Sampling sites, sampled birds and plants of young larch plantations in Tokachi district, eastern Hokkaido, northern Japan, 2011

Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a variety of study designs and allows the inclusion of additional environmental covariates.

Flying vs. climbing: Factors controlling arboreal seed removal in oak-beech forests

Nuts are heavy and nutritious seeds that need animals to be successfully dispersed. Most studies address nut removal by a single animal species once seeds fall onto the ground. However, nuts are also accessible before the seed drop and usually to a wide guild of seed foragers. This study examines the factorscontrollingarborealseedremoval in oak–beechforests within the whole guild of nut foragers. We found that seed-dispersing rodents (Apodemus sylvaticus) were the main acorn removers in the oaks (up to 3.75 m height), with a rapid seed encounter and a high removal rate. However, rodents did not climb the beech trees, probably due to their smoother bark in comparison to oak bark and/or the lower nutritional value of beechnuts with regard to acorns. Jays (Garrulus glandarius) were more abundant in oak stands (both dense and scattered) and clearly preferred acorns to beechnuts whereas nuthatches (Sitta europaea) were more abundant in beech stands and preferred beechnuts to acorns. Non-storing birds such as great tits (Parus major) also removed acorns and beechnuts, especially in the stands where oaks are dominant. Jays and rodents preferred sound seeds over insect-infested seeds but such a preference was not found for nuthatches. This study highlights that pure beech stands showed a reduced guild of arboreal nut foragers in comparison to oak stands. This different guild could probably affect the spatial patterns of seed dispersal, with a proportionally higher number of long dispersal events for acorns (mostly jay-dispersed) than for beechnuts (mostly nuthatch-dispersed). Long-distance dispersal of beechnuts (by jays) is determined by the presence of other preferred species (oaks) and their frequency of non-mast years. Seed location in different habitats strongly determines the contribution of different arboreal removers (including climbing rodents) and their removal speed, leading to a differential seed fate that will eventually affect tree regeneration. As nuthatches are sedentary birds, it is important to maintain old and dead trees where they can breed (crevices), forage (arthropods) and store seeds in order to favor beechnut dispersal and gene flow. By maintaining or favoring oak trees within beech stands we will ensure a wider guild of arboreal nut dispersers.

Si(100) versus Ge(100): Watching the interface formation for the growth of III-V-based solar cells on abundant substrates

We investigated the atomic surface properties of differently prepared silicon and germanium (100) surfaces during metal-organic vapour phase epitaxy/chemical vapour deposition (MOVPE/MOCVD), in particular the impact of the MOVPE ambient, and applied reflectance anisotropy/difference spectroscopy (RAS/RDS) in our MOVPE reactor to in-situ watch and control the preparation on the atomic length scale for subsequent III-V-nucleation. The technological interest in the predominant opto-electronic properties of III-V-compounds drives the research for their heteroepitaxial integration on more abundant and cheaper standard substrates such as Si(100) or Ge(100). In these cases, a general task must be accomplished successfully, i.e. the growth of polar materials on non-polar substrates and, beyond that, very specific variations such as the individual interface formation and the atomic step structure, have to be controlled. Above all, the method of choice to grow industrial relevant high-performance device structures is MOVPE, not normally compatible with surface and interface sensitive characterization tools, which are commonly based on ultrahigh vacuum (UHV) ambients. A dedicated sample transfer system from MOVPE environment to UHV enabled us to benchmark the optical in-situ spectra with results from various surfaces science instruments without considering disruptive contaminants. X-ray photoelectron spectroscopy (XPS) provided direct observation of different terminations such as arsenic and phosphorous and verified oxide removal under various specific process parameters. Absorption lines in Fourier-transform infrared (FTIR) spectra were used to identify specific stretch modes of coupled hydrides and the polarization dependence of the anti-symmetric stretch modes distinguished different dimer orientations. Scanning tunnelling microscopy (STM) studied the atomic arrangement of dimers and steps and tip-induced H-desorption proved the saturation of dangling bonds after preparati- n. In-situ RAS was employed to display details transiently such as the presence of H on the surface at lower temperatures (T <; 800°C) and the absence of Si-H bonds at elevated annealing temperature and also surface terminations. Ge buffer growth by the use of GeH4 enables the preparation of smooth surfaces and leads to a more pronounced amplitude of the features in the spectra which indicates improvements of the surface quality.

A single response mechanism is responsible for evolutionary adaptive variation in a bird’s laying date

Many proximate factors determine a bird’s laying date, including environmental and social stimuli as well as individual responses to internal and external factors. However, the relative importance of these factors has not been experimentally demonstrated. Here we show that (i) large differences in the onset of first clutches between different populations result from variation in different responses to photoperiod and not from variation in responses to any other proximate factors and (ii) the same response mechanism causes maladaptive laying dates in habitats modified by humans. We present, to our knowledge, the first experimental demonstration that a single response mechanism is responsible for evolutionary adaptive intraspecific variation in a vertebrate life history trait.

Abundant empty class II MHC molecules on the surface of immature dendritic cells

A monoclonal antibody specific for the empty conformation of class II MHC molecules revealed the presence of abundant empty molecules on the surface of spleen- and bone marrow-derived dendritic cells (DC) among various types of antigen-presenting cells. The empty class II MHC molecules are developmentally regulated and expressed predominantly on immature DC. They can capture peptide antigens directly from the extracellular medium and present bound peptides to antigen-specific T lymphocytes. The ability of the empty cell-surface class II MHC proteins to bind peptides and present them to T cells without intracellular processing can serve to extend the spectrum of antigens able to be presented by DC, consistent with their role as sentinels in the immune system.

Prehistoric birds from New Ireland, Papua New Guinea: Extinctions on a large Melanesian island

At least 50 species of birds are represented in 241 bird bones from five late Pleistocene and Holocene archaeological sites on New Ireland (Bismarck Archipelago, Papua New Guinea). The bones include only two of seabirds and none of migrant shorebirds or introduced species. Of the 50 species, at least 12 (petrel, hawk, megapode, quail, four rails, cockatoo, two owls, and crow) are not part of the current avifauna and have not been recorded previously from New Ireland. Larger samples of bones undoubtedly would indicate more extirpated species and refine the chronology of extinction. Humans have lived on New Ireland for ca. 35,000 years, whereas most of the identified bones are 15,000 to 6,000 years old. It is suspected that most or all of New Ireland’s avian extinction was anthropogenic, but this suspicion remains undetermined. Our data show that significant prehistoric losses of birds, which are well documented on Pacific islands more remote than New Ireland, occurred also on large, high, mostly forested islands close to New Guinea.

Batrachotoxin alkaloids from passerine birds: A second toxic bird genus (Ifrita kowaldi) from New Guinea

Batrachotoxins, including many congeners not previously described, were detected, and relative amounts were measured by using HPLC-mass spectrometry, in five species of New Guinean birds of the genus Pitohui as well as a species of a second toxic bird genus, Ifrita kowaldi. The alkaloids, identified in feathers and skin, were batrachotoxinin-A cis-crotonate (1), an allylically rearranged 16-acetate (2), which can form from 1 by sigmatropic rearrangement under basic conditions, batrachotoxinin-A and an isomer (3 and 3a, respectively), batrachotoxin (4), batrachotoxinin-A 3′-hydroxypentanoate (5), homobatrachotoxin (6), and mono- and dihydroxylated derivatives of homobatrachotoxin. The highest levels of batrachotoxins were generally present in the contour feathers of belly, breast, or legs in Pitohui dichrous, Pitohui kirhocephalus, and Ifrita kowaldi. Lesser amounts are found in head, back, tail, and wing feathers. Batrachotoxin (4) and homobatrachotoxin (6) were found only in feathers and not in skin. The levels of batrachotoxins varied widely for different populations of Pitohui and Ifrita, a result compatible with the hypothesis that these birds are sequestering toxins from a dietary source.

Paired Ig-like receptor homologs in birds and mammals share a common ancestor with mammalian Fc receptors

Paired Ig-like receptors (PIR) that can reciprocally modulate cellular activation have been described in mammals. In the present study, we searched expressed sequence tag databases for PIR relatives to identify chicken expressed sequence tags predictive of ≈25% amino acid identity to mouse PIR. Rapid amplification of cDNA ends (RACE)-PCR extension of expressed sequence-tag sequences using chicken splenic cDNA as a template yielded two distinct cDNAs, the sequence analysis of which predicted protein products with related extracellular Ig-like domains. Chicken Ig-like receptor (CHIR)-A was characterized by its transmembrane segment with a positively charged histidine residue and short cytoplasmic tail, thereby identifying CHIR-A as a candidate-activating receptor. Conversely, CHIR-B was characterized by its nonpolar transmembrane segment and cytoplasmic tail with two immunoreceptor tyrosine-based inhibitory motifs, indicating that it may serve as an inhibitory receptor. The use of CHIR amino acid sequences in a search for other PIR relatives led to the recognition of mammalian Fc receptors as distantly related genes. Comparative analyses based on amino acid sequences and three-dimensional protein structures provided molecular evidence for common ancestry of the PIR and Fc receptor gene families.

Multiple independent origins of mitochondrial gene order in birds

Mitochondrial genomes of all vertebrate animals analyzed to date have the same 37 genes, whose arrangement in the circular DNA molecule varies only in the relative position of a few genes. This relative conservation suggests that mitochondrial gene order characters have potential utility as phylogenetic markers for higher-level vertebrate taxa. We report discovery of a mitochondrial gene order that has had multiple independent originations within birds, based on sampling of 137 species representing 13 traditionally recognized orders. This provides evidence of parallel evolution in mitochondrial gene order for animals. Our results indicate operation of physical constraints on mitochondrial gene order changes and support models for gene order change based on replication error. Bird mitochondria have a displaced OL (origin of light-strand replication site) as do various other Reptilia taxa prone to gene order changes. Our findings point to the need for broad taxonomic sampling in using mitochondrial gene order for phylogenetic analyses. We found, however, that the alternative mitochondrial gene orders distinguish the two primary groups of songbirds (order Passeriformes), oscines and suboscines, in agreement with other molecular as well as morphological data sets. Thus, although mitochondrial gene order characters appear susceptible to some parallel evolution because of mechanistic constraints, they do hold promise for phylogenetic studies.

Geometric constraints explain much of the species richness pattern in African birds

The world contains boundaries (e.g., continental edge for terrestrial taxa) that impose geometric constraints on the distribution of species ranges. Thus, contrary to traditional thinking, the expected species richness pattern in absence of ecological or physiographical factors is unlikely to be uniform. Species richness has been shown to peak in the middle of a bounded one-dimensional domain, even in the absence of ecological or physiographical factors. Because species ranges are not linear, an extension of the approach to two dimensions is necessary. Here we present a two-dimensional null model accounting for effects of geometric constraints. We use the model to examine the effects of continental edge on the distribution of terrestrial animals in Africa and compare the predictions with the observed pattern of species richness in birds endemic to the continent. Latitudinal, longitudinal, and two-dimensional patterns of species richness are predicted well from the modeled null effects alone. As expected, null effects are of high significance for wide ranging species only. Our results highlight the conceptual significance of an until recently neglected constraint from continental shape alone and support a more cautious analysis of species richness patterns at this scale.