pinecone/core-2020-05-10-deduplication huggingface dataset:
Phylogenetic plant community structure along elevation is lineage specific

The trend of closely related taxa to retain similar environmental preferences mediated by inherited traits suggests that several patterns observed at the community scale originate from longer evolutionary processes. While the effects of phylogenetic relatedness have been previously studied within a single genus or family, lineage-specific effects on the ecological processes governing community assembly have rarely been studied for entire communities or flora. Here, we measured how community phylogenetic structure varies across a wide elevation gradient for plant lineages represented by thirty-five families, using a co-occurrence index and net relatedness index (NRI). We propose a framework that analyses each lineage separately and reveals the trend of ecological assembly at tree nodes. We found prevailing phylogenetic clustering for more ancient nodes and overdispersion in more recent tree nodes. Closely related species may thus rapidly evolve new environmental tolerances to radiate into distinct communities, while older lineages likely retain inherent environmental tolerances to occupy communities in similar environments, either through efficient dispersal mechanisms or the exclusion of older lineages with more divergent environmental tolerances. Our study illustrates the importance of disentangling the patterns of community assembly among lineages to better interpret the ecological role of traits. It also sheds light on studies reporting absence of phylogenetic signal, and opens new perspectives on the analysis of niche and trait conservatism across lineages
A species assemblage approach to comparative phylogeography of birds in southern Australia

We present a novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data. We use coalescent-based hierarchical approximate Bayesian computation (HABC) methods (MsBayes) to estimate the number and timing of discrete divergences across a putative barrier and to assign species to their appropriate period of co-divergence. We then apply a coalescent-based full Bayesian model of divergence (IMa) to suites of species shown to have simultaneously diverged. The full Bayesian model results in reduced credibility intervals around divergence times and allows other parameters associated with divergence to be summarized across species assemblages. We apply this approach to 10 bird species that are wholly or patchily discontinuous in semi-arid habitats between Australia's southwest (SW) and southeast (SE) mesic zones. There was substantial support for up to three discrete periods of divergence. HABC indicates that two species wholly restricted to more mesic habitats diverged earliest, between 594,382 and 3,417,699 years ago, three species from semi-arid habitats diverged between 0 and 1,508,049 years ago, and four diverged more recently, between 0 and 396,843 years ago. Eight species were assigned to three periods of co-divergence with confidence. For full Bayesian analyses, we accounted for uncertainty in the two remaining species by analyzing all possible suites of species. Estimates of divergence times from full Bayesian divergence models ranged between 429,105 and 2,006,355; 67,172 and 663,837; and 24,607 and 171,085 for the earliest, middle, and most recent periods of co-divergence, respectively. This single-locus approach uses the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research using multilocus and genomic tools applied to an understudied biome.Gaynor Dolman & Leo Josep
Multidisciplinary population monitoring when demographic data are sparse: a case study of remote trout populations

The potential of genetic, genomic, and phenotypic metrics for monitoring population trends may be especially high in isolated regions, where traditional demographic monitoring is logistically difficult and only sporadic sampling is possible. This potential, however, is relatively underexplored empirically. Over eleven years, we assessed several such metrics along with traditional ecological knowledge and catch data in a socioeconomically important trout species occupying a large, remote lake. The data revealed largely stable characteristics in two populations over 2–3 generations, but possible contemporary changes in a third population. These potential shifts were suggested by reduced catch rates, reduced body size, and changes in selection implied at one gene-associated single nucleotide polymorphism. A demographic decline in this population, however, was ambiguously supported, based on the apparent lack of temporal change in effective population size, and corresponding traditional knowledge suggesting little change in catch. We illustrate how the pluralistic approach employed has practicality for setting future monitoring efforts of these populations, by guiding monitoring priorities according to the relative merits of different metrics and availability of resources. Our study also considers some advantages and disadvantages to adopting a pluralistic approach to population monitoring where demographic data are not easily obtained
Evaluating the carbon balance estimate from an automated ground-level flux chamber system in artificial grass mesocosms.

Measuring and modeling carbon (C) stock changes in terrestrial ecosystems are pivotal in addressing global C-cycling model uncertainties. Difficulties in detecting small short-term changes in relatively large C stocks require the development of robust sensitive flux measurement techniques. Net ecosystem exchange (NEE) ground-level chambers are increasingly used to assess C dynamics in low vegetation ecosystems but, to date, have lacked formal rigorous field validation against measured C stock changes. We developed and deployed an automated and multiplexed C-flux chamber system in grassland mesocosms in order rigorously to compare ecosystem total C budget obtained using hourly C-flux measurements versus destructive net C balance. The system combines transparent NEE and opaque respiration chambers enabling partitioning of photosynthetic and respiratory fluxes. The C-balance comparison showed good agreement between the two methods, but only after NEE fluxes were corrected for light reductions due to chamber presence. The dark chamber fluxes allowed assessing temperature sensitivity of ecosystem respiration (Reco) components (i.e., heterotrophic vs. autotrophic) at different growth stages. We propose that such automated flux chamber systems can provide an accurate C balance, also enabling pivotal partitioning of the different C-flux components (e.g., photosynthesis and respiration) suitable for model evaluation and developments
What shall I do now? State-dependent variations of life-history traits with aging in Wandering Albatrosses

Allocation decisions depend on an organism's condition which can change with age. Two opposite changes in life-history traits are predicted in the presence of senescence: either an increase in breeding performance in late age associated with terminal investment or a decrease due to either life-history trade-offs between current breeding and future survival or decreased efficiency at old age. Age variation in several life-history traits has been detected in a number of species, and demographic performances of individuals in a given year are influenced by their reproductive state the previous year. Few studies have, however, examined state-dependent variation in life-history traits with aging, and they focused mainly on a dichotomy of successful versus failed breeding and non-breeding birds. Using a 50-year dataset on the long-lived quasi-biennial breeding wandering albatross, we investigated variations in life-history traits with aging according to a gradient of states corresponding to potential costs of reproduction the previous year (in ascending order): non-breeding birds staying at sea or present at breeding grounds, breeding birds that failed early, late or were successful. We used multistate models to study survival and decompose reproduction into four components (probabilities of return, breeding, hatching, and fledging), while accounting for imperfect detection. Our results suggest the possible existence of two strategies in the population: strict biennial breeders that exhibited almost no reproductive senescence and quasi-biennial breeders that showed an increased breeding frequency with a strong and moderate senescence on hatching and fledging probabilities, respectively. The patterns observed on survival were contrary to our predictions, suggesting an influence of individual quality rather than trade-offs between reproduction and survival at late ages. This work represents a step further into understanding the evolutionary ecology of senescence and its relationship with costs of reproduction at the population level. It paves the way for individual-based studies that could show the importance of intra-population heterogeneity in those processes
Life-history of the Glanville fritillary butterfly in fragmented versus continuous landscapes

Habitat loss and fragmentation threaten the long-term viability of innumerable species of plants and animals. At the same time, habitat fragmentation may impose strong natural selection and lead to evolution of life histories with possibleconsequences for demographic dynamics. The Baltic populations of the Glanville fritillary butterfly (Melitaea cinxia) inhabit regions with highly fragmented habitat (networks of small dry meadows) as well as regions with extensive continuous habitat (calcareous alvar grasslands). Here, we report the results of common garden studies on butterflies originating from two highly fragmented landscapes (FL) in Finland and Sweden and from two continuous landscapes (CL) in Sweden andEstonia, conducted in a large outdoor cage (32 by 26 m) and in the laboratory. We investigated a comprehensive set of 51 life-history traits, including measures of larval growth and development, flight performance, and adult reproductive behavior. Seventeen of the 51 traits showed a significant difference between fragmented versus CL. Most notably, the growth rate of postdiapause larvae and several measures of flight capacity, including flight metabolic rate, were higher in butterflies from fragmented than CL. Females from CL had shorter intervals between consecutive egg clutches and somewhat higher life-time egg production,but shorter longevity, than females from FL. These results are likely to reflect theconstant opportunities for oviposition in females living in continuous habitats, while the more dispersive females from FL allocate more resources to dispersal capacity at the cost of egg maturation rate. This study supports theoretical predictions about small population sizes and high rate of population turnover in fragmented habitats selecting for increased rate of dispersal, but the results also indicate that many other life-history traits apart from dispersal are affected by the degree of habitat fragmentation
Long-term fertilization of a boreal Norway spruce forest increases the temperature sensitivity of soil organic carbon mineralization

Boreal ecosystems store one-third of global soil organic carbon (SOC) and are particularly sensitive to climate warming and higher nutrient inputs. Thus, a better description of how forest managements such as nutrient fertilization impact soil carbon (C) and its temperature sensitivity is needed to better predict feedbacks between C cycling and climate. The temperature sensitivity of in\ud
situ soil C respiration was investigated in a boreal forest, which has received long-term nutrient fertilization (22 years), and compared with the temperature sensitivity of C mineralization measured in the laboratory. We found that the fertilization treatment increased both the response of soil in situ CO2 effluxes\ud
to a warming treatment and the temperature sensitivity of C mineralization measured in the laboratory (Q10). These results suggested that soil C may be more sensitive to an increase in temperature in long-term fertilized in comparison with nutrient poor boreal ecosystems. Furthermore, the fertilization treatment modified the SOC content and the microbial community composition, but we found no direct relationship between either SOC or microbial changes and the temperature sensitivity of C mineralization. However, the relation between the soil C:N ratio and the fungal/bacterial ratio was changed in the combined warmed and fertilized treatment compared with the other treatments, which suggest that strong interaction mechanisms may occur between nutrient input and warming in boreal soils. Further research is needed to unravel into more details in how far soil organic matter and microbial community composition changes are responsible for the change in the temperature sensitivity of soil C under increasing mineral N inputs. Such research would help to take into account the effect of fertilization managements on soil C storage in C cycling\ud
numerical models
Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae)

In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa
Interactions between assembly order and temperature can alter both short- and long-term community composition

Both the order in which species arrive in a community, and environmental conditions, such as temperature, are known to affect community structure. Little is known, however, about the potential for, and occurrence of, interactions between assembly history and the environment. Of particular, interest may be the interaction between temperature and community assembly dynamics, especially in the light of predicted global climatic change and the fundamental processes that are governed, through metabolic rate, by an individual's environmental temperature. We present, to our knowledge, the first experimental exploration of how the influence of assembly history, temperature, and the interaction between the two alters the structure of communities of competitors, using small-scale protist microcosm communities where temperature and assembly order were manipulated factorially. In our experiment, the most important driver of long-term abundance was temperature but long-lasting assembly order effects influenced the relationship between temperature and abundance. Any advantage of early colonization proved to be short-lived, and there was rarely any long-term advantage to colonizing a habitat before other species. The results presented here suggest that environmental conditions shape community composition, but that occasionally temperature could interact with the stochastic nature of community assembly to significantly alter future community composition, especially where temperature change has been large. This could have important implications for the dynamics of both rare and invasive species
Divergence of feeding channels within the soil food web determined by ecosystem type.

Crotty, F. V., Blackshaw, R. P., Adl, S. M., Inger, R., Murray, P. J. (2014). Divergence of feeding channels within the soil food web determined by ecosystem type.Ecology and Evolution, 4 (1), 1-13Understanding trophic linkages within the soil food web (SFW) is hampered by its opacity, diversity, and limited niche adaptation. We need to expand our insight between the feeding guilds of fauna and not just count biodiversity. The soil fauna drive nutrient cycling and play a pivotal, but little understood role within both the carbon (C) and nitrogen (N) cycles that may be ecosystem dependent. Here, we define the structure of the SFW in two habitats (grassland and woodland) on the same soil type and test the hypothesis that land management would alter the SFW in these habitats. To do this, we census the community structure and use stable isotope analysis to establish the pathway of C and N through each trophic level within the ecosystems. Stable isotope ratios of C and N from all invertebrates were used as a proxy for trophic niche, and community-wide metrics were obtained. Our empirically derived C/N ratios differed from those previously reported, diverging from model predictions of global C and N cycling, which was unexpected. An assessment of the relative response of the different functional groups to the change from agricultural grassland to woodland was performed. This showed that abundance of herbivores, microbivores, and micropredators were stimulated, while omnivores and macropredators were inhibited in the grassland. Differences between stable isotope ratios and community-wide metrics, highlighted habitats with similar taxa had different SFWs, using different basal resources, either driven by root or litter derived resources. Overall, we conclude that plant type can act as a top-down driver of community functioning and that differing land management can impact on the whole SFW.publishersversionPeer reviewe
Defining conservation units in a stocking-induced genetic melting pot: unraveling native and multiple exotic genetic imprints of recent and historical secondary contact in Adriatic grayling

The definition of conservation units is crucial for the sustainable management of endangered species, though particularly challenging when recent and past anthropogenic and natural gene flow might have played a role. The conservation of the European grayling, Thymallus thymallus, is particularly complex in its southern distribution area, where the Adriatic evolutionary lineage is endangered by a long history of anthropogenic disturbance, intensive stocking and potentially widespread genetic introgression. We provide mtDNA sequence and microsatellite data of 683 grayling from 30 sites of Adriatic as well as Danubian and Atlantic origin. We apply Bayesian clustering and Approximate Bayesian Computation (ABC) to detect microgeographic population structure and to infer the demographic history of the Adriatic populations, to define appropriate conservation units. Varying frequencies of indigenous genetic signatures of the Adriatic grayling were revealed, spanning from marginal genetic introgression to the collapse of native gene pools. Genetic introgression involved multiple exotic source populations of Danubian and Atlantic origin, thus evidencing the negative impact of few decades of stocking. Within the Adige River system, a contact zone of western Adriatic and eastern Danubian populations was detected, with ABC analyses suggesting a historical anthropogenic origin of eastern Adige populations, most likely founded by medieval translocations. Substantial river-specific population substructure within the Adriatic grayling Evolutionary Significant Unit points to the definition of different conservation units. We finally propose a catalog of management measures, including the legal prohibition of stocking exotic grayling and the use of molecular markers in supportive- and captive-breeding program
Increasing pCO<inf>2</inf> correlates with low concentrations of intracellular dimethylsulfoniopropionate in the sea anemone Anemonia viridis

Marine anthozoans maintain a mutualistic symbiosis with dinoflagellates that are prolific producers of the algal secondary metabolite dimethylsulfoniopropionate (DMSP), the precursor of the climate-cooling trace gas dimethyl sulfide (DMS). Surprisingly, little is known about the physiological role of DMSP in anthozoans and the environmental factors that regulate its production. Here, we assessed the potential functional role of DMSP as an antioxidant and determined how future increases in seawater pCO2 may affect DMSP concentrations in the anemone Anemonia viridis along a natural pCO2 gradient at the island of Vulcano, Italy. There was no significant difference in zooxanthellae genotype and characteristics (density of zooxanthellae, and chlorophyll a) as well as protein concentrations between anemones from three stations along the gradient, V1 (3232 μatm CO2), V2 (682 μatm) and control (463 μatm), which indicated that A. viridis can acclimate to various seawater pCO2. In contrast, DMSP concentrations in anemones from stations V1 (33.23 ± 8.30 fmol cell-1) and V2 (34.78 ± 8.69 fmol cell-1) were about 35% lower than concentrations in tentacles from the control station (51.85 ± 12.96 fmol cell-1). Furthermore, low tissue concentrations of DMSP coincided with low activities of the antioxidant enzyme superoxide dismutase (SOD). Superoxide dismutase activity for both host (7.84 ± 1.37 U·mg-1 protein) and zooxanthellae (2.84 ± 0.41 U·mg-1 protein) at V1 was 40% lower than at the control station (host: 13.19 ± 1.42; zooxanthellae: 4.72 ± 0.57 U·mg-1 protein). Our results provide insight into coastal DMSP production under predicted environmental change and support the function of DMSP as an antioxidant in symbiotic anthozoans. © 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd