ALBERT

Description: Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems. Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information : Supplementary data are available at Bioinformatics online.

Description: : Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify 〉175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. Availability and implementation: The source code can be downloaded at http://www.heiderlab.de Contact: d.heider@wz-straubing.de

Description: : We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org

Description: : AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net . Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of 〉97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock . Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online

Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ . Contact: sjh@cmp.uea.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. Availability and implementation: DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB Contact: avi.maayan@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation : Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent ‘third-generation’ sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. Results : We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly. Availability and implementation : MultiBreak-SV is available at http://compbio.cs.brown.edu/software/ . Contact : annaritz@vt.edu or braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. Results: We propose here an original method, called M ind T he G ap , for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. M ind T he G ap uses an efficient k -mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. M ind T he G ap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, M ind T he G ap detected and correctly assembled insertions 〉1 kb, using at most 14 GB of memory. Availability and implementation: http://mindthegap.genouest.org Contact: guillaume.rizk@inria.fr or claire.lemaitre@inria.fr

Description: Motivation: Most tumor samples are a heterogeneous mixture of cells, including admixture by normal (non-cancerous) cells and subpopulations of cancerous cells with different complements of somatic aberrations. This intra-tumor heterogeneity complicates the analysis of somatic aberrations in DNA sequencing data from tumor samples. Results: We describe an algorithm called THetA2 that infers the composition of a tumor sample—including not only tumor purity but also the number and content of tumor subpopulations—directly from both whole-genome (WGS) and whole-exome (WXS) high-throughput DNA sequencing data. This algorithm builds on our earlier Tumor Heterogeneity Analysis (THetA) algorithm in several important directions. These include improved ability to analyze highly rearranged genomes using a variety of data types: both WGS sequencing (including low ~7 x coverage) and WXS sequencing. We apply our improved THetA2 algorithm to WGS (including low-pass) and WXS sequence data from 18 samples from The Cancer Genome Atlas (TCGA). We find that the improved algorithm is substantially faster and identifies numerous tumor samples containing subclonal populations in the TCGA data, including in one highly rearranged sample for which other tumor purity estimation algorithms were unable to estimate tumor purity. Availability and implementation: An implementation of THetA2 is available at http://compbio.cs.brown.edu/software Contact: layla@cs.brown.edu or braphael@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Ecology, Volume 95, Issue 1, Page 68-77, January 2014. Delayed life history effects (DLHEs) occur when fitness in one life stage affects fitness in subsequent life stages. Given their biphasic life cycle, pond-breeding amphibians provide a natural system for studying DLHEs, although these effects are not restricted to species with biphasic life histories. In this study, we used multiple mark–recapture techniques enabled by a large trapping array to monitor components of fitness and resulting DLHEs in a population of the endangered California tiger salamander (Ambystoma californiense). We found that DLHEs are prominent across all life stage transitions and that there is variation in whether selection acts primarily at the individual or cohort level. We also demonstrated that there is more than an order of magnitude variation in mean cohort fitness, providing tremendous variation for DLHEs to act upon. We documented an evolutionary trade-off between mass at emergence and date of emergence, which may play a role in maintaining the variation in mass (fitness) at emergence. A literature review revealed that such high levels of intercohort variation occur in many other pond-breeding amphibians, and that appropriately documenting the magnitude of intercohort variation requires long-term studies (roughly two population turnovers). Given the profound effect that DLHEs can have on population dynamics, quantifying intercohort variation in mean fitness and the level(s) at which selection acts will be very important for developing accurate models of population dynamics. In general, when developing models of population dynamics, more attention should be paid to variation in mean fitness and not just variation in total numbers.

Description: Ecology, Volume 95, Issue 1, Page 30-36, January 2014. Competition plays an important role in structuring the community dynamics of phytophagous insects. As the number and impact of biological invasions increase, it has become increasingly important to determine whether competitive differences exist between native and exotic insects. We conducted a meta-analysis to test the hypothesis that native/exotic status affects the outcome of herbivore competition. Specifically, we used data from 160 published studies to assess plant-mediated competition in phytophagous insects. For each pair of competing herbivores, we determined the native range and coevolutionary history of each herbivore and host plant. Plant-mediated competition occurred frequently, but neither native nor exotic insects were consistently better competitors. Spatial separation reduced competition in native insects but showed little effect on exotics. Temporal separation negatively impacted native insects but did not affect competition in exotics. Insects that coevolved with their host plant were more affected by interspecific competition than herbivores that lacked a coevolutionary history. Insects that have not coevolved with their host plant may be at a competitive advantage if they overcome plant defenses. As native/exotic status does not consistently predict outcomes of competitive interactions, plant–insect coevolutionary history should be considered in studies of competition.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Predicting the future trend and viability of populations is an essential task in ecology. Because many populations respond to changing environments, uncertainty surrounding environmental responses must be incorporated into population assessments. However, understanding the effects of environmental variation on population dynamics requires information on several important demographic parameters which are often difficult to estimate. Integrated population models facilitate the integration of time-series data on population size and all existing demographic information from a species, allowing the estimation of demographic parameters for which limited or no empirical data exist. Although these models are ideal for assessments of population viability, they have so far not included environmental uncertainty. We incorporated environmental variation in an integrated population model to account for both demographic and environmental uncertainty in an assessment of population viability. In addition, we used this model to estimate true juvenile survival, an important demographic parameter for population dynamics that is difficult to estimate empirically. We applied this model to assess the past and future population trend of a rare island endemic songbird, the Montserrat Oriole Icterus oberi, which is threatened by volcanic activity. Montserrat Orioles experienced lower survival in years with volcanic ash-fall, causing periodic population declines that were compensated by higher seasonal fecundity in years with high pre-breeding season rainfall. Due to the inclusion of both demographic and environmental uncertainty in the model, the estimated population growth rate in the immediate future was highly imprecise (95% credible interval 0.844 - 1.105), and the probability of extinction after three generations (in the year 2028) was low (2.1%). This projection demonstrates that accounting for both demographic and environmental sources of uncertainty provides a more realistic assessment of the viability of populations under unknown future environmental conditions.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Evidence of age-dependent changes in foraging behavior of free-ranging individuals is scarce, especially at older stages. Using the isotopic niche as a proxy of the trophic niche during both the breeding (blood) and inter-nesting (feather) periods, we report here empirical evidence for age-, gender- and breeding status-dependent foraging ecology and examine its potential consequences on subsequent reproduction and survival in an extremely long-lived species, the wandering albatross. Immature wandering albatrosses of both sexes forage in the subtropics (δ13C) and feed at the same trophic position (δ15N) than the adults. In contrast to immature birds, adult females forage on average at northern latitudes than males, with both sexes feeding in the subtropics during the inter-nesting period, and males, not females, favouring subantartic waters during incubation. In contrast to adult females, males showed a unique pattern among birds and mammals of a continuous change with age in their main feeding habitat by foraging progressively further south in colder waters during both the breeding and inter-nesting periods. In males, foraging at higher latitudes (lower feather δ13C values) is associated with a lower probability to breed during the following years compared to other birds, but with no effect on their probability to survive. Foraging in cold and windy waters may be linked to foraging impairment that might explain different life history trade-offs and lower investment in reproduction with age. This key point requires further longitudinal investigations and/or studies examining foraging success and energy budget of birds feeding in different water masses.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Interactions between plants and scatterhoarding animals may shift from mutualism to predation as a function of resources available to those animals. Because seed species differ in their nutrient content and defenses to predation, resource selection and cache management by scatterhoarders, and thus seed fate, may also depend on the relative availability of different seed types. We tracked the fates of tagged Castanea dentata, Quercus alba, and Q. rubra seeds presented to rodents in pairwise combinations and found that C. dentata, which has moderate dormancy prior to germination, survived better in the presence of Q. alba (no dormancy) than with Q. rubra (longer dormancy). Decisions made by scatterhoarders in response to the composition of available seed resources can alter the relationship between masting and seed dispersal effectiveness in individual tree species and may have influenced the evolution of asynchrony among species-specific masting patterns in temperate forests. In theory, preferential allocation of certain seed species to storage or consumption may also result in indirect apparent predation by one seed species on another.

Description: Motivation: We have recently characterized an instance of alternative splicing that differs from the canonical gene transcript by deletion of a length of sequence not divisible by three, but where translation can be rescued by an alternative start codon. This results in a predicted protein in which the amino terminus differs markedly in sequence from the known protein product(s), as it is translated from an alternative reading frame. Automated pipelines have annotated thousands of splice variants but have overlooked these protein isoforms, leading to them being underrepresented in current databases. Results: Here we describe 1849 human and 733 mouse transcripts that can be transcribed from an alternate ATG. Of these, 〉80% have not been annotated previously. Those conserved between human and mouse genomes (and hence under likely evolutionary selection) are identified. We provide mass spectroscopy evidence for translation of selected transcripts. Of the described splice variants, only one has previously been studied in detail and converted the encoded protein from an activator of cell-function to a suppressor, demonstrating that these splice variants can result in profound functional change. We investigate the potential functional effects of this splicing using a variety of bioinformatic tools. The 2582 variants we describe are involved in a wide variety of biological processes, and therefore open many new avenues of research. Contact: aude.fahrer@anu.edu.au Supplementary Inforation: Supplementary data are available at Bioinformatics online.

Description: Motivation : High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifacts. Results : We investigated the impact of library amplification bias on the identification of allele-specific (AS) molecular events from high-throughput sequencing data derived from chromatin immunoprecipitation assays (ChIP-seq). Putative AS DNA binding activity for RNA polymerase II was determined using ChIP-seq data derived from lymphoblastoid cell lines of two parent–daughter trios. We found that, at high-sequencing depth, many significant AS binding sites suffered from an amplification bias, as evidenced by a larger number of clonal reads representing one of the two alleles. To alleviate this bias, we devised an amplification bias detection strategy, which filters out sites with low read complexity and sites featuring a significant excess of clonal reads. This method will be useful for AS analyses involving ChIP-seq and other functional sequencing assays. Availability : The R package absfilter for library clonality simulations and detection of amplification-biased sites is available from http://updepla1srv1.epfl.ch/waszaks/absfilter Contact : sebastian.waszak@epfl.ch or bart.deplancke@epfl.ch Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation : Recently, investigators have proposed state-of-the-art Identity-by-descent (IBD) mapping methods to detect IBD segments between purportedly unrelated individuals. The IBD information can then be used for association testing in genetic association studies. One approach for this IBD association testing strategy is to test for excessive IBD between pairs of cases (‘pairwise method’). However, this approach is inefficient because it requires a large number of permutations. Moreover, a limited number of permutations define a lower bound for P -values, which makes fine-mapping of associated regions difficult because, in practice, a much larger genomic region is implicated than the region that is actually associated. Results: In this article, we introduce a new pairwise method ‘Fast-Pairwise’. Fast-Pairwise uses importance sampling to improve efficiency and enable approximation of extremely small P -values. Fast-Pairwise method takes only days to complete a genome-wide scan. In the application to the WTCCC type 1 diabetes data, Fast-Pairwise successfully fine-maps a known human leukocyte antigen gene that is known to cause the disease. Availability: Fast-Pairwise is publicly available at: http://genetics.cs.ucla.edu/graphibd . Contact: eeskin@cs.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Measurements are commonly taken from two phenotypes to build a classifier, where the number of data points from each class is predetermined, not random. In this ‘separate sampling’ scenario, the data cannot be used to estimate the class prior probabilities. Moreover, predetermined class sizes can severely degrade classifier performance, even for large samples. Results: We employ simulations using both synthetic and real data to show the detrimental effect of separate sampling on a variety of classification rules. We establish propositions related to the effect on the expected classifier error owing to a sampling ratio different from the population class ratio. From these we derive a sample-based minimax sampling ratio and provide an algorithm for approximating it from the data. We also extend to arbitrary distributions the classical population-based Anderson linear discriminant analysis minimax sampling ratio derived from the discriminant form of the Bayes classifier. Availability: All the codes for synthetic data and real data examples are written in MATLAB. A function called mmratio, whose output is an approximation of the minimax sampling ratio of a given dataset, is also written in MATLAB. All the codes are available at: http://gsp.tamu.edu/Publications/supplementary/shahrokh13b . Contact: edward@ece.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation:  Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains. Results:  Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language. Availability and implementation:  The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org . GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license. Contact:   peccoud@vt.edu Supplementary Information:   Supplementary data are available at Bioinformatics online.

Description: Motivation: Homology search methods are dominated by the central paradigm that sequence similarity is a proxy for common ancestry and, by extension, functional similarity. For determining sequence similarity in proteins, most widely used methods use models of sequence evolution and compare amino-acid strings in search for conserved linear stretches. Probabilistic models or sequence profiles capture the position-specific variation in an alignment of homologous sequences and can identify conserved motifs or domains. While profile-based search methods are generally more accurate than simple sequence comparison methods, they tend to be computationally more demanding. In recent years, several methods have emerged that perform protein similarity searches based on domain composition. However, few methods have considered the linear arrangements of domains when conducting similarity searches, despite strong evidence that domain order can harbour considerable functional and evolutionary signal. Results: Here, we introduce an alignment scheme that uses a classical dynamic programming approach to the global alignment of domains. We illustrate that representing proteins as strings of domains (domain arrangements) and comparing these strings globally allows for a both fast and sensitive homology search. Further, we demonstrate that the presented methods complement existing methods by finding similar proteins missed by popular amino-acid–based comparison methods. Availability: An implementation of the presented algorithms, a web-based interface as well as a command-line program for batch searching against the UniProt database can be found at http://rads.uni-muenster.de . Furthermore, we provide a JAVA API for programmatic access to domain-string–based search methods. Contact: terrapon.nicolas@gmail.com or ebb@uni-muenster.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA. Results: Here, we present a major update of the R/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor’s annotation databases to facilitate annotation of specific genomic regions. Availability and implementation: The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http://www.bioconductor.org . Contact: lienhard@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation:  Most methods for estimating differential expression from RNA-seq are based on statistics that compare normalized read counts between treatment classes. Unfortunately, reads are in general too short to be mapped unambiguously to features of interest, such as genes, isoforms or haplotype-specific isoforms. There are methods for estimating expression levels that account for this source of ambiguity. However, the uncertainty is not generally accounted for in downstream analysis of gene expression experiments. Moreover, at the individual transcript level, it can sometimes be too large to allow useful comparisons between treatment groups. Results:  In this article we make two proposals that improve the power, specificity and versatility of expression analysis using RNA-seq data. First, we present a Bayesian method for model selection that accounts for read mapping ambiguities using random effects. This polytomous model selection approach can be used to identify many interesting patterns of gene expression and is not confined to detecting differential expression between two groups. For illustration, we use our method to detect imprinting, different types of regulatory divergence in cis and in trans and differential isoform usage, but many other applications are possible. Second, we present a novel collapsing algorithm for grouping transcripts into inferential units that exploits the posterior correlation between transcript expression levels. The aggregate expression levels of these units can be estimated with useful levels of uncertainty. Our algorithm can improve the precision of expression estimates when uncertainty is large with only a small reduction in biological resolution. Availability and implementation:  We have implemented our software in the mmdiff and mmcollapse multithreaded C++ programs as part of the open-source MMSEQ package, available on https://github.com/eturro/mmseq . Contact:   et341@cam.ac.uk Supplementary information:   Supplementary data are available at Bioinformatics online.

Description: Motivation:  Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis—intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps. Results:  Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster. Availability and implementation:  Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/ ; the pipeline is implemented in C++ and uses the Message Passing Interface (MPI) standard for distributed computing. Contact:  mering@imls.uzh.ch Supplementary Information:  Supplementary data are available at Bioinformatics online.

Description: : High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different ‘-omics’. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies. Availability and implementation: tRanslatome is available in Bioconductor. Contact : t.tebaldi@unitn.it Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : DoMosaics is an application that unifies protein domain annotation, domain arrangement analysis and visualization in a single tool. It simplifies the analysis of protein families by consolidating disjunct procedures based on often inconvenient command-line applications and complex analysis tools. It provides a simple user interface with access to domain annotation services such as InterProScan or a local HMMER installation, and can be used to compare, analyze and visualize the evolution of domain architectures. Availability and implementation: DoMosaics is licensed under the Apache License, Version 2.0, and binaries can be freely obtained from www.domosaics.net . Contact: radmoore@uni-muenster.de or e.bornberg@uni-muenster.de

Description: Motivation: A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables—usually molecules and their interactions. Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data. Results: Topological augmentation starts from a simple model that is unable to explain the experimental data and augments its topology by adding new terms that capture the experimental behavior. This process is guided by representing the uncertainty in the model topology through stochastic differential equations whose trajectories contain information about missing model parts. We first apply this semiautomatic procedure to a pharmacokinetic model. This example illustrates that a global sampling of the parameter space is critical for inferring a correct model structure. We also use our method to improve our understanding of glutamine transport in yeast. This analysis shows that transport dynamics is determined by glutamine permeases with two different kinds of kinetics. Topological augmentation can not only be applied to biochemical systems, but also to any system that can be described by ordinary differential equations. Availability and implementation: Matlab code and examples are available at: http://www.csb.ethz.ch/tools/index . Contact: mikael.sunnaker@bsse.ethz.ch ; andreas.wagner@ieu.uzh.ch Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot—a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to 〉28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. Availability: Freely available on the web at http://seqdepot.net/ . REST access via http://seqdepot.net/api/v1 . Database files and scripts may be downloaded from http://seqdepot.net/download . Contact: ulrich.luke+sci@gmail.com

Description: Motivation: Microarray data analysis is often applied to characterize disease populations by identifying individual genes linked to the disease. In recent years, efforts have shifted to focus on sets of genes known to perform related biological functions (i.e. in the same pathways). Evaluating gene sets reduces the need to correct for false positives in multiple hypothesis testing. However, pathways are often large, and genes in the same pathway that do not contribute to the disease can cause a method to miss the pathway. In addition, large pathways may not give much insight to the cause of the disease. Moreover, when such a method is applied independently to two datasets of the same disease phenotypes, the two resulting lists of significant pathways often have low agreement. Results: We present a powerful method, PFSNet, that identifies smaller parts of pathways (which we call subnetworks), and show that significant subnetworks (and the genes therein) discovered by PFSNet are up to 51% (64%) more consistent across independent datasets of the same disease phenotypes, even for datasets based on different platforms, than previously published methods. We further show that those methods which initially declared some large pathways to be insignificant would declare subnetworks detected by PFSNet in those large pathways to be significant, if they were given those subnetworks as input instead of the entire large pathways. Availability: http://compbio.ddns.comp.nus.edu.sg:8080/pfsnet/ Contact: kevinl@comp.nus.edu.sg Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: :  Pathway Commons is a resource permitting simultaneous queries of multiple pathway databases. However, there is no standard mechanism for using these data (stored in BioPAX format) to annotate and build quantitative mathematical models. Therefore, we developed a new module within the virtual cell modeling and simulation software. It provides pathway data retrieval and visualization and enables automatic creation of executable network models directly from qualitative connections between pathway nodes. Availability and implementation:  Available at Virtual Cell ( http://vcell.org/ ). Application runs on all major platforms and does not require registration for use on the user’s computer. Tutorials and video are available at user guide page. Contact:   vcell_support@uchc.edu

Description: : myChEMBL is a completely open platform, which combines public domain bioactivity data with open source database and cheminformatics technologies. myChEMBL consists of a Linux (Ubuntu) Virtual Machine featuring a PostgreSQL schema with the latest version of the ChEMBL database, as well as the latest RDKit cheminformatics libraries. In addition, a self-contained web interface is available, which can be modified and improved according to user specifications. Availability and implementation: The VM is available at: ftp://ftp.ebi.ac.uk/pub/databases/chembl/VM/myChEMBL/current . The web interface and web services code is available at: https://github.com/rochoa85/myChEMBL . Contact: jpo@ebi.ac.uk

Description: Motivation: The identification of cell cycle-regulated genes through the cyclicity of messenger RNAs in genome-wide studies is a difficult task due to the presence of internal and external noise in microarray data. Moreover, the analysis is also complicated by the loss of synchrony occurring in cell cycle experiments, which often results in additional background noise. Results: To overcome these problems, here we propose the LEON (LEarning and OptimizatioN) algorithm, able to characterize the ‘cyclicity degree’ of a gene expression time profile using a two-step cascade procedure. The first step identifies a potentially cyclic behavior by means of a Support Vector Machine trained with a reliable set of positive and negative examples. The second step selects those genes having peak timing consistency along two cell cycles by means of a non-linear optimization technique using radial basis functions. To prove the effectiveness of our combined approach, we use recently published human fibroblasts cell cycle data and, performing in vivo experiments, we demonstrate that our computational strategy is able not only to confirm well-known cell cycle-regulated genes, but also to predict not yet identified ones. Availability and implementation: All scripts for implementation can be obtained on request. Contact: lorenzo.farina@uniroma1.it or gurtner@ifo.it Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: RNA-seq technology has been widely adopted as an attractive alternative to microarray-based methods to study global gene expression. However, robust statistical tools to analyze these complex datasets are still lacking. By grouping genes with similar expression profiles across treatments, cluster analysis provides insight into gene functions and networks, and hence is an important technique for RNA-seq data analysis. Results: In this manuscript, we derive clustering algorithms based on appropriate probability models for RNA-seq data. An expectation-maximization algorithm and another two stochastic versions of expectation-maximization algorithms are described. In addition, a strategy for initialization based on likelihood is proposed to improve the clustering algorithms. Moreover, we present a model-based hybrid-hierarchical clustering method to generate a tree structure that allows visualization of relationships among clusters as well as flexibility of choosing the number of clusters. Results from both simulation studies and analysis of a maize RNA-seq dataset show that our proposed methods provide better clustering results than alternative methods such as the K-means algorithm and hierarchical clustering methods that are not based on probability models. Availability and implementation: An R package, MBCluster.Seq, has been developed to implement our proposed algorithms. This R package provides fast computation and is publicly available at http://www.r-project.org . Contact: sy@swufe.edu.cn ; pliu@iastate.edu Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation:  Modern biomedical and epidemiological studies often measure hundreds or thousands of biomarkers, such as gene expression or metabolite levels. Although there is an extensive statistical literature on adjusting for ‘multiple comparisons’ when testing whether these biomarkers are directly associated with a disease, testing whether they are biological mediators between a known risk factor and a disease requires a more complex null hypothesis, thus offering additional methodological challenges. Results:  We propose a permutation approach that tests multiple putative mediators and controls the family wise error rate. We demonstrate that, unlike when testing direct associations, replacing the Bonferroni correction with a permutation approach that focuses on the maximum of the test statistics can significantly improve the power to detect mediators even when all biomarkers are independent. Through simulations, we show the power of our method is 2–5 x larger than the power achieved by Bonferroni correction. Finally, we apply our permutation test to a case-control study of dietary risk factors and colorectal adenoma to show that, of 149 test metabolites, docosahexaenoate is a possible mediator between fish consumption and decreased colorectal adenoma risk. Availability and implementation:  R-package included in online Supplementary Material. Contact:   joshua.sampson@nih.gov Supplementary information:   Supplementary materials are available at Bioinformatics online.

Description: Ecology, Volume 95, Issue 1, Page 98-109, January 2014. Grazing, fire, and climate shape mesic grassland communities. With global change altering all three factors, understanding how grasslands respond to changes in these combined drivers may aid in projecting future changes in grassland ecosystems. We manipulated rainfall and simulated grazing (clipping) in two long-term fire experiments in mesic grasslands in North America (NA) and South Africa (SA). Despite their common drivers, grasslands in NA and SA differ in evolutionary history. Therefore, we expected community structure and production in NA and SA to respond differently to fire, grazing, and drought. Specifically, we hypothesized that NA plant community composition and production would be more responsive than the SA plant communities to changes in the drivers and their interactions, and that despite this expected stability of SA grasslands, drought would be the dominant factor controlling production, but grazing would play the primary role in determining community composition at both sites. Contrary to our hypothesis, NA and SA grasslands generally responded similarly to grazing, drought, and fire. Grazing increased diversity, decreased grass cover and production, and decreased belowground biomass at both sites. Drought alone minimally impacted plant community structure, and we saw similar treatment interactions at the two sites. Drought was not the primary driver of grassland productivity, but instead drought effects were similar to or less than grazing and fire. Even though these grasslands differed in evolutionary history, they responded similarly to our fire, grazing, and climate manipulations. Overall, we found community and ecosystem convergence in NA and SA grasslands. Grazing and fire are as important as climate in controlling mesic grassland ecosystems on both continents.

Description: Ecology, Volume 95, Issue 1, Page 173-184, January 2014. Biodiversity has been shown to increase the temporal stability of community and ecosystem attributes through multiple mechanisms, but these same mechanisms make less consistent predictions about the effects of richness on population stability. The overall effects of biodiversity on population and community stability will therefore depend on the dominant mechanisms that are likely to vary with the nature of biodiversity loss and the degree of environmental variability. We conducted a mesocosm experiment in which we generated a gradient in zooplankton species richness by directly manipulating dominant species and by allowing/preventing immigration from a metacommunity. The mesocosms were maintained under either constant or variable nutrient environments. Population, community, and ecosystem data were collected for five months. We found that zooplankton population and community stability is enhanced in species-rich communities in both constant and variable environments. Species richness increased primarily through the addition of species with low abundance. The communities that were connected to a metacommunity via immigration were the most diverse and the most stable, indicating the importance of both metacommunity dynamics and rare species for stability. We found little evidence for selection effects or overyielding as stabilizing forces. We did find support for asynchronous dynamics and statistical averaging, both of which predict destabilizing effects at the population level. We also found support for weak interactions, which predicts that both populations and communities will become more stable as richness increases. In order to understand the effects of biodiversity loss on stability, we will need to understand when different stabilizing mechanisms tend to operate but also how multiple mechanisms interact.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Theory of invasion ecology indicates that the number of invading individuals (propagule size) and the timing of invasion are important for invasion success. Propagule size affects establishment success due to an Allee effect and the effect of demographic stochasticity, whereas the timing of invasion does so via niche opportunity produced by fluctuating predation pressure and resource abundance. We propose a synthesis of these two mechanisms by a time-varying dose-response curve where the dose is propagule size and the response is establishment probability. We show an example of the synthesis in a simple predator-prey model where successful invasion occurs as a demographic regime shift because of the bistability of the system. The two mechanisms are not independent, but simultaneously determine invasion success in our model. We found that positive growth rate of an invading species does not ensure its establishment, especially when its propagule size is small or when its growth rate is in a decreasing trend. We suggest the difficulty of understanding invasion process based on a dose-response curve of propagule size as no unique curve can be determined due to the effects of invasion timing (i.e., the threshold of demographic regime shift is time-varying). The results of our model analysis also have an implication on the phase relationship between population cycles of predators and prey.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Grasslands have been lost and degraded in the USA since Euro-American settlement due to agriculture, development, introduced invasive species, and changes in fire regimes. Fire is frequently used in prairie restoration to control invasion by trees and shrubs, but may have additional consequences. For example, fire might reduce damage by herbivore and pathogen enemies by eliminating litter, which harbors eggs and spores. Less obviously, fire might influence enemy loads differently for native and introduced plant hosts. We used a controlled burn in a Willamette Valley (Oregon) prairie to examine these questions. We expected that without fire, introduced host plants should have less damage than native host plants because the introduced species are likely to have left many of their enemies behind when they were transported to their new range (the enemy release hypothesis, or ERH). If the ERH holds, then fire, which should temporarily reduce enemies on all species, should give an advantage to the natives because they should see greater total reduction in damage by enemies. Prior to the burn, we censused herbivore and pathogen attack on eight plant species (five of non-native origin: Bromus hordaceous, Cynosuros echinatus, Galium divaricatum, Schedonorus arundinaceus (=Festuca arundinacea), Sherardia arvensis; and three natives: Danthonia californica, Epilobium minutum, and Lomatium nudicale). The same plots were monitored for two years post-fire. Prior to the burn, native plants had more kinds of damage and more pathogen damage than introduced plants, consistent with the ERH. Fire reduced pathogen damage relative to the controls more for the native than the introduced species, but the effects on herbivory were negligible. Pathogen attack was correlated with plant reproductive fitness, whereas herbivory was not. These results suggest that fire may be useful for promoting some native plants in prairies due to its negative effects on their pathogens.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Complementary resource use and redundancy of species that fulfill the same ecological role are two mechanisms that can respectively increase and stabilize process rates in ecosystems. For example, predator complementarity and redundancy can determine prey consumption rates and their stability, yet few studies take into account the multiple predator species attacking multiple prey at different rates in natural communities. Thus, it remains unclear whether these biodiversity mechanisms are important determinants of consumption in entire predator-prey assemblages, such that food-web interaction structure determines community-wide consumption and stability. Here, we use empirical quantitative food-webs to study the community-wide effects of functional complementarity and redundancy of consumers (parasitoids) on herbivore control in temperate forests. We find that complementarity in host resource use by parasitoids was a strong predictor of absolute parasitism rates at the community level, and that redundancy in host-use patterns stabilised community-wide parasitism rates in space, but not through time. These effects can potentially explain previous contradictory results from predator diversity research. Phylogenetic diversity (measured using taxonomic distance) did not explain functional complementarity or parasitism rates, so could not serve as a surrogate measure for functional complementarity. Our study shows that known mechanisms underpinning predator diversity effects on both functioning and stability can easily be extended to link food webs to ecosystem functioning.

Description: Motivation: For samples of unrelated individuals, we propose a general analysis framework in which hundred thousands of genetic loci can be tested simultaneously for association with complex phenotypes. The approach is built on spatial-clustering methodology, assuming that genetic loci that are associated with the target phenotype cluster in certain genomic regions. In contrast to standard methodology for multilocus analysis, which has focused on the dimension reduction of the data, our multilocus association-clustering test profits from the availability of large numbers of genetic loci by detecting clusters of loci that are associated with the phenotype. Results: The approach is computationally fast and powerful, enabling the simultaneous association testing of large genomic regions. Even the entire genome or certain chromosomes can be tested simultaneously. Using simulation studies, the properties of the approach are evaluated. In an application to a genome-wide association study for chronic obstructive pulmonary disease, we illustrate the practical relevance of the proposed method by simultaneously testing all genotyped loci of the genome-wide association study and by testing each chromosome individually. Our findings suggest that statistical methodology that incorporates spatial-clustering information will be especially useful in whole-genome sequencing studies in which millions or billions of base pairs are recorded and grouped by genomic regions or genes, and are tested jointly for association. Availability and implementation: Implementation of the approach is available upon request. Contact : daq412@mail.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Floral nectar of many plant species is prone to colonization by microbial organisms such as yeasts. Their presence and metabolism of nectar chemical components have the potential to modify a suite of floral traits important for pollinator attraction, including nectar quality and scent. However, studies on the direct and indirect effects of nectar-inhabiting microogranisms on pollinator behavior and plant reproductive success remain rare. To determine their potential to affect pollinator behavior and plant fitness, we experimentally manipulated the common nectar-inhabiting yeast Metschnikowia reukaufii in the nectar of Delphinium nuttallianum, a short-lived montane perennial herb. We detected positive indirect, pollinator-mediated effects of yeasts on male plant fitness measured as pollen donation using powdered fluorescent dyes. However, we detected no direct or indirect effects on components of female fitness. Matching effects on male plant fitness, pollinators responded positively to the presence of yeasts, removing more nectar from flowers treated with M. reukaufii. Our results provide evidence of effects of nectar-inhabiting yeasts on male plant fitness and highlight the importance of microorganisms in mediating plant-pollinator interactions and subsequent plant fitness.

Description: Ecology, Volume 95, Issue 1, Page 3-8, January 2014. Periodical cicadas (Magicicada spp.) mature in 13 or 17 years, the longest development times for any non-diapausing insects. Selection may favor prolonged development since nymphs experience little mortality and individuals taking 17 years have been shown to have greater fecundity than those taking 13 years. Why don't periodical cicadas take even longer to develop? Nymphs feed on root xylem fluid and move little. Ovipositing females prefer fast-growing trees at forest edges. I hypothesized that (1) adults emerging at edges would be heavier than those from forest interiors and (2) habitat changes could limit development time. I collected newly eclosed females that had neither fed as adults nor moved from their site of development. For M. septendecim, females from edges were 4.9% heavier than those from the interior. I assumed that emergence density indicated habitat quality and measured density at eight sites in 1979, 1996, and 2013. Over three generations, variation in densities was great; densities at two sites crashed, and at one site they exploded to 579/m2. Habitat transience may limit development time because only adults can reassess habitats and reposition offspring. In conclusion, cicadas are affected by habitat characteristics, habitats change over 17 years, and cicadas may emerge, mate, and redistribute their offspring to track habitat dynamics.

Description: Ecology, Volume 95, Issue 1, Page 56-67, January 2014. Predation has been suggested to be especially important in simple food webs and less productive ecosystems such as the arctic tundra, but very few data are available to evaluate this hypothesis. We examined the hypothesis that avian predators could drive the population dynamics of two cyclic lemming species in the Canadian Arctic. A dense and diverse suite of predatory birds, including the Snowy Owl (Bubo scandiacus), the Rough-legged Hawk (Buteo lagopus), and the Long-tailed Jaeger (Stercorarius longicaudus), inhabits the arctic tundra and prey on collared (Dicrostonyx groenlandicus) and brown (Lemmus trimucronatus) lemmings during the snow-free period. We evaluated the predation pressure exerted by these predators by combining their numerical (variation in breeding and fledgling numbers) and functional (variation in diet and daily consumption rates) responses to variations in lemming densities over the 2004–2010 period. Breeding density and number of fledglings produced by the three main avian predators increased sharply without delay in response to increasing lemming densities. The proportion of collared lemmings in the diet of those predators was high at low lemming density (both species) but decreased as lemming density increased. However, we found little evidence that their daily consumption rates vary in relation to changes in lemming density. Total consumption rate by avian predators initially increased more rapidly for collared lemming but eventually leveled off at a much higher value for brown lemmings, the most abundant species at our site. The combined daily predation rate of avian predators exceeded the maximum daily potential growth rates of both lemming species except at the highest recorded densities for brown lemmings. We thus show, for the first time, that predation pressure exerted without delay by avian predators can limit populations of coexisting lemming species during the snow-free period, and thus, that predation could play a role in the cyclic dynamic of these species in the tundra.

Description: Ecology, Volume 95, Issue 1, Page 238-239, January 2014.

Description: Ecology, Volume 95, Issue 1, Page 238-239, January 2014.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Successful dispersal can enhance both individual fitness and population persistence, but the process of dispersal is often inherently risky. The interplay between the costs and benefits of dispersal are poorly documented for species with complex life-histories due to the difficulty of tracking dispersing individuals. Here we investigate variability in dispersal histories of a freshwater fish, Awaous stamineus, across the species' entire geographic range in the Hawaiian archipelago. Like many animals endemic to tropical island streams, these gobies have an amphidromous life cycle in which a brief marine larval phase enables dispersal among isolated freshwater habitats. Using otolith microchemistry, we document three distinct marine dispersal pathways, all of which are observed on every island. Surprisingly, we also find that 62% of individuals complete their life cycle entirely within freshwater, in contrast to the assumption that amphidromy is obligate in Hawaiian stream gobies. Comparing early life history outcomes based on daily otolith growth rings, we find that individuals with marine dispersal have shorter larval durations and faster larval growth, and their growth advantage over purely-freshwater counterparts continues to some degree into adult life. These individual benefits of maintaining a marine dispersal phase presumably balance against the challenge of finding and re-entering an island stream from the ocean. The facultative nature of amphidromy in this species highlights the selective balance between costs and benefits of dispersal in life history evolution. Accounting for alternative dispersal strategies will be essential for conservation of the amphidromous species that often dominate tropical island streams, many of which are at risk of extinction.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Climate change forecasts of more frequent climate extremes suggest that such events will become increasingly important drivers of future ecosystem dynamics and function. Because the rarity and unpredictability of naturally occurring climate extremes limits assessment of their ecological impacts, we experimentally imposed extreme drought and a mid-summer heat wave over two years in a central US grassland. While the ecosystem was resistant to heat waves, it was not resistant to extreme drought, which reduced aboveground net primary productivity (ANPP) below the lowest level measured in this grassland in almost thirty years. This extreme reduction in ecosystem function was a consequence of reduced productivity of both C4 grasses and C3 forbs. However, the dominant forb was negatively impacted by the drought more than the dominant grass, and this led to a reordering of species abundances within the plant community. Although this change in community composition persisted post-drought, ANPP recovered completely the year after drought due to rapid demographic responses by the dominant grass, compensating for loss of the dominant forb. Overall, these results show that an extreme reduction in ecosystem function attributable to climate extremes (e.g., low resistance) does not preclude rapid ecosystem recovery. Given that dominance by a few species is characteristic of most ecosystems, knowledge of the traits of these species and their responses to climate extremes will be key for predicting future ecosystem dynamics and function.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. The resource quality of the host has been shown to affect parasite transmission success, prevalence and virulence. Seasonal availability of environmental nutrients alters density and stoichiometric quality (carbon-nutrient ratios) of both producers and consumers, suggesting that nutrient availability may drive fluctuations in parasite prevalence patterns observed in nature. We examined the interactions between the population dynamics of a keystone herbivore Daphnia and its parasites, and their associations with water nutrient concentrations, resource quantity and quality and other environmental variables (temperature, pH, oxygen concentration) in a small lake, using general linear models. We found that the prevalence of two gut endoparasites were positively related to food source and quality as well as nitrogen content of Daphnia - whereas the prevalence of an epibiont and overall parasite species richness were negatively related to phosphorus content of Daphnia. When only endoparasite species richness was considered, no connections to nutrients were found. Daphnia density was not connected to parasites, but we found interactions between Daphnia fecundity and parasite prevalence. Overall, our results suggest that environmental nutrient concentrations and stoichiometric quality of the host have a potential to affect seasonality in parasite epidemics, but the connections between environmental carbon:nutrient ratios and parasite prevalence patterns are diverse and species-specific.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. The Tibetan Plateau (TP) is experiencing high rates of climatic change. We present a novel combined mechanistic-bioclimatic modeling approach to determine (i) how changes in precipitation and temperature on the TP may impact net primary production (NPP) in four major biomes (forest, shrub, grass, desert); and (ii) if there exists a maximum rain use efficiency (RUEMAX) that represents a "boundary that constrain(s) site-level productivity and efficiency" (Huxman et al. 2004). We used a daily mechanistic ecosystem model to generate 40-y outputs using observed climatic data for scenarios of (i) decreased precipitation (25 to 100%); (ii) increased air temperature (1 to 6°C); (iii) simultaneous changes in both precipitation ( ± 50%, ± 25%) and air temperature (+1 to +6°C); and (iv) increased interannual variability (IAV) of precipitation (+1σ to +3σ, with fixed means). We fitted model output from these scenarios to Huxman et al.'s RUEMAX bioclimatic model, NPP = α +RUE•PPT (where α = intercept, RUE is rain use efficiency and PPT is annual precipitation). Based on these analyses we conclude that: (i) there is strong support (when not explicit, then trend-wise) for Huxman et al.'s assertion that biomes converge to a common RUEMAX during the driest years at a site, thus representing the boundary for highest rain use efficiency; (ii) the interactive effects of simultaneously decreasing precipitation and increasing temperature on NPP for the TP is smaller than might be expected from additive, single-factor changes in these drivers; and (iii) that increasing IAV of precipitation may ultimately have a larger impact on biomes of the Tibetan Plateau than changing amounts of rainfall and air temperature alone.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Niche differentiation is a major hypothesized determinant of species distributions, but its practical importance is heavily debated and underlying mechanisms are poorly understood. Trait-based approaches have been used to infer niche differentiation and predict species distributions. For understanding underlying mechanisms, individual traits should be scaled up to whole-plant performance, which hardly has been done. We measured seven key traits that are important for carbon and water balance for 37 tropical tree species. We used a process-based plant physiological model to simulate the carbon budget of saplings along gradients of light and water availability, and quantified the performance of the species in terms of their light compensation points (a proxy for shade tolerance), water compensation points (proxy for drought tolerance) and maximum carbon gain rates (proxy for potential growth rate). We linked species performances to their observed distributions (the realized niches) at two spatial scales in Bolivian lowland forests: along a canopy openness gradient at local scale (~1 km2) and along a rainfall gradient (1100-2200 mm/y) at regional (~1000 km) scale. We show that the water compensation point was the best predictor of species distributions along water and light resource gradients within and across tropical forests. A sensitivity analysis suggests that the stomatal regulation of minimum leaf water potentials, rather than stem hydraulic traits (sapwood area and specific conductivity), contributed to the species differences in the water compensation point of saplings. The light compensation point and maximum carbon gain - both driven by leaf area index and the leaf nitrogen concentration - also contributed to differential species distributions at the local scale, but not or only marginally at the regional scale. Trait-and-physiology-based simulations of whole-plant performance thus help to evaluate the possible roles of individual traits in physiological processes underlying species performance along environmental gradients. The development of such whole plant concepts will improve our ability to understand responses of plant communities to shifts in resource availability and stress under global change.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Birds and their population dynamics are often used to understand and document anthropogenic effects on biodiversity. Nest success is a critical component of the breeding output of birds in different environments; but to obtain the complete picture of how bird populations respond to perturbations, we also need an estimate of nest abundance or density. The problem is that raw counts generally underestimate actual nest numbers because detection is imperfect and because some nests may fail or fledge before being subjected to detection efforts. Here we develop a state-space superpopulation capture-recapture approach in which inference about detection probability is based on the age at first detection, as opposed to the sequence of re-detections in standard capture-recapture models. We apply the method to ducks in which 1) the age of the nests and their initiation dates can be determined upon detection and 2) the duration of the different stages of the breeding cycle is a priori known. We fit three model variants with or without assumptions about the phenology of nest initiation dates, and use simulations to evaluate the performance of the approach in challenging situations. In an application to blue-winged teal Anas discors breeding at study sites in North and South Dakota, USA, nesting stage (egg-laying or incubation) markedly influenced nest survival and detection probabilities. Two individual covariates (one binary covariate: presence of grazing cattle at the nest site, and one continuous covariate: Robel index of vegetation) had only weak effects. We estimated that 5-10% of the total number of nests were available for detection but missed by field crews. An additional 6-15% were never available for detection. These proportions are expected to be larger in less intense, more typical sampling designs. User-friendly software nestAbund is provided to assist users in implementing the method.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Disease is often expected to limit host populations, but diseases do not always dramatically reduce host numbers and often have no effect. The impact of a fungal pathogen (Entomophaga grylli pathotype 1) on grasshopper (Camnula pellucida) populations was studied in a field experiment. We tested whether the effects of disease on grasshopper survival were 1) additive, with disease mortality summing with other mortality sources to determine the total population mortality rate or 2) compensatory, where disease mortality simply replaces mortality from other sources so that the total population mortality rate remains unchanged. We examined grasshopper survival in relation to differences in disease exposure, host density levels, and host developmental stage. The effects of disease varied with grasshopper developmental stage and density. Disease mortality increased by 60% at high grasshopper density compared to low density treatments, and decreased when grasshoppers fully matured. Despite increased rates of disease mortality at high densities, the total mortality rate was not notably higher in diseased grasshoppers (87%) compared to disease-free counterparts at high densities (83%), indicating that a large proportion of disease mortality simply replaced mortality from food limitation. Additive responses were supported in early and late instars, with disease exposure resulting in decreased grasshopper survival. In contrast, the effect of disease on adults was inconclusive. Yet, the disease did not affect adult survival suggesting that adult disease mortality is compensatory. Therefore, disease reduction of grasshopper populations (additive mortality) is more likely to occur during earlier developmental stages when hosts are most vulnerable to disease and at low host densities when food is abundant. Combined, our results emphasize the importance of host dynamics and food availability in how this host-pathogen system responds to disease. Accordingly, compensatory versus additive mortality may need to be considered when examining how disease ultimately affects host population dynamics.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Urbanization and global climate change can profoundly alter biological systems, yet scientists often analyze their effects separately. We test how the timing of life cycle events (phenology) is jointly influenced by these two components of global change. To do so, we use a long-term phenological dataset of 20 common butterfly species from 83 sites across the state of Ohio, USA, with sites that range from rural undeveloped areas to moderately sized cities. These sites span a several °C latitudinal gradient in mean temperature, mimicking the range of projected global climate warming effects through the end of the century. Although shifts toward earlier phenology are typical of species' responses to either global climate change or urbanization, we found that their interaction delayed several Ohio butterfly species' first appearance and peak abundance phenology. Exploitative species exhibited smaller delays in first appearance and peak abundance phenology in areas that were urbanized and geographically warm. Our results show that phenological responses to urbanization are contingent upon geographic variation in temperature, and that the impacts of urbanization and global climate change should be considered simultaneously when developing forecasts of biological responses to environmental change.

Description: Ecology, Volume 0, Issue 0, Ahead of Print. Fertilization via agricultural inputs and nutrient deposition is one of the major threats to global terrestrial plant richness, yet we still do not fully understand the mechanisms by which fertilization decreases plant richness. Tall clonal species have recently been proposed to cause declines in plant species richness by increasing in abundance in response to fertilization and competing strongly with other species. We tested this hypothesis in a fertilization experiment in a low productivity grassland by using a novel experimental manipulation of the presence vs. absence of clonal species and by examining the role of height within these treatments. We found that fertilization decreased species richness more in the presence than absence of clonal species. We also found that only tall species increased in biomass in response to fertilization. In the absence of clonal species, fertilization increased biomass of tall non-clonal species. However, in the presence of clonal species, fertilization decreased tall non-clonal biomass and only tall clonal biomass increased. Fertilization caused almost all short species to be lost in the presence, but not the absence, of clonal species and caused greater declines in the mean and variance of light levels in the presence of clonal species. These results show that the traits of species in a community can determine the magnitude of species loss due to fertilization. The strongly negative effect of tall clonals on species richness in fertilized plots is likely a result of their capacity to decrease light levels to a greater extent and more uniformly than non-clonal species, and thereby drive the exclusion of short species. These results help clarify the mechanisms whereby fertilization decreases grassland plant species richness and suggest that efforts to prevent the loss of species under fertilized conditions may be most effective when they focus on controlling the biomass of tall clonal species.

Description: Ecology, Ahead of Print. Predicting the future trend and viability of populations is an essential task in ecology. Because many populations respond to changing environments, uncertainty surrounding environmental responses must be incorporated into population assessments. However, understanding the effects of environmental variation on population dynamics requires information on several important demographic parameters which are often difficult to estimate. Integrated population models facilitate the integration of time-series data on population size and all existing demographic information from a species, allowing the estimation of demographic parameters for which limited or no empirical data exist. Although these models are ideal for assessments of population viability, they have so far not included environmental uncertainty. We incorporated environmental variation in an integrated population model to account for both demographic and environmental uncertainty in an assessment of population viability. In addition, we used this model to estimate true juvenile survival, an important demographic parameter for population dynamics that is difficult to estimate empirically. We applied this model to assess the past and future population trend of a rare island endemic songbird, the Montserrat Oriole Icterus oberi, which is threatened by volcanic activity. Montserrat Orioles experienced lower survival in years with volcanic ash-fall, causing periodic population declines that were compensated by higher seasonal fecundity in years with high pre-breeding season rainfall. Due to the inclusion of both demographic and environmental uncertainty in the model, the estimated population growth rate in the immediate future was highly imprecise (95% credible interval 0.844 - 1.105), and the probability of extinction after three generations (in the year 2028) was low (2.1%). This projection demonstrates that accounting for both demographic and environmental sources of uncertainty provides a more realistic assessment of the viability of populations under unknown future environmental conditions.

Description: Ecology, Ahead of Print. Grasslands have been lost and degraded in the USA since Euro-American settlement due to agriculture, development, introduced invasive species, and changes in fire regimes. Fire is frequently used in prairie restoration to control invasion by trees and shrubs, but may have additional consequences. For example, fire might reduce damage by herbivore and pathogen enemies by eliminating litter, which harbors eggs and spores. Less obviously, fire might influence enemy loads differently for native and introduced plant hosts. We used a controlled burn in a Willamette Valley (Oregon) prairie to examine these questions. We expected that without fire, introduced host plants should have less damage than native host plants because the introduced species are likely to have left many of their enemies behind when they were transported to their new range (the enemy release hypothesis, or ERH). If the ERH holds, then fire, which should temporarily reduce enemies on all species, should give an advantage to the natives because they should see greater total reduction in damage by enemies. Prior to the burn, we censused herbivore and pathogen attack on eight plant species (five of non-native origin: Bromus hordaceous, Cynosuros echinatus, Galium divaricatum, Schedonorus arundinaceus (=Festuca arundinacea), Sherardia arvensis; and three natives: Danthonia californica, Epilobium minutum, and Lomatium nudicale). The same plots were monitored for two years post-fire. Prior to the burn, native plants had more kinds of damage and more pathogen damage than introduced plants, consistent with the ERH. Fire reduced pathogen damage relative to the controls more for the native than the introduced species, but the effects on herbivory were negligible. Pathogen attack was correlated with plant reproductive fitness, whereas herbivory was not. These results suggest that fire may be useful for promoting some native plants in prairies due to its negative effects on their pathogens.

Description: Ecology, Ahead of Print. Floral nectar of many plant species is prone to colonization by microbial organisms such as yeasts. Their presence and metabolism of nectar chemical components have the potential to modify a suite of floral traits important for pollinator attraction, including nectar quality and scent. However, studies on the direct and indirect effects of nectar-inhabiting microogranisms on pollinator behavior and plant reproductive success remain rare. To determine their potential to affect pollinator behavior and plant fitness, we experimentally manipulated the common nectar-inhabiting yeast Metschnikowia reukaufii in the nectar of Delphinium nuttallianum, a short-lived montane perennial herb. We detected positive indirect, pollinator-mediated effects of yeasts on male plant fitness measured as pollen donation using powdered fluorescent dyes. However, we detected no direct or indirect effects on components of female fitness. Matching effects on male plant fitness, pollinators responded positively to the presence of yeasts, removing more nectar from flowers treated with M. reukaufii. Our results provide evidence of effects of nectar-inhabiting yeasts on male plant fitness and highlight the importance of microorganisms in mediating plant-pollinator interactions and subsequent plant fitness.

Description: Ecology, Ahead of Print. Complementary resource use and redundancy of species that fulfill the same ecological role are two mechanisms that can respectively increase and stabilize process rates in ecosystems. For example, predator complementarity and redundancy can determine prey consumption rates and their stability, yet few studies take into account the multiple predator species attacking multiple prey at different rates in natural communities. Thus, it remains unclear whether these biodiversity mechanisms are important determinants of consumption in entire predator-prey assemblages, such that food-web interaction structure determines community-wide consumption and stability. Here, we use empirical quantitative food-webs to study the community-wide effects of functional complementarity and redundancy of consumers (parasitoids) on herbivore control in temperate forests. We find that complementarity in host resource use by parasitoids was a strong predictor of absolute parasitism rates at the community level, and that redundancy in host-use patterns stabilised community-wide parasitism rates in space, but not through time. These effects can potentially explain previous contradictory results from predator diversity research. Phylogenetic diversity (measured using taxonomic distance) did not explain functional complementarity or parasitism rates, so could not serve as a surrogate measure for functional complementarity. Our study shows that known mechanisms underpinning predator diversity effects on both functioning and stability can easily be extended to link food webs to ecosystem functioning.

Description: Ecology, Ahead of Print. Understanding the way in which species are associated in communities is a fundamental question in ecology. Yet there remains a tension between communities as highly structured units or as coincidental collections of individualistic species. We explore these ideas using a new statistical approach that clusters species based on their environmental response- a species archetype, rather than clustering sites based on their species composition. We find that there are groups of species, which are consistently highly correlated, but that these groups are not unique to any set of locations and overlap spatially. The species present at a single site are a realisation of species from the (multiple) archetype groups that are likely to be present at that location based on their response to the environment.

Description: Ecology, Ahead of Print. Invasive alien predators can impose strong selection on native prey populations and induce rapid evolutionary change in the invaded communities. However, studies on evolutionary responses to invasive predators are often complicated by the lack of replicate populations differing in coexistence time with the predator, which would allow determining how prey traits change during the invasion. The red swamp crayfish Procambarus clarkii has invaded many freshwater areas worldwide, with negative impacts for native fauna. Here, we examined how coexistence time shapes antipredator responses of the Iberian waterfrog (Pelophylax perezi) to the invasive crayfish by raising tadpoles from five populations differing in historical exposure to P. clarkii (30 years, 20 years or no coexistence). Tadpoles from non-invaded populations responded to the presence of P. clarkii with behavioral plasticity (reduced activity), whereas long-term invaded populations showed canalized antipredator behavior (constant low activity level). Tadpoles from one of the long-term invaded populations responded to the crayfish with inducible morphological defenses (deeper tails), reflecting the use of both constitutive and inducible antipredator defenses against the exotic predator by this population. Our results suggest that, while naive P. perezi populations responded behaviorally to P. clarkii, the strong predation pressure imposed by the crayfish has induced the evolution of qualitatively different antipredator defenses in populations with longer coexistence time. These responses suggest that strong selection by invasive predators may drive rapid evolutionary change in invaded communities. Examining responses of prey species to biological invasions using multiple populations will help us better forecast the impact of invasive predators in natural communities.

Description: Ecology, Ahead of Print. Imbalances in phosphorus (P) intake relative to demand negatively affect animal growth, but their consequences are less understood for vertebrates, in which bone represents a significant and potentially flexible pool of P. Flexibility in body-P content could buffer vertebrates from the effects of imbalances between P intake and demand, reducing the likelihood of a sharp stoichiometric "knife-edge" in the relationship between growth rate and diet-P level. We conducted a meta-analysis of published aquaculture experiments that tested effects of diet %P on fish growth rate (49 studies, 28 species) and body-P content (27 of the studies in the main data set, 20 species). Our meta-analysis revealed significant P limitation of growth, as well as significant negative effects of excess P on growth rate. Diet-P thresholds for these effects occurred at ecologically relevant levels (mean ± SD optimal diet-P of 1.2 ± 0.45% under experimental conditions of high ration). Finally, the analysis also suggested a pattern of relatively shallow relationships between growth rate and diet-P level, coupled with surprisingly flexible body-P content in fishes. This result is consistent with fish using flexible body-P content (presumably mediated through bone P) to buffer imbalances between P intake and demand. Together, our results provide evidence for a relatively "dull" stoichiometric "knife-edge" in fishes, driven in part by flexible body-P content.

Description: Ecology, Ahead of Print. Community ecologists use functional groups based on the rarely tested assumption that within-group responses to ecological processes are similar and thus members are functionally equivalent. However, recent research suggests functional equivalency may break down with human impacts. We tested the equivalency assumption and model predictions of responses to simulated human alterations in nutrients and large herbivores for two models of coral reef algae, the Relative Dominance Model (RDM) and the Functional Group Model (FGM). Results of both mesocosm and field experiments using assembled communities were compared to model predictions and within- and between-group variability were assessed. Both models' predictions of group response to herbivory matched experimental outcomes, but only the RDM predicted response to nutrients. However, within-group variability was dramatic, as the RDM grouped species with opposite responses to herbivory and the FGM grouped species with unique responses to nutrients. These heterogeneous responses resulted in loss of information and masked strong interactions between herbivory and nutrients that were not included in the models. As humans continue to impact major ecological processes in ecosystems globally, we postulate that functional-group models may need to be reformulated to account for shifting baselines.

Description: Ecology, Ahead of Print. Flowering plants often occur in mixed-species groups where interactions between them can occur both pre- and post-pollination. In post-pollination interactions conspecific (CP) and heterospecific pollen (HP) interact on the style and previous work indicates that these interactions, often, but not always, lead to reduced fitness. However, over half of insect-pollinated species display a mixed mating system, where both self and outcross CP could interact with HP, yet no study has evaluated the effects on both types of CP. We present and test hypotheses for the differential effects of HP depending on CP source and timing of HP arrival with a mixed-mating plant, M. guttatus, and one of its HP donors (Helianthus exilis). We found H. exilis pollen reduced tube growth and fertilization success of M. guttatus self pollen to a greater degree than outcross pollen, but only when CP and HP were applied simultaneously. Our results indicate that for mixed-mating plants the fitness consequences of HP receipt can be more detrimental than previously thought. Furthermore, our findings suggest that HP receipt, which can be high in biodiverse areas, has the potential to influence mating system and genetic diversity of the plant populations within them.

Description: Ecology, Ahead of Print. Factors that control tree seedling dynamics are critical determinants of forest diversity. We examined the role of density-dependent mortality and abiotic factors in the differential establishment and survival of tree seedlings at three large mapped forest plots in Indiana, Virginia and Wisconsin, USA. We tested whether seedling densities and seedling survival are related to local biotic and abiotic factors with generalized linear mixed models. Spatial point pattern analyses were utilized to determine if the distribution patterns of seedlings and saplings are consistent with a pattern generated by negative density-dependent mortality with respect to conspecific trees. Initial sampled seedling density for nearly a third of species showed a positive correlation with increasing conspecific basal area indicating dispersal limitation, but few had any association with abiotic variables. By contrast, survival of seedlings over one year significantly declined with increasing conspecific basal area. Point pattern analyses indicated that nearly one third of tree species had significantly over-dispersed point patterns of conspecific seedlings and saplings relative to adult densities; the majority of other species exhibited random spatial arrangements. Our results demonstrate that negative conspecific density-dependent mortality of seedlings could generate the spatial patterns observed at later life stages. By differentially favoring seedlings of other species, this process may contribute to the maintenance of tree diversity in temperate forests, just as others have demonstrated for tropical forests.

Description: Ecology, Ahead of Print. Communities are comprised of individual species that respond to changes in their environment depending in part on their niche requirements. These species comprise the biodiversity of any given community. Common biodiversity metrics such as richness, evenness, and the species abundance distribution are frequently used to describe biodiversity across ecosystems and taxonomic groups. While it is increasingly clear that researchers will need to forecast changes in biodiversity, ecology currently lacks a framework for understanding the natural background variability in biodiversity or how biodiversity patterns will respond to environmental change. We predict that while species populations depend on local ecological mechanisms (e.g., niche processes) and should respond strongly to disturbance, community-level properties that emerge from these species should generally be less sensitive to disturbance because they depend on regional mechanisms (e.g., compensatory dynamics). Using published data from terrestrial animal communities, we show that community-level properties were generally resilient under a suite of artificial and natural manipulations. In contrast, species responded readily to manipulation. Our results suggest that community-level measures are poor indicators of change, perhaps because many systems display strong compensatory dynamics maintaining community-level properties. We suggest that ecologists consider using multiple metrics that measure composition and structure in biodiversity response studies.

Description: Ecology, Ahead of Print. In colonial-breeding species, prebreeders often emigrate temporarily from natal reproductive colonies then subsequently return for one or more years before producing young. Variation in attendance/nonattendance patterns can have implications for subsequent recruitment. We used open robust-design multi-state models and 27 years of encounter data for prebreeding female Weddell seals (Leptonychotes weddellii Lesson) to evaluate hypotheses about (1) the relationships of temporary emigration (TE) probabilities to environmental and population size covariates, (2) motivations for attendance and consequences of nonattendance for subsequent probability of recruitment to the breeding population. TE probabilities were density-dependent (= 0.66, = 0.17) (βBPOP = 0.66, SE = 0.17)and increased when the fast-ice edge was distant from the breeding colonies (βDIST = 0.75, SE = 0.04), and were strongly age- and state-dependent. These results suggest that tradeoffs between potential benefits and costs of colony attendance vary annually and might influence motivation to attend colonies. Recruitment probabilities were greatest for seals that consistently attended colonies in 2 or more years (e.g.,ψage10 = 0.56, sd = 0.17) and lowest for seals that never or inconsistently attended prior to recruitment (e.g., ψage10 = 0.32, sd = 0.15). In colonial-breeding seabirds repeated colony attendance increases subsequent probability of recruitment to the adult breeding population; our results suggest similar implications for a marine mammal and are consistent with the hypothesis that prebreeders were motivated to attend reproductive colonies to gain reproductive skills or perhaps to optimally synchronize estrus through close association with mature breeding females.

Description: Ecology, Ahead of Print. Fertilization via agricultural inputs and nutrient deposition is one of the major threats to global terrestrial plant richness, yet we still do not fully understand the mechanisms by which fertilization decreases plant richness. Tall clonal species have recently been proposed to cause declines in plant species richness by increasing in abundance in response to fertilization and competing strongly with other species. We tested this hypothesis in a fertilization experiment in a low productivity grassland by using a novel experimental manipulation of the presence vs. absence of clonal species and by examining the role of height within these treatments. We found that fertilization decreased species richness more in the presence than absence of clonal species. We also found that only tall species increased in biomass in response to fertilization. In the absence of clonal species, fertilization increased biomass of tall non-clonal species. However, in the presence of clonal species, fertilization decreased tall non-clonal biomass and only tall clonal biomass increased. Fertilization caused almost all short species to be lost in the presence, but not the absence, of clonal species and caused greater declines in the mean and variance of light levels in the presence of clonal species. These results show that the traits of species in a community can determine the magnitude of species loss due to fertilization. The strongly negative effect of tall clonals on species richness in fertilized plots is likely a result of their capacity to decrease light levels to a greater extent and more uniformly than non-clonal species, and thereby drive the exclusion of short species. These results help clarify the mechanisms whereby fertilization decreases grassland plant species richness and suggest that efforts to prevent the loss of species under fertilized conditions may be most effective when they focus on controlling the biomass of tall clonal species.

Description: Ecology, Ahead of Print. Nutrient pollution constitutes a major threat to biodiversity - one whose magnitude is predicted to increase greatly in the near future. While the negative effects of excessive nitrogen and phosphorus loading on local species diversity are widely appreciated, a growing body of evidence indicates that increases in productivity (a correlate of nutrient supply) can also reduce predictability in community composition by driving community divergence and increases in beta diversity (or compositional dissimilarity among communities). Stochastic variation in dispersal history has frequently been cited as a cause of such patterns. However, underlying mechanisms have not received strong experimental scrutiny. I present results of a microcosm experiment testing the effects of enrichment and dispersal mode on zooplankton community structure. I show that beta diversity increases with enrichment but only in the presence of sequential dispersal and variation in dispersal history. Sequential dispersal and enrichment enhanced beta diversity by driving increases in temporal compositional turnover (or beta diversity in time). These results suggest that nutrient enrichment and dispersal may have interactive effects on community organization by facilitating persistent compositional flux and reducing our ability to predict the structure of communities in both space and time.

Description: Ecology, Ahead of Print. Climate change forecasts of more frequent climate extremes suggest that such events will become increasingly important drivers of future ecosystem dynamics and function. Because the rarity and unpredictability of naturally occurring climate extremes limits assessment of their ecological impacts, we experimentally imposed extreme drought and a mid-summer heat wave over two years in a central US grassland. While the ecosystem was resistant to heat waves, it was not resistant to extreme drought, which reduced aboveground net primary productivity (ANPP) below the lowest level measured in this grassland in almost thirty years. This extreme reduction in ecosystem function was a consequence of reduced productivity of both C4 grasses and C3 forbs. However, the dominant forb was negatively impacted by the drought more than the dominant grass, and this led to a reordering of species abundances within the plant community. Although this change in community composition persisted post-drought, ANPP recovered completely the year after drought due to rapid demographic responses by the dominant grass, compensating for loss of the dominant forb. Overall, these results show that an extreme reduction in ecosystem function attributable to climate extremes (e.g., low resistance) does not preclude rapid ecosystem recovery. Given that dominance by a few species is characteristic of most ecosystems, knowledge of the traits of these species and their responses to climate extremes will be key for predicting future ecosystem dynamics and function.

Description: Ecology, Ahead of Print. Thresholds profoundly affect our understanding and management of ecosystem dynamics, but we have yet to develop practical techniques to assess the risk that thresholds will be crossed. Combining ecological knowledge of critical system interdependencies with a large-scale experiment we tested for breaks in the ecosystem interaction network to identify threshold potential in real world ecosystem dynamics. Our experiment on marine sandflats demonstrated that reductions in incident sunlight changed the interaction network between sediment biogeochemical fluxes, productivity and macrofauna. By demonstrating loss of positive feedbacks and changes in the architecture of the network, we provide mechanistic evidence that stressors lead to breakpoints in dynamics, which theory predicts pre-dispose a system to a critical transition.

Description: Ecology, Ahead of Print. Pendulous lichens dominate canopies of boreal forests, with dark Bryoria species in upper versus light Alectoria and Usnea species in lower canopy. These genera offer important ecosystem services like winter forage for reindeer and caribou. The mechanism behind this niche separation is poorly understood. We tested the hypothesis that species-specific sun-screening fungal pigments protect underlying symbiotic algae differently against high light, and thus shape the vertical canopy gradient of epiphytes. Three pale species with the reflecting pigment usnic acid (Alectoria sarmentosa, Usnea dasypoga, U. longissima) and three with dark, absorbing melanins (Bryoria capillaris, B. fremontii, B. fuscescens) were compared. We subjected the lichens to desiccation stress with and without light, and assessed their performance with chlorophyll fluorescence. Desiccation alone only affected U. longissima. By contrast, light in combination with desiccation caused photoinhibitory damage in all species. Usnic lichens were significantly more susceptible to light during desiccation than melanic ones. Thus, melanin is a more efficient light-screening pigment than usnic acid. Thereby, the vertical gradient of pendulous lichens in forest canopies is consistent with a shift in type and functioning of sun-screening pigments, from high-light tolerant Bryoria in the upper to susceptible Alectoria and Usnea in the lower canopy.

Description: Ecology, Ahead of Print. Predicting the effects of climate change on ecological communities requires an understanding of how environmental factors influence both physiological processes and species interactions. Specifically, the net impact of temperature on community structure depends on the relative response of physiological energetic costs (metabolism) and energetic gains (ingestion of resources) that mediate the flow of energy throughout a food web. However, the relative temperature scaling of metabolic and ingestion rates have rarely been measured for multiple species within an ecological assemblage and it is not known how, and to what extent, these relative scaling differences vary among species. To investigate the relative influence of these processes, I measured the temperature scaling of metabolic and ingestion rates for a suite of rocky intertidal species using a multiple regression experimental design. I compared oxygen consumption rates (as a proxy for metabolic rate) and ingestion rates by estimating the temperature scaling parameter of the 'universal temperature dependence' (UTD) model, a theoretical model derived from first principles of biochemical kinetics and allometry. The results show that consumer metabolic rates (energetic costs) tend to be more sensitive to temperature than ingestion rates (energetic gains). Thus, as temperature increases, metabolic rates tend to increase faster relative to ingestion rates, causing the overall energetic efficiencies of these rocky intertidal invertebrates to decline. Metabolic and ingestion rates largely scaled in accordance with the UTD model; however, non-linearity was evident in several cases, particularly at higher temperatures, in which alternative models were more appropriate. There are few studies where multiple rate dependencies are measured on multiple species from the same ecological community. These results indicate that there may be general patterns across species in the temperature scaling of biological rates, with important implications for forecasting temperature effects on ecological communities.

Description: Ecology, Ahead of Print. Metacommunity theory generally predicts that regional dispersal of organisms among local habitat patches should influence spatial patterns of species diversity. In particular, increased dispersal rates are generally expected to increase local (α) diversity, yet homogenize local communities across the region (decreasing β-diversity), resulting in no change in regional (γ) diversity. Although the effect of dispersal on α-diversity has garnered much experimental attention, the influence of dispersal rates on diversity at larger spatial scales (β and γ) is poorly understood. Furthermore, these theoretical predictions are not well tested in the field, where other environmental factors (e.g., habitat size, resource density) likely also influence species diversity. Here, we use a system of freshwater rock pools on Appledore Island, Maine, USA to test the effects of dispersal rate on species diversity in metacommunities. The pools exist in clusters (metacommunities) that experience different levels of dispersal imposed by gulls (Larus spp.), which we show to be frequent passive dispersers of rock-pool invertebrates. Although previous research has suggested that waterbirds may disperse aquatic invertebrates, our study is the first to quantify the rate at which such dispersal occurs and determine its effects on species diversity. In accordance with theory, we found that metacommunities experiencing higher dispersal rates had significantly more homogeneous local communities (reduced β-diversity) and that γ-diversity was not influenced by dispersal rate. Contrary to theoretical predictions, however, α-diversity in the rock pools was not significantly influenced by dispersal. Rather, local diversity was significantly positively related to local habitat size and both α- and γ-diversity were influenced by the physicochemical environment of the pools. These results provide an important field test of metacommunity theory, highlighting how local and regional factors interact to drive patterns of species diversity in metacommunities, and demonstrate that waterbirds are indeed important dispersal vectors for aquatic invertebrates.

Description: Ecology, Ahead of Print. Given the health and economic burden associated with the widespread occurrence of co-infections in human and agricultural animals, understanding how co-infections contribute to host heterogeneity to infection and transmission is critical if we are to assess risk of infection based on host characteristics. Here, we examine whether host heterogeneity to infection leads to similar heterogeneity in transmission in a population of rabbits single and co-infected with two helminths and monitored monthly for eight years. Compared to single infections, co-infected rabbits carried higher Trichostrongylus retortaeformis intensities, longer worms with fewer eggs in utero and shed a similar numbers of parasite eggs. In contrast, the same co-infected rabbits harbored fewer Graphidium strigosum with longer bodies and more eggs in utero, and shed more eggs of this helminth. A positive density-dependent relationship between fecundity and intensity was found for T. retortaeformis but not G. strigosum in co-infected rabbits. Juvenile rabbits contributed to most of the infection and shedding of T. retortaeformis while adult hosts were more important for G. strigosum dynamics of infection and transmission, and this pattern was consistent in single and co-infected individuals. This host-parasite system suggests that we cannot predict pattern of parasite shedding during co-infections based on intensity of infection alone. We suggest that a mismatching between susceptibility and infectiousness should be expected in helminth co-infections and should not be overlooked.

Description: Ecology, Ahead of Print. Large pelagic predators play important roles in oceanic ecosystems and may migrate vast distances to utilize resources in different marine ecoregions. Understanding movement patterns of migratory marine animals is critical for effective management, but often challenging due to the cryptic habitat of pelagic migrators and the difficulty of assessing past movements. Chemical tracers can partially circumvent these challenges by reconstructing recent migration patterns. Pacific bluefin tuna (Thunnus orientalis; PBFT) inhabit the western and eastern Pacific Ocean and are in steep decline due to overfishing. Understanding age-specific eastward trans-Pacific migration patterns can improve management practices but these migratory dynamics remain largely unquantified. Here, we combine a Fukushima-derived radiotracer (134Cs) with bulk tissue- and amino acid-stable isotope analyses of PBFT to distinguish recent migrants from residents of the eastern Pacific Ocean. The proportion of recent migrants to residents decreased in older year classes, though the proportion of older PBFT that recently migrated across the Pacific was greater than previous estimates. This novel toolbox of biogeochemical tracers can be applied to any species that crosses the North Pacific Ocean.

Description: Ecology, Ahead of Print. The emission of volatile monoterpenes from coniferous trees impacts the oxidative state of the troposphere and multi-trophic signaling between plants and animals. Previous laboratory studies have revealed that climate anomalies and herbivory alter the rate of tree monoterpene emissions. However, no studies to date have been conducted to test these relations in situ. We conducted a two-year field experiment at two semi-arid sites dominated by pinyon pine (Pinus edulis) during outbreaks of a specialist herbivore, the southwestern tiger moth (Lophocampa ingens: Arctiidae). We discovered that during the early spring, when herbivory rates were highest, monoterpene emission rates were approximately two to six times higher from undamaged needles on damaged trees, with this increase in emissions due to α-pinene, β-pinene, and camphene at both sites. During mid-summer, emission rates did not differ between previously damaged and undamaged trees at the site on the Western Slope of the Rocky Mountains, but rather tracked changes in the temperature and precipitation regime characteristic of the region. As the mid-summer drought progressed at the Eastern Slope site, emission rates were low but differences between previously damaged and undamaged trees were not statistically significant. Despite no difference in emissions, mid-summer tissue monoterpene concentrations were significantly lower in previously damaged trees at both sites. With the onset of monsoon rains during late summer, emission rates from previously damaged trees increased to levels higher than those of undamaged trees despite the lack of herbivory. We conclude (1) herbivory systemically increases the flux of terpenes to the atmosphere during the spring, (2) drought overrides the effect of past herbivory as the primary control over emissions during the mid-summer, and (3) that a release from drought and the onset of late-summer rains is correlated with a secondary increase in emissions, particularly from herbivore-damaged trees, possibly due to a drought-delayed stimulation of induced monoterpene synthesis and/or increases in stomatal conductance. A greater understanding of the interactive effects of seasonality and herbivory on monoterpene emissions provides much needed information regarding the atmospheric and ecological consequences these compounds will have on semi-arid ecosystems.

Description: Ecology, Ahead of Print. Fires are the major natural disturbance in the boreal forest, and their frequency and intensity will likely increase as the climate warms. Terrestrial nutrients released by fires may be transported to boreal lakes, stimulating increased primary productivity, which may radiate through multiple trophic levels. Using a before-after-control-impact (BACI) design, with pre- and post-fire data from burned and unburned areas, we examined effects of a natural fire across several trophic levels of boreal lakes, from nutrient and chlorophyll levels to macroinvertebrates to waterbirds. Concentrations of total nitrogen and phosphorus were not affected by the fire. Chlorophyll a levels were also unaffected, likely reflecting the stable nutrient concentrations. For aquatic invertebrates, we found that densities of 3 functional feeding groups did not respond to the fire (filterers, gatherers, scrapers), while 2 groups increased (shredders, predators). Amphipods accounted for 98% of shredder numbers, and we hypothesize that fire-mediated habitat changes may have favored their generalist feeding and habitat ecology. This increase in amphipods may have in turn driven increased predator densities, as amphipods were the most numerous invertebrate in our lakes and are commonly taken as prey. Finally, abundance of waterbird young, which feed primarily on aquatic invertebrates, was not affected by the fire. Overall, ecosystems of our study lakes were largely resilient to forest fires, likely due to their high initial nutrient concentrations and small catchment sizes. Moreover, this resilience spanned multiple trophic levels, a significant result for ecologically similar boreal regions, especially given the high potential for increased fires with future climate change.

Description: Ecology, Ahead of Print. The importance of terrestrial-derived organic matter for lake zooplankton communities remains debated, partly because little is known about the basic pathways by which allochthonous carbon is transferred to zooplankton, and whether these vary among the major taxonomic and functional groups. We quantified allochthony of three zooplankton groups (Cladocera, Calanoida and Cyclopoida) across 18 lakes in Québec, spanning broad gradients of dissolved organic matter (DOM) and lake trophy, using a multi-isotope (δ2H + δ13C), multi-source (terrestrial, phytoplanktonic, benthic) approach. All three zooplankton groups had significant levels of allochthony, but differed greatly in their respective patterns across lakes. Allochthony in Calanoida and Cyclopoida was linked to detrital food chains based on particulate organic matter (POM) and on DOM, respectively, whereas in Cladocera it appeared related to both pathways; not surprisingly this latter group had the highest mean allochthony (0.31; compared to 0.18 in Cyclopoida and 0.16 in Calanoida). This study highlights the complexity of the pathways of delivery and transfer of terrestrial organic matter in freshwaters, and underscores the role that microbial food webs play in this transfer.

Description: Ecology, Ahead of Print. Consumer growth can be affected by imbalances between the nutrient content of the consumer and its food resource. Although ontogenetic-driven changes in animal composition are well-documented, their potential consequences for organism's sensitivity to food quality constraints have remained elusive. Here we show that the potential growth response of the copepod Mixodiaptomus laciniatus (as %RNA and RNA:DNA ratio) to the natural gradient of seston carbon (C):nutrient ratio is unimodal and stage-specific. Solution of the equation given by the first derivative function provided the optimum C:nutrient ratio for maximum stage-specific growth, which increased during ontogeny. The peakedness of the function indicated that animal vulnerability to suboptimal food quality decreased as juveniles reached adulthood. Consistent with these results, a field-experiment demonstrated that potential consumer growth responded to variations in seston C:phosphorus ratio and that early-life stages were particularly vulnerable to suboptimal food quality.

Description: Ecology, Ahead of Print. Soils host diverse communities of interacting microbes and the nature of interspecific interactions is increasingly recognised to affect ecosystem-level processes. Antagonistic interactions between bacteria and fungi are of particular relevance for soil functioning. A number of soil bacteria produce secondary metabolites that inhibit eukaryotic growth. Antibiosis may be stimulated in the presence of competing bacteria, and we tested if biodiversity within bacterial communities affects their antagonistic activity against fungi and fungal-like species. We set up Pseudomonas fluorescens communities of increasing diversity and measured the production of the broad spectrum antifungal compound 2,4-DAPG and their antagonistic activity against different eukaryotes. Diversity increased DAPG concentration and antifungal activity, an effect due to a combination of identity and interactions between species. Our results indicate that investment of pseudomonads into broad spectrum anti-eukaryotic traits is determined by both community composition and diversity and this provides new avenues to understand interactions between bacterial and fungal communities.

Description: Ecology, Ahead of Print. In some mutualisms cooperation in symbionts is promoted by hosts sanctioning 'cheats' who obtain benefits but fail to reciprocate. In fig-wasp mutualisms agaonid wasps pollinate the trees (Ficus spp.) but are also exploitative by using some flowers as larval food. Ficus can sanction cheats that fail to pollinate by aborting some un-pollinated figs. However, in those un-pollinated figs retained by trees cheats successfully reproduce. When this occurs wasp broods are reduced, suggesting sanctions increase offspring mortality within un-pollinated figs. We investigated sanction mechanisms of abortion and larval mortality against wasp cheats in the monoecious Ficus racemosa, by introducing into figs 1,3,5,7 or 9 female wasps (foundresses) that were either all pollen-laden (P+) or all pollen-free (P-) The abortion rates of P- figs were highest (~60%) when single foundresses were present. Abortion declined with increased foundresses and ceased with seven or more wasps present, irrespective of pollination. In un-aborted figs, wasp fitness (mean offspring per foundress) declined as foundress number increased, especially in P- figs. Reduced broods in P- figs resulted from increased larval mortality of female offspring as foundress number increased, resulting in more male biased sex ratios. Overall sanctions estimated from both abortion rates and reduced offspring production strengthened as the number of cheats increased. In a second experiment we decoupled pollination from wasp oviposition by introducing one pollen-free foundress followed 24h later by seven pollen-laden ovipositor-excised wasps. Compared with P+ and P- single foundress figs, delayed pollination resulted in intermediate larval mortality and wasp fitness, which concurred with patterns of female offspring production. We conclude that fig abortion reflects both pollinator numbers and pollen presence. Sanctions within P- figs initiate soon after oviposition and discriminate against female offspring, thus reducing the benefits to cheats from adaptively biasing their offspring sex ratios. We suggest that costs to cheats via these discriminative sanctions are likely to promote stability in this mutualism.

Description: Ecology, Ahead of Print. Plants, bacteria and fungi produce essential amino acids (EAAs) with distinctive patterns of δ13C values that can be used as naturally occurring fingerprints of biosynthetic origin of EAAs in a food web. Because animals cannot synthesize EAAs and must obtain them from food, their tissues reflect δ13CEAA patterns found in diet, but it is not known how microbes responsible for hindgut fermentation in some herbivores influence the δ13C values of EAAs in their host's tissues. We examined whether distinctive δ13C fingerprints of hindgut flora are evident in the tissues of green turtles (Chelonia mydas), which are known to be facultative hindgut fermenters. We determined δ13CEAA values in tissues of green turtles foraging herbivorously in neritic habitats of Hawaii and compared them with those from green, olive ridley and loggerhead turtles foraging carnivorously in oceanic environments of the central and south-east Pacific Ocean. Results of multivariate statistical analysis revealed two distinct groups that could be distinguished based on unique δ13CEAA patterns. A three-end member predictive linear discriminant model indicated that δ13CEAA fingerprints existed in the tissues of carnivorous turtles that resembled patterns found in microalgae, which form the base of an oceanic food web, whereas herbivorous turtles derive EAAs from a bacterial or seagrass source. This study demonstrates the capacity for δ13C fingerprinting to establish the biosynthetic origin of EAAs in higher consumers, and that marine turtles foraging on macroalgal diets appear to receive nutritional supplementation from bacterial symbionts in their digestive system.

Description: Ecology, Ahead of Print. A longstanding concept in community ecology is that closely related species compete more strongly than distant relatives. Ecologists have invoked this 'limiting similarity hypothesis' to explain patterns in the structure and function of biological communities and to inform conservation, restoration, and invasive species management. However, few studies have empirically tested the validity of the limiting similarity hypothesis. Here we report the results of a laboratory microcosm experiment in which we used a model system of 23 common, co-occurring North American freshwater green algae to quantify the strength of 216 pair-wise species' interactions (the difference in population density when grown alone vs. in the presence of another species) along a manipulated gradient of evolutionary relatedness (phylogenetic distance, as the sum of branch lengths separating species on a molecular phylogeny). Interspecific interactions varied widely in these bicultures of phytoplankton, ranging from strong competition (relative yield in poly:monoculture 〈 〈 1) to moderate facilitation (relative yield 〉 1). Yet, we found no evidence that the strength of species' interactions was influenced by their evolutionary relatedness. There was no relationship between phylogenetic distance and the average, minimum (inferior competitor), nor maximum (superior competitor) interaction strength across all biculture communities (respectively, P = 0.19; P = 0.17, P = 0.14, N = 428). When we examined each individual species, only 17% of individual species' interactions strengths varied as a function of phylogenetic distance, and none of these relationships remained significant after Bonferoni correction for multiple tests (N = 23). Lastly, when we grouped interactions into five qualitatively different types, the frequency of these types was not related to phylogenetic distance among species pairs (F = 1.63, P = 0.15). Our empirical study adds to several others that suggest the biological underpinnings of competition may not be evolutionarily conserved, and thus, ecologists may need to re-evaluate the previously assumed generality of the limiting similarity hypothesis.

Description: Ecology, Ahead of Print. Environmental pulses, or sudden, marked changes to the conditions within an ecosystem, can be important drivers of resource availability in many systems. In this study, we investigated the effect of tidal pulsing on the fluxes of nitrous oxide (N2O), a powerful greenhouse gas, from a marine intertidal mudflat on the north shore of Massachusetts, USA. We found these tidal flat sediments to be a sink of N2O at low tide with an average uptake rate of -6.7 ± 2 μmol m-2 h-1. Further, this N2O sink increased the longer sediments were tidally exposed. These field measurements, in conjunction with laboratory nutrient additions, revealed that this flux appears to be driven primarily by sediment denitrification. Additionally, N2O uptake was most responsive to DIN+DIP addition suggesting that the N2O consumption process may be P limited. Furthermore, nutrient addition experiments suggest that dissimilatory nitrate reduction to ammonium (DNRA) releases N2O at the highest levels of nitrate fertilization. Our findings indicate that tidal flats are important sinks of N2O, potentially capable of offsetting the release of this potent greenhouse gas by other, nearby ecosystems.

Description: Ecology, Ahead of Print. Fear of predation produces large effects on prey population dynamics through indirect risk effects that can cause even greater impacts than direct predation mortality. As yet, there is no general theoretical framework for predicting when and how these population risk effects will arise in specific prey populations, meaning there is often little consideration given to the key role predator risk effects can play in understanding conservation and wildlife management challenges. Here, we propose population predator risk effects can be predicted through an extension of individual risk trade-off theory and show for the first time that this is the case in a wild vertebrate system. Specifically, we demonstrate that the timing (in specific months of the year), occurrence (at low food availability), cause (reduction in individual energy reserves) and type (starvation mortality) of a population level predator risk effect can be successfully predicted from individual responses using a widely applicable theoretical framework (individual based risk trade-off theory). Our results suggest individually-based risk-trade-off frameworks could allow a wide range of population level predator risk effects to be predicted from existing ecological theory, which would enable risk effects to be more routinely integrated into consideration of population processes and in applied situations such as conservation.

Description: Ecology, Ahead of Print. The timing of fine root production and turnover strongly influences both the seasonal potential for soil resource acquisition among competing root systems and the plant fluxes of root carbon into soil pools. However, basic patterns and variability in the rates and timing or fine root production and turnover are generally unknown among perennial plants species. We address this shortfall using a heuristic model relating root phenology to turnover together with three-years of minirhizotron observations of root dynamics in 12 temperate tree species grown in a common garden. We specifically investigated how the amount and the timing of root production differ among species and how they impact estimates of fine root turnover. Across the 12 species there was wide variation in the timing of root production with some species producing a single root flush in early summer and others producing roots either more uniformly over the growing season or in multiple pulses. Additionally, the pattern and timing of root production appeared to be consistent across years for some species but varied in others. Root turnover rate was related to total root production (P 〈 0.001) as species with greater root production typically had faster root turnover rates. We also found that within species, annual root production varied up to three-fold between years which led to large interannual differences in turnover rate. Results from the heuristic model indicated that shifting the pattern or timing of root production can impact estimates of root turnover rates for root populations with lifespans less than one year while estimates of root turnover rate for longer lived roots were unaffected by changes in root phenology. Overall, we suggest that more detailed observations of root phenology and production will improve fidelity of root turnover estimates. Future efforts should link patterns of root phenology and production with whole plant life history traits and variation in annual and seasonal climate.

Description: Ecology, Ahead of Print. The movements of some long-distance migrants are driven by innate compass headings that they follow on their first migrations (e.g., some birds and insects), whilst the movements of other first time migrants are learnt by following more experienced conspecifics (e.g., baleen whales). However, the overall roles of innate, learnt and social behaviors in driving migration goals in many taxa are poorly understood. To look for evidence of whether migration routes are innate or learnt for sea turtles, here for 42 sites around the World we compare the migration routes of 〉 400 satellite adults of multiple species of sea turtle with c.45,000 Lagrangian hatchling turtle drift scenarios. In so doing, we show that the migration routes of adult turtles are strongly related to hatchling drift patterns, implying that adult migration goals are learnt through their past experiences dispersing with ocean currents. The diverse migration destinations of adults consistently reflected the diversity in sites they would have encountered as drifting hatchlings. Our findings reveal how a simple mechanism, juvenile passive drift, can explain the ontogeny of some of the longest migrations in the animal kingdom and ensure that adults find suitable foraging sites.

Description: Ecology, Ahead of Print. Taylor's law, one of the most widely accepted generalizations in ecology, states that the variance of a population abundance time series scales as a power-law of its mean. Here we re-examine this law and the empirical evidence presented in support of it. Specifically we show that the exponent generally depends on the length of the time series and its value reflects the combined effect of many underlying mechanisms. Moreover, sampling errors alone, when presented on a double logarithmic scale, are sufficient to produce an apparent power-law. This raises questions regarding the usefulness of Taylor's law for understanding ecological processes. As an alternative approach, we focus on short-term fluctuations and derive a generic null model for the variance-mean ratio in population time-series from a demographic model that incorporates the combined effects of demographic and environmental stochasticity. After comparing the predictions of the proposed null model with the fluctuations observed in empirical datasets, we suggest an alternative expression for fluctuation scaling in population time series. Analyzing population fluctuations as we have proposed here may provide new applied (e.g., estimation of species persistence times) and theoretical (e.g., the neutral theory of biodiversity) insights that can be derived from more generally available short-term monitoring data.

Description: Ecology, Ahead of Print. Species exist within communities of other interacting species, so an exogenous force that directly affects one species can indirectly affect all other members of the community. In the case of climate change, many species may be affected directly and subsequently initiate numerous indirect effects that propagate throughout the community. Therefore, the net effect of climate change on any one species is a function of the direct and indirect effects. We investigated the direct and indirect effects of climate warming on corn leaf aphids, a pest of corn and other grasses, by performing an experimental manipulation of temperature, predators, and two common aphid-tending ants. Although warming had a positive direct effect on aphid population growth rate, warming reduced aphid abundance when ants and predators were present. This occurred because winter ants, which aggressively defend aphids from predators under control temperatures, were less aggressive towards predators and less abundant when temperatures were increased. In contrast, warming increased the abundance of cornfield ants, but they did not protect aphids from predators with the same vigor as winter ants. Thus, warming broke down the ant-aphid mutualism and counter-intuitively reduced the abundance of this agricultural pest.

Description: Ecology, Ahead of Print. Interactions between plants can have strong effects on community structure and function. Variability in the morphological, developmental, physiological and biochemical traits of plants can influence the outcome of plant interactions and thus have important ecological consequences. However, the ecological ramifications of trait variability in plants are poorly understood and have rarely been tested in the field. We experimentally tested the effects of morphological variation in root architecture of Quercus douglasii trees in the field on interactions between understory plants and community composition. Our results indicate that variability among Q. douglasii tree root systems initiates a striking reversal in the competitive effects of a dominant understory grass species on a less common species. Trees with a deep-rooted morphology facilitated exotic annual grasses and these annual grasses in turn competitively excluded the native perennial bunchgrass, Stipa pulchra. In contrast, Q. douglasii trees with shallow-rooted morphologies directly suppressed the growth of exotic annual grasses and indirectly released S. pulchra individuals from competition with these annual grasses. Morphological variation in the root architecture of Q. douglasii created substantial conditionality in the outcomes of competition among species which enhanced the potential for indirect interactions to sustain coexistence and increase community diversity.

Description: Ecology, Ahead of Print. Hurricane winds can have large impacts on forest structure and dynamics. To date, most evaluations of hurricane impacts have focused on short-term responses after a hurricane, often lack pre-hurricane measurements, and miss responses occurring over longer time scales. Here we use a long-term dataset (1974-2009, 35 years) of tree stems (〉 3 cm in diameter at 1.3 m) in four sites (0.35 ha in total) in montane rain forest (c.1600 m) in Jamaica to investigate the patterns of crown damage in individual stems by Hurricane Gilbert in 1988, and how subsequent growth and mortality were affected by hurricane damage, sprouting, and the incidence of multiple stems. Topographical position on a mountain ridge was the best predictor of crown damage, followed by crown size and species identity. The average diameter growth rate of stems that survived the hurricane was greater than that pre-hurricane for the whole 21 year post-hurricane period. Growth of stems with damaged crowns increased less than those with undamaged crowns; differences in growth rate between damaged and undamaged trees disappeared after eleven years. Hurricane-damaged stems had 2 to 8 times higher mortality than undamaged stems for up to 16 years post hurricane. Many stems sprouted shortly after the hurricane, but few sprouts managed to establish (grow to 〉 3 cm diameter at breast height). However, sprouting and multi-stemming were associated with reduced mortality rate, particularly in damaged trees. From an initial population of 1670 stems in 1974, 54% were still alive in 2009 (21 years after the hurricane). We conclude that despite the high frequency of hurricane damage to tree crowns and the subsequent increased mortality rate in this hurricane-prone tropical montane forest, many stems will be hit and recover from several hurricanes in their lifetime.

Description: Ecology, Ahead of Print. The Tibetan Plateau (TP) is experiencing high rates of climatic change. We present a novel combined mechanistic-bioclimatic modeling approach to determine (i) how changes in precipitation and temperature on the TP may impact net primary production (NPP) in four major biomes (forest, shrub, grass, desert); and (ii) if there exists a maximum rain use efficiency (RUEMAX) that represents a "boundary that constrain(s) site-level productivity and efficiency" (Huxman et al. 2004). We used a daily mechanistic ecosystem model to generate 40-y outputs using observed climatic data for scenarios of (i) decreased precipitation (25 to 100%); (ii) increased air temperature (1 to 6°C); (iii) simultaneous changes in both precipitation ( ± 50%, ± 25%) and air temperature (+1 to +6°C); and (iv) increased interannual variability (IAV) of precipitation (+1σ to +3σ, with fixed means). We fitted model output from these scenarios to Huxman et al.'s RUEMAX bioclimatic model, NPP = α +RUE•PPT (where α = intercept, RUE is rain use efficiency and PPT is annual precipitation). Based on these analyses we conclude that: (i) there is strong support (when not explicit, then trend-wise) for Huxman et al.'s assertion that biomes converge to a common RUEMAX during the driest years at a site, thus representing the boundary for highest rain use efficiency; (ii) the interactive effects of simultaneously decreasing precipitation and increasing temperature on NPP for the TP is smaller than might be expected from additive, single-factor changes in these drivers; and (iii) that increasing IAV of precipitation may ultimately have a larger impact on biomes of the Tibetan Plateau than changing amounts of rainfall and air temperature alone.

Description: Ecology, Ahead of Print. Birds and their population dynamics are often used to understand and document anthropogenic effects on biodiversity. Nest success is a critical component of the breeding output of birds in different environments; but to obtain the complete picture of how bird populations respond to perturbations, we also need an estimate of nest abundance or density. The problem is that raw counts generally underestimate actual nest numbers because detection is imperfect and because some nests may fail or fledge before being subjected to detection efforts. Here we develop a state-space superpopulation capture-recapture approach in which inference about detection probability is based on the age at first detection, as opposed to the sequence of re-detections in standard capture-recapture models. We apply the method to ducks in which 1) the age of the nests and their initiation dates can be determined upon detection and 2) the duration of the different stages of the breeding cycle is a priori known. We fit three model variants with or without assumptions about the phenology of nest initiation dates, and use simulations to evaluate the performance of the approach in challenging situations. In an application to blue-winged teal Anas discors breeding at study sites in North and South Dakota, USA, nesting stage (egg-laying or incubation) markedly influenced nest survival and detection probabilities. Two individual covariates (one binary covariate: presence of grazing cattle at the nest site, and one continuous covariate: Robel index of vegetation) had only weak effects. We estimated that 5-10% of the total number of nests were available for detection but missed by field crews. An additional 6-15% were never available for detection. These proportions are expected to be larger in less intense, more typical sampling designs. User-friendly software nestAbund is provided to assist users in implementing the method.

Description: Ecology, Ahead of Print. What determines the seasonal and interannual variation of growth rates in trees in a tropical forest? We explore this question with a novel four-year high temporal resolution dataset of carbon allocation from two forest plots in the Bolivian Amazon. The forests show strong seasonal variation in tree wood growth rates which are largely explained by shifts in carbon allocation, and not by shifts in total productivity. At the deeper soil plot, there was a clear seasonal trade-off between wood and canopy NPP, while the shallower soils plot showed a contrasting seasonal trade-off between wood and fine roots. Although a strong 2010 drought reduced photosynthesis, NPP remained constant and increased in the six month period following the drought, which indicates usage of significant non-structural carbohydrate stores. Following the drought, carbon allocation increased initially towards the canopy, and then in the following year, allocation increased towards fine root production. Had we only measured woody growth at these sites and inferred total NPP, we would have misinterpreted both the seasonal and interannual responses. In many tropical forest ecosystems, we propose that changing tree growth rates are more likely to reflect shifts in allocation rather than changes in overall productivity. Only a whole NPP allocation perspective can correctly interpret the relationship between changes in growth and changes in productivity.

Description: Ecology, Ahead of Print. Dispersal affects processes as diverse as habitat selection, population growth and gene flow. Inference about dispersal and its variation is thus crucial for assessing population and evolutionary dynamics. Two approaches are generally used to estimate dispersal in free-ranging animals. First, multisite capture-recapture models estimate movement rates among sites while accounting for survival and detection probabilities. This approach is however limited in the number of sites that can be considered. Second, diffusion models estimate movements within discrete habitat using a diffusion coefficient resulting in a continuous processing of space. However, this approach has been rarely used because of its mathematical and implementation complexity. Here, we develop a multievent capture-recapture approach that circumvents the issue of too many sites while being relatively simple to be implemented in existing software. Moreover, this new approach allows quantifying memory effects whereby the decision of dispersing or not on a given year impacts on the survival or dispersal likelihood of the following year. We illustrate our approach using a long-term dataset on the breeding ecology of a declining passerine in southern Québec, Canada, the Tree swallow (Tachycineta bicolor).

Description: Ecology, Ahead of Print. Fungal plant pathogens are common in natural communities where they affect plant physiology, plant survival and biomass production. Conversely, pathogen transmission and infection may be regulated by plant-community characteristics such as plant-species diversity and functional composition that favor pathogen diversity through increases in host diversity while simultaneously reducing pathogen infection via increased variability in host density and spatial heterogeneity. Therefore, a comprehensive understanding of multi-host-multi-pathogen interactions is of high significance in the context of biodiversity-ecosystem functioning. We investigated the relationship between plant diversity and aboveground obligate parasitic fungal pathogen ("pathogens" hereafter) diversity and infection in grasslands of a long-term, large-scale biodiversity experiment with varying plant-species (1-60 species) and plant functional group diversity (1-4 groups). To estimate pathogen infection of the plant communities, we visually assessed pathogen-group presence (i.e., rusts, powdery mildews, downy mildews, smuts, and leaf-spot diseases) and overall infection levels (combining incidence and severity of each pathogen group) in 82 experimental plots on all aboveground organs of all plant species per plot during four surveys in 2006. Pathogen diversity, assessed as the cumulative number of pathogen groups on all plant species per plot, increased log-linearly with plant-species diversity. However, pathogen incidence and severity and hence overall infection decreased with increasing plant-species diversity. In addition, co-infection of plant individuals by two or more pathogen groups was less likely with increasing plant-community diversity. We conclude that plant-community diversity promotes pathogen-community diversity while at the same time reducing pathogen infection-levels of plant individuals.