Marianne Elias

Limited performance of DNA barcoding in a diverse community of tropical butterflies.

DNA ‘barcoding’ relies on a short fragment of mitochondrial DNA to infer identification of specimens. The method depends on genetic diversity being markedly lower within than between species. Closely related species are most likely to share genetic variation in communities where speciation rates are rapid and effective population sizes are large, such that coalescence times are long. We assessed the applicability of DNA barcoding (here the 5′ half of the cytochrome c oxidase I) to a diverse community of butterflies from the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference. Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in species represented in the analyses by more than one geographical race and at least one congener. The use of additional mitochondrial sequence data hardly improved species identification, while a fragment of a nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes when morphological characters are ambiguous or unknown, but we also recommend the addition of nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse habitats of our planet.

The evolutionary ecology of clonally propagated domesticated plants.

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy–Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.

Traditional management of cassava morphological and genetic diversity by the Makushi Amerindians (Guyana, South America): perspectives for on-farm conservation of crop genetic resources

In this paper we present original data on morphological and genetic diversity of cassava managed by the Makushi Amerindians from Guyana. Although they propagate cassava exclusively vegetatively by means of stem cuttings, many Amerindian farmers also use and multiply volunteer plants grown from seeds produced by sexual reproduction. Morphological characters were recorded for 29 varieties cultivated by the Makushi and two populations of plants originating from volunteer cassava seedlings. Genetic characterisation with AFLP markers was available for 21 of the examined varieties. The morphological and agronomic characters were highly variable among varieties. Every variety could be differentiated from any other one, except for one pair of varieties. However, high intra-varietal variability existed, which might lead to confusions between phenotypically similar varieties by the Makushi. Seedlings were on average different from the pool of the varieties studied, but 67% were found to resemble closely enough one of the varieties to be liable to be assigned to it. Confusion between very similar varieties, as well as assignment of seedlings to a variety, should generate genetic variability within varieties, which was detected with AFLP markers. As in other sites in Amazonia, there was only a weak correlation between inter-varietal distances assessed with molecular and with morphological markers, suggesting that diversification of morphological characters has taken place repeatedly and independently across the Amazonian range of the crop. Diversifying selection, exchanges of varieties between farmers, and incorporation of sexually produced volunteer plants are key mechanisms responsible for the high diversity observed. Strategies of conservation of genetic resources should take these dynamic processes into account.

Out of the Andes: patterns of diversification in clearwing butterflies

Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated species‐level phylogenies to investigate the time course of speciation and to infer ancestral elevation ranges for two diverse genera. We show that both genera likely originated at middle elevations in the Andes in the Middle Miocene, contrasting with most published results in vertebrates that point to a lowland origin. Although we detected a signature of vicariance caused by the uplift of the Andes at the Miocene–Pliocene boundary, most sister species were parapatric without any obvious vicariant barrier. Combined with an overall decelerating speciation rate, these results suggest an important role for ecological speciation and adaptive radiation, rather than simple vicariance.

Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers

Despite the urgent need to conserve domesticated plant genetic resources, and developing ‘on farm’ strategies of conservation, the impact of traditional farming practices and of their interaction with ecological factors on the structure and evolutionary dynamics of the genetic variability of crop populations has been little documented. We assessed the genetic variability of 31 varieties of cassava (M. esculenta Crantz) traditionally grown by Makushi Amerindians from Guyana, using AFLP markers. We used a sample of 38 varieties from an ex situ core collection as a reference. Accessions of wild cassava were also included. While clonality of the varieties was expected due to the vegetative propagation of cassava, 21 varieties presented intravarietal polymorphism. Among the varieties from a single site in Guyana, genetic diversity was the same as that in the accessions from the core collection. We suggest that incorporation of volunteer seedlings, produced by sexual reproduction, into the stock of varieties grown by the Makushi plays a major role in explaining both intravarietal polymorphism and the high level of genetic diversity. No correspondence was found between the structure of molecular diversity and variation observed for agronomic traits that are targets for selection by cultivators. As found in previous studies, all wild forms of cassava clustered together and separately from the cultivated varieties in a Neighbour-Joining dendrogram. These results are consistent with the hypothesis of a limited domestication event in a restricted area, followed by rapid diffusion of cultivated phenotypes and convergent evolution. Our results show that local varieties are an important source of genetic diversity, and highlight the importance of the interaction between human and ecological factors in the dynamics of this diversity.

Mitochondrial DNA barcoding detects some species that are real, and some that are not

Mimicry and extensive geographical subspecies polymorphism combine to make species in the ithomiine butterfly genus Mechanitis (Lepidoptera; Nymphalidae) difficult to determine. We use mitochondrial DNA (mtDNA) barcoding, nuclear sequences and amplified fragment length polymorphism (AFLP) genotyping to investigate species limits in this genus. Although earlier biosystematic studies based on morphology described only four species, mtDNA barcoding revealed eight well‐differentiated haplogroups, suggesting the presence of four new putative ‘cryptic species’. However, AFLP markers supported only one of these four new ‘cryptic species’ as biologically meaningful. We demonstrate that in this genus, deep genetic divisions expected on the basis of mtDNA barcoding are not always reflected in the nuclear genome, and advocate the use of AFLP markers as a check when mtDNA barcoding gives unexpected results.

Genetic diversity of traditional South American landraces of cassava (Manihot esculenta Crantz): An analysis using microsatellites

The extent and structure of the genetic variability of traditional varieties of cassava (Manihot esculenta Crantz) have been little documented, despite considerable evidence for this cropś great varietal diversity in traditional agroecosystems. We used microsatellite markers to assess the genetic structure of traditional landraces of sweet and bitter cassava collected from five South American sites. As reference, we used a sample of 38 accessions from a world collection of cultivated cassava. For a total of 10 loci examined, we found 15 alleles that were not represented in this sample. Ten of these had been previously detected in wild Manihot species. The geographical structure of genetic variability was weak, but the genetic differentiation between bitter and sweet landraces was significant, suggesting that each form had evolved separately after domestication. Our results showed that traditional landraces form an important source of genetic diversity and merit more attention from managers of crop genetic resources.RésuméA extensão e a estruturação da variabilidade genética de variedades tradicionais de mandioca (Manihot esculenta Crantz) têm sido pouco documentadas, apesar de existirem evidências sugerindo uma grande diversidade varietal desta cultura em agroecosistemas tradicionais. No presente trabalho, foram usados marcadores de DNA, do tipo microssatélite, para avaliar a estrutura genética de variedades tradicionais de mandioca brava e mandioca de mesa coletadas em cinco localidades da América do Sul. Como referência, usou-se um conjunto de 38 acessos de uma coleção mundial de germoplasma de mandioca. Entre as variedades tradicionais, foram encontrados 15 alelos que não estavam presentes nesta amostragem da coleção mundial. Dez destes alelos já haviam sido detectados em espécies silvestres de Manihot. Apenas uma leve estruturação geográfica da variabilidade foi observada. No entanto, foi evidenciada uma diferenciação genética entre variedades bravas e de mesa, sugerindo que cada forma tenha evoluído separadamente após a domesticaç~ao. Nossos resultados mostram que variedades tradicionais constituem uma importante fonte de diversidade genética e deveriam receber maior atenção no manejo de recursos genéticos de plantas cultivadas.

Germination Ecology of Cassava (Manihot Esculenta Crantz, Euphorbiaceae) in Traditional Agroecosystems: Seed and Seedling Biology of a Vegetatively Propagated Domesticated Plant1

Cassava is clonally propagated, but Amerindian farmers also use plants from volunteer seedlings to prepare stem cuttings. Although sexual reproduction plays a role in cassava’s evolution it is poorly studied. We examined one aspect of cassava reproductive ecology, seed dormancy and germination. Volunteer seedlings emerge from a soil bank of seeds produced during the previous cycle of cultivation that remain ungerminated through the fallow period, then germinate synchronously after vegetation is slashed and burned. Laboratory experiments showed that germination can be enhanced by mechanical scarification and also by dry heat treatment, suggesting that burning after field clearing could help break dormancy. Germination was also stimulated by high temperatures (35°C) that in nature indicate bare soils, and inhibited by temperatures (25°C) close to those in soil shaded by vegetation and by light. Seeds of both wild and domesticated cassava exhibit physiological dormancy, an adaptation for germination in periodically disturbed habitats. In addition to these preadaptations, preliminary results also suggest specific adaptations of domesticated cassava to the distinctive disturbance regimes of swidden agriculture.

The unmanaged reproductive ecology of domesticated plants in traditional agroecosystems: An example involving cassavaand a call for data§

Abstract Although cassava is a strictly vegetatively propagated crop, in many traditional Amazonian agroecosystems, Amerindian farmers recognise volunteer seedlings of cassava and allow them to grow. If their properties are deemed desirable, plants originating from seedlings are included in the harvest of tuberous roots, and their stems are used to prepare cuttings for propagation. Incorporation of these products of spontaneous sexual reproduction appears to be important in origin and maintenance of genetic diversity in this clonally propagated plant. Our observations conducted in an Amerindian village in Guyana suggest that volunteer seedlings arise from a bank of viable seeds stored in soil, and that dispersal and burial of seeds by ants may be important in its constitution. Future investigations of the dynamics of genetic diversity in this crop in traditional agroecosystems must consider the role of the ‘wild’ sexual reproduction that occurs in parallel with vegetative propagation. We suggest that unmanaged processes of sexual reproduction play important but neglected roles in the evolutionary ecology of many domesticated plants in traditional agroecosystems.