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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 955 records · Page 53Linked to original sources

bioRxiv2015

Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation.

1Biological soil crusts (BSC) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N2-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N2-fixation is largely attributed to heterocystous cyanobacteria, however, early successional crusts possess few N2-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development. DNA stable isotope probing (DNA-SIP) with 15N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate 15N2 in early successional crusts. The Clostridiaceae identified are divergent from previously characterized isolates, though N2fixation has previously been observed in this family. The Proteobacteria identified share >98.5 %SSU rRNA gene sequence identity with isolates from genera known to possess diazotrophs (e.g. Pseudomonas, Klebsiella, Shigella, and Ideonella). The low abundance of these heterotrophic diazotrophs in BSC may explain why they have not been characterized previously. Diazotrophs play a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSC in arid ecosystems.

Microbiology↗

bioRxiv2015

The genetics of resistance to Morinda fruit toxin during the postembryonic stages in Drosophila sechellia

Many phytophagous insect species are ecologic specialists that have adapted to utilize a single host plant. Drosophila sechellia is a specialist that utilizes the ripe fruit of Morinda citrifolia, which is toxic to its sibling species, D. simulans. Here we apply multiplexed shotgun genotyping and QTL analysis to examine the genetic basis of resistance to M. citrifolia fruit toxin in interspecific hybrids. We find that at least four dominant and four recessive loci interact additively to confer resistance to the M. citrifolia fruit toxin. These QTL include a dominant locus of large effect on the third chromosome (QTL-IIIsima) that was not detected in previous analyses. The small-effect loci that we identify overlap with regions that were identified in selection experiments with D. simulans on octanoic acid and in QTL analyses of adult resistance to octanoic acid. Our high-resolution analysis sheds new light upon the complexity of M. citrifolia resistance, and suggests that partial resistance to lower levels of M. citrifolia toxin could be passed through introgression from D. sechellia to D. simulans in nature. The identification of a locus of major effect, QTL-IIIsima, is an important step towards identifying the molecular basis of host plant specialization by D. sechellia.

Evolutionary Biology↗

bioRxiv2015

More than meets the eye: diversity and geographic patterns in sea cucumbers

Estimates for the number of species in the sea vary by orders of magnitude. Molecular taxonomy can greatly speed up screening for diversity and evaluating species boundaries, while gaining insights into the biology of the species. DNA barcoding with a region of cytochrome oxidase 1 (COI) is now widely used as a first pass for molecular evaluation of diversity, as it has good potential for identifying cryptic species and improving our understanding of marine biodiversity. We present the results of a large scale barcoding effort for holothuroids (sea cucumbers). We sequenced 3048 individuals from numerous localities spanning the diversity of habitats in which the group occurs, with a particular focus in the shallow tropics (Indo-Pacific and Caribbean) and the Antarctic region. The number of cryptic species is much higher than currently recognized. The vast majority of sister species have allopatric distributions, with species showing genetic differentiation between ocean basins, and some are even differentiated among archipelagos. However, many closely related and sympatric forms, that exhibit distinct color patterns and/or ecology, show little differentiation in, and cannotbe separatedby, COI sequence data. This pattern is much more common among echinoderms than among molluscs or arthropods, and suggests that echinoderms acquire reproductive isolation at a much faster pace than other marine phyla. Understanding the causes behind such patterns will refine our understanding of diversification and biodiversity in the sea.

Evolutionary Biology↗

bioRxiv2015

Community stability and selective extinction during Earth’s greatest mass extinction

We modelled the resilience and transient dynamics of terrestrial paleocommunities from the Karoo Basin, South Africa, around the Permian-Triassic mass extinction. Using recently refined biostratigraphic data that suggest two pulses of extinction leading up to the Permian-Triassic boundary, we show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became stable during the mass extinction. Modelled food webs before and after the mass extinction have lower resilience and less stable transient dynamics compared to random food webs lacking in functional structure but of equal species richness. They are, however, more stable than random food webs of equal richness but with randomized functional structure. In contrast, models become increasingly more resilient and have more stable transient dynamics, relative to the random models, as the mass extinction progressed. The increased stability of the community that resulted from the first pulse of extinction was driven by significant selective extinction against small-bodied amniotes, and significantly greater probabilities of survival of large-bodied amniotes. These results point to a positive relationship between evolved patterns of functional diversity and emergent community dynamics, with observed patterns being more stable than alternative possibilities.\n\nSignificanceAnthropogenic impacts on modern ecosystems have no precedents in human history. The fossil record does contain episodes of severe biodiversity crises, but incomplete preservation and low temporal resolution make it difficult to equate fossil data to modern ecological processes. We examined terrestrial paleocommunities from Earths most severe mass extinction, the Permian-Triassic mass extinction (PTME), and modelled their dynamic stabilities. We show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became more stable during the mass extinction. Increased stability resulted mostly from selective extinction and survival based on vertebrate body size. Whether modern communities will behave similarly depends on the similarity between human drivers and those of the PTME.

Paleontology↗

bioRxiv2015

Genomic Diversity and Climate Adaptation in Brachypodium

The Brachypodium genus contains the model grasses B. distachyon, B. stacei and B. hybridum, that are useful for molecular and physiological studies relevant to grain, pasture and bioenergy crops, as well as ecology. In this chapter we discuss the natural variation in climate/geography, genotypic and phenotypic diversity that exists within these species. We describe utilisation of this diversity via two methods, Genome Wide Association Studies and Landscape Genomics, to examine the interaction between specific genetic variants, phenotype, and environment. The aim is to identify adaptive loci that control specific traits in specific environments and understand the contribution of background polygenetic variation shaped by demographic processes. With recent developments in high throughput phenotyping, cheaper genotyping by sequencing and higher spatial/temporal resolution of climate data, these approaches can exploit the diversity of the Brachypodium. Experiments using this toolkit will reveal alleles, genes and pathways underlying agriculturally important and environmentally sensitive traits for use in grass breeding.

Plant Biology↗

bioRxiv2015

Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

Evolutionary Biology↗

bioRxiv2015

Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

Documenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterflies Heliconius melpomene and Heliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.

Evolutionary Biology↗

bioRxiv2015

No association between plant mating system & geographic range overlap

Premise of the StudyAutomatic self-fertilization may influence the geography of speciation, promote reproductive isolation between incipient species, and lead to ecological differentiation. As such, selfing taxa are predicted to co-occur more often with their closest relatives than are outcrossing taxa. Despite suggestions that this pattern may be general, the extent to which mating system influences range overlap in close relatives has not been tested formally across a diverse group of plant species pairs.\n\nMethodsWe test for a difference in range overlap between species pairs where zero, one, or both species are selfers, using data from 98 sister species pairs in 20 genera across 15 flowering plant families. We also use divergence time estimates from time-calibrated phylogenies to ask how range overlap changes with divergence time and whether this effect depends on mating system.\n\nKey ResultsWe find no evidence that automatic self-fertilization influences range overlap of closely related plant species. Sister pairs with more recent divergence times had modestly greater range overlap, but this effect did not depend on mating system.\n\nConclusionsThe absence of a strong influence of mating system on range overlap suggests that mating system plays a minor or inconsistent role compared to many other mechanisms potentially influencing the co-occurrence of close relatives.

Evolutionary Biology↗

bioRxiv2015

Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

Studying the evolutionary dynamics of an alien species surviving and continuing to expand after several generations can provide fundamental information on the relevant features of clearly successful invasions. Here, we tackle this task by investigating the dynamics of the genetic diversity in invasive crested porcupine (Hystrix cristata) populations, introduced to Italy about 1500 years ago, which are still growing in size, distribution range and ecological niche. Using genome-wide RAD markers, we describe the structure of the genetic diversity and the demographic dynamics of the H. cristata invasive populations and compare their genetic diversity with that of native African populations of both H. cristata and its sister species, H. africaeaustralis. First, we demonstrate that genetic diversity is lower in both the invasive Italian and the North Africa source range relative to other native populations from Sub-Saharan and South Africa. Second, we find evidence of multiple introduction events in the invasive range followed by very limited gene flow. Through coalescence-based demographic reconstructions, we also show that the bottleneck at introduction was mild and did not affect the introduced genetic diversity. Finally, we reveal that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. We conclude that the level of genome-wide diversity of H. cristata invasive populations is less important in explaining its successful invasion than species-specific life-history traits or the phylogeographic history in the native source range.

Evolutionary Biology↗

bioRxiv2015

Phylogenomic analyses support traditional relationships within Cnidaria

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.

Evolutionary Biology↗

bioRxiv2015

Multiple new species of Ophiocordyceps on ants

In tropical forests, one of the most common relationships between parasites and insects is that between the fungus Ophiocordyceps (Ophiocordycipitaceae, Hypocreales, Ascomycota) and ants, especially within the tribe Camponotini. These fungi have the ability to penetrate the exoskeleton of the ant and to manipulate the behavior of the host, making it leave the nest and ascend understorey shrubs, to die biting onto the vegetation: hence, the term zombie-ant fungi to describe this behavioral changes on the host. It is posited that this behavioral change aids spore dispersal and thus increases the chances of infection. Despite their undoubted importance for ecosystem functioning, these fungal pathogens are still poorly documented, especially regarding their diversity, ecology and evolutionary relationships. Here, we describe multiple new and host-specific species of the genus Ophiocordyceps on Camponotus and Polyrhachis ants from the central Amazonian region of Brazil, USA, Australia and Japan, which can readily be separated using classic taxonomic criteria, in particular ascospore morphology.

Microbiology↗

bioRxiv2015

Open science resources for the discovery and analysis of Tara Oceans Data

The Tara Oceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.

Systems Biology↗

bioRxiv2015

Molecular Fossils from Microorganisms Preserved in Glacial Ice

The study of microbial evolution is hindered by the fact that microbial populations leave few fossils. We hypothesized that bacterial cells preserved in ancient ice could be used as a molecular fossil record if their DNA could be extracted and sequenced. Channels formed along triple junctions of ice crystals contain liquid \"veins\" in which microbial cells may be preserved intact. Since vertical motion through the ice matrix is impossible, microbes found in ice cores are representative of microbes present at the time the ice was formed. We detected chlorophyll fluorescence in intact ice cores taken from Greenland and Antarctica. Flow cytometric analysis localized at least some of this fluorescence to particles < 1 m in diameter. Metagenomic analysis of meltwater indeed revealed sequences similar to modern strains of the picocyanobacterial genera Synechococcus and Prochlorococcus, and some of these sequences were distinct from any sequences known from modern oceans or glacial environments. Our study is a first proof-of-concept of the use of ice cores as records of microbial evolution, and we suggest that future genetic studies with higher vertical resolution in the cores might shed light on the pace and character of evolution of these ecologically important cells.

Evolutionary Biology↗

bioRxiv2015

Stochastic models of evidence accumulation in changing environments

Organisms and ecological groups accumulate evidence to make decisions. Classic experiments and theoretical studies have explored this process when the correct choice is fixed during each trial. However, the natural world constantly changes. Using sequential analysis we derive a tractable model of evidence accumulation when the correct option changes in time. Our analysis shows that ideal observers discount prior evidence at a rate determined by the volatility of the environment, and that the dynamics of evidence accumulation is governed by the information gained over an average environmental epoch. A plausible neural implementation of an optimal observer in a changing environment shows that, in contrast to previous models, neural populations representing alternate choices are coupled through excitation.

Neuroscience↗

bioRxiv2015

RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa

Species delimitation is problematic in many taxa due to the difficulty of evaluating predictions from species delimitation hypotheses, which chiefly relay on subjective interpretations of morphological observations and/or DNA sequence data. This problem is exacerbated in recalcitrant taxa for which genetic resources are scarce and inadequate to resolve questions regarding evolutionary relationships and uniqueness. In this case study we demonstrate the empirical utility of restriction site associated DNA sequencing (RAD-seq) by unambiguously resolving phylogenetic relationships among recalcitrant octocoral taxa with divergences greater than 80 million years. We objectively infer robust species boundaries in the genus Paragorgia, which contains some of the most important ecosystem engineers in the deep-sea, by testing alternative taxonomy-guided or unguided species delimitation hypotheses using the Bayes factors delimitation method (BFD*) with genome-wide single nucleotide polymorphism data. We present conclusive evidence rejecting the current morphological species delimitation model for the genus Paragorgia and indicating the presence of cryptic species boundaries associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences in divergent taxa cannot be assessed in terms of absolute time, but depend on taxon-specific factors such as mutation rate, generation time and effective population size. We show that classic morphological taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypothesis. Our results pave the way for addressing further questions in biogeography, species ranges, community ecology, population dynamics, conservation, and evolution in octocorals and other marine taxa.

Evolutionary Biology↗

bioRxiv2015

A new idea on the evolution of biodiversity

The understanding of the mechanisms that allow the origin of species has shed light on many processes such as speciation, adaptation and extinction, but how to explain the existence of such a huge diversity of species on Earth still remains a mystery. Many theories and evidence have corroborated the processes that allow species to evolve or become extinct. Currently there are different hypotheses but no clear demonstrations of the factors that maintain the species diversity of ecosystems. Those based on competitive principles have been criticized from both theoretical and empirical approaches. Only by studying biodiversity in the context of evolution, natural history and ecology (taking into consideration the avoidance of competition and dispersal abilities, the phenotypic plasticity, the heterogeneous landscape, the facilitation and the endogenosymbiosis) we can understand values and gaps of past theories trying to provide a broader understanding of life on Earth towards a Unified Theory of Biodiversity.

Evolutionary Biology↗

bioRxiv2015

When does high-dose antimicrobial chemotherapy prevent the evolution of resistance?

High-dose chemotherapy has long been advocated as a means of controlling drug resistance in infectious diseases but recent empirical and theoretical studies have begun to challenge this view. We show how high-dose chemotherapy engenders opposing evolutionary processes involving the mutational input of resistant strains and their release from ecological competition. Whether such therapy provides the best approach for controlling resistance therefore depends on the relative strengths of these processes. These opposing processes lead to a unimodal relationship between drug pressure and resistance emergence. As a result, the optimal drug dose always lies at either end of the therapeutic window of clinically acceptable concentrations. We illustrate our findings with a simple model that shows how a seemingly minor change in parameter values can alter the outcome from one where high-dose chemotherapy is optimal to one where using the smallest clinically effective dose is best. A review of the available empirical evidence provides broad support for these general conclusions. Our analysis opens up treatment options not currently considered as resistance management strategies, and greatly simplifies the experiments required to determine the drug doses which best retard resistance emergence in patients.\n\nSignificance StatementThe evolution of antimicrobial resistant pathogens threatens much of modern medicine. For over one hundred years, the advice has been to hit hard, in the belief that high doses of antimicrobials best contain resistance evolution. We argue that nothing in evolutionary theory supports this as a good rule of thumb in the situations that challenge medicine. We show instead that the only generality is to either use the highest tolerable drug dose or the lowest clinically effective dose; that is, one of the two edges of the therapeutic window. This approach suggests treatment options not currently considered, and greatly simplifies the experiments required to identify the dose that best retards resistance evolution.

Microbiology↗

bioRxiv2015

The discovery, distribution and evolution of viruses associated with Drosophila melanogaster

AO_SCPLOWBSTRACTC_SCPLOWDrosophila melanogaster is a valuable invertebrate model for viral infection and antiviral immunity, and is a focus for studies of insect-virus coevolution. Here we use a metagenomic approach to identify more than 20 previously undetected RNA viruses and a DNA virus associated with wild D. melanogaster. These viruses not only include distant relatives of known insect pathogens, but also novel groups of insect-infecting viruses. By sequencing virus-derived small RNAs we show that the viruses represent active infections of Drosophila. We find that the RNA viruses differ in the number and properties of their small RNAs, and we detect both siRNAs and a novel miRNA from the DNA virus. Analysis of small RNAs also allows us to identify putative viral sequences that lack detectable sequence similarity to known viruses. By surveying >2000 individually collected wild adult Drosophila we show that more than 30% of D. melanogaster carry a detectable virus, and more than 6% carry multiple viruses. However, despite a high prevalence of the Wolbachia endosymbiont--which is known to be protective against virus infections in Drosophila--we were unable to detect any relationship between the presence of Wolbachia and the presence of any virus. Using publicly available RNA-seq datasets we show that the community of viruses in Drosophila laboratories is very different from that seen in the wild, but that some of the newly discovered viruses are nevertheless widespread in laboratory lines and are ubiquitous in cell culture. By sequencing viruses from individual wild-collected flies we show that some viruses are shared between D. melanogaster and D. simulans. Our results provide an essential evolutionary and ecological context for host-virus interaction in Drosophila, and the newly reported viral sequences will help develop D. melanogaster further as a model for molecular and evolutionary virus research.\n\nDO_SCPLOWATAC_SCPLOW AO_SCPLOWVAILABILITYC_SCPLOWAll of the relevant data can be found within the paper and its Supporting Information files, with the exception of raw metagenomic sequence data which are deposited at NCBI Sequence Read Archive (SRP056120), and sequence data which are deposited at Genbank (KP714070-KP714108, KP757922-KP757936 and KP757937-KP757993)

Microbiology↗