Half a century ago, MacArthur & Wilson proposed that the number of species on islands tends t... more Half a century ago, MacArthur & Wilson proposed that the number of species on islands tends towards a dynamic equilibrium diversity around which species richness fluctuates. The current prevailing view in island biogeography accepts the fundamentals of MacArthur & Wilson's theory, but questions whether their prediction of equilibrium can be fulfilled over evolutionary time scales, given the unpredictable and ever-changing nature of island geological and biotic features. Here we conduct a complete molecular phylogenetic survey of the terrestrial bird species from four oceanic archipelagos that make up the diverse Macaronesian bioregion - Azores, Canary Islands, Cape Verde and Madeira. We estimate the times at which birds colonized and speciated in the four archipelagos, including many previously unsampled endemic and non-endemic taxa and their closest continental relatives. We develop and fit a new multi-archipelago dynamic stochastic model to these data, explicitly incorporating information from 91 taxa, both extant and extinct. Remarkably, we find that all four archipelagos have independently achieved and maintained a dynamic equilibrium over millions of years. Biogeographical rates are homogenous across archipelagos, except for the Canary Islands, which exhibit higher speciation and colonization. Our finding that the avian communities of the four Macaronesian archipelagos display an equilibrium diversity pattern indicates that a diversity plateau may be rapidly achieved on islands where rates of in situ radiation are low and extinction is high. This study reveals that equilibrium processes may be more prevalent than recently proposed, supporting MacArthur & Wilson's 50 year old theory
The application of state-dependent speciation and extinction models to phylogenetic trees has sho... more The application of state-dependent speciation and extinction models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration, and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction, and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trai...
The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees h... more The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has revealed an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. Here, we perform a robustness study to identify how trait-dependence in rates of island colonization, extinction and speciation (CES rates) affects the estimation accuracy of a phylogenetic model that assumes no rate variation between trait states. We extend the DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) simulation model to include state-dependent rates, and evaluate the robustness of the DAISIE inference model using simulated data. Our results show that when the CES rate differences between trait states are moderate, DAISIE shows negligible error for a variety of island diversity metrics. However, for large differences in speciation ...
Diversity-dependent diversification models have been extensively used to study the effect of ecol... more 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. 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 canno...
Being part of a group facilitates cooperation between group members, but also creates competition... more Being part of a group facilitates cooperation between group members, but also creates competition for limited resources. This conundrum is problematic for gravid females who benefit from being in a group, but whose future offspring may struggle for access to nutrition in larger groups. Females should thus modulate their reproductive output depending on their social context. Although social-context dependent modulation of reproduction is documented in a broad range of species, its underlying mechanisms and functions are poorly understood. In the fruit flyDrosophila melanogaster,females actively attract conspecifics to lay eggs on the same resources, generating groups in which individuals may cooperate or compete. The tractability of the genetics of this species allows dissecting the mechanisms underlying physiological adaptation to their social context.Here, we show that females produce eggs increasingly faster as group size increases. By laying eggs faster in group than alone, femal...
ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly cons... more ABSTRACTAlthough 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, however, is just a statistical distribution of mutation rates without any 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 acr...
SummaryIn the field of phylogenetics, BEAST2 is one of the most widely used software tools. It co... more SummaryIn 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 cumbersome.Here, we present a free, libre and open-source package, babette: ‘BEAUti 2, BEAST2 and Tracer for R’, for the R programming language. babette creates BEAST2 input files, runs BEAST2 and parses its results, all from an R function call.We describe babette’s usage and the novel functionality it provides compared to the original tools and we give some examples.As babette is designed to be of high quality and extendable, we conclude by describing the further development of the package.
AimIsland biogeography theory describes how island size and isolation determine population coloni... more AimIsland 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 from the mainland. However, local conditions on islands are often different from those on the mainland; therefore, populations on recently colonized islands also need to adapt. Island size and isolation are known to impact the build‐up of genetic variation necessary for adaptation; hence, we integrated island biogeography with evolution experimentally to gain a better understanding of the roles of island size and isolation in biodiversity patterns.LocationLaboratory, Ghent University, Belgium.Time periodOctober 2013 to June 2014.Major taxa studiedTwo‐spotted spider mite (Tetranychus urticae).MethodsUsing experimental evolution, we studied ...
Half a century ago, MacArthur & Wilson proposed that the number of species on islands tends t... more Half a century ago, MacArthur & Wilson proposed that the number of species on islands tends towards a dynamic equilibrium diversity around which species richness fluctuates. The current prevailing view in island biogeography accepts the fundamentals of MacArthur & Wilson's theory, but questions whether their prediction of equilibrium can be fulfilled over evolutionary time scales, given the unpredictable and ever-changing nature of island geological and biotic features. Here we conduct a complete molecular phylogenetic survey of the terrestrial bird species from four oceanic archipelagos that make up the diverse Macaronesian bioregion - Azores, Canary Islands, Cape Verde and Madeira. We estimate the times at which birds colonized and speciated in the four archipelagos, including many previously unsampled endemic and non-endemic taxa and their closest continental relatives. We develop and fit a new multi-archipelago dynamic stochastic model to these data, explicitly incorporating information from 91 taxa, both extant and extinct. Remarkably, we find that all four archipelagos have independently achieved and maintained a dynamic equilibrium over millions of years. Biogeographical rates are homogenous across archipelagos, except for the Canary Islands, which exhibit higher speciation and colonization. Our finding that the avian communities of the four Macaronesian archipelagos display an equilibrium diversity pattern indicates that a diversity plateau may be rapidly achieved on islands where rates of in situ radiation are low and extinction is high. This study reveals that equilibrium processes may be more prevalent than recently proposed, supporting MacArthur & Wilson's 50 year old theory
The application of state-dependent speciation and extinction models to phylogenetic trees has sho... more The application of state-dependent speciation and extinction models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration, and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction, and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trai...
The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees h... more The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has revealed an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. Here, we perform a robustness study to identify how trait-dependence in rates of island colonization, extinction and speciation (CES rates) affects the estimation accuracy of a phylogenetic model that assumes no rate variation between trait states. We extend the DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) simulation model to include state-dependent rates, and evaluate the robustness of the DAISIE inference model using simulated data. Our results show that when the CES rate differences between trait states are moderate, DAISIE shows negligible error for a variety of island diversity metrics. However, for large differences in speciation ...
Diversity-dependent diversification models have been extensively used to study the effect of ecol... more 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. 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 canno...
Being part of a group facilitates cooperation between group members, but also creates competition... more Being part of a group facilitates cooperation between group members, but also creates competition for limited resources. This conundrum is problematic for gravid females who benefit from being in a group, but whose future offspring may struggle for access to nutrition in larger groups. Females should thus modulate their reproductive output depending on their social context. Although social-context dependent modulation of reproduction is documented in a broad range of species, its underlying mechanisms and functions are poorly understood. In the fruit flyDrosophila melanogaster,females actively attract conspecifics to lay eggs on the same resources, generating groups in which individuals may cooperate or compete. The tractability of the genetics of this species allows dissecting the mechanisms underlying physiological adaptation to their social context.Here, we show that females produce eggs increasingly faster as group size increases. By laying eggs faster in group than alone, femal...
ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly cons... more ABSTRACTAlthough 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, however, is just a statistical distribution of mutation rates without any 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 acr...
SummaryIn the field of phylogenetics, BEAST2 is one of the most widely used software tools. It co... more SummaryIn 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 cumbersome.Here, we present a free, libre and open-source package, babette: ‘BEAUti 2, BEAST2 and Tracer for R’, for the R programming language. babette creates BEAST2 input files, runs BEAST2 and parses its results, all from an R function call.We describe babette’s usage and the novel functionality it provides compared to the original tools and we give some examples.As babette is designed to be of high quality and extendable, we conclude by describing the further development of the package.
AimIsland biogeography theory describes how island size and isolation determine population coloni... more AimIsland 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 from the mainland. However, local conditions on islands are often different from those on the mainland; therefore, populations on recently colonized islands also need to adapt. Island size and isolation are known to impact the build‐up of genetic variation necessary for adaptation; hence, we integrated island biogeography with evolution experimentally to gain a better understanding of the roles of island size and isolation in biodiversity patterns.LocationLaboratory, Ghent University, Belgium.Time periodOctober 2013 to June 2014.Major taxa studiedTwo‐spotted spider mite (Tetranychus urticae).MethodsUsing experimental evolution, we studied ...
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