A novel approach to understanding bird communities using informed diversity estimates at local and regional scales in northern California and southern Oregon

Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence–absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of “informed diversity” indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the “informed diversity” concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species‐rich naïve communities were in fact species‐poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat.     

Iterative character weighting based on mutation frequency: A new method for constructing phyletic trees

Summary In this paper we present an iterative character weighting method for the construction of phyletic trees. An initial tree is used to calculate the character weights, which are the number of mutations normalized so that the possible range is corrected for. The weights obtained are used to adjust the tree; this process is iterated until a stable tree is found. Using data generated according to a model tree, we show that the trees constructed by the iterative character weighting method converge to the true underlying tree. Using biological data, the trees become closer to the systematic classification of the species concerned, and patterns conflicting with the phylogenetic pattern can be singled out. The method involves a combination of minimal length methods and similarity methods, whereby the strict parsimony criterion is relaxed.     

Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity.

An unexpected structural similarity is described between the pleckstrin homology (PH) domain and verotoxin. This similarity has escaped detection primarily due to the differences in topology that exist between the two proteins. By comparing this result with two previously reported similarities for the PH domain, one with the lipocalins and another with the FK506 binding protein, we discuss the problems of measuring and assessing structural similarities.     

Differential Expression and Network Inferences through Functional Data Modeling

Summary .  Time course microarray data consist of mRNA expression from a common set of genes collected at different time points. Such data are thought to reflect underlying biological processes developing over time. In this article, we propose a model that allows us to examine differential expression and gene network relationships using time course microarray data. We model each gene-expression profile as a random functional transformation of the scale, amplitude, and phase of a common curve. Inferences about the gene-specific amplitude parameters allow us to examine differential gene expression. Inferences about measures of functional similarity based on estimated time-transformation functions allow us to examine gene networks while accounting for features of the gene-expression profiles. We discuss applications to simulated data as well as to microarray data on prostate cancer progression.     

Functional group based Ligand binding affinity scoring function at atomic environmental level

Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure.     

High white-tailed deer densities benefit graminoids and contribute to biotic homogenization of forest ground-layer vegetation

Biotic homogenization, with its emphasis on invasions, extinctions, and convergence in taxonomic similarity, provides an important framework for investigating changes in biodiversity across scales. Through their selective foraging, large populations of white-tailed deer are altering population sizes, driving extirpations, and facilitating invasions of plants throughout the eastern United States. I hypothesize that deer can drive biotic homogenization in forest understory communities by shifting species composition to one dominated by grasses, sedges, and ferns (all wind-pollinated plants). I report the effects of 16 years of deer exclusion in a hemlock-northern hardwood stand in N Wisconsin using a block design. Species composition showed greater convergence in control plots than exclosure plots, indicating deer can drive biotic homogenization at the stand level. Total percent cover is nearly 4 times greater in exclosure plots. Percent cover by woody plants, broadleaf herbs, and ferns is 150, 63, and 20 times greater in exclosure plots, respectively, while cover by sedges and grasses is 3.8 and 2.2 times greater in control plots. Cover by species with showy, insect-pollinated flowers is 79 times greater in exclosures. Graminoid-dominated control plots represent a novel state not observed fifty years ago, and could reflect the emergence of a grazing lawn. The increase in graminoids at this study area and throughout the region could under some global change scenarios be an early stage of conversion from forest to savanna or wood pasture.     

Selecting for extinction: nonrandom disease-associated extinction homogenizes amphibian biotas

Studying the patterns in which local extinctions occur is critical to understanding how extinctions affect biodiversity at local, regional and global spatial scales. To understand the importance of patterns of extinction at a regional spatial scale, we use data from extirpations associated with a widespread pathogenic agent of amphibian decline, Batrachochytrium dendrobatidis ( Bd ) as a model system. We apply novel null model analyses to these data to determine whether recent extirpations associated with Bd have resulted in selective extinction and homogenization of diverse tropical American amphibian biotas. We find that Bd -associated extinctions in this region were nonrandom and disproportionately, but not exclusively, affected low-occupancy and endemic species, resulting in homogenization of the remnant amphibian fauna. The pattern of extirpations also resulted in phylogenetic homogenization at the family level and ecological homogenization of reproductive mode and habitat association. Additionally, many more species were extirpated from the region than would be expected if extirpations occurred randomly. Our results indicate that amphibian declines in this region are an extinction filter, reducing regional amphibian biodiversity to highly similar relict assemblages and ultimately causing amplified biodiversity loss at regional and global scales.     

When can we distinguish between neutral and non‐neutral processes in community dynamics under ecological drift?

Determining whether the composition of ecological communities (species presence and abundance), can be predicted from species demographic traits, rather than being a result of neutral drift, is a key ecological question. Here we compare the similarity of community composition, from different community assembly models run under identical environmental conditions, where interspecific competition is assumed to be either neutral or niche-based. In both cases, species colonize a focal patch from a network of neighbouring patches in a metacommunity. We highlight the circumstances (rate and spatial scale of dispersal, and the relative importance of ecological drift) where commonly used community similarity metrics or species rank–abundance relationships are likely to give similar results, regardless of the underlying processes (neutral or non-neural) driving species' dynamics. As drift becomes more important in driving species abundances, deterministic niche structure has a smaller influence. Our ability to discriminate between different underlying processes driving community organization depends on the relative importance of different drift processes that operate on different spatial scales.     

Niches versus neutrality: uncovering the drivers of diversity in a species-rich community

Ecological models suggest that high diversity can be generated by purely niche-based, purely neutral or by a mixture of niche-based and neutral ecological processes. Here, we compare the degree to which four contrasting hypotheses for coexistence, ranging from niche-based to neutral, explain species richness along a body mass niche axis. We derive predictions from these hypotheses and confront them with species body-mass patterns in a highly sampled marine phytoplankton community. We find that these patterns are consistent only with a mechanism that combines niche and neutral processes, such as the emergent neutrality mechanism. In this work, we provide the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community. We suggest this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities.     

Preference–performance relationship and influence of plant relatedness on host use by Pityogenes chalcographus L.

• 1 Pityogenes chalcographus L. (Coleoptera: Scolytinae) causes damage in European coniferous forests, primarily on Picea abies L. Karst., but is also recorded on other native and exotic Pinaceae species. Estimating the adequacy between adult preference and larval performance of this beetle among its host‐range, as well as the influence of plant taxonomic relatedness on these parameters, would provide useful information on the beetle's ability to shift onto novel hosts.
• 2 Choice and no‐choice assays were conducted under laboratory conditions. Adult preference and larval performance parameters among two native (Pinus sylvestris L. and Picea abies) and three exotic north American [Pinus contorta Dougl., Picea sitchensis (Bong.) Carr. and Pseudotsuga menziesii Mirbel (Franco)] conifer species were measured.
• 3 Pityogenes chalcographus exhibited a significant positive relationship between preference and performance. Picea abies was both the preferred and the most suitable host species for larval development. The closest relative, P. sitchensis, was the second best choice in terms of preference and performance. Pseudotsuga menziesii occupied an intermediate position for both beetle preference and performance, and Pinus spp. were the least suitable hosts for beetle development.
• 4 Adult preference and larval performance ranking among hosts provides little support to the plant taxonomic relatedness hypothesis. Taxonomic relatedness could play a role on the diet breadth, although only at a limited scale, within the genus Picea. At higher taxonomic levels, other factors such as bark thickness might be decisive.