Genomic pattern of adaptive divergence in Arabidopsis halleri, a model species for tolerance to heavy metal

The Serum Levels of the Heavy Metals Cu, Zn, Cd, and Pb and Progression of COPD-A Preliminary Study

There is evidence in previous studies that high levels of heavy metals may play a key role in the development of COPD due to the induction of chronic inflammation and oxidative stress. In this preliminary study, we used atomic absorption spectrophotometry to measure the levels of four heavy metals (Cu, Zn, Cd, and Pb) in blood serum of COPD patients and controls over 2 years. Clinical data on disease progression or absence were collected in patients living in the industrial region of Stara Zagora, Bulgaria. The mean values of Cu in the serum of patients with COPD and the control group were 374.29 ± 15.03 μg/L and 238.55 ± 175.31 μg/L, Zn—2010.435 ± 670.006 μg/L and 1672.78 ± 934.27 μg/L, Cd—0.334 ± 0.0216 μg/L and 0.395 ± 0.110 μg/L and Pb—0.0732 ± 0.009 μg/L and 0.075 ± 0.0153 μg/L. This is probably because these elements are biogenic and are used in the body for its anti-oxidant protection. In fact, it cannot be stated with certainty that elevated levels of Cu and Zn in the environment have a negative impact in COPD patients. There was a trend towards higher levels of the toxicants lead and cadmium in COPD patients compared to the control group of patients. There is a statistically unproven trend toward higher levels of lead and cadmium in COPD patients compared to controls, which to some extent supports our hypothesis that there is a relationship between environmental lead and cadmium levels and the COPD manifested. In COPD patients, a positive correlation was found between BMI and serum Cu levels (r = 0.413, p = 0.005). A higher concentration of serum Cu was found in men with BMI ≥ 30, compared to those with BMI < 30. There is also a positive correlation to a lesser extent between CRP and cadmium (r = 0.380; p = 0.019) and lead (r = 0.452; p = 0.004). The correlation of lead and cadmium with PSA also shows that these elements may also be associated with the presence of inflammatory processes. A significant negative correlation exists between Pb in the serum of patients with COPD and their blood hemoglobin (r = −356; p = 0.028). The results of our study suggest that higher doses of the trace elements Cu and Zn do not always have a negative effect in patients with COPD, while the toxicants Pb and Cd may be involved in COPD exacerbation and can be used as prognostic biomarkers for progression. Further studies are warranted to confirm these preliminary results.

Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot

Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with "resident" species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.

Can zinc pollution promote adaptive evolution in plants? Insights from a one-generation selection experiment

Human activities generate environmental stresses that can lead plant populations to become extinct. Population survival would require the evolution of adaptive responses that increase tolerance to these stresses. Thus, in pseudometallophyte species that have colonized anthropogenic metalliferous habitats, the evolution of increased metal tolerance is expected in metallicolous populations. However, the mechanisms by which metal tolerance evolves remain unclear. In this study, parent populations were created from non-metallicolous families of Noccaea caerulescens. They were cultivated for one generation in mesocosms and under various levels of zinc (Zn) contamination to assess whether Zn in soil represents a selective pressure. Individual plant fitness estimates were used to create descendant populations, which were cultivated in controlled conditions with moderate Zn contamination to test for adaptive evolution in functional traits. The number of families showing high fitness estimates in mesocosms was progressively reduced with increasing Zn levels in soil, suggesting increasing selection for metal tolerance. In the next generation, adaptive evolution was suggested for some physiological and ecological traits in descendants of the most exposed populations, together with a significant decrease of Zn hyperaccumulation. Our results confirm experimentally that Zn alone can be a significant evolutionary pressure promoting adaptive divergence among populations.

Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: The case of zinc hyperaccumulation in Arabidopsis halleri

Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here, we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and nonmetalliferous sampling sites in southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic subregions, rather than to ecological types (i.e., metallicolous vs. nonmetallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some nonmetallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and nonmetallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and nonmetalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways-towards higher levels at nonmetalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.

Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri

Zinc (Zn) hyperaccumulation and hypertolerance are highly variable traits in Arabidopsis halleri. Metallicolous populations have evolved from nearby nonmetallicolous populations in multiple independent adaptation events. To determine whether these events resulted in similar or divergent adaptive strategies to high soil Zn concentrations, we compared two A. halleri metallicolous populations from distant genetic units in Europe (Poland (PL22) and Italy (I16)). The ionomic (Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES)) and transcriptomic (RNA sequencing (RNA-Seq)) responses to growth at 5 and 150 μM Zn were analyzed in root and shoot tissues to examine the contribution of the geographic origin and treatment to variation among populations. These analyses were enabled by the generation of a reference A. halleri transcriptome assembly. The genetic unit accounted for the largest variation in the gene expression profile, whereas the two populations had contrasting Zn accumulation phenotypes and shared little common response to the Zn treatment. The PL22 population displayed an iron deficiency response at high Zn in roots and shoots, which may account for higher Zn accumulation. By contrast, I16, originating from a highly Zn-contaminated soil, strongly responded to control conditions. Our data suggest that distinct mechanisms support adaptation to high Zn in soils among A. halleri metallicolous populations.

Divergent biology of facultative heavy metal plants

Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current literature favours the idea that hyperaccumulation of heavy metals serves plants as deterrent against attack by feeding animals (termed elemental defense hypothesis). The capability to hyperaccumulate heavy metals in A. halleri and N. caerulescens is achieved by duplications and alterations of the cis-regulatory properties of genes coding for heavy metal transporting/excreting proteins. Several metallophytes have developed ecotypes with a varying content of such heavy metal transporters as an adaption to the specific toxicity of a heavy metal site.

Genomic studies of adaptive evolution in outcrossing Arabidopsis species

Large-scale population genomic approaches have very recently been fruitfully applied to the Arabidopsis relatives Arabidopsis halleri, A. lyrata and especially A. arenosa. In contrast to A. thaliana, these species are obligately outcrossing and thus the footprints of natural selection are more straightforward to detect. Furthermore, both theoretical and empirical studies indicate that outcrossers are better able to evolve in response to selection pressure. As a result, recent work in these species serves as a paradigm of population genomic studies of adaptation both to environmental as well as intracellular challenges.

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex

Metal hyperaccumulation is an uncommon but highly distinctive adaptation found in certain plants that can grow on metalliferous soils. Here we review what is known about evolution of metal hyperaccumulation in plants and describe a population-genetic analysis of the Alyssum serpyllifolium (Brassicaceae) species complex that includes populations of nickel-hyperaccumulating as well as non-accumulating plants growing on serpentine (S) and non-serpentine (NS) soils, respectively. To test whether the S and NS populations belong to the same or separate closely related species, we analysed genetic variation within and between four S and four NS populations from across the Iberian peninsula. Based on microsatellites, genetic variation was similar in S and NS populations (average Ho=0.48). The populations were significantly differentiated from each other (overall FST=0.23), and the degree of differentiation between S and NS populations was similar to that within these two groups. However, high S versus NS differentiation was observed in DNA polymorphism of two genes putatively involved in adaptation to serpentine environments, IREG1 and NRAMP4, whereas no such differentiation was found in a gene (ASIL1) not expected to play a specific role in ecological adaptation in A. serpyllifolium. These results indicate that S and NS populations belong to the same species and that nickel hyperaccumulation in A. serpyllifolium appears to represent a case of adaptation to growth on serpentine soils. Further functional and evolutionary genetic work in this system has the potential to significantly advance our understanding of the evolution of metal hyperaccumulation in plants.

Potential preadaptation to anthropogenic pollution: evidence from a common quantitative trait locus for zinc and cadmium tolerance in metallicolous and nonmetallicolous accessions of Arabidopsis halleri

As a drastic environmental change, metal pollution may promote the rapid evolution of genetic adaptations contributing to metal tolerance. In Arabidopsis halleri, genetic bases of zinc (Zn) and cadmium (Cd) tolerance have been uncovered only in a metallicolous accession, although tolerance is species-wide. The genetic determinants of Zn and Cd tolerance in a nonmetallicolous accession were thus investigated for the first time. The genetic architecture of tolerance was investigated in a nonmetallicolous population (SK2) by using first backcross progeny obtained from crosses between SK2 and Arabidopsis lyrata petraea, a nonmetallophyte species. Only one significant and common quantitative trait locus (QTL) region was identified explaining 22.6% and 31.2% of the phenotypic variation for Zn and Cd tolerance, respectively. This QTL co-localized with HEAVY METAL ATPASE 4 (AhHMA4), which was previously validated as a determinant of Zn and Cd tolerance in a metallicolous accession. Triplication and high expression of HMA4 were confirmed in SK2. In contrast, gene duplication and high expression of METAL TOLERANT PROTEIN 1A (MTP1A), which was previously associated with Zn tolerance in a metallicolous accession, were not observed in SK2. Overall, the results support the role of HMA4 in tolerance capacities of A. halleri that may have pre-existed in nonmetallicolous populations before colonization of metal-polluted habitats. Preadaptation to metal-contaminated sites is thus discussed.

AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect

Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies.

Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China

Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies.

Lower selfing rates in metallicolous populations than in non-metallicolous populations of the pseudometallophyte Noccaea caerulescens (Brassicaceae) in Southern France

BACKGROUND AND AIMS

The pseudometallophyte Noccaea caerulescens is an excellent model to study evolutionary processes, as it grows both on normal and on heavy-metal-rich, toxic soils. The evolution and demography of populations are critically impacted by mating system and, yet, information about the N. caerulescens mating system is limited.

METHODS

Mean selfing rates were assessed using microsatellite loci and a robust estimation method (RMES) in five metallicolous and five non-metallicolous populations of N. caerulescens in Southern France, and this measure was replicated for two successive reproductive seasons. As a part of the study, the patterns of gene flow among populations were analysed. The mating system was then characterized at a fine spatial scale in three populations using the MLTR method on progeny arrays.

KEY RESULTS

The results confirm that N. caerulescens has a mixed mating system, with selfing rates ranging from 0·2 to 0·5. Selfing rates did not vary much among populations within ecotypes, but were lower in the metallicolous than in the non-metallicolous ecotype, in both seasons. Effective population size was also lower in non-metallicolous populations. Biparental inbreeding was null to moderate. Differentiation among populations was generally high, but neither ecotype nor isolation by distance explained it.

CONCLUSIONS

The consequences of higher selfing rates on adaptation are expected to be weak to moderate in non-metallicolous populations and they are expected to suffer less from inbreeding depression, compared to metallicolous populations.

Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain

The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty-four samples from 17 locations from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of positive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair-wise genetic distance of the AFLP dataset and AFLP-positive outliers dataset. AFLP-positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.

Genetic structure of Mugil cephalus L. populations from the northern coast of Egypt

AIM

The gray mullet, Mugil cephalus, has been farmed in semi-intensive ponds with tilapia and carps in Egypt for years. The current study used the fluorescent amplified fragment length polymorphism (F-AFLP) technique to search for genetic differences between the populations of M. cephalus in the northern region of Egypt and to detect the gene flow between sampled locations and the homogeneity within M. cephalus genetic pool in Egypt.

MATERIALS AND METHODS

To fulfill the study objectives 60 (15/location) samples were collected from four northern coast governorates of Egypt (Alexandria "sea," Kafr El-Sheikh "farm," Damietta "farm" and Port Said "sea"). Three replicates of bulked DNA (5 samples/replicate) for each location were successfully amplified using the standard AFLP protocol using fluorescent primers. DNA polymorphism, genetic diversity, and population structure were assessed while positive outlier loci were successfully detected among the sampled locations. Based on the geographical distribution of sampling sites, the gene flow, the genetic differentiation, and correlations to sampling locations were estimated.

RESULTS

A total of 1890 polymorphic bands were scored for all locations, where 765, 1054, 673, and 751 polymorphic bands were scored between samples from Alexandria, Kafr El-Sheikh, Damietta and Port Said, respectively. The effective number of alleles (ne) for all bulked samples combined together was 1.42. The expected heterozygosity under Hardy-Weinberg assumption (He) for all bulked samples combined together was 0.28. Bulked samples from Damietta yielded the lowest ne (1.35) and the lowest He (0.23) when inbreeding coefficient (FIS) = 1. Bulked samples from Kafr El-Sheikh scored the highest ne (1.55) and the highest He (0.37). Bulked samples from Alexandria scored 1.40 for ne and 0.26 for He, while bulked samples from Port Said scored 1.39 for ne and 0.26 for He. The observed bulked samples formed three sub-population groups, where none is limited to a certain sampling location. A high differentiation among locations was detected, however, is not fully isolating the locations. Gene flow was 0.58. Positive outliers loci (117) were detected among the four sampled locations while weak significant correlation (r=0.15, p=0.03) was found for the distance between them.

CONCLUSION

Even though this species is cultivated in Egypt, the wild population is still present and by the current study a flow of its genes is still exchanged through the northern coast of Egypt. Which contribute to the cultivated populations leading to heterogeneity in its genetic pool and consequently affects the production consistency of M. cephalus in Egypt.

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

A more complete picture of metal hyperaccumulation through next-generation sequencing technologies

The mechanistic understanding of metal hyperaccumulation has benefitted immensely from the use of molecular genetics tools developed for Arabidopsis thaliana. The revolution in DNA sequencing will enable even greater strides in the near future, this time not restricted to the family Brassicaceae. Reference genomes are within reach for many ecologically interesting species including heterozygous outbreeders. They will allow deep RNA-seq transcriptome studies and the re-sequencing of contrasting individuals to unravel the genetic basis of phenotypic variation. Cell-type specific transcriptome analyses, which will be essential for the dissection of metal translocation pathways in hyperaccumulators, can be achieved through the combination of RNA-seq and translatome approaches. Affordable high-resolution genotyping of many individuals enables the elucidation of quantitative trait loci in intra- and interspecific crosses as well as through genome-wide association mapping across large panels of accessions. Furthermore, genome-wide scans have the power to detect loci under recent selection. Together these approaches will lead to a detailed understanding of the evolutionary path towards the emergence of hyperaccumulation traits.

Taxonomy and systematics are key to biological information: Arabidopsis, Eutrema (Thellungiella), Noccaea and Schrenkiella (Brassicaceae) as examples

Taxonomy and systematics provide the names and evolutionary framework for any biological study. Without these names there is no access to a biological context of the evolutionary processes which gave rise to a given taxon: close relatives and sister species (hybridization), more distantly related taxa (ancestral states), for example. This is not only true for the single species a research project is focusing on, but also for its relatives, which might be selected for comparative approaches and future research. Nevertheless, taxonomical and systematic knowledge is rarely fully explored and considered across biological disciplines. One would expect the situation to be more developed with model organisms such as Noccaea, Arabidopsis, Schrenkiella and Eutrema (Thellungiella). However, we show the reverse. Using Arabidopsis halleri and Noccaea caerulescens, two model species among metal accumulating taxa, we summarize and reflect past taxonomy and systematics of Arabidopsis and Noccaea and provide a modern synthesis of taxonomic, systematic and evolutionary perspectives. The same is presented for several species of Eutrema s. l. and Schrenkiella recently appeared as models for studying stress tolerance in plants and widely known under the name Thellungiella.

Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae)

The present study investigated the genetic diversity, population structure, F_ST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

Contrasting patterns of genetic divergence in two sympatric pseudo-metallophytes: Rumex acetosa L. and Commelina communis L

BACKGROUND

Patterns of genetic divergence between populations of facultative metallophytes have been investigated extensively. However, most previous investigations have focused on a single plant species making it unclear if genetic divergence shows common patterns or, conversely, is species-specific. The herbs Rumex acetosa L. and Commelina communis L. are two pseudo-metallophytes thriving in both normal and cupriferous soils along the middle and lower reaches of the Yangtze River in China. Their non-metallicolous and metallicolous populations are often sympatric thus providing an ideal opportunity for comparative estimation of genetic structures and divergence under the selective pressure derived from copper toxicity.

RESULTS

In the present study, patterns of genetic divergence of R. acetosa and C. communis , including metal tolerance, genetic structure and genetic relationships between populations, were investigated and compared using hydroponic experiments, AFLP, ISSR and chloroplast genetic markers. Our results show a significant reduction in genetic diversity in metallicolous populations of C. communis but not in R. acetosa . Moreover, genetic differentiation is less in R. acetosa than in C. communis , the latter species also shows a clustering of its metallicolous populations.

CONCLUSIONS

We propose that the genetic divergences apparent in R. acetosa and C. communis , and the contrasting responses of the two species to copper contamination, might be attributed to the differences in their intrinsic physiological and ecological properties. No simple and generalised conclusions on genetic divergence in pseudo-metallophytes can thus be drawn.

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

Genome scans have become a common approach to identify genomic signatures of natural selection and reproductive isolation, as well as the genomic bases of ecologically relevant phenotypes, based on patterns of polymorphism and differentiation among populations or species. Here, we review the results of studies taking genome scan approaches in plants, consider the patterns of genomic differentiation documented and their possible causes, discuss the results in light of recent models of genomic differentiation during divergent adaptation and speciation, and consider assumptions and caveats in their interpretation. We find that genomic regions of high divergence generally appear quite small in comparisons of both closely and more distantly related populations, and for the most part, these differentiated regions are spread throughout the genome rather than strongly clustered. Thus, the genome scan approach appears well-suited for identifying genomic regions or even candidate genes that underlie adaptive divergence and/or reproductive barriers. We consider other methodologies that may be used in conjunction with genome scan approaches, and suggest further developments that would be valuable. These include broader use of sequence-based markers of known genomic location, greater attention to sampling strategies to make use of parallel environmental or phenotypic transitions, more integration with approaches such as quantitative trait loci mapping and measures of gene flow across the genome, and additional theoretical and simulation work on processes related to divergent adaptation and speciation.

Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance, Arabidopsis halleri (Brassicaceae)

Arabidopsis halleri is a pseudometallophyte involved in numerous molecular studies of the adaptation to anthropogenic metal stress. In order to test the representativeness of genetic accessions commonly used in these studies, we investigated the A. halleri population genetic structure in Europe. Microsatellite and nucleotide polymorphisms from the nuclear and chloroplast genomes, respectively, were used to genotype 65 populations scattered over Europe. The large-scale population structure was characterized by a significant phylogeographic signal between two major genetic units. The localization of the phylogeographic break was assumed to result from vicariance between large populations isolated in southern and central Europe, on either side of ice sheets covering the Alps during the Quaternary ice ages. Genetic isolation was shown to be maintained in western Europe by the high summits of the Alps, whereas admixture was detected in the Carpathians. Considering the phylogeographic literature, our results suggest a distinct phylogeographic pattern for European species occurring in both mountain and lowland habitats. Considering the evolution of metal adaptation in A. halleri, it appears that recent adaptations to anthropogenic metal stress that have occurred within either phylogeographic unit should be regarded as independent events that potentially have involved the evolution of a variety of genetic mechanisms.

Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing

AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier detection with 454 sequencing of AFLP fragments to obtain sequences from outlier loci. We applied this approach to the study of resistance to Bacillus thuringiensis israelensis (Bti) toxins in the dengue vector Aedes aegypti. A genome scan of Bti-resistant and Bti-susceptible A. aegypti laboratory strains was performed based on 432 AFLP markers. Fourteen outliers were detected using two different population genetic algorithms. Out of these, 11 were successfully sequenced. Three contained transposable elements (TEs) sequences, and the 10 outliers that could be mapped at a unique location in the reference genome were located on different supercontigs. One outlier was in the vicinity of a gene coding for an aminopeptidase potentially involved in Bti toxin-binding. Patterns of sequence variability of this gene showed significant deviation from neutrality in the resistant strain but not in the susceptible strain, even after taking into account the known demographic history of the selected strain. This gene is a promising candidate for future functional analysis.

DETSEL: an R-package to detect marker loci responding to selection

In the new era of population genomics, surveys of genetic polymorphism ("genome scans") offer the opportunity to distinguish locus-specific from genome-wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DETSEL has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations. Recently, two major improvements have been made: the analysis of dominant markers is now supported, and the estimation of empirical P-values has been implemented. These features, which are described below, have been incorporated into an R package, which replaces the stand-alone DETSEL software package.

Two methods to easily obtain nucleotide sequences from AFLP loci of interest

Genome scans based on anonymous Amplified Fragment Length Polymorphism (AFLP) markers scattered throughout the genome are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation in natural populations. A shortcoming of this approach is that despite its efficiency to detect signatures of selection, it can hardly help pinpoint the specific genomic region(s), gene(s), or mutation(s) targeted by selection. Here, we present two methods to be undertaken after performing an AFLP-based genome scan to easily obtain the sequences of AFLP loci detected as outliers by population genomics approaches. The first one is based on the gel excision of the target AFLP fragment, after simplification of the AFLP fingerprint and separation of the fragments by migration. The second one is a combination of classical AFLP protocol and 454 pyrosequencing.

In silico fingerprinting (ISIF): a user-friendly in silico AFLP program

The Amplified fragment Length Polymorphism (AFLP) is one of the cost-effective and useful fingerprinting techniques to study non-model species. One crucial AFLP step in the AFLP procedure is the choice of restriction enzymes and selective bases providing good-quality AFLP profiles. Here, we present a user-friendly program (ISIF) that allows carrying out in silico AFLPs on species for which whole genome sequences are available. Carrying out in silico analyses as preliminary tests can help to optimize the experimental work by allowing a rapid screening of candidate restriction enzymes and the combinations of selective bases to be used. Furthermore, using in silico AFLPs is of great interest to limit homoplasy and amplification of repetitive elements to target genomic regions of interest or to optimize complex and costly high-throughput genomic experiments.

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

BACKGROUND

It is essential to understand and predict the effects of changing environments on plants. This review focuses on the sexual reproduction of plants, as previous studies have suggested that this trait is particularly vulnerable to climate change, and because a number of ecologically and evolutionarily relevant genes have been identified.

SCOPE

It is proposed that studying gene functions in naturally fluctuating conditions, or gene functions in natura, is important to predict responses to changing environments. First, we discuss flowering time, an extensively studied example of phenotypic plasticity. The quantitative approaches of ecological and evolutionary systems biology have been used to analyse the expression of a key flowering gene, FLC, of Arabidopsis halleri in naturally fluctuating environments. Modelling showed that FLC acts as a quantitative tracer of the temperature over the preceding 6 weeks. The predictions of this model were verified experimentally, confirming its applicability to future climate changes. Second, the evolution of self-compatibility as exemplifying an evolutionary response is discussed. Evolutionary genomic and functional analyses have indicated that A. thaliana became self-compatible via a loss-of-function mutation in the male specificity gene, SCR/SP11. Self-compatibility evolved during glacial-interglacial cycles, suggesting its association with mate limitation during migration. Although the evolution of self-compatibility may confer short-term advantages, it is predicted to increase the risk of extinction in the long term because loss-of-function mutations are virtually irreversible.

CONCLUSIONS

Recent studies of FLC and SCR have identified gene functions in natura that are unlikely to be found in laboratory experiments. The significance of epigenetic changes and the study of non-model species with next-generation DNA sequencers is also discussed.

Metal hyperaccumulation and hypertolerance: a model for plant evolutionary genomics

In the course of evolution, plants adapted to widely differing metal availabilities in soils and therefore represent an important source of natural variation of metal homeostasis networks. Research on plant metal homeostasis can thus provide insights into the functioning, regulation and adaptation of biological networks. Here, we describe major recent breakthroughs in the understanding of the genetic and molecular basis of metal hyperaccumulation and associated hypertolerance, a naturally selected complex trait which represents an extreme adaptation of the metal homeostasis network. Investigations in this field reveal further the molecular alterations underlying the evolution of natural phenotypic diversity and provide a highly relevant framework for comparative genomics.

Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species

It has recently been shown that the European corn borer, a major pest of maize crops, is actually composed of two genetically differentiated and reproductively isolated taxa, which are found in sympatry over a wide geographical range in Eurasia. Each taxon is adapted to specific host plants: Ostrinia nubilalis feeds mainly on maize, while O. scapulalis feeds mainly on hop or mugwort. Here, we present a genome scan approach as a first step towards an integrated molecular analysis of the adaptive genomic divergence between O. nubilalis and O. scapulalis. We analysed 609 AFLP marker loci in replicate samples of sympatric populations of Ostrinia spp. collected on maize, hop and mugwort, in France. Using two genome scan methods based on the analysis of population differentiation, we found a set of 28 outlier loci that departed from the neutral expectation in one or the other method (of which a subset of 14 loci were common to both methods), which showed a significantly increased differentiation between O. nubilalis and O. scapulalis, when compared to the rest of the genome. A subset of 12 outlier loci were sequenced, of which 7 were successfully re-amplified as target candidate loci. Three of these showed homology with annotated lepidopteran sequences from public nucleotide databases.

Genetic basis of pearl millet adaptation along an environmental gradient investigated by a combination of genome scan and association mapping

Identifying the molecular bases of adaptation is a key issue in evolutionary biology. Genome scan is an efficient approach for identifying important molecular variation involved in adaptation. Association mapping also offers an opportunity to gain insight into genotype-phenotype relationships. Using these two approaches coupled with environmental data should help to come up with a refined picture of the evolutionary process underlying adaptation. In this study, we first conducted a selection scan analysis on a transcription factor gene family. We focused on the MADS-box gene family, a gene family which plays a crucial role in vegetative and flower development. Twenty-one pearl millet populations were sampled along an environmental gradient in West Africa. We identified one gene, i.e. PgMADS11, using Bayesian analysis to detect selection signatures. Polymorphism at this gene was also associated with flowering time variation in an association mapping framework. Finally, we found that PgMADS11 allele frequencies were closely associated with annual rainfall. Overall, we determined an efficient way to detect functional polymorphisms associated with climate variation in non-model plants by combining genome scan and association mapping. These results should help monitor the impact of recent climatic changes on plant adaptation.

Amplified fragment length homoplasy: in silico analysis for model and non-model species

BACKGROUND

AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

RESULTS

In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

CONCLUSIONS

These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

Adapting genomics to study the evolution and ecology of agricultural systems

In the face of global change, agriculture increasingly requires germplasm with high yields on marginal lands. Identifying pathways that are adaptive under marginal conditions is increasingly possible with advances at the intersection of evolutionary ecology, population genetics, and functional genomics. Trait-based (reverse ecology) approaches have connected flowering time in Arabidopsis thaliana to single alleles with environment-specific effects. Similarly, genetic dissection of rice flooding tolerance enabled the production of near-isogenic lines exhibiting tolerance and high yields. An alternative gene-forward (forward ecology) approach identified candidate genes for local adaptation of Arabidopsis lyrata to heavy-metal rich soils. A global perspective on plant adaptation and trait correlations provides a foundation for breeding tolerant crops and suggests populations adapted to marginal habitats be conservation priorities.

Selection pressures have caused genome-wide population differentiation of Anthoxanthum odoratum despite the potential for high gene flow

The extent to which divergent selection can drive genome-wide population differentiation remains unclear. Theory predicts that in the face of ongoing gene flow, population differentiation should be apparent only at those markers that are directly or indirectly (i.e. through linkage) under selection. However, if reproductive barriers limit gene flow, genome-wide population differentiation may occur even in geographically proximate populations. Some insight into the link between selection and genetic differentiation in the presence of ongoing gene flow can come from long-term experiments such as The Park Grass Experiment, which has been running for over 150 years, and provides a unique example of a heterogeneous environment with a long and detailed history. Fertilizer treatments applied in the Park Grass Experiment have led to rapid evolutionary change in sweet vernal grass Anthoxanthum odoratum, but until now, nothing was known of how these changes would be reflected in neutral molecular markers. We have genotyped ten A. odoratum populations from the Park Grass Experiment using Amplified Fragment Length Polymorphisms (AFLPs). Our data show that nutrient additions have resulted in genome-wide divergence among plots despite the high potential for ongoing gene flow. This provides a well-documented example of concordance between genomes and environmental conditions that has arisen in continuous populations across a time span of fewer than 75 generations.

Variability of zinc tolerance among and within populations of the pseudometallophyte species Arabidopsis halleri and possible role of directional selection

We estimated the level of quantitative polymorphism for zinc (Zn) tolerance in neighboring metallicolous and nonmetallicolous populations of Arabidopsis halleri and tested the hypothesis that divergent selection has shaped this polymorphism. A short-term hydroponic test was used to capture the quantitative polymorphism present between edaphic types, among and within populations. We measured six morphological and physiological traits on shoots and roots to estimate the response of A. halleri to Zn. In order to assess the adaptive value of Zn tolerance polymorphism, we compared differentiation of quantitative traits with that of molecular markers. Zinc tolerance of metallicolous populations was, on average, higher than that of nonmetallicolous populations according to the morphological and physiological traits measured. Phenotypic variability within edaphic types was very high and mainly explained by polymorphism among individuals within populations. Genetic differentiation for photosystem II yield of leaves (a measure of photosynthetic efficiency) was greater than the differentiation for microsatellite and thus, probably shaped by divergent selection. Overall, these results suggest that, in the sampled populations, Zn tolerance has been increased in metallicolous populations through selection on standing genetic variation within local nonmetallicolous ancestral populations.

Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations

Background

Genome scans are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation, but on their own, they are often helpless at identifying the specific gene(s) or mutation(s) targeted by selection. This shortcoming is hopefully bound to disappear in the near future, thanks to the wealth of new genomic resources that are currently being developed for many species. In this article, we provide a foretaste of this exciting new era by conducting a genome scan in the mosquito Aedes aegypti with the aim to look for candidate genes involved in resistance to Bacillus thuringiensis subsp. israelensis (Bti) insecticidal toxins.

Results

The genome of a Bti-resistant and a Bti-susceptible strains was surveyed using about 500 MITE-based molecular markers, and the loci showing the highest inter-strain genetic differentiation were sequenced and mapped on the Aedes aegypti genome sequence. Several good candidate genes for Bti-resistance were identified in the vicinity of these highly differentiated markers. Two of them, coding for a cadherin and a leucine aminopeptidase, were further examined at the sequence and gene expression levels. In the resistant strain, the cadherin gene displayed patterns of nucleotide polymorphisms consistent with the action of positive selection (e.g. an excess of high compared to intermediate frequency mutations), as well as a significant under-expression compared to the susceptible strain.

Conclusion

Both sequence and gene expression analyses agree to suggest a role for positive selection in the evolution of this cadherin gene in the resistant strain. However, it is unlikely that resistance to Bti is conferred by this gene alone, and further investigation will be needed to characterize other genes significantly associated with Bti resistance in Ae. aegypti. Beyond these results, this article illustrates how genome scans can build on the body of new genomic information (here, full genome sequence and MITE characterization) to finally hold their promises and help pinpoint candidate genes for adaptation and speciation.