BMC Ecology - Latest Articles

Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers

Michael Robeson — 2009-12-11T00:00:00Z

Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms.Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. Results: The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism. Conclusion: The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils.

Temporal development and collapse of an Arctic plant-pollinator network

Clementine Pradal — 2009-12-04T00:00:00Z

Background: The temporal dynamics and formation of plant-pollinator networks are difficult to study as it requires detailed observations of how the networks change over time. Understanding the temporal dynamics might provide insight into sustainability and robustness of the networks and how they react to environmental changes, such as global warming. Here we study an Arctic plant-pollinator network in two consecutive years using a simple mathematical model and describe the temporal dynamics (daily assembly and disassembly of links) by random mechanisms. Results: We develop a mathematical model with parameters governed by the probabilities for entering, leaving and making connections in the nework and demonstrate that A. The dynamics is described by very similar parameters in both years despite a strong turnover in the composition of the pollinator community and different climate conditions, B. There is a drastic change in the temporal behaviour a few days before the end of the season in both years. This change leads to the collapse of the network and does not correlate with weather parameters, C. We estimate that the number of available pollinator species is about 80 species of which 75-80\% are observed in each year, D. The network does not reach an equilibrium state (as defined by our model) before the collapse set in and the season is over. Conclusions: We have shown that the temporal dynamics of an Arctic plant-pollinator network can be described by a simple mathematical model and that the model allows us to draw biologically interesting conclusions. Our model makes it possible to investigate how the network topology changes with changes in parameter values and might provide means to study the effect of climate on plant-pollinator networks.

Spurious and functional correlates of the isotopic composition of a generalist across a tropical rainforest landscape

Terrence McGlynn — 2009-11-24T00:00:00Z

Background: The isotopic composition of generalist consumers may be expected to vary in space as a consequence of spatial heterogeneity in isotope ratios, the abundance of resources, and competition. We aim to account for the spatial variation in the carbon and nitrogen isotopic composition of a generalized predatory species across a 500 ha. tropical rain forest landscape. We test competing models to account for relative influence of resources and competitors to the carbon and nitrogen isotopic enrichment of gypsy ants (Aphaenogaster araneoides), taking into account site-specific differences in baseline isotope ratios. Results: We found that 75% of the variance in the fraction of 15N in the tissue of A. araneoides was accounted by one environmental parameter, the concentration of soil phosphorus. After taking into account landscape-scale variation in baseline resources, the most parsimonious model indicated that colony growth and leaf litter biomass accounted for nearly all of the variance in the δ15N discrimination factor, whereas the δ13C discrimination factor was most parsimoniously associated with colony size and the rate of leaf litter decomposition. There was no indication that competitor density or diversity accounted for spatial differences in the isotopic composition of gypsy ants. Conclusion: Across a 500 ha. landscape, soil phosphorus accounted for spatial variation in baseline nitrogen isotope ratios. The δ15N discrimination factor of a higher order consumer in this food web was structured by bottom-up influences - the quantity and decomposition rate of leaf litter. Stable isotope studies on the trophic biology of consumers may benefit from explicit spatial design to account for edaphic properties that alter the baseline at fine spatial grains.

Impacts of feral horses on a desert environment

Stacey Ostermann-Kelm — 2009-11-10T00:00:00Z

Background: Free-ranging horses (Equus caballus) in North America are considered to be feral animals since they are descendents of non-native domestic horses introduced to the continent. We conducted a study in a southern California desert to understand how feral horse movements and horse feces impacted this arid ecosystem. We evaluated five parameters susceptible to horse trampling: soil strength, vegetation cover, percent of nonnative vegetation, plant species diversity, and macroinvertebrate abundance. We also tested whether or not plant cover and species diversity were affected by the presence of horse feces. Results: Horse trailing resulted in reduced vegetation cover, compacted soils, and in cases of intermediate intensity disturbance, increased plant species diversity. The presence of horse feces did not affect plant cover, but it did increase native plant diversity. Conclusion: Adverse impacts, such as soil compaction and increased erosion potential, were limited to established horse trails. In contrast, increased native plant diversity near trails and feces could be viewed as positive outcomes. Extensive trailing can result in a surprisingly large impact area: we estimate that < 30 horses used > 25 km2 of trails in our study area.

Generalist dinoflagellate endosymbionts and host genotype diversity detected from mesophotic (67-100m depths) coral Leptoseris

Yvonne Chan — 2009-09-11T00:00:00Z

Background: Mesophotic corals (light-dependent corals in the deepest half of the photic zone at depths of 30 - 150 m) provide a unique opportunity to study the limits of the interactions between corals and endosymbiotic dinoflagellates in the genus Symbiodinium. We sampled Leptoseris spp. in Hawaii via manned submersibles across a depth range of 67 - 100 m. Both the host and Symbiodinium communities were genotyped, using a non-coding region of the mitochondrial ND5 intron (NAD5) and the nuclear ribosomal internal transcribed spacer region 2 (ITS2), respectively. Results: Coral colonies harbored endosymbiotic communities dominated by previously identified shallow water Symbiodinium ITS2 types (C1_ AF333515, C1c_ AY239364, C27_ AY239379, and C1b_ AY239363) and exhibited genetic variability at mitochondrial NAD5. Conclusion: This is one of the first studies to examine genetic diversity in corals and their endosymbiotic dinoflagellates sampled at the limits of the depth and light gradients for hermatypic corals. The results reveal that these corals associate with generalist endosymbiont types commonly found in shallow water corals and implies that the composition of the Symbiodinium community (based on ITS2) alone is not responsible for the dominance and broad depth distribution of Leptoseris spp. The level of genetic diversity detected in the coral NAD5 suggests that there is undescribed taxonomic diversity in the genus Leptoseris from Hawaii.

Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms

Lorraine Pariset — 2009-09-02T00:00:00Z

Background: SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results: A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion: Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.

Patterns of genetic structuring in the coral Pocillopora damicornis on reefs in East Africa

Petra Souter — 2009-08-26T00:00:00Z

Background: Studies of population genetic structures provide an indication of direction and magnitude of larval transport and hence are an important component in the assessment of the ability of reefs to recover from severe disturbance. This paper reports data on population genetic structures in the coral Pocillopora damicornis from 26 reefs in Kenya and Tanzania. Results: Gene flow among reefs was found to be variable, with a significant overall genetic subdivision (FST = 0.023 ± 0.004 SE; p < 0.001), however, only 34% of all pairwise population comparisons showed significant differentiation. Panmixia could not be rejected between reefs separated by as much as 697 km, while other sites, separated by only a single kilometre, were found to be significantly differentiated. An analysis of molecular variance indicated that population genetic differentiation was significant only at the smaller spatial scale (< 10 km), whereas panmixia could not be rejected between groups of samples separated by over 100 km. Estimates of contemporary gene flow showed similar results, with numbers of first generation migrants within each population ranging from 0 to 4 (~5% of the total number of colonies sampled) and likely dispersal distances ranging between 5 and 500 km. Conclusion: This study showed that population differentiation in P. damicornis varied over spatial scales and that this variability occurred at both evolutionary and ecological time scales. This paradox is discussed in light of stochastic recruitment and small scale population structures found in other species of coral. The study also identifies potential source reefs, such as those within Mnemba Conservation area near Zanzibar and genetically isolated reefs such as those within Malindi Marine National Park and Reserve in northern Kenya.

The effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

Richard Sibly — 2009-06-23T00:00:00Z

Background: Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results: Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion: Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms of density dependence. The importance of our results lies in our demonstration that the effects of spatial and temporal heterogeneity must be accounted for if we are to have accurate predictive models for use in management and conservation. This is an area which until now has lacked an adequate theoretical framework and methodology.

Ecological niche partitioning between Anopheles gambiae molecular forms in Cameroon: the ecological side of speciation

Frederic Simard — 2009-05-21T00:00:00Z

Background: Speciation among members of the Anopheles gambiae complex is thought to be promoted by disruptive selection and ecological divergence acting on sets of adaptation genes protected from recombination by polymorphic paracentric chromosomal inversions. However, shared chromosomal polymorphisms between the M and S molecular forms of An. gambiae and insufficient information about their relationship with ecological divergence challenge this view. We used Geographic Information Systems, Ecological Niche Factor Analysis, and Bayesian multilocus genetic clustering to explore the nature and extent of ecological and chromosomal differentiation of M and S across all the biogeographic domains of Cameroon in Central Africa, in order to understand the role of chromosomal arrangements in ecological specialisation within and among molecular forms. Results: Species distribution modelling with presence-only data revealed differences in the ecological niche of both molecular forms and the sibling species, An. arabiensis. The fundamental environmental envelope of the two molecular forms, however, overlapped to a large extent in the rainforest, where they occurred in sympatry. The S form had the greatest niche breadth of all three taxa, whereas An. arabiensis and the M form had the smallest niche overlap. Correspondence analysis of M and S karyotypes confirmed that molecular forms shared similar combinations of chromosomal inversion arrangements in response to the eco-climatic gradient defining the main biogeographic domains occurring across Cameroon. Savanna karyotypes of M and S, however, segregated along the smaller-scale environmental gradient defined by the second ordination axis. Population structure analysis identified three chromosomal clusters, each containing a mixture of M and S specimens. In both M and S, alternative karyotypes were segregating in contrasted environments, in agreement with a strong ecological adaptive value of chromosomal inversions. Conclusion: Our data suggest that inversions on the second chromosome of An. gambiae are not causal to the evolution of reproductive isolation between the M and S forms. Rather, they are involved in ecological specialization to a similar extent in both genetic backgrounds, and most probably predated lineage splitting between molecular forms. However, because chromosome-2 inversions promote ecological divergence, resulting in spatial and/or temporal isolation between ecotypes, they might favour mutations in other ecologically significant genes to accumulate in unlinked chromosomal regions. When such mutations occur in portions of the genome where recombination is suppressed, such as the pericentromeric regions known as speciation islands in An. gambiae, they would contribute further to the development of reproductive isolation.

Living at the edge: biogeographic patterns of habitat segregation conform to speciation by niche expansion in Anopheles gambiae

Carlo Costantini — 2009-05-21T00:00:00Z

Background: Ongoing lineage splitting within the African malaria mosquito Anopheles gambiae is compatible with ecological speciation, the evolution of reproductive isolation by divergent natural selection acting on two populations exploiting alternative resources. Divergence between two molecular forms (M and S) identified by fixed differences in rDNA, and characterized by marked, although incomplete, reproductive isolation is occurring in West and Central Africa. To elucidate the role that ecology and geography play in speciation, we carried out a countrywide analysis of An. gambiae M and S habitat requirements, and that of their chromosomal variants, across Burkina Faso. Results: Maps of relative abundance by geostatistical interpolators produced a distinct pattern of distribution: the M-form dominated in the northernmost arid zones, the S-form in the more humid southern regions. Maps of habitat suitability, quantified by Ecological Niche Factor Analysis based on 15 eco-geographical variables revealed less contrast among forms. M was peculiar as it occurred proportionally more in habitat of marginal quality. Measures of ecological niche breadth and overlap confirmed the mismatch between the fundamental and realized patterns of habitat occupation: forms segregated more than expected from the extent of divergence of their environmental envelope – a signature of niche expansion. Classification of chromosomal arm 2R karyotypes by multilocus genetic clustering identified two clusters loosely corresponding to molecular forms, with 'mismatches' representing admixed individuals due to shared ancestral polymorphism and/or residual hybridization. In multivariate ordination space, these karyotypes plotted in habitat of more marginal quality compared to non-admixed, 'typical', karyotypes. The distribution of 'typical' karyotypes along the main eco-climatic gradient followed a consistent pattern within and between forms, indicating an adaptive role of inversions at this geographical scale. Conclusion: Ecological segregation between M and S is consistent with niche expansion into marginal habitats by chromosomal inversion variants during early lineage divergence; presumably, this process is promoted by inter-karyotype competition in the higher-quality core habitat. We propose that the appearance of favourable allelic combinations in other regions of suppressed recombination (e.g. pericentromeric portions defining speciation islands in An. gambiae) fosters development of reproductive isolation to protect linkage between separate chromosomal regions.