Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers

Genetic Structure of Natural Northern Range-Margin Mainland, Peninsular, and Island Populations of Northern Red Oak (Quercus rubra L.)

Plant populations at the leading edge of the species’ native range often exhibit genetic structure as a result of genetic drift and adaptation to harsh environmental conditions. Hence, they are likely to harbour rare genetic adaptations to local environmental conditions and therefore are of particular interest to understand climate adaptation. We examined genetic structure of nine northern marginal mainland, peninsular and isolated island natural populations of northern red oak (Quercus rubraL.), a valuable long-lived North American hardwood tree species, covering a wide climatic range, using 17 nuclear microsatellites. We found pronounced genetic differentiation of a disjunct isolated island population from all mainland and peninsular populations. Furthermore, we observed remarkably strong fine-scale spatial genetic structure (SGS) in all investigated populations. Such high SGS values are uncommon and were previously solely observed in extreme range-edge marginal oak populations in one other study. We found a significant correlation between major climate parameters and SGS formation in northern range-edge red oak populations, with more pronounced SGS in colder and drier regions. Most likely, the harsh environment in leading edge populations influences the density of reproducing trees within the populations and therefore leads to restricted overlapping of seed shadows when compared to more central populations. Accordingly, SGS was negatively correlated with effective population size and increased with latitude of the population locations. The significant positive association between genetic distances and precipitation differences between populations may be indicative of isolation by adaptation in the observed range-edge populations. However, this association was not confirmed by a multiple regression analysis including geographic distances and precipitation distances, simultaneously. Our study provides new insights in the genetic structure of long-lived tree species at their leading distribution edge.

Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus

The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.

New Insight into Taxonomy of European Mountain Pines, Pinus mugo Complex, Based on Complete Chloroplast Genomes Sequencing

The Pinus mugo complex is a large group of closely related mountain pines, which are an important component of the ecosystems of the most important mountain ranges, such as the Alps, Carpathians and Pyrenees. The phylogenetic relationships between taxa in this complex have been under discussion for many years. Despite the use of many different approaches, they still need to be clarified and supplemented with new data, especially those obtained with high-throughput methods. Therefore, in this study, the complete sequences of the chloroplast genomes of the three most recognized members of the Pinus mugo complex, i.e., Pinus mugo, Pinus rotundata and Pinus uncinata, were sequenced and analyzed to gain new insight into their phylogenetic relationships. Comparative analysis of their complete chloroplast genome sequences revealed several mutational hotspots potentially useful for the genetic identification of taxa from the Pinus mugo complex. Phylogenetic inference based on sixteen complete chloroplast genomes of different coniferous representatives showed that pines from the Pinus mugo complex form one distinct monophyletic group. The results obtained in this study provide new and valuable omics data for further research within the European mountain pine complex. They also indicate which regions may be useful in the search for diagnostic DNA markers for the members of Pinus mugo complex and set the baseline in the conservation of genetic resources of its endangered taxa.

Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

Genetic Diversity and Classification of the Cytoplasm of Chinese Elite Foxtail Millet [Setaria italica (L.) P. Beauv.] Parental Lines Revealed by Chloroplast Deoxyribonucleic Acid Variation

Due to the maternal inheritance of cytoplasm, using foxtail millet [Setaria italica (L.) P. Beauv.] male sterile lines with a single cytoplasmic source as the female parent will inevitably lead to a narrow source of cytoplasm in hybrids, which may make them vulnerable to infection by cytoplasm-specific pathogens, ultimately leading to destructive yield losses. To assess cytoplasmic genetic diversity in plants, molecular markers derived from chloroplast DNA (cpDNA) have been used. However, such markers have not yet been applied to foxtail millet. In this study, we designed and screened nine pairs of polymorphic foxtail millet-specific primers based on its completely sequenced cpDNA. Using these primers, we analyzed the genetic diversity and cytoplasmic types of 130 elite foxtail millet parental lines collected in China. Our results revealed that the cytoplasmic genetic diversity of these accessions was low and needs to be increased. The parental lines were divided into four cytoplasmic types according to population structure analysis and a female parent-derivative evolutionary graph, indicating that the cytoplasmic types of elite foxtail millet lines were rather limited. A principal component analysis (PCA) plot was linked with the geographic and ecological distribution of accessions for each cytoplasmic type, as well as their basal maternal parents. Collectively, our results suggest that enriching cytoplasmic sources through the use of accessions from diverse ecological regions and other countries as the female parent may improve foxtail millet breeding programs, and prevent infection by cytoplasm-specific pathogens.

Genetic structure of the Canarian palm tree (Phoenix canariensis) at the island scale: does the 'island within islands' concept apply to species with high colonisation ability?

Oceanic islands are dynamic settings that often promote within-island patterns of strong population differentiation. Species with high colonisation abilities, however, are less likely to be affected by genetic barriers, but island size may impact on species genetic structure regardless of dispersal ability. The aim of the present study was to identify the patterns and factors responsible for the structure of genetic diversity at the island scale in Phoenix canariensis, a palm species with high dispersal potential. To this end, we conducted extensive population sampling on the three Canary Islands where the species is more abundant and assessed patterns of genetic variation at eight microsatellite loci, considering different within-island scales. Our analyses revealed significant genetic structure on each of the three islands analysed, but the patterns and level of structure differed greatly among islands. Thus, genetic differentiation fitted an isolation-by-distance pattern on islands with high population densities (La Gomera and Gran Canaria), but such a pattern was not found on Tenerife due to strong isolation between colonised areas. In addition, we found a positive correlation between population geographic isolation and fine-scale genetic structure. This study highlights that island size is not necessarily a factor causing strong population differentiation on large islands, whereas high colonisation ability does not always promote genetic connectivity among neighbouring populations. The spatial distribution of populations (i.e. landscape occupancy) can thus be a more important driver of plant genetic structure than other island, or species' life-history attributes.

Genetic diversity patterns and functional traits of Bradyrhizobium strains associated with Pterocarpus officinalis Jacq. in Caribbean islands and Amazonian forest (French Guiana)

Pterocarpus officinalis Jacq. is a legume tree native to the Caribbean islands and South America growing as a dominant species in swamp forests. To analyze (i) the genetic diversity and (ii) the symbiotic properties of its associated nitrogen-fixing soil bacteria, root nodules were collected from P. officinalis distributed in 16 forest sites of the Caribbean islands and French Guiana. The sequencing of the 16S-23S ribosomal RNA intergenic spacer region (ITS) showed that all bacteria belonged to the Bradyrhizobium genus. Bacteria isolated from insular zones showed very close sequence homologies with Bradyrhizobium genospecies V belonging to the Bradyrhizobium japonicum super-clade. By contrast, bacteria isolated from continental region displayed a larger genetic diversity and belonged to B. elkanii super-clade. Two strains from Puerto Rico and one from French Guiana were not related to any known sequence and could be defined as a new genospecies. Inoculation experiments did not show any host specificity of the Bradyrhizobium strains tested in terms of infectivity. However, homologous Bradyrhizobium sp. strain-P. officinalis provenance associations were more efficient in terms of nodule production, N acquisition, and growth than heterologous ones. The dominant status of P. officinalis in the islands may explain the lower bacterial diversity compared to that found in the continent where P. officinalis is associated with other leguminous tree species. The specificity in efficiency found between Bradyrhizobium strains and host tree provenances could be due to a coevolution process between both partners and needs to be taken in consideration in the framework of rehabilitation plantation programs.

Signatures of volcanism and aridity in the evolution of an insular pine (Pinus canariensis Chr. Sm. Ex DC in Buch)

Oceanic islands of volcanic origin provide useful templates for the study of evolution because they are subjected to recurrent perturbations that generate steep environmental gradients that may promote adaptation. Here we combine population genetic data from nuclear genes with the analysis of environmental variation and phenotypic data from common gardens to disentangle the confounding effects of demography and selection to identify the factors of importance for the evolution of the insular pine P. canariensis. Eight nuclear genes were partially sequenced in a survey covering the entire species range, and phenotypic traits were measured in four common gardens from contrasting environments. The explanatory power of population substrate age and environmental indices were assessed against molecular and phenotypic diversity estimates. In addition, neutral genetic variability (FST) and the genetic differentiation of phenotypic variation (QST) were compared in order to identify the evolutionary forces acting on these traits. Two key factors in the evolution of the species were identified: (1) recurrent volcanic activity has left an imprint in the genetic diversity of the nuclear genes; (2) aridity in southern slopes promotes local adaptation in the driest localities of P. canariensis, despite high levels of gene flow among populations.

The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp. guanchica

Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations, but their consequences in species with high dispersal abilities have not been tested at large scales. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a wind-pollinated, zoochorous tree (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Isolation-by-distance differentiation was observed for nDNA but not for cpDNA, in agreement with other metapopulation studies. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance.

Genetically depauperate in the continent but rich in oceanic islands: Cistus monspeliensis (Cistaceae) in the Canary Islands

Background

Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus.

Methodology/Principal Findings

We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP).

Conclusions/Significance

The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent.

Phylogeography of Pinus subsection Australes in the Caribbean Basin

BACKGROUND AND AIMS

Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas.

METHODS

Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin.

KEY RESULTS

In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (R(ST) = 0·671 > permuted R(ST) = 0·101; P < 0·0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima.

CONCLUSIONS

Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8.

Characterization of demographic expansions from pairwise comparisons of linked microsatellite haplotypes

This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations

Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.

Genetic variation and phylogeography of Stauracanthus (Fabaceae, Genisteae) from the Iberian Peninsula and northern Morocco assessed by chloroplast microsatellite (cpSSR) markers

The tribe Genisteae includes genera of great ecological importance in Mediterranean countries because they are dominant elements of many plant communities. Genetic variation and diversification patterns in Stauracanthus (Genisteae) provide information relevant for the study of the processes of diversification in relation to the environmental history of the western Mediterranean. Nineteen populations of S. boivinii and S. genistoides were assessed by 11 chloroplast microsatellite markers, revealing 44 haplotypes. Both species had different haplotypes and contrasting patterns of karyological, morphological, and genetic variation. In the minimum spanning tree of the haplotypes, AMOVA analysis, and nested clade analysis, S. boivinii had high levels of differentiation and restricted gene flow among populations. Allopatric differentiation occurred between the Moroccan and Iberian populations of S. genistoides, although S. genistoides subsp. spectabilis and subsp. vicentinus had high levels of differentiation among populations (F(ST)), whereas S. genistoides subsp. genistoides had a low F(ST). Genetic patterns are discussed in relation to the Messinian salinity crisis (MSC): hard conditions drove plants to refuge habitats along the Atlantic coast and higher altitude areas in the Moroccan mountains (S. genistoides subsp. spectabilis and S. boivinii). After the MSC, S. boivinii underwent polyploidization and expansion, whereas S. genistoides expanded and continued diversifying into S. genistoides subspp. genistoides and vicentinus.

Molecular and quantitative trait variation across the native range of the invasive speciesHypericum canariense: evidence for ancient patterns of colonization via pre-adaptation?

To understand the success of invasive species, it is important to know whether colonization events are facilitated by adaptive evolution or are limited to sites where a species is pre-adapted to thrive. Studies of the ancient colonization patterns of an invader in its native range provide an opportunity to examine its natural history of adaptation and colonization. This study uses molecular (internal transcribed spacer sequence and amplified fragment length polymorphism) and common garden approaches to assess the ancient patterns of establishment and quantitative trait evolution in the invasive shrub Hypericum canariense. This species has an unusually small and discrete native range in the Canary Islands. Our data reveal two genetic varieties with divergent life histories and different colonization patterns across the islands. Although molecular divergence within each variety is large (pairwise FST from 0.18 to 0.32 between islands) and nearly as great as divergence between them, life-history traits show striking uniformity within varieties. The discrepancy between molecular and life-history trait divergence points to the action of stabilizing selection within varieties and the influence of pre-adaptation on patterns of colonization. The colonization history of H. canariense reflects how the relationship between selective environments in founding and source populations can dictate establishment by particular lineages and their subsequent evolutionary stasis or change.

Genetic diversity of relictual and endangered plant Abies ziyuanensis (Pinaceae) revealed by AFLP and SSR markers

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Phist (AFLP) = 0.550 and Phist (SSR) = 0.289) and among regions (Phict (AFLP) = 0.139 and Phict (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.

Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine

Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the F(S) test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the F(S) test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands.

Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range-wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (G(ST) = N(ST) = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (G(ST) = 0.362; R(ST) = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (G(ST) > R(ST); and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation-drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.

Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed.

Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe

We used chloroplast polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) and chloroplast microsatellites to assess the structure of genetic variation and postglacial history across the entire natural range of the common ash (Fraxinus excelsior L.), a broad-leaved wind-pollinated and wind-dispersed European forest tree. A low level of polymorphism was observed, with only 12 haplotypes at four polymorphic microsatellites in 201 populations, and two PCR-RFLP haplotypes in a subset of 62 populations. The clear geographical pattern displayed by the five most common haplotypes was in agreement with glacial refugia for ash being located in Iberia, Italy, the eastern Alps and the Balkan Peninsula, as had been suggested from fossil pollen data. A low chloroplast DNA mutation rate, a low effective population size in glacial refugia related to ash's life history traits, as well as features of postglacial expansion were put forward to explain the low level of polymorphism. Differentiation among populations was high (GST= 0.89), reflecting poor mixing among recolonizing lineages. Therefore, the responsible factor for the highly homogeneous genetic pattern previously identified at nuclear microsatellites throughout western and central Europe (Heuertz et al. 2004) must have been efficient postglacial pollen flow. Further comparison of variation patterns at both marker systems revealed that nuclear microsatellites identified complex differentiation patterns in south-eastern Europe which remained undetected with chloroplast microsatellites. The results suggest that data from different markers should be combined in order to capture the most important genetic patterns in a species.

Patterns of pollen dispersal in a small population of Pinus sylvestris L. revealed by total-exclusion paternity analysis

Patterns of pollen dispersal were investigated in a small, isolated, relict population of Pinus sylvestris L., consisting of 36 trees. A total-exclusion battery comprising four chloroplast and two nuclear microsatellites (theoretical paternity exclusion probability EP=0.996) was used to assign paternity to 813 seeds, collected from 34 trees in the stand. Long-distance pollen immigration accounted for 4.3% of observed matings. Self-fertilization rate was very high (0.25), compared with typical values in more widespread populations of the species. The average effective pollen dispersal distance within the stand was 48 m (or 83 m excluding selfs). Half of effective pollen was dispersed within 11 m, and 7% beyond 200 m. A strong correlation was found between the distance to the closest tree and the mean mating-distance calculated for single-tree progenies. The effective pollen dispersal distribution showed a leptokurtic shape, with a large and significant departure from that expected under uniform dispersal. A maximum-likelihood procedure was used to fit an individual pollen dispersal distance probability density function (dispersal kernel). The estimated kernel indicated fairly leptokurtic dispersal (shape parameter b=0.67), with an average pollen dispersal distance of 135 m, and 50% of pollen dispersed beyond 30 m. A marked directionality pattern of pollen dispersal was found, mainly caused by the uneven distribution of trees, coupled with restricted dispersal and unequal male success. Overall, results show that the number and distribution of potential pollen donors in small populations may strongly influence the patterns of effective pollen dispersal.