Chloroplast DNA phylogeography of European ashes,Fraxinussp. (Oleaceae): roles of hybridization and life history traits

The Role of the Hercynian Mountains of Central Europe in Shaping Plant Migration Patterns in the Pleistocene-A Review

The climatic changes that took place in Europe during the Quaternary period influenced plant habitats as well as their species and vegetation composition. In this article, biogeographical studies on Hercynian mountain plants that include data for the Alps, Carpathians, and European lowlands are reviewed in order to discuss the phylogeographical structure and divergence of the Hercynian populations from those in other European mountain ranges, Scandinavia, and lowlands. The analyzed studies show specific phylogeographical relations between the Hercynian mountains, Alps, Scandinavia, Carpathians, and European lowlands. The results also indicate that the genetic patterns of plant populations in the Hercynian Mountains may differ significantly in terms of origin. The main migration routes of species to the Hercynian ranges began in the Alps or Carpathians. Some species, such as Rubus chamaemorus L., Salix lapponum L., and Salix herbacea L., are glacial relics that may have arrived and settled in the Hercynian Mountains during the Ice Age and that survived in isolated habitats. The Hercynian Mountains are composed of various smaller mountain ranges and are a crossroads of migration routes from different parts of Europe; thus, intensive hybridization has occurred between the plant populations therein, which is indicated by the presence of several divergent genetic lines.

Expansion of Ash Dieback towards the scattered Fraxinus excelsior range of the Italian peninsula

Hymenoscyphus fraxineus, causal agent of Ash Dieback, has posed a threat to Fraxinus excelsior (common ash) in Europe since the 1990s. In south-western Europe, optimal climatic conditions for H. fraxineus become scattered and host density decreases, reducing disease spread rates. To date, the Ash Dieback agent has not been reported from southern and most of central Italy, where native F. excelsior is present as small fragmented populations. This study examines the expansion of Ash Dieback into central Italy, and it considers the consequences of further local spread with regards to the loss of F. excelsior genetic resource. Symptomatic F. excelsior were sampled from sixteen sites in northern and central Italy during 2020. Specimens were analyzed with a culturomics and a quantitative PCR approach. A bibliographic search of F. excelsior floristic reports was conducted for the creation of a detailed range map. The combined use of both techniques confirmed the presence of H. fraxineus in all the sites of central Italy where host plants were symptomatic. These new records represent the southern limit of the current known distribution of this pathogen in Italy, and together with Montenegro, in Europe. The characterization of the F. excelsior scattered range suggests that further spread of Ash Dieback across southern Italy is a realistic scenario. This presents a threat not just to the southern European proveniences of F. excelsior, but to the species as a whole, should Ash Dieback lead to the loss of warm climate adapted genetic material, which may become increasingly valuable under climate change.

The Impact of Biotic and Abiotic Stress Factors on Development of European Ash Tissue Cultures

Fraxinus excelsior L. is threatened by a variety of environmental factors causing a decline of the species. The most important biotic factors negatively affecting the condition of the F. excelsior population are fungi such as the pathogen Hymenoscyphus fraxineus. Abiotic factors with potentially harmful effect to the F. excelsior population are the accumulation of heavy metals and salinity in soils. Thus, the aim of this study was to investigate the impact of selected biotic and abiotic stress factors to determine which of them pose a threat to European ash. The study was conducted using in vitro techniques based on callus and seedlings regenerated via indirect organogenesis. Tissue cultures exclude the influence of other factors, including the environmental impact on ash extinction. The results confirmed very strong pathogenic potential of H. fraxineus in which after 14 days the callus tissue cells died as the tissue failed to activate its defense mechanisms. Experiments showed the high toxicity of cadmium in concentration of 0.027 mmol/L. Salinity caused the activity of oxidation enzymes to vary among seedlings and calluses in the control suggesting the enzymes play a role in controlling the morphogenetic development of tissue cultures.

Genetic Distinctiveness Highlights the Conservation Value of a Sicilian Manna Ash Germplasm Collection Assigned to Fraxinus angustifolia (Oleaceae)

The cosmopolitan genus Fraxinus comprises about 40 species occupying several habitats in the Northern Hemisphere. With some species hybridizing and sharing genetic variants, questions remain on the species assignment of germplasm within the genus Fraxinus despite numerous species-specific assessments. A multidisciplinary approach was employed to provide a definitive insight into the genetics of an endangered Fraxinus “manna ash” collection, located in a rich plant biodiversity hotspot of the Madonie Mountains (Sicily). Although the collection size was small, genetic diversity, assessed by chloroplast (cpSSR) and nuclear (nSSR) microsatellites (SSR—Simple Sequence Repeats), allowed identifying three different chloroplast haplotypes, with one (H5) dominant, and several polymorphic loci, able to discriminate most of the local accessions studied. Molecular data were linked to cytofluorimetric and phenotypic evaluations and, contrary to popular belief that manna ash is Fraxinus ornus L., the germplasm currently used for manna production belongs to Fraxinus angustifolia Vahl. Interestingly, joint analysis of our genetic panel with a large European dataset of Fraxinus spp. suggested the presence of a possible glacial refuge in Sicily, confirming its importance as biodiversity source. Our results will be helpful for the design of long-term conservation programs for genetic resources, such as in situ and ex situ conservation, seed collection and tree reintroduction.

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid Cardamine majovskyi evolved at least twice in different regions by autopolyploidy from diploid Cardamine matthioli. The extensive genome size and genetic variation of Cardamine rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations

Hybridization is a widespread phenomenon present in numerous lineages across the tree of life. Its evolutionary consequences range from effects on the origin and maintenance, to the loss of biodiversity. We studied genetic diversity and intra- and interspecific gene flow between two sympatric populations of closely-related species, Pitcairnia flammea and P. corcovadensis (Bromeliaceae), which are adapted to naturally fragmented Neotropical inselbergs, based on nuclear and plastidial DNA. Our main results indicate a strong reproductive isolation barrier, although low levels of interspecific gene flow were observed in both sympatric populations. The low rates of intraspecific gene flow observed for both P. corcovadensis and P. flammea populations corroborate the increasing body of evidence that inselberg bromeliad species are maintained as discrete evolutionary units despite the presence of low genetic connectivity. Nuclear patterns of genetic diversity and gene flow revealed that hybridization and introgression might not cause species extinction via genetic assimilation of the rare P. corcovadensis. In the face of reduced intraspecific gene exchange, hybridization and introgression may be important aspects of the Pitcairnia diversification process, with a positive evolutionary impact at the bromeliad community level, and thus contribute to increasing and maintaining genetic diversity in local isolated inselberg populations.

A first assessment of Fraxinus excelsior (common ash) susceptibility to Hymenoscyphus fraxineus (ash dieback) throughout the British Isles

Ash dieback (ADB), caused by Hymenoscyphus fraxineus, has severely damaged a large proportion of ash trees (Fraxinus excelsior) in continental Europe. We have little damage data for the British Isles where the disease was found only five years ago in the Southeast, and is still spreading. A large-scale screening trial to evaluate ADB damage to provenances of F. excelsior sourced from throughout the British Isles was planted in 2013 in the southeast of England. In 2016, we scored trees by their level of ADB damage observed in field at the two worst affected (based on assessments in 2015) of the 14 sites. Significant differences were found in average ADB damage among planting sites and seed source provenances. Trees from certain provenances in Scotland were the least damaged by ADB, whereas trees from Wales and Southeast England were the most badly damaged in both trial sites. Thus the levels of ADB damage currently seen in ash populations in Southeast England may not be an accurate predictor of the damage expected in future throughout the British Isles. Given all provenances contained some healthy trees, a breeding programme to produce genetically variable native ash tree populations with lower ADB susceptibility may be feasible.

Genome sequence and genetic diversity of European ash trees

Ash trees (genus Fraxinus, family Oleaceae) are widespread throughout the Northern Hemisphere, but are being devastated in Europe by the fungus Hymenoscyphus fraxineus, causing ash dieback, and in North America by the herbivorous beetle Agrilus planipennis. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we re-analyse association transcriptomic data, yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.

Genetic admixture and lineage separation in a southern Andean plant

Mountain uplifts have generated new ecologic opportunities for plants, and triggered evolutionary processes, favouring an increase on the speciation rate in all continents. Moreover, mountain ranges may act as corridors or barriers for plant lineages and populations. In South America a high rate of diversification has been linked to Andean orogeny during Pliocene/Miocene. More recently, Pleistocene glacial cycles have also shaped species distribution and demography. The endemic genus Escallonia is known to have diversified in the Andes. Species with similar morphology obscure species delimitation and plants with intermediate characters occur naturally. The aim of this study is to characterize genetic variation and structure of two widespread species of Escallonia: E. alpina and E. rubra We analyzed the genetic variation of populations of the entire distribution range of the species and we also included those with intermediate morphological characters; a total of 94 accessions from 14 populations were used for the Amplified Fragment Length Polymorphism (AFLP) analysis. Plastid DNA sequences (trnS-trnG, 3'trnV-ndhC intergenic spacers and the ndhF gene) from sixteen accessions of Escallonia species were used to construct a Statistical Parsimony network. Additionally, we performed a geometric morphometrics analysis on 88 leaves from 35 individuals of the two E. alpina varieties to further study their differences. Wright's Fst and analysis of molecular variance tests performed on AFLP data showed a significant level of genetic structure at the species and population levels. Intermediate morphology populations showed a mixed genetic contribution from E. alpina var. alpina and E. rubra both in the Principal Coordinates Analysis (PCoA) and STRUCTURE. On the other hand, E. rubra and the two varieties of E. alpina are well differentiated and assigned to different genetic clusters. Moreover, the Statistical Parsimony network showed a high degree of divergence between the varieties of E. alpina: var. alpina is more closely related to E. rubra and other species than to its own counterpart E. alpina var. carmelitana Geometric morphometrics analysis (Elliptic Fourier descriptors) revealed significant differences in leaf shape between varieties. We found that diversity in Escallonia species analyzed here is geographically structured and deep divergence between varieties of E. alpina could be associated to ancient evolutionary events like orogeny. Admixture in southern populations could be the result of hybridization at the margins of the parental species' distribution range.

Heteroploid Knautia drymeia includes K. gussonei and cannot be separated into diagnosable subspecies

PREMISE OF THE STUDY

Knautia drymeia is a morphologically variable, diploid and tetraploid temperate forest understory species distributed in southeastern Europe and adjacent areas. The species is an excellent system to explore the influence of polypoidy on taxonomic delineations, the role of hybridization among genetically distant populations in polyploid evolution, and the impact of glacial refugia on the evolution of polyploids.

METHODS

Amplified fragment length polymorphism fingerprinting and multivariate analyses of morphological characters were performed on 57 populations spanning the distribution area of K. drymeia. K-means clustering, comparison of in-silico tetraploids and observed tetraploids, and a phylogeographic analysis using relaxed random walks were used to explore the genetic structure within the diploids, to infer the origin of the tetraploids and to reconstruct range expansion through time. Further, we contrasted the morphology and genetic groups with current taxonomy and evaluated the status of the tetraploid Apennine endemic K. gussonei and the intraspecific taxa of K. drymeia.

KEY RESULTS

The genetic structure was strongly geographically correlated and yielded four genetic groups; K. gussonei was inseparable from K. drymeia. Distributions of diploid lineages are suggestive of glacial refugia in the northwesternmost and southeastern Balkan Peninsula. Polyploids originated at least two times, as autopolyploids and probably additionally also as allopolyploids. Morphological divergence corresponded with neither genetic groups nor current taxonomy.

CONCLUSIONS

Genetic and morphometric data confirmed neither divergence of K. gussonei nor recognition of subspecies within K. drymeia. We therefore propose treating K. drymeia as a morphologically and genetically variable species without infraspecific taxa.

Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation

We reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe. To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals). Analysis of haplotype and microsatellite diversity revealed that southeastern refugial populations situated in the Carpathians and the Balkan Peninsula did not spread north and cannot be considered as important source populations for postglacial recolonization of Europe; populations in Eastern Europe did not establish Fennoscandian populations; populations in Fennoscandia and Eastern Europe have no unique genetic cluster, but represent a mix with a predominant cluster typical for Central Europe; and that colonization of Fennoscandia and Eastern Europe took place from Central Europe. Our findings highlight the importance of an effective refugium in Central Europe located outside classical southern refugia confirming the existence of northern refugia for boreal trees in Europe. The postglacial range expansion of A. incana did not follow the model established for Picea abies. Fennoscandian populations are not derived from Eastern European ones, but from Central European ones.

Halfway encounters: meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica

The Patagonian region is characterized by a complex biogeographic history, with evidence of deep phylogeographic breaks shared among species. Of particular interest to conservation is the nature of colonization and settlement patterns after the last glacial period, including the detection of secondary contact between different lineages and/or hybridization among related species around phylogeographic breaks. Here we studied population demography and past hybridization of two widespread tree species endemic to South America, Nothofagus pumilio and N. antarctica. Using 8 nuclear microsatellites we genotyped 41 populations of both species. Genetic variation and structure across the geographic region were evaluated within and among species and the past demographic history of hybridization between the two species was inferred using Approximate Bayesian Computation (ABC). Northern and southern lineages were identified in each species, and Bayesian clustering revealed their convergence at mid latitudes (42°S). Spatial genetic structure (SGS) also indicated the existence of a genetic discontinuity at these latitudes, which is in agreement with previous data from maternal DNA markers. Several populations around 42-44°S presented high levels of genetic diversity with a decrease toward southern populations. Even though the species are clearly differentiated (G'ST=0.335), admixed gene pools were observed in both species. Two independent runs of ABC suggested that inter species admixture-like patterns occurred within the timescale of the Last Glacial Maximum (around 20,000 BP). We also provide evidences of recent and bi-directional hybridization/introgression between the two Nothofagus species and describe features of the populationś demography in the past. The settlement of a secondary contact zone in Nothofagus species around 42-44°S coincides with the phylogeographic breaks and hotspots of genetic diversity found in other plant and animal species in Patagonia, highlighting its importance as reservoir of diversity. The characterization of the population history of native species can contribute substantially to long-term conservation and management policies.

A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology

Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995-2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.

Genetic diversity, genetic structure and demographic history of Cycas simplicipinna (Cycadaceae) assessed by DNA sequences and SSR markers

BACKGROUND

Cycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species.

RESULTS

Analyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna. A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene.

CONCLUSIONS

Some genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively.

The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation

To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.

Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.

Dynamic conservation of forest genetic resources in 33 European countries

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan-European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species-oriented strategy in which national conservation networks are specifically designed for key target species and a site-oriented strategy in which multiple-target units include so-called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however, <2% of the conserved populations seem to be at risk of extinction. On the basis of our results, we recommend combining species-oriented and site-oriented strategies.

Evolutionary history of almond tree domestication in the Mediterranean basin

Genetic diversity of contemporary domesticated species is shaped by both natural and human-driven processes. However, until now, little is known about how domestication has imprinted the variation of fruit tree species. In this study, we reconstruct the recent evolutionary history of the domesticated almond tree, Prunus dulcis, around the Mediterranean basin, using a combination of nuclear and chloroplast microsatellites [i.e. simple sequence repeat (SSRs)] to investigate patterns of genetic diversity. Whereas conservative chloroplast SSRs show a widespread haplotype and rare locally distributed variants, nuclear SSRs show a pattern of isolation by distance with clines of diversity from the East to the West of the Mediterranean basin, while Bayesian genetic clustering reveals a substantial longitudinal genetic structure. Both kinds of markers thus support a single domestication event, in the eastern side of the Mediterranean basin. In addition, model-based estimation of the timing of genetic divergence among those clusters is estimated sometime during the Holocene, a result that is compatible with human-mediated dispersal of almond tree out of its centre of origin. Still, the detection of region-specific alleles suggests that gene flow from relictual wild preglacial populations (in North Africa) or from wild counterparts (in the Near East) could account for a fraction of the diversity observed.

A European phylogeography of Rhinanthus minor compared to Rhinanthus angustifolius: unexpected splits and signs of hybridization

Rhinanthus minor and Rhinanthus angustifolius (Orobanchaceae) are annual hemiparasites, which occur sympatrically in Europe and are known to hybridize. We studied chloroplast and nuclear (amplified fragment length polymorphism [AFLP]) diversity in R. minor and compared genetic structuring in this species with R. angustifolius by analyzing the AFLP data for both species simultaneously. The AFLP data revealed that populations in Italy, Greece, and southeast Russia initially identified as R. minor were so distant from the other R. minor populations that they probably belong to another, yet unidentified taxon, and we refer to them as Rhinanthus sp. R. minor s.s. showed a clear geographic genetic structure in both the chloroplast DNA (cpDNA) and nuclear genome. The simultaneous analysis of both species shed new light on the previously published findings for R. angustifolius, because some populations now turned out to belong to R. minor. The admixture analysis revealed very few individuals of mixed R. minor–R.angustifolius ancestry in the natural populations in the west of Europe, while admixture levels were higher in the east. The combined haplotype network showed that haplotype H1 was shared among all species and is likely to be ancestral. H2 was more abundant in R. angustifolius and H3 in R. minor, and the latter probably arose from H1 in this species in the east of Europe. The occurrence of H3 in R. angustifolius may be explained by introgression from R. minor, but without interspecific admixture, these are likely to have been old hybridization events. Our study underlines the importance of including related species in phylogeographic studies.

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA "universal" barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed.

Back to the suture: the distribution of intraspecific genetic diversity in and around anatolia

The effect of ice ages in speciation and diversification is well established in the literature. In Europe, the Iberian, the Italian and the Balkan peninsulas comprise the main glacial refugia, where the subsequent re-population of Europe started. Though not studied as extensively, Anatolia has also been hinted to be a potential glacial refugium for Europe, and with its proximity to the Caucasus and the Middle East at the same time, has potential to exhibit high levels of intraspecific diversity. The more ubiquitous use and cheaper availability of molecular methods globally now makes it possible to better understand molecular ecology and evolution of the fauna and flora in the genetically understudied regions of the world, such as Anatolia. In this review, the molecular genetic studies undertaken in Anatolia in the last decade, for 29 species of plants and animals, are examined to determine general phylogeographic patterns. In this regard, two major patterns are observed and defined, showing genetic breaks within Anatolia and between Anatolia and the Balkans. A third pattern is also outlined, which suggests Anatolia may be a center of diversity for the surrounding regions. The patterns observed are discussed in terms of their relevance to the location of suture zones, postglacial expansion scenarios, the effect of geographic barriers to gene flow and divergence time estimates, in order to better understand the effect of the geological history of Anatolia on the evolutionary history of the inhabitant species. In view of the current state of knowledge delineated in the review, future research directions are suggested.

Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs

The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot.

Genomic profiling of plastid DNA variation in the Mediterranean olive tree

BACKGROUND

Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.

RESULTS

Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations.

CONCLUSIONS

We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.

Diversity gradients and phylogeographic patterns in Santiria trimera (Burseraceae), a widespread African tree typical of mature rainforests

PREMISE OF THE STUDY

New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests.

METHODS

We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations.

RESULTS

Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of São Tomé, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogooué River, suggesting refuges on both sides of the river bed.

CONCLUSIONS

The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity.

CpDNA-based species identification and phylogeography: application to African tropical tree species

Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations.

Disjunct distribution of chloroplast DNA haplotypes in the understory perennial Veratrum album ssp. oxysepalum (Melanthiaceae) in Japan as a result of ancient introgression

• The Quaternary climatic changes resulted in range shifts of species, providing chances for hybridization. However, the genetic signatures of such ancient introgression have rarely been reported. To investigate such signatures, we performed a phylogeographical study on the perennial plant Veratrum album ssp. oxysepalum, which may have hybridized long ago with another congeneric species, V. stamineum. • Sequence variations in chloroplast DNA (cpDNA) were examined in 43 populations in Japan and adjacent areas. Phylogenetic analyses of different cpDNA haplotypes were conducted on the basis of cpDNA and nuclear ribosomal internal transcribed spacer (nrITS) variations. • In the Japanese archipelago, two major groups of haplotypes were detected, one of which was distributed in a disjunct pattern. The major haplotype, occupying the central part of the species' distribution, formed a monophyletic group with V. stamineum in phylogenetic trees on the basis of cpDNA variation, although the two species did not form a monophyletic group in phylogenetic trees on the basis of nrITS variation. • Historical hybridization between V. album ssp. oxysepalum and V. stamineum in refugia during the Quaternary climatic oscillations, and the resulting chloroplast capture of V. stamineum by V. album ssp. oxysepalum, are most probably responsible for the disjunct distribution of cpDNA in V. album ssp. oxysepalum.

Disentangling phylogeography, polyploid evolution and taxonomy of a woodland herb (Veronica chamaedrys group, Plantaginaceae s.l.) in southeastern Europe

Southeastern Europe is a centre of European biodiversity, but very little is known about factors causing the observed richness. Here, we contribute to fill this gap by reconstructing the spatio-temporal diversification of the cytologically variable and taxonomically intricate complex of Veronica chamaedrys (Plantaginaceae s.l.), growing in open forests, forest edges and grasslands, with flow cytometry, molecular markers (AFLPs, plastid DNA sequences) and morphometry. Our results show that both diploid and tetraploid cytotypes are widespread, but diploids predominate on the southern Balkan Peninsula. Plastid sequences suggest a first split into three main lineages in the mid-Pleistocene and a continuous diversification during the last 0.4 my. Two of the identified plastid lineages coincide with geographically distinct AFLP clusters. Altogether, the genetic data suggest forest refugia on the southern-most Balkan Peninsula (Greece), in Bulgaria, Istria (Croatia and Slovenia) and maybe the southeastern Carpathians (Romania). Morphometric and genetic data show little congruence with current taxonomy.

The history of extant Ilex species (Aquifoliaceae): evidence of hybridization within a Miocene radiation

The history and diversification of the genus Ilex (Aquifoliaceae), based on 108 different species (116 specimens), are inferred from the analysis of two nuclear (ITS and nepGS) and three plastid (rbcL, trnL-F and atpB-rbcL) sequences. Nuclear and plastid trees are highly incongruent and the nuclear tree is more compatible with current taxonomic classifications than the plastid one. The most recent common ancestor (MRCA) of extant species is dated from the Miocene, although the Ilex stem lineage can be traced back to the late Cretaceous, according to fossil records. This suggests extensive lineage extinctions between the Cretaceous and Miocene and may also explain the difficulties encountered in defining the relationships between Ilex and its closest relatives. The MRCA ancestral area was identified as being in the North Hemisphere (North America and/or East Asia). Several bidirectional North America/East Asia and North America/South America dispersal events are proposed to explain observed geographic and phylogenetic patterns. Hybridization and introgression events between distantly related lineages are also inferred, indicating weak reproductive barriers between species in Ilex.

Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison

BACKGROUND

The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions discriminating among the agronomically and economically important olive cultivars have been identified. The objective of this study was to sequence the entire plastome of olive and analyze many potential polymorphic regions to develop new inter-cultivar genetic markers.

RESULTS

The complete plastid genome of the olive cultivar Frantoio was determined by direct sequence analysis using universal and novel PCR primers designed to amplify all overlapping regions. The chloroplast genome of the olive has an organisation and gene order that is conserved among numerous Angiosperm species and do not contain any of the inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses that have been found in the chloroplast genomes of the genera Jasminum and Menodora, from the same family as Olea.The annotated sequence was used to evaluate the content of coding genes, the extent, and distribution of repeated and long dispersed sequences and the nucleotide composition pattern. These analyses provided essential information for structural, functional and comparative genomic studies in olive plastids. Furthermore, the alignment of the olive plastome sequence to those of other varieties and species identified 30 new organellar polymorphisms within the cultivated olive.

CONCLUSIONS

In addition to identifying mutations that may play a functional role in modifying the metabolism and adaptation of olive cultivars, the new chloroplast markers represent a valuable tool to assess the level of olive intercultivar plastome variation for use in population genetic analysis, phylogenesis, cultivar characterisation and DNA food tracking.

Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae)

The impact of the Pleistocene climate oscillations on the structure of biodiversity in tropical regions remains poorly understood. In this study, the forest refuge theory is examined at the molecular level in Milicia excelsa, a dioecious tree with a continuous range throughout tropical Africa. Eight nuclear microsatellites (nSSRs) and two sequences and one microsatellite from chloroplast DNA (cpDNA) showed a deep divide between samples from Benin and those from Lower Guinea. This suggests that these populations were isolated in separate geographical regions, probably for several glacial cycles of the Pleistocene, and that the nuclear gene pools were not homogenized despite M. excelsa's wind-pollination syndrome. The divide could also be related to seed dispersal patterns, which should be largely determined by the migration behaviour of M. excelsa's main seed disperser, the frugivorous bat Eidolon helvum. Within Lower Guinea, a north-south divide, observed with both marker types despite weak genetic structure (nSSRs: F(ST) = 0.035, cpDNA: G(ST)  = 0.506), suggested the existence of separate Pleistocene refugia in Cameroon and the Gabon/Congo region. We inferred a pollen-to-seed dispersal distance ratio of c.1.8, consistent with wide-ranging gene dispersal by both wind and bats. Simulations in an Approximate Bayesian Computation framework suggested low nSSR and cpDNA mutation rates, but imprecise estimates of other demographic parameters, probably due to a substantial gene flow between the Lower Guinean gene pools. The decline of genetic diversity detected in some Gabonese populations could be a consequence of the relatively recent establishment of a closed canopy forest, which could negatively affect M. excelsa's reproductive system.

Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences

The phylogenetic relationships between the five dioecious species in Silene section Melandrium (Caryophyllaceae) and their putative hermaphrodite relatives are investigated based on an extensive geographic and taxonomic sample, using DNA sequence data from the chloroplast genome and the nuclear ribosomal ITS region. The hermaphrodite S. noctiflora (the type species of section Elisanthe) is distantly related to the dioecious species. With the exception of chloroplast sequences in one S. latifolia population from Turkey, the dioecious taxa form a strongly supported monophyletic group (Silene section Melandrium). The phylogenetic structure within section Melandrium differs between chloroplast and nuclear sequences. While there is extensive sharing of chloroplast haplotypes among all the dioecious species (the observed patterns reflect geographic structure), the nuclear ITS phylogeny shows a higher degree of taxonomic structure. Chloroplast-sharing by the section Melandrium species is most plausibly explained by a history of hybridization and extensive backcrossing.

Chloroplast DNA phylogeography of Betula maximowicziana, a long-lived pioneer tree species and noble hardwood in Japan

Betula maximowicziana is an ecologically and economically important tree species in Japan. In order to examine the phylogeographical pattern of the species in detail, maternally inherited chloroplast (cp) DNA variations of 25 natural populations of Betula maximowicziana and a total of 12 populations of three related species were evaluated by PCR-RFLP analysis. Two main haplotypic groups of B. maximowicziana populations (northern and southern) were detected, with the main boundary passing through the Tohoku region in northeastern Japan; in addition there was high genetic differentiation among the 25 populations studied (GST = 0.950, G'ST =0:977). The phylogeographical pattern exhibited by B. maximowicziana was much more similar to that of alpine plants than to that of beech and oak. Comparison of the patterns of genetic structure obtained from the cpDNA with previously and newly acquired data on bi-parentally inherited nuclear DNA indicates that the nuclear genome was transferred via pollen from the northern haplotypic group to the southern group more frequently than it moved in the opposite direction. Although common haplotypes were detected among B. maximowicziana and the two related species examined, these haplotypes were not shared sympatrically, suggesting very rare hybridization among the species currently occurring in their natural populations.

Ancient and current gene flow between two distantly related Mediterranean oak species, Quercus suber and Q. ilex

BACKGROUND AND AIMS

Quercus suber and Q. ilex are distantly related and their distributions partially overlap. They hybridize occasionally, but the complete replacement of Q. suber chloroplast DNA (cpDNA) by that of Q. ilex was identified in two specific geographical areas. The objective of this study was to determine whether the contrasting situation reflected current or recent geographical interspecies gene flow variation or was the result of ancient introgression.

METHODS

cpDNA PCR-RFLPs (restriction fragment length polymorphisms) and variation at ten nuclear microsatellite loci were analysed in populations of each species, in 16 morphologically intermediate individuals and the progeny of several of them. Interspecies nuclear introgression was based on individual admixture rates using a Bayesian approach with no a priori species assignment, and on a maximum-likelihood (ML) method, using allele frequencies in the allopatric populations of each species as controls. Gene flow was compared specifically between populations located within and outside the specific areas.

KEY RESULTS

High interspecies nuclear genetic differentiation was observed, with twice the number of alleles in Q. ilex than in Q. suber. According to Bayesian assignment, approx. 1 % of individuals had a high probability of being F(1) hybrids, and bidirectional nuclear introgression affected approx. 4 % of individuals in each species. Hybrid and introgressed individuals were identified predominantly in mixed stands and may have a recent origin. Higher proportions including allospecific genes recovered from past hybridization were obtained using the ML method. Similar rates of hybridization and of nuclear introgression, partially independent of cpDNA interspecies transfer suggestive of gene filtering, were obtained in the populations located within and outside the areas of complete cpDNA replacement.

CONCLUSIONS

The results did not provide evidence for geographical variation in interspecies gene flow. In contrast, historical introgression is supported by palynological records and constitutes the more reliable origin of cpDNA replacement in specific regions.

Haplotype richness in refugial areas: phylogeographical structure of Saxifraga callosa

This paper illustrates the phylogeographical structure of Saxifraga callosa in order to describe its genetic richness in refugial areas and to reconstruct its glacial history. S. callosa is a species spread throughout south-east France and Italy with a high distribution in the Maritime Alps. Four chloroplast microsatellite and AFLP markers were analyzed in populations of S. callosa. The size variants of all tested loci amount to 11 different haplotypes. Intrapopulational haplotype variation was found in two of the populations analyzed: on the Mt. Toraggio in the Maritime Alps, and in the Apuan Alps. On the other hand, no intrapopulational variation was found in 25 populations, most of which were sampled from isolated areas. Analysis of the haplotype distribution showed that population subdivision across all populations was high (G (ST) = 0.899). Moreover, its genetic structure was studied using AMOVA and STRUCTURE analysis. The study legitimated inferred conclusions about the phylogeographical structure of the species and identified centers of diversity. Considerations concerning genetic structure and divergence among three major clades (Maritime Alps, Apuan Alps and Apennines), the patchy distribution of haplotypes, and the high number of private haplotypes support the proposal that S. callosa survived in some refugia within the Italian Peninsula refugium, and that mainly northern populations of refugia were involved in postglacial recolonization.

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex)

Powerful and accurate detection of first-generation (F1) hybrids and backcrosses in nature is needed to achieve a better understanding of the function and dynamics of introgression. To document the frequency of ongoing interspecific gene exchange between two Mediterranean evergreen oaks, the cork oak (Quercus suber) and the holm oak (Q. ilex), we analyzed 1487 individuals originating from across the range of the two species using eight microsatellite loci and two Bayesian clustering approaches (implemented in the programs STRUCTURE and NEWHYBRIDS). Simulated data were used to assess the differences between the two clustering methods and to back up the choice of the threshold value for the posterior probability to discriminate admixed from pure individuals. We found that the use of STRUCTURE resulted in the highest power to detect hybrids, whereas NEWHYBRIDS provided the highest accuracy. Irrespective of the approach, the two species were clearly distinguished as independent genetic entities without any prior information. In contrast with previous reports, we found no evidence for unidirectional introgression. The overall hybridization rate was very low (<2% of introgressed individuals). Only two individuals were identified as F1 hybrids and five as early backcrosses. This work shows that the combined application of the two complementary Bayesian approaches and their systematic validation with simulations, fit for the case at hand, helps gain resolution in the identification of admixed individuals.

Divergence in the face of gene flow: the case of two newts (amphibia: salamandridae)

Understanding the process of divergence requires the quantitative characterization of patterns of gene flow between diverging taxa. New and powerful coalescent-based methods give insight into these processes in unprecedented details by enabling the reconstruction of the temporal distribution of past gene flow. Here, we use sequence variation at eight nuclear markers and mitochondrial DNA (mtDNA) in multiple populations to study diversity, divergence, and gene flow between two subspecies of a salamander, the smooth newt (Lissotriton vulgaris kosswigi and Lissotriton vulgaris vulgaris) in Turkey. The ranges of both subspecies encompass mainly the areas of this important glacial refugial area. Populations in refugia where species have been present for a long time and differentiated in situ should better preserve the record of past gene flow than young populations in postglacial expansion areas. Sequence diversity in both subspecies was substantial (nuclear pi(sil) = 0.69% and 1.31%). We detected long-term demographic stability in these refugial populations with large effective population sizes (N(e)) of the order of 1.5-3 x 10(5) individuals. Gene trees and the isolation with migration (IM) analysis complemented by tests of nested IM models showed that despite deep, pre-Pleistocene divergence of the studied newts, asymmetric introgression from vulgaris to kosswigi has occurred, with signatures of recent gene flow in mtDNA and an anonymous nuclear marker, and evidence for more ancient introgression in nuclear introns. The distribution of migration times raises the intriguing possibility that even the initial divergence may have occurred in the face of gene flow.

Repeated adaptive introgression at a gene under multiallelic balancing selection

Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193) is about four times lower than the genomic background (K = 0.0743). We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the species stopped forming fertile hybrids, thereby complementing the average portrait of divergence between species provided by genomic data.

The role of natural selection in promoting or preventing genomic divergence between nascent species remains highly debated. As long as reproductive barriers remain incomplete, genetic material from one species is indeed exposed to natural selection into the genomic background of the other species. In some cases, genomic co-adaptations developing independently in each species are believed to select against such transfers. Yet, theory predicts that the transfer of some chromosomal fragments may be favored by natural selection. In particular, this should occur for alleles at genes evolving under a particular form of natural selection, i.e., multi-allelic balancing selection. We test this prediction using two closely related Arabidopsis species, and find a four-fold lower divergence at alleles at the gene controlling pistil self-incompatibility specificity than at the genomic background. We conclude that alleles at this gene have been transferred more readily between the two species than the genomic background. We suggest that natural selection may efficiently allow the maintenance of high allelic diversity and divergence across many species at S-loci as well as at all other loci under multi-allelic balancing selection, such as the MHC in vertebrates or disease resistance genes in plants.