Phylogenetic context and Basal metazoan model systems

In comparative studies using model organisms, extant taxa areoften referred to as basal. The term suggests that such taxaare descendants of lineages that diverged early in the historyof some larger taxon. By this usage, the basal metazoans comprisejust four phyla (Placozoa, Porifera, Cnidaria, and Ctenophora)and the large clade Bilateria. We advise against this practicebecause basal refers to a region at the base or root of a phylogenetictree. Thus, referring to an extant taxon or species as basal,or as more basal than another, can be misleading. While muchprogress has been made toward understanding some of the phylogeneticrelationships within these groups, the relationships among themare still largely not known with certainty. Thus, sound inferencesfrom comparative studies of model organisms demand continuedillumination of phylogeny. Hypotheses about the mechanisms underlyingmetazoan evolution can be drawn from the study of model organismsin Cnidaria, Ctenophora, Placozoa, and Porifera, but it is clearthat these model organisms are likely to be derived in manyrespects. Therefore, testing these hypotheses requires the studyof yet additional model organisms. The most effective testsare those that investigate model organisms with phylogeneticpositions among two sister groups comprising a larger cladeof interest.     

Character evolution in Hydrozoa (phylum Cnidaria)

The diversity of hydrozoan life cycles, as manifested in the wide range of polyp, colony, and medusa morphologies, has been appreciated for centuries. Unraveling the complex history of characters involved in this diversity is critical for understanding the processes driving hydrozoan evolution. In this study, we use a phylogenetic approach to investigate the evolution of morphological characters in Hydrozoa. A molecular phylogeny is reconstructed using ribosomal DNA sequence data. Several characters involving polyp, colony, and medusa morphology are coded in the terminal taxa. These characters are mapped onto the phylogeny and then the ancestral character states are reconstructed. This study confirms the complex evolutionary history of hydrozoan morphological characters. Many of the characters involving polyp, colony, and medusa morphology appear as synapomorphies for major hydrozoan clades, yet homoplasy is commonplace.     

Fossil wood charcoal assemblages from Elands Bay Cave, South Africa: implications for Late Quaternary vegetation and climates in the winter-rainfall fynbos biome

Aim The aim of this paper is to analyse fossil charcoal deposits, largely identified to the species level and spanning a sequence from the late Holocene to < 40,000 BP , in order to reconstruct Late Quaternary vegetation and climatic patterns in the western (winter-rainfall) fynbos biome of South Africa. Location The charcoals were excavated from the Elands Bay Cave (32°19S, 18°20E) on the semiarid (200–250 mmyr^?1), winter-rainfall coastline of the western fynbos biome. Methods Patterns in the charcoal data set over time were sought by manual sorting of the charcoal×sample matrix, as well as by subjecting the data to multivariate analysis. Palaeoclimatic reconstruction was attempted by comparing the climatic controls on contemporary vegetation communities that resembled the fossil assemblages. Charcoal diversity was modelled using sample age and number of charcoal fragments as explanatory variables. Results The fossil assemblages ranged from xeric communities (similar to those presently occurring at the site) during the Holocene, to more mesic thicket and fynbos vegetation in the terminal Pleistocene, to Afromontane forest and riverine woodland communities after about 18,000 BP . Diversity of the charcoal samples increased monotonically with increasing sample age. Main conclusions The results suggest that, unlike the eastern fynbos biome, which is under fundamentally different climatic controls, soil moisture conditions in the western part of the biome were higher in the Last Glacial than during the Holocene. This scenario may help to explain the higher regional richness and associated diversification in the western than eastern part of the biome.     

Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages

Understanding the nature and timing of metazoan origins is oneof the most important, yet elusive, questions in evolutionarybiology. Fossil data provide the most tangible evidence forthe origin of early animal lineages, although additional evidencefrom molecular phylogenetics, molecular clock studies, and developmenthas contributed to our current understanding. We review severallines of evidence to explore the nature and timing of earlymetazoan evolution and discuss how these data, when consideredtogether, provide a more cohesive picture of the origin of animaldiversity. We discuss how trace fossils and biomarkers providecompelling evidence for the origins of Bilateria and siliceoussponges. Using a molecular phylogenetic framework for metazoans,we discuss how fossils can be used to date the origin of clades.We use these fossil dates to perform a relaxed molecular clockanalysis for estimating dates of nodes when no fossils are available.We also discuss current data from developmental biology thatsuggest that early metazoans possessed a sophisticated moleculartoolkit for building complex body plans. We conclude that thebest evidence for the origin of major metazoan lineages liesin the careful interpretation of the fossil record and thatthese data, when considered with phylogenetic and developmentalevidence, support the notion that the Cambrian radiation isa real phenomenon that marks a critically important time inthe history of life.     

Resource use by salmonids in riverine,lacustrine and marine environments: Evidence from stable isotope analysis

Synopsis We measured stable isotope ratios (δ¹³C and δ¹⁵N) of invertebrates, Atlantic salmon, Salmo salar, and brook trout, Salvelinus fontinalis, in three distinct freshwater environments (headwater tributary, ultra-oligotrophic lake, and main-stem river) in the Western Brook system, Newfoundland, Canada. Large differences in the stable carbon signatures of invertebrates allowed the identification of organic matter assimilation from each environment by resident parr and migrating smolts. Brook trout captured in the headwater tributary in June had a carbon signature characteristic of the tributary, while those collected in August had enriched ¹³C (maximum = −15.6‰) and ¹⁵N (maximum = 12.8‰) values. These enriched carbon and nitrogen signatures were indicative of foraging at sea. There was a low correlation between δ¹³C and δ¹⁵N (r² = 0.198) for individual fish that was likely due to the confounding influence of trout feeding in the lake and the lower main-stem of the river, where δ¹³C of food sources was high but δ¹⁵N was low. Smolts emigrating from Western Brook Pond where they had been foraging (based on lacustrine carbon signatures) were significantly larger than those emigrating from a nursery brook and the main river in the same basin, despite having the same median age. These results suggest better growth opportunities in the lake environment. Trout fork length was positively correlated with δ¹³C and δ¹⁵N, demonstrating that larger individuals had been feeding outside the brook. These results support previous studies that found increased growth potential for salmonids in lacustrine and marine environments, and further, indicate possible adaptive advantages for salmonid movement away from natal brooks.     

SpecAlign--processing and alignment of mass spectra datasets

SUMMARY: Pre-processing of chromatographic profile or mass spectral data is an important aspect of many types of proteomics and biomarker discovery experiments. Here we present a graphical computational tool, SpecAlign, that enables simultaneous visualization and manipulation of multiple datasets. SpecAlign not only provides all common processing functions, but also uniquely implements an algorithm that enables the complete alignment of each mass spectrum within a loaded dataset. We demonstrate its utility by aligning two datasets each containing six spectra; one set was acquired prior to instrument calibration and the other following calibration. AVAILABILITY: The software is free of charge and available for download from http://ptcl.chem.ox.ac.uk/~jwong/specalign. Supports Windows operating systems including Windows 9X/NT/2000/XP.     

Culture Conditions Affect Colonization of Watermelon by Colletotrichum Orbiculare

Area of lesions produced by Colletotrichum orbiculare on watermelon (Citrullus lanatus) seedlings was not affected by amount of culture medium on which the fungus was grown, and decreased as length of time the fungus was in culture increased. Internal integrity of C. orbiculare spores appeared degraded, and this was coincident with decreases in lesion area.