Genetic structure of gall oak (<Emphasis Type="Italic">Quercus infectoria</Emphasis>) characterized by nuclear and chloroplast SSR markers

Quercus infectoria, commonly known as gall oak, is a small shrub found in Iran. Unfortunately, it is subjected to genetic erosion, and so, its conservation and evaluation are desirable. Thus, in the current research, 16 microsatellite primer pairs (seven nuclear simple sequence repeats (nSSRs) and nine chloroplast simple sequence repeats (cpSSRs)) were used in an attempt to assess the genetic diversity of 121 individuals of Q. infectoria belonging to 11 populations from three provinces in northern Zagros forests of Iran. In total, 69 alleles of nSSR and 18 alleles of cpSSR were detected among the individuals. The results of the overall analysis of molecular variance based on nSSRs indicated that 89.00% of the variation was due to differences within populations and 11.00% occurred among populations, while according to cpSSRs, 94.00% of the variation resided among populations, and only 6.00% could be attributed to variation within populations. A higher genetic differentiation of Q. infectoria populations was found according to cpSSR data in comparison to nSSR data. Cophenetic correlation coefficient values were statistically insignificant between nSSR and cpSSR data. The unweighted pair group method with arithmetic mean and Bayesian cluster analyses grouped the studied individuals into two main clusters based on both nSSR and cpSSR data. nSSR data could not completely clustered individuals next each other according to their geographical collection area. Information detailed by nSSR loci revealed that north-Zagros gall oak preserves average levels of genetic diversity at the species level, high level of within-population genetic diversity, and moderate level of genetic variation among populations. The present results provide valuable data for in situ or ex situ conservation and utilization of the studied germplasm.     

Population Structure of and Conservation Strategies for Wild Pyrus ussuriensis Maxim. in China

Pyrus ussriensis Maxim. is native to the northern part of China, but whose habitats are currently being destroyed by environmental changes and human deforestation. An investigation of population structure and genetic diversity of wild Ussurian pear is a priority in order to acquire fundamental knowledge for conservation. A total of 153 individuals of wild Ussurian pear from the main habitats, Heilongjiang, Jilin, and Inner Mongolia in China, possessed low genetic diversity as a result of habitat fragmentation. The genetic diversity of the populations in Inner Mongolia and north east of Heilongjiang was especially low and there was the possibility of inbreeding. Wild Ussurian pears were divided into 5 groups based on the Bayesian clustering method using 20 nuclear SSRs (nSSRs) and 5 groups by haplotype distributions using 16 chloroplast SSRs (cpSSRs), and the populations in Inner Mongolia and north east of Heilongjiang represented unique genotypes. AMOVA indicated there was a 20.05% variation in nSSRs and a 44.40% variation in cpSSRs among populations. These values are relatively high when compared to those of other tree species. Haplotype E, positioned in the center of the cpSSR analysis network and showed the largest number of connections with other haplotypes, represented the most important haplotype. Inner Mongolia and the north east of Heilongjiang are two areas that need urgent conservation because of their genetic vulnerability and peculiarity. We determined 4 conservation units based on the clustering by nSSRs and cpSSRs, and geographic factor. This information is helpful in deciding the conservation strategies for wild Ussurian pear in China.     

A range wide geographic pattern of genetic diversity and population structure of Castanea mollissima populations inferred from nuclear and chloroplast microsatellites

Understanding geographical pattern of genetic diversity and population structure is of great importance for formulating conservation and utilization strategies. In this study, we investigated the genetic diversity and population structure of 28 natural populations of Castanea mollissima in China using eight nuclear and six chloroplast microsatellite makers (nSSRs and cpSSRs). Populations from central China harbored the highest genetic diversity at both nSSR and cpSSR markers (nSSR: H _E?=?0.705; cpSSR: H?=?0.461). The standardized measure of genetic differentiation estimated as G′ _ST was 0.447 for nSSR and 0.803 for cpSSR, respectively. The G′_ST-based pollen to seed flow ratio is 3.043, indicating that pollen flow is not extensive among C. mollissima populations. No obvious population genetic structure by geographical locations was found by STRUCTURE analysis based on nSSR data, and similarly, no signal of phylogeographic structure was detected for cpSSR analysis. Five boundaries defining zones of maximum genetic differences within the network of the C. mollissima populations were found, and the locations of those barriers were consistent with those of four mountains, i.e., Daloushan Mountain, Dabashan Mountain, Wushan Mountain, and Qingliangfeng Mountain, indicating that those mountains might act as genetic barriers obstructing the genetic exchange among natural C. mollissima populations. These results provide valuable baseline data for conservation and utilization of this species.     

Genetic structure of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill populations at gene-based EST-SSR and nuclear SSR markers

Sympatric hybridizing oak species provide a model system for studying local adaptation. Disjunct populations of Quercus rubra L. and Quercus ellipsoidalis E. J. Hill at the northern edge of their distribution may harbor important reservoirs of adaptive genetic variation. Genic (expressed sequence tag- simple sequence repeat?=?EST-SSR) and non-genic nuclear microsatellite (nuclear SSR?=?nSSR) markers were used to estimate neutral and potentially adaptive genetic variation in these two supposedly interfertile oak species showing different adaptations to drought. Eleven populations of putative Q. rubra and Q. ellipsoidalis located in the Western Upper Peninsula of Michigan were characterized using seven EST-SSRs and eight nSSRs. Bayesian cluster analysis revealed two distinct groups corresponding to each species with evidence of low levels of potential introgression. A comparison of the genetic structure of adult trees and seedlings revealed no evidence for selection against hybrids. Overall, similar levels of genetic variation and differentiation between populations and species were found at both EST-SSRs and nSSRs indicating that most EST-SSRs chosen reflect neutral variation. Two loci, 3A05 (nSSR) and GOT021 (EST-SSR, putative histidine kinase 4-like), were identified as putative outlier loci between species showing largely reduced variation in Q. ellipsoidalis. Future analyses of an increased number of EST-SSRs located in functional genes will allow the identification of genes involved in the reproductive isolation between both species.     

High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans‐Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within‐population genetic diversity was high (mean h_S = 0.72), and among‐population genetic differentiation showed a strong phylogeographic structure (N_ST = 0.630 > G_ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.     

Development and Characterization of Genomic and Gene-Based Microsatellite Markers in North American Red Oak Species

Oaks (Quercus: Fagaceae) are ecological and economic keystones of many forested ecosystems but effective genetic management strategies are hindered by high levels of phenotypic plasticity within species and frequent hybridization among them. These same features, however, make oak communities suited for the study of speciation, hybridization, and genetic adaptation. Efforts to develop new and to adapt existing genomic resources to less-studied members of this genus should not only improve oak conservation and management but also aid the study of fundamental evolutionary processes. Here, we present a suite of 27 highly polymorphic simple sequence repeat (SSR) markers tested in four North American red oak (Quercus section Lobatae) species: Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina. Five markers are genomic SSRs (gSSRs) — four novel and one previously transferred from Q. petraea — and 22 are gene-based SSRs derived from Q. robur and Q. petraea expressed sequence tags (EST-SSRs). Overall, levels of polymorphism detected with these primer pairs were high, with gene diversity (H _e) averaging 0.66 across all loci in natural populations. In addition, we show that EST-SSR markers may have the potential to detect divergent selection at stress-resistance candidate genes among closely related oak species.     

A set of primers for the amplification of chloroplast microsatellites in Quercus

The increase in demand for the certification of oak seed lots, as well as control of the geographical origin of oak wood, has led us to develop powerful genetic markers permitting us to discriminate among provenance regions. With the aim of detecting new chloroplast variants, we have identified 17 potential cpSSRs motifs from available oak sequences and tested their variability among French oak populations. Six loci were polymorphic at the intraspecific level in Quercus petraea and Q. robur. Moreover, conservation of the primer pairs was checked on a set of 21 forest tree species and they were all shown to work well on several Quercus species, and even within Fagacaea.     

Conservation genetics of rare trees restricted to subtropical montane cloud forests in southern China: a case study from <Emphasis Type="Italic">Quercus arbutifolia</Emphasis> (Fagaceae)

Montane cloud forests (MCFs), with their isolated nature, offer excellent opportunities to study the long-term effects of habitat fragmentation and the impacts of climate change. Quercus arbutifolia is a rare oak in MCFs of southern China and Vietnam. Its isolated populations, small population size and unique ecological niche make this species vulnerable to climate change and habitat loss. In this study, we used chloroplast (cpDNA) and nuclear (ITS) DNA sequences to investigate genetic divergence patterns and demographic history of five of the six known populations of Q. arbutifolia. Considering its small population size and fragmentation, Q. arbutifolia has unexpectedly high genetic diversity. The time since the most recent common ancestor of all cpDNA haplotypes was c. 10.25 Ma, and the rapid diversification of haplotypes occurred during the Quaternary. The maximum clade credibility chronogram of cpDNA haplotypes suggests that the DM population (Daming Mountain, Guangxi province) diverged early and rapidly became isolated from other populations. The Pearl River drainage system may have been the main geographic barrier between DM and other populations since the late Miocene. ITS data suggests that population expansion occurred during the last interglacial of the Quaternary. The combined effects of pre-Quaternary and Quaternary climatic and geological changes were the main drivers to the current genetic diversity and distribution pattern of Q. arbutifolia. Because of the high between-population genetic differentiation and high within-population genetic diversity of Q. arbutifolia, conservation efforts should be implemented for all populations, but if conservation resources are limited, populations DM, YZ (Mang Mountain, Hunan province) and ZZ (Daqin Mountain, Fujian province) should have priority.     

Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican <Emphasis Type="Italic">Quercus</Emphasis> (Fagaceae) species

The northern Neotropical region is characterized by a heterogeneous geological and climatic history. Recent studies have shown contrasting patterns regarding the role of geographic elements as barriers that could have determined phylogeographic structure in various species. Recently, the phylogeography and biogeography of Quercus species have been studied intensively, and the patterns observed so far suggest contrasting evolutionary histories for Neotropical species in comparison with their Holarctic relatives. The goal of this study was to describe the phylogeographic structure of two Neotropical oak species (Quercus insignis and Quercus sapotifolia) in the context of the geological and palaeoclimatic history of the northern Neotropics. Populations through the distribution range of both species were collected and characterized using nine chloroplast DNA microsatellite loci. Both oak species showed high levels of genetic diversity and strong phylogeographic structure. The distribution of genetic variation in Q. insignis suggested an influence of two major barriers, the Isthmus of Tehuantepec and the Nicaraguan Depression, while Q. sapotifolia exhibited a genetic structure defined by the heterogeneity of the Chortis highlands. The haplotype networks of both species indicated complex histories, suggesting that colonization from the Sierra Madre de Chiapas to central Mexico and from the north of the Nicaraguan Depression to the Costa Rican mountains may have occurred during different stages, and apparently more than one time. In conclusion, the phylogeographic structure of Neotropical oak species seems to be defined by a combination of geological and climatic events.     

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

Given the low intraspecific chloroplast diversity detected in northern red oak (Quercus rubra L.), more powerful genetic tools are necessary to accurately characterize Q. rubra chloroplast diversity and structure. We report the sequencing, assembly, and annotation of the chloroplast genome of northern red oak via pyrosequencing and a combination of de novo and reference-guided assembly (RGA). Chloroplast DNA from 16 individuals was separated into four MID-tagged pools for a Genome Sequencer 20 quarter-run (Roche Life Sciences, Indianapolis, IN, USA). A four-step assembly method was used to generate the Q. rubra chloroplast consensus sequence: (1) reads were assembled de novo into contigs, (2) de novo contigs were aligned to a reference genome and merged to produce a consensus sequence, (3) the consensus sequence was aligned to the reference sequence and gaps between contigs were filled with reference sequence to generate a "pseudoreference", and (4) reads were mapped to the pseudoreference using RGA to generate the draft chloroplast genome. One hundred percent of the pseudoreference sequence was covered with a minimum coverage of 2× and an average coverage of 43.75×. The 161,304-bp Q. rubra chloroplast genome draft sequence contained 137 genes and one rps19 pseudogene. The sequence was compared to that of Quercus robur and Q. nigra with 951 and 186 insertion/deletion or SNP polymorphisms detected, respectively. A total of 51 intraspecific polymorphisms were detected among four northern red oak individuals. The fully sequenced and annotated Q. rubra chloroplast genome containing locations of interspecific and intraspecific polymorphisms will be essential for studying population differentiation, phylogeography, and evolutionary history of this species as well as meeting management goals such as monitoring reintroduced populations, tracking wood products, and certifying seed lots and forests.     

Clonal and genetic structure of two Mexican oaks: Quercus eduardii and Quercus potosina (Fagaceae)

Quercus eduardii and Q. potosina are dominant oak species in Sierra Fría, Aguascalientes, Mexico. These species have been exploited for multiple purposes since the 16th century. Both species produce clonal offspring through root suckering and acorns through sexual reproduction. To understand clonality for the implementation of the most adequate actions for the conservation of these species, we addressed the following questions: (a) what is the spatial clonal structure of both species? (b) How much clonal and genetic diversity is maintained in these species? Random Amplified Polymorphic DNAs (RAPDs) were used as molecular markers for these analyses. Genets of both species have few ramets and these grow close the parent tree. Autocorrelation analyses at the ramet level showed an aggregated distribution at short distances and a random spatial distribution at larger distances. Also, at the genet level the autocorrelation analyses showed a random distribution. Clonal diversity was high in both species (Q. eduardii: D=0.963, G/N=0.60; Q. potosina: D=0.985, G/N=0.65). Genetic diversity was high within populations (Q. eduardii: H _e =0.33±0.11; Q. potosina: H _e =0.35±0.11). Low levels of genetic differentiation among populations were observed (Q. eduardii ? _st =0.19, P < 0.002; Q. potosina ? _st =0.13, P < 0.002). Both species maintain high levels of clonal and genetic diversity, probably due to successful sexual reproduction, which allows gene flow among populations. Conservation and/or reforestation programs must include seed collections and germplasm banks. Due to the small genet size and the high clonal diversity of these species, seeds can be collected in any place in Sierra Fría, Aguascalientes.     

Effects of plant hybridization on the structure and composition of a highly rich community of cynipid gall wasps: the case of the oak hybrid complex <Emphasis Type="Italic">Quercus magnoliifolia</Emphasis> x <Emphasis Type="Italic">Quercus resinosa</Emphasis> in Mexico

The richness and composition of herbivore communities can be influenced by the genetic variation of host plants. Hybrid plant populations are ideal to test these effects because they usually harbor high genetic variation and display a mosaic of phenotypic characters. The goal of this study was to examine the effect of hybridization between two Mexican white oaks, Q. magnoliifolia and Q. resinosa, on the composition and diversity of the associated cynipid gall wasp community. We used eight nuclear microsatellite markers to genotype 150 oak individuals sampled at three different altitudes at the Tequila volcano and conducted monthly samplings of galls in each individual over the course of 2 years. A Bayesian assignment analysis indicated genetic admixture between the two oak species at the study site and allowed classifying individuals as Q. magnoliifolia, Q. resinosa or hybrids. Gall morphospecies richness was significantly higher in the hybrids, intermediate in Q. magnoliifolia and lower in Q. resinosa. Overall, 48 different gall morphospecies were found, with 21 of them being shared among the three groups of plants, 13 between two groups of plants, and 14 were unique to one group of plants, with eight of these being found in hybrids. Several of the shared galls showed differences in abundance among plant groups. Therefore, genetic structure in this oak complex significantly influences the diversity and composition of the associated gall wasp community, and hybrid individuals are probably acting as potential sinks and bridges for the colonization of plant hosts by these highly specialized insect species.     

Extent of nuclear genome sharing among white oak species (Quercus L. subgen. Lepidobalanus (Endl.) Oerst.) in Slovakia estimated by allozymes

European white oak species (Quercus subg. Lepidobalanus) are known to share a substantial part of the nuclear and cytoplasmic genome. In spite of this fact, they have preserved their integrity. We analyzed genetic variation at thirteen isozyme loci in nine Quercus robur, ten Q. petraea, two Q. pubescens and two mixed (two-species) populations in Slovakia to assess the extent of allele sharing. Moreover, a detailed morphometric study based on thirteen leaf traits was done in the mixed stands. A Bayesian analysis of population structure in the set of pure populations revealed the existence of three clusters, which coincided with the supposed taxonomical identity of populations. However, the distribution of posterior probabilities of data was bimodal with a second peak at six groups, what indicates a possible substructure in the gene pools of the investigated oak species. Moreover, gene admixture was close to 50% in all investigated populations. Morphometric analysis of the two mixed stands revealed a clear morphological separation of the studied oak species, sharply contrasting with a high degree of gene admixture. Differentiation is not uniformly distributed over the genome. High levels of differentiation (F _ST > 0.10) were observed at only three out of thirteen loci. The hypotheses explaining extensive allele sharing (shared ancestral polymorphisms vs. high levels of interspecific gene flow) are briefly discussed.     

Genetic diversity and population structure in wild Sichuan rhesus macaques

Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy–Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity.     

Natural hybridisation among Quercus glabrescens,Q. rugosa and Q. obtusata (Fagaceae): Microsatellites and secondary metabolites markers

• Natural hybridisation has significant ecological, genetic and evolutionary consequences altering morphological and chemical characters of individuals. Quercus glabrescens, Q. rugosa and Q. obtusata are white oak species well separated by their morphological characters when they occur in allopatry in Mexican temperate forests. However, in sympatry, individuals with atypical morphology have been observed, suggesting hybridisation events.
• In this study, we determined, with microsatellites and secondary metabolites, if interspecific gene flow occurs when these three oak species coexist in sympatry. In total, 180 individuals belonging to seven populations [three allopatric (one for each parental species) and four sympatric sites] were analysed.
• Allopatric populations represent well‐defined genetic groups and the sympatric populations showed genetic evidence of hybridisation between Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata. The hybridisation percentage varied between sites and combination of involved species. We registered the presence of unique flavonoid compounds for Q. glabrescens (caffeic acid and flavonol 2), Q. rugosa (flavonol 5) and Q. obtusata (flavonol 1). Three compounds (quercetin rhamnoside, flavonol 3 and alkyl coumarate) were expressed in all taxa. Finally, the hybrid genotypes identified in this study (Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata) showed specific chemical profiles, resulting from a combination of those of their parental species.
• These results show that hybridisation events between these oak species alter chemical expression of secondary metabolites, creating a mosaic of resources and conditions that provide the substrate for different combinations of foliar‐associated species such as herbivores, endophytic fungi or epiphyte plants.

     

Molecular phylogeny and genetic diversity of Tunisian Quercus species using chloroplast DNA CAPS markers

Chloroplast DNA variation was studied in five evergreen Quercus species from the Western part of Tunisia using Cleaved Amplified Polymorphic Sequence (CAPS) technique. Five primer pair/endonuclease combinations have been used. Chlorotypes of Quercus species have been identified. The enzyme HinfI was more efficient in detecting polymorphism in oak species than TaqI. The phenogram showed five groups defining the five studied oak species: suber group, afares group, coccifera group, canariensis group and ilex group. The topology of phenogram showed that the classification depends only on species and independently of their geographic origin. The principal component analysis (ACP) corroborated the results of the tree branching and confirmed the existence of five species groups. Our results showed a genetic proximity between Quercus afares and Quercus coccifera species that may be due to temperature tolerance or the demographic history of these species. Nevertheless, a high value of G_ST calculated (G_ST = 1), suggesting that the maximum of variation is maintained among oak species. This result was confirmed by the low value of the genetic diversity within species (h_S = 0), the value obtained of the total genetic diversity (h_T = 0.378) and the absence of gene flow between species (N_m = 0). A high genetic proximity has been registered between Q. afares, Quercus suber and Quercus canariensis. Moreover, Q. afares shared the chlorotype of Q. suber and Q. canariensis which suggests its hybrid origin.     

High genetic variation among closely related red oak (<Emphasis Type="Italic">Quercus rubra</Emphasis>) populations in an ecosystem under metal stress: analysis of gene regulation

Metal toxicity is a major abiotic stressor of plants. It has been established that changes in genetic variation occur very rapidly in plants in response to environmental stressors such as increased levels of metals. Quercus rubra (red oak) is a pioneer species in mining regions contaminated with metals in Northern Ontario (Canada). The objectives of the study were to (1) determine the level of genetic variation in Q. rubra populations from mining damaged ecosystems using RAPD marker system and (2) assess the level of gene expression of candidate genes for nickel resistance. Total gene diversity (H_T) and the mean gene diversity among populations (H_S) were 0.22 and 0.19, respectively. The percent of polymorphic loci within populations was high ranging from 61 % (Capreol) to 72 % (Daisy Lake) despite a high level of gene flow (2.4). The population differentiation (G_ST) value was low (0.17). No significant difference was found among the contaminated and reference sites for all the genetic parameters estimated. Hence, all the Q. rubra populations from the metal-contaminated and damaged ecosystems are genetically sustainable. Moreover, this study reveals that all populations were genetically closely related with genetic distance values varying from 0.17 to 0.35. A zinc finger protein of Arabidopsis thaliana (ZAT11) gene involved in nickel resistance was differentially expressed in samples analyzed. There was a 120 times higher of ZAT11 expression in samples from metal contaminated areas of Wahnapitae Dam compared to other metal contaminated and uncontaminated sites, but no association between soil metal levels and expression of ZAT11 was established.     

Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico

Background and Aims

Interspecific gene flow can occur in many combinations among species within the genus Quercus, but simultaneous hybridization among more than two species has been rarely analysed. The present study addresses the genetic structure and morphological variation in a triple hybrid zone formed by Q. hypoleucoides, Q. scytophylla and Q. sideroxyla in north-western Mexico.

Methods

A total of 247 trees from ten reference and 13 presumed intermediate populations were characterized using leaf shape variation and geometric morphometrics, and seven nuclear microsatellites as genetic markers. Discriminant function analysis was performed for leaf shape variation, and estimates of genetic diversity and structure, and individual Bayesian genetic assignments were obtained.

Key Results

Reference populations formed three completely distinct groups according to discriminant function analysis based on the morphological data, and showed low, but significant, genetic differentiation. Populations from the zone of contact contained individuals morphologically intermediate between pairs of species in different combinations, or even among the three species. The Bayesian admixture analysis found that three main genetic clusters best fitted the data, with good correspondence of reference populations of each species to one of the genetic clusters, but various degrees of admixture evidenced in populations from the contact area.

Conclusions

The three oak species have formed a complex hybrid zone that is geographically structured as a mosaic, and comprising a wide range of genotypes, including hybrids between different species pairs, backcrosses and probable triple hybrids.     

Chloroplast DNA Microsatellites Reveal Contrasting Phylogeographic Structure in Mahogany (Swietenia macrophylla King, Meliaceae) from Amazonia and Central America

Big-leaf mahogany (Swietenia macrophylla King) is one of the most valuable and overharvested timber trees of tropical America. In order to better characterize geographic patterns of genetic variation, we performed a phylogeographic analysis of S. macrophylla based on six polymorphic chloroplast genome simple sequence repeat loci (cpSSRs) analyzed in 16 populations (N?=?245 individuals) distributed across Central America and the Brazilian Amazon. Of the 31 total cpDNA haplotypes identified, 16 occurred in Central America and 15 in Amazonia with no single haplotype shared between the two regions. Populations from Central America showed moderate differentiation (F _ST ?=?0.36) while within population genetic diversity was generally high (mean Nei’s H _E ?=?0.639). In contrast, the Amazonian populations were strongly differentiated (F _ST ?=?0.91) and contained relatively low genetic diversity (mean H _E ?=?0.176), except for one highly diverse population (H _E ?=?0.925) from eastern Amazonia. Spatial analysis of molecular variance (SAMOVA) identified a single Central American phylogroup and four Amazonian phylogroups, indicating stronger phylogeographic structure within Amazonia. The results demonstrate distinctive regional patterns of S. macrophylla differentiation, and the first evidence of a strong phylogeographic break between Central American and South American mahogany populations. We suggest that the frequent occurrence of hurricanes in Central America, the differences in the glacial histories and in the duration and intensity of anthropogenic disturbance during the late Holocene may have played important roles in the geographic structuring of cpDNA lineages in the two regions. The high private haplotype diversity in Brazilian populations suggests that cpSSRs can be used as DNA barcodes for regional timber certification.     

Allozyme variation in cork oak (Quercus suber L.): the role of phylogeography and genetic introgression by other Mediterranean oak species and human activities

 Genetic variation in the cork oak (Quercus suber L.) was investigated using 11 loci from seven enzyme systems in 40 populations sampled over the entire distribution of this species in the western Mediterranean Basin. Mean heterozygosity values over the polymorphic loci (Ho=0.283), the percentage of polymorphic populations (M=0.76), and the total genetic diversity (Ht=0.31) from which 11% was accounted for among-population variation, are among the highest recorded in oak species. In contrast to previous results in holm oak (Q. ilex L.), another evergreen species in the same area, cork oak possessed a smaller allele pool and a lower average number of alleles per locus and per population (A=2.0). More particularly, very few low-frequency alleles were observed in cork oak except for eight populations in which allozyme polymorphism at locus Pgi 1, diagnostic between both species, indicates that these low-frequency alleles are introgressed from holm oak. On the basis of the genetic distance estimated from allozyme frequencies, 32 of the 40 cork oak populations studied were classified into two very distinct sets which also corresponded to distinct geographic areas. One set gathered together the 18 populations from the Iberian peninsula and two adjacent areas in France, i.e. the centre of origin of cork oak, according to paleobotanical data. This set was characterized by a larger allele pool, a higher within-population genetic diversity and a lower differentiation between populations than was observed in the other set, which comprised the populations from North Africa, Sicily, Sardinia, Corsica, continental Italy and the region of Provence (southeastern France). In these more southern and eastern disjunct areas, cork oak migration from Iberia may have occurred at different periods since the end of the Tertiary. The possible effect of human activity on cork oak genetic structure, i.e. the selection of good-quality cork, acorn over-use for animal food, and even human nutrition, is discussed. Received: 3 March 1998 / Accepted: 19 March 1998