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Background: The low bacterial load in samples acquired from the lungs, have made studies on the airway microbiome vulnerable to contamination from bacterial DNA introduced during sampling and laboratory processing. We have examined the impact of laboratory contamination on samples collected from the lower airways by protected (through a sterile catheter) bronchoscopy and explored various in silico approaches to dealing with the contamination post-sequencing. Our analyses included quantitative PCR and targeted amplicon sequencing of the bacterial 16S rRNA gene. Results: The mean bacterial load varied by sample type for the 23 study subjects (oral wash>1st fraction of protected bronchoalveolar lavage>protected specimen brush>2nd fraction of protected bronchoalveolar lavage; p < 0.001). By comparison to a dilution series of know bacterial composition and load, an estimated 10-50% of the bacterial community profiles for lower airway samples could be traced back to contaminating bacterial DNA introduced from the laboratory. We determined the main source of laboratory contaminants to be the DNA extraction kit (FastDNA Spin Kit). The removal of contaminants identified using tools within the Decontam R package appeared to provide a balance between keeping and removing taxa found in both negative controls and study samples. Conclusions: The influence of laboratory contamination will vary across airway microbiome studies. By reporting estimates of contaminant levels and taking use of contaminant identification tools (e.g. the Decontam R package) based on statistical models that limit the subjectivity of the researcher, the accuracy of inter-study comparisons can be improved.
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Sexual size dimorphism (SSD) is ubiquitous across animals with female bias most prominent in snakes and other ectothermic organisms. To understand how SSD evolves across species, Rensch’s Rule predicts that in taxa where males are larger, SSD increases with body size. In contrast, where females are larger, SSD decreases with body size. While this rule holds for many taxa, it may be ambiguous for others, particularly ectothermic vertebrates. Importantly, this rule suggests that the outcomes of SSD over phylogenetic time scales depends on the direction of dimorphism predicated on the difference in reproductive efforts between males and females. Here we examine SSD in the context of Rensch’s Rule in Thamnophiini, the garter and waternsakes, a prominent group composing the North American snake biota. Using a dated phylogeny, measurements of gape, body and tail size, we show that these snakes do not follow Rensch’s Rule, but rather female-biased SSD increases with body size. We in turn find that this allometry is most pronounced with gape and is correlated with both neonate and litter size, suggesting that acquiring prey of increased size may be directly related to fecundity selection. These changes in SSD are not constrained to any particular clade; we find no evidence of phylogenetic shifts in those traits showing SSD. We suggest several ways forward to better understand the anatomical units of selection for SSD and modularity
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Preferential dissolution of the biogenic carbonate polymorph aragonite promotes preservational bias in shelly marine faunas. Whilst field studies have documented the impact of preferential aragonite dissolution on fossil molluscan diversity, its impact on regional and global biodiversity metrics is debated. Epicontinental seas are especially prone to conditions which both promote and inhibit preferential dissolution, which may result in spatially extensive zones with variable preservation. Here we present a multi-faceted evaluation of aragonite dissolution within the late Cretaceous Western Interior Seaway of North America. Occurrence data of molluscs from two time intervals (Cenomanian-Turonian boundary, early Campanian) are plotted on new high-resolution paleogeographies to assess aragonite preservation within the seaway. Fossil occurrences, diversity estimates and sampling probabilities for calcitic and aragonitic fauna were compared in zones defined by depth and distance from the seaway margins. Apparent range sizes, which could be influenced by differential preservation potential of aragonite between separate localities, were also compared. Our results are consistent with exacerbated aragonite dissolution within specific depth zones for both time slices, with aragonitic bivalves additionally showing a statistically significant decrease in range size compared to calcitic fauna within carbonate-dominated Cenomanian-Turonian strata. However, we are unable to conclusively show that aragonite dissolution impacted diversity estimates. Therefore, whilst aragonite dissolution is likely to have affected the preservation of fauna in specific localities, time averaging and instantaneous preservation events preserve regional biodiversity. Our results suggest that the spatial expression of taphonomic biases should be an important consideration for paleontologists working on paleobiogeographic problems.
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The taxonomic and ecologic composition of Earth’s biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota towards the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.
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The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip‐calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip‐calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip‐calibrations. In particular, we focus on the effect of using tip‐calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence‐time estimates and demonstrate that concentrating tip‐calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip‐dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating.
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Müllerian mimicry theory states that frequency dependent selection should favour geographic convergence of harmful species onto a shared colour pattern. As such, mimetic patterns are commonly circumscribed into discrete mimicry complexes each containing a predominant phenotype. Outside a few examples in butterflies, the location of transition zones between mimicry complexes and the factors driving mimicry zones has rarely been examined. To infer the patterns and processes of Müllerian mimicry, we integrate large-scale data on the geographic distribution of colour patterns of social bumble bees across the contiguous United States and use these to quantify colour pattern mimicry using an innovative, unsupervised machine learning approach based on computer vision. Our data suggest that bumble bees exhibit geographically clustered, but sometimes imperfect colour patterns and that mimicry patterns gradually transition spatially, rather than exhibit discrete boundaries. Additionally, examination of colour pattern transition zones of three comimicking, polymorphic species, where active selection is driving phenotype frequencies, revealed their transition zones to differ in location within a broad region of poor mimicry. Potential factors influencing mimicry transition zone dynamics are discussed.
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Aim: Soils and their biological communities face increasing pressure from multiple global drivers, including land management and climate change. In soils, earthworms play key roles in ecosystem functioning, but the environmental controls on their global communities are not fully understood. Here, an earthworm dataset was compiled to investigate the effects of environmental controls and land management on global earthworm communities. Location: 40 ° S – 65 ° N. Time period: 1962 to 2016. Major taxa studied: Earthworms Methods: A dataset of 899 earthworm community observations, together with environmental variables, was compiled across 169 globally distributed sites. Sites included natural forests and grasslands or managed arable, pasture or plantation ecosystems. Total, anecic, endogeic and epigeic abundances were compared in natural and managed ecosystems to quantify the effects of land management across climates. A hierarchical model was used to test interactions between earthworm communities with environmental controls and management across eighteen ecosystem types. Results: Land management prompted little change in total earthworm abundance at the global scale, but reduced species richness and shifted community composition. Endogeic earthworms were more abundant in managed ecosystems, while anecic and epigeic earthworms show variable responses across ecosystem types. Global relationships between total earthworm species richness and abundance were explained by climate, soil pH and land management. Main conclusions: Land management modulates the effects of environmental controls on global earthworm communities, through direct disturbance and indirect changes in edaphic conditions.
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We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a common garden trial of 281 lodgepole pine (Pinus contorta) provenances from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype-associated loci are equivalent or slightly superior to climate data for describing local adaptation in seedling traits, but that climate data is superior to bulk genomic data that have not been selected for phenotypic associations. We also find agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with the experimental traits occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than are indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.
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In coastal habitats, mussels are exposed to microplastic (MP; plastic 1,250 particles/ml) but was not affected at equivalent silt concentrations. These findings suggest high MP concentrations inhibit mussel clearance rate, more than expected by changes in particle concentration or the proportion of abiotic particles. As plastic production increases, mussel exposure to MP will increase, potentially reducing energy transfer, benthic-pelagic coupling, and water clarity.
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Aim: Current species distributions are shaped by present and past biotic and abiotic factors. Here we assessed whether abiotic factors (habitat availability) in combination with past connectivity and a biotic factor (body mass) can explain the unique distribution pattern of Southeast Asian mammals, which are separated by the enigmatic biogeographic transition zone, the Isthmus of Kra (IoK), for which no strong geophysical barrier exists. Location: Southeast Asia Taxon: Mammals Methods: We projected habitat suitability for 125 mammal species using climate data for the present period and for two historic periods: mid-Holocene (6 kya) and last glacial maximum (LGM 21 kya). Next, we employed a phylogenetic linear model to assess how present species distributions were affected by the suitability of areas in these different periods, habitat connectivity during LGM and species body mass. Results: Our results show that cooler climate during LGM provided suitable habitat south of IoK for species presently distributed north of IoK (in mainland Indochina). However, the potentially suitable habitat for these Indochinese species did not stretch very far southwards onto the exposed Sunda Shelf. Instead, we found that the emerged landmasses connecting Borneo and Sumatra provided suitable habitat for forest dependent Sundaic species. We show that for species whose current distribution ranges are mainly located in Indochina, the area of the distribution range that is located south of IoK is explained by the suitability of habitat in the past and present in combination with the species body mass. Main conclusions: We demonstrate that a strong geophysical barrier may not be necessary for maintaining a biogeographic transition zone for mammals, but that instead a combination of abiotic and biotic factors may suffice.
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