy for introduction likelihood. This revealed high potential for P. parva to invade regions well beyond its current invasive range. These included areas in all modelled continents, with several hotspots of climatic suitability and risk of introduction. We believe that these methods are easily adapted for a variety of other invasive species and that such risk maps could be used by policy-makers and managers in hotspots to formulate increased surveillance and early-warning systems that aim to prevent introductions and subsequent invasions.

Identification of a 49-kDa hydrophobic cell wall mannoprotein present in velum yeast which may be implicated in velum formation

Analysis of velum-forming yeast cell wall components released by beta-1,3-glucanase treatment were compared with those of a non velum-forming yeast. SDS-PAGE electrophoresis and Western blotting with ConA-peroxidase staining of mannoproteins allowed us to identify a 49-kDa mannoprotein present in the cell wall of the velum-forming yeast and hardly visible in the control. The cell wall nature of this protein was confirmed by labelling with the non-permeable sulfosuccinimydiyl-6-(biotinamido)hexanoate reagent. A partial purification of this mannoprotein by anion exchange HPLC followed by surface hydrophobicity determination revealed that the fraction containing the 49-kDa mannoprotein was the most hydrophobic. Since cell surface hydrophobicity plays an important role in aggregate formation, it is likely that this mannoprotein is involved in velum formation.

Melanin-based coloration and host-parasite interactions under global change

The role of parasites in shaping melanin-based colour polymorphism, and the consequences of colour polymorphism for disease resistance, remain debated. Here we review recent evidence of the links between melanin-based coloration and the behavioural and immunological defences of vertebrates against their parasites. First we propose that (1) differences between colour morphs can result in variable exposure to parasites, either directly (certain colours might be more or less attractive to parasites) or indirectly (variations in behaviour and encounter probability). Once infected, we propose that (2) immune variation between differently coloured individuals might result in different abilities to cope with parasite infection. We then discuss (3) how these different abilities could translate into variable sexual and natural selection in environments varying in parasite pressure. Finally, we address (4) the potential role of parasites in the maintenance of melanin-based colour polymorphism, especially in the context of global change and multiple stressors in human-altered environments. Because global change will probably affect both coloration and the spread of parasitic diseases in the decades to come, future studies should take into account melanin-based coloration to better predict the evolutionary responses of animals to changing disease risk in human-altered environments.

The disruption of dominance hierarchies by a non-native species: an individual-based analysis

We studied the effects of the exotic rainbow trout (Oncorhynchus mykiss) on the performance and the dominance hierarchy of native Atlantic salmon (Salmo salar) at the group and individual level using laboratory and semi-natural experiments. At the group level, we compared the effects of interspecific and intraspecific competition (substitutive and additive design) on behavioural responses and growth of young-of-the-year Atlantic salmon. At the individual level, the same design was used to evaluate: (1) the temporal consistency of behavioural responses, dominance hierarchy and growth rate of Atlantic salmon; (2) the pattern of correlations between behaviours; and (3) the relationship between individual growth rate and behaviour. In the laboratory, group-level analyses revealed a weak but similar effect of rainbow trout and intraspecific competition on the behaviour and growth of Atlantic salmon. In contrast, individual-based analyses demonstrated that rainbow trout (but not intraspecific competition) strongly affected behavioural strategy, dominance hierarchy and growth trajectory of individual Atlantic salmon. Specifically, behaviours, dominance status and growth rate of salmon were temporally consistent in the intraspecific environment, while these patterns were disrupted when rainbow trout were present. Similarly, we found that rainbow trout strongly affected behavioural correlations and the relationships between individual growth rate and behaviour. The semi-natural experiments confirmed these results as interspecific competition affected relationships between individual growth rate of salmon, initial weight and activity index. Overall, individual-based analyses highlighted important mechanisms that were concealed at the group level, and that may be crucial to understand ecological and evolutionary consequences of exotic species. Moreover, these results demonstrated that competition with an exotic species disrupts the hierarchical relationship among native individuals and may therefore represent a potential for a shift in selective pressure.

Characterization of cDNAs encoding the chick retinoic acid receptor gamma 2 and preferential distribution of retinoic acid receptor gamma transcripts during chick skin development

Retinoic acid receptors alpha, beta and gamma (RAR alpha, beta and gamma) are ligand-inductible transcriptional activators which belong to the steroid/thyroid hormone receptor superfamily. At least two major isoforms (1 and 2) of each RAR arise by differential use of two promoters and alternative splicing. In mouse, the three RAR genes are expressed in stage- and tissue-specific patterns during embryonic development. In order to understand the role of the different RARs in chick, RAR gamma 2 cDNAs were isolated from an 8.5-day (stage 35 of Hamburger and Hamilton) chick embryo skin library. The deduced chick RAR gamma 2 amino acid sequence displays uncommon features such as 21 specific amino acid replacements, 12 of them being clustered in the amino-terminal region (domains A2 and B), and a truncated acidic carboxy-terminal region (F domain). However, the pattern of RAR gamma expression in chick embryo resembles that reported in mouse, particularly in skin where RAR gamma expression occurs in both the dermal and epidermal layers at the beginning of feather formation, and is subsequently restricted to the differentiating epidermal cells. Northern blot analysis suggests that different RAR gamma isoforms could be successively required during chick development.

Cognitive processes involved in delayed non-matching-to-sample performance in Parkinson's disease

Visual recognition memory was assessed in terms of delay duration, memory load and amount of interference(s) in non-demented patients with Parkinson's disease (PD) using an automated delayed non-matching-to-sample (DNMS) task with trial-unique stimuli. Special attention was focused on the different cognitive functions engaged by these patients in solving this recognition memory task. Thirteen patients with PD, carefully selected according to their stable regimen and anticholinergic medication, were compared to 12 controls matched by age and educational level. Besides the DNMS task, a neuropsychological battery that included tasks carefully selected according to processes potentially required to perform the DNMS task (e.g. attention, executive functions, visual discrimination and motor speed) was administered to the subjects. As compared with controls, patients with PD showed a deficit on most DNMS subscores, except those requiring the least cognitive load. The correlative analysis between the DNMS and other neuropsychological tasks suggests involvement of long-term memory mainly in the DNMS performance for the control group, contrasting with a major involvement of executive functions for the patients with PD. These data indicate that visual recognition memory impairment in non-demented patients with PD is largely due to an executive dysfunction, notably in working memory. Several hypotheses are proposed concerning the neuronal substrates underlying the impairment on the visual DNMS task in PD.

Evidence of plasticity in the reproduction of a trematode parasite: the effect of host removal

The parasitic trematode Proctoeces lintoni requires 3 hosts (intertidal mussels, keyhole limpets, and clingfish) to complete its life cycle. The densities and size structure of host communities are modified by selective human harvesting. This study examined clutch and egg size of P. lintoni in 3 adjacent sites in rocky intertidal areas of central Chile presenting differences in the levels of human disturbance (i.e., from a fully protected marine reserve to free open-access areas). We found significant differences in parasite fecundity among sites. An increase in number of eggs was observed inside protected marine areas compared with open-access areas, suggesting a plastic response of the parasite reproductive strategies to the host community modification. These results show that host removal by humans in coastal ecosystems can strongly influence parasite life history traits.

Isolation and characterization of a cDNA encoding a chicken actin-like protein

We report the isolation and characterization of a chicken cDNA which putatively encodes an actin-like protein (chACTL). This 394-amino-acid (aa) polypeptide shares sequence homology (81, 70 and 67% identical aa, respectively) with three actin-related proteins (ARP) described for Drosophila melanogaster (ARP14D), Caenorhabditis elegans (ACTL) and Saccharomyces cerevisiae (ACT2). At least six chACTL transcripts were detected in different tissues during chick embryogenesis. Sequence analysis suggests that at least three groups of ARP have been evolutionarily conserved.

To boldly climb: behavioural and cognitive differences in migrating European glass eels

European eel (Anguilla anguilla) is a catadromous fish species that received substantial attention as its population has markedly declined in the last three decades. The possible causes of this decline include habitat fragmentation factors such as dams and weirs. In some cases, these obstacles are equipped with fish friendly passage devices that may select young eels according to their climbing behaviour. We tested how individual climbing tendency was related to the event of fishway passage experienced in the field and classified fish climbing profiles as climbing 'leaders', 'followers', 'finishers' and 'no climbers'. Moreover, we analysed the brain transcription level of genes related to neurogenesis and synaptic plasticity and compared it to climbing profiles. We found that fish from the upstream segments of an impounded river had a higher climbing propensity. Their behaviour was also more repeatable throughout the whole test than the obstacle-naive fish from the downstream segment. Moreover, we found that boldly climbing 'leaders' had lower levels of transcription of synapse-related genes than the climbing 'followers'. These differences could be related to coping styles of fish, where proactive 'leaders' express a routine and risky behaviour, whereas reactive fish need an environmental assessment before exploratory behaviour. Our study showed that differences in climbing propensity exist in glass eels separated by water obstacles. Moreover, eels could adopt climbing different strategies according to the way they deal with environmental stress and to the cognitive abilities they possess.

Individual genetic tagging for teleosts: an empirical validation and a guideline for ecologists

The efficiency of individual genetic tagging was determined by using passive integrated transponders (PIT) as a comparative conventional tagging method. Fifty-five common dace Leuciscus leuciscus were captured in the wild, PIT tagged and fin clipped (for DNA analysis). Thirty fish were recaptured on three occasions and tissue samples were collected. Using 18 microsatellite loci, 79-94% of the recaptures were correctly assigned. Experience with scoring L. leuciscus microsatellites led to more individuals correctly assigned. Allowing matches that differed by one or two alleles resulted in 100% of all recaptures successfully assigned irrespective of the observer. Reducing the set of loci to five to six loci appropriately selected did not affect the assignment rate, demonstrating that costs can be subsequently reduced. Despite their potential benefits, the application of genetic tags for teleosts has been limited. Here, it was demonstrated that genetic tagging could be applied, and a clear guideline (flowchart) is provided on how this method can be developed for teleosts and other organisms, with subsequent practical applications to ecology, evolutionary biology and conservation management.

Both retinoic acid receptors alpha (RARalpha) and gamma (RARgamma) are able to initiate mouse upper-lip skin glandular metaplasia

Embryonic mouse upper-lip skin explants treated with 16.7 microM all-trans retinoic acid (tRA) give rise to a glandular metaplasia of hair vibrissa follicles; however, at this concentration, tRA can activate not only the three retinoic acid receptors (RARalpha, beta, and gamma), but also the retinoid X receptors (RXRalpha, beta, and gamma) as a consequence of its isomerization to 9-cis retinoic acid. We therefore studied the respective roles of the RXR and RAR by treating RARalpha(-/-), beta(-/-), and gamma(-/-) skin explants with tRA and wild-type explants with synthetic retinoids specific for RXR or for each of the RAR. The null mutation of the RARalpha, RARbeta, and RARgamma genes did not prevent tRA-induced hair glandular metaplasia, but RARgamma inactivation dramatically reduced its ratio. As demonstrated by treating explants with a RAR- or a RXR-specific panagonist (CD367 and Ro25-7386, respectively), RAR are primarily responsible for this metaplasia. The use of two retinoids (Ro40-6055, 8 x 10(-3) microM, or CD437, 7.7 x 10(-2) microM) that are believed to act, respectively, as a RARalpha- or a RARgamma-specific agonist showed that both these receptors can initiate a metaplasia. In contrast, BMS453, a RARbeta-specific agonist, was unable to give rise to any metaplasia. Nevertheless, the highest degrees and ratios of metaplasia were only obtained after treatment with the CD367 RAR panagonist, or with either Ro40-6055 or CD437 at a concentration sufficient to allow the activation of the three RAR, suggesting that RARbeta activation is required for a metaplasia of all vibrissae.