pinecone/core-2020-05-10-deduplication huggingface dataset:
Changes in pollinator fauna affect altitudinal variation of floral size in a bumblebee-pollinated herb

Geographic trait variations are often caused by locally different selection regimes. As a steep environmental cline along altitude strongly influences adaptive traits, mountain ecosystems are ideal for exploring adaptive differentiation over short distances. We investigated altitudinal floral size variation of Campanula punctata var. hondoensis in 12 populations in three mountain regions of central Japan to test whether the altitudinal floral size variation was correlated with the size of the local bumblebee pollinator and to assess whether floral size was selected for by pollinator size. We found apparent geographic variations in pollinator assemblages along altitude, which consequently produced a geographic change in pollinator size. Similarly, we found altitudinal changes in floral size, which proved to be correlated with the local pollinator size, but not with altitude itself. Furthermore, pollen removal from flower styles onto bees (plant\u27s male fitness) was strongly influenced by the size match between flower style length and pollinator mouthpart length. These results strongly suggest that C. punctata floral size is under pollinator-mediated selection and that a geographic mosaic of locally adapted C. punctata exists at fine spatial scale
Parasitism in early life: environmental conditions shape within-brood variation in responses to infection

Parasites play key ecological and evolutionary roles through the costs they impose on their host. In wild populations, the effect of parasitism is likely to vary considerably with environmental conditions, which may affect the availability of resources to hosts for defense. However, the interaction between parasitism and prevailing conditions is rarely quantified. In addition to environmental variation acting on hosts, individuals are likely to vary in their response to parasitism, and the combined effect of both may increase heterogeneity in host responses. Offspring hierarchies, established by parents in response to uncertain rearing conditions, may be an important source of variation between individuals. Here, we use experimental antiparasite treatment across 5 years of variable conditions to test how annual population productivity (a proxy for environmental conditions) and parasitism interact to affect growth and survival of different brood members in juvenile European shags (Phalacrocorax aristotelis). In control broods, last-hatched chicks had more plastic growth rates, growing faster in more productive years. Older siblings grew at a similar rate in all years. Treatment removed the effect of environment on last-hatched chicks, such that all siblings in treated broods grew at a similar rate across environmental conditions. There were no differences in nematode burden between years or siblings, suggesting that variation in responses arose from intrinsic differences between chicks. Whole-brood growth rate was not affected by treatment, indicating that within-brood differences were driven by a change in resource allocation between siblings rather than a change in overall parental provisioning. We show that gastrointestinal parasites can be a key component of offspring's developmental environment. Our results also demonstrate the value of considering prevailing conditions for our understanding of parasite effects on host life-history traits. Establishing how environmental conditions shape responses to parasitism is important as environmental variability is predicted to increase
Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity

Dothistroma septosporum is a haploid fungal pathogen that causes a serious needle
blight disease of pines, particularly as an invasive alien species on Pinus radiata
in the Southern Hemisphere. During the course of the last two decades,
the pathogen has also incited unexpected epidemics on native and non-native
pine hosts in the Northern Hemisphere. Although the biology and ecology of
the pathogen has been well documented, there is a distinct lack of knowledge
regarding its movement or genetic diversity in many of the countries where it
is found. In this study we determined the global population diversity and structure
of 458 isolates of D. septosporum from 14 countries on six continents using
microsatellite markers. Populations of the pathogen in the Northern Hemisphere,
where pines are native, displayed high genetic diversities and included
both mating types. Most of the populations from Europe showed evidence for
random mating, little population differentiation and gene flow between countries.
Populations in North America (USA) and Asia (Bhutan) were genetically
distinct but migration between these continents and Europe was evident. In the
Southern Hemisphere, the population structure and diversity of D. septosporum
reflected the anthropogenic history of the introduction and establishment of
plantation forestry, particularly with Pinus radiata. Three introductory lineages
in the Southern Hemisphere were observed. Countries in Africa, that have had
the longest history of pine introductions, displayed the greatest diversity in the
pathogen population, indicating multiple introductions. More recent introductions
have occurred separately in South America and Australasia where the
pathogen population is currently reproducing clonally due to the presence of
only one mating type.The Department
of Science and Technology (DST)/National
Research Foundation (NRF), the Tree
Protection Co-operative Programme (TPCP),
the Claude Leon Foundation and the THRIP
initiative of the Department of Trade and
Industry, South Africa.http://onlinelibrary.wiley.comjournal/10.1002/(ISSN)2045-7758am201
Abundance, diversity, and feeding behavior of coral reef butterflyfishes at Lord Howe Island

Endemic species are assumed to have a high risk of extinction because their restricted geographic range is often associated with low abundance and high ecological specialization. This study examines the abundance of Chaetodon butterflyfishes at Lord Howe Island in the south-west Pacific, and compares interspecific differences in local abundance to the feeding behavior and geographic range of these species. Contrary to expected correlations between abundance and geographic range, the single most abundant species of butterflyfish was Chaetodon tricinctus, which is endemic to Lord Howe Island and adjacent reefs; densities of C. tricinctus (14.1 ± 2.1 SE fish per 200m(2)) were >3 times higher than the next most abundant butterflyfish (Chaetodon melannotus), and even more abundant than many other geographically widespread species. Dietary breadth for the five dominant butterflyfishes at Lord Howe Island was weakly and generally negative correlated with abundance. The endemic C. tricinctus was a distinct outlier in this relationship, though our extensive feeding observations suggest some issues with the measurements of dietary breadth for this species. Field observations revealed that all bites taken on benthic substrates by C. tricinctus were from scleractinian corals, but adults rarely, if ever, took bites from the benthos, suggesting that they may be feeding nocturnally and/or using mid-water prey, such as plankton. Alternatively, the energetic demands of C. tricinctus may be fundamentally different to other coral-feeding butterflyfishes. Neither dietary specialization nor geographic range accounts for interspecific variation in abundance of coral reef butterflyfishes at Lord Howe Island, while much more work on the foraging behavior and population dynamics of C. tricinctus will be required to understand its' abundance at this location.Funding was provided by ARC Centre ofExcellence for Coral Reef Studies
Interactive effect of warming, nitrogen and phosphorus limitation on phytoplankton cell size

Cell size is one of the ecologically most important traits of phytoplankton. The cell size variation is frequently related to temperature and nutrient limitation. In order to disentangle the role of both factors, an experiment was conducted to determine the possible interactions of these factors. Baltic Sea water containing the natural plankton community was used. We performed a factorial combined experiment of temperature, type of nutrient limitation (N vs. P), and strength of nutrient limitation. The type of nutrient limitation was manipulated by altering the N:P ratio of the medium (balanced, N and P limitation) and strength by the dilution rate (0% and 50%) of the semicontinuous cultures. The negative effect of temperature on cell size was strongest under N limitation, intermediate under P limitation, and weakest when N and P were supplied at balanced ratios. However, temperature also influenced the intensity of nutrient imitation, because at higher temperature there was a tendency for dissolved nutrient concentrations to be lower, while the C:N or C:P ratio being higher... higher at identical dilution rates and medium composition. Analyzing the response of cell size to C:N ratios (as index of N limitation) and C:P ratios (as index of P limitation) indicated a clear dominance of the nutrient effect over the direct temperature effect, although the temperature effect was also significant
Are all species necessary to reveal ecologically important patterns?

While studying ecological patterns at large scales, ecologists are often unable to identify all collections, forcing them to either omit these unidentified records entirely, without knowing the effect of this, or pursue very costly and time-consuming efforts for identifying them. These "indets" may be of critical importance, but as yet, their impact on the reliability of ecological analyses is poorly known. We investigated the consequence of omitting the unidentified records and provide an explanation for the results. We used three large-scale independent datasets, (Guyana/ Suriname, French Guiana, Ecuador) each consisting of records having been identified to a valid species name (identified morpho-species - IMS) and a number of unidentified records (unidentified morpho-species - UMS). A subset was created for each dataset containing only the IMS, which was compared with the complete dataset containing all morpho-species (AMS: = IMS + UMS) for the following analyses: species diversity (Fisher's alpha), similarity of species composition, Mantel test and ordination (NMDS). In addition, we also simulated an even larger number of unidentified records for all three datasets and analyzed the agreement between similarities again with these simulated datasets. For all analyses, results were extremely similar when using the complete datasets or the truncated subsets. IMS predicted ≥91% of the variation in AMS in all tests/analyses. Even when simulating a larger fraction of UMS, IMS predicted the results for AMS rather well. Using only IMS also out-performed using higher taxon data (genus-level identification) for similarity analyses. Finding a high congruence for all analyses when using IMS rather than AMS suggests that patterns of similarity and composition are very robust. In other words, having a large number of unidentified species in a dataset may not affect our conclusions as much as is often thought
Diversity of honey stores and their impact on pathogenic bacteria of the honeybee, Apis mellifera

Honeybee colonies offer an excellent environment for microbial pathogen
development. The highest virulent, colony killing, bacterial agents are Paenibacillus
larvae causing American foulbrood (AFB), and European foulbrood (EFB)
associated bacteria. Besides the innate immune defense, honeybees evolved
behavioral defenses to combat infections. Foraging of antimicrobial plant compounds
plays a key role for this “social immunity” behavior. Secondary plant
metabolites in floral nectar are known for their antimicrobial effects. Yet, these
compounds are highly plant specific, and the effects on bee health will depend
on the floral origin of the honey produced. As worker bees not only feed themselves,
but also the larvae and other colony members, honey is a prime candidate
acting as self-medication agent in honeybee colonies to prevent or decrease
infections. Here, we test eight AFB and EFB bacterial strains and the growth
inhibitory activity of three honey types. Using a high-throughput cell growth
assay, we show that all honeys have high growth inhibitory activity and the two
monofloral honeys appeared to be strain specific. The specificity of the monofloral
honeys and the strong antimicrobial potential of the polyfloral honey suggest
that the diversity of honeys in the honey stores of a colony may be highly
adaptive for its “social immunity” against the highly diverse suite of pathogens
encountered in nature. This ecological diversity may therefore operate similar
to the well-known effects of host genetic variance in the arms race between host
and parasite.The project
RoBeeTech (grant POS CCE 206/20.07.2010
SMIS code 618/12460 to LAM, DSD, RFAM)
and an ERASMUS MUNDUS exchange
program grant (AD, RFAM).http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)2045-7758hb201
Intraspecific competition reduces niche width in experimental populations

Intraspecific competition is believed to drive niche expansion, because otherwise suboptimal resources can provide a refuge from competition for preferred resources. Competitive niche expansion is well supported by empirical observations, experiments, and theory, and is often invoked to explain phenotypic diversification within populations, some forms of speciation, and adaptive radiation. However, some foraging models predict the opposite outcome, and it therefore remains unclear whether competition will promote or inhibit niche expansion. We conducted experiments to test whether competition changes the fitness landscape to favor niche expansion, and if competition indeed drives niche expansion as expected. Using Tribolium castaneum flour beetles fed either wheat (their ancestral resource), corn (a novel resource) or mixtures of both resources, we show that fitness is maximized on a mixed diet. Next, we show that at higher population density, the optimal diet shifts toward greater use of corn, favoring niche expansion. In stark contrast, when beetles were given a choice of resources, we found that competition caused niche contraction onto the ancestral resource. This presents a puzzling mismatch between how competition alters the fitness landscape, versus competition's effects on resource use. We discuss several explanations for this mismatch, highlighting potential reasons why optimality models might be misleading
4P: fast computing of population genetics statistics from large DNA polymorphism panels

Massive DNA sequencing has significantly increased the amount of data avail- able for population genetics and molecular ecology studies. However, the paral- lel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymor- phism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run explor- atory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation stud- ies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations
Variability in sperm form and function in the context of sperm competition risk in two Tupinambis lizards

In polyandrous species, sperm morphometry and sperm velocity are under strong sexual selection. Although several hypotheses have been proposed to explain the role of sperm competition in sperm trait variation, this aspect is still poorly understood. It has been suggested that an increase in sperm competition pressure could reduce sperm size variation or produce a diversity of sperm to maximize male fertilization success. We aim at elucidating the variability of sperm morphometric traits and velocity in two Tupinambis lizards in the context of sperm competition risk. Sperm traits showed substantial variation at all levels examined: between species, among males within species, and within the ejaculate of individual males. Sperm velocity was found to be positively correlated with flagellum:midpiece ratio, with relatively longer flagella associated with faster sperm. Our results document high variability in sperm form and function in lizards.Fil: Blengini, Cecilia Soledad. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Naretto, Sergio. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Cardozo Milanesio, Gabriela Alejandra. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Giojalas, Laura Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas; ArgentinaFil: Chiaraviglio,  Margarita. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; Argentin
Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central-western and south-eastern Patagonia, consistent with long-term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.Fil: Nicola, Marcela Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Nicola, Marcela Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Pozner, Raul Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Johnson, Leigh. University Brigham Young; Estados Unido
A phylogenetic analysis of the British flora sheds light on the evolutionary and ecological factors driving plant invasions

Darwin's naturalization hypothesis predicts that invasive species should perform better in their novel range in the absence of close relatives in the native flora due to reduced competition. Evidence from recent taxonomic and phylogenetic-based studies, however, is equivocal. We test Darwin's naturalization hypothesis at two different spatial scales using a fossil-dated molecular phylogenetic tree of the British native and alien flora (ca. 1600 species) and extensive, fine-scale survey data from the 1998 Countryside Survey. At both landscape and local scales, invasive species were neither significantly more nor less related to the native flora than their non-invasive alien counterparts. Species invasiveness was instead correlated with higher nitrogen and moisture preference, but not other life history traits such as life-form and height. We argue that invasive species spread in Britain is hence more likely determined by changes in land use and other anthropogenic factors, rather than evolutionary history. Synthesis. The transition from non-invasive to invasive is not related to phylogenetic distinctiveness to the native community, but instead to their environmental preferences. Therefore, combating biological invasions in the Britain and other industrialized countries need entirely different strategies than in more natural environments.publishersversionPeer reviewe