Integrated global assessment of the natural forest carbon potential

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2-5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellite-derived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151-363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

The global biogeography of tree leaf form and habit

Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4 Gt), 54% (335.7 Gt), 22% (136.2 Gt) and 3% (18.7 Gt), respectively. We further project that, depending on future emissions pathways, 17-34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling.

Native diversity buffers against severity of non-native tree invasions

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species1,2. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies3,4. Here, leveraging global tree databases5-7, we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.

Co-limitation towards lower latitudes shapes global forest diversity gradients

The latitudinal diversity gradient (LDG) is one of the most recognized global patterns of species richness exhibited across a wide range of taxa. Numerous hypotheses have been proposed in the past two centuries to explain LDG, but rigorous tests of the drivers of LDGs have been limited by a lack of high-quality global species richness data. Here we produce a high-resolution (0.025° × 0.025°) map of local tree species richness using a global forest inventory database with individual tree information and local biophysical characteristics from ~1.3 million sample plots. We then quantify drivers of local tree species richness patterns across latitudes. Generally, annual mean temperature was a dominant predictor of tree species richness, which is most consistent with the metabolic theory of biodiversity (MTB). However, MTB underestimated LDG in the tropics, where high species richness was also moderated by topographic, soil and anthropogenic factors operating at local scales. Given that local landscape variables operate synergistically with bioclimatic factors in shaping the global LDG pattern, we suggest that MTB be extended to account for co-limitation by subordinate drivers.

Southeast Asian Dipterocarp origin and diversification driven by Africa-India floristic interchange

The evolution and diversification of ancient megathermal angiosperm lineages with Africa-India origins in Asian tropical forests is poorly understood because of the lack of reliable fossils. Our palaeobiogeographical analysis of pollen fossils from Africa and India combined with molecular data and fossil amber records suggest a tropical-African origin of Dipterocarpaceae during the mid-Cretaceous and its dispersal to India during the Late Maastrichtian and Paleocene, leading to range expansion of aseasonal dipterocarps on the Indian Plate. The India-Asia collision further facilitated the dispersal of dipterocarps from India to similar climatic zones in Southeast Asia, which supports their out-of-India migration. The dispersal pathway suggested for Dipterocarpaceae may provide a framework for an alternative biogeographic hypothesis for several megathermal angiosperm families that are presently widely distributed in Southeast Asia.

Genome Sequence Resource of Bacillus velezensis EB14, a Native Endophytic Bacterial Strain with Biocontrol Potential Against the Poplar Stem Canker Causative Pathogen, Sphaerulina musiva

Bacillus velezensis EB14, isolated from a leaf of Populus × jackii, possesses antagonistic activity against Sphaerulina musiva, a fungal pathogen of Populus sp. that causes leaf spots and stem cankers on poplars, limiting the utility of hybrid poplars as plantation trees. We sequenced the genome of B. velezensis EB14 to gain insights into the underlying basis of its antagonistic activity. Here, we report the complete genome sequence of B. velezensis EB14, a gram-positive bacterium of the family Bacillaceae. Through antiSMASH analysis, we predicted several gene clusters coding for the biosynthesis of antimicrobial compounds and several genes involved in plant bacterial interactions. These findings support the potential of developing B. velezensis EB14 as a biocontrol agent against S. musiva in poplar plantations. The genome of B. velezensis EB14 along with genome sequences of closely related B. velezensis species are invaluable for comparative genomic analyses to gain insights into bacterial, fungal, and host plant interactions.

Plants endophytes: unveiling hidden agenda for bioprospecting toward sustainable agriculture

Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host-endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host-endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.

Ecosystem-level carbon storage and its links to diversity, structural and environmental drivers in tropical forests of Western Ghats, India

Tropical forests are rich in biodiversity with great potential for carbon (C) storage. We estimated ecosystem-level C stock using data from 70 forest plots in three major forest types: tropical dry deciduous (TDD I and TDD II), tropical semi-evergreen (TSE I and TSE II) and tropical evergreen forests (TEF I, TEF II and TEF III) of Kanyakumari Wildlife Sanctuary, Western Ghats, India. The average C stock in these forests was 336.8 Mg C/ha, of which 231.3, 3.0, 2.4, 15.2 and 84.9 Mg C/ha were stored in woody vegetation, understorey, litter, deadwood and soil respectively. The live vegetation, detritus and soil contributed 65.5%, 5.5% and 29% respectively to the total ecosystem-level C stock and distributed in forest types in the order: TEF III > TEF II > TEF I > TSE I > TDD II > TSE II > TDD I. The plant diversity, structural attributes and environmental factors showed significant positive correlations with C stocks and accounted for 6.7, 77.2 and 16% of variance. These findings indicate that the tropical forests in the Western Ghats store large amount of C, and resulting data are invaluable for planning and monitoring forest conservation and management programs to enhance C storage in tropical forests.

Ecological niche modeling for conservation planning of an endemic snail in the verge of becoming a pest in cardamom plantations in the Western Ghats biodiversity hotspot

Conservation managers and policy makers are often confronted with a challenging dilemma of devising suitable strategies to maintain agricultural productivity while conserving endemic species that at the early stages of becoming pests of agricultural crops. Identification of environmental factors conducive to species range expansion for forecasting species distribution patterns will play a central role in devising management strategies to minimize the conflict between the agricultural productivity and biodiversity conservation. Here, we present results of a study that predicts the distribution of Indrella ampulla, a snail endemic to the Western Ghats biodiversity hotspot, which is becoming a pest in cardamom (Ellettaria cardamomum) plantations. We determined the distribution patterns and niche overlap between I. ampulla and Ellettaria cardamomum using maximum entropy (MaxEnt) niche modeling techniques under current and future (2020-2080) climatic scenarios. The results showed that climatic (precipitation of coldest quarter and isothermality) and soil (cation exchange capacity of soil [CEC]) parameters are major factors that determine the distribution of I. ampulla in Western Ghats. The model predicted cardamom cultivation areas in southern Western Ghats are highly sensitive to invasion of I. ampulla under both present and future climatic conditions. While the land area in the central Western Ghats is predicted to become unsuitable for I. ampulla and Ellettaria cardamomum in future, we found 71% of the Western Ghats land area is suitable for Ellettaria cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of 35% between two species. The resulting distribution maps are invaluable for policy makers and conservation managers to design and implement management strategies minimizing the conflicts to sustain agricultural productivity while maintaining biodiversity in the region.

Genetic structure and diversity of natural and domesticated populations of Citrus medica L. in the Eastern Himalayan region of Northeast India

Citron (Citrus medica L.) is a medicinally important species of citrus native to India and occurs in natural forests and home gardens in the foothills of the eastern Himalayan region of northeast India. The wild populations of citron in the region have undergone rapid decline due to natural and anthropogenic disturbances and most of the remaining individuals of citron are found in fragmented natural forests and home gardens in the region. In order to assess the genetic structure and diversity of citron in wild and domesticated populations, we analyzed 219 individuals of C. medica collected from four wild and eight domesticated populations using microsatellite markers. The genetic analysis based on five polymorphic microsatellite loci revealed an average of 13.40 allele per locus. The mean observed and expected heterozygosity values ranged between 0.220–0.540 and 0.438–0.733 respectively among the wild and domesticated populations. Domesticated populations showed close genetic relationships as compared to wild populations and pairwise Nei's genetic distance ranged from 0.062 to 2.091 among wild and domesticated populations. Analysis of molecular variance (AMOVA) showed higher genetic diversity among‐ than within populations. The analysis of population structure revealed five groups. Mixed ancestry of few individuals of different populations revealed exchange of genetic materials among farmers in the region. Citron populations in the region show high genetic variation. The knowledge gained through this study is invaluable for devising genetically sound strategies for conservation of citron genetic resources in the region.

Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene

BACKGROUND

Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes.

FINDINGS

The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes.

CONCLUSION

The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

Genetic Structure, Diversity and Long Term Viability of a Medicinal Plant, Nothapodytes nimmoniana Graham. (Icacinaceae), in Protected and Non-Protected Areas in the Western Ghats Biodiversity Hotspot

Background and Question

The harvesting of medicinal plants from wild sources is escalating in many parts of the world, compromising the long-term survival of natural populations of medicinally important plants and sustainability of sources of raw material to meet pharmaceutical industry needs. Although protected areas are considered to play a central role in conservation of plant genetic resources, the effectiveness of protected areas for maintaining medicinal plant populations subject to intense harvesting pressure remain largely unknown. We conducted genetic and demographic studies of Nothapodytes nimmoniana Graham, one of the extensively harvested medicinal plant species in the Western Ghats biodiversity hotspot, India to assess the effectiveness of protected areas in long-term maintenance of economically important plant species.

Methodology/Principal Findings

The analysis of adults and seedlings of N. nimmoniana in four protected and four non-protected areas using 7 nuclear microsatellite loci revealed that populations that are distributed within protected areas are subject to lower levels of harvesting and maintain higher genetic diversity (H_e = 0.816, H_o = 0.607, A = 18.857) than populations in adjoining non-protected areas (H_e = 0.781, H_o = 0.511, A = 15.571). Furthermore, seedlings in protected areas had significantly higher observed heterozygosity (H_o = 0.630) and private alleles as compared to seedlings in adjoining non-protected areas (H_o = 0.426). Most populations revealed signatures of recent genetic bottleneck. The prediction of long-term maintenance of genetic diversity using BOTTLESIM indicated that current population sizes of the species are not sufficient to maintain 90% of present genetic diversity for next 100 years.

Conclusions/Significance

Overall, these results highlight the need for establishing more protected areas encompassing a large number of adult plants in the Western Ghats to conserve genetic diversity of economically and medicinally important plant species.

Phylogeny reconstruction and hybrid analysis of populus (Salicaceae) based on nucleotide sequences of multiple single-copy nuclear genes and plastid fragments

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.

Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India

Background

During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus.

Results

No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (π_tot = 0.0053) than nonglutinous type varieties (π_tot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (π_tot = 0.0010) than in the colored apiculus varieties (π_tot = 0.0023).

Conclusions

The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.

Functional androdioecy in critically endangered Gymnocladus assamicus (Leguminosae) in the Eastern Himalayan Region of Northeast India

Gymnocladus assamicus is a critically endangered tree species endemic to Northeast India, and shows sexual dimorphism with male and hermaphrodite flowers on separate trees. We studied phenology, reproductive biology and mating system of the species. The flowers are small, tubular, odorless and last for about 96 hours. Pollen grains in both morphs were viable and capable of fertilization leading to fruit and seed set. Scanning electron micrographs revealed morphologically similar pollen in both male and hermaphrodite flowers. The fruit set in open pollinated flowers was 43.61 percent, while controlled autogamous and geitonogamous pollinations yielded 76.81 and 65.58 percent fruit set respectively. Xenogamous pollinations between male and hermaphrodite flowers resulted in 56.85 percent fruit set and pollinations between hermaphrodite flowers yielded 67.90 percent fruit set. This indicates a functionally androdioecious mating system and pollination limited fruit set in G. assamicus. Phylogenetic analyses of Gymnocladus and the sister genus Gleditsia are needed to assess if the androdioecious mating system in G. assamicus evolved from dioecy as a result of selection for hermaphrodites for reproductive assurance during colonization of pollination limited high altitude ecosystems.

Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India

The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.

Tertiary origin and pleistocene diversification of dragon blood tree (Dracaena cambodiana-Asparagaceae) populations in the Asian tropical forests

Background

The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests.

Methods

We analyzed nucleotide sequence data of two chloroplast DNA (cpDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs.

Results

A significant phylogeographic structure (N_ST = 0.876, G_ST = 0.796, F_ST-SSR =0.329, R_ST =0.449; N_ST>G_ST, R_ST>F_ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period.

Conclusions

The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.

Structure, function, and evolution of plant O-methyltransferases

Plant O-methyltransferases (OMTs) constitute a large family of enzymes that methylate the oxygen atom of a variety of secondary metabolites including phenylpropanoids, flavonoids, and alkaloids. O-Methylation plays a key role in lignin biosynthesis, stress tolerance, and disease resistance in plants. To gain insights into the evolution of the extraordinary diversity of plant O-methyltransferases, and to develop a framework phylogenetic tree for improved prediction of the putative function of newly identified OMT-like gene sequences, we performed a comparative and phylogenetic analysis of 61 biochemically characterized plant OMT protein sequences. The resulting phylogenetic tree revealed two major groups. One of the groups included two sister clades, one comprising the caffeoyl CoA OMTs (CCoA OMTs) that methylate phenolic hydroxyl groups of hydroxycinnamoyl CoA esters, and the other containing the carboxylic acid OMTs that methylate aliphatic carboxyl groups. The other group comprised the remaining OMTs, which act on a diverse group of metabolites including hydroxycinnamic acids, flavonoids, and alkaloids. The results suggest that some OMTs may have undergone convergent evolution, while others show divergent evolution. The high number of unique conserved regions within the CCoA OMTs and carboxylic acid OMTs provide an opportunity to design oligonucleotide primers to selectively amplify and characterize similar OMT genes from many plant species.

Asymmetrical natural hybridization betweenPopulus deltoidesandP.balsamifera(Salicaceae)This note is one of a selection of papers published in the Special Issue on Poplar Research in Canada

Natural hybridization has long been recognized as a means for gene flow between species and has important evolutionary consequences. Although hybridization is generally considered to be symmetrical, with both hybridizing species being equally likely to be the male or female parent, several studies have demonstrated the presence of asymmetrical hybridization and introgression from one species to the other. We investigated the direction of natural hybridization between two sympatric forest tree species in North America ( Populus deltoides Bartr. ex Marsh. and Populus balsamifera L.) using species-specific single nucleotide polymorphism (SNP) markers in both the nuclear and chloroplast genomes. All natural hybrid individuals, identified from morphological traits, had nuclear alleles corresponding to both parental species, while the chloroplast genotypes showed similarity to P. deltoides, indicating asymmetrical hybridization with P. deltoides as the maternal and P. balsamifera as the paternal donor species. This observed asymmetrical hybridization may be attributable to cytonuclear interactions.

Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae)

Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine.

Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA

The species of the genus Populus, collectively known as poplars, are widely distributed over the northern hemisphere and well known for their ecological, economical, and evolutionary importance. The extensive interspecific hybridization and high morphological diversity in this group pose difficulties in identifying taxonomic units for comparative evolutionary studies and systematics. To understand the evolutionary relationships among poplars and to provide a framework for biosystematic classification, we reconstructed a phylogeny of the genus Populus based on nucleotide sequences of three noncoding regions of the chloroplast DNA (intron of trnL and intergenic regions of trnT-trnL and trnL-trnF) and ITS1 and ITS2 of the nuclear rDNA. The resulting phylogenetic trees showed polyphyletic relationships among species in the sections Tacamahaca and Aigeiros. Based on chloroplast DNA sequence data, P. nigra had a close affinity to species of section Populus, whereas nuclear DNA sequence data suggested a close relationship between P. nigra and species of the section Aigeiros, suggesting a possible hybrid origin for P. nigra. Similarly, the chloroplast DNA sequences of P. tristis and P. szechuanica were similar to that of the species of section Aigeiros, while the nuclear sequences revealed a close affinity to species of the section Tacamahaca, suggesting a hybrid origin for these two Asiatic balsam poplars. The incongruence between phylogenetic trees based on nuclear- and chloroplast-DNA sequence data suggests a reticulate evolution in the genus Populus.

Molecular systematics of some North American species of Diplostomum (Digenea) based on rDNA-sequence data and comparisons with European congeners

The systematics of Diplostomum species, common intestinal parasites of piscivorous birds, has long been problematic, owing to phenotypic plasticity and the paucity of morphological features that are often subject to age- and host-induced variation. We sequenced the ITS1–5.8S–ITS2 regions of the rDNA from adult Diplostomum huronense, Diplostomum indistinctum, and Diplostomum baeri obtained from experimentally infected ring-bill gulls (Larus delawarensis) and compared them with partial ITS1 sequences from several species of Diplostomum in GenBank. The three North American species were distinguishable on the basis of ITS sequences. Sequences from D. huronense differed from those of D. indistinctum at 12 sites in ITS1 and 4 sites in ITS2, supporting morphological and morphometric data that indicate the two are distinct species. Sequences of D. huronense and D. indistinctum differed from those of D. baeri at 27 and 24 sites, respectively, in ITS1 and 15 and 12 sites, respectively, in ITS2. Phylogenetic analysis of partial ITS1 sequences revealed that the North American and European species of Diplostomum formed separate groups, with the former being basal to the latter. The results indicated that D. huronense and D. indistinctum from North America are distinct from Diplostomum spathaceum and other similar species from Europe. Furthermore, sequences from specimens identified as D. baeri from North America differed from those of D. baeri from Europe by 3.8% in ITS1 (23 sites). While morphologically similar, the two are not conspecific. Sequences of the North American species have been deposited in GenBank (AY 123042–123044).

Genetic relatedness among developing seeds and intra fruit seed abortion in Dalbergia sissoo (Fabaceae)

Dalbergia sissoo, a wind-dispersed tropical tree, exhibits high intrafruit seed abortion. Of the four to five ovules in the flower, generally one and occasionally two or three develop to maturity. It has been proposed that the seed abortion is a consequence of intense sibling competition for maternal resources and that this competition occurs as an inverse function of the genetic relatedness among the developing seeds. Accordingly, developing seeds compete intensely when they are genetically less related but tend to develop together when genetically more related. We tested this hypothesis by comparing the genetic similarity among the pairs of seeds developing within a pod with that among (a) random pairs from the pool of all seeds, (b) random pairs from single-seeded pods, and (c) random pairs from two-seeded pods, using both randomly amplified polymorphic DNA (RAPD) and isozymes in five trees. We found that the pairs of seeds developing within a pod are genetically more similar than any random pairs of seeds in a tree. Thus the formation of two-seeded pods appear to be associated with increased genetic relatedness among the developing seeds. We discuss the results in the context of possible fitness advantages and then discuss the possible mechanisms that promote tolerance among related seeds.

Isolation, characterization, inheritance and linkage of microsatellite DNA markers in white spruce (Picea glauca) and their usefulness in other spruce species

Microsatellite DNA/simple-sequence-repeat (SSR) loci were identified, isolated and characterized in white spruce (Picea glauca) by screening both a non-enriched partial genomic library and a partial genomic library enriched for (AG/TC)n-containing clones. Inheritance and linkage of polymorphic SSR loci were determined in F1 progeny of four controlled crosses. We also assessed the compatibility and usefulness of the P. glauca microsatellite DNA markers in five other Picea species. Twenty-four microsatellites were identified by sequencing 32 clones selected from screens of 5,400 clones from the two libraries. The (AG/TC)n microsatellites were the most abundant in the non-enriched library. Eight microsatellite DNA loci were of the single-copy type, and six of these were polymorphic. A total of 87 alleles were detected at the six polymorphic SSR loci in 32 P. glauca individuals drawn from several populations. The number of alleles found at these six SSR loci ranged from 2 to 22, with an average of 14.5 alleles per locus, and the observed heterozygosity ranged from 0.48 to 0.91, with a mean of 0.66 per locus. Parents of the controlled crosses were polymorphic for five of the six polymorphic SSR loci. Microsatellite DNA variants at each of these five SSR loci followed a single-locus, codominant, Mendelian inheritance pattern. Joint two-locus segregation tests indicated complete linkage between PGL13 and PGL14, and no linkage between any of the remaining SSR loci. Each of the 32 P. glauca individuals examined had unique single or two-locus genotypes. With the exception of non-amplification of PGL12 in P. sitchensis, P. mariana, and P. abies and the monomorphic nature of PGL7 in P. mariana, primer pairs for all six polymorphic SSR loci successfully amplified specific fragments from genomic DNA and resolved polymorphic microsatellites of comparable sizes in P. engelmanni, P. sitchensis, P. mariana, P. rubens, and P. abies. The closely related species P. mariana and P. rubens, and P. glauca and P. sitchensiss could be distinguished by the PGL12 SSR marker. The microsatellite DNA markers developed and reported here could be used for assisting various genetics, breeding, biotechnology, tree forensics, genome mapping, conservation, restoration, and sustainable forest management programs in spruce species.

Microsatellite DNA markers in Populus tremuloides

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars.

Microsatellite DNA markers in Populus tremuloides

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars.

Key words: poplar, microsatellites, genetic mapping, simple sequence repeat (SSR) markers, DNA fingerprinting.

Population structure delineated with microsatellite markers in fragmented populations of a tropical tree, carapa guianensis (Meliaceae)

Deforestation and selective logging in the tropics may have serious consequences on genetic processes in tropical tree populations, affecting long-term survival of a given species as well as tropical forest communities. Because understanding the effects of human-induced changes on genetic processes is of utmost importance in formulating sound conservation and management plans for tropical forest communities, we developed microsatellite or simple sequence repeat (SSR) markers for the tropical tree Carapa guianensis (Meliaceae) and assessed the polymorphism of SSRs in adult and sapling populations in a large contiguous forest and in selectively logged and fragmented forests. The number of alleles in polymorphic loci ranged between 4 and 28. No inbreeding was detected in saplings or adult cohorts, but the allelic richness was lower in the sapling cohort of the isolated fragment. Genetic distances, Nei's D and (delta&mgr;)2, and RST values among saplings were greater than among adult cohorts, suggesting restriction of gene flow due to deforestation and habitat fragmentation. These SSR loci may be used to address many related questions regarding the population and conservation genetics of tropical trees.

Phylogeny of the tropical tree family Dipterocarpaceae based on nucleotide sequences of the chloroplast RBCL gene

The Dipterocarpaceae, well-known trees of the Asian rain forests, have been variously assigned to Malvales and Theales. The family, if the Monotoideae of Africa (30 species) and South America and the Pakaraimoideae of South America (one species) are included, comprises over 500 species. Despite the high diversity and ecological dominance of the Dipterocarpaceae, phylogenetic relationships within the family as well as between dipterocarps and other angiosperm families remain poorly defined. We conducted parsimony analyses on rbcL sequences from 35 species to reconstruct the phylogeny of the Dipterocarpaceae. The consensus tree resulting from these analyses shows that the members of Dipterocarpaceae, including Monotes and Pakaraimaea, form a monophyletic group closely related to the family Sarcolaenaceae and are allied to Malvales. The present generic and higher taxon circumscriptions of Dipterocarpaceae are mostly in agreement with this molecular phylogeny with the exception of the genus Hopea, which forms a clade with Shorea sections Anthoshorea and Doona. Phylogenetic placement of Dipterocarpus and Dryobalanops remains unresolved. Further studies involving representative taxa from Cistaceae, Elaeocarpaceae, Hopea, Shorea, Dipterocarpus, and Dryobalanops will be necessary for a comprehensive understanding of the phylogeny and generic limits of the Dipterocarpaceae.

Conservation of microsatellites among tropical trees (Leguminosae)

Although microsatellites or simple sequence repeats (SSRs) have become a popular tool in genetic mapping and gene flow studies, their utility is limited due to paucity of information about DNA sequences in plants. We tested the utility of microsatellite markers characterized for the tropical tree Pithecellobium elegans as a genetic tool for related species. The results indicate that SSR loci are conserved among closely related species, and SSR primers developed for P. elegans could be successfully used as a genetic tool in several species of the tribe Ingeae. This study indicates that there is high potential for the transfer of SSR markers among closely related taxa, circumventing laborious cloning and screening procedures involved in characterizing SSR loci for many species.