Population structure and genetic diversity of Lithocarpus litseifolius (Fagaceae) assessed using microsatellite markers

Lithocarpus litseifolius (Fagaceae), known as tree of Chinese sweet tea, is a native commercial plant distributed in south China and adjacent areas. This study used ten microsatellite markers to investigate the genetic variation and population structure of 11 populations of L. litseifolius from the main production regions in China. All of the tested loci proved to be effective for the species. The number of alleles per locus ranged between 3 and 39, and mean observed and expected heterozygosity was 0.43 and 0.52, respectively. The deficiency in heterozygosity may be the result of human interference and harvesting activities. Analysis of molecular variance revealed that most of the variation was within populations, whereas differentiation among populations was insignificant, and that there was no significant correlation between genetic distance and geographic distance (r = 0.4089, p = 0.9940). However, A Bayesian model‐based analysis sorted all 11 populations into two (when k = 2) or three (when k = 3) clusters with higher probabilities and showed a geographical pattern which is probably related to the topography of China. Our results provide important information for protecting, sustainably using, and improving the current resources of L. litseifolius.     

Effect of a red oak species gradient on genetic structure and diversity of Quercus castanea (Fagaceae) in Mexico

Incipient reproductive barriers are a common characteristic of oak species. Disruption of these barriers promotes changes in diversity and genetic structure of the species involved. Quercus castanea is a red oak with wide geographic distribution in Mexico, which presents atypically high morphological variability when it occurs in sympatry with other red oak species, suggesting that hybridization may explain the observed variation. We tested if the genetic structure and diversity levels of Q. castanea are related to the number of red oak species growing in sympatry. In total, 14 microsatellite (SSRs) primers (six nSSRs and eight cpSSRs) were used in 120 Q. castanea individuals (20/site) belonging to six populations, where the number of red oak species associated varied from zero to five. Results showed a positive and significant relationship between the genetic diversity of Q. castanea and the number of red oak species growing in sympatry, regardless of the marker type or the parameter of genetic diversity analyzed. Also, we found a higher genetic differentiation of Q. castanea populations using cpSSRs in comparison with nSSRs. Our results suggest that temperate forests with high red oaks species richness co-dominated by Q. castanea promote the increase in this species genetic diversity. From a conservation perspective, high genetic diversity levels of foundation species such as Q. castanea may have positive cascade effects extending to other species in the community.     

Genetic architecture in bur oak,Quercus macrocarpa (Fagaceae), inferred by means of spatial autocorrelation analysis

Allozyme variation at seven putative polymorphic gene loci (Fle, Idh, Mdh-2, Mdh-3, 6 Pgd-2, Pgi-2, Pgm) was quantified in an isolatedQuercus macrocarpa population in northwestern Ontario, Canada. The bur oaks studied were slightly less genetically variable (H _e = 0.196,A = 3.43) than theQuercus subg.Lepidobalanus average. To assess the genetic differentiation within the topodeme,Moran's spatial autocorrelation coefficients were used for the nearest-neighbor map and correlograms. Results indicate that most alleles were randomly distributed in space. However, significant genetic patches were detected for twoFle-alleles. Patch width was inferred to be less than 10m. This spatial substructure may be due to limited gene flow and/or demographic factors. Spatially varying selection can be probably excluded as a spatial evolutionary force, since site conditions were very homogeneous.     

Drought response of two Mexican oak species, Quercus laceyi and Q. sideroxyla (Fagaceae), in relation to elevational position

To investigate the relationship between the altitudinal distribution of Quercus laceyi and Q. sideroxyla and their physiological responses to drought, we measured relative water content (RWC), water potentials (Ψ(predawn) and Ψ(midday)), photosynthesis (A(max)), stomatal conductance (g), chlorophyll fluorescence (F(v)/F(m)), and spectral reflectance (400-1100 nm) five times during a 7 wk acute drought. Quercus laceyi was drought tolerant, while Q. sideroxyla was a drought avoider; Q. laceyi tolerated lower RWC (Q. sideroxyla = 54%, Q. laceyi = 44%), Ψ(pd) (Q. sideroxyla = -2.6 MPa, Q. laceyi = -3.3 MPa), and Ψ(md) (Q. sideroxyla = -4.5 MPa, Q. laceyi = -6.6 MPa). The F(v)/F(m) also declined first in Q. sideroxyla in wk 6, whereas F(v)/F(m) did not decline in Q. laceyi until wk 7. A(max) and g fell in wk 4, 6, and 7 in drought seedlings of both species, suggesting a decline in CO(2) assimilation during the drought. Leaf spectral reflectance increased with time in response to decreases in leaf photosynthetic pigment concentrations in latter weeks of the drought. The results suggest a close association between the altitudinal distributions of these species and their adaptation to water stress.     

Genetic diversity in Nothofagus alessandrii (Fagaceae), an endangered endemic tree species of the coastal maulino forest of Central Chile

BACKGROUND AND AIMS: The endemic tree Nothofagus alessandrii (Fagaceae) has been historically restricted to the coastal range of Region VII of central Chile, and its forests have been increasingly destroyed and fragmented since the end of the 19th century. In this study, the patterns of within- and among-population genetic diversity in seven fragments of this endangered narrowly endemic tree were examined. METHODS: Allozyme electrophoresis of seven loci of N. alessandrii was used to estimate genetic diversity, genetic structure and gene flow. KEY RESULTS: High levels of genetic diversity were found as shown by mean expected heterozygosity (H(e) = 0.182 +/- 0.034), percentage of polymorphic loci (P(p) = 61.2 %), mean number of alleles per locus (A = 1.8) and mean number of alleles per polymorphic locus (A(p) = 2.3). Genetic differentiation was also high (G(ST) = 0.257 and Nm = 0.7). These values are high compared with more widespread congeneric species. CONCLUSIONS: Despite its endemic status and restricted geographical range N. alessandrii showed high levels of genetic diversity. The observed patterns of diversity are explained in part by historical processes and more recent human fragmentation.     

Impact of sudden oak death on tree mortality in the Big Sur ecoregion of California

The Big Sur ecoregion in coastal California is a botanically and ecologically diverse area that has recently experienced substantial mortality of oak (Quercus spp.) and tanoak (Lithocarpus densiflorus) trees due to the emerging forest disease sudden oak death, caused by the invasive pathogen Phytophthora ramorum. In response to the urgent need to examine environmental impacts and create management response strategies, we quantified the impact of P. ramorum invasion on tree mortality across the Big Sur ecoregion using high-resolution aircraft imagery and field data. Using the imagery, we mapped all detectable oak and tanoak trees possibly killed by P. ramorum infection within redwood-tanoak forests and mixed oak woodlands. To validate and improve our remote assessment, we quantified the number, size, and infection status of host trees in 77 field plots (0.25 ha). The field data showed that our remote assessment underestimated mortality due to the occurrence of dead trees in the forest understory. For each forest type, we developed regression models that adjusted our remote assessments of tree mortality in relation to field observations of mortality and local habitat variables. The models significantly improved remote assessment of oak mortality, but relationships were stronger for mixed oak woodlands (r ² = 0.77) than redwood-tanoak forests (r ² = 0.66). Using the field data, we also modeled the amount of dead tree basal area (m²) in relation to the density of mapped dead trees in mixed oak woodlands (r ² = 0.73) and redwood-tanoak forests (r ² = 0.54). Application of the regression models in a GIS estimated 235,678 standing dead trees in 2005 and 12,650 m² of tree basal area removed from the ecoregion, with 63% of mortality occurring in redwood-tanoak forests and 37% in mixed oak woodlands. Integration of the remote assessment with population estimates of host abundance, obtained from an independent network of 175 field plots (0.05 ha each), indicated similar prevalence of mortality in redwood-tanoak forests (20.0%) and mixed oak woodlands (20.5%) at this time. This is the first study to quantify a realistic number of dead trees impacted by P. ramorum over a defined ecological region. Ecosystem impacts of such widespread mortality will likely be significant.

Genetic diversity and structure of Atta robusta (Hymenoptera,Formicidae, Attini), an endangered species endemic to the restinga ecoregion

The genetic diversity and structure of the ant Atta robusta were assessed by ISSR (inter-simple sequence repeats) in 72 colonies collected from 10 localities in the Brazilian states of Espírito Santo (48 colonies) and Rio de Janeiro (24 colonies). The ISSR pattern included 67 bands, 51 of them (76.1%) polymorphic. Analysis of molecular variance (AMOVA) revealed a high level (57.4%) of inter-population variation, which suggested a high degree of genetic structure that was confirmed by UPGMA (unweighted pair-group method using an arithmetic average) cluster analysis. The significant correlation between genetic and geographic distances (r = 0.64, p < 0.05) indicated isolation that reflected the distance between locations. Overall, the populations were found to be genetically divergent. This finding indicates the need for management plans to preserve and reduce the risk of extinction of A. robusta.     

Clonal population structure and genetic variation in sand-shinnery oak,Quercus havardii (Fagaceae)

We investigated clonal population structure and genetic variation in Quercus havardii (sand-shinnery oak), a deciduous rhizomatous shrub that dominates vegetation by forming uninterrupted expanses of ground cover over sandy deposits on the plains of western Texas, western Oklahoma, and eastern New Mexico. Isozyme electrophoresis (15 loci coding 11 enzymes) was used to recognize and map clones arrayed in a 2000-m transect (50-m sample intervals) and a 200 × 190 m grid (10-m sample intervals). Ninety-four clones were discovered, 38 in the transect and 56 in the grid, resulting in an estimated density of ～15 clones per hectare. Clones varied greatly in size (～100-7000 m), shape, and degree of fragmentation. The larger clones possessed massive interiors free of intergrowth by other clones, while the smaller clones varied in degree of intergrowth. The population maintained substantial levels of genetic variation (P = 60%, A = 2.5, H(exp) = 0.289) comparable to values obtained for other Quercus spp. and for other long-lived perennials. The population was outcrossing as evidenced by conformance of most loci to Hardy-Weinberg expected genotype proportions, although exceptions indicated a limited degree of population substructuring. These data indicate that despite apparent reproduction primarily through vegetative means, Q. havardii possesses conventional attributes of a sexual population.     

Genetic diversity of Allium munzii (Amaryllidaceae), a rare southern California species and implication for its conservation

An understanding of genetic diversity within and among populations of rare plant species is a prerequisite to develop effective conservation management strategies and reintroduction programs. Allium munzii is a narrow endemic species distributed in western Riverside County, California, USA and known from 18 extant element occurrences. We sampled 119 individuals from 11 element occurrences and investigated within and among population genetic diversity using two variable chloroplast markers (rpL32–trnL intergenic spacer and rpoC1 intron). Of the total genetic variation detected in A. munzii, 87.65% was due to differences among occurrences. Furthermore, our results revealed that most of the element occurrences are strongly genetically differentiated. There are low levels of gene flow between occurrences, not due to isolation by distance but possibly resulting from habitat fragmentation. Non-significant values of Tajima's D and Fu's Fs were found in all occurrences suggesting no demographic expansion in A. munzii. Ex situ seed and bulb conservation is recommended to enable introduction of individuals to occurrences with low abundance and genetic diversity.     

Predicting species responses to climate change: demography and climate microrefugia in California valley oak (Quercus lobata)

Anticipating species movement under climate change is a major focus in conservation. Bioclimate models are one of the few predictive tools for adaptation planning, but are limited in accounting for (i) climatic tolerances in preadult life stages that are potentially more vulnerable to warming; and (ii) local‐scale movement and use of climatic refugia as an alternative or complement to large‐scale changes in distribution. To assess whether these shortfalls can be addressed with field demographic data, we used California valley oak (Quercus lobata Nee), a long‐lived species with juvenile life stages known to be sensitive to climate. We hypothesized that the valley oak bioclimate model, based on adults, would overpredict the species' ability to remain in the projected persisting area, due to higher climate vulnerability of young life stages; and underpredict the potential for the species to remain in the projected contracting area in local‐scale refugia. We assessed the bioclimate model projections against actual demographic patterns in natural populations. We found that saplings were more constricted around surface water than adults in the projected contracting area. We also found that the climate envelope for saplings is narrower than that for adults. Saplings disappeared at a summer maximum temperature 3 °C below that associated with adults. Our findings indicate that rather than a complete shift northward and upward, as predicted by the species bioclimate model, valley oaks are more likely to experience constriction around water bodies, and eventual disappearance from areas exceeding a threshold of maximum temperature. Ours is the first study we know of to examine the importance of discrete life stage climate sensitivities in determining bioclimate modeling inputs, and to identify current climate change‐related constriction of a species around microrefugia. Our findings illustrate that targeted biological fieldwork can be central to understanding climate change‐related movement for long‐lived, sessile species.     

A comparative study of oak (Quercus, Fagaceae) seedling physiology during summer drought in southern California

Natural recruitment of oaks appears to be declining throughout the northern hemisphere. Summer drought poses a potentially important barrier to oak recruitment in southern California. To evaluate this barrier, we grew evergreen Quercus agrifolia and deciduous Q. lobata from seeds near parental trees. We measured water relations, chlorophyll fluorescence, and gas exchange during these seedlings' fourth and fifth summers and compared them to neighboring adults. Most seedlings had substantially lower values for predawn xylem pressure potential (Ψ(pd)), minimum photosystem II (PSII) quantum efficiency (Φ(PSIIMIN)), maximum quantum efficiency for PSII under dark-adapted leaf conditions (Fv/Fm), and maximum photosynthetic assimilation (Amax), and higher values for maximum nonphotochemical quenching (NPQmax) than did conspecific adults. The high, unvarying Ψ(pd) values of the adults suggest they use perennially available groundwater. Quercus lobata seedlings commonly had lower values for Ψ(pd) than did Q. agrifolia, and values for Ψ(pd) and Φ(PSIIMIN) were significantly related to size in Q. lobata but not in Q. agrifolia. These data suggest important interspecific differences in root architecture. Lower values for Φ(PSIIMIN), Fv/Fm, and higher NPQmax in Q. agrifolia indicate that Q. agrifolia seedlings were usually under more stress than Q. lobata, which typically had higher Amax rates than did Q. agrifolia seedlings. Diurnal photosynthesis curves were quite flat for Q. agrifolia, but they peaked in the morning for Q. lobata. Established seedlings appeared to be under more stress than adults, but this stress did not appear severe enough to cause death. Access to perennially available groundwater may be crucial for the seedling to sapling transition.     

Genetic diversity and local population structure in Ambrosina bassii (Araceae,Ambrosineae), a Mediterranean relict species

The effects of habitat fragmentation on the genetic structure of Ambrosina bassii are analyzed. The species, whose reproductive biology is mostly unknown, is the only representative of its genus and tribe and it is endemic to the central Mediterranean area. The selected study area was the island of Sicily, in which wild populations show a wide morphological variability and ecological amplitude. Patterns of within- and among-population genetic diversity in eleven Sicilian populations, occurring in six disjunct areas, were examined by means of allozyme electrophoresis. High levels of genetic diversity were found as shown by the mean expected heterozygosity (H_e = 0.263), the percentage of polymorphic loci (P₉₅ = 65.3), the mean number of alleles per locus (A = 2.0). Genetic differentiation between populations was relatively low (mean F_ST = 0.091 and Nm = 1.98). A very weak correlation exists between genetic distances and geographic distances between populations. Despite its restricted and fragmented geographical range, A. bassii showed (i) high levels of genetic diversity, mainly within populations; (ii) no genetic differentiation between populations and morphotypes.     

Genetic diversity and population structure of Swertia tetraptera (Gentianaceae), an endemic species of Qinghai-Tibetan Plateau

Swertia tetraptera Maxim is an annual alpine herb endemic to the Qinghai-Tibetan Plateau (QTP). Its populations are locally scattered as isolated patches throughout this region. Genetic variation within and among thirty-four populations of this species was assessed using ISSR fingerprinting with 10 primers. High levels of genetic diversity exist within species (P = 98.9%, I = 0.3475; He = 0.2227), while the within-population diversity is low (P = 32.7%, I = 0.177; He = 0.12). High levels of genetic differentiation were detected among populations based on various statistics, including Nei’s genetic diversity analysis (G_ST = 0.4608), Bayesian analysis (θ^B = 0.476) and AMOVA (F_ST = 0.57). That is, populations shared low levels of genetic identity (I = 0.2622–0.0966). This genetic structure was probably due to severe genetic drift, breeding system and limited gene flow. The observed genetic structure of the populations implies that different populations across the distribution range of the species should be sampled to maintain high genetic diversity when a conservation strategy is implemented.     

Population structure, genetic diversity, and clone formation in Quercus chrysolepis (Fagaceae)

Stands of canyon live oak (Quercus chrysolepis, Fagaceae) are maintained for fuelwood, fire management, recreation, and as habitat for wildlife. Information about the link between the oak's reproductive ecology and its extent of genetic diversity is important in developing land management policies that will maintain the long-term viability of populations. Basal sprouting is the primary means of reproduction following fire or cutting, and stands frequently include groups of visibly connected trees in a clustered distribution that suggests cloning. We determined the extent to which clusters of trees were clonal and defined the spatial pattern and diversity of genotypes for six populations across nearly the entire east-west extent of the San Bernardino Mountains in southern California. We mapped over 100 trees at each of five sites and genotyped each tree for allozymes at seven polymorphic loci. We identified clones using these multilocus genotypes and detected an average of 34.4 ± 7.3 (SD) clones per site, most of which had unique genotypes. In general, clustered trees belong to single clones and most clones consist of few trees (mean = 3.4 ± 0.6 trees per clone). However, clone size increased significantly with increased individual heterozygosity, suggesting that selection may favor highly heterozygous clones. Clonal diversity and evenness were high relative to reports for most other clonal species; an average of 97% of clones had distinct genotypes, and Simpson's index of diversity averaged 0.95 ± 0.02. Population genetic analyses of 319 clones from six sites revealed high genetic diversity within sites (mean HS = 0.443). Only a small proportion of the total genetic diversity was explained by variation among sites (mean GST = 0.018), which is consistent with high gene flow among sites (Nm = 9.5). We found no significant substructure among plots within sites, and fixation indices within sites were generally small, suggesting that either little inbreeding occurs, and/or few inbred progeny survive. However, spatial autocorrelation analysis of clones indicated fine-scale genetic structure at distances under 4 m, possibly due to limited seed dispersal. Our data suggest that guidelines for seed collection of canyon live oak for use in restoration can be specified in a manner similar to that recommended for conifer species within the region studied.     

Genetic diversity and population structure in four Cirsium (Asteraceae) species

The present study considers genetic diversity of 38 populations in 4 Cirsium species of the genus Cirsium Mill. (Asteraceae), occurring in different ecological regions and tries to compare degree of genetic variability among the species with wide geographical distribution versus endemic C. pyramidale showing confined geographical distribution. The results showed that the endemic species has similar value of genetic diversity parameters as the species with wider distribution. We also studied the possible admixture nature of these populations and tried to understand the relation between genetic changes, geographical distribution and polyploidy level and chromosome pairing in these species. ISSR analysis showed population difference in allele composition and frequency. Clustering and PcoA ordination produced different groupings in each species, while STRUCTURE and reticulation analyses revealed high degree of genetic admixture and gene exchange among populations as well as allelic rearrangement. No significant correlation was observed between geographical distance and genetic distance of the populations and AMOVA test revealed no significant difference among populations in each species studied. However, high amount of within population variation occurred in all 4 species indicating their cross-pollination nature and high genetic admixture. The populations also varied in chiasma frequency and chromosome pairing as well as the occurrence of heterozygote translocations all creating more variability to be used by plants for local adaptation.     

Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population

The Finnish wolf population (Canis lupus) was sampled during three different periods (1996-1998, 1999-2001 and 2002-2004), and 118 individuals were genotyped with 10 microsatellite markers. Large genetic variation was found in the population despite a recent demographic bottleneck. No spatial population subdivision was found even though a significant negative relationship between genetic relatedness and geographic distance suggested isolation by distance. Very few individuals did not belong to the local wolf population as determined by assignment analyses, suggesting a low level of immigration in the population. We used the temporal approach and several statistical methods to estimate the variance effective size of the population. All methods gave similar estimates of effective population size, approximately 40 wolves. These estimates were slightly larger than the estimated census size of breeding individuals. A Bayesian model based on Markov chain Monte Carlo simulations indicated strong evidence for a long-term population decline. These results suggest that the contemporary wolf population size is roughly 8% of its historical size, and that the population decline dates back to late 19th century or early 20th century. Despite an increase of over 50% in the census size of the population during the whole study period, there was only weak evidence that the effective population size during the last period was higher than during the first. This may be caused by increased inbreeding, diminished dispersal within the population, and decreased immigration to the population during the last study period.