Abstract: The European genus Ophrys (Orchidaceae) is famous for its insect-like floral morphology, an adaptation for pseudocopulatory pollination strategy involving Hymenoptera males. A large number of endemic Ophrys species have recently been described, especially within the Mediterranean Basin, one of the major species-diversity hotspots. Subtle morphological variations and specific pollinator dependence are the two main perceptible criteria for describing numerous endemic taxa. However, the degree to which endemics differ genetically remains a challenging question. In addition, the knowledge of factors potentially underlying the emergence of such endemic entities is limited.
In order to bring new insights to speciation processes in Ophrys, we test species boundaries in the Fly Orchid group (O. insectifera sensu lato) considering morphological, ecological and genetic evidence. Classically, authors recognize one widespread taxon (O. insectifera) and two endemics (O. aymoninii from France and O. subinsectifera from Spain). Our research is the first to identify clear morphological and ecological segregating factors among these taxa. However, species show limited genetic differentiation, as evidenced by gene sequencing and AFLP genotyping. Still, our results show weak but noticeable phylogeographic clustering that partially correlates with the described species. In particular, we report several isolated haplotypes and genetic clusters in central and south-eastern Europe.
Abstract: Introgression of sequences from crop species in wild relatives is of fundamental and practical concern. Here, we address gene flow between cultivated wheat and its widespread polyploid relative, Aegilops triuncialis, using 12 EST-SSR markers mapped on wheat chromosomes. The presence of wheat diagnostic alleles in natural populations of the barbed goatgrass growing in proximity to cultivated fields highlights that substantial gene flow occurred when both species coexisted. Furthermore, loci from the A subgenome of wheat were significantly less introgressed than sequences from other subgenomes, indicating differential introgression into Ae. triuncialis. Gene flow between such species sharing nonhomeologous chromosomes addresses the evolutionary outcomes of hybridization and may be important for efficient gene containment.
Abstract: Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic
genome evolution. Among eukaryotes, polyploidy has likely had the largest evolutionary
impact on vascular plants where many contemporary species are of recent polyploid origin.
Genomic analyses have uncovered evidence of at least one round of polyploidy in the
ancestry of most plants, fueling speculation that genome duplications lead to increases in net
diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that
recently-formed polyploid species have higher extinction rates than their diploid relatives.
These results suggest that despite leaving a substantial legacy in plant genomes, only rare
polyploids survive over the long term and most are evolutionary dead-ends.
Abstract: Aim: To predict the fate of alpine interactions involving specialised species, using a
monophagous beetle and its host-plant as a case study. Location: The Alps.
Methods: We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host-plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from the Shape theory that we use for the first time in comparative phylogeography. Finally, we simulated recolonisation of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonisation process as well as dispersal capacities of associated species could explain the observed pattern. Results: Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice-based model suggested these empirical patterns arose during or soon after recolonisation, long after the estimated origin of the interaction ca. 0.5 million years ago. Conclusion: Species-specific interactions are scarce in alpine habitats because glacial cycles have limited opportunities for coevolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are concerted at large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host-dependence of the beetle that locally limits the establishment of dispersing insects.
Notes: Notes: * These authors contributed equally to this work
Abstract: We briefly introduce R2G2, an R CRAN package to visualize spatially-explicit biological data within the Google Earth interface. Our package combines a collection of basic graph-editing features, including automated placement of dots, segments, polygons, images (including graphs produced with R), along with several complex three-dimensional (3D) representations such as phylogenies, histograms, and pie charts. We briefly present some example datasets and show the immediate benefits in communication gained from using the Google Earth interface to visually explore biological results. The package is distributed with detailed help pages providing examples and annotated source scripts with the hope that users will have an easy time using and further developing this package. R2G2 is distributed on http://cran.r-project.org/web/packages.
Abstract: Deschampsia littoralis is an endemic tetraploid
Poaceae occurring on the shores of pre-Alpine lakes. It is
closely related to the diploid and widespread D. cespitosa.
Several D. littoralis populations from Lake Constance are
vegetatively propagating through pseudoviviparous spik-
elets. These latter populations were formerly described as a
separate species, D. rhenana. Still, the species status of
D. rhenana has been questioned since, apart from
pseudovivipary, no morphological differentiation from
D. littoralis is observed. Both species are highly endan-
gered and accurate assessment of taxon status is needed for
conservation management. We used ampliï¬ed fragment
length polymorphism ï¬ngerprinting to assess whether
D. rhenana from Lake Constance (43 specimens) was
genetically differentiated from D. littoralis (11 specimens
collected at Lac de Joux, incl. Lac Brenet) and the wide-
spread D. cespitosa (48 specimens). An analysis of
molecular variance (AMOVA) showed that 12 % of the
genetic diversity occurred among the three species, 7 %
occurred among populations within species and 81 %
within populations. Principal coordinate analysis and fuzzy
c-means clustering showed that D. rhenana was genetically
distinct from D. littoralis. In addition, both species differed in
levels of genetic diversity and clustering, with D. rhenana
being the most divergent and structured species.
D. littoralis appeared as genetically intermediate between
D. rhenana and D. cespitosa. These results suggested that
(1) all species are closely related, (2) genetic variation
within populations is high even in the asexually propa-
gating D. rhenana and (3) D. rhenana is more distinct from
D. cespitosa than is D. littoralis. We therefore suggest to
treat D. rhenana from Lake Constance and D. littoralis
from Lac de Joux as independent evolutionary units in
conservation management.
Abstract: Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies have investigated spontaneous gene flow among wild and domesticated <i>Prunus</i> species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild <i>Prunus</i> species is needed. Combining nuclear and chloroplastic microsatellites, we investigated gene flow and hybridization among two key almond tree species, the cultivated <i>P. dulcis</i> and one of the most widespread wild relative <i>P. orientalis</i> in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetrical gene flow between the domesticated <i>P. dulcis</i> and the wild <i>P. orientalis</i>. These results were discussed in light of cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad-hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the Western Mediterranean.
Abstract: Background
Within the Coleoptera, the largest order in the animal kingdom, the exclusively herbivorous Chrysomelidae are recognized as one of the most species rich beetle families. The evolutionary processes that have fueled radiation into the more than thirty-five thousand currently recognized leaf beetle species remain partly unresolved. The prominent role of leaf beetles in the insect world, their omnipresence across all terrestrial biomes and their economic importance as common agricultural pest organisms make this family particularly interesting for studying the mechanisms that drive diversification. Here we specifically focus on two ecotypes of the alpine leaf beetle Oreina speciosissima (Scop.), which have been shown to exhibit orphological differences in male genitalia roughly corresponding to the subspecies Oreina speciosissima sensu stricto and Oreina speciosissima troglodytes. In general the two ecotypes segregate along an elevation gradient and by host plants: Oreina speciosissima sensu stricto colonizes high forb vegetation at low altitude and Oreina speciosissima troglodytes is found in stone run vegetation at higher elevations. Both host plants and leaf beetles have a patchy geographical distribution. Through use of gene sequencing and genome fingerprinting (AFLP) we analyzed the genetic structure and habitat use of Oreina speciosissima populations from the Swiss Alps to examine whether the two ecotypes have a genetic basis. By investigating a wide range of altitudes and focusing on the structuring effect of habitat types, we aim to provide answers regarding the factors that drive adaptive radiation in this phytophagous leaf beetle.
Results
While little phylogenetic resolution was observed based on the sequencing of four DNA regions, the topology and clustering resulting from AFLP genotyping grouped specimens according to their habitat, mostly defined by plant associations. A few specimens with intermediate morphologies clustered with one of the two ecotypes or formed separate clusters consistent with habitat differences. These results were discussed in an ecological speciation framework.
Conclusions
The question of whether this case of ecological differentiation occurred in sympatry or allopatry remains open. Still, the observed pattern points towards ongoing divergence between the two ecotypes which is likely driven by a recent shift in host plant use.
Notes: * These authors contributed equally to this work
Abstract: We used experimental cattle ungrazed and grazed sites to evaluate what impact different intensities of cattle grazing have on deer mice (<i>Peromyscus maniculatus</i> Wagner, 1845) and meadow voles (<i>Microtus pennsylvanicus</i> Ord, 1815). Live-trapping of these small rodents was conducted on paired treatment plots (grazed and ungrazed) at Sheep River Provincial Park in South-western Alberta, Canada. Before grazing started, both rodent species were equally abundant in either grazed or ungrazed sites. Introduction of grazing resulted in strong, but differing responses by both rodent species. Deer mice had higher population density in the grazed than in ungrazed plots, but their body mass was negatively correlated with increasing grazing pressure. Meadow voles were more heavily affected by grazing as a strong avoidance of cattle-grazed plots was observed already at low grazing intensity. In addition, cattle grazing had noticeable effects, impacting the survival, sex and age ratio and the ectoparasite prevalence of these two rodent populations. We conclude that there are diverse and different levels of impact of cattle grazing on those two rodents, leading to much more complex species interactions than previously thought. We suggest that the presence/absence, density and body condition of small mammals could be used as a tool for ecosystem health assessment.
Abstract: Aquatic plants, and especially the emblematic genus Baldellia (Alismataceae), are among the most threatened organisms, due to unprecedented human-driven habitat destructions. Therefore protection plans are crucially needed and call for thoroughly documenting the genetic diversity and clarifying the taxonomy of this endangered genus. Our sampling included 282 individuals from 42 natural populations and covered the whole geographical range of the genus, across Europe and the Mediterranean. We combined sequencing of nuclear internal transcribed spacer (ITS) and chloroplastic trnL-ndhF regions with amplified fragment length polymorphism (AFLP) genotyping to investigate the Alismataceae phylogeny, and produce a phylogeography of Baldellia. Our phylogeny strongly supported the monophyly of Baldellia and placed it as the sister clade to Luronium and Alisma, therefore excluding, as previously supposed, a close genetic relatedness to the predominantly neotropical genus Echinodorus. The phylogeography of Baldellia outlined patterns consistent with a hypothesis considering glacial refugia located in the Iberian Peninsula and the Italy/Balkan region from which two distinct genetic lineages re-colonized Europe. These two lineages corresponded respectively to Baldellia ranunculoides (Italy/Balkan derived populations) and Baldellia repens (populations recovered from the Iberian Peninsula refuge), therefore supporting differences outlined between the two taxa in previous ecological and morphological studies. These results allowed clarifying taxonomic uncertainties by confirming the genetic distinctness of B. repens according to B. ranunculoides. A third lineage, Baldellia alpestris, originated and remained endemic to the mountainous regions of the Iberian Peninsula. Unexpectedly, B. repens populations collected in northern Africa, appeared to be genetically distinct from their European counterparts, this calls for further investigation to fully address their genetic and conservation status. Finally, we detected a large hybridization zone in northwestern Europe between B. repens and B. ranunculoides. These results were discussed in light of conservation approaches for Baldellia populations.
Abstract: Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.
Abstract: This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species. *We combined chloroplast DNA (cpDNA) sequencing, analysed using statistical parsimony network, with nonhierarchical K-means clustering of amplified fragment length polymorphism (AFLP) genotyping, to unravel patterns of genetic structure across the native range of Ae. geniculata. The AFLP dataset was further explored by measurement of the regional genetic diversity and the detection of isolation by distance patterns. *Both cpDNA and AFLP suggest an eastern Mediterranean origin of Ae. geniculata. Two lineages have spread independently over northern and southern Mediterranean areas. Northern populations show low genetic diversity but strong phylogeographical structure among the main peninsulas, indicating a major influence of glacial cycles. By contrast, low genetic structuring and a high genetic diversity are detected in southern Mediterranean populations. Finally, we highlight human-mediated dispersal resulting in substantial introgression between resident and migrant populations. *We have shown that the evolutionary trajectories of ruderal plants can be similar to those of wild species, but are interfered by human activities, promoting range expansions through increased long-distance dispersal and the creation of suitable habitats.
Abstract: Aimâ
Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersalâextinctionâcladogenesis (DEC), against a parsimony-based method, dispersalâvicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.
Locationâ
World-wide.
Methodsâ
Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years.
Resultsâ
Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events â which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node.
Main conclusionsâ
By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.
Abstract: The alpine white-flowered buttercup, Ranunculus kuepferi Greuter & Burdet, is a polyploid complex with diploids endemic to the southwestern Alps and polyploids - which have been previously described as apomictic - widespread throughout European mountains. Due to the polymorphic status of both its ploidy level and its reproductive mode, R. kuepferi represents a key species for understanding the evolution of polyploid lineages in alpine habitats. To disentangle the phylogeography of this polyploid taxon, we used cpDNA sequences and AFLP (amplified fragment length polymorphism) markers in 33 populations of R. kuepferi representative of its ploidy level and distribution area. Polyploid individuals were shown to be the result of at least two polyploidization events that may have taken place in the southwestern Alps. From this region, one single main migration of tetraploids colonized the entire Alpine range, the Apennines and Corsica. Genetic recombination among tetraploids was also observed, revealing the facultative nature of the apomictic reproductive mode in R. kuepferi polyploids. Our study shows the contrasting role played by diploid lineages mostly restricted to persistent refugia and by tetraploids, whose dispersal abilities have permitted their range extension all over the previously glaciated Alpine area and throughout neighbouring mountain massifs.
Abstract: Since the transfer and application of modern sequencing technologies to the analysis of amplified fragment-length polymorphisms (AFLP), evolutionary biologists have included an increasing number of samples and markers in their studies. Although justified in this context, the use of automated scoring procedures may result in technical biases that weaken the power and reliability of further analyses.
Using a new scoring algorithm, RawGeno, we show that scoring errors--in particular "bin oversplitting" (i.e. when variant sizes of the same AFLP marker are not considered as homologous) and "technical homoplasy" (i.e. when two AFLP markers that differ slightly in size are mistakenly considered as being homologous)--induce a loss of discriminatory power, decrease the robustness of results and, in extreme cases, introduce erroneous information in genetic structure analyses. In the present study, we evaluate several descriptive statistics that can be used to optimize the scoring of the AFLP analysis, and we describe a new statistic, the information content per bin (Ibin) that represents a valuable estimator during the optimization process. This statistic can be computed at any stage of the AFLP analysis without requiring the inclusion of replicated samples. Finally, we show that downstream analyses are not equally sensitive to scoring errors. Indeed, although a reasonable amount of flexibility is allowed during the optimization of the scoring procedure without causing considerable changes in the detection of genetic structure patterns, notable discrepancies are observed when estimating genetic diversities from differently scored datasets.
Our algorithm appears to perform as well as a commercial program in automating AFLP scoring, at least in the context of population genetics or phylogeographic studies. To our knowledge, RawGeno is the only freely available public-domain software for fully automated AFLP scoring, from electropherogram files to user-defined working binary matrices. RawGeno was implemented in an R CRAN package (with an user-friendly GUI) and can be found at http://sourceforge.net/projects/rawgeno.
Abstract: The emergence of comparative phylogeography requires tools that allow comparing quantitatively the genetic structures between species. Whereas numerous methods have been developed to compare trees inferred from two species, comparison methods involving population structures issued from Bayesian inferences or maximum likelihood criterion have been poorly investigated. Here, we present a method implemented in an r (CRAN) scripts collection, SIMIL, based on the mean absolute differences computed from structure 2 outputs. The scripts collection is illustrated by the computation of unweighted and weighted genetic-structure-similarity (GSS) indices in three alpine plants. Different weighting procedures â taking into account the level of overlap between the species sampling areas â are compared among the different species pairs and among the different numbers of gene pools considered in structure.
Abstract: Gene flow from crops to wild relatives by sexual reproduction is one of the major issues in risk assessment for the cultivation of genetically engineered (GE) plants. The main factors which influence hybridization and introgression, the two processes of gene flow, as well as the accompanying containment measures of the transgene, are reviewed. The comparison of risks between Switzerland and Europe highlights the importance of regional studies. Differences were assessed for barley, beet and wheat. Moreover, transgene flow through several wild species acting as bridge (bridge species) has been up to now poorly investigated. Indeed, transgene flow may go beyond the closest wild relative, as in nature several wild species complexes hybridize. Its importance is assessed by several examples in Poaceae. Finally, the transgene itself has genetic and ecological consequences that are reviewed. Transgenic hybrids between crops and wild relatives may have lower fitness than the wild relatives, but in several cases, no cost was detected. On the other hand, the transgene provides advantages to the hybrids, in the case of selective value as a Bt transgene in the presence of herbivores. Genetic and ecological consequences of a transgene in a wild species are complex and depend on the type of transgene, its insertion site, the density of plants and ecological factors. More studies are needed for understanding the short and long term consequences of escape of a transgene in the wild.
Abstract: The genus Vitis is represented by several coexisting species in Europe. Our study focuses on naturalised rootstocks that originate in viticulture. The consequences of their presence to the landscape and to native European species (Vitis vinifera ssp. silvestris) are evaluated. This study compares ecological traits (seven qualitative and quantitative descriptors) and the genetic diversity (10 SSR markers) of populations of naturalised rootstocks and native wild grapevines. 18 large naturalised rootstock populations were studied in the Rhône watershed. Wild European grapevines are present in four main habitats (screes, alluvial forests, hedges, and streamside hedges). In contrast, naturalised rootstock populations are mainly located in alluvial forests, but they clearly take advantage of alluvial system dynamics and connectivity at the landscape level. These latter populations appear to reproduce sexually, and show a higher genetic diversity than Vitis vinifera ssp. silvestris. The regrouping of naturalised rootstocks in interconnected populations tends to create active hybrid swarms of rootstocks. The rootstocks show characters of invasive plants. The spread of naturalised rootstocks in the environment, the acceleration of the decline of the European wild grapevine, and the propagation of genes of viticultural interest in natural populations are potential consequences that should be kept in mind when undertaking appropriate management measures.
Abstract: Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including for instance population genomics, phylogeography and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e. the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, vizualizing and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (i) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems, (ii) performing quality checks, (iii) defining bins and proceeding to scoring, (iv) filtering non-optimal bins and (v) exporting results in different formats.
DOI 
