SEARCH · Search bioRxiv

Results for “Ecology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources

bioRxiv2016

Eco-evolutionary dynamics of social dilemmas

Social dilemmas are an integral part of social interactions. Cooperative actions, ranging from secreting extra-cellular products in microbial populations to donating blood in humans, are costly to the actor and hence create an incentive to shirk and avoid the costs. Nevertheless, cooperation is ubiquitous in nature. Both costs and benefits often depend non-linearly on the number and types of individuals involved-as captured by idioms such as too many cooks spoil the broth where additional contributions are discounted, or two heads are better than one where cooperators synergistically enhance the group benefit. Interaction group sizes may depend on the size of the population and hence on ecological processes. This results in feedback mechanisms between ecological and evolutionary processes, which jointly affect and determine the evolutionary trajectory. Only recently combined eco-evolutionary processes became experimentally tractable in microbial social dilemmas. Here we analyse the evolutionary dynamics of non-linear social dilemmas in settings where the population fluctuates in size and the environment changes over time. In particular, cooperation is often supported and maintained at high densities through ecological fluctuations. Moreover, we find that the combination of the two processes routinely reveals highly complex dynamics, which suggests common occurrence in nature.

Evolutionary Biology↗

bioRxiv2016

Evolution of simple multicellularity increases environmental complexity

Multicellularity--the integration of previously autonomous cells into a new, more complex organism--is one of the major transitions in evolution. Multicellularity changed evolutionary possibilities and facilitated the evolution of increased complexity. Transitions to multicellularity are associated with rapid diversification and increased ecological opportunity but the potential mechanisms are not well understood. In this paper we explore the ecological mechanisms of multicellular diversification during experimental evolution of the brewers yeast, Saccharomyces cerevisiae. The evolution from single cells into multicellular clusters modifies the structure of the environment, changing the fluid dynamics and creating novel ecological opportunities. This study demonstrates that even in simple conditions, incipient multicellularity readily changes the environment, facilitating the origin and maintenance of diversity.

Evolutionary Biology↗

bioRxiv2016

Modeling time-series data from microbial communities

As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (e.g. skin, soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open, thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but given the big data nature of these studies, there are currently no methods capable of utilizing the breadth of the data to infer ecological interactions from these longitudinal data. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that 1) takes advantage of the fact that the data are time series; 2) constrains estimates to allow for the possibility of many more interactions than data; and 3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

Microbiology↗

bioRxiv2016

Intra- and inter-specific variations of gene expression levels in yeast are largely neutral

It is commonly, although not universally, accepted that most intra- and inter-specific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only [~]0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra- and inter-specific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution.

evolutionary biology↗

bioRxiv2016

VIRUS-HOST INFECTION DYNAMICS OF MARINE SINGLE-CELLED EUKARYOTES RESOLVED FROM METATRANSCRIPTOMICS

Metatranscriptomics has emerged as a tool in microbial ecology that can resolve the functional landscape of both prokaryotes and eukaryotes within a community. In this study, we extend the potential of metatranscriptomics to probe active virus infections and virus-host relationships in marine systems. Polyadenylation-selected RNA-seq data were examined from microbial communities in two productive marine environments: a brown tide bloom event dominated by Aureococcus anophagefferens in Quantuck Bay, NY, and a diatom-dominated plankton community in Narragansett Bay, RI. Active infections by diverse giant viruses (NCLDVs) of algal and non-algal hosts were found at both sites. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) were observed during both the peak and decline of the bloom. Bloom decline was also accompanied by increased activity for viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution revealed active NCLDVs with both boom-and-bust as well as steady-state infection-like ecologies. Statistical co-occurrence examinations of the dsDNA, ssRNA and dsRNA markers within the data revealed a broad spectrum of statistically strong and significant virus-host relationships that included both known as well as novel interactions. Our approach offers a method for screening the diversity and dynamics of active viral infections in natural systems and develops links between viruses and their potential hosts in situ.\n\nSignificanceViruses are important partners in ecosystem scale ecology, yet their study to date is primarily limited to single virus-host infection models in the laboratory or limited to \"potential-actions\" derived from metagenomics analyses. Using metatranscriptomic sequences from polyadenylated-RNA selected samples, we have simultaneously captured information regarding eukaryotic diversity and active infection by viruses with dsDNA genomes, resulting in a statistical opportunity to predict \"who is infecting whom\". This approach further provides concurrent insight regarding viruses with ssRNA and dsRNA genomes, capturing dynamics for the communities of viruses infecting single-celled eukaryotes. Given the central role of these plankton in global scale processes, our efforts result in a transformational step-forward regarding the study of in situ virus-host interactions.

microbiology↗

bioRxiv2016

Cleanliness in context: reconciling hygiene with a modern microbial perspective

The concept of hygiene is rooted in the relationship between cleanliness and the maintenance of good health. Since the widespread acceptance of the germ theory of disease, hygiene has become increasingly conflated with that of sterilization. Recent research on microbial ecology is demonstrating that humans have intimate and evolutionarily significant relationships with a diverse assemblage of microorganisms (our microbiota). Human skin is home to a diverse, skin habitat specific community of microorganisms; this includes members that exist across the ecological spectrum from pathogen through commensal to mutualist. Most evidence suggests that the skin microbiota is likely of direct benefit to the host, and only rarely exhibits pathogenicity. This complex ecological context suggests that the conception of hygiene as a unilateral reduction or removal of microbes has outlived its usefulness. As such, we suggest the explicit definition of hygiene as those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease. To examine the implications of this definition, we review the literature related to hand drying as an aspect of hand hygienic practice. Research on hand drying generally focuses on hygienic efficacy, a concept not typically defined explicitly, but nearly always including alterations to bulk microbial load. The corresponding literature is differentiable into two divisions: research supporting the use of forced air dryers, which typically includes effectiveness of drying as an aspect of hygienic efficacy; and research supporting the use of paper towels, which typically includes risk of aerosolized spread of microbes from hands as an aspect of hygienic efficacy. Utilizing a definition of hygiene that explicitly relies on reduction in disease spread rather than alterations to bulk microbial load would address concerns raised on both sides of the debate. Future research should take advantage of cultivation-independent techniques, working to bridge the gap between the two existing divisions of research by using health outcomes (such as the spread of disease) as dependent variables, taking into account the microbial community context of the skin microbiota, and focusing on understanding the relative contribution of bioaerosols and residual moisture to the risk of disease transmission.

microbiology↗

bioRxiv2017

Targeted sequencing of venom genes from cone snail genomes reveals coupling between dietary breadth and conotoxin diversity

Although venomous taxa provide an attractive system to study the genetic basis of adaptation and speciation, the slow pace of toxin gene discovery through traditional laboratory techniques (e.g., cDNA cloning) have limited their utility in the study of ecology and evolution. Here, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and non-toxin loci from the genomes of 32 species of cone snails (family, Conidae), a hyper diverse group of carnivorous marine gastropods that capture their prey using a cocktail of neurotoxic proteins (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species sequenced in this study with high confidence (> 100X coverage). We found that conotoxin gene superfamilies are composed of 1-6 exons and adjacent noncoding regions are not enriched for simple repetitive elements. Additionally, we provided further evidence for several genetic factors shaping venom composition in cone snails, including positive selection, extensive gene turnover, expression regulation, and potentially, presence-absence variation. Using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin gene superfamily size evolution, dietary breadth was positively correlated with total conotoxin gene diversity. These results continue to emphasize the importance of dietary breadth in shaping venom evolution, an underappreciated ecological correlate in venom biology. Finally, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification.

evolutionary biology↗

bioRxiv2017

Temporal fitness fluctuations in experimental Arabidopsis thaliana populations

Understanding the genetics of lifetime fitness is crucial to understand a species ecological preferences and ultimately predict its ability to cope with novel environmental conditions. Yet, there is a dearth of information regarding the impact of the ecological variance experienced by natural populations on expressed phenotypic and fitness differences. Here, we follow the natural dynamics of experimental A. thaliana populations over 5 successive plantings whose timing was determined by the natural progression of the plants life cycle and disentangle the environmental and genetic factors that drive plant ecological performance at a given locality. We show that, at the intermediate latitude where the experiment was conducted, a given genotype can experience different life cycles across successive seasons. Lifetime fitness across these seasons varied strongly, with a fall planting yielding 36-fold higher fitness compared to a spring planting. In addition, the actual life-stage at which plant overwinter oscillated across years, depending on the timing of the end of the summer season. We observed a rare but severe fitness differential after inadequate early flowering in one of the five planting. Substrate variation played a comparatively minor role, but also contributed to modulate the magnitude of fitness differentials between genotypes. Finally, reciprocal introgressions on chromosome 4 demonstrated that the fitness effect of a specific chromosomal region is strongly contingent on micro-geographic and seasonal fluctuations. Our study contributes to emphasize the extent to which the fitness impact of phenotypic traits and the genes that encode them in the genome can fluctuate. Experiments aiming at dissecting the molecular basis of local adaptation must apprehend the complexity introduced by temporal fluctuations because they massively affect the expression of phenotype and fitness differences.

evolutionary biology↗

bioRxiv2017

General Environmental Heterogeneity As The Explanation Of Sexuality? Comparative Study Shows That Ancient Asexual Taxa Are Associated With Both Biotically And Abiotically Homogeneous Environments

Ecological theories of sexual reproduction assume that sexuality is advantageous in certain conditions, for example, in biotically or abiotically more heterogeneous environments. Such theories thus could be tested by comparative studies. However, the published results of these studies are rather unconvincing. Here we present the results of a new comparative study based solely on the ancient asexual clades. The association with biotically or abiotically homogeneous environments in these asexual clades was compared with the same association in their sister, or closely related, sexual clades. Using the conservative definition of ancient asexuals (i.e. age > 1 million years), we found six pairs for which relevant ecological data are available. The difference between the homogeneity type of environment associated with the sexual and asexual species was then compared in an exact binomial test. Based on available literature, the results showed that the vast majority of ancient asexual clades tend to be associated with biotically or abiotically, biotically, and abiotically more homogeneous environments than their sexual controls. In the exploratory part of the study, we found that the ancient asexuals often have durable resting stages, enabling life in subjectively homogeneous environments, live in the absence of intense biotic interactions, and are very often sedentary, inhabiting benthos and soil. The consequences of these findings for the ecological theories of sexual reproduction are discussed.

evolutionary biology↗

bioRxiv2017

The Relationship Between Cancer Progression And Social Environment In Drosophila

The influence of oncogenic phenomena on the ecology and evolution of animal species is fast becoming an important research topic. Similar to host-pathogen interactions, cancer negatively affects host fitness, which should lead to the selection of host control mechanisms, including behavioral traits that best minimize the proliferation of malignant cells. Social behavior is one such trait, which is suggested to influence cancer progression. While the ecological benefits of sociality in gregarious species are widely acknowledged, only limited data are available on the role of the social environment on cancer progression. Here, we exposed adult Drosophila, with colorectal-like tumors, to different social environments. First, we show that cancerous flies kept in complete isolation exhibit increased tumor progression. Yet, more surprisingly, we find that cancerous flies, kept in groups with other noncancerous individuals, also develop tumors at a faster rate compared to those kept with other cancerous conspecifics, suggesting a strong impact of social group composition on cancer growth. Finally, we show that flies can discriminate between individuals at different stages of tumor growth and selectively choose their social environment accordingly. Control flies actively avoid flies with cancer but only at the later stages of tumor development, whereas cancerous flies display strong social interactions with cancerous flies in the early stages of tumor growth. Our study demonstrates the reciprocal links between cancer and social interactions, as well as highlighting how sociality impacts health and fitness in animals and its potential implications for disease ecology and ecosystem dynamics.

animal behavior and cognition↗

bioRxiv2017

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms

Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery for the first time of extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping which increases the diversity of transcripts to regulate gene expression in response to nutrient limitations. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.

bioinformatics↗

bioRxiv2017

Decoupled Maternal and Zygotic Genetic Effects Shape the Evolution of Development

Many animals develop indirectly via a larval stage that is morphologically and ecologically distinct from its adult form. Hundreds of lineages across animal phylogeny have secondarily lost larval forms, instead producing offspring that directly develop into adult form without a distinct larval ecological niche1-7. Indirect development in the sea is typically planktotrophic: females produce large numbers of small offspring that require exogenous planktonic food to develop before metamorphosing into benthic juveniles. Direct development is typically lecithotrophic: females produce a smaller number of larger eggs, each developing into a juvenile without the need for larval feeding, provisioned by yolk. Evolutionary theory suggests that these alternative developmental strategies represent stable alternative fitness peaks, while intermediate states are disfavored4,8-11. Transitions from planktotrophy to lecithotrophy thus require crossing a fitness valley and represent radical and coordinated transformations of life-history, fecundity, ecology, dispersal, and development7,12-16. Here we dissect this transition in Streblospio benedicti, the sole genetically tractable species that harbors both states as heritable variation17-19. We identify large-effect loci that act maternally to influence larval size and independent, unlinked large-effect loci that act zygotically to affect discrete aspects of larval morphology. Because lecithotrophs and planktotrophs differ in both size and morphology, the genetic basis of larval form exhibits strong maternal-by-zygotic epistasis for fitness20. The fitness of zygotic alleles depends on their maternal background, creating a positive frequency-dependence that may homogenize local populations. Developmental and population genetics interact to shape larval evolution.

evolutionary biology↗

bioRxiv2017

TaxAss: Leveraging Custom Databases Achieves Fine-Scale Taxonomic Resolution

Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater datasets using the comprehensive Silva database and the freshwater-specific FreshTrain database. TaxAss increased the percent of the dataset classified compared to using only Silva, especially at fine-resolution family-species taxa levels, while across the freshwater test-datasets classifications increased by as much as 11-40 percent of total reads. A similar increase in classifications was not observed in a control mouse gut dataset, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxa-levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxa levels incorrect classifications became significant. We validated TaxAss using simulated amplicon data with known taxonomy and found that 96-99% of test sequences were correctly classified at fine resolution. TaxAss splits a datasets sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source, and available at www.github.com/McMahonLab/TaxAss.\n\nIMPORTANCEMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon datasets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at phylum, class, and order level lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are dataset-dependent and cannot be compared between datasets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between datasets.

bioinformatics↗

bioRxiv2017

Competitive ability of a tetraploid selfing species (Capsella bursa-pastoris) across its expansion range and comparison with its sister species

Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy in Grimes Competitive-Stress-tolerant-Ruderal (CSR) classification of ecological strategies. Consequently, selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. Although suggested by meta-analyses, these predictions have not been directly tested yet. We compared the competitive ability of four Capsella species differing by their mating system and ploidy level. We found that the two diploid selfing species (C. rubella and C. orientalis) were more sensitive to competition than the diploid outcrosser (C. grandiflora), and that the tetraploid selfer (C. bursa-pastoris) was intermediate. Within C. bursa-pastoris, we also found that sensitivity to competition increased in parallel to range expansion. These results highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.

evolutionary biology↗

bioRxiv2017

Mechanisms that maintain coexistence of antibiotic sensitivity and resistance also promote high frequencies of multidrug resistance

Resistance against different antibiotics appears on the same bacterial strains more often than expected by chance, leading to high frequencies of multidrug resistance. There are multiple explanations for this observation, but these tend to be specific to subsets of antibiotics and/or bacterial species, whereas the trend is pervasive. Here, we consider the question in terms of strain ecology: explaining why resistance to different antibiotics is often seen on the same strain requires an understanding of the competition between strains with different resistance profiles. This work builds on models originally proposed to explain another aspect of strain competition: the stable coexistence of antibiotic sensitivity and resistance observed in a number of bacterial species. We first demonstrate a partial structural similarity in these models of coexistence. We then generalise this unified underlying model to multidrug resistance and show that models with this structure predict high levels of association between resistance to different drugs and high multidrug resistance frequencies. We test predictions from this model in six bacterial datasets and find them to be qualitatively consistent with observed trends. The higher than expected frequencies of multidrug resistance are often interpreted as evidence that these strains are out-competing strains with lower resistance multiplicity. Our work provides an alternative explanation that is compatible with long-term stability in resistance frequencies.\n\nAuthor summaryAntibiotic resistance is a serious public health concern, yet the ecology and evolution of drug resistance are not fully understood. This impacts our ability to design effective interventions to combat resistance. From a public health point of view, multidrug resistance is particularly problematic because resistance to different antibiotics is often seen on the same bacterial strains, which leads to high frequencies of multidrug resistance and limits treatment options. This work seeks to explain this trend in terms of strain ecology and the competition between strains with different resistance profiles. Building on recent work exploring why resistant bacteria are not out-competing sensitive bacteria, we show that models originally proposed to explain this observation also predict high multidrug resistance frequencies. These models are therefore a unifying explanation for two pervasive trends in resistance dynamics. In terms of public health, the implication of our results is that new resistances are likeliest to be found on already multidrug resistant strains and that changing patterns of prescription may not be enough to combat multidrug resistance.

evolutionary biology↗

bioRxiv2018

New insights on adaptation and population structure of cork oak using genotyping by sequencing

Species respond to global climatic changes in a local context. Understanding this process is paramount due to the pace of these changes. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. The potential response of Q. suber to global climatic changes has also been studied, under ecological modelling. In this work, \"Genotyping by Sequencing\" (GBS) is used to derive 2,547 SNP markers to assess the species evolutionary history from a nuclear DNA perspective, gain insights on how local adaptation may be shaping the species genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal an essentially unstructured species, where a balance between gene flow and local adaptation keeps the species gene pool somewhat homogeneous across its distribution, but at the same time allows variation clines for the individuals to cope with local conditions. \"Risk of Non-Adaptedness\" (RONA) analyses, suggest that for the considered variables and most sampled locations, the cork oak does not require large shifts in allele frequencies to survive the predicted climatic changes. However, more research is required to integrate these results with those of ecological modelling.

evolutionary biology↗

bioRxiv2018

New formula and conversion factor to compute tree species basic wood density from a global wood technology database.

Premise of the studyBasic wood density is an important ecological trait for woody plants. It is used to characterize species performance and fitness in community ecology, and to compute tree and forest biomass in carbon cycle studies. While wood density has been historically measured at 12% moisture, it is convenient for ecological purposes to convert this measure to basic wood density, i.e. the ratio of dry mass over green volume. Basic wood density can then be used to compute tree dry biomass from living tree volume.\n\nMethodsHere, we derive a new, exact formula to compute the basic wood density Db from the density at moisture content w denoted Dw, the fibre saturation point S, and the volumetric shrinkage coefficient R. We estimated a new conversion factor using a global wood technology database where values to use this formula are available for 4022 trees collected in 64 countries (mostly tropical) and representing 872 species.\n\nKey resultsWe show that previous conversion factors used to convert densities at 12% moisture into basic wood densities are inconsistent. Based on theory and data, we found that basic wood density could be inferred from the density at 12% moisture using the following formula: Db = 0.828D122. This value of 0.828 provides basic wood density estimates 4-5% smaller than values inferred from previous conversion factors.\n\nConclusionsThis new conversion factor should be used to derive basic wood densities in global wood density databases. This would prevent overestimating global forest carbon stocks and allow predicting better tree species community dynamics from wood density.

plant biology↗

bioRxiv2018

Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

The genomes of species that are ecological specialists will likely contain signatures of genomic adaptation to their niche. However, distinguishing genes related to their ecological specialism from other sources of selection and more random changes is a challenge. Here we describe the genome of Drosophila montana, the most extremely cold-adapted Drosophila species. We describe the genome, which is similar in size and gene content to most Drosophila species. We look for evidence of accelerated divergence from a previously sequenced relative, and do not find strong evidence for divergent selection on coding sequence variation. We use branch tests to identify genes showing accelerated divergence in contrasts between cold- and warm adapted species and identify about 250 genes that show differences, possibly driven by a lower synonymous substitution rate in cold-adapted species. Divergent genes are involved in a variety of functions, including cuticular and olfactory processes. We also re-sequenced three populations of D. montana representing its ecological and geographic range. Outlier loci were more likely to be found on the X chromosome and there was a greater than expected overlap between population outliers and those genes implicated in cold adaptation between Drosophila species, implying some continuity of selective process at these different evolutionary scales.

genomics↗