Biology subjects

Etienne, R. S.

Publications and source records attributed to Etienne, R. S..

At least 19 recordsLinked to original sources

bioRxiv2026

An expanded urine culturing workflow to cultivate and characterize diverse urobiome isolates

Despite increased recognition of the diverse resident microbiome of the urinary tract (i.e., the urobiome) in postmenopausal women, the roles and functions of these microbes remain largely unknown. Further empirical research is needed to understand the physiology, interactions, and antibiotic resistance evolution of urobiome members with pathogenic potential. However, experimental work relies on viable, culturable isolates. Standard urine culturing practices are designed for identifying a narrow set of known urinary microbes, and are thus poorly suited for cultivating taxa from the resident urobiome. Here we expand the urine culturing toolkit to reliably recover diverse urobiome taxa for downstream empirical research. Urine samples collected from postmenopausal women with recurrent urinary tract infections were shipped at ambient temperature to a central point for culturing. Microbial viability was maintained using boric acid preservative tubes during multi-day transport of sample aliquots. Selective media incubated under specialized conditions were used to promote recovery of diverse urobiome members, including fastidious taxa. Under 5% CO2 -enriched atmospheric conditions and with longer incubation times, we leveraged a chromogenic agar (UTIC) to further differentiate isolates based on colony color and morphology. We evaluated the workflow for its ability to isolate and characterize urobiome taxa, as determined by morphological differentiation and taxonomic identification. Across 108 urine samples, 6.3 {+/-} 3.2 distinct isolates were recovered, with no detectable relationship between sample shipment duration and isolate richness. On chromogenic agar, colony growth and color intensity was improved with CO2 -enriched atmospheric conditions and extended incubation times. We identified diverse taxa that are typically underrepresented in standard diagnostic culture and provide novel morphological characterizations for members of the genera Actinotignum, Aerococcus, Facklamia, Lactobacillus, Latilactobacillus, Limosilactobacillus, and Streptococcus species, which have not been previously described on UTIC chromogenic agar. Using this novel workflow, we recovered a diverse collection of urobiome isolates from urine samples shipped over multiple days. We also demonstrated the utility of a chromogenic agar for the visual differentiation of key urobiome taxa. While sequencing approaches have enhanced our understanding of urobiome composition, culturing is needed to investigate microbial interactions, virulence mechanisms, and antimicrobial susceptibility. This protocol adds to the growing toolkit for the cultivation of diverse urobiome isolates needed to support downstream empirical studies and advance urinary tract infection research.

microbiology↗

bioRxiv2025

Sociability is a multidimensional trait in Drosophila melanogaster

Sociability--the propensity of an individual to engage in group activities--is a trait present in all social species. In humans and many animals, sociability varies between individuals yet remains consistent across contexts, qualifying it as a personality trait. Sociability influences health and physiology, but the mechanisms underlying sociability and its inter-individual variation remain poorly understood. The genetically tractable fruit fly, Drosophila melanogaster, is increasingly used to study social behavior and exhibits a wide range of sociability phenotypes. However, previous studies have relied on distinct behavioral paradigms, limiting cross-context comparisons and motivating a more extensive characterization of sociability in this species. Here, we quantified sociability in D. melanogaster using a multidimensional approach encompassing three paradigms that capture engagement in group activities across contexts: (1) preference for communal versus solitary egg-laying, (2) egg-laying latency in a group, and (3) frequency and duration of spontaneous social interactions and interindividual distance. We assessed these behaviors in 105 lines of the Drosophila Genetic Reference Panel and observed substantial variation in responses to conspecific presence across paradigms. Sociability-related behaviors differed between genetically distinct lines, indicating a genetic component. However, the three sociability traits were uncorrelated, demonstrating that sociability in D. melanogaster is multidimensional. These findings suggest that sociability is not governed by a single central mechanism, but instead arises from multiple context-dependent pathways.

animal behavior and cognition↗

bioRxiv2025

Trait-dependent diversification and spatio-ecological limits drive angiosperm diversity unevenness across the Canary Islands archipelago

Island biotas often show highly uneven species richness among lineages, influenced by clade age, diversification rates, and/or spatio-ecological limits. However, disentangling these drivers has been challenging due to the lack of comprehensive datasets across multiple lineages in the same geographical arena. The flora of the Canary Islands includes hundreds of plant lineages with contrasting species richness and harbours the highest number of species that evolved their woodiness in-situ ("insular woodiness"). Here, we present a phylogenomic reconstruction for Canary Island angiosperms and show that diversity unevenness in the flora is not driven by lineage age but by trait-dependent diversification and spatio-ecological limits. Our phylogenomic dataset, based on 1,244 newly generated and 501 published DNA sequences for 669 Canary Island species and 771 closely related mainland taxa, allows us to simultaneously study 435 plant lineages ([~]50% of total). Applying dynamic stochastic modelling, we find the flora is shaped by high extinction and colonisation rates, maintaining a macroevolutionary equilibrium. Additionally, insular woody lineages exhibit higher diversification rates than the remaining flora. Our results suggest the uneven diversity of a highly dynamic insular region can be explained by the interaction of trait evolution and ecological constraints, providing insights into island biodiversity dynamics.

evolutionary biology↗

bioRxiv2024

Colonisation lags predict sympatric diversity in birds

Speciation is the ultimate source of biodiversity. However, because most species arise in spatial isolation (allopatry), how speciation shapes patterns of co-occurring (sympatry) species richness remains unclear. Here we examine how the history of past speciation events influences the maximum sympatric species richness attained across passerine bird clades (n = 40 families). Using a phylogenetic model, we infer that the rate at which species assemble in sympatry is extremely slow, and on average millions of years after speciation onset. As a result, having accounted for clade size, sympatric species richness varies substantially across families, being highest in small or ancient clades comprised of older species that have had more time to accumulate in sympatry. While our analysis does not test the ecological or evolutionary processes causing the slow build-up of sympatric assemblages, our results show that speciation history has left an indelible legacy on current species richness patterns.

evolutionary biology↗

bioRxiv2024

Phylogenetic tree statistics: a systematic overview using the new R package 'treestats'

Phylogenetic trees are believed to contain a wealth of information on diversification processes. Comparing phylogenetic trees is not straightforward due to their high dimensionality. Researchers have therefore defined a wide range of one-dimensional summary statistics. However, it remains unexplored to what extent these summary statistics cover the same underlying information and what summary statistics best explain observed variation across phylogenies. Furthermore, a large subset of available summary statistics focusses on measuring the topological features of a phylogenetic tree, but are often only explored at the extreme edge cases of the fully balanced or unbalanced tree and not for trees of intermediate balance. Here, we introduce a new R package that provides speed optimized code to compute 54 summary statistics. We study correlations between summary statistics on empirical trees and on trees simulated using several diversification models. Furthermore, we introduce an algorithm to create intermediately balanced trees in a well-defined manner, in order to explore variation in summary statistics across a balance gradient. We find that almost all summary statistics are correlated with tree size, and it is difficult if not impossible to correct for tree size, unless the tree generating model is known. Furthermore, we find that across empirical and simulated trees, at least two large clusters of correlated summary statistics can be found, where statistics group together based on information used (topology or branching times). However, the finer grained correlation structure appears to depend strongly on either the taxonomic group studied (in empirical studies) or the diversification model (in simulation studies). Nevertheless, we can identify multiple groups of summary statistics that are strongly and consistently correlated, indicating that these statistics measure the same underlying property of a tree. Lastly, we find that almost all topological summary statistics vary non-linearly and sometimes even non-monotonically with our intuitive balance gradient. Therefore, in order to avoid introducing biases and missing underlying information, we advocate for selecting as many summary statistics as possible in phylogenetic analyses. With the introduction of the treestats package, which provides fast and reliable calculations, such an approach is now routinely possible.

bioinformatics↗

bioRxiv2023

Exponential diversity-dependent diversification emerges from an individual-based model with Lotka-Volterra competition

AbstractA long-standing question in macroevolution is whether diversification is governed by the same processes that structure diversity at ecological scales, particularly competition. This competition has led to the development of a model where diversification rates depend on diversity, analogous to density-dependence in population growth models. Various versions of this model have been widely used for inference, where the rate of speciation and/or extinction can be either a linear or a power function of species number. It is, however, unknown if either approximates the diversification process that arises from the general ecological setting proposed to lead to diversity-dependence. This is of concern for inference, as failure to include a model that appropriately represents the hypothesized scenario is likely to lead to erroneous inference. Here we use an individual-based model adapted from adaptive dynamics, where fitness is governed by resource availability and the density of competitors, to determine the shape of the diversity-dependence functions. We find that the diversity-dependent rate of speciation produced by the individual-based model is best approximated by an exponential function of species diversity, consistent with a view of macroevolution where diversity increases rapidly after mass extinctions or when new adaptive space becomes available. Although we do find diversity-dependence in the extinction rate, it remains low over the entire process and erases its own signal, so it cannot be recovered from reconstructed phylogenies. The support for a linear relationship for diversity-dependent diversification found in many empirical phylogenies suggests that either our adaptive dynamics model of speciation is inadequate or there is too little information contained in reconstructed phylogenies. We indeed find evidence for the latter when pruning extinct species from our simulated phylogenies, but this does not rule out the former.

evolutionary biology↗

bioRxiv2023

DAISIEprep: an R package for the extraction and formatting of data for the island biogeography model DAISIE

O_LIPhylogenetic trees are commonly used to answer questions on biogeographical and diversification histories of different groups. C_LIO_LIRecently, new approaches have been developed that use community phylogenetic trees requiring a data structure distinct from the single phylogenetic trees that are commonly used, which may be a barrier to the utilisation of these approaches. C_LIO_LIDAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from phylogenetic data across insular communities, as well as simulate islands under those rates. C_LIO_LIHere we describe the DAISIEprep R package, a set of pre-processing tools to aid the extraction of data from one or many phylogenetic trees to generate data in a format interpretable by DAISIE for the application of island biogeography inference models. We present examples to illustrate the various data types that can be used. C_LIO_LIThe package includes simple algorithms to extract data on island colonists and account for bio-geographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when phylogenetic data are not available. C_LIO_LIDAISIEprep enables reproducible and user-friendly data extraction and formatting, and will facili-tate addressing questions about island biogeography, diversification and anthropogenic impacts in insular systems. C_LI

evolutionary biology↗

bioRxiv2022

Direct estimation of genome mutation rates from pedigrees in free-ranging baleen whales

Current low germline mutation rate () estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Petos Paradox). We demonstrate the feasibility of estimating from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on .

genetics↗

bioRxiv2022

The limits to ecological limits to diversification

AO_SCPLOWBSTRACTC_SCPLOWWhile the theory of micro-evolution by natural selection assigns a crucial role to competition, its role in macroevolution is less clear. Phylogenetic evidence for a decelerating accumulation of lineages suggests a feedback of lineage diversity on diversification, i.e., ecological limits to diversification. However, does this feedback only occur between close relatives, or do distant relatives also influence their diversification? In other words: are there phylogenetic limits to these ecological limits? Islands form ideal systems to answer these questions, because their boundedness facilitates an overview of all potential competitors. The DAISIE (Dynamic Assembly of Island biota through Speciation Immigration and Extinction) framework allows for testing the presence of diversity-dependence on islands given phylogenetic data on colonization and branching times. The current inference models in DAISIE assume that this diversity-dependence only applies within a colonizing clade, which we term clade-specific (CS) diversity-dependence. Here we introduce a new DAISIE model that assumes that diversity-dependence applies to all species regardless of their ancestry, i.e. diversity-dependence applies both to species within the same clade and between different clades. We call this island-wide (IW) diversity-dependence. Here we present a method to compute a likelihood for this model and develop a statistical procedure based on likelihood ratio bootstrapping to compare it to the likelihood of the CS model in order to overcome biases known for standard model selection. We apply it to the diversification of Eleutherodactylus frogs on Hispaniola. Across the Greater Antilles archipelago, this radiation shows repeated patterns of diversification in ecotypes which are similar across clades. This could be suggestive of overlapping niche space and hence between-clade interactions, i.e. IW diversity-dependence. But it could also be suggestive of only within-clade interactions, because between-clade interactions would have blocked the same ecotype re-appearing. We find that the CS model fits the data much better than the IW model, indicating that different colonizations, while resulting in similar ecotypes, are sufficiently distinct to avoid interacting strongly. We argue that non-overlapping distributions between clades (both spatially and in terms of ecotypes) cannot be used as evidence of CS diversity-dependence, because this pattern may be a consequence of IW diversity-dependence. By contrast, by using phylogenetic data rather than distributional data our method does allow for inferring the phylogenetic limits to ecological limits to diversification. We discuss how our new IW model advances our understanding also in other ways, ranging from identifying priority effects to modelling the spread of an epidemic in island-like systems, such as schools or hospitals.

evolutionary biology↗

bioRxiv2022

The effect of mainland dynamics on data and parameter estimates in island biogeography

Understanding macroevolution on islands requires knowledge of the closest relatives of is-land species on the mainland. The evolutionary relationships between island and mainland species can be reconstructed using phylogenies, to which models can be fitted to understand the dynamical processes of colonisation and diversification. But how much information on the mainland is needed to gain insight into macroevolution on islands? Here we first test whether species turnover on the mainland and incomplete mainland sampling leave recognis-able signatures in community phylogenetic data. We find predictable phylogenetic patterns: colonisation times become older and the perceived proportion of endemic species increases as mainland turnover and incomplete knowledge increase. We then analyse the influence of these factors on the inference performance of the island biogeography model DAISIE, a whole-island community phylogenetic model that assumes that mainland species do not diversify, and that the mainland is fully sampled in the phylogeny. We find that colonisation and diversification rate are estimated with little bias in the presence of mainland extinction and incomplete sampling. By contrast, the rate of anagenesis is overestimated under high levels of mainland extinction and incomplete sampling, because these increase the perceived level of island endemism. We conclude that community-wide phylogenetic and endemism datasets of island species carry a signature of mainland extinction and sampling. The ro-bustness of parameter estimates suggests that island diversification and colonisation can be studied even with limited knowledge of mainland dynamics.

evolutionary biology↗

bioRxiv2021

The robustness of a simple dynamic model of island biodiversity to geological and eustatic change

AimBiodiversity on islands is affected by various geo-physical processes and sea-level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, followed by a decline as islands shrink. Continental islands have species upon formation (when disconnected from the mainland) and may have transient land-bridge connections. Theoretical predictions for the effects of these geo-processes on rates of colonisation, speciation and extinction have been proposed, but methods of phylogenetic inference assume only oceanic island scenarios without accounting for island ontogeny, sea-level changes or past landmass connections. Here, we analyse to what extent ignoring geodynamics affects the inference performance of a phylogenetic island model, DAISIE, when confronted with simulated data that violate its assumptions. LocationSimulation of oceanic and continental islands. MethodsWe extend the DAISIE simulation model to include: area-dependent rates of colonisation and diversification associated with island ontogeny and sea-level fluctuations, and continental islands with biota present upon separation from the mainland, and shifts in rates to mimic temporary land-bridges. We quantify the error made when geo-processes are not accounted for by applying DAISIEs inference method to geodynamic simulations. ResultsWe find that the robustness of the model to dynamic island area is high (error is small) for oceanic islands and for continental islands that have been separated for a long time, suggesting that, for these island types, it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of DAISIE is low, and inference results should not be trusted. Main conclusions: This study highlights that under a large proportion of island biogeographic geo-scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring development of a new inference model.

evolutionary biology↗

bioRxiv2021

Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids

Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of Vitamin A1/A2-derived chromophores (i.e. the light-sensitive component of the visual pigment, bound to the opsin protein), where higher proportions of A2 cause a more red-shifted wavelength absorbance. Here, we explore variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the enzyme CYP27C1 that catalyses the conversion of Vitamin A1-into A2. We focus on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands, but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid-water than from clear-water locations, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear- and turbid-water locations. To assess the contribution of heritable versus environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Establishing the biological importance of this variation requires testing the link between cyp27c1 expression and A1/A2 ratios in the eye, as well as its consequences for visual performance.

evolutionary biology↗

bioRxiv2021

DETECTING PHYLODIVERSITY-DEPENDENT DIVERSIFICATION WITH A GENERAL PHYLOGENETIC INFERENCE FRAMEWORK

AO_SCPLOWBSTRACTC_SCPLOWDiversity-dependent diversification models have been extensively used to study the effect of ecological limits and feedback of community structure on species diversification processes, such as speciation and extinction. Current diversity-dependent diversification models characterise ecological limits by carrying capacities for species richness. Such ecological limits have been justified by niche filling arguments: as species diversity increases, the number of available niches for diversification decreases. However, as species diversify they may diverge from one another phenotypically, which may open new niches for new species. Alternatively, this phenotypic divergence may not affect the species diversification process or even inhibit further diversification. Hence, it seems natural to explore the consequences of phylogenetic diversity-dependent (or phylodiversity-dependent) diversification. Current likelihood methods for estimating diversity-dependent diversification parameters cannot be used for this, as phylodiversity is continuously changing as time progresses and species form and become extinct. Here, we present a new method based on Monte Carlo Expectation-Maximization (MCEM), designed to perform statistical inference on a general class of species diversification models and implemented in the R package emphasis. We use the method to fit phylodiversity-dependent diversification models to 14 phylogenies, and compare the results to the fit of a richness-dependent diversification model. We find that in a number of phylogenies, phylogenetic divergence indeed spurs speciation even though species richness reduces it. Not only do we thus shine a new light on diversity-dependent diversification, we also argue that our inference framework can handle a large class of diversification models for which currently no inference method exists.

evolutionary biology↗

bioRxiv2021

Competition and environmental gradients structure Canidae assemblages across the planet

The phylogenetic information of assemblages carries the signature of ecological and evolutionary processes that assembled these communities. Identifying the mechanisms that shape communities is not simple, as they can vary spatially. Here, we investigated how the phylogenetic structure of Canidae across the globe is affected by the environment and competition. We first identified phylogenetically clustered and overdispersed assemblages of canids over the planet taking into account regional pools of species in South and North America, Eurasia, and Africa. Then, we applied Structural Equation Models in these communities in order to identify the effect of temperature, vegetation cover, human impact, and body size dissimilarity on the spatial distribution of the phylogenetic information of canids. Only southern South America and the Middle East had strong phylogenetic clustered patterns, while the rest of the planet predominantly showed overdispersed assemblages. Body size dissimilarity and vegetation cover were the most important variables to explain the spatial patterns of phylogenetic structure in clustered and overdispersed communities, respectively. Canidae community composition across the world presents significant patterns of clustering and overdispersion, which vary following mainly the environmental gradient, suggesting habitat filtering as the main force acting on Canidae assemblages.

evolutionary biology↗

bioRxiv2021

Explosive diversification following continental colonizations by canids

Colonization of a new environment may trigger an explosive radiation process, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger explosive radiations is still an open question. We studied the worldwide dispersal of the subfamily Caninae, to investigate whether the invasion of new continents resulted in explosive radiations. We used a combination of phylogenetic analyses and ancestral area reconstructions to estimate ancestral ranges of 56 extant and extinct species of Caninae, as well as variation in speciation and extinction rates through time and across clades. Our findings indicate that canids experienced an explosive radiation event when lineages were able to cross the Bering Strait and the Isthmus of Panama to reach Eurasia and South America, respectively, around 11 million years ago. This large number of species arising in a short period of time suggests that canids experienced ecological opportunity events within the new areas, implying that the differences in the ecological settings between continents may be responsible for the variation in clade dynamics. We argue that interaction with other carnivores probably also affected the diversification dynamics of canids.

evolutionary biology↗

bioRxiv2020

Nucleotide substitutions during speciation may explain substitution rate variation

Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

evolutionary biology↗

bioRxiv2019

Quantifying the importance of an inference model in Bayesian phylogenetics

O_LIPhylogenetic trees are currently routinely reconstructed from an alignment of character sequences (usually nucleotide sequences). Bayesian tools, such as MrBayes, RevBayes and BEAST2, have gained much popularity over the last decade, as they allow joint estimation of the posterior distribution of the phylogenetic trees and the parameters of the underlying inference model. An important ingredient of these Bayesian approaches is the species tree prior. In principle, the Bayesian framework allows for comparing different tree priors, which may elucidate the macroevolutionary processes underlying the species tree. In practice, however, only macroevolutionary models that allow for fast computation of the prior probability are used. The question is how accurate the tree estimation is when the real macroevolutionary processes are substantially different from those assumed in the tree prior. C_LIO_LIHere we present pirouette, a free and open-source R package that assesses the inference error made by Bayesian phylogenetics for a given macroevolutionary diversification model. pirouette makes use of BEAST2, but its philosophy applies to any Bayesian phylogenetic inference tool. C_LIO_LIWe describe pirouettes usage providing full examples in which we interrogate a model for its power to describe another. C_LIO_LILast, we discuss the results obtained by the examples and their interpretation. C_LI

evolutionary biology↗

bioRxiv2019

The role of preadaptation, propagule pressure and competition in the colonization of new habitats

To successfully colonize new habitats, organisms not only need to gain access to it, but also need to cope with the selective pressures imposed by the local biotic and abiotic conditions. The number of immigrants, the preadaptation to the local habitat and the presence of competitors are important factors determining the success of colonization. Here, using an experimental set-up, we test the combined effect of propagule pressure, preadaptation and interspecific competition on the colonization success of new habitats using the two-spotted spider mite (Tetranychus urticae) as our model system and the red spider mite (Tetranychus evansi) as a competitor. Our results show that propagule pressure and preadaptation positively affect colonization success. More successful populations reach larger final population sizes either by having higher per capita growth rate (due to preadaptation effect) or by starting a population with a larger number of individuals. Although populations are more successful colonizing non-competitive environments than competitive ones, propagule pressure and preadaptation counteract the negative effects of competition, promoting colonization success. Our results show the importance of propagule pressure and preadaptation to cope both with the exigencies of the new environment and the community context for successful colonization of new habitats.

evolutionary biology↗