Phylogeny of Trichomonads Based On Partial Sequences of Large Subunit Rrna and On Cladistic Analysis of Morphological Data

ABSTRACT. Several domains of large subunit rRNA from nine trichomonad species have been sequenced. Molecular phylogenies obtained with parsimony and distance methods demonstrate the trichomonads are a monophyletic group which branches very early in the eukaryotic tree. the topology of the trees is in general agreement with traditional views on evolutionary and systematic relationships of trichomonads. A clear dichotomy is noted between the subfamily Trichomonadinae and the subfamily Tritrichomonadinae. In the latter subfamily, a second division separates the " Tritrichomonas muris -type" species from the " Tritrichomonas augusta -type" ones. Previous evolutionary schemes in which the Monocercomonadidae were regarded as the most "primitive" and the Trichomonadidae as more "evolved" are not in agreement with our molecular data. the emergence of Monocercomonas and Hypotrichomonas at the base of the Tritrichomonas lineage suggests a secondary loss of some cytoskeletal structures, the costa and undulating membrane in these genera. This is corroborated by the early branching position of Trichomitus. which possesses a costa and an undulating membrane and has usually been placed among the Trichomonadidae on the basis of cytological characters. A cladistic analysis was applied to the available morphological characters in order to produce a hierarchical grouping of the taxa reflecting their morphological diversity. Supplementary key words. Evolution, molecular phylogeny, morphological cladistic analysis.     

Population dynamics of American horseshoe crabs—historic climatic events and recent anthropogenic pressures

Populations of the American horseshoe crab, Limulus polyphemus, have declined, but neither the causes nor the magnitude are fully understood. In order to evaluate historic demography, variation at 12 microsatellite DNA loci surveyed in 1218 L. polyphemus sampled from 28 localities was analysed with Bayesian coalescent‐based methods. The analysis showed strong declines in population sizes throughout the species’ distribution except in the geographically isolated southern‐most population in Mexico, where a strong increase in population size was inferred. Analyses suggested that demographic changes in the core of the distribution occurred in association with the recolonization after the Ice Age and also by anthropogenic effects, such as the past overharvest of the species for fertilizer or the current use of the animals as bait for American eel (Anguilla rostrata) and whelk (Busycon spp.) fisheries. This study highlights the importance of considering both climatic changes and anthropogenic effects in efforts to understand population dynamics—a topic which is highly relevant in the ongoing assessments of the effects of climate change and overharvest.     

EFFECT OF MEAT APPEARANCE ON SOUTH KOREAN CONSUMERS' CHOICE OF PORK CHOPS DETERMINED BY IMAGE METHODOLOGY

The effect of appearance characteristics of fresh pork on Korean consumers' preferences was assessed using images of pork chops. Consumers (1015) in six provinces selected their preferred chop from 16 images modified systematically to give two levels each of fat cover, color, marbling and drip. Meat color was the most important characteristic; similar numbers of consumers chose the dark and light red meat colored pork. Almost two‐thirds of the consumers chose consistently the option without drip. A strong characteristic was that almost half of the Korean consumers chose the marbled pork, although fat cover was not an important selection criterion. Similar preferences were observed on a regional basis, except for color, which varied according to region. More female, particularly the married ones, than male consumers preferred the light red, no drip and marbled options.     

Functional morphology of neck musculature in the Tyrannosauridae (Dinosauria, Theropoda) as determined via a hierarchical inferential approach

With multiple well-preserved specimens, tyrannosaurid dinosaurs are ideal subjects for exploring the role of the neck for feeding in an extinct amniote clade. Detailed exploration of the morphology of avian and crocodilian neck muscles grounds phylogenetic inference of musculature of tyrannosaurids. Introduced methods of kinematic and physiological inference explicate action and function of tyrannosaurid neck muscles, and the explicit method of extant behavioural interpolation (EBI) allows inference of generalized behaviours. Anteriorly originating craniocervical muscles of tyrannosaurids, and insertions of the neck dorsiflexor m. transversospinalis cervicis, were similar to those of birds, while the major respective head dorsiflexor and lateroflexor, m. transversospinalis capitis and m. longissimus capitis superficialis, resembled their homologues in crocodilians. Because the proposed inferential methods are cumulative and emphasize mutual falsification, behavioural effects of muscle function become immediately testable rather than assumed. Kinematic inference of muscle moment topology, and bracketed and unipolar inference of muscle activity, facilitate EBI of rapid gaze shifts, lateral and sagittal strikes, inertial feeding, and tearing of flesh by specific permutational actions of tyrannosaurid neck muscles. Several examples of EBI are tested further through biomechanical considerations.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 759–808.     

Effects of an experimental drought and recovery on soil emissions of carbon dioxide,methane, nitrous oxide,and nitric oxide in a moist tropical forest

Changes in precipitation in the Amazon Basin resulting from regional deforestation, global warming, and El Niño events may affect emissions of carbon dioxide (CO₂), methane (CH₄), nitrous oxide (N₂O), and nitric oxide (NO) from soils. Changes in soil emissions of radiatively important gases could have feedback implications for regional and global climate. Here, we report the final results of a 5‐year, large‐scale (1 ha) throughfall exclusion experiment, followed by 1 year of recovery with natural throughfall, conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N₂O emissions in four out of five treatment years (a natural drought year being the exception), and then recovered during the first year after the drought treatment stopped. Similarly, consumption of atmospheric CH₄ increased under drought treatment, except during a natural drought year, and it also recovered to pretreatment values during the first year that natural throughfall was permitted back on the plot. No treatment effect was detected for NO emissions during the first 3 treatment years, but NO emissions increased in the fourth year under the extremely dry conditions of the exclusion plot during a natural drought. Surprisingly, there was no treatment effect on soil CO₂ efflux in any year. The drought treatment provoked significant tree mortality and reduced the allocation of C to stems, but allocation of C to foliage and roots were less affected. Taken together, these results suggest that the dominant effect of throughfall exclusion on soil processes during this 6‐year period was on soil aeration conditions that transiently affected CH₄, N₂O, and NO production and consumption.     

Scaling environmental change through the community-level: a trait-based response-and-effect framework for plants

Predicting ecosystem responses to global change is a major challenge in ecology. A critical step in that challenge is to understand how changing environmental conditions influence processes across levels of ecological organization. While direct scaling from individual to ecosystem dynamics can lead to robust and mechanistic predictions, new approaches are needed to appropriately translate questions through the community level. Species invasion, loss, and turnover all necessitate this scaling through community processes, but predicting how such changes may influence ecosystem function is notoriously difficult. We suggest that community‐level dynamics can be incorporated into scaling predictions using a trait‐based response–effect framework that differentiates the community response to environmental change (predicted by response traits) and the effect of that change on ecosystem processes (predicted by effect traits). We develop a response‐and‐effect functional framework, concentrating on how the relationships among species' response, effect, and abundance can lead to general predictions concerning the magnitude and direction of the influence of environmental change on function. We then detail several key research directions needed to better scale the effects of environmental change through the community level. These include (1) effect and response trait characterization, (2) linkages between response‐and‐effect traits, (3) the importance of species interactions on trait expression, and (4) incorporation of feedbacks across multiple temporal scales. Increasing rates of extinction and invasion that are modifying communities worldwide make such a research agenda imperative.     

Evolutionary morphology of the Tenrecoidea (Mammalia) carpal complex

The mammalian carpus can be difficult to interpret both phylogenetically and functionally. It is evolutionarily constrained in terms of functional morphology, yet there is considerable variation among many eutherian and metatherian lower and higher level taxa. The ecologically diverse Tenrecoidea (Mammalia) is a useful model for morphological interpretation of the interplay between function and phylogenetic constraint. Elements from the wrist and hand of 13 tenrecoid species, and one species each from Macroscelididae, Solenodontidae, and Erinaceidae, were compared to test form–function hypotheses of specific carpal, metacarpal, and phalangeal characters. Qualitative comparisons illustrate that several aspects of the tenrecoid carpus can be correlated with positional behaviour. Convergences within Tenrecoidea, and between tenrecoids and nontenrecoids with similar locomotor regimes, confirm a small number of carpal characters and a larger number of distal forearm, metacarpal, and phalangeal characters that reliably correspond with functional expectations. In addition, several features of the carpus appear to be phylogenetically constrained and indicate specific affinities within Tenrecoidea. Finally, there are a significant number of carpal features that vary among the studied taxa and remain ambiguous in terms of phylogenetic and/or functional significance.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 267–288.     

Demography of Black Bears in Hunted and Unhunted Areas of the Boreal Forest of Ontario

Abstract: We estimated relative density, survival, and reproduction of American black bears (Ursus americanus) from capture-recapture and telemetry data collected from 1989 to 1999 in the unhunted Chapleau Crown Game Preserve (CCGP) and nearby hunted areas in the boreal forest of Ontario, Canada. We tested for combinations of effects of age class, sex, year, years of food shortage, encumbrance status, and residency (on or off the Game Preserve) on vital rates. Results from live captures, remote captures, and bait-station hit rates indicated that density was highest inside CCGP. Total survival of adult females, subadults, and cubs were similar among residents and nonresidents of CCGP, but yearling survival was lower among CCGP residents. Adult females were approximately twice as likely to die and nearly 10 times as likely to be cannibalized (risk ratio [RR] = 9.62, 95% CI = 2.088–44.29) while encumbered with cubs of the year. Nonresidents of CCGP had greater risk of being harvested (RR = 4.00, 95% CI = 1.19–13.46) but similar risk of being cannibalized (RR = 0.875, 95% CI = 0.300–2.55) relative to CCGP residents, suggesting that harvest mortality was additive to other forms of mortality. Residents of CCGP had older ages at primiparity and lower litter-production rates than bears resident in hunted areas. Few litters were produced in years following food shortages, but litter size was unaffected. We recommend that managers allow for additive harvest mortality and reduced survival of bears encumbered with cubs of the year, and we caution that assuming density-compensatory increases in cub production could optimistically bias estimates of population growth.     

Selection on domestication traits and quantitative trait loci in crop–wild sunflower hybrids

The strength and extent of gene flow from crops into wild populations depends, in part, on the fitness of the crop alleles, as well as that of alleles at linked loci. Interest in crop–wild gene flow has increased with the advent of transgenic plants, but nontransgenic crop–wild hybrids can provide case studies to understand the factors influencing introgression, provided that the genetic architecture and the fitness effects of loci are known. This study used recombinant inbred lines (RILs) generated from a cross between crop and wild sunflowers to assess selection on domestication traits and quantitative trait loci (QTL) in two contrasting environments, in Indiana and Nebraska, USA. Only a small fraction of plants (9%) produced seed in Nebraska, due to adverse weather conditions, while the majority of plants (79%) in Indiana reproduced. Phenotypic selection analysis found that a mixture of crop and wild traits were favoured in Indiana (i.e. had significant selection gradients), including larger leaves, increased floral longevity, larger disk diameter, reduced ray flower size and smaller achene (seed) mass. Selection favouring early flowering was detected in Nebraska. QTLs for fitness were found at the end of linkage groups six (LG6) and nine (LG9) in both field sites, each explaining 11–12% of the total variation. Crop alleles were favoured on LG9, but wild alleles were favoured on LG6. QTLs for numerous domestication traits overlapped with the fitness QTLs, including flowering date, achene mass, head number, and disk diameter. It remains to be seen if these QTL clusters are the product of multiple linked genes, or individual genes with pleiotropic effects. These results indicate that crop trait values and alleles may sometimes be favoured in a noncrop environment and across broad geographical regions.