Thijs Janzen

Can clade age alone explain the relationship between body size and diversity

One of the most striking patterns observed among animals is that smaller-bodied taxa are generally much more diverse than larger-bodied taxa. This observation seems to be explained by the mere fact that smaller-bodied taxa tend to have an older evolutionary origin and have therefore had more time to diversify. A few studies, based on the prevailing null model of diversification (i.e. the stochastic constant-rate birth–death model), have suggested that this is indeed the correct explanation, and body-size dependence of speciation and extinction rates does not play a role. However, there are several potential shortcomings to these studies: a suboptimal statistical procedure and a relatively narrow range of body sizes in the analysed data. Here, we present a more coherent statistical approach, maximizing the likelihood of the constant-rate birth–death model with allometric scaling of speciation and extinction rates, given data on extant diversity, clade age and average body size in each clade. We applied our method to a dataset compiled from the literature that includes a wide range of Metazoan taxa (range from midges to elephants). We find that the higher diversity among small animals is indeed, partly, caused by higher clade age. However, it is also partly caused by the body-size dependence of speciation and extinction rates. We find that both the speciation rate and extinction rate decrease with body size such that the net diversification rate is close to 0. Even more interestingly, the allometric scaling exponent of speciation and extinction rates is approximately −0.25, which implies that the per generation speciation and extinction rates are independent of body size. This suggests that the observed relationship between diversity and body size pattern can be explained by clade age alone, but only if clade age is measured in generations rather than years. Thus, we argue that the most parsimonious explanation for the observation that smaller-bodied taxa are more diverse is that their evolutionary clock ticks faster.

A new modeling approach estimates the relative importance of different community assembly processes

The relative importance of niche-based (e.g., competitive or stress-based) and stochastic (e.g., random dispersal) processes in structuring ecological communities is frequently analyzed by studying trait distributions of co-occurring species. While filtering processes, such as the exclusion of stress-intolerant species from particular habitats, increase the trait similarity between co-occurring species, other processes, such as resource competition, can limit the similarity of co-occurring species. Comparing the observed trait distribution patterns in communities to null expectations from randomized communities (e.g., a draw of the same observed richness from the regional pool) therefore gives a first indication of the dominant process driving community assembly. However, such comparisons do not inform us about the relative contribution of these different processes in shaping community compositions in case of their joint operation (a likely scenario). Using an Approximate Bayesian Computation approach, we develop a new method that allows inference of the relative importance of dispersal, filtering, and limiting similarity processes for the assembly of observed communities with known species and trait composition. We applied this approach to a tree community data set, collected across 20 plots along strong rainfall and fire gradients in a South African savanna. Based on comparisons with simulations, we find that our new approach is powerful in identifying which community assembly scenario has the highest probability to generate the observed trait distribution patterns, while traditional null model comparisons perform poorly in detecting signs of limiting similarity. For the studied savanna tree communities, our analysis yields that dispersal processes are most important in shaping the functional trait distribution patterns. Furthermore, our models indicate that filtering processes were relatively most important in areas with high fire frequencies, while limiting similarity processes were relatively most important in areas with low fire frequency and high rainfall. We conclude that our new method is a promising improvement on current approaches to estimate the relative importance of community assembly processes across different species groups, ecosystems, and biomes. Future model modifications (e.g., the inclusion of individual-based processes) could provide further steps in uncovering the underlying assembly processes behind observed community patterns.

Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT

Molecular phylogenies form a potential source of information on rates of diversification, and the mechanisms that underlie diversification patterns. Diversification models have become increasingly complex over the past decade, and we have reached a point where the computation of the analytical likelihood of the model given a phylogeny is either unavailable or intractable. For such models, a likelihood-free approach such as Approximate Bayesian Computation (ABC) offers a solution. ABC is a Bayesian framework that uses one or more summary statistics instead of the likelihood function. Crucial to the performance of an ABC algorithm is the choice of summary statistics. Here, we analyse the applicability of three traditional and often-used summary statistics (Gamma statistic, Phylogenetic Diversity and tree size) within an ABC framework and propose a new summary statistic: the normalized Lineages-Through-Time (nLTT) statistic. We find that the traditional summary statistics perform poorly and should not be used as a substitute of the likelihood. By contrast, we find that the nLTT statistic performs on par with the likelihood. We suggest to include the nLTT statistic in future ABC applications within phylogenetics. We argue that the use of ABC in diversification rate analysis is a promising new approach, but that care should be taken which summary statistics are chosen.

A sampling formula for ecological communities with multiple dispersal syndromes

Over the past decade, the neutral theory of biodiversity has stirred up community assembly theory considerably by suggesting that stochasticity in the form of ecological drift is an important factor determining community composition and community turnover. The neutral theory assumes that all species within a community are functionally equivalent (the neutrality assumption), and therefore applies best to communities of trophically similar species. Evidently, trophically similar species may still differ in dispersal ability, and therefore may not be completely functionally equivalent. Here we present a new sampling formula that takes into account the partitioning of a community into two guilds that differ in immigration rate. We show that, using this sampling formula, we can accurately detect a subdivision into guilds from species abundance distributions, given ecological data about dispersal ability. We apply our sampling formula to tropical tree data from Barro Colorado Island, Panama. Tropical trees are divided depending on their dispersal mode, where biotically dispersed trees are grouped as one guild, and abiotically dispersed trees represent another guild. We find that breaking neutrality by adding guild structure to the neutral model significantly improves the fit to data and provides a better understanding of community assembly on BCI. Our findings are thus an important step towards an integration of neutral and niche theory.

Cyclical succession in grazed ecosystems: The importance of interactions between different-sized herbivores and different-sized predators

Body size of vertebrate herbivores is strongly linked to other life history traits, most notably (1) tolerance of low quality forage and (2) vulnerability to predation, which both impact the composition and dynamics of natural communities. However, no study has thus far explored how the combination of these two body-size related traits affects the long-term composition and dynamics of the herbivore and plant communities. We made a simple model of ordinary differential equations and simulated a grassland system with three herbivore species (small, medium, large) and two predator species (small, large) to investigate how the combination of low-quality tolerance and predation-vulnerability structure the herbivore and plant community. We found that facilitation and competition between different-sized herbivores and predation by especially small predators stimulate coexistence among herbivore species. Furthermore, the interaction between different-sized herbivores and predators generated cyclical succession in the plant community, i.e. alternating periods of short vegetation dominated by high-quality plants, with periods of tall vegetation dominated by low-quality plants. Our results suggest that cyclical succession in plant communities is more likely to occur when a predator predominantly preys on small herbivore species. Large predators also play an important role, as their addition relaxed the set of conditions under which cyclical succession occurred. Consequently, our model predictions suggest that a diverse predator community plays an important role in the long-term dynamics and maintenance of diversity in both the herbivore and plant community.

Modeling the contributions of chromosome segregation errors and aneuploidy to Saccharomyces hybrid sterility

Errors in meiosis can be important postzygotic barriers between different species. In Saccharomyces hybrids, chromosomal missegregation during meiosis I produces gametes with missing or extra chromosomes. Gametes with missing chromosomes are inviable, but we do not understand how extra chromosomes (disomies) influence hybrid gamete inviability. We designed a model predicting rates of missegregation in interspecific hybrid meioses assuming several different mechanisms of disomy tolerance, and compared predictions from the model with observations of sterility in hybrids between Saccharomyces yeast species. Sterility observations were consistent with the hypothesis that chromosomal missegregation causes hybrid sterility, and the model indicated that missegregation probabilities of 13–50% per chromosome can cause observed values of 90–99% hybrid sterility regardless of how cells tolerate disomies. Missing chromosomes in gametes are responsible for most infertility, but disomies may kill as many as 11% of the gametes produced by hybrids between Saccharomyces cerevisiae and Saccharomyces paradoxus. Copyright

The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites

When a lineage originates from hybridization genomic blocks of contiguous ancestry from different ancestors are fragmented through genetic recombination. The resulting blocks are delineated by so called junctions, which accumulate with every generation that passes. Modeling the accumulation of ancestry block junctions can elucidate processes and timeframes of genomic admixture. Previous models have not addressed ancestry block dynamics for chromosomes that consist of a finite number of recombination sites. However, genomic data typically consist of informative markers that are interspersed with fragments for which no ancestry information is available. Hence, repeated recombination events may occur between markers, effectively removing existing junctions. Here, we present an analytical treatment of the dynamics of the mean number of junctions over time, taking into account the number of recombination sites per chromosome, population size, genetic map length, and the frequency of the ancestral species in the founding hybrid swarm. We describe the expected number of junctions using equidistant molecular markers and estimate the number of junctions using random markers. This extended theory of junctions thus reflects properties of empirical data and can serve to study the genomic patterns following admixture.

Community assembly in Lake Tanganyika cichlid fish : Quantifying the contributions of both niche-based and neutral processes

Abstract 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 short, ecological timescales. Here, we investigate the relative importance of niche‐based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche‐based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche‐based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche‐based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche‐based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche‐based or neutral‐based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.

Stochastic processes dominate community assembly in cichlid communities in Lake Tanganyika

The African Great Lakes are characterized by an extraordinary diversity of endemic cichlid fish species. The cause of this diversity is still largely unknown. Most studies have tried to solve this question by focusing on macro-evolutionary processes, such as speciation. However, the ecological processes determining local cichlid diversity have so far been understudied, even though knowledge on these might be crucial for understanding larger scale biodiversity patterns. Using trait, environmental and abundance data of cichlid fishes along 36 transects, we have studied how differences in local environmental conditions influence cichlid community assembly in the littoral of Lake Tanganyika, Zambia. We investigated changes in average trait values and in trait-based community assembly processes along three key environmental gradients. Species diversity and local abundance decreased with increasing sand cover and diet-associated traits changed with depth. Analyses on within-community trait diversity patterns indicated that cichlid community assembly was mainly driven by stochastic processes, to a smaller extent by processes that limit the similarity among co-existing species and least by filtering processes that limit the range of species traits occurring in an environment. Despite, the low impact of habitat filtering processes, we find community dissimilarity to increase with increasing environmental difference. Our results suggest that local environmental conditions determine cichlid abundance, while the predominance of stochastic community assembly across all environments explains why the communities with the highest abundances contain most species.

Inferring the role of habitat dynamics in driving diversification: evidence for a species pump in Lake Tanganyika cichlids

Geographic isolation that drives speciation is often assumed to slowly increase over time, for instance through the formation of rivers, the formation of mountains or the movement of tectonic plates. Cyclic changes in connectivity between areas may occur with the advancement and retraction of glaciers, with water level fluctuations in seas between islands or in lakes that have an uneven bathymetry. These habitat dynamics may act as a driver of allopatric speciation and propel local diversity. Here we present a parsimonious model of the interaction between cyclical (but not necessarily periodic) changes in the environment and speciation, and provide an ABC-SMC method to infer the rates of allopatric and sympatric speciation from a phylogenetic tree. We apply our approach to the posterior sample of an updated phylogeny of the Lamprologini, a tribe of cichlid fish from Lake Tanganyika where such cyclic changes in water level have occurred. We find that water level changes play a crucial role in driving diversity in Lake Tanganyika. We note that if we apply our analysis to the Most Credible Consensus tree, we do not find evidence for water level changes influencing diversity in the Lamprologini, suggesting that the MCC tree is a misleading representation of the true species tree. Furthermore, we note that the signature of habitat dynamics is found in the posterior sample despite the fact that this sample was constructed using a species tree prior that ignores habitat dynamics. However, in other cases this species tree prior might erase this signature. Hence we argue that in order to improve inference of the effect of habitat dynamics on biodiversity, phylogenetic reconstruction methods should include tree priors that explicitly take into account such dynamics.