Patterns of species ranges, speciation, and extinction

The exact nature of the relationship among species range sizes, speciation, and extinction events is not well understood. The factors that promote larger ranges, such as broad niche widths and high dispersal abilities, could increase the likelihood of encountering new habitats but also prevent local adaptation due to high gene flow. Similarly, low dispersal abilities or narrower niche widths could cause populations to be isolated, but such populations may lack advantageous mutations due to low population sizes. Here we present a large-scale, spatially explicit, individual-based model addressing the relationships between species ranges, speciation, and extinction. We followed the evolutionary dynamics of hundreds of thousands of diploid individuals for 200,000 generations. Individuals adapted to multiple resources and formed ecological species in a multidimensional trait space. These species varied in niche widths, and we observed the coexistence of generalists and specialists on a few resources. Our model shows that species ranges correlate with dispersal abilities but do not change with the strength of fitness trade-offs; however, high dispersal abilities and low resource utilization costs, which favored broad niche widths, have a strong negative effect on speciation rates. An unexpected result of our model is the strong effect of underlying resource distributions on speciation: in highly fragmented landscapes, speciation rates are reduced.     

Plant evolution: pulses of extinction and speciation in gymnosperm diversity

Living gymnosperms represent the survivors of ancient seed plant lineages whose fossil record reaches back 270 million years. Two recent studies find that recent pulses of extinction and speciation have shaped today's gymnosperm diversity, contradicting the widespread assumption that gymnosperms have remained largely unchanged for tens of millions of years.     

Animal body size distributions: patterns, mechanisms and implications

Documenting the shape of the frequency distribution of species body sizes for an animal taxon appears at first sight a straightforward task. However, a variety of patterns has been reported, and a consensus is only now being reached through an understanding of how potential biases may affect observed shapes of distributions. A new body of evidence suggests that, at large scales, size distributions are right-skewed, even on logarithmic axes. If body size distributions can be described with certainty, this will allow assessment of the mechanisms proposed to generate them, and will be an important step towards understanding the structure and dynamics of animal assemblages.     

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.     

Inferring speciation and extinction rates under different sampling schemes

The birth-death process is widely used in phylogenetics to model speciation and extinction. Recent studies have shown that the inferred rates are sensitive to assumptions about the sampling probability of lineages. Here, we examine the effect of the method used to sample lineages. Whereas previous studies have assumed random sampling (RS), we consider two extreme cases of biased sampling: "diversified sampling" (DS), where tips are selected to maximize diversity and "cluster sampling (CS)," where sample diversity is minimized. DS appears to be standard practice, for example, in analyses of higher taxa, whereas CS may occur under special circumstances, for example, in studies of geographically defined floras or faunas. Using both simulations and analyses of empirical data, we show that inferred rates may be heavily biased if the sampling strategy is not modeled correctly. In particular, when a diversified sample is treated as if it were a random or complete sample, the extinction rate is severely underestimated, often close to 0. Such dramatic errors may lead to serious consequences, for example, if estimated rates are used in assessing the vulnerability of threatened species to extinction. Using Bayesian model testing across 18 empirical data sets, we show that DS is commonly a better fit to the data than complete, random, or cluster sampling (CS). Inappropriate modeling of the sampling method may at least partly explain anomalous results that have previously been attributed to variation over time in birth and death rates.     

Estimating a binary character's effect on speciation and extinction

Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values.     

Shifting distributions and speciation: species divergence during rapid climate change

Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species distributions.     

Stochastic epidemic models with random environment: quasi-stationarity, extinction and final size

We investigate stochastic $SIS$ and $SIR$ epidemic models, when there is a random environment that influences the spread of the infectious disease. The inclusion of an external environment into the epidemic model is done by replacing the constant transmission rates with dynamic rates governed by an environmental Markov chain. We put emphasis on the algorithmic evaluation of the influence of the environmental factors on the performance behavior of the epidemic model.     

Reducing liposome size with ultrasound: bimodal size distributions

Sonication is a simple method for reducing the size of liposomes. We report the size distributions of liposomes as a function of sonication time using three different techniques. Liposomes, mildly sonicated for just 30 sec, had bimodal distributions when surface-weighted with modes at about 140 and 750 nm. With extended sonication, the size distribution remains bimodal but the average diameter of each population decreases and the smaller population becomes more numerous. Independent measurements of liposome size using Dynamic Light Scattering (DLS), transmission electron microscopy (TEM), and the nystatin/ergosterol fusion assay all gave consistent results. The bimodal distribution (even when number-weighted) differs from the Weibull distribution commonly observed for liposomes sonicated at high powers over long periods of time and suggests that a different mechanism may be involved in mild sonication. The observations are consistent with the following mechanism for decreasing liposome size. During ultrasonic irradiation, cavitation, caused by oscillating microbubbles, produces shear fields. Large liposomes that enter these fields form long tube-like appendages that can pinch-off into smaller liposomes. This proposed mechanism is consistent with colloidal theory and the observed behavior of liposomes in shear fields.     

Sympatric speciation and extinction driven by environment dependent sexual selection

A theoretical model is studied to investigate the possibility of sympatric speciation driven by sexual selection and ecological diversification. In particular we focus on the rock-dwelling haplochromine cichlid species in Lake Victoria. The high speciation rate in these cichlids has been explained by their apparent ability to specialize rapidly to a large diversity of feeding niches. Seehausen and colleagues however, demonstrated the importance of sexual selection in maintaining reproductive barriers between species. Our individual-orientated model integrates both niche differentiation and a Fisherian runaway process, which is limited by visibility constraints. The model shows rapid sympatric speciation or extinction of species, depending on the strength of sexual selection.     

Diversity,speciation, endemism and extinction in Devonian reef and level-bottom communities,eastern North America

Lower Devonian late Emsian (Bois Blanc and Clear Creek Limestones; Schoharie Formation) level-bottom communities in New York, Michigan and Illinois were moderately cosmopolitan and diverse and dominated by brachiopods and solitary rugose corals. Subsequently (Early Eifelian?), there was an important episode of cratonal patch reef building in New York (Edgecliff Member, Onondaga Limestone), southwestern Ontario (Formosa Reef Limestone, lower Detroit River Group), and the Hudson Bay Lowland (Kwataboahegan Formation) by highly diverse endemic communities. The Edgecliff reefs were built by corals whereas the Formosa and Kwataboahegan reefs were built primarily by stromatoporoids. The strong correlation between high diversity and high endemism during the reef-building episode suggests that these communities contained numberous, small species populations belonging to several major taxa — an example of rapid speciation by geographic isolation and genetic drift.     

Evolutionary dynamics at high latitudes: speciation and extinction in polar marine faunas

Ecologists have long been fascinated by the flora and fauna of extreme environments. Physiological studies have revealed the extent to which lifestyle is constrained by low temperature but there is as yet no consensus on why the diversity of polar assemblages is so much lower than many tropical assemblages. The evolution of marine faunas at high latitudes has been influenced strongly by oceanic cooling during the Cenozoic and the associated onset of continental glaciations. Glaciation eradicated many shallow-water habitats, especially in the Southern Hemisphere, and the cooling has led to widespread extinction in some groups. While environmental conditions at glacial maxima would have been very different from those existing today, fossil evidence indicates that some lineages extend back well into the Cenozoic. Oscillations of the ice-sheet on Milankovitch frequencies will have periodically eradicated and exposed continental shelf habitat, and a full understanding of evolutionary dynamics at high latitude requires better knowledge of the links between the faunas of the shelf, slope and deep-sea. Molecular techniques to produce phylogenies, coupled with further palaeontological work to root these phylogenies in time, will be essential to further progress.     

Genome size and extinction risk in vertebrates

The hypothesis of 'selfish DNA' is tested for the case of animals using the relation between genome size and conservation status of a given species. In contrast to plants, where the larger genome was previously shown to increase the likelihood of extinction, the picture is more complicated in animals. At the within-families and within-orders levels, the larger genome increases the risk of extinction only in reptiles and birds (which have the smallest genomes among tetrapods). In fishes and amphibians, the effect is caused by the higher taxonomic levels (above order). In several phylogenetic lineages of anamniotes, there is a correlation between a higher fraction of threatened species and a lower number of extant species in a lineage with the larger genome. In mammals, no effect was observed at any taxonomic level. The obtained data support the concept of hierarchical selection. It is also shown that, in plants and reptiles, the probability of being threatened increases from less than 10% to more than 80% with the increase in genome size, which can help in establishing conservation priorities.     

Relation between extinction angle and molecular size

The relation between the observed extinction angle of flow birefringence measurements and the dimensions of the dissolved macromolecules is presented in graphical form for rapid computation. The calculations are based on a rigid ellipsoidal model for the solute particles.     

Trilobite size-frequency distributions, recognition of instars, and phyletic size changes

Size-frequency analysis of over 5,000 Ordovician trilobites from the Teretiusculus Shales of the Builth inlier, central Wales, has revealed size distributions with counter intuitive shapes. Not only do most species show normal or slightly skewed distributions, despite the preponderance of moults, but there is no evidence of instar peaks. Such features can, however, be explained by reference to steady-state population structures of Recent marine arthropods, in which small individuals often form only a minor proportion of the post-larval population structure. Trilobite steady-state population structures would have differed in detail from species to species, but certain distribution shapes may have been characteristic of particular environments. These findings necessitate a reappraisal of previous work on trilobite size-frequency distributions, survivorship and recognition of instars. The Builth data also show the first clear evidence of phyletic size increase and parallel size changes in trilobites. ▭ Trilobites, size-frequency distributions, steady-state populations, instars, phyletic size changes.     

Local extinction and recolonization, species effective population size, and modern human origins

A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.