bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal change in spatial variability of eelgrass epifaunal community in relation to gradients of abiotic and biotic factors
Authors: Momota Kyosuke , Nakaoka Masahiro 
Published: October 2018

AbstractSeagrass‐associated macroinvertebrates (epifauna) play important roles as mediators between primary producers and higher consumers in seagrass beds. However, many aspects of the variation in the epifaunal community in seagrass beds remain to be investigated. In this study, we examined how the epifaunal community structure varied seasonally and spatially with abiotic and biotic factors in an eelgrass bed of Akkeshi, northeastern Japan. We predict that abiotic factors are more definitive of the variation in the epifaunal community than biotic factors when the eelgrass bed is less productive in early spring and late autumn, whereas biotic factors including macro‐epibiotic organisms (epiphytic macroalgae and sessile animals on eelgrass blades) are more influential when the eelgrass bed is more productive from late spring to early autumn. The epifaunal community composition varied greatly with season, and its spatial variation was correlated with different sets of abiotic and biotic factors in different seasons. Epibiotic organisms, in addition to other abiotic and biotic factors, explained some of the variation, especially in the productive summer seasons, despite the relatively low biomass of epibiotic organisms compared to that of eelgrass and epiphytic microalgae. Inconsistent with our prediction, abiotic factors were more definitive of the spatial patterns of the epifaunal communities from spring to summer when the productivity of the eelgrass bed was increasing, whereas biotic factors were found to be more important in the autumn when the productivity declined. Our result highlights the importance of epibiotic organisms on eelgrass blades to the epifaunal community, which was underappreciated in previous studies.
Mind your neighbourhood: Biotic and abiotic factors shaping the small‐scale spatial distribution of sponges (Demospongiae) in tropical urban beaches
Authors: Oliveira Franciele S. , Lanna Emilio 
Published: October 2018

AbstractThe distribution and abundance of a species can be determined by the interaction of that species with both the biotic and abiotic characteristics of the environment it inhabits. The Demospongiae Aplysina solangeae, Cladocroce caelum, Desmapsamma anchorata, Dysidea janiae and Tedania ignis are commonly found in urban beaches along the tropical Brazilian coast. They reproduce year round in these localities and are thus good model species candidates for studies of evolutionary developmental biology, ecotoxicology and bioprospecting. Here, we investigate how substrate and community requirements modulate the density of these species in two urban beaches in Todos os Santos Bay, Brazil, in order to better comprehend the species’ needs for settlement and growth. We assessed the density of the target species by sampling quadrats during SCUBA dives at these two beaches. Generalised additive models were used to assess how the per cent coverage of benthic organisms co‐occurring with these species influenced the density of the target species. As expected, we found that each species had different requirements for their spatial distribution, with most species being generalists. The only exception to this was found with C. caelum, which appeared to be more specialist, requiring a higher number of explanatory variables in terms of neighbouring benthos despite being the most abundant target species in both localities. A comparison of the differences observed in small‐scale localities and the regional scale is presented. Our findings on how selective these species are about their “neighbourhood” allow us to better comprehend their life histories and predict their dynamics in a changing environment.
Inbreeding tolerance as a pre‐adapted trait for invasion success in the invasive ant Brachyponera chinensis
Authors: Eyer Pierre‐André , Matsuura Kenji , Vargo Edward L. , Kobayashi Kazuya , Yashiro Toshihisa , Suehiro Wataru , Himuro Chihiro , Yokoi Tomoyuki , Guénard Benoit , Dunn Robert R. , Tsuji Kazuki 
Published: October 2018

AbstractIdentifying traits that facilitate species introductions and successful invasions of ecosystems represents a key issue in ecology. Following their establishment into new environments, many non‐native species exhibit phenotypic plasticity with post‐introduction changes in behaviour, morphology or life history traits that allow them to overcome the presumed loss of genetic diversity resulting in inbreeding and reduced adaptive potential. Here, we present a unique strategy in the invasive ant Brachyponera chinensis (Emery), in which inbreeding tolerance is a pre‐adapted trait for invasion success, allowing this ant to cope with genetic depletion following a genetic bottleneck. We report for the first time that inbreeding is not a consequence of the founder effect following introduction, but it is due to mating between sister queens and their brothers that pre‐exists in native populations which may have helped it circumvent the cost of invasion. We show that a genetic bottleneck does not affect the genetic diversity or the level of heterozygosity within colonies and suggest that generations of sib‐mating in native populations may have reduced inbreeding depression through purifying selection of deleterious alleles. This work highlights how a unique life history may pre‐adapt some species for biological invasions.
The obligate alkalophilic soda‐lake fungus Sodiomyces alkalinus has shifted to a protein diet
Authors: Grum‐Grzhimaylo Alexey A. , Falkoski Daniel L. , van den Heuvel Joost , Valero‐Jiménez Claudio A. , Min Byoungnam , Choi In‐Geol , Lipzen Anna , Daum Chris G. , Aanen Duur K. , Tsang Adrian , Henrissat Bernard , Bilanenko Elena N. , de Vries Ronald P. , van Kan Jan A. L. , Grigoriev Igor V. , Debets Alfons J. M. 
Published: October 2018

AbstractSodiomyces alkalinus is one of the very few alkalophilic fungi, adapted to grow optimally at high pH. It is widely distributed at the plant‐deprived edges of extremely alkaline lakes and locally abundant. We sequenced the genome of S. alkalinus and reconstructed evolution of catabolic enzymes, using a phylogenomic comparison. We found that the genome of S. alkalinus is larger, but its predicted proteome is smaller and heavily depleted of both plant‐degrading enzymes and proteinases, when compared to its closest plant‐pathogenic relatives. Interestingly, despite overall losses, S. alkalinus has retained many proteinases families and acquired bacterial cell wall‐degrading enzymes, some of them via horizontal gene transfer from bacteria. This fungus has very potent proteolytic activity at high pH values, but slowly induced low activity of cellulases and hemicellulases. Our experimental and in silico data suggest that plant biomass, a common food source for most fungi, is not a preferred substrate for S. alkalinus in its natural environment. We conclude that the fungus has abandoned the ancestral plant‐based diet and has become specialized in a more protein‐rich food, abundantly available in soda lakes in the form of prokaryotes and small crustaceans.
Long‐term effects of superoxide and DNA repair on lizard telomeres
Authors: Olsson Mats , Friesen Christopher R. , Rollings Nicky , Sudyka Joanna , Lindsay Willow , Whittington Camilla M. , Wilson Mark 
Published: October 2018

AbstractTelomeres are the non‐coding protein‐nucleotide “caps” at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in cell culture, but other researchers have failed to find such effects in free‐living vertebrates. Here, we use a novel approach to measure free radicals (superoxide), mitochondrial “content” (a combined measure of mitochondrial number and size in cells), telomere length and DNA damage at two primary time points during the mating season of an annual lizard species (Ctenophorus pictus). Superoxide levels early in the mating season vary widely and elevated levels predict shorter telomeres both at that time as well as several months later. These effects are likely driven by mitochondrial content, which significantly impacts late season superoxide (cells with more mitochondria have more superoxide), but superoxide effects on telomeres are counteracted by DNA repair as revealed by 8‐hydroxy‐2′‐deoxyguanosine assays. We conclude that reactive oxygen species and DNA repair are fundamental for both short‐ and long‐term regulation of lizard telomere length with pronounced effects of early season cellular stress detectable on telomere length near lizard death.
Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions
Authors: Feng Youzhi , Chen Ruirui , Stegen James C. , Guo Zhiying , Zhang Jianwei , Li Zhongpei , Lin Xiangui 
Published: October 2018

AbstractBelowground microbial communities strongly influence ecosystem function such that predicting function may rely on understanding ecological processes that assemble communities. Uncertainty remains, however, in what governs the relative contributions of different ecological processes. To help fill this knowledge gap, we test the general hypothesis that both initial state and degree of change in environmental conditions govern the relative contributions of different ecological assembly processes. To do so, we leveraged regional‐scale nutrient and organic matter addition experiments and used soil organic matter (SOM) as a proxy of integrated soil environmental conditions. Consistent with our hypothesis, we found that both the initial amount of SOM and the degree of change in SOM—in response to nutrient addition—influenced the relative contributions of different ecological assembly processes. These influences were most clearly observed at the regional scale, suggesting potential scale dependence. More specifically, nutrient additions homogenized bacterial community composition due to enhanced influences of homogenizing dispersal when SOM content was initially high. In contrast, nutrient additions led to divergence in community composition due to variable selection when initial SOM was low and/or when SOM increased significantly in response to nutrient additions. Our findings indicate important connections among initial conditions, degree of change in environmental variables and microbial community assembly processes that may influence ecosystem processes. These conceptual inferences highlight a need to strengthen connections between ecological theory and biogeochemical modelling.
A synergistic role for two predicted inner membrane proteins of Escherichia coli in cell envelope integrity
Authors: Mychack Aaron , Amrutha R. N. , Chung Charlie , Cardenas Arevalo Karla , Reddy Manjula , Janakiraman Anuradha 
Published: October 2018

SummaryThe bacterial cytoplasmic membrane is a principal site of protein translocation, lipid and peptidoglycan biogenesis, signal transduction, transporters and energy generating components of the respiratory chain. Although 25–30% of bacterial proteomes consist of membrane proteins, a comprehensive understanding of their influence on fundamental cellular processes is incomplete. Here, we show that YciB and DcrB, two small cytoplasmic membrane proteins of previously unknown functions, play an essential synergistic role in maintaining cell envelope integrity of Escherichia coli. Lack of both YciB and DcrB results in pleiotropic cell defects including increased levels of lipopolysaccharide, membrane vesiculation, dynamic shrinking and extension of the cytoplasmic membrane accompanied by lysis and cell death. The stalling of an abundant outer membrane lipoprotein, Lpp, at the periplasmic face of the inner membrane leads to lethal inner membrane–peptidoglycan linkages. Additionally, the periplasmic chaperone Skp contributes to yciB dcrB mutant cell death by possibly mistargeting stalled porins into the inner membrane. Consistent with the idea of a compromised envelope in the yciB dcrB mutant, multiple envelope stress response systems are induced, with Cpx signal transduction being required for growth. Taken together, our results suggest a fundamental role for YciB and DcrB in cell envelope biogenesis.
Acoustic monitoring reveals the times and tides of harbor porpoise (Phocoena phocoena) distribution off central Oregon, U.S.A.
Authors: Holdman Amanda K. , Haxel Joseph H. , Klinck Holger , Torres Leigh G. 
Published: October 2018

AbstractHarbor porpoises (Phocoena phocoena) are commonly observed in Oregon's nearshore marine environment yet knowledge of their ecosystem use and behavior remains limited, generating concerns for potential impacts on this species from future coastal development. Passive acoustic monitoring was used to investigate spatial and temporal variations in the presence and foraging activity of harbor porpoises off the Oregon coast from May through October 2014. Digital monitoring devices (DMONs) were deployed to record acoustic data (320 kHz sample rate) in two neighboring but bathymetrically different locations off the Oregon coast: (1) a site on the 30 m isobath in close proximity (<50 m) to a rocky reef, and (2) a site on the 60 m isobath in an open sandy environment. Data were analyzed with respect to two dynamic cyclic variables: diel and tidal phase. Porpoise presence at the rocky reef site was aligned with the ebb phase of the tidal forcing, while, harbor porpoise presence and foraging at the offshore, sandy bottom site was associated with night‐time foraging. The spatial and temporal patterns identified in this study suggest harbor porpoise habitat use is modulated by specific environmental conditions particular to each site that maximize foraging efficiency.
Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean
Authors: Leslie Matthew S. , Archer Frederick I. , Morin Phillip A. 
Published: October 2018

AbstractSpinner dolphins (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because understanding population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical taxonomic levels. Results show differences between subspecies of spinner and spotted dolphins, but no support for the division of existing offshore stocks of spotted dolphins. We compare these results to previous results of genome‐wide nuclear SNP data and suggest high haplotype diversity, female dispersal, and/or relative power of the two data sets explains the differences observed. Interestingly, increasing the amount of mitochondrial data (base pairs and genes) did not increase ability to delimit population units. This study supports a genetic basis for management units at the subspecies level, and provides critical information for mitigating historical and continued fisheries impacts.
Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution
Authors: Cavender‐Bares Jeannine 
Published: October 2018

ContentsSummary669I.Model clades for the study and integration of ecology and evolution670II.Oaks: an important model clade671III.Insights from the history of the American oaks for understanding community assembly and ecosystem dominance673IV.Bridging the gap between micro‐ and macroevolutionary processes relevant to ecology679V.How do we reconcile evidence for adaptive evolution with niche conservatism and long‐term stasis?682VI.High plasticity and within‐population genetic variation contribute to population persistence683VII.Emerging technologies for tracking functional change685VIII.Conclusions685Acknowledgements686References686SummaryEcologists and evolutionary biologists are concerned with explaining the diversity and composition of the natural world and are aware of the inextricable linkages between ecological and evolutionary processes that maintain the Earth's life support systems. Yet examination of these linkages remains challenging due to the contrasting nature of focal systems and research approaches. Model clades provide a critical means to integrate ecology and evolution, as illustrated by the oaks (genusQuercus), an important model clade, given their ecological dominance, remarkable diversity, and growing phylogenetic, genomic, and ecological data resources. Studies of the clade reveal that their history of sympatric parallel adaptive radiation continues to influence community assembly today, highlighting questions on the nature and extent of coexistence mechanisms. Flexible phenology and hydraulic traits, despite evolutionary stasis, may have enabled adaptation to a wide range of environments within and across species, contributing to their high abundance and diversity. The oaks offer fundamental insights at the intersection of ecology and evolution on the role of diversification in community assembly processes, on the importance of flexibility in key functional traits in adapting to new environments, on factors contributing to persistence of long‐lived organisms, and on evolutionary legacies that influence ecosystem function.
The extent of adaptive wild introgression in crops
Authors: Janzen Garrett M. , Wang Li , Hufford Matthew B. 
Published: October 2018

SummaryThe study of crop evolution has focused primarily on the process of initial domestication. Post‐domestication adaptation during the expansion of crops from their centers of origin has received considerably less attention. Recent research has revealed that, in at least some instances, crops have received introgression from their wild relatives that has facilitated adaptation to novel conditions encountered during expansion. Such adaptive introgression could have an important impact on the basic study of domestication, affecting estimates of several evolutionary processes of interest (e.g. the strength of the domestication bottleneck, the timing of domestication, the targets of selection during domestication). Identification of haplotypes introgressed from the wild may also help in the identification of alleles that are beneficial under particular environmental conditions. Here we review mounting evidence for substantial adaptive wild introgression in several crops and consider the implications of such gene flow to our understanding of crop histories.
Light regulation of coccolithophore host–virus interactions
Authors: Thamatrakoln Kimberlee , Talmy David , Haramaty Liti , Maniscalco Christopher , Latham Jason R. , Knowles Ben , Natale Frank , Coolen Marco J. L. , Follows Michael J. , Bidle Kay D. 
Published: October 2018

SummaryViruses that infect photoautotrophs have a fundamental relationship with light, given the need for host resources.We investigated the role of light onCoccolithovirus(EhV) infection of the globally distributed coccolithophore,Emiliania huxleyi. Light was required for EhV adsorption, and viral production was highest when host cultures were maintained in continuous light or at irradiance levels of 150–300 μmol m−2 s−1. During the early stages of infection, photosynthetic electron transport remained high, while RuBisCO expression decreased concomitant with an induction of the pentose phosphate pathway, the primary source ofde novonucleotides. A mathematical model developed and fitted to the laboratory data supported the hypothesis that EhV replication was controlled by a trade‐off between host nucleotide recycling andde novosynthesis, and that photoperiod and photon flux could toggle this switch.Laboratory results supported field observations that light was the most robust driver of EhV replication withinE. huxleyipopulations collected across a 2000 nautical mile transect in the North Atlantic.Collectively, these findings demonstrate that light can drive host–virus interactions through a mechanistic interplay between host metabolic processes, which serve to structure infection and phytoplankton mortality in the upper ocean.
Whole‐tree nonstructural carbohydrate storage and seasonal dynamics in five temperate species
Authors: Furze Morgan E. , Huggett Brett A. , Aubrecht Donald M. , Stolz Claire D. , Carbone Mariah S. , Richardson Andrew D. 
Published: October 2018

SummaryDespite the importance of nonstructural carbohydrates (NSC) for growth and survival in woody plants, we know little about whole‐treeNSCstorage. The conventional theory suggests thatNSCreserves will increase over the growing season and decrease over the dormant season. Here, we compare storage in five temperate tree species to determine the size and seasonal fluctuation of whole‐tree totalNSCpools as well as the contribution of individual organs.NSCconcentrations in the branches, stemwood, and roots of 24 trees were measured across 12 months. We then scaled up concentrations to the whole‐tree and ecosystem levels using allometric equations and forest stand inventory data.While whole‐tree totalNSCpools followed the conventional theory, sugar pools peaked in the dormant season and starch pools in the growing season. Seasonal depletion of totalNSCs was minimal at the whole‐tree level, but substantial at the organ level, particularly in branches. Surprisingly, roots were not the major storage organ as branches stored comparable amounts of starch throughout the year, and root reserves were not used to support springtime growth.Scaling upNSCconcentrations to the ecosystem level, we find that commonly used, process‐based ecosystem and land surface models all overpredictNSCstorage.
Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers
Authors: Qiu Fan , Baack Eric J. , Whitney Kenneth D. , Bock Dan G. , Tetreault Hannah M. , Rieseberg Loren H. , Ungerer Mark C. 
Published: October 2018

Summary

Flowering plants serve as a powerful model for studying the evolution of nuclear genome size (GS) given the tremendous GS variation that exists both within and across angiosperm lineages.

Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse habitats and vary in ploidy level. In the current study, we generated a comprehensive GS database for 49 Helianthus species using flow cytometric approaches. We examined variability across the genus and present a comparative phylogenetic analysis of GS evolution in diploid Helianthus species.

Results demonstrated that different clades of diploid Helianthus species showed evolutionary patterns of GS contraction, expansion and relative stasis, with annual diploid species evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of diploids revealed significant negative associations of GS with temperature seasonality and cell production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed.

The Helianthus GS database presented here and corresponding analyses of environmental and phenotypic correlates will facilitate ongoing and future research on the ultimate drivers of GS evolution in this well‐studied North American plant genus.