In 2000, Jamaica ranked third in the world in murders per capita (2). By the end of 2005, police crime data indicated a record number of annual homicides (63.0 per 100 000 inhabitants), a rate

Aim The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution.Location Worldwide.Methods Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program 'BioGeoBEARS'. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events. ResultsOur best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America.Main conclusions For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build-up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework.

Although the importance of regulatory and functional sequence evolution in generating species differences has been studied to some extent, much less is known about the role of other types of genomic changes, such as fluctuation in gene copy number. Here, we apply analyses of gene function and expression of anthocyanin pigment pathway genes, as well as cosegregation analyses in backcross populations, to examine the genetic changes involved in the shift from blue to red flowers in Andean Iochroma (Solanaceae). We demonstrate that deletion of a gene coding for an anthocyanin pathway enzyme was necessary for the transition to red floral pigmentation. The downregulation of a second pathway gene was also necessary for the novel flower color, and this regulatory pattern parallels the genetic change in the two other red-flowered species in the sister family Convolvulaceae in which flower color change has been examined genetically. Finally, we document a shift in enzymatic function at a third locus, but the importance of this change in the transition to red flowers depends on the exact order with which the three changes occurred. This study shows that gene inactivation or loss can be involved in the origin of phenotypic differences between species, thereby restricting the possibility of reversion to the ancestral state. It also demonstrates that parallel evolution of red flowers in three different species occurs via a common developmental/regulatory change but by mutations in different genes.

Differences in floral traits among plant species have often been attributed to adaptation to pollinators. We explored the importance of pollinator shifts in explaining floral divergence among 15 species of Iochroma. We examined four continuously varying floral traits: corolla length, nectar reward, display size, and flower color. Pollinator associations were characterized with a continuously varying measure of pollinator importance (the product of visitation and pollen deposition) for four groups of pollinators: hummingbirds, Hymenoptera, Lepidoptera, and Diptera. A phylogenetic generalized least squares approach was used to estimate correlations between pollinator groups and floral traits across a sample of Bayesian trees using different models of trait evolution. Multivariate analyses were also employed to identify suites of traits associated with each pollinator group. We found that nonphylogenetic models typically fit the data better than phylogenetic models (Brownian motion, Ornstein-Uhlenbeck), and thus results varied little across trees. Our results indicated that species with high nectar reward and large displays are significantly more likely to be pollinated by hummingbirds and less likely to be pollinated by all groups of insects. Corolla length and flower color did not show any consistently significant associations with pollinator groups. For these two traits, we discuss alternative evolutionary forces, including phylogenetic inertia and community-level factors.

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.