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Phylogenetic Analysis of Local-Scale Tree Soil Associations in a Lowland Moist Tropical Forest

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Background: Local plant-soil associations are commonly studied at the species-level, while associations at the level of nodes within a phylogeny have been less well explored. Understanding associations within a phylogenetic context, however, can improve our ability to make predictions across systems and can advance our understanding of the role of evolutionary history in structuring communities. Methodology/Principal Findings: Here we quantified evolutionary signal in plant-soil associations using a DNA sequence-based community phylogeny and several soil variables (e. g., extractable phosphorus, aluminum and manganese, pH, and slope as a proxy for soil water). We used published plant distributional data from the 50-ha plot on Barro Colorado Island (BCI), Republic of Panama. Our results suggest some groups of closely related species do share similar soil associations. Most notably, the node shared by Myrtaceae and Vochysiaceae was associated with high levels of aluminum, a potentially toxic element. The node shared by Apocynaceae was associated with high extractable phosphorus, a nutrient that could be limiting on a taxon specific level. The node shared by the large group of Laurales and Magnoliales was associated with both low extractable phosphorus and with steeper slope. Despite significant node-specific associations, this study detected little to no phylogeny-wide signal. We consider the majority of the 'traits' (i.e., soil variables) evaluated to fall within the category of ecological traits. We suggest that, given this category of traits, phylogeny-wide signal might not be expected while node-specific signals can still indicate phylogenetic structure with respect to the variable of interest. Conclusions: Within the BCI forest dynamics plot, distributions of some plant taxa are associated with local-scale differences in soil variables when evaluated at individual nodes within the phylogenetic tree, but they are not detectable by phylogeny-wide signal. Trends highlighted in this analysis suggest how plant-soil associations may drive plant distributions and diversity at the local-scale.

Understanding ecosystem retrogression

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Over time scales of thousands to millions of years, and in the absence of rejuvenating disturbances that initiate primary or early secondary succession, ecosystem properties such as net primary productivity, decomposition, and rates of nutrient cycling undergo substantial declines termed ecosystem retrogression. Retrogression results from the depletion or reduction in the availability of nutrients, and can only be reversed through rejuvenating disturbance that resets the system; this differs from age-related declines in forest productivity that are driven by shorter-term depression of nutrient availability and plant ecophysiological process rates that occur during succession. Here we review and synthesize the findings from studies of long-term chronosequences that include retrogressive stages for systems spanning the boreal, temperate, and subtropical zones. Ecosystem retrogression has been described by ecologists, biogeochemists, geologists, and pedologists, each of which has developed somewhat independent conceptual frameworks; our review seeks to unify this literature in order to better understand the causes and consequences of retrogression. Studies of retrogression have improved our knowledge of how long-term pedogenic changes drive shorter-term biological processes, as well as the consequences of these changes for ecosystem development. Our synthesis also reveals that similar patterns of retrogression (involving reduced soil fertility, predictable shifts in organismic traits, and ecological processes) occur in systems with vastly different climatic regimes, geologic substrates, and vegetation types, even though the timescales and mechanisms driving retrogression may vary greatly among sites. Studies on retrogression also provide evidence that in many regions, high biomass or "climax" forests are often transient, and do not persist indefinitely in the absence of rejuvenating disturbance. Finally, our review highlights that studies on retrogressive chronosequences in contrasting regions provide unparalleled opportunities for developing general principles about the long-term feedbacks between biological communities and pedogenic processes, and how these control ecosystem development.

Landscape matrix and species traits mediate responses of Neotropical resident birds to forest fragmentation in Jamaica

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Land cover and land use surrounding, fragmented habitat can greatly impact species persistence by altering resource availability, edge effects, or the movement of individuals throughout a landscape. Despite the potential importance of the landscape matrix, ecologists still have limited understanding of the relative effects of different types of land cover and land uses on species patterns and processes in natural systems. Here we investigated whether Neotropical resident bird communities in limestone forest patches differed if they were embedded in three different human-dominated matrix types (agriculture, pert-urban development, and bauxite mining) relative to sites in continuous forest in central Jamaica. We found that species richness, community composition, and abundances were matrix-dependent, with agricultural landscapes supporting greater avian diversity and more intact community assemblages than either pen-urban or bauxite landscapes. Abundance of almost 70% of species differed in forest embedded in the different landscape matrix types. Traits related to resource use best predicted species responses, including diet guild, nest height, habitat association, and foraging strata. Insectivores, frugivores, canopy nesters, understory and canopy foragers, and forest-restricted species rarely observed in matrix habitats had lower abundances in forest fragments embedded in human-dominated matrix types than in continuous forest. In contrast, nectarivores, omnivores, granivores, ground and multi-strata nesters, ground foragers, and species regularly in matrix habitats were least sensitive to forest fragmentation. Results suggest that structure, composition, and land use disturbance regimes in matrix areas impact overall habitat quality in landscapes by potentially mediating resource availability inside as well as outside forest habitat. This study reinforces the importance of differentiating among land cover and land uses in fragmentation research and lends support to the hypothesis that resource availability may be a primary factor driving Neotropical bird responses to fragmentation.

A New Coronuloid Barnacle Subfamily, Genus and Species from Cheloniid Sea Turtles

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During a survey of the commensal barnacles of nesting and foraging sea turtles from the coastal waters of Florida and Georgia, USA, an undescribed species of platylepadid coronuloid barnacle was encountered, embedded within the carapace and plastron regions of host turtles. This new genus and species is described herein as Calyptolepas bjorndalae gen. et sp. nov. and is compared with other members of the family Platylepadidae. While similar in some respects to members of currently recognized platylepadid subfamilies, particularly Cylindrolepas darwiniana Pilsbry (Cylindrolepadinae Ross and Frick) and Platylepas decorata Darwin (Platylepadidae Newman and Ross), this new species bears an amalgamation of characters from these two subfamilies that require it to be placed into a new subfamily, Calyptolepadinae subfam. nov., also described herein.

Movements and morphology under sexual selection: tsetse fly genitalia

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Shon (2009, Ethology Ecology Evolution 21: 161-172) pointed out that in order to understand the functional morphology of sexually selected structures that are used as signaling devices in birds, it is crucial to understand how these structures move during sexual interactions. This insight applies not only to bird feathers, but also to many other types of possible signaling devices, including male genitalia. This note highlights the need for studies of the behavior of genitalia, and describes two promising techniques, using a tsetse fly as an example. Observations of this species revealed otherwise cryptic, highly rhythmic and forceful thrusting, pinching, pressing, and scraping movements by the male's genitalia within the female's body that have no obvious relation to sperm transfer. Thus even though on the outside the male`s body is nearly motionless during long lapses during copulation, the female is subject to a barrage of possible stimulation from his genitalia during copulation. Similar studies are needed in other groups to understand the functional significance of genital morphology.

Tetralogy of Fallot in a cat

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Vaccine-induced canine distemper in a lesser panda

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A fatal disease occurred in a lesser panda (Ailurus fulgens) 2 weeks after vaccination with modified live distemper vaccine. The disease clinically resembled canine distemper. Pathologically there was giant cell pneumonia, with canine distemper viral inclusion bodies in pulmonary and digestive tract epithelium. Viral isolates were indicative of an attenuated strain rather than virulent types.

Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot

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Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Plant-soil associations in a lower montane tropical forest: physiological acclimation and herbivore-mediated responses to nitrogen addition

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1. Soil nutrients influence plant productivity and community composition in tropical forests. In lower montane tropical forests in western Panama, the distribution of understory palm species over a scale of 1201320 km correlates with differences in soil nitrogen (N). We hypothesized that soil N determines seedling performance in the forest understory, and, may therefore influence species distributions along the soil N gradient. 2. We explored the potential for N availability to generate species-habitat associations through species-specific differences in biomass allocation, photosynthetic capacity, N use-efficiency, and susceptibility to herbivory. Seedlings of nine palm species from two sub-families and four habitat types were transplanted into N-addition and control plots at a low N site. Growth, mortality, biomass allocation, photosynthesis, foliar N content and herbivory were measured over 21 months. 3. Foliar N increased for all species (15201368%) following N addition. Most species showed strong (202013200%) increases in photosynthetic rates with N addition except two species with marginal decreases in photosynthetic rates (5201315%). However, shifts in physiological traits did not increase relative growth rate or change in biomass allocation for any species or N treatment combination. Rather, increased leaf quality contributed to greater levels of herbivory in species associated with soils of intermediate and high inorganic N availability. 4. Thus, potential increases in overall growth with N addition were masked by herbivory, resulting in no apparent growth response with increased N. We suggest that for understory palms, and potentially other montane forest plants, distribution patterns are driven by a combination of physiological and herbivore-mediated responses to soil nutrient availability.
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