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Birer, C., Tysklind, N., Zinger, L., & Duplais, C. (2017). Comparative analysis of DNA extraction methods to study the body surface microbiota of insects: A case study with ant cuticular bacteria. Mol Ecol Resour, 17(6), e34–e45.
Abstract: High-throughput sequencing of the 16S rRNA gene has considerably helped revealing the essential role of bacteria living on insect cuticles in the ecophysiology and behaviour of their hosts. However, our understanding of host-cuticular microbiota feedbacks remains hampered by the difficulties of working with low bacterial DNA quantities as with individual insect cuticle samples, which are more prone to molecular biases and contaminations. Herein, we conducted a methodological benchmark on the cuticular bacterial loads retrieved from two Neotropical ant species of different body size and ecology: Atta cephalotes (~15 mm) and Pseudomyrmex penetrator (~5 mm). We evaluated the richness and composition of the cuticular microbiota, as well as the amount of biases and contamination produced by four DNA extraction protocols. We also addressed how bacterial community characteristics would be affected by the number of individuals or individual body size used for DNA extraction. Most extraction methods yielded similar results in terms of bacterial diversity and composition for A. cephalotes (~15 mm). In contrast, greater amounts of artefactual sequences and contaminations, as well as noticeable differences in bacterial community characteristics were observed between extraction methods for P. penetrator (~5 mm). We also found that large (~15 mm) and small (~5 mm) A. cephalotes individuals harbour different bacterial communities. Our benchmark suggests that cuticular microbiota of single individual insects can be reliably retrieved provided that blank controls, appropriate data cleaning, and individual body size and functional role within insect society are considered in the experiment.
Keywords: 16S rRNA; bacterial communities; cuticular microbiome; insect cuticle; metabarcoding
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Sommeria-Klein, G., Zinger, L., Coissac, E., Iribar, A., Schimann, H., Taberlet, P., et al. (2020). Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA-based census of soil biodiversity from a tropical forest. Mol. Ecol. Resour., 20(2), 371–386.
Abstract: High-throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such data sets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA samples into overlapping assemblages of co-occurring taxa. It is a flexible model-based method adapted to uneven sample sizes and to large and sparse data sets. Here, we compare LDA performance on abundance and occurrence data, and we quantify the robustness of the LDA decomposition by measuring its stability with respect to the algorithm's initialization. We then apply LDA to a survey of 1,131 soil DNA samples that were collected in a 12-ha plot of primary tropical forest and amplified using standard primers for bacteria, protists, fungi and metazoans. The analysis reveals that bacteria, protists and fungi exhibit a strong spatial structure, which matches the topographical features of the plot, while metazoans do not, confirming that microbial diversity is primarily controlled by environmental variation at the studied scale. We conclude that LDA is a sensitive, robust and computationally efficient method to detect and interpret the structure of large DNA-based biodiversity data sets. We finally discuss the possible future applications of this approach for the study of biodiversity. © 2019 John Wiley & Sons Ltd
Keywords: community ecology; environmental DNA; metabarcoding; OTU presence–absence; soil microbiome; topic modelling; bacterium; biodiversity; biology; classification; eukaryote; fungus; genetics; high throughput sequencing; isolation and purification; microbiology; parasitology; procedures; soil; Bacteria; Biodiversity; Computational Biology; Eukaryota; Fungi; High-Throughput Nucleotide Sequencing; Soil; Soil Microbiology
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Coutant, O., Richard-Hansen, C., de Thoisy, B., Decotte, J. - B., Valentini, A., Dejean, T., et al. (2021). Amazonian mammal monitoring using aquatic environmental DNA. Molecular Ecology Resources, 21(6), 1875–1888.
Abstract: Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
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Le Guen, V., Rodier-Goud, M., Troispoux, V., Xiong, T. C., Brottier, P., Billot, C., et al. (2004). Characterization of polymorphic microsatellite markers for Microcyclus ulei, causal, agent of South American leaf blight of rubber trees. Mol. Ecol. Notes, 4(1), 122–124.
Abstract: South American leaf blight caused by the ascomycete Microcyclus Wei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus).
Keywords: Hevea brasiliensis; Microcyclus ulei; microsatellite markers; phytopathogenic fungi; South American leaf blight
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Duminil, J., Caron, H., Scotti, I., Cazal, S. O., & Petit, R. J. (2006). Blind population genetics survey of tropical rainforest trees. Mol. Ecol., 15(12), 3505–3513.
Abstract: Rainforest tree species can be difficult to identify outside of their period of reproduction. Vascular tissues from Carapa spp. individuals were collected during a short field trip in French Guiana and analysed in the laboratory with nuclear and chloroplast markers. Using a Bayesian approach, > 90% of the samples could be assigned to one of two distinct clusters corresponding to previously described species, making it possible to estimate the genetic structure of each species and to identify cases of introgression. We argue that this blind procedure represents a first-choice rather than a fallback option whenever related taxa are investigated.
Keywords: Bayesian assignment tests; genetic diversity; geographical structure; South America; species delimitation
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Hardy, O. J., Maggia, L., Bandou, E., Breyne, P., Caron, H., Chevallier, M. H., et al. (2006). Fine-scale genetic structure and gene dispersal inferences in 10 Neotropical tree species. Mol. Ecol., 15(2), 559–571.
Abstract: The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.
Keywords: French Guiana; gene dispersal; seed dispersal; spatial genetic structure; tropical trees
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Foucaud, J., Orivel, J., Fournier, D., Delabie, J. H. C., Loiseau, A., Le Breton, J., et al. (2009). Reproductive system, social organization, human disturbance and ecological dominance in native populations of the little fire ant, Wasmannia auropunctata. Mol. Ecol., 18(24), 5059–5073.
Abstract: The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non-dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non-dominant native populations in natural and human-modified habitats. Microsatellite and mtDNA data indicated that dominant and non-dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human-modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species' ecological features and the adaptive potential of clonal reproductive systems.
Keywords: biological invasion; clonality; human disturbance; parthenogenesis; social organization; Wasmannia auropunctata
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Latouche-Halle, C., Ramboer, A., Bandou, E., Caron, H., & Kremer, A. (2004). Long-distance pollen flow and tolerance to selfing in a neotropical tree species. Mol. Ecol., 13(5), 1055–1064.
Abstract: Outcrossing rates, pollen dispersal and male mating success were assessed in Dicorynia guianensis Amshoff, a neotropical tree endemic to the Guiana shield. All adult trees within a continuous area of 40 ha (n = 157) were mapped, and were genotyped with six microsatellite loci. In addition, progenies were genotyped from 22 mature trees. At the population level, the species was mostly outcrossing (t(m) = 0.89) but there was marked variation among individuals. One tree exhibited mixed mating, confirming earlier results obtained with isozymes that D. guianensis can tolerate selfing. A Bayesian extension of the fractional paternity method was used for paternity analysis, and was compared with the neighbourhood method used widely for forest trees. Both methods indicated that pollen dispersal was only weakly related to distance between trees within the study area, and that the majority (62%) of pollen came from outside the study stand. Using maximum likelihood, male potential population size was estimated to be 1119, corresponding to a neighbourhood size of 560 hectares. Male mating success was, however, related to the diameter of the stem and to flowering intensity assessed visually. The mating behaviour of D. guianensis is a combination of long-distance pollen flow and occasional selfing. The species can still reproduce when it is extremely rare, either by selfing or by dispersing pollen at long distances. These results, together with the observation that male mating success was correlated with the size of the trees, could be implemented in management procedures aiming at regenerating the species.
Keywords: Dicorynia guianensis; microsatellites; outcrossing rate; pollen flow; reproductive success; tropical tree
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Dutech, C., Seiter, J., Petronelli, P., Joly, H. I., & Jarne, P. (2002). Evidence of low gene flow in a neotropical clustered tree species in two rainforest stands of French Guiana. Mol. Ecol., 11(4), 725–738.
Abstract: The spatial genetic structure of the neotropical, clustered tree species Vouacapoua americana (Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci, V. americana is characterized by a marked genetic structure at small spatial distances (under 30-60 m), in agreement with the limited seed dispersal by rodent species. Gene flow through pollen is also shown to be mainly restricted to less than 100 m. This result suggests that most pollination events (mediated through small insects) are probably limited to within-patches of individuals, which might explain the high genetic differentiation among patches (F-ST = 0.11) separated by less than 2 km. We also assume that stronger genetic structure in Paracou is likely to be due to lower seed dispersal by rodents, large spatial distances separating patches, or a recent recolonization event.
Keywords: Caesalpiniaceae; gene flow; recolonization process; spatial genetic structure; tropical rainforest; Vouacapoua americana
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Csilléry, K., Lalague, H., Vendramin, G. G., González-Martínez, S. C., Fady, B., & Oddou-Muratorio, S. (2014). Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations. Molecular Ecology, 23(19), 4696–4708.
Abstract: Detecting signatures of selection in tree populations threatened by climate change is currently a major research priority. Here, we investigated the signature of local adaptation over a short spatial scale using 96 European beech (Fagus sylvatica L.) individuals originating from two pairs of populations on the northern and southern slopes of Mont Ventoux (south-eastern France). We performed both single and multilocus analysis of selection based on 53 climate-related candidate genes containing 546 SNPs. FST outlier methods at the SNP level revealed a weak signal of selection, with three marginally significant outliers in the northern populations. At the gene level, considering haplotypes as alleles, two additional marginally significant outliers were detected, one on each slope. To account for the uncertainty of haplotype inference, we averaged the Bayes factors over many possible phase reconstructions. Epistatic selection offers a realistic multilocus model of selection in natural populations. Here, we used a test suggested by Ohta based on the decomposition of the variance of linkage disequilibrium. Overall populations, 0.23% of the SNP pairs (haplotypes) showed evidence of epistatic selection, with nearly 80% of them being within genes. One of the between gene epistatic selection signals arose between an FST outlier and a nonsynonymous mutation in a drought response gene. Additionally, we identified haplotypes containing selectively advantageous allele combinations which were unique to high or low elevations and northern or southern populations. Several haplotypes contained nonsynonymous mutations situated in genes with known functional importance for adaptation to climatic factors.
Keywords: abiotic stress; budburst phenology; FST outlier; gene network; haplotype; Ohta's test; variance components of linkage disequilibrium
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