Rampal S. Etienne

Rampal S. Etienne
University of Groningen | RUG · Groningen Institute for Evolutionary Life Sciences

PhD

About

199
Publications
38,408
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8,858
Citations
Additional affiliations
September 2002 - present
Rijksuniversiteit Groningen
February 1998 - August 2002
Wageningen University & Research
Position
  • Wageningen University

Publications

Publications (199)
Article
Full-text available
Microbiomes are involved in most vital processes, such as immune response, detoxification, and digestion and are thereby elementary to organismal functioning and ultimately the host’s fitness. In turn, the microbiome may be influenced by the host and by the host’s environment. To understand microbiome dynamics during the process of adaptation to ne...
Code
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See e.g. Valente et al. 2015. Ecology Letters 18: 844-852, <doi:10.1111/ele.12461>. See https://cran.r-project.org/web/packages/DAISIE/index.html for details.
Article
Full-text available
ABSTRACT The process of adaptation towards novel environments is directly connected to the acquisition of a higher fitness relative to others. Such an increased fitness is obtained by changes in life history traits that may directly impact population dynamics. From a functional perspective, increased fitness can be achieved through a higher resourc...
Preprint
Full-text available
Understanding macroevolution on islands requires knowledge of the closest relatives of island 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 inform...
Article
Full-text available
Herbivore diets are often generalistic, and communities of herbivores tend to share much of their diets. In the tropical lowlands of Malaysian Borneo, tens of different noncarnivorous land snail species are able to coexist in communities on limestone outcrops. We tried to answer the question whether diet differentiation plays a role in their coexis...
Article
Full-text available
Low-elevation regions harbour the majority of the world’s species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics,...
Article
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Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the con...
Preprint
Full-text available
Aim: Biodiversity 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...
Preprint
Full-text available
Diversity-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. Suc...
Preprint
DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is a framework for a dynamic stochastic model of island biogeography that can be used to estimate the rates of colonisation, speciation and extinction (CES rates) from phylogenetic trees of insular communities by maximum likelihood, and to simulate such data sets gi...
Article
Full-text available
Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co‐occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other la...
Article
Full-text available
Most ecological communities are facing changing environments, particularly due to global change. When migration is impossible, adaptation to these altered environments is necessary to survive. Yet, we have little theoretical understanding how ecological communities respond both ecologically and evolutionarily to such environmental change. Here we i...
Preprint
Full-text available
Low elevation regions harbor the majority of the world’s species diversity compared to high elevation areas. This global elevational diversity gradient, suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands (either due to higher ecological limits or intrinsically higher div...
Article
Full-text available
Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co‐occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other la...
Article
Full-text available
Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein-Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abio...
Article
Full-text available
Aim Rates of colonization, speciation and extinction determine species richness and endemism in insular systems. The general dynamic model of island biogeography (GDM) predicts that speciation and extinction rates depend on island area and elevation via their control on ecological limits to diversification and therefore covary with an island's geol...
Article
Full-text available
To successfully colonize new habitats, organisms not only need to gain access to it, they 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. H...
Article
Full-text available
Background A central tenet of the evolutionary theory of communities is that competition impacts evolutionary processes such as local adaptation. Species in a community exert a selection pressure on other species and may drive them to extinction. We know, however, very little about the influence of unsuccessful or ghost species on the evolutionary...
Preprint
Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein-Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abio...
Preprint
The Janzen-Connell (J-C) hypothesis states that species-specific natural enemies (pathogens, predators) induce local-density dependence which explains high diversity observed in tropical tree communities. However, these natural enemies often attack phylogenetically related species as well. Here, we use a spatially explicit model in which the contin...
Article
Full-text available
Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness1–6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island7,8. Notably, there has been no robust global test of this predictio...
Article
Full-text available
Vascular epiphytes form a diverse group of almost 30 000 species, yet theory concerning their community structure is still largely lacking. We therefore employed the simplest models of biodiversity, (near‐)neutral models, to generate hypotheses concerning their community structure. With recently developed tools for (near‐)neutral models we analyzed...
Preprint
Full-text available
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. He...
Article
Full-text available
Local adaptation is determined by the strength of selection and the level of gene flow within heterogeneous landscapes. The presence of benign habitat can act as an evolutionary stepping stone for local adaptation to challenging environments by providing the necessary genetic variation. At the same time, migration load from benign habitats will hin...
Article
Full-text available
Aim Islands are often hotspots of endemism due to their isolation, making colonization a rare event and hence facilitating allopatric speciation. Dispersal usually occurs between nearby locations according to a stepping‐stone model. We aimed to reconstruct colonization and speciation processes in an endemic‐rich system of land‐based islands that do...
Article
Full-text available
Aim The great variation in range sizes among species has fascinated ecologists for decades. Reef‐associated fish species live in highly spatially structured habitats and adopt a wide range of dispersal strategies. We consequently expect species with greater dispersal ability to occupy larger ranges. However, empirical evidence for such a positive r...
Article
Full-text available
Aim Island biogeography theory describes how island size and isolation determine population colonization success. Large islands sustain larger populations than small ones and experience less demographic stochasticity, thus a lower extinction risk. Nearby islands are more likely to be colonized than distant ones, because they receive more immigrants...
Article
Full-text available
Dispersal is thought to be an important process determining range size, especially for species in highly spatially structured habitats, such as tropical reef fishes. Despite intensive research efforts, there is conflicting evidence about the role of dispersal in determining range size. We hypothesize that traits related to dispersal drive range siz...
Preprint
Full-text available
A report for the Malacological Society of London, who awarded me an Early Career Research Grant for fieldwork on microsnail communities on Borneo in November 2017. Some first results of our metabarcoding study are included.
Data
Table S1. Parameter values explored in the simulations.
Article
Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The State-dependent Speciation and Extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (Multiple-States dependent Specia...
Article
Coinfecting parasites and pathogens remain a leading challenge for global public health due to their consequences for individual-level infection risk and disease progression. However, a clear understanding of the population-level consequences of coinfection is lacking. Here, we constructed a model that includes three individual-level effects of coi...
Article
Full-text available
The role of ecological limits in regulating the distribution and diversification of species remains controversial. Although such limits must ultimately arise from constraints on local species coexistence, this spatial context is missing from most macroevolutionary models. Here, we develop a stochastic, spatially explicit model of species diversific...
Data
Fig. S1. A list of phylogenetic trees of Scenario 2. Fig. S2. A list of phylogenetic trees of Scenario 3. Fig. S3. Parameter estimations for Scenario 2 versus Scenarios 4 and 5. Fig. S4. Parameter estimations for Scenario 3 versus Scenarios 4 and 5. Fig. S5. P‐values and powers of the test of spatial Scenario 2 versus non‐spatial Scenarios 4 an...
Article
Full-text available
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification - extinction rates in particular - can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossili...
Article
1.In the field of phylogenetics, BEAST2 is one of the most widely used software tools. It comes with the graphical user interfaces BEAUti 2, DensiTree and Tracer, to create BEAST2 configuration files and to in‐terpret BEAST2's output files. However, when many different alignments or model setups are required, a workflow of graphical user interfaces...
Article
Full-text available
Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum likelihood method to detect diversity‐dependent diversification from phylogenetic branching times exists, but it assumes...
Preprint
Full-text available
In the field of phylogenetics, BEAST2 is one of the most widely used software tools. It comes with the graphical user interfaces BEAUti 2, DensiTree and Tracer, to create BEAST2 configuration files and to interpret BEAST2’s output files. However, when many different alignments or model setups are required, a workflow of graphical user interfaces is...
Article
Island biogeography aims at inferring the processes that govern the assembly of communities in space and time. Molecular phylogenies can tell us about the timings of island colonisations and diversification, but have rarely been used for the estimation of colonisation, speciation and extinction rates on islands. In this study we illustrate the effe...
Article
Full-text available
The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speci...
Preprint
Full-text available
Aim The great variation in range sizes among species has fascinated ecologists for decades. In reef-associated fish species, which live in fragmented habitats and adopt a wide range of dispersal strategies, we may expect species with greater dispersal ability to spread over larger ranges. However, empirical evidence for such a positive relationship...
Article
Full-text available
Co-infecting parasites and pathogens remain a leading challenge for global public health due to their consequences for individual-level infection risk and disease progression. However, a clear understanding of the population-level consequences of co-infection is lacking. Here, we constructed a model that includes three individual-level effects of c...
Article
Full-text available
The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic process...
Poster
Full-text available
The tropical lowland of the Kinabatangan Floodplain in northern Borneo, Malaysia, is characterized by limestone outcrops dotted through the rainforest, forming an island system. The calcareous substrate attracts many, often microscopically small, snail species, using the calcium carbonate to build their shells. Each outcrop can hold over 50 species...
Article
Full-text available
Dispersal and competition have both been suggested to drive variation in adaptability to a new environment, either positively or negatively. A simultaneous experimental test of both mechanisms is however lacking. Here, we experimentally investigate how population dynamics and local adaptation to a new host plant in a model species, the two-spotted...
Article
Half a century ago, MacArthur and Wilson proposed that the number of species on islands tends toward a dynamic equilibrium diversity around which species richness fluctuates [1]. The current prevailing view in island biogeography accepts the fundamentals of MacArthur and Wilson’s theory [2] but questions whether their prediction of equilibrium can...
Article
Full-text available
The development of neutral community theory has shown that the assumption of species neutrality, although implausible on the level of individual species, can lead to reasonable predictions on the community level. While Hubbell's neutral model and several of its variants have been analyzed in quite some detail, the comparison of theoretical predicti...
Article
Full-text available
The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively sh...
Article
Full-text available
Islands are ideal systems to model temporal changes in biodiversity and reveal the influence of humans on natural communities. Although theory predicts biodiversity on islands tends towards an equilibrium value, the recent extinction of large proportions of island biotas complicates testing this model. The well-preserved subfossil record of Caribbe...
Article
Full-text available
Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for hete...