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1.  Limited impacts of extensive human land use on dominance, specialization, and biotic homogenization in boreal plant communities 
BMC Ecology  2015;15(1):5.
Niche theory predicts that human disturbance should influence the assembly of communities, favouring functionally homogeneous communities dominated by few but widespread generalists. The decline and loss of specialists leaves communities with species that are functionally more similar. Evenness of species occupancy declines, such that species become either widespread of rare. These patterns have often been observed, but it is unclear if they are a general result of human disturbance or specific to communities that are rich in species, in complex, spatially heterogeneous environments where the problem has often been investigated. We therefore tested whether human disturbance impacts dominance/evenness of species occupancy in communities, specialism/generalism of species, and functional biotic homogenization in the spatially relatively homogeneous, species poor boreal forest region of Alberta, Canada. We investigated 371 boreal vascular plant communities varying 0 – 100% in proportion of human land use.
Rank species occupancy curves revealed high species dominance regardless of disturbance: within any disturbance class a few species occupied nearly every site and most species were found in a low proportion of sites. However, species were more widespread and displayed more even occupancy in intermediately disturbed communities than among communities of either low or high disturbance. We defined specialists and generalists based on turnover in co-occupants and thereby assessed impacts of human disturbance on specialization of species and community homogenization. Generalists were not disproportionately found at higher disturbance sites, and did not occupy more sites. Communities with greater human disturbance were not more functionally homogeneous; they did not harbor communities with more generalists.
We unexpectedly did not observe strong linkages between species specialism/generalism and disturbance, nor between community homogenization and disturbance. These results contrast previous findings in more species rich, complex or spatially heterogeneous systems and ecological models. We suggest that broad occupancy-based intercommunity patterns are insensitive to human land use extent in boreal vascular plants, perhaps because of ubiquity of generalists, low species richness, and history of natural disturbance. The poor sensitivity of these metrics to disturbance presents challenges for monitoring and managing impacts to biodiversity in this region.
PMCID: PMC4328035
Anthropogenic disturbance; Biodiversity; Biotic homogenization; Boreal forest; Community structure; Human land use; Niche width; Rank species occupancy curve; Specialization; Vascular plants
2.  High-throughput sequencing of nematode communities from total soil DNA extractions 
BMC Ecology  2015;15:3.
Nematodes are extremely diverse and numbers of species are predicted to be more than a million. Studies on nematode diversity are difficult and laborious using classical methods and therefore high-throughput sequencing is an attractive alternative. Primers that have been used in previous sequence-based studies are not nematode specific but also amplify other groups of organisms such as fungi and plantae, and thus require a nematode enrichment step that may introduce biases.
In this study an amplification strategy which selectively amplifies a fragment of the SSU from nematodes without the need for enrichment was developed. Using this strategy on DNA templates from a set of 22 agricultural soils, we obtained 64.4% sequences of nematode origin in total, whereas the remaining sequences were almost entirely from other metazoans. The nematode sequences were derived from a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida.
Our amplification and sequencing strategy for assessing nematode diversity was able to collect a broad diversity without prior nematode enrichment and thus the method will be highly valuable in ecological studies of nematodes.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-014-0034-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4331302
Nematode; Community; Next-generation sequencing; SSU; Diversity; 18S; rDNA
3.  Nectar sugars and bird visitation define a floral niche for basidiomycetous yeast on the Canary Islands 
BMC Ecology  2015;15(1):2.
Studies on the diversity of yeasts in floral nectar were first carried out in the late 19th century. A narrow group of fermenting, osmophilous ascomycetes were regarded as exclusive specialists able to populate this unique and species poor environment. More recently, it became apparent that microorganisms might play an important role in the process of plant pollination. Despite the importance of these nectar dwelling yeasts, knowledge of the factors that drive their diversity and species composition is scarce.
In this study, we linked the frequencies of yeast species in floral nectars from various host plants on the Canary Islands to nectar traits and flower visitors. We estimated the structuring impact of pollination syndromes (nectar volume, sugar concentration and sugar composition) on yeast diversity.
The observed total yeast diversity was consistent with former studies, however, the present survey yielded additional basidiomycetous yeasts in unexpectedly high numbers. Our results show these basidiomycetes are significantly associated with ornithophilous flowers. Specialized ascomycetes inhabit sucrose-dominant nectars, but are surprisingly rare in nectar dominated by monosaccharides.
There are two conclusions from this study: (i) a shift of floral visitors towards ornithophily alters the likelihood of yeast inoculation in flowers, and (ii) low concentrated hexose-dominant nectar promotes colonization of flowers by basidiomycetes. In the studied floral system, basidiomycete yeasts are acknowledged as regular members of nectar. This challenges the current understanding that nectar is an ecological niche solely occupied by ascomycetous yeasts.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-015-0036-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4318194  PMID: 25638173
Basidiomycetes; Bird pollination; Boraginaceae; Canary Islands; Nectar-dwelling yeast
4.  Suppression of the invasive plant mile-a-minute (Mikania micrantha) by local crop sweet potato (Ipomoea batatas) by means of higher growth rate and competition for soil nutrients 
BMC Ecology  2015;15(1):1.
There are a variety of ways of increasing crop diversity to increase agricultural sustainability and in turn having a positive influence on nearby natural ecosystems. Competitive crops may provide potent management tools against invasive plants. To elucidate the competitive mechanisms between a sweet potato crop (Ipomoea batatas) and an invasive plant, mile-a-minute (Mikania micrantha), field experiments were carried out in Longchuan County of Yunnan Province, Southwest China, utilizing a de Wit replacement series. The trial incorporated seven ratios of sweet potato and mile-a-minute plants in 25 m2 plots.
In monoculture, the total biomass, biomass of adventitious root, leafstalk length, and leaf area of sweet potato were all higher than those of mile-a-minute, and in mixed culture the plant height, branch, leaf, stem node, adventitious root, flowering and biomass of mile-a-minute were suppressed significantly (P < 0.05). The relative yield (RY) of mile-a-minute and sweet potato was less than 1.0 in mixed culture, indicating that intraspecific competition was less than interspecific competition. The competitive balance index of sweet potato demonstrated a higher competitive ability than mile-a-minute. Except pH, other soil nutrient contents of initial soil (CK) were significantly higher than those of seven treatments. The concentrations of soil organic matter, total N, total K, available N, available P, available K, exchange Ca, exchange Mg, available Mn, and available B were significantly greater (P < 0.05) in mile-a-minute monoculture soil than in sweet potato monoculture soil, and were reduced by the competition of sweet potato in the mixture.
Evidently sweet potato has a competitive advantage in terms of plant growth characteristics and greater absorption of soil nutrients. Thus, planting sweet potato is a promising technique for reducing infestations of mile-a-minute, providing weed management benefits and economic returns from harvest of sweet potatoes. This study also shows the potential value of replacement control methods which may apply to other crop-weed systems or invaded natural ecosystems.
PMCID: PMC4325956  PMID: 25626963
Sweet potato; Mile-a-minute; Competition interactions; Soil nutrients; Biological control
5.  Experimental infection of a periodical cicada (Magicicada cassinii) with a parasitoid (Emblemasoma auditrix) of a proto-periodical cicada (Okanagana rimosa) 
BMC Ecology  2014;14(1):31.
The proto-periodical cicada Okanagana rimosa is subject to infection by the acoustically orientating parasitoid fly Emblemasoma auditrix. Furthermore, it is also the only known host of E. auditrix. Here we test the question, whether the highly adapted parasitoid can also infect other cicadas, like the periodical cicada (Magicicada cassinii) and which steps of the parasitization process can be completed. The experiments might also reveal whether such a parasitoid could hypothetically have been involved in the evolution of periodicity.
The hearing threshold of E. auditrix matches with the spectrum of the calling song of M. cassinii, indicating potential host localization. Behaviourally, host localization is possible by the parasitoid as it approaches a loudspeaker broadcasting the buzz part of the calling song of M. cassinii. Magicicada cassinii is readily accepted as host and for host infection the parasitoid uses the same behavioural sequence as for its host O. rimosa. A larva is deposited into the timbal of the cicada. By contrast to O. rimosa the development of the fly larva is delayed and eventually suppressed in M. cassinii.
The host range of E. auditrix is mainly determined by acoustic parameters. This filter is important, as other sensory cues seem not to be involved in the host selection process and larva will not develop in unsuited host. Although the recent parasitoid-host system seems to be stable in terms of coexistence of both species, an acoustically hunting parasitoid could have been a selective force during evolution of prime numbered periodicity in cicadas.
PMCID: PMC4269849  PMID: 25496534
Host location; Host suitability; Evolution of periodicity; Auditory system
6.  Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability 
BMC Ecology  2014;14(1):26.
Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian “Llanos”. We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the “single tree effect” by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses.
The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10–20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0–5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10–20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation.
A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-014-0026-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4261983  PMID: 25476419
7.  Gastrointestinal helminths may affect host susceptibility to anthrax through seasonal immune trade-offs 
BMC Ecology  2014;14(1):27.
Most vertebrates experience coinfections, and many pathogen-pathogen interactions occur indirectly through the host immune system. These interactions are particularly strong in mixed micro-macroparasite infections because of immunomodulatory effects of helminth parasites. While these trade-offs have been examined extensively in laboratory animals, few studies have examined them in natural systems. Additionally, many wildlife pathogens fluctuate seasonally, at least partly due to seasonal host immune changes. We therefore examined seasonality of immune resource allocation, pathogen abundance and exposure, and interactions between infections and immunity in plains zebra (Equus quagga) in Etosha National Park (ENP), Namibia, a system with strongly seasonal patterns of gastrointestinal (GI) helminth infection intensity and concurrent anthrax outbreaks. Both pathogens are environmentally transmitted, and helminth seasonality is driven by environmental pressures on free living life stages. The reasons behind anthrax seasonality are currently not understood, though anthrax is less likely directly driven by environmental factors.
We measured a complex, interacting set of variables and found evidence that GI helminth infection intensities, eosinophil counts, IgE and IgGb antibody titers, and possibly IL-4 cytokine signaling were increased in wetter seasons, and that ectoparasite infestations and possibly IFN-γ cytokine signaling were increased in drier seasons. Monocyte counts and anti-anthrax antibody titers were negatively associated with wet season eosinophilia, and monocytes were negatively correlated with IgGb and IgE titers. Taken together, this supports the hypothesis that ENP wet seasons are characterized by immune resource allocation toward Th-2 type responses, while Th1-type immunity may prevail in drier seasons, and that hosts may experience Th1-Th2 trade-offs. We found evidence that this Th2-type resource allocation is likely driven by GI parasite infections, and that these trade-offs may render hosts less capable of concurrently mounting effective Th1-type immune responses against anthrax.
This study is one of the first to examine laboratory-demonstrated Th1-Th2 trade-offs in a natural system. It provides evidence that seasonally bound pathogens may affect, through immunology, transmission dynamics of pathogens that might otherwise not be seasonally distributed. It suggests that, by manipulating the internal host ecosystem, GI parasites may influence the external ecosystem by affecting the dynamics of another environmentally transmitted pathogen.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-014-0027-3) contains supplementary material, which is available to authorized users.
PMCID: PMC4247756  PMID: 25388877
Bacteria; Ecological immunology; Endoparasites; Host-parasite interactions; Microparasites; Coinfections immunological trade-offs; Disease ecology; Seasonality
8.  Coexistence mechanisms at multiple scales in mosquito assemblages 
BMC Ecology  2014;14(1):30.
Species coexistence in mosquito assemblages may depend on mechanisms related to interspecific resource partitioning occurring at multiple scales. In the present work we investigated co-occurrence or spatial segregation in mosquito assemblages sharing resources at micro-habitat, habitat and landscape scales. Environmental characteristics, mosquito fauna as adults and larvae were assessed along vegetation gradient in a natural landscape of tropical rainforest. Huisman-Olff-Fresco (HOF) and Generalized Additive (GAM) models were employed to explore relationships between abundances of potential competitors in mosquito assemblages and vegetation gradient (e.g., scrublands, mixed arboreal vegetation and dense ombrophilous forest). We tested hypotheses concerning mosquito species co-occurrence or spatial segregation employing binomial logistic regression models.
Co-occurrences and spatial segregation of mosquito species showed evidences of three scales of coexistence mechanisms: 1) micro-habitat - scale 1: different behaviors in response to food availability in specific vertical strata within larval container; 2) habitat - scale 2: specialized strategies related to heterogeneity of resource availability among larval containers and 3) landscape - scale 3: asymmetrical competition dependent upon the context of abiotic and biotic variables.
Results of the present work suggest that coexistence mechanisms can concomitantly work at multiple scales.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-014-0030-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4247778  PMID: 25384802
Biodiversity; Biotic interactions; Coexistence; Community; Ecology; Mosquitoes; Resource partitioning; Tropical rainforest
9.  Phosphorus limitation enhances parasite impact: feedback effects at the population level 
BMC Ecology  2014;14(1):29.
Nutrient deficiency affects the growth and population dynamics of consumers. Endoparasites can be seen as consumers that drain carbon (C) or energy from their host while simultaneously competing for limiting resources such as phosphorus (P). Depending on the relative demands of the host and the parasite for the limiting nutrient, intensified resource competition under nutrient limitation can either reduce the parasite’s effect on the host or further reduce the fitness of the nutrient-limited host. So far, knowledge of how nutrient limitation affects parasite performance at the host population level and how this affects the host populations is limited.
We followed the population growth of Daphnia magna that were uninfected or experimentally infected with a microsporidian, Glugoides intestinalis. The Daphnia were fed either P-sufficient or P-limited algae. The P-limited diet decreased the population density and biomass compared with the populations fed with the P-sufficient algae. In the P-sufficient populations, infection with the parasite reduced the population density but not the biomass of Daphnia, while in the P-limited populations, both the density and biomass of Daphnia decreased toward the end of the 32 day experiment compared with the uninfected controls. The infected animals from the P-limited populations had higher parasite spore cluster counts, while, in a separate experiment, host diet quality did not affect the number of parasites in individually kept Daphnia.
Because host diet quality did not affect parasite numbers at the individual level, we suggest that the higher parasite load in the P-limited populations is a result of feedback effects arising at the population level. Because of the density-dependent transmission of the parasite and the time lag between exposure and transmission, the lower host population density in the P-limited populations led to a higher spore:host ratio. This effect may have been further reinforced by decreases in filtration rates caused by crowding in the P-sufficient populations and/or increases in filtration rates as a response to poor food quality in the P-limited populations. The increases in exposure led to a higher parasite load and aggravated the negative effects of parasite infection at the population level.
Electronic supplementary material
The online version of this article (doi:10.1186/s12898-014-0029-1) contains supplementary material, which is available to authorized users.
PMCID: PMC4223164  PMID: 25366521
Daphnia magna; Ecological stoichiometry; Epidemiology; Glugoides intestinalis; Parasite; Transmission; Zooplankton
10.  The Hawaiian freshwater algae biodiversity survey (2009–2014): systematic and biogeographic trends with an emphasis on the macroalgae 
BMC Ecology  2014;14:28.
A remarkable range of environmental conditions is present in the Hawaiian Islands due to their gradients of elevation, rainfall and island age. Despite being well known as a location for the study of evolutionary processes and island biogeography, little is known about the composition of the non-marine algal flora of the archipelago, its degree of endemism, or affinities with other floras. We conducted a biodiversity survey of the non-marine macroalgae of the six largest main Hawaiian Islands using molecular and microscopic assessment techniques. We aimed to evaluate whether endemism or cosmopolitanism better explain freshwater algal distribution patterns, and provide a baseline data set for monitoring future biodiversity changes in the Hawaiian Islands.
1,786 aquatic and terrestrial habitats and 1,407 distinct collections of non-marine macroalgae were collected from the islands of Kauai, Oahu, Molokai, Maui, Lanai and Hawaii from the years 2009–2014. Targeted habitats included streams, wet walls, high elevation bogs, taro fields, ditches and flumes, lakes/reservoirs, cave walls and terrestrial areas. Sites that lacked freshwater macroalgae were typically terrestrial or wet wall habitats that were sampled for diatoms and other microalgae. Approximately 50% of the identifications were of green algae, with lesser proportions of diatoms, red algae, cyanobacteria, xanthophytes and euglenoids. 898 DNA sequences were generated representing eight different markers, which enabled an assessment of the number of taxonomic entities for genera collected as part of the survey. Forty-four well-characterized taxa were assessed for global distribution patterns. This analysis revealed no clear biogeographic affinities of the flora, with 27.3% characterized as “cosmopolitan”, 11.4% “endemic”, and 61.3% as intermediate.
The Hawaiian freshwater algal biodiversity survey represents the first comprehensive effort to characterize the non-marine algae of a tropical region in the world using both morphological and molecular tools. Survey data were entered in the Hawaiian Freshwater Algal Database, which serves as a digital repository of photographs and micrographs, georeferenced localities and DNA sequence data. These analyses yielded an updated checklist of the non-marine macroalgae of the Hawaiian Islands, and revealed varied biogeographic affinities of the flora that are likely a product of both natural and anthropogenic dispersal.
PMCID: PMC4222836  PMID: 25343968
Algal distribution; Biodiversity survey; Biogeography; Cyanobacteria; Dispersal; Freshwater algae; Hawaiian Islands; Molecular characterization; Taxonomy; UPA
11.  Plant genetic variation mediates an indirect ecological effect between belowground earthworms and aboveground aphids 
BMC Ecology  2014;14:25.
Interactions between aboveground and belowground terrestrial communities are often mediated by plants, with soil organisms interacting via the roots and aboveground organisms via the shoots and leaves. Many studies now show that plant genetics can drive changes in the structure of both above and belowground communities; however, the role of plant genetic variation in mediating aboveground-belowground interactions is still unclear. We used an earthworm-plant-aphid model system with two aphid species (Aphis fabae and Acyrthosiphon pisum) to test the effect of host-plant (Vicia faba) genetic variation on the indirect interaction between the belowground earthworms (Eisenia veneta) on the aboveground aphid populations.
Our data shows that host-plant variety mediated an indirect ecological effect of earthworms on generalist black bean aphids (A. fabae), with earthworms increasing aphid growth rate in three plant varieties but decreasing it in another variety. We found no effect of earthworms on the second aphid species, the pea aphid (A. pisum), and no effect of competition between the aphid species. Plant biomass was increased when earthworms were present, and decreased when A. pisum was feeding on the plant (mediated by plant variety). Although A. fabae aphids were influenced by the plants and worms, they did not, in turn, alter plant biomass.
Previous work has shown inconsistent effects of earthworms on aphids, but we suggest these differences could be explained by plant genetic variation and variation among aphid species. This study demonstrates that the outcome of belowground-aboveground interactions can be mediated by genetic variation in the host-plant, but depends on the identity of the species involved.
PMCID: PMC4209454  PMID: 25331082
Aboveground-belowground interactions; Aphis fabae; Acyrthosiphon pisum; Genetic interactions; Plant genotype; Vicia faba
12.  BMC Ecology image competition 2014: the winning images 
BMC Ecology  2014;14:24.
BMC Ecology showcases the winning entries from its second Ecology Image Competition. More than 300 individual images were submitted from an international array of research scientists, depicting life on every continent on earth. The journal’s Editorial Board and guest judge Caspar Henderson outline why their winning selections demonstrated high levels of technical skill and aesthetic sense in depicting the science of ecology, and we also highlight a small selection of highly commended images that we simply couldn’t let you miss out on.
PMCID: PMC4236560  PMID: 25178017
13.  Evidence for functional convergence in genes upregulated by herbivores ingesting plant secondary compounds 
BMC Ecology  2014;14:23.
Nearly 40 years ago, Freeland and Janzen predicted that liver biotransformation enzymes dictated diet selection by herbivores. Despite decades of research on model species and humans, little is known about the biotransformation mechanisms used by mammalian herbivores to metabolize plant secondary compounds (PSCs). We investigated the independent evolution of PSC biotransformation mechanisms by capitalizing on a dramatic diet change event—the dietary inclusion of creosote bush (Larrea tridentata)—that occurred in the recent evolutionary history of two species of woodrats (Neotoma lepida and N. bryanti).
By comparing gene expression profiles of two populations of woodrats with evolutionary experience to creosote and one population naïve to creosote, we identified genes either induced by a diet containing creosote PSCs or constitutively higher in populations with evolutionary experience of creosote. Although only one detoxification gene (an aldo-keto reductase) was induced by both experienced populations, these populations converged upon functionally equivalent strategies to biotransform the PSCs of creosote bush by constitutively expressing aldehyde and alcohol dehydrogenases, Cytochromes P450s, methyltransferases, glutathione S-transferases and sulfotransferases. The response of the naïve woodrat population to creosote bush was indicative of extreme physiological stress.
The hepatic detoxification system of mammals is notoriously complex, with hundreds of known biotransformation enzymes. The comparison herein of woodrat taxa that differ in evolutionary and ecological experience with toxins in creosote bush reveals convergence in the overall strategies used by independent species after a historical shift in diet. In addition, remarkably few genes seemed to be important in this dietary shift. The research lays the requisite groundwork for future studies of specific biotransformation pathways used by woodrats to metabolize the toxins in creosote and the evolution of diet switching in woodrats. On a larger level, this work advances our understanding of the mechanisms used by mammalian herbivores to process toxic diets and illustrates the importance of the selective relationship of PSCs in shaping herbivore diversity.
PMCID: PMC4153740  PMID: 25123454
Herbivory; Diet switching; Mammalian herbivores; Neotoma; Biotransformation; Microarray
14.  How do climate-linked sex ratios and dispersal limit range boundaries? 
BMC Ecology  2014;14:19.
Geographic ranges of ectotherms such as reptiles may be determined strongly by abiotic factors owing to causal links between ambient temperature, juvenile survival and individual sex (male or female). Unfortunately, we know little of how these factors interact with dispersal among populations across a species range. We used a simulation model to examine the effects of dispersal, temperature-dependent juvenile survival and sex determining mechanism (temperature-dependent sex determination (TSD) and genotypic sex determination (GSD)) and their interactions, on range limits in populations extending across a continuous range of air temperatures. In particular, we examined the relative importance of these parameters for population persistence to recommend targets for future empirical research.
Dispersal influenced the range limits of species with TSD to a greater extent than in GSD species. Whereas male dispersal led to expanded species ranges across warm (female-producing) climates, female dispersal led to expanded ranges across cool (male-producing) climates. Two-sex dispersal eliminated the influence of biased sex ratios on ranges.
The results highlight the importance of the demographic parameter of sex ratio in determining population persistence and species range limits.
PMCID: PMC4090346  PMID: 25011492
Dispersal; GSD; Population dynamics; Range limits; Reptiles; Sex ratio; TSD
15.  Causes and consequences of fine-scale population structure in a critically endangered freshwater seal 
BMC Ecology  2014;14:22.
Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.
Microsatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.
Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.
PMCID: PMC4106222  PMID: 25005257
Cryptic population structure; Effective population size; Gene flow; Genetic erosion; Landscape genetics; Small population
16.  High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid 
BMC Ecology  2014;14:20.
Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci.
We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations.
The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.
PMCID: PMC4099500  PMID: 24998243
17.  Fine-scale genetic structure analyses suggest further male than female dispersal in mountain gorillas 
BMC Ecology  2014;14:21.
Molecular studies in social mammals rarely compare the inferences gained from genetic analyses with field information, especially in the context of dispersal. In this study, we used genetic data to elucidate sex-specific dispersal dynamics in the Virunga Massif mountain gorilla population (Gorilla beringei beringei), a primate species characterized by routine male and female dispersal from stable mixed-sex social groups. Specifically, we conducted spatial genetic structure analyses for each sex and linked our genetically-based observations with some key demographic and behavioural data from this population.
To investigate the spatial genetic structure of mountain gorillas, we analysed the genotypes of 193 mature individuals at 11 microsatellite loci by means of isolation-by-distance and spatial autocorrelation analyses. Although not all males and females disperse, female gorillas displayed an isolation-by-distance pattern among groups and a signal of dispersal at short distances from their natal group based on spatial autocorrelation analyses. In contrast, male genotypes were not correlated with spatial distance, thus suggesting a larger mean dispersal distance for males as compared to females. Both within sex and mixed-sex pairs were on average genetically more related within groups than among groups.
Our study provides evidence for an intersexual difference in dispersal distance in the mountain gorilla. Overall, it stresses the importance of investigating spatial genetic structure patterns on a sex-specific basis to better understand the dispersal dynamics of the species under investigation. It is currently poorly understood why some male and female gorillas disperse while others remain in the natal group. Our results on average relatedness within and across groups confirm that groups often contain close relatives. While inbreeding avoidance may play a role in driving female dispersal, we note that more detailed dyadic genetic analyses are needed to shed light on the role of inbreeding avoidance as an ultimate cause of female dispersal in mountain gorillas.
PMCID: PMC4113491  PMID: 25001262
Dispersal; Inbreeding avoidance; Microsatellite; Mountain gorilla; Philopatry; Social mammal; Spatial genetic structure
18.  Forced monogamy in a multiply mating species does not impede colonisation success 
BMC Ecology  2014;14:18.
The guppy (Poecilia reticulata) is a successful invasive species. It is also a species that mates multiply; previous studies have demonstrated that this strategy carries fitness benefits. Guppies are routinely introduced to tanks and troughs in regions outside their native range for mosquito-control purposes, and often spread beyond these initial confines into natural water bodies with negative ecological consequences. Here, using a mesocosm set up that resembles the containers into which single guppies are typically introduced for mosquito control, we ask whether singly-mated females are at a disadvantage, relative to multiply-mated females, when it comes to founding a population. Treatments were monitored for one year.
A key finding was that mating history did not predict establishment success, which was 88% in both treatments. Furthermore, analysis of behavioural traits revealed that the descendants of singly-mated females retained antipredator behaviours, and that adult males showed no decrease in courtship vigour. Also, we detected no differences in behavioural variability between treatments.
These results suggest that even when denied the option of multiple mating, singly-mated female guppies can produce viable populations, at least at the founder stage. This may prove to be a critical advantage in typical introduction scenarios where few individuals are released into enclosed water bodies before finding their way into natural ecosystems.
PMCID: PMC4067062  PMID: 24925225
Poecilia reticulata; Polyandry; Invasive species; Mesocosms; Population viability
19.  Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche 
BMC Ecology  2014;14:11.
Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche and parasite prevalence data indicate strong ecological divergence between marine-oriented wolves inhabiting islands and individuals on the coastal mainland that interact primarily with terrestrial prey. Local holders of traditional ecological knowledge, who distinguish between mainland and island wolf forms, also informed our hypothesis that genetic differentiation might occur between wolves from these adjacent environments.
We used microsatellite genetic markers to examine data obtained from wolf faecal samples. Our results from 116 individuals suggest the presence of a genetic cline between mainland and island wolves. This pattern occurs despite field observations that individuals easily traverse the 30 km wide study area and swim up to 13 km among landmasses in the region.
Natal habitat-biased dispersal (i.e., the preference for dispersal into familiar ecological environments) might contribute to genetic differentiation. Accordingly, this working hypothesis presents an exciting avenue for future research where marine resources or other components of ecological heterogeneity are present.
PMCID: PMC4050401  PMID: 24915756
Canis lupus; Ecological divergence; Marine resources; Niche; Population genetic structure; Traditional ecological knowledge; Wolf
20.  Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution 
BMC Ecology  2014;14:16.
The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity.
By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition.
Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.
PMCID: PMC4047435  PMID: 24886397
Metagenomics; Microbial ecology; Hydrothermal ecosystems; Geochemistry; Markov clustering
21.  The interplay between seasonality and density: consequences for female breeding decisions in a small cyclic herbivore 
BMC Ecology  2014;14:17.
Cyclic rodent population dynamics are subjected to both intrinsic regulatory processes such as density-dependence and extrinsic environmental forcing. Among extrinsic factors, seasonal environmental variation is understood to facilitate cycles. In rodents, these processes have been studied mostly independently and their relative importance for population dynamics is poorly known.
We performed a detailed analysis of common vole (Microtus arvalis) reproduction in a cyclic population using a spatially extensive data set over 17 years in central-western France. Environmental seasonality was the main source of explained variation in common vole reproduction. Additionally, inter-annual variation in the environment explained a smaller part of the variance in reproduction in spring and summer than in winter, whereas the effect of density was only found in autumn and winter. In particular, we detected a strong impact of plant productivity on fecundity during the breeding season, with low vegetation productivity being able to bring vole reproduction nearly to a halt. In contrast, vole reproduction during autumn and winter was mainly shaped by intrinsic factors, with only the longer and heavier females being able to reproduce. The effect of population density on reproduction was negative, mediated by direct negative effects on the proportion of breeders in autumn and winter during outbreak years and by a delayed negative effect on litter size the following year.
During the main breeding season, variability of female vole reproduction is predominantly shaped by food resources, suggesting that only highly productive environment may induce vole outbreaks. During fall and winter, variability of female vole reproduction is mainly controlled by intrinsic factors, with high population density suppressing reproduction. This suggests, in this cyclic population, that negative direct density dependence on reproduction could explain winter declines after outbreaks.
PMCID: PMC4049426  PMID: 24886481
Seasonality; Population cycles; Common vole; Density-dependence; Fecundity
22.  Secondary reproduction in the herbaceous monocarp Lobelia inflata: time-constrained primary reproduction does not result in increased deferral of reproductive effort 
BMC Ecology  2014;14:15.
Although semelparity is a life history characterized by a single reproductive episode within a single reproductive season, some semelparous organisms facultatively express a second bout of reproduction, either in a subsequent season (“facultative iteroparity”) or later within the same season as the primary bout (“secondary reproduction”). Secondary reproduction has been explained as the adaptive deferral of reproductive potential under circumstances in which some fraction of reproductive success would otherwise have been lost (due, for example, to inopportune timing). This deferral hypothesis predicts a positive relationship between constraints on primary reproduction and expression of secondary reproduction. The herbaceous monocarp Lobelia inflata has been observed occasionally to express a secondary reproductive episode in the field. However, it is unknown whether secondary reproduction is an example of adaptive reproductive deferral, or is more parsimoniously explained as the vestigial expression of iteroparity after a recent transition to semelparity. Here, we experimentally manipulate effective season length in each of three years to test whether secondary reproduction is a form of adaptive plasticity consistent with the deferral hypothesis.
Our results were found to be inconsistent with the adaptive deferral explanation: first, plants whose primary reproduction was time-constrained exhibited decreased (not increased) allocation to subsequent secondary reproduction, a result that was consistent across all three years; second, secondary offspring—although viable in the laboratory—would not have the opportunity for expression under field conditions, and would thus not contribute to reproductive success.
Although alternative adaptive explanations for secondary reproduction cannot be precluded, we conclude that the characteristics of secondary reproduction found in L. inflata are consistent with predictions of incomplete or transitional evolution to annual semelparity.
PMCID: PMC4030501  PMID: 24886288
Life-history evolution; Semelparity; Iteroparity; Facultative iteroparity; Lobelia inflata
23.  Mistaken identity? Visual similarities of marine debris to natural prey items of sea turtles 
BMC Ecology  2014;14:14.
There are two predominant hypotheses as to why animals ingest plastic: 1) they are opportunistic feeders, eating plastic when they encounter it, and 2) they eat plastic because it resembles prey items. To assess which hypothesis is most likely, we created a model sea turtle visual system and used it to analyse debris samples from beach surveys and from necropsied turtles. We investigated colour, contrast, and luminance of the debris items as they would appear to the turtle. We also incorporated measures of texture and translucency to determine which of the two hypotheses is more plausible as a driver of selectivity in green sea turtles.
Turtles preferred more flexible and translucent items to what was available in the environment, lending support to the hypothesis that they prefer debris that resembles prey, particularly jellyfish. They also ate fewer blue items, suggesting that such items may be less conspicuous against the background of open water where they forage.
Using visual modelling we determined the characteristics that drive ingestion of marine debris by sea turtles, from the point of view of the turtles themselves. This technique can be utilized to determine debris preferences of other visual predators, and help to more effectively focus management or remediation actions.
PMCID: PMC4032385  PMID: 24886170
Chelonia mydas; Chromatic space; Eretmochelys imbricata; Marine debris; Vorobyev-Osorio model
24.  Individual quality explains association between plumage colouration, arrival dates and mate acquisition in yellow warblers (Setophaga petechia) 
BMC Ecology  2014;14:13.
In many bird species colour traits influence social dominance and breeding success. In our study we first evaluated whether the colour of the basic plumage (tail feathers grown at the end of the breeding season), that provides an index of individual quality, influenced winter habitat use by yellow warblers. We then evaluated whether winter habitat use (inferred using δ13C and δ15N signatures of winter grown greater-coverts) influenced alternate plumage colouration, after controlling for individual quality using basic plumage colouration. Finally, we investigated whether basic and alternate plumage colouration influenced arrival dates, mate acquisition, breeding phenology and reproductive success of yellow warblers breeding in southern (Revelstoke, B.C.) and arctic (Inuvik, N.W.T.) Canada.
The colour (chroma and hue) of tail feathers, grown on the breeding grounds, was not related to subsequent winter habitat use. Greater covert and tail feather colour (chroma and hue) were correlated, suggesting genetics and/or individual quality played a role in pigment deposition. After controlling for individual difference in tail colour, δ13C values did not explain any variation in greater covert colour, but birds with high δ15N signatures had greater coverts with higher chroma. Male arrival dates varied with tail chroma in Revelstoke and tail hue in Inuvik. Males that arrived early paired with older and/or more colourful mates that initiated clutches earlier, and at one site (Revelstoke) were more likely to fledge young. In addition, in Revelstoke (but not Inuvik) males with high tail hue also acquired more colourful mates. In contrast, after controlling for individual differences in tail colour, greater covert colour did not affect male arrival date, the quality of the mate obtained or reproductive success in either population.
Our results suggest that plumage colour effects on breeding phenology and mate acquisition result from differences in the intrinsic quality of individuals rather than a carry-over effect of winter habitat use.
PMCID: PMC4024118  PMID: 24886073
Carry-over effects; Seasonal interactions; Breeding phenology; Plumage colour; Carotenoid-based colouration; Yellow warbler; American redstart
25.  Effects of Bromelia pinguin (Bromeliaceae) on soil ecosystem function and fungal diversity in the lowland forests of Costa Rica 
BMC Ecology  2014;14:12.
Bromelia pinguin (Bromeliaceae) is a terrestrial bromeliad commonly found under forest stands throughout the Neotropics that has been shown to have antifungal activity in vitro. We have hypothesized that this bromeliad would also have an effect on the fungal populations in nearby soil by decreasing fungaldiversity and negatively impacting C and N cycle-related activities. A previous study in the lowland forest of Costa Rica showed the soil beneath these bromeliads had decreased fungal ITS DNA and differences in C and N levels compared to adjacent primary forest soils.
In this follow-up study, we found that the bromeliad soils had lower rates of C and N biomass development and lower phenol oxidase activity (suggesting less decreased fungal decomposition activity). The results of T-RFLP and cloning-based taxonomic analyses showed the community level diversity and abundance of fungal ITS DNA was less in bromeliad soils. Sequence analysis of fungal ITS DNA clones showed marked differences in fungal community structure between habitats of Basidiomycota (Tremellales, Agricales, Thelephorales), Ascomycota (Helotiales), and Zycomycota populations.
The data show there to be differences in the soil nutrient dynamics and fungal community structure and activity associated with these bromeliads, as compared to the adjacent primary forest. This suggests the possibility that the anti-fungal activity of the bromeliad extends into the soil. The bromeliad-dense regions of these primary forest habitats provide a unique natural micro-habitat within the forests and the opportunity to better identify the role of fungal communities in the C and N cycles in tropical soils.
PMCID: PMC4020870  PMID: 24885984
Carbon biomass; Nitrogen biomass; Bromelia pinguin; Fungal diversity; Soil ecosystems

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