Population genetic structure of mahogany (Swietenia macrophylla King, Meliaceae) across the Brazilian Amazon, based on variation at microsatellite loci: implications for conservation

Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in Melia dubia Cav

Melia dubia Cav. (Meliaceae), a fast-growing tropical tree finds use in plywood, pulp and high-value solid wood products. To increase its productivity, we must essentially capture genetic diversity and identify genotypes with superior wood properties. This study aimed to develop novel microsatellite markers from genomic data and validate the markers in M. dubia. Direct Seq-to-SSR approach was adopted and using an in-house Perl script, 426,390 SSR markers identified. For validation, selected 151 markers, of which 50 were genomic markers chosen randomly, and 101 were genic markers identified through BLAST2GO. Amplification was observed in all loci, and 81.4% generated high-quality, reproducible amplicons of the expected size. Out of 50 genomic markers, we used ten highly polymorphic markers to assess genetic diversity among 75 genotypes from three populations. One hundred fourteen alleles were recorded, with a moderate level of diversity and a positive fixation index. Twenty-nine genic markers representing 13 enzymes showing polymorphism for wood stiffness were selected for diversity assessment of 24 genotypes (12 genotypes each with high and low-stress wave velocity). The product size ranged from 87 to 279, covering the majority of the genome. Cluster and structure analysis segregated ~ 80% of the genotypes based on the trait. This is the first report of the development of genic markers from a genomic survey and has proved efficient in differentiating genotypes based on the trait. The markers developed in this study will be useful for genetic mapping, diversity estimation, marker-assisted selection for desired traits and breeding for wood traits in M. dubia.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02858-w.

Development of nuclear SNP markers for Mahogany (Swietenia spp.)

Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.

Preliminary Evidence for Domestication Effects on the Genetic Diversity of Guazuma crinita in the Peruvian Amazon

Guazuma crinita, a fast-growing timber tree species, was chosen for domestication in the Peruvian Amazon because it can be harvested at an early age and it contributes to the livelihood of local farmers. Although it is in an early stage of domestication, we do not know the impact of the domestication process on its genetic resources. Amplified fragment length polymorphic (AFLP) fingerprints were used to estimate the genetic diversity of G. crinita populations in different stages of domestication. Our objectives were (i) to estimate the level of genetic diversity in G. crinita using AFLP markers, (ii) to describe how the genetic diversity is distributed within and among populations and provenances, and (iii) to assess the genetic diversity in naturally regenerated, cultivated and semi-domesticated populations. We generated fingerprints for 58 leaf samples representing eight provenances and the three population types. We used seven selective primer combinations. A total of 171 fragments were amplified with 99.4% polymorphism at the species level. Nei’s genetic diversity and Shannon information index were slightly higher in the naturally regenerated population than in the cultivated and semi-domesticated populations (He = 0.10, 0.09 and 0.09; I = 0.19, 0.15 and 0.16, respectively). The analysis of molecular variation showed higher genetic diversity within rather than among provenances (84% and 4%, respectively). Cluster analysis (unweighted pair group method with arithmetic mean) and principal coordinate analysis did not show correspondence between genetic and geographic distance. There was significant genetic differentiation among population types (Fst = 0.12 at p ˂ 0.001). The sample size was small, so the results are considered as preliminary, pending further research with larger sample sizes. Nevertheless, these results suggest that domestication has a slight but significant effect on the diversity levels of G. crinita and this should be considered when planning a domestication program.

Genetic diversity in populations of African mahogany (Khaya grandioliola C. DC.) introduced in Brazil

Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Para. These populations are among the oldest plantations (>15 years) in Brazil and, therefore, the country's main seed sources. The average number of alleles per locus was 5.9, expected heterozygosity was moderate (^=0.56) and lower than the high observed heterozygosity (H_O=0.74). Therefore, the intrapopulation fixation index was negative (f=-0.31) indicating the possibility that selection of superior trees might have favored heterozygous plants with heterosis. No genetic structure was observed between provenances. The genetic diversity observed within selected trees, with an effective population size (Ne) of 30.4, is comparable to that of natural populations of African and Brazilian mahoganies. Therefore, our results contradict the idea that the genetic diversity of K. grandifoliola introduced in Brazil is low and show that our germplasm can be exploited for breeding purposes.

Tropical Trees as Time Capsules of Anthropogenic Activity

After the ice caps, tropical forests are globally the most threatened terrestrial environments. Modern trees are not just witnesses to growing contemporary threats but also legacies of past human activity. Here, we review the use of dendrochronology, radiocarbon analysis, stable isotope analysis, and DNA analysis to examine ancient tree management. These methods exploit the fact that living trees record information on environmental and anthropogenic selective forces during their own and past generations of growth, making trees living archaeological 'sites'. The applicability of these methods across prehistoric, historic, and industrial periods means they have the potential to detect evolving anthropogenic threats and can be used to set conservation priorities in rapidly vanishing environments.

Machine Learning Models with Quantitative Wood Anatomy Data Can Discriminate between Swietenia macrophylla and Swietenia mahagoni

Illegal logging and associated trade aggravate the over-exploitation of Swietenia species, of which S. macrophylla King, S. mahagoni (L.) Jacq, and S. humilis Zucc. have been listed in Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Appendix Ⅱ. Implementation of CITES necessitates the development of efficient forensic tools to identify wood species accurately, and ideally ones readily deployable in wood anatomy laboratories across the world. Herein, a method using quantitative wood anatomy data in combination with machine learning models to discriminate between three Swietenia species is presented, in addition to a second model focusing only on the two historically more important species S. mahagoni and S. macrophylla. The intra- and inter-specific variations in nine quantitative wood anatomical characters were measured and calculated based on 278 wood specimens, and four machine learning classifiers—Decision Tree C5.0, Naïve Bayes (NB), Support Vector Machine (SVM), and Artificial Neural Network (ANN)—were used to discriminate between the species. Among these species, S. macrophylla exhibited the largest intraspecific variation, and all three species showed at least partly overlapping values for all nine characters. SVM performed the best of all the classifiers, with an overall accuracy of 91.4% and a per-species correct identification rate of 66.7%, 95.0%, and 80.0% for S. humilis, S. macrophylla, and S. mahagoni, respectively. The two-species model discriminated between S. macrophylla and S. mahagoni with accuracies of over 90.0% using SVM. These accuracies are lower than perfect forensic certainty but nonetheless demonstrate that quantitative wood anatomy data in combination with machine learning models can be applied as an efficient tool to discriminate anatomically between similar species in the wood anatomy laboratory. It is probable that a range of previously anatomically inseparable species may become identifiable by incorporating in-depth analysis of quantitative characters and appropriate statistical classifiers.

Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives

BACKGROUND

Tree species in the genus Cedrela P. Browne are threatened by timber overexploitation across the Neotropics. Genetic identification of processed timber can be used to supplement wood anatomy to assist in the taxonomic and source validation of protected species and populations of Cedrela. However, few genetic resources exist that enable both species and source identification of Cedrela timber products. We developed several 'omic resources including a leaf transcriptome, organelle genome (cpDNA), and diagnostic single nucleotide polymorphisms (SNPs) that may assist the classification of Cedrela specimens to species and geographic origin and enable future research on this widespread Neotropical tree genus.

RESULTS

We designed hybridization capture probes to enrich for thousands of genes from both freshly preserved leaf tissue and from herbarium specimens across eight Meliaceae species. We first assembled a draft de novo transcriptome for C. odorata, and then identified putatively low-copy genes. Hybridization probes for 10,001 transcript models successfully enriched 9795 (98%) of these targets, and analysis of target capture efficiency showed that probes worked effectively for five Cedrela species, with each species showing similar mean on-target sequence yield and depth. The probes showed greater enrichment efficiency for Cedrela species relative to the other three distantly related Meliaceae species. We provide a set of candidate SNPs for species identification of four of the Cedrela species included in this analysis, and present draft chloroplast genomes for multiple individuals of eight species from four genera in the Meliaceae.

CONCLUSIONS

Deforestation and illegal logging threaten forest biodiversity globally, and wood screening tools offer enforcement agencies new approaches to identify illegally harvested timber. The genomic resources described here provide the foundation required to develop genetic screening methods for Cedrela species identification and source validation. Due to their transferability across the genus and family as well as demonstrated applicability for both fresh leaves and herbarium specimens, the genomic resources described here provide additional tools for studies examining the ecology and evolutionary history of Cedrela and related species in the Meliaceae.

Elevation, Not Deforestation, Promotes Genetic Differentiation in a Pioneer Tropical Tree

The regeneration of disturbed forest is an essential part of tropical forest ecology, both with respect to natural disturbance regimes and large-scale human-mediated logging, grazing, and agriculture. Pioneer tree species are critical for facilitating the transition from deforested land to secondary forest because they stabilize terrain and enhance connectivity between forest fragments by increasing matrix permeability and initiating disperser community assembly. Despite the ecological importance of early successional species, little is known about their ability to maintain gene flow across deforested landscapes. Utilizing highly polymorphic microsatellite markers, we examined patterns of genetic diversity and differentiation for the pioneer understory tree Miconia affinis across the Isthmus of Panama. Furthermore, we investigated the impact of geographic distance, forest cover, and elevation on genetic differentiation among populations using circuit theory and regression modeling within a landscape genetics framework. We report marked differences in historical and contemporary migration rates and moderately high levels of genetic differentiation in M. affinis populations across the Isthmus of Panama. Genetic differentiation increased significantly with elevation and geographic distance among populations; however, we did not find that forest cover enhanced or reduced genetic differentiation in the study region. Overall, our results reveal strong dispersal for M. affinis across human-altered landscapes, highlighting the potential use of this species for reforestation in tropical regions. Additionally, this study demonstrates the importance of considering topography when designing programs aimed at conserving genetic diversity within degraded tropical landscapes.

In Vitro Cytoprotective Effects and Antioxidant Capacity of Phenolic Compounds from the Leaves of Swietenia macrophylla

Swietenia macrophylla (mahogany) is a highly valued timber species, whereas the leaves are considered to be waste product. A total of 27 phenolic compounds were identified in aqueous extracts from mahogany leaves by comparing retention times and mass spectra data with those of authentic standards using LC-ESI-MS/MS. Polyphenols play an important role in plants as defense mechanisms against pests and pathogens and have potent antioxidant properties. In terms of health applications, interest has increased considerably in naturally occurring antioxidant sources, since they can retard the progress of many important neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. The antioxidant capacities of two aqueous extracts, M1 (decoction) and M2 (infusion), were measured using TEAC and Folin-Ciocalteau methods. Additionally, M1 was used in order to investigate its potential cytoprotective effects on an in vitro model of neurodegeneration, by using primary cerebellar cultures exposed to methyl mercury (MeHg). Under experimental sub-chronic conditions (72 h), concomitant exposure of the same cultures to MeHg and M1 extract resulted in a statistically significant increase in cell viability in all three concentrations tested (10, 50 and 100 μg/mL), strongly suggesting that due to its high content of antioxidant compounds, the M1 extract provides significant cytoprotection against the MeHg-induced in vitro neurotoxicity.

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.

Biological activities and phytochemicals of Swietenia macrophylla King

Swietenia macrophylla King (Meliaceae) is an endangered and medicinally important plant indigenous to tropical and subtropical regions of the World. S. macrophylla has been widely used in folk medicine to treat various diseases. The review reveals that limonoids and its derivatives are the major constituents of S. macrophylla. There are several data in the literature indicating a great variety of pharmacological activities of S. macrophylla, which exhibits antimicrobial, anti-inflammatory, antioxidant effects, antimutagenic, anticancer, antitumor and antidiabetic activities. Various other activities like anti-nociceptive, hypolipidemic, antidiarrhoeal, anti-infective, antiviral, antimalarial, acaricidal, antifeedant and heavy metal phytoremediation activity have also been reported. In view of the immense medicinal importance of S. macrophylla, this review aimed at compiling all currently available information on its ethnomedicinal uses, phytochemistry and biological activities of S. macrophylla, showing its importance.

Verifying the geographic origin of mahogany (Swietenia macrophylla King) with DNA-fingerprints

Illegal logging is one of the main causes of ongoing worldwide deforestation and needs to be eradicated. The trade in illegal timber and wood products creates market disadvantages for products from sustainable forestry. Although various measures have been established to counter illegal logging and the subsequent trade, there is a lack of practical mechanisms for identifying the origin of timber and wood products. In this study, six nuclear microsatellites were used to generate DNA fingerprints for a genetic reference database characterising the populations of origin of a large set of mahogany (Swietenia macrophylla King, Meliaceae) samples. For the database, leaves and/or cambium from 1971 mahogany trees sampled in 31 stands from Mexico to Bolivia were genotyped. A total of 145 different alleles were found, showing strong genetic differentiation (δ(Gregorious)=0.52, F(ST)=0.18, G(ST(Hedrick))=0.65) and clear correlation between genetic and spatial distances among stands (r=0.82, P<0.05). We used the genetic reference database and Bayesian assignment testing to determine the geographic origins of two sets of mahogany wood samples, based on their multilocus genotypes. In both cases the wood samples were assigned to the correct country of origin. We discuss the overall applicability of this methodology to tropical timber trading.

Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity

Khaya senegalensis (African mahogany or dry-zone mahogany) is a high-value hardwood timber species with great potential for forest plantations in northern Australia. The species is distributed across the sub-Saharan belt from Senegal to Sudan and Uganda. Because of heavy exploitation and constraints on natural regeneration and sustainable planting, it is now classified as a vulnerable species. Here, we describe the development of microsatellite markers for K. senegalensis using next-generation sequencing to assess its intra-specific diversity across its natural range, which is a key for successful breeding programs and effective conservation management of the species. Next-generation sequencing yielded 93,943 sequences with an average read length of 234 bp. The assembled sequences contained 1030 simple sequence repeats, with primers designed for 522 microsatellite loci. Twenty-one microsatellite loci were tested with 11 showing reliable amplification and polymorphism in K. senegalensis. The 11 novel microsatellites, together with one previously published, were used to assess 73 accessions belonging to the Australian K. senegalensis domestication program, sampled from across the natural range of the species. STRUCTURE analysis shows two major clusters, one comprising mainly accessions from west Africa (Senegal to Benin) and the second based in the far eastern limits of the range in Sudan and Uganda. Higher levels of genetic diversity were found in material from western Africa. This suggests that new seed collections from this region may yield more diverse genotypes than those originating from Sudan and Uganda in eastern Africa.

Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa

While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.

Microsatellites for mahoganies: twelve new loci for Swietenia macrophylla and its high transferability to Khaya senegalensis

PREMISE OF THE STUDY

A new set of 12 microsatellite markers was developed and characterized for big-leaf mahogany (Swietenia macrophylla King, Meliaceae) and its transferability assayed in the African mahogany, Khaya senegalensis (Desr.) A. Juss. (Meliaceae), to study population and conservation genetics of these threatened tropical timber species.

METHODS AND RESULTS

Using an enriched library approach twelve novel microsatellite loci were identified for S. macrophylla. The number of alleles per locus ranged from 5 to 14 and mean observed and expected heterozygosities were 0.819 and 0.822, respectively. Twenty microsatellite loci developed for S. macrophylla (12 from this study and eight previously published) were tested for K. senegalensis and 10 polymorphic were characterized.

CONCLUSIONS

The results show the highly informative content of the new SSR loci for Swietenia macrophylla and the high effectiveness of these microsatellites for population genetics, gene flow, and mating system studies in Khaya senegalensis.

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

BACKGROUND AND AIMS

The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest.

METHODS

Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers.

KEY RESULTS

For nuclear microsatellites, allelic richness (R) and heterozygosity (H(e,nuc)) differed between types of forest: R = 7.36 and R = 9.55, H(e,nuc) = 0.64 and H(e,nuc) = 0.80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N(a,nuc)) and the fixation index F(IS) differed significantly: N(a,nuc) = 9.41 and N(a,nuc) = 13.18, F(IS) = 0.06 and F(IS) = 0.15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F(ST,nuc) = 0.08) and moderate for chloroplast microsatellites (F(ST,cp) = 0.49). A clear relationship was observed between genetic and geographic distance (r = 0.42 P < 0.01 and r = 0.42 P = 0.03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations.

CONCLUSIONS

Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.

High levels of genetic variability and inbreeding in two Neotropical dioecious palms with contrasting life histories

We characterized the population genetics of two Neotropical dioecious palm species of Chamaedorea with contrasting life strategies from the region that is both the northernmost extent and most species rich of the genus. Chamaedorea tepejilote is a common, wind-pollinated arboreal understory palm. Although most adult plants reproduce each year, only a few individuals produce the majority of flowers and seeds. Chamaedorea elatior, conversely, is an uncommon climbing subcanopy palm with entomophilous flowers (insect-pollinated characteristics). Most of the mature palms do not reproduce in consecutive years and fruiting is episodic. Isozymes with a total of 107 alleles for 27 loci of 17 enzymes from six populations were assessed. For both species, co-occurrence of high levels of genetic variation and homozygosity was observed (C. tepejilote: He: 0.385-0.442, f: 0.431-0.486; C. elatior: He: 0.278-0.342, f: 0.466-0.535). Genetic differentiation of C. elatior was much lower (theta=0.0315) than that for C. tepejilote (theta=0.152). The contrast in differentiation may be influenced by differences in the spatial scale of the genetic neighborhoods of the two species. The simultaneous maintenance of inbreeding and of a large number of alleles within the populations is attributable to the low and variable number of mating pairs. Demographic studies indicate that this pattern could be explained by low reproductive frequency among individuals and over years in C. elatior and by reproductive dominance in C. tepejilote.

Optimal sampling strategy for estimation of spatial genetic structure in tree populations

Fine-scale spatial genetic structure (SGS) in natural tree populations is largely a result of restricted pollen and seed dispersal. Understanding the link between limitations to dispersal in gene vectors and SGS is of key interest to biologists and the availability of highly variable molecular markers has facilitated fine-scale analysis of populations. However, estimation of SGS may depend strongly on the type of genetic marker and sampling strategy (of both loci and individuals). To explore sampling limits, we created a model population with simulated distributions of dominant and codominant alleles, resulting from natural regeneration with restricted gene flow. SGS estimates from subsamples (simulating collection and analysis with amplified fragment length polymorphism (AFLP) and microsatellite markers) were correlated with the 'real' estimate (from the full model population). For both marker types, sampling ranges were evident, with lower limits below which estimation was poorly correlated and upper limits above which sampling became inefficient. Lower limits (correlation of 0.9) were 100 individuals, 10 loci for microsatellites and 150 individuals, 100 loci for AFLPs. Upper limits were 200 individuals, five loci for microsatellites and 200 individuals, 100 loci for AFLPs. The limits indicated by simulation were compared with data sets from real species. Instances where sampling effort had been either insufficient or inefficient were identified. The model results should form practical boundaries for studies aiming to detect SGS. However, greater sample sizes will be required in cases where SGS is weaker than for our simulated population, for example, in species with effective pollen/seed dispersal mechanisms.

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali

In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano-Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d'Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6-3.0 alleles/locus; H(E) = 0.25-0.42) and the fixation index (F(IS) = -0.227-0.186) was not significantly different from zero suggesting that Hardy-Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q(ST) = 0.055-0.283, Q(STmean) = 0.189) strongly exceeds that in eight microsatellite loci (F(ST) = -0.011-0.142, F(STmean) = 0.047). Global and pairwise F(ST) values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters.

Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago

We present a study of the genetic diversity and structure of a tropical tree in an insular system. Santalum austrocaledonicum is endemic to the archipelago of New Caledonia and is exploited for oil extraction from heartwood. A total of 431 individuals over 17 populations were analysed for eight polymorphic microsatellite loci. The number of alleles per locus ranged from 3 to 33 and the observed heterozygosity per population ranged from 0.01 in Mare to 0.74 in Ile des Pins. The genetic diversity was lowest in the most recent islands, the Loyautes, and highest in the oldest island, Grande Terre, as well as the nearby small Ile des Pins. Significant departures from panmixia were observed for some loci-population combinations (per population FIS = 0-0.03 on Grande-Terre and Ile des Pins, and 0-0.67 on Loyautes). A strong genetic differentiation among all islands was observed (FST = 0.22), and the amount of differentiation increased with geographic distance in Iles Loyaute and in Grande Terre. At both population and island levels, island age and isolation seem to be the main factors influencing the amount of genetic diversity. In particular, populations from recent islands had large average FIS that could not be entirely explained by null alleles or a Wahlund effect. This result suggests that, at least in some populations, selfing occurred extensively. Conclusively, our results indicate a strong influence of insularity on the genetic diversity and structure of Santalum austrocaledonicum.

Long-distance gene flow and cross-Andean dispersal of lowland rainforest bees (Apidae: Euglossini) revealed by comparative mitochondrial DNA phylogeography

Euglossine bees (Apidae; Euglossini) exclusively pollinate hundreds of orchid species and comprise up to 25% of bee species richness in neotropical rainforests. As one of the first studies of comparative phylogeography in a neotropical insect group, we performed a mitochondrial DNA (mtDNA)-based analysis of 14 euglossine species represented by populations sampled across the Andes and/or across the Amazon basin. The mtDNA divergences within species were consistently low; across the 12 monophyletic species the mean intraspecific divergence among haplotypes was 0.9% (range of means, 0-1.9%). The cytochrome oxidase 1 (CO1) divergence among populations separated by the Andes (N = 11 species) averaged 1.1% (range 0.0-2.0%). The mtDNA CO1 data set displayed homogeneous rates of nucleotide substitution, permitting us to infer dispersal across the cordillera long after the final Andean uplift based on arthropod molecular clocks of 1.2-1.5% divergence per million years. Gene flow across the 3000-km breadth of the Amazon basin was inferred from identical cross-Amazon haplotypes found in five species. Although mtDNA haplotypes for 12 of the 14 euglossine species were monophyletic, a reticulate CO1 phylogeny was recovered in Euglossa cognata and E. mixta, suggesting large ancestral populations and recent speciation. Reference to closely related outgroups suggested recent speciation for the majority of species. Phylogeographical structure across a broad spatial scale is weaker in euglossine bees than in any neotropical group previously examined, and may derive from a combination of Quaternary speciation, population expansion and/or long-distance gene flow.

Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis

While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation.

Molecular systematic analysis reveals cryptic tertiary diversification of a widespread tropical rain forest tree

The broad geographic range of many Neotropical rain forest tree species implies excellent dispersal abilities or range establishment that preceded the formation of current dispersal barriers. In order to initiate historical analyses of such widespread Neotropical trees, we sequenced the nuclear ribosomal spacer (ITS) region of Symphonia globulifera L. f. (Clusiaceae) from populations spanning the Neotropics and western Africa. This rain forest tree has left unmistakable Miocene fossils in Mesoamerica (15.5-18.2 Ma) and in South America ( approximately 15 Ma). Although marine dispersal of S. globulifera is considered improbable, our study establishes three marine dispersal events leading to the colonization of Mesoamerica, the Amazon basin, and the West Indies, thus supporting the paleontological data. Our phylogeographic analysis revealed the spatial extent of the three Neotropical S. globulifera clades, which represent trans-Andes (Mesoamerica+west Ecuador), cis-Andes (Amazonia+Guiana), and the West Indies. Strong phylogeographic structure found among trans-Andean populations of S. globulifera stands in contrast to an absence of ITS nucleotide variation across the Amazon basin and indicates profound regional differences in the demographic history of this rain forest tree. Drawing from these results, we provide a historical biogeographic hypothesis to account for differences in the patterns of beta diversity within Mesoamerican and Amazonian forests.