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bioRxiv2014

Genetic drift suppresses bacterial conjugation in spatially structured populations

Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.

Biophysics↗

bioRxiv2014

Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)

Premise of the studyThe teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the genes expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte.\n\nMethodsPrevalence of the Hopscotch element was assessed across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Population genetic summaries were calculated for a subset of individuals from four teosinte populations in central Mexico. Phenotypic data were also collected using seed from a single teosinte population where Hopscotch was found segregating at high frequency.\n\nKey resultsGenotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on this locus revealing a potential ecological role for Hopscotch in teosinte, but a greenhouse experiment does not detect a strong association between tb1 and tillering in teosinte.\n\nConclusionsOur findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.

Evolutionary Biology↗

bioRxiv2014

Concerning RNA-Guided Gene Drives for the Alteration of Wild Populations

Gene drives may be capable of addressing ecological problems by altering entire populations of wild organisms, but their use has remained largely theoretical due to technical constraints. Here we consider the potential for RNA-guided gene drives based on the CRISPR nuclease Cas9 to serve as a general method for spreading altered traits through wild populations over many generations. We detail likely capabilities, discuss limitations, and provide novel precautionary strategies to control the spread of gene drives and reverse genomic changes. The ability to edit populations of sexual species would offer substantial benefits to humanity and the environment. For example, RNA-guided gene drives could potentially prevent the spread of disease, support agriculture by reversing pesticide and herbicide resistance in insects and weeds, and control damaging invasive species. However, the possibility of unwanted ecological effects and near-certainty of spread across political borders demand careful assessment of each potential application. We call for thoughtful, inclusive, and well-informed public discussions to explore the responsible use of this currently theoretical technology.

Synthetic Biology↗

bioRxiv2014

Applying Geospatial Semantic Array Programming for a Reproducible Set of Bioclimatic Indices in Europe

Bioclimate-driven regression analysis is a widely used approach for modelling ecological niches and zonation. Although the bioclimatic complexity of the European continent is high, a particular combination of 12 climatic and topographic covariates was recently found able to reliably reproduce the ecological zoning of the Food and Agriculture Organization of the United Nations (FAO) for forest resources assessment at pan-European scale, generating the first fuzzy similarity map of FAO ecozones in Europe. The reproducible procedure followed to derive this collection of bioclimatic indices is now presented. It required an integration of data-transformation modules (D-TM) using geospatial tools such as Geographic Information System (GIS) software, and array-based mathematical implementation such as semantic array programming (SemAP). Base variables, intermediate and final covariates are described and semantically defined by providing the workflow of D-TMs and the mathematical formulation following the SemAP notation. Source layers to derive base variables were extracted by exclusively relying on global-scale public open geodata in order for the same set of bioclimatic covariates to be reproducible in any region worldwide. In particular, two freely available datasets were exploited for temperature and precipitation (WorldClim) and elevation (Global Multi-resolution Terrain Elevation Data). The working extent covers the European continent to the Urals with a resolution of 30 arc-second. The proposed set of bioclimatic covariates will be made available as open data in the European Forest Data Centre (EFDAC). The forthcoming complete set of D-TM codelets will enable the 12 covariates to be easily reproduced and expanded through free software.

Preprint↗

bioRxiv2014

Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex

Anopheles gambiae, the primary vector of human malaria in sub-Saharan Africa, exists as a series of ecologically specialized subgroups that are phylogenetically nested within the Anopheles gambiae species complex. These species and subgroups exhibit varying degrees of reproductive isolation, sometimes recognized as distinct subspecies. We have sequenced 32 complete genomes from field-captured individuals of Anopheles gambiae, Anopheles gambiae M form (recently named A. coluzzii), sister species A. arabiensis, and the recently discovered \"GOUNDRY\" subgroup of A. gambiae that is highly susceptible to Plasmodium. Amidst a backdrop of strong reproductive isolation and adaptive differentiation, we find evidence for introgression of autosomal chromosomal regions among species and subgroups, some of which have facilitated adaptation. The X chromosome, however, is strongly differentiated among all species and subgroups, pointing to a disproportionately large effect of X chromosome genes in driving speciation among anophelines. Strikingly, we find that autosomal introgression has occurred from contemporary hybridization among A. gambiae and A. arabiensis despite strong divergence ({bsim}5x higher than autosomal divergence) and isolation on the X chromosome. We find a large region of the X chromosome that has swept to fixation in the GOUNDRY subgroup within the last 100 years, which may be an inversion that serves as a partial barrier to contemporary gene flow. We show that speciation with gene flow results in genomic mosaicism of divergence and introgression. Such a reticulate gene pool connecting vector species and subgroups across the speciation continuum has important implications for malaria control efforts.\n\nAuthor SummarySubdivision of species into ecological specialized subgroups allows organisms to access a wider variety of environments and sometimes leads to the formation of species complexes. Adaptation to distinct environments tends to result in differentiation among closely related subgroups, although hybridization can facilitate sharing of globally adaptive alleles. Here, we show that differentiation and hybridization have acted in parallel in a species complex of Anopheles mosquitoes that vector human malaria. In particular, we show that extensive adaptive differentiation and partial reproductive isolation has led to genomic differentiation among mosquito species and subgroups, especially on the X chromosome. However, we also find evidence for exchange of genes on the autosomes that has provided the raw material for recent rapid adaptation. For example, we show that A. arabiensis has shared a mutation conferring insecticide resistance with two subgroups of A. gambiae within the last 60 years, illustrating the fluid nature of species boundaries among even more advanced species pairs. Our results underscore the expected challenges in deploying vector-based disease control strategies since many of the worlds most devastating human pathogens are transmitted by arthropod species complexes.

Evolutionary Biology↗

bioRxiv2014

Limits to adaptation along environmental gradients

Brief SummaryWhy do species ranges often end when no obvious change in the environment suggests they should? Our theory explains that there is an inherent limit to adaptation arising in any (finite) natural population, and identifies the key parameters that determine this limit to a species range. Two observable parameters describe the threshold when adaptation fails: i) the loss of fitness due to dispersal to a different environment, and ii) the efficacy of selection relative to stochastic effects in finite populations.\n\nAbstractWhy do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: while it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that when the environment varies across space, \"swamping\" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. Yet, current deterministic theory shows that when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary time scales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment, and ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.

Evolutionary Biology↗

bioRxiv2014

Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

Coexistence of multiple populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present a theoretical framework for measuring the functional form of frequency-dependent fitness by accounting for changes in abundance and relative fitness during a competition assay. Using two examples of ecological coexistence that arose in a long-term evolution experiment with Escherichia coli, we illustrate accurate quantification of the functional form of frequency-dependent relative fitness. Using a Monod-type model of growth dynamics, we show that two ecotypes in a typical cross-feeding interaction--such as when one bacterial population uses a byproduct generated by another--yields relative fitness that is linear with relative frequency.

Evolutionary Biology↗

bioRxiv2014

Real-world Interaction Networks Buffer Impact of Small Evolutionary Shifts On Biodiversity

Biodiversity maintenance and community evolution depend on the species interaction network. The \"diversity-stability debate\" has revealed that the complex interaction structure within real-world ecosystems determines how ecological communities respond to environmental changes, but can have opposite effects depending on the community type. Here we quantify the influence of shifts on community diversity and stability at both the species level and the community level. We use interaction networks from 19 real-world mutualistic communities and simulate shifts to antagonism. We demonstrate that both the placement of the shifting species in the community, as well as the structure of the interaction network as a whole contribute to stability and diversity maintenance under shifts. Our results suggest that the interaction structure of natural communities generally enhances community robustness against small ecological and evolutionary changes, but exacerbates the consequences of large changes.

Preprint↗

bioRxiv2015

Cline coupling and uncoupling in a stickleback hybrid zone

Strong ecological selection on a genetic locus can maintain allele frequency differences between populations in different environments, even in the face of hybridization. When alleles at divergent loci come into tight linkage disequilibria, selection acts on them as a unit and can significantly reduce gene flow. For populations interbreeding across a hybrid zone, linkage disequilibria between loci can force clines to share the same slopes and centers. However, strong ecological selection can push clines away from the others, reducing linkage disequilibria and weakening the barrier to gene flow. We looked for this cline uncoupling effect in a hybrid zone between stream resident and anadromous sticklebacks at two genes known to be under divergent natural selection (Eda and ATP1a1) and five morphological traits that repeatedly evolve in freshwater stickleback. We used 10 anonymous SNPs to characterize the shape of the zone. We found that the clines at Eda, ATP1a1, and four morphological traits were concordant and coincident, suggesting that direct selection on each is outweighed by the indirect selection generated by linkage disequilibria. Interestingly, the cline for pectoral fin length was much steeper and displaced 200m downstream, and two anonymous SNPs also had steep clines.

Evolutionary Biology↗

bioRxiv2015

Brain composition in Heliconius butterflies, post-eclosion growth and experience dependent neuropil plasticity

Behavioral and sensory adaptations are often based in the differential expansion of brain components. These volumetric differences represent changes in investment, processing capacity and/or connectivity, and can be used to investigate functional and evolutionary relationships between different brain regions, and between brain composition and behavioral ecology. Here, we describe the brain composition of two species of Heliconius butterflies, a long-standing study system for investigating ecological adaptation and speciation. We confirm a previous report of striking mushroom body expansion, and explore patterns of post-eclosion growth and experience-dependent plasticity in neural development. This analysis uncovers age-and experience-dependent post-emergence mushroom body growth comparable to that in foraging hymenoptera, but also identifies plasticity in several other neuropil. An interspecific analysis indicates that Heliconius display remarkable levels of investment in mushroom bodies for a lepidopteran, and indeed rank highly compared to other insects. Our analyses lay the foundation for future comparative and experimental analyses that will establish Heliconius as a useful case study in evolutionary neurobiology.

Evolutionary Biology↗

bioRxiv2015

Is there such a thing as Landscape Genetics?

For a scientific discipline to be interdisciplinary it must satisfy two conditions; it must consist of contributions from at least two existing disciplines and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this paper, I examine the complete body of peer-reviewed literature self-identified as landscape genetics using the statistical approaches of text mining and natural language processing. The goal here is to quantify the kinds of questions being addressed in landscape genetic studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published landscape genetic papers examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual- and population-based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if landscape genetics is to serve as a real bridge connecting evolution and ecology sensu lato.

Evolutionary Biology↗

bioRxiv2015

Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Transposable elements (TEs) are major drivers of genomic and phenotypic evolution, yet many questions about their biology remain poorly understood. Here, we compare TE abundance between populations of the two sister species D. mauritiana und D. simulans and relate it to the more distantly related D. melanogaster. The low population frequency of most TE insertions in D. melanogaster and D. simulans has been a key feature of several models of TE evolution. In D. mauritiana, however, the majority of TE insertions are fixed (66%). We attribute this to a lower transposition activity of up to 47 TE families in D. mauritiana, rather than stronger purifying selection. Only three families, including the extensively studied Mariner, may have a higher activity in D. mauritiana. This remarkable difference in TE activity between two recently diverged Drosophila species ({approx} 250,000 years), also supports the hypothesis that TE copy numbers in Drosophila may not reflect a stable equilibrium where the rate of TE gains equals the rate of TE losses by negative selection. We propose that the transposition rate heterogeneity results from the contrasting ecology of the two species: the extent of vertical extinction of TE families and horizontal acquisition of active TE copies may be very different between the colonizing D. simulans and the island endemic D. mauritiana. Our findings provide novel insights in the evolution of TEs in Drosophila and suggest that the ecology of the host species could be a major, yet underappreciated, factor governing the evolutionary dynamics of TEs.

Evolutionary Biology↗

bioRxiv2015

Endorsing Darwin – Global biogeography of the epipelagic goose barnacles Lepas spp. (Cirripedia, Lepadomorpha) proves cryptic speciation

AimWe studied different species of gooseneck barnacles from the globally distributed rafting genus Lepas to examine whether the most widespread species are true cosmopolitans and to explore the factors influencing the phylogeny and biogeography of these epipelagic rafters.\n\nLocationTemperate and tropical parts of the Atlantic, Pacific, and Indic oceans.\n\nMethodsWe used a phylogenetic approach based on mitochondrial 16S and coI sequences, and the nuclear 18S gene to elucidate patterns of inter- and intra-species divergence. Altogether, five species of Lepas from 18 confined regions of the Atlantic, Pacific and Indic oceans were analyzed.\n\nResultsA combination of nuclear and mitochondrial sequences provided robust phylogenetic signals for biogeographic classification of subgroups in Lepas species. Lepas australis, restricted to cold-temperate waters of the southern hemisphere shows two separate populations in the southern hemisphere (coastal Chile, other circum-Antarctic sampling sites) most probably related to temperature differences in the southern Pacific current systems. A more complex differentiation is seen for the cosmopolitan L. anatifera that thrives in warmer waters. In total, it is differentiated in four regional subgroups (coastal Chile, Oregon, Indopacific in general, Atlantic) and a global group, which might be either an ancient stemgroup, but more probably is an anthropogenic artefact. Separation into subgroups likely reflect geological vicariance effects. For Lepas, these were closure of the Isthmus of Panama, installation of the cool Benguela Current in the later Miocene including its persistence into the Present, Pleistocene current systems in the western Pacific differing from today, and in general lowered Pleistocene temperatures, and finally present-day current systems. The extreme ecological generalists L. anserifera and L. pectinata are not differentated according to available data and might represent true global species. Data for L. testudinata remain ambiguous.\n\nMain conclusionsOur data indicate cryptic speciation in some but not all species of the cosmopolitan epipelagic genus Lepas. Regional distribution of genetically different populations rely on a wealth of in part interacting inherited geological factors and modern traits. Controlling factors differ between species according to their ecospace limits and demonstrate the need for studies on species level to avoid unjustified generalizations. Data indicate that allopatric speciation is the main mode of divergence. True global species, if existent at all, need to be extreme ecological generalists, like Lepas pectinata and L. anserifera.

Evolutionary Biology↗

bioRxiv2015

Evolution of organismal stoichiometry in a 50,000-generation experiment with Escherichia coli

Organismal stoichiometry refers to the relative proportion of chemical elements in the biomass of organisms, and it can have important effects on ecological interactions from population to ecosystem scales. Although stoichiometry has been studied extensively from an ecological perspective, little is known about rates and directions of evolutionary changes in elemental composition in response to nutrient limitation. We measured carbon, nitrogen, and phosphorus content of Escherichia coli evolved under controlled carbon-limited conditions for 50,000 generations. The bacteria evolved higher relative nitrogen and phosphorus content, consistent with selection for increased use of the more abundant elements. Total carbon assimilated also increased, indicating more efficient use of the limiting element. Altogether, our study shows that stoichiometry evolved over a relatively short time-period, and that it did so in a predictable direction given the carbon-limiting environment.

Evolutionary Biology↗

bioRxiv2015

Phylogenetic relationships of the Helmeted Woodpecker (Dryocopus galeatus): A case of interspecific mimicry?

Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. Herein, we document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multi-locus phylogenetic analyses unequivocally place D. galeatus within Celeus, indicating the former has subsequently converged in appearance upon the distantly related and syntopic Dryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpeckers ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game theory models and the interspecific social dominance mimicry hypothesis (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant to Celeus and Dryocopus foraging behavior. In light of our results, we recommend taxonomic transfer of D. galeatus to Celeus and emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimics acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.

Zoology↗

bioRxiv2015

How can we study the evolution of animal minds?

AbstractDuring the last 50 years, comparative cognition and neurosciences have improved our understanding of animal minds while evolutionary ecology has revealed how selection acts on traits through evolutionary time. We describe how this evolutionary approach can be used to understand the evolution of animal cognition. We recount how comparative and fitness methods have been used to understand the evolution of cognition and outline how these methods could be extended to gain new insights into cognitive evolution. The fitness approach, in particular, offers unprecedented opportunities to study the evolutionary mechanisms responsible for variation in cognition within species and could allow us to investigate both proximate (ie: neural and developmental) and ultimate (ie: ecological and evolutionary) underpinnings of animal cognition together. Our goal in this review is to build a bridge between cognitive neuroscientist and evolutionary biologists, illustrate how their research could be complementary, and encourage evolutionary ecologists to include explicit attention to cognitive processes in their studies of behaviour. We believe that in doing so, we can break new ground in our understanding of the evolution of cognition as well as gain a much better understanding of animal behaviour.

Animal Behavior and Cognition↗

bioRxiv2015

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection ecology approach and compare the genetic and phenotypic divergence of temporally sampled seed progenies of Ipomoeapurpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that this bottleneck may have occurred prior to 2003. Further, a greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.

Evolutionary Biology↗

bioRxiv2015

Changes in Forest Composition, Stem Density, and Biomass from the Settlement Era (1800s) to Present in the Upper Midwestern United States

EuroAmerican land use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Gridded (8x8km) estimates of pre-settlement (1800s) forests from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan) using 19th Century Public Land Survey (PLS) records provide relative composition, biomass, stem density, and basal area for 26 tree genera. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection.\n\nWe compare pre-settlement to modern forests using Forest Inventory and Analysis (FIA) data, with respect to structural changes and the prevalence of lost forests, pre-settlement forests with no current analogue, and novel forests, modern forests with no past analogs. Differences between PLSS and FIA forests are spatially structured as a result of differences in the underlying ecology and land use impacts in the Upper Midwestern United States. Modern biomass is higher than pre-settlement biomass in the northwest (Minnesota and northeastern Wisconsin, including regions that were historically open savanna), and lower in the east (eastern Wisconsin and Michigan), due to shifts in species composition and, presumably, average stand age. Modern forests are more homogeneous, and ecotonal gradients are more diffuse today than in the past. Novel forest assemblages represent 29% of all FIA cells, while 25% of pre-settlement forests no longer exist in a modern context.\n\nLost forests are centered around the forests of the Tension Zone, particularly in hemlock dominated forests of north-central Wisconsin, and in oak-elm-basswood forests along the forest-prairie boundary in south central Minnesota and eastern Wisconsin. Novel FIA forest assemblages are distributed evenly across the region, but novelty shows a strong relationship to spatial distance from remnant forests in the upper Midwest, with novelty predicted at between 20 to 60km from remnants, depending on historical forest type.\n\nThe spatial relationships between remnant and novel forests, shifts in ecotone structure and the loss of historic forest types point to significant challenges to land managers if landscape restoration is a priority in the region. The spatial signals of novelty and ecological change also point to potential challenges in using modern spatial distributions of species and communities and their relationship to underlying geophysical and climatic attributes in understanding potential responses to changing climate. The signal of human settlement on modern forests is broad, spatially varying and acts to homogenize modern forests relative to their historic counterparts, with significant implications for future management.

Preprint↗