Nonstochastic variation of species-level diversification rates within angiosperms

Variations in the origination and extinction rates of species over geological time often are linked with a range of factors, including the evolution of key innovations, changes in ecosystem structure, and environmental factors such as shifts in climate and physical geography. Before hypothesizing causality of a single factor, it is critical to demonstrate that the observed variation in diversification is significantly greater than one would expect due to natural stochasticity in the evolutionary branching process. Here, we use a likelihood-ratio test to compare taxonomic rate heterogeneity to a neutral birth-death model, using data on well-supported sister pairs of taxa and their species richness. We test the likelihood that the distribution of extant species among angiosperm genera and families could be the result of constant diversification rates. Results strongly support the conclusion that there is significantly more heterogeneity in diversity at the species level within angiosperms than would be expected due to stochastic processes. This result is consistent in datasets of genus pairs and family pairs and is not affected significantly by degrading pairs to simulate inaccuracy in the assumption of simultaneous origin of sister taxa. When we parse taxon pairs among higher groups of angiosperms, results indicate that a constant rates model is not rejected by rosid and basal eudicot pairs but is rejected by asterid and eumagnoliid pairs. These results provide strong support for the hypothesis that species-level rates of origination and/or extinction have varied nonrandomly within angiosperms and that the magnitude of heterogeneity varies among major groups within angiosperms.     

Environmental regulation of mutation rates at specific sites

Recent studies on bacterial adaptation to stress suggest that bacteria can regulate the generation of mutations at specific sites in response to environmental conditions. Here, we review these findings and discuss the circumstances under which these mechanisms might prove advantageous.     

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies in yeast or plants have shown that the effects of such duplications can be mediated by a complex pattern of gene retention and changes in evolutionary pressure. To explore such patterns in fishes, we have determined by phylogenetic analysis the evolutionary origin of 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species of actinopterygian fishes. The subset of genes, which was retained in double after the genome duplication, is enriched in development, signaling, behavior, and regulation functional categories. The evolutionary rate of duplicate fish genes appears to be determined by 3 forces: 1) fish proteins evolve faster than mammalian orthologs; 2) the genes kept in double after genome duplication represent the subset under strongest purifying selection; and 3) following duplication, there is an asymmetric acceleration of evolutionary rate in one of the paralogs. These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals.     

Rate asymmetry after genome duplication causes substantial long-branch attraction artifacts in the phylogeny of Saccharomyces species

Whole-genome duplication (WGD) produces sets of gene pairs that are all of the same age. We therefore expect that phylogenetic trees that relate these pairs to their orthologs in other species should show a single consistent topology. However, a previous study of gene pairs formed by WGD in the yeast Saccharomyces cerevisiae found conflicting topologies among neighbor-joining (NJ) trees drawn from different loci and suggested that this conflict was the result of "asynchronous functional divergence" of duplicated genes (Langkjaer, R. B., P. F. Cliften, M. Johnston, and J. Piskur. 2003. Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature 421:848-852). Here, we test whether the conflicting topologies might instead be due to asymmetrical rates of evolution leading to long-branch attraction (LBA) artifacts in phylogenetic trees. We constructed trees for 433 pairs of WGD paralogs in S. cerevisiae with their single orthologs in Saccharomyces kluyveri and Candida albicans. We find a strong correlation between the asymmetry of evolutionary rates of a pair of S. cerevisiae paralogs and the topology of the tree inferred for that pair. Saccharomyces cerevisiae gene pairs with approximately equal rates of evolution tend to give phylogenies in which the WGD postdates the speciation between S. cerevisiae and S. kluyveri (B-trees), whereas trees drawn from gene pairs with asymmetrical rates tend to show WGD pre-dating this speciation (A-trees). Gene order data from throughout the genome indicate that the "A-trees" are artifacts, even though more than 50% of gene pairs are inferred to have this topology when the NJ method as implemented in ClustalW (i.e., with Poisson correction of distances) is used to construct the trees. This LBA artifact can be ameliorated, but not eliminated, by using gamma-corrected distances or by using maximum likelihood trees with robustness estimated by the Shimodaira-Hasegawa test. Tests for adaptive evolution indicated that positive selection might be the cause of rate asymmetry in a substantial fraction (19%) of the paralog pairs.     

Potential rates and pathways of microbial nitrate reduction in coastal sediments

Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal sediments. Potential rates of nitrate reduction were measured on undisturbed sediment slices from two eutrophic coastal environments using flow-through reactors (FTR). Maximum potential nitrate reduction rates ranged over an order of magnitude, with values of up to 933 nmol cm(-3) h(-1), whereas affinity constants for NO(3) (-) fell mostly between 200 and 600 microM. Homogenized sediment slurries systematically yielded higher rates of nitrate reduction than the FTR experiments. Dentrification was the major nitrate removal pathway in the sediments, although excess ammonium production indicated a contribution of dissimilatory nitrate reduction to ammonium under nitrate-limiting conditions.     

Recent progress in understanding the evolution of carnivorous lentibulariaceae (lamiales)

Carnivorous plants have emerged as model systems for addressing many ecological and evolutionary questions, and since Lentibulariaceae comprise more than half of all known carnivorous species (325 spp.), they are of particular interest. Studies using various molecular markers have established that Lentibulariaceae and their three genera are monophyletic with Pinguicula being sister to a Genlisea-Utricularia-clade, while the closest relatives of the family remain uncertain. Character states of the carnivorous syndrome in related proto-carnivorous lamialean families apparently emerged independently. In Utricularia, the terrestrial habit has been reconstructed as plesiomorphic, and an extension of subgenus Polypompholyx is warranted. In the protozoan-attracting Genlisea, subgenus Tayloria is revealed as basal lineage. In Pinguicula, the six major lineages found reflect radiations in clearly defined geographic regions, whereas most previously recognized subgeneric taxa are non-monophyletic. Genlisea and Utricularia exhibit substitutional rates that rank among the highest in angiosperms for the molecular markers analyzed. One possible explanation for this lies in selective constraints on a wide range of genomic regions that may have been lowered due to the use of an alternative mode of acquiring nutrients.     

Factors affecting the distribution, abundance and diversity of fishes of small, soft-substrata tidal pools within Moreton Bay, Australia

Clearance rates of Limnoperna fortunei (Bivalvia) were investigated in laboratory experiments using monocultures of the alga Chlorella vulgaris. Experimental conditions included two mollusc sizes (15 and 23 mm), and three water temperatures (15, 20 and 25 °C) covering the normal seasonal range in the lower Paraná river and Río de la Plata estuary. Filtration rates obtained were, for the larger mussels: 9.9, 13.1 and 17.7 ml mg tissue dry weight^–1 h^–1 at 15, 20 and 25 °C, respectively; and for the smaller ones: 17.7, 20.8 and 29.5 ml mg^–1 h^–1. Differences between sizes and between temperatures (except 15 vs. 20 °C) were statistically significant. In absolute terms larger animals have higher clearance rates, but as a function of body mass smaller individuals feed more actively. Within the range of experimental values used, filtration rates were positively associated with water temperature. These clearance rates (125–350 ml individual^–1 h^–1) are among the highest reported for suspension feeding bivalves, including the invasive species Dreissena polymorpha, D. bugensis and Corbicula fluminea. High filtration rates, associated with the very high densities of this mollusc in the Paraná watershed (up to over 200,000 ind m^–2) suggest that its environmental impact may be swiftly changing ecological conditions in the areas colonized.     

Maximum body size in a radiating clade as a function of time

The behavior of the maximum body size (body length) in an evolving clade is exemplified by the evolutionary histories of Bivalvia, Cetacea, and Camerata (Crinoidea). Changes of the maximum size with time track closely diversification history: when a clade diversifies exponentially, the maximum size also increases exponentially, and when the number of species changes irregularly (at varying rates), the maximum size also changes in that manner. However, within any given clade, the maximum body size changes at lower rates than diversity does. The observed shifts in maximum body size approximate the rate of diversification per unit of time to the power of about 0.5.     

Herkogamy and mating patterns in the self-compatible daffodil Narcissus longispathus

BACKGROUND AND AIMS: Floral design in self-compatible plants can influence mating patterns. This study investigated Narcissus longispathus, a self-compatible bee-pollinated species with wide variation in anther-stigma separation (herkogamy), to determine the relationship between variation in this floral trait and the relative amounts of cross- and self-fertilization. METHODS: Anther-stigma separation was measured in the field in six populations of N. longispathus from south-eastern Spain. Variation in herkogamy during the life of individual flowers was also quantified. Multilocus outcrossing rates were estimated from plants differing in herkogamy using allozyme markers. KEY RESULTS: Anther-stigma separation varied considerably among flowers within the six populations studied (range = 1-10 mm). This variation was nearly one order of magnitude larger than the slight, statistically non-significant developmental variation during the lifespan of individual flowers. Estimates of multilocus outcrossing rate for different herkogamy classes (t(m) range = 0.49-0.76) failed to reveal a monotonic increase with increasing herkogamy. CONCLUSIONS: It is suggested that the lack of a positive relationship between herkogamy and outcrossing rate, a result that has not been previously documented for other species, could be mostly related to details of the foraging behaviour of pollinators.