Inter- and intraspecific genetic and morphological variation in a sibling pair of carabid species

Background

Pogonus littoralis and Pogonus chalceus are very close related species with quite different ecological preferences within salt marshes. We study the evolutionary processes in and between these presumably young species. Therefore, we compare the variation in ecologically relevant characters and the genetic variation within one of the species (intraspecific differentiation) with the variation of the two types of characters between the two species (interspecific variation). Data are compared between two independent sets of populations, one set at a small geographical scale (the ecologically diverse Guérande area in France) and the other set at a Atlantic-Mediterranean scale.

Results

Body and relative wing size and IDH1 allozyme data show that the intraspecific variation in P. chalceus is high and in the same range as the interspecific variation (P. chalceus versus P. littoralis). Based on neutral markers (other allozymes and mitochondrial DNA) on the other hand, the intraspecific variation in P. chalceus is much lower in comparison to the interspecific variation.

Conclusion

The different ecotypes in the highly polytypic species P. chalceus are as highly differentiated in ecological characters as true species, but are not recognised as such by screening neutral DNA polymorphisms. This can be interpreted as a case of ongoing speciation driven by natural selection adapting each ecotype to its respective ecological niche. The same ecological process can be recognised in the differentiation between the two sister species, where en plus reproductive isolation between the two gene pools occurred, allowing independent drift and mutation accumulation in neutral genetic characters.     

Interspecific competition in Arabidopsis thaliana: root hairs are important for competitive effect, but not for competitive response

Background and aims

The role of root hairs in intraspecific competition for Phosporus (P) is well examined, but their importance during interaction with other plant species is unknown, as is the differential meaning for competitive effect and response. This study aims to fill this gap of knowledge.

Methods

Competitive abilities of Arabidopsis thaliana wildtype and mutants with aberrant root hair phynotypes (root hair deficient, rhd2-1 or excessive root hair density, prc1-1) were examined in a pot-experiment with P-deficient sand. Competitive effects on a phytometer (Hieracium pilosella) or on A. thaliana itself were assessed as well as competitive responses to species mixtures.

Results

In intraspecific interaction, the competitive effect of wildtype was superior to that of rhd2-1 or prc1-1. This was much less pronounced in interspecific interaction. Competitive response was entirely uniform between Arabidopsis root phenotypes.

Conclusions

The notion that root hairs are important for competition for P should be differentiated. With A. thaliana root hairs less important in inter- than in intraspecific interaction and with root hairs entirely unimportant for competitive response, functional mechanisms of competition for P appear quite complex. Such differential importance of root traits in different facets of competition might well be more common than previously thought.     

Different ecological conditions support individual specialization in closely related,ecologically similar species

Individual generalist predators often have more specialized diets than their populations do. Individual specialization (IS) is influenced by ecological opportunity, intraspecific competition, and interspecific competition, although the effects of these parameters are inconsistent across studies. We investigated IS in five species of frogs and toads, Anaxyrus americanus, A. fowleri, Lithobates catesbeianus, L. clamitans, and L. sphenocephalus. We used the natural history and ecology of each species to predict which parameters would influence IS. Our predictions were supported for some species but not others. We predicted IS would be positively influenced by resource diversity in all species, but this prediction held for only three species, with the relationship significant in A. fowleri and L. catesbeianus and marginally significant in A. americanus. We also predicted that interspecific competition would have a negative relationship with IS in L. clamitans because L. catesbeianus is competitively superior to L. clamitans and likely to suppress its foraging options. This prediction was upheld. Finally, we predicted that IS in A. americanus, A. fowleri, and L. clamitans would be influenced by intraspecific competition. However, IS was not influenced by intraspecific competition in any species, a surprising result given that intraspecific competition has traditionally been assumed to be the ecological parameter with the strongest effects on IS. Many previous studies did not simultaneously consider all three ecological parameters, which may have increased the apparent importance of intraspecific competition for IS. Our results revealed that the ecological parameters affected IS differently even across closely related and ecologically similar species, and demonstrated that these differences are sometimes predictable based on natural history. This study also suggests that sympatric ecological speciation based on IS may be rare because the ecological parameters driving IS are inconsistent across species, and the strength of their effects on intraspecific diet variation varies in space.     

Integrated response of intercropped maize and potatoes to heterogeneous nutrients and crop neighbours

Background and Aims

In communities, plants often simultaneously interact with intra- and inter-specific neighbours and heterogeneous nutrients. How plants respond under these conditions and then affect the structure and function of communities remain important questions.

Methods

Maize (Zea mays L.) was intercropped with potatoes (Solanum tuberosum L.). In the field experiment, we applied fertilizer both homogeneously and heterogeneously under monocropping and intercropping conditions. The heterogeneous nutrient treatment in intercropping was designed with different fertilizer placements, at intraspecific and interspecific rows, respectively. In the pot experiment, crops were grown under both homogeneous and heterogeneous nitrogen conditions with single plant, intraspecific and interspecific competition. Shoot and root biomass and yield were measured to analyse crop performance.

Results

In the field experiment, the heterogeneous nitrogen, compared with the homogenous one, enhanced the performance of the intercropped crop. Importantly, this effect of heterogeneous nitrogen was greater when fertilizer was applied at interspecific rows, rather than at intraspecific rows. Moreover, in pot experiments, the root foraging precision of the two crops was increased by interspecific neighbours, but only that of potatoes was increased by intraspecific neighbours.

Conclusions

The integrated responses of plants to heterogeneous neighbours and nutrients depend on the position of nutrient-rich patches, which deepen our understanding of the function of plant diversity, and show that fertilizer placement within multi-cropping systems merits more attention. Moreover, the enhanced utilization of heterogeneous nitrogen could drive overyielding in multi-cropping systems.     

Worldwide population differentiation at disease-associated SNPs

Background

Recent genome-wide association (GWA) studies have provided compelling evidence of association between genetic variants and common complex diseases. These studies have made use of cases and controls almost exclusively from populations of European ancestry and little is known about the frequency of risk alleles in other populations. The present study addresses the transferability of disease associations across human populations by examining levels of population differentiation at disease-associated single nucleotide polymorphisms (SNPs).

Methods

We genotyped ~1000 individuals from 53 populations worldwide at 25 SNPs which show robust association with 6 complex human diseases (Crohn's disease, type 1 diabetes, type 2 diabetes, rheumatoid arthritis, coronary artery disease and obesity). Allele frequency differences between populations for these SNPs were measured using Fst. The Fst values for the disease-associated SNPs were compared to Fst values from 2750 random SNPs typed in the same set of individuals.

Results

On average, disease SNPs are not significantly more differentiated between populations than random SNPs in the genome. Risk allele frequencies, however, do show substantial variation across human populations and may contribute to differences in disease prevalence between populations. We demonstrate that, in some cases, risk allele frequency differences are unusually high compared to random SNPs and may be due to the action of local (i.e. geographically-restricted) positive natural selection. Moreover, some risk alleles were absent or fixed in a population, which implies that risk alleles identified in one population do not necessarily account for disease prevalence in all human populations.

Conclusion

Although differences in risk allele frequencies between human populations are not unusually large and are thus likely not due to positive local selection, there is substantial variation in risk allele frequencies between populations which may account for differences in disease prevalence between human populations.     

Validation of the theoretical domains framework for use in behaviour change and implementation research

Background

An integrative theoretical framework, developed for cross-disciplinary implementation and other behaviour change research, has been applied across a wide range of clinical situations. This study tests the validity of this framework.

Methods

Validity was investigated by behavioural experts sorting 112 unique theoretical constructs using closed and open sort tasks. The extent of replication was tested by Discriminant Content Validation and Fuzzy Cluster Analysis.

Results

There was good support for a refinement of the framework comprising 14 domains of theoretical constructs (average silhouette value 0.29): ??Knowledge??, ??Skills??, ??Social/Professional Role and Identity??, ??Beliefs about Capabilities??, ??Optimism??, ??Beliefs about Consequences??, ??Reinforcement??, ??Intentions??, ??Goals??, ??Memory, Attention and Decision Processes??, ??Environmental Context and Resources??, ??Social Influences??, ??Emotions??, and ??Behavioural Regulation??.

Conclusions

The refined Theoretical Domains Framework has a strengthened empirical base and provides a method for theoretically assessing implementation problems, as well as professional and other health-related behaviours as a basis for intervention development.     

Analysis of disruptive selection in subdivided populations

Background

Analytical methods have been proposed to determine whether there are evolutionarily stable strategies (ESS) for a trait of ecological significance, or whether there is disruptive selection in a population approaching a candidate ESS. These criteria do not take into account all consequences of small patch size in populations with limited dispersal.

Results

We derive local stability conditions which account for the consequences of small and constant patch size. All results are derived from considering R_m, the overall production of successful emigrants from a patch initially colonized by a single mutant immigrant. Further, the results are interpreted in term of concepts of inclusive fitness theory. The condition for convergence to an evolutionarily stable strategy is proportional to some previous expressions for inclusive fitness. The condition for evolutionary stability stricto sensu takes into account effects of selection on relatedness, which cannot be neglected. It is function of the relatedness between pairs of genes in a neutral model and also of a three-genes relationship. Based on these results, I analyze basic models of dispersal and of competition for resources. In the latter scenario there are cases of global instability despite local stability. The results are developed for haploid island models with constant patch size, but the techniques demonstrated here would apply to more general scenarios with an island mode of dispersal.

Conclusions

The results allow to identity and to analyze the relative importance of the different selective pressures involved. They bridge the gap between the modelling frameworks that have led to the R_m concept and to inclusive fitness.

     

Genetic variation in wild Prunus L. subgen. Cerasus germplasm from Iran characterized by nuclear and chloroplast SSR markers

Key message

The selected material of Cerasus subgen. will be useful for conservation and management and important for Prunus breeding programs.

Abstract

Knowledge of relationships among the cultivated and wild species of Cerasus is important for recognizing gene pools in germplasm and developing effective conservation and management strategies. In this study, genetic and phylogenetic relationships of wild Cerasus subgenus species naturally growing in Iran, including P. avium (mazzard), P. mahaleb, P. brachypetala, P. incana, P. yazdiana, P. microcarpa subsp. microcarpa, P. microcarpa subsp. diffusa and P. pseudoprostrata and three commercial species, sweet cherry (P. avium), sour cherry (P. cerasus) and duke cherry (P. x gondouinii) was investigated based on 16 nuclear SSR and five chloroplast SSR. Very high level of polymorphism was detected among the studied species based these molecular markers, indicating high inter and intraspecific genetic variation. Inter and intraspecific genetic similarity coefficients varied from 0.00 to 1.00, indicating high genetic variation in studied germplasm. These two molecular markers types could distinguish differences between all species so that accessions of each species were placed into a single group. Based on molecular markers, a close correlation was observed between intraspecific variation and geographical distribution. Furthermore, based on nuSSR primers, most wild species showed 2–4 alleles and may be tetraploid. In conclusion, the conservation of these highly diverse native populations of Iranian wild Cerasus germplasm is recommended for future breeding activity.     

Natural selection drives the fine-scale divergence of a coevolutionary arms race involving a long-mouthed weevil and its obligate host plant

Background

One of the major recent advances in evolutionary biology is the recognition that evolutionary interactions between species are substantially differentiated among geographic populations. To date, several authors have revealed natural selection pressures mediating the geographically-divergent processes of coevolution. How local, then, is the geographic structuring of natural selection in coevolutionary systems?

Results

I examined the spatial scale of a "geographic selection mosaic," focusing on a system involving a seed-predatory insect, the camellia weevil (Curculio camelliae), and its host plant, the Japanese camellia (Camellia japonica). In this system, female weevils excavate camellia fruits with their extremely-long mouthparts to lay eggs into seeds, while camellia seeds are protected by thick pericarps. Quantitative evaluation of natural selection demonstrated that thicker camellia pericarps are significantly favored in some, but not all, populations within a small island (Yakushima Island, Japan; diameter ca. 30 km). At the extreme, camellia populations separated by only several kilometers were subject to different selection pressures. Interestingly, in a population with the thickest pericarps, camellia individuals with intermediate pericarp thickness had relatively high fitness when the potential costs of producing thick pericarps were considered. Also importantly, some parameters of the weevil - camellia interaction such as the severity of seed infestation showed clines along temperature, suggesting the effects of climate on the fine-scale geographic differentiation of the coevolutionary processes.

Conclusion

These results show that natural selection can drive the geographic differentiation of interspecific interactions at surprisingly small spatial scales. Future studies should reveal the evolutionary/ecological outcomes of the "fine scale geographic mosaics" in biological communities.     

Ecology, genetic diversity and phylogeography of the Iberian endemic plant Jurinea pinnata (Lag.) DC. (Compositae) on two special edaphic substrates: dolomite and gypsum

Background and aims

Jurinea pinnata is an Iberian vascular plant which only grows on gypsum and dolomite, two types of rocks associated with their exclusive endemic floras. In addition, the plant has an island-like distribution which could affect the differentiation and the genetic variability of wild populations. Thus, the species provides a unique opportunity for comparing (bio)geographical and ecological (edaphic) differentiation by means of molecular markers.

Methods

For our investigation we took 24 soil samples paired with a similar number of foliar samples for nutritional analyses. Our molecular-marker approach (AFLPs) involved 16 populations.

Results

The edaphic parameters revealed significant dissimilarities between dolomitic and gypsum soils. These differences are also found in the mineral composition of the leaves. However, molecular data revealed that the differentiation between populations correlates better with geographical isolation than with the substrate character.

Conclusions

The populations showing the greatest genetic diversity are those of the East Baetic territory where the species grow on both substrates and its populations are closer together. The plant tolerance to gypsum and dolomite can be explained either as a result of common adaptive mechanisms or of a more general adaptation to arid environments.     

Excitability decreasing central motor plasticity is retained in multiple sclerosis patients

Background

Essential tremor (ET) is one of the commonest movement disorders though the prevalence varies globally. There is paucity of data on ET prevalence in sub-Saharan Africa. The study aimed to determine the prevalence of ET in a Nigerian community.

Methods

This door-to-door survey was conducted in two stages. In Stage 1, 3000 randomly selected residents of an urban centre in Lagos, Nigeria, were screened using a questionnaire to detect symptoms of movement disorder. 234 participants who responded positively regarding presence of tremors were rescreened using an ET-specific questionnaire, a face-to-face interview and neurological examination. Diagnosis of ET was based on the Movement Disorders Society (MDS) consensus diagnostic criteria for ET.

Results

Of the 3000 participants, forty responded positively to the ET screening questionnaire, of which 36 (19 females and 17 males) had a final diagnosis of ET, giving a crude prevalence of 12 per 1000 (95% CI?=?8.1- 15.9). Gender specific prevalence was 10.3 /1000 in males and 14.3/1000 in females. Age specific prevalence increased with advancing age in both sexes. Age adjusted prevalence (WHO New world population) was 23.8 per 1000.

Conclusions

We documented a high prevalence of ET in this study, with typical increasing prevalence with advancing age as previously reported in other populations.     

Intraspecific eye color variability in birds and mammals: a recent evolutionary event exclusive to humans and domestic animals

Background

Human populations and breeds of domestic animals are composed of individuals with a multiplicity of eye (= iris) colorations. Some wild birds and mammals may have intraspecific eye color variability, but this variation seems to be due to the developmental stage of the individual, its breeding status, and/or sexual dimorphism. In other words, eye colour tends to be a species-specific trait in wild animals, and the exceptions are species in which individuals of the same age group or gender all develop the same eye colour. Domestic animals, by definition, include bird and mammal species artificially selected by humans in the last few thousand years. Humans themselves may have acquired a diverse palette of eye colors, likewise in recent evolutionary time, in the Mesolithic or in the Upper Paleolithic.

Presentation of the hypothesis

We posit two previously unrecognized hypotheses regarding eye color variation: 1) eye coloration in wild animals of every species tends to be a fixed trait. 2) Humans and domestic animal populations, on the contrary, have eyes of multiple colors. Sexual selection has been invoked for eye color variation in humans, but this selection mode does not easily apply in domestic animals, where matings are controlled by the human breeder.

Testing the hypothesis

Eye coloration is polygenic in humans. We wish to investigate the genetics of eye color in other animals, as well as the ecological correlates.

Implications of the hypothesis

Investigating the origin and function of eye colors will shed light on the reason why some species may have either light-colored irises (e.g., white, yellow or light blue) or dark ones (dark red, brown or black). The causes behind the vast array of eye colors across taxa have never been thoroughly investigated, but it may well be that all Darwinian selection processes are at work: sexual selection in humans, artificial selection for domestic animals, and natural selection (mainly) for wild animals.

     

Neuropeptide-inducible upregulation of proteasome activity precedes nuclear factor kappa B activation in androgen-independent prostate cancer cells

Background

Upregulation of nuclear factor kappa B (NF??B) activity and neuroendocrine differentiation are two mechanisms known to be involved in prostate cancer (PC) progression to castration resistance. We have observed that major components of these pathways, including NF??B, proteasome, neutral endopeptidase (NEP) and endothelin 1 (ET-1), exhibit an inverse and mirror image pattern in androgen-dependent (AD) and -independent (AI) states in vitro.

Methods

We have now investigated for evidence of a direct mechanistic connection between these pathways with the use of immunocytochemistry (ICC), western blot analysis, electrophoretic mobility shift assay (EMSA) and proteasome activity assessment.

Results

Neuropeptide (NP) stimulation induced nuclear translocation of NF??B in a dose-dependent manner in AI cells, also evident as reduced total inhibitor ??B (I??B) levels and increased DNA binding in EMSA. These effects were preceded by increased 20?S proteasome activity at lower doses and at earlier times and were at least partially reversed under conditions of NP deprivation induced by specific NP receptor inhibitors, as well as NF??B, I??B kinase (IKK) and proteasome inhibitors. AD cells showed no appreciable nuclear translocation upon NP stimulation, with less intense DNA binding signal on EMSA.

Conclusions

Our results support evidence for a direct mechanistic connection between the NPs and NF??B/proteasome signaling pathways, with a distinct NP-induced profile in the more aggressive AI cancer state.     

Mode of competition for light and water amongst juvenile beech and spruce trees under ambient and elevated levels of O3 and CO2

Key message

Our study provides evidence that neither elevated CO ₂ nor elevated O ₃ alters the positive asymmetric competition for light and the symmetric competition for water among beech and spruce individuals grown in monoculture. We conclude that the mechanism of competition (i.e. symmetric/asymmetric) above (e.g shading or overtopping effect) and belowground (e.g. non-preemption or foraging) rather than abiotic treatments such as elevated CO ₂ , O ₃ and CO ₂ /O ₃ regimes, plays a dominant role for ensuring competitive success among tree saplings.

Abstract

Despite numerous studies conducted on plant responses to increasing CO₂ and O₃ concentrations, there is still a gap in understanding on how these gasses would affect the mode of competition (e.g., the ability by which larger and smaller plants capture resources) at the individual level of intra-specific beech and spruce saplings. Using empirical data and simulations from the plant-growth model PLATHO, we analyzed underlying mechanisms of competition and extrapolated effects beyond the time span of the experiment. We hypothesized that among juvenile beech and spruce trees planted in monoculture, +CO₂ would diminish the positive asymmetric competition for light. Conversely, +O₃ would enhance this outcome. In addition, we hypothesized that the symmetric mode of competition belowground for water would remain unchanged, irrespective of +CO₂ and/or +O₃ treatments. Our results showed that +CO₂ and/or +O₃ treatments did not alter the mode of competition aboveground for light. Conversely, we accepted our hypothesis that the mode of competition for water would remain unchanged under both treatments. Overall, we conclude that neither +CO₂ nor +O₃ alters the positive asymmetric competition for light and the symmetric competition for water among beech and spruce individuals grown in monoculture. We further conclude that competitive mechanism above (e.g., shading or overtopping effect) and belowground (e.g., non-preemption or foraging) rather than abiotic treatments, such as elevated CO₂, O₃ and CO₂/O₃ regimes, plays a dominant role for ensuring competitive success among tree saplings.     

Climate-driven diversification in two widespread Galerida larks

Background

The major impact of Plio-Pleistocene climatic oscillations on the current genetic structure of many species is widely recognised but their importance in driving speciation remains a matter of controversies. In addition, since most studies focused on Europe and North America, the influence of many other biogeographic barriers such as the Sahara remains poorly understood. In this paper, climate-driven diversification was investigated by using a comparative phylogeographic approach in combination with phenotypic data in two avian species groups distributed on both sides of the deserts belt of Africa and Asia. In particular, we tested whether: 1) vicariance diversification events are concomitant with past climatic events; and 2) current ecological factors (using climate and competition as proxies) contribute to phenotypic divergence between allopatric populations.

Results

Mitochondrial and nuclear sequence data indicated that the crested and Thekla lark species groups diverged in the early Pliocene and that subsequent speciation events were congruent with major late Pliocene and Pleistocene climatic events. In particular, steep increase in aridity in Africa near 2.8 and 1.7 million years ago were coincident with two north-south vicariance speciation events mediated by the Sahara. Subsequent glacial cycles of the last million years seem to have shaped patterns of genetic variation within the two widespread species (G. cristata and G. theklae). The Sahara appears to have allowed dispersal from the tropical areas during climatic optima but to have isolated populations north and south of it during more arid phases. Phenotypic variation did not correlate with the history of populations, but was strongly influenced by current ecological conditions. In particular, our results suggested that (i) desert-adapted plumage evolved at least three times and (ii) variation in body size was mainly driven by interspecific competition, but the response to competition was stronger in more arid areas.

Conclusion

Climatic fluctuations of the Plio-Pleistocene strongly impacted diversification patterns in the Galerida larks. Firstly, we found that cladogenesis coincides with major climatic changes, and the Sahara appears to have played a key role in driving speciation events. Secondly, we found that morphology and plumage were strongly determined by ecological factors (interspecific competition, climate) following vicariance.     

A single origin of the photosynthetic organelle in different Paulinella lineages

Background

Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders.

Results

At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects.

Conclusion

While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.     

Optimizing the allocation of resources for genomic selection in one breeding cycle

Key message

We developed a universally applicable planning tool for optimizing the allocation of resources for one cycle of genomic selection in a biparental population. The framework combines selection theory with constraint numerical optimization and considers genotype? ×? environment interactions.

Abstract

Genomic selection (GS) is increasingly implemented in plant breeding programs to increase selection gain but little is known how to optimally allocate the resources under a given budget. We investigated this problem with model calculations by combining quantitative genetic selection theory with constraint numerical optimization. We assumed one selection cycle where both the training and prediction sets comprised double haploid (DH) lines from the same biparental population. Grain yield for testcrosses of maize DH lines was used as a model trait but all parameters can be adjusted in a freely available software implementation. An extension of the expected selection accuracy given by Daetwyler et al. (2008) was developed to correctly balance between the number of environments for phenotyping the training set and its population size in the presence of genotype?×?environment interactions. Under small budget, genotyping costs mainly determine whether GS is superior over phenotypic selection. With increasing budget, flexibility in resource allocation increases greatly but selection gain leveled off quickly requiring balancing the number of populations with the budget spent for each population. The use of an index combining phenotypic and GS predicted values in the training set was especially beneficial under limited resources and large genotype × environment interactions. Once a sufficiently high selection accuracy is achieved in the prediction set, further selection gain can be achieved most efficiently by massively expanding its size. Thus, with increasing budget, reducing the costs for producing a DH line becomes increasingly crucial for successfully exploiting the benefits of GS.