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Testing a short nuclear marker for inferring staphylinid beetle diversity in an African tropical rain forest.

ABSTRACT: The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, there are only few attempts to use DNA markers for inventorying all animal species found in environmental samples to describe variations of biodiversity patterns.In this study, an analysis of the nuclear D3 region of the 28S rRNA gene to delimit species-like units is compared to results based on distinction of morphospecies. Data derived from both approaches are used to assess diversity and composition of staphylinid beetle communities of a Guineo-Congolian rain forest in Kenya. Beetles were collected with a standardized sampling design across six transects in primary and secondary forests using pitfall traps. Sequences could be obtained of 99% of all individuals. In total, 76 molecular operational taxonomic units (MOTUs) were found in contrast to 70 discernible morphospecies. Despite this difference both approaches revealed highly similar biodiversity patterns, with species richness being equal in primary and secondary forests, but with divergent species communities in different habitats. The D3-MOTU approach proved to be an efficient tool for biodiversity analyses.Our data illustrate that the use of MOTUs as a proxy for species can provide an alternative to morphospecies identification for the analysis of changes in community structure of hyperdiverse insect taxa. The efficient amplification of the D3-marker and the ability of the D3-MOTUs to reveal similar biodiversity patterns as analyses of morphospecies recommend its use in future molecular studies on biodiversity.

SUBMITTER: Thormann B

PROVIDER: S-EPMC3069053 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

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Testing a short nuclear marker for inferring staphylinid beetle diversity in an African tropical rain forest.

Thormann Birthe B Raupach Michael J MJ Wagner Thomas T Wägele Johann W JW Peters Marcell K MK

PloS one 20110331 3

<h4>Background</h4>The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, ...[more]

PMID: 21483872

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Project description:BACKGROUND: The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa. RESULTS: A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods. CONCLUSIONS: Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.

Project description:BackgroundTropical rain forests are the most diverse terrestrial ecosystems on the planet. How this diversity evolved remains largely unexplained. In Africa, rain forests are situated in two geographically isolated regions: the West-Central Guineo-Congolian region and the coastal and montane regions of East Africa. These regions have strong floristic affinities with each other, suggesting a former connection via an Eocene pan-African rain forest. High levels of endemism observed in both regions have been hypothesized to be the result of either 1) a single break-up followed by a long isolation or 2) multiple fragmentation and reconnection since the Oligocene. To test these hypotheses the evolutionary history of endemic taxa within a rain forest restricted African lineage of the plant family Annonaceae was studied. Molecular phylogenies and divergence dates were estimated using a Bayesian relaxed uncorrelated molecular clock assumption accounting for both calibration and phylogenetic uncertainties.ResultsOur results provide strong evidence that East African endemic lineages of Annonaceae have multiple origins dated to significantly different times spanning the Oligocene and Miocene epochs. Moreover, these successive origins (c. 33, 16 and 8 million years--Myr) coincide with known periods of aridification and geological activity in Africa that would have recurrently isolated the Guineo-Congolian rain forest from the East African one. All East African taxa were found to have diversified prior to Pleistocene times.ConclusionMolecular phylogenetic dating analyses of this large pan-African clade of Annonaceae unravels an interesting pattern of diversification for rain forest restricted trees co-occurring in West/Central and East African rain forests. Our results suggest that repeated reconnections between the West/Central and East African rain forest blocks allowed for biotic exchange while the break-ups induced speciation via vicariance, enhancing the levels of endemicity. These results provide an explanation for present day distribution patterns and origins of endemicity for African rain forest trees. Moreover, given the pre-Pleistocene origins of all the studied endemic East African genera and species, these results also offer important insights for setting conservation priorities in these highly diversified but threatened ecosystems.

Project description:Soil characteristics have been hypothesised as one of the possible mechanisms leading to monodominance of Gilbertiodendron dewerei in some areas of Central Africa where higher-diversity forest would be expected. However, the differences in soil characteristics between the G. dewevrei-dominated forest and its adjacent mixed forest are still poorly understood. Here we present the soil characteristics of the G. dewevrei forest and quantify whether soil physical and chemical properties in this monodominant forest are significantly different from the adjacent mixed forest.We sampled top soil (0-5, 5-10, 10-20, 20-30 cm) and subsoil (150-200 cm) using an augur in 6 × 1 ha areas of intact central Africa forest in SE Cameroon, three independent patches of G. dewevrei-dominated forest and three adjacent areas (450-800 m apart), all chosen to be topographically homogeneous. Analysis--subjected to Bonferroni correction procedure--revealed no significant differences between the monodominant and mixed forests in terms of soil texture, median particle size, bulk density, pH, carbon (C) content, nitrogen (N) content, C:N ratio, C:total NaOH-extractable P ratio and concentrations of labile phosphorous (P), inorganic NaOH-extractable P, total NaOH-extractable P, aluminium, barium, calcium, copper, iron, magnesium, manganese, molybdenum, nickel, potassium, selenium, silicon, sodium and zinc. Prior to Bonferroni correction procedure, there was a significant lower level of silicon concentration found in the monodominant than mixed forest deep soil; and a significant lower level of nickel concentration in the monodominant than mixed forest top soil. Nevertheless, these were likely to be the results of multiple tests of significance.Our results do not provide clear evidence of soil mediation for the location of monodominant forests in relation to adjacent mixed forests. It is also likely that G. dewevrei does not influence soil chemistry in the monodominant forests.

Dataset Information

Testing a short nuclear marker for inferring staphylinid beetle diversity in an African tropical rain forest.

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Testing a short nuclear marker for inferring staphylinid beetle diversity in an African tropical rain forest.

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