Genetic differentiation and trade among populations of peach palm ( Bactris gasipaes Kunth) in the Peruvian Amazon-implications for genetic resource management

From ethnobotany to mainstream agriculture: socially modified Cinderella species capturing 'trade-ons' for 'land maxing'

Over the last 25 years, the process of domesticating culturally-important, highly-nutritious, indigenous food-tree species. Integrating these over-looked 'Cinderella' species into conventional farming systems as new crops is playing a critical role in raising the productivity of staple food crops and improving the livelihoods of poor smallholder farmers. This experience has important policy implications for the sustainability of tropical/sub-tropical agriculture, the rural economy and the global environment. A participatory domestication process has been implemented in local communities using appropriate horticultural technologies to characterize genetic variation in non-timber forest products and produce putative cultivars by the vegetative propagation of elite trees in rural resource centers. When integrated into mainstream agriculture, these new crops diversify farmers' fields and generate income. Together, these outcomes address land degradation and social deprivation-two of the main constraints to staple food production-through beneficial effects on soil fertility, agroecosystem functions, community livelihoods, local trade and employment. Thus, the cultivation of these 'socially modified crops' offers a new strategy for the sustainable intensification of tropical agriculture based on the maximization of total factor productivity with minimal environmental and social trade-offs.

Genetic analysis identifies the region of origin of smuggled peach palm seeds

Seeds of a plant, supposedly a palm tree known popularly as peach palm (Bactris gasipaes), were seized by the Federal Police in the state of Pará, Brazil, without documentation of legal origin to authorize transportation and marketing in Brazil. They were alleged to be from the western part of Amazonas, Brazil, near the frontier with Peru and Colombia, justifying the lack of documentation. The species was confirmed to be peach palm. To determine the likely place of origin, a genetic analysis was performed to determine the relationship between the seized seeds and representative populations of peach palm from all of Amazonia, maintained in the Peach palm Core Collection, at the National Research Institute for Amazonia, using nine microsatellite loci. Reynolds' coancestry analysis showed a strong relationship between the seeds and the Pampa Hermosa landrace, around Yurimaguas, Peru. The Structure program, used to infer the probability of an individual belonging to a given population, showed that most seeds grouped with populations close to Yurimaguas, Peru, corroborating the coancestry analysis. The Pampa Hermosa landrace is the main source of spineless peach palm seeds used in the Brazilian heart-of-palm agribusiness, which motivated the smugglers to attempt this biopiracy.

An Integrated Hypothesis on the Domestication of Bactris gasipaes

Peach palm (Bactris gasipaes Kunth) has had a central place in the livelihoods of people in the Americas since pre-Columbian times, notably for its edible fruits and multi-purpose wood. The botanical taxon includes both domesticated and wild varieties. Domesticated var gasipaes is believed to derive from one or more of the three wild types of var. chichagui identified today, although the exact dynamics and location of the domestication are still uncertain. Drawing on a combination of molecular and phenotypic diversity data, modeling of past climate suitability and existing literature, we present an integrated hypothesis about peach palm’s domestication. We support a single initial domestication event in south western Amazonia, giving rise to var. chichagui type 3, the putative incipient domesticate. We argue that subsequent dispersal by humans across western Amazonia, and possibly into Central America allowed for secondary domestication events through hybridization with resident wild populations, and differential human selection pressures, resulting in the diversity of present-day landraces. The high phenotypic diversity in the Ecuadorian and northern Peruvian Amazon suggest that human selection of different traits was particularly intense there. While acknowledging the need for further data collection, we believe that our results contribute new insights and tools to understand domestication and dispersal patterns of this important native staple, as well as to plan for its conservation.

Conservation implications of the mating system of the Pampa Hermosa landrace of peach palm analyzed with microsatellite markers

Peach palm (Bactris gasipaes) is cultivated by many indigenous and traditional communities from Amazonia to Central America for its edible fruits, and is currently important for its heart-of-palm. The objective of this study was to investigate the mating system of peach palm, as this is important for conservation and breeding. Eight microsatellite loci were used to genotype 24 open-pollinated progenies from three populations of the Pampa Hermosa landrace maintained in a progeny trial for genetic improvement. Both the multi-locus outcrossing rates (0.95 to 0.99) and the progeny level multi-locus outcrossing rates (0.9 to 1.0) were high, indicating that peach palm is predominantly allogamous. The outcrossing rates among relatives were significantly different from zero (0.101 to 0.202), providing evidence for considerable biparental inbreeding within populations, probably due to farmers planting seeds of a small number of open-pollinated progenies in the same plot. The correlations of paternity estimates were low (0.051 to 0.112), suggesting a large number of pollen sources (9 to 20) participating in pollination of individual fruit bunches. Effective population size estimates suggest that current germplasm collections are insufficient for long-term ex situ conservation. As with most underutilized crops, on farm conservation is the most important component of an integrated conservation strategy.

Genetic divergence among populations and accessions of the spineless peach palm from Pampa Hermosa landrace used in the heart-of-palm agribusiness in Brazil

Although originally domesticated for its fruit, exploitation of the peach palm (Bactris gasipaes Kunth) in the production of gourmet heart-of-palm has also become an important activity, hence the need for improved material for large-scale production, on employing the Pampa Hermosa landrace as the seed source. In this study 11 microsatellite markers were used to evaluate genetic divergence among 96 elite plants representing four populations of spineless peach palm from the above cited source. Genetic variability was high (H_T = 0.82). The low levels of divergence [F_ST (0.023), G_ST’ (0.005)] and the high number of migrants (Nm - 3.8 to 52.2) indicated significant interpopulation gene flow. Some of the plants presented high levels of genetic divergence, but the plants were grouped independently of their geographic origins. When combined with morpho-agronomic evaluation, the results found could substantially contribute towards mounting an efficient tool for obtaining superior genotypes with wide genetic variability for improvement programs.

Parallelization and optimization of genetic analyses in isolation by distance web service

Background

The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and returns vector based graphs. The more than 60 citations since 2005 confirm the popularity and utility of this website. Despite its usefulness, the data sets with over 65 populations can take hours or days to complete due to the computational intensity of the statistical tests. This is especially troublesome for web-based software analysis, since users tend to expect real-time results on the order of seconds, or at most, minutes. Moreover, as genetic data continue to increase and diversify, so does the demand for more processing power. In order to increase the speed and efficiency of IBDWS, we first determined which aspects of the code were most time consuming and whether they might be amenable to improvements by parallelization or algorithmic optimization.

Results

Runtime tests uncovered two areas of IBDWS that consumed significant amounts of time: randomizations within the Mantel test and the RMA calculations. We found that these sections of code could be restructured and parallelized to improve efficiency. The code was first optimized by combining two similar randomization routines, implementing a Fisher-Yates shuffling algorithm, and then parallelizing those routines. Tests of the parallelization and Fisher-Yates algorithmic improvements were performed on a variety of data sets ranging from 10 to 150 populations. All tested algorithms showed runtime reductions and a very close fit to the predicted speedups based on time-complexity calculations. In the case of 150 populations with 10,000 randomizations, data were analyzed 23 times faster.

Conclusion

Since the implementation of the new algorithms in late 2007, datasets have continued to increase substantially in size and many exceed the largest population sizes we used in our test sets. The fact that the website has continued to work well in "real-world" tests, and receives a considerable number of new citations provides the strongest testimony to the effectiveness of our improvements. However, we soon expect the need to upgrade the number of nodes in our cluster significantly as dataset sizes continue to expand. The parallel implementation can be found at .

Taxonomy and conservation: A case study from Chamaedorea alternans

BACKGROUND AND AIMS

The establishment of justified recommendations in conservation biology requires robust taxonomic treatments for the group(s) being considered. Controversial or poorly developed taxonomies can have a negative impact on conservation assessments. One example of a taxonomically difficult and controversial species complex that is important in conservation involves two species of Mexican palms, Chamaedorea tepejilote and C. alternans. The goal of this study was to investigate whether C. alternans and C. tepejilote are genetically distinct within the Los Tuxtlas region of Veracruz.

METHODS

Individuals corresponding to the morphology of C. alternans and C. tepejilote were collected from sympatric and allopatric regions within the Los Tuxtlas Biological Station. Eighty-eight samples were genotyped using amplified fragment length polymorphism (AFLP) markers. Cluster and ordination analyses were used to investigate patterns of differentiation.

KEY RESULTS

UPGMA and PCO analyses of AFLP profiles recovered two divergent clusters corresponding to morphologically defined C. tepejilote and C. alternans. No intermediate genotypes were observed and five of the 45 loci were fixed for either the presence or absence between the species. The patterns of divergence observed do not identify a role for sympatric speciation.

CONCLUSIONS

The observed patterns of differentiation support the recognition of C. alternans as distinct from C. tepejilote. A suite of vegetative and reproductive morphological features can be used to help distinguish these taxa in the field, but they can be difficult to differentiate from preserved material. Previous treatments of the variation found within the complex (C. alternans and C. tepejilote) as intraspecific variance is unjustified. Given that the Los Tuxtlas region has suffered from historical and ongoing deforestation and that Chamaedorea includes numerous endangered taxa, retaining conservation status for C. alternans serves to help safeguard individuals of the species as well as a region and larger taxonomic group all under considerable threat from human activities.