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.

Understanding long-term hunting statistics: the case of Spain (1972-2007)

Hunting is assuming a growing role in the current European forestry and agroforestry landscape. However, consistent statistical sources that provide quantitative information for policy-making, planning and management of game resources are often lacking. In addition, in many instances statistical information can be used without sufficient evaluation or criticism. Recently, the European Commission has declared the importance of high quality hunting statistics and the need to set up a common scheme in Europe for their collection, interpretation and proper use. This work aims to contribute to this current debate on hunting statistics in Europe by exploring data from the last 35 years of Spanish hunting statistics. The analysis focuses on the three major pillars underpinning hunting activity: hunters, hunting grounds and game animals. First, the study aims to provide a better understanding of official hunting statistics for use by researchers, game managers and other potential users. Second, the study highlights the major strengths and weaknesses of the statistical information that was collected. The results of the analysis indicate that official hunting statistics can be incomplete, dispersed and not always homogeneous over a long period of time. This is an issue of which one should be aware when using official hunting data for scientific or technical work. To improve statistical deficiencies associated with hunting data in Spain, our main suggestion is the adoption of a common protocol on data collection to which different regions agree. This protocol should be in accordance with future European hunting statistics and based on robust and well-informed data collection methods. Also it should expand the range of biological, ecological and economic concepts currently included to take account of the profound transformations experienced by the hunting sector in recent years. As much as possible, any future changes in the selection of hunting statistics should allow for comparisons between new variables with the previous ones.

Estudio y análisis para la elaboración de un modelo de certificado de calidad cinegética en España = Study and analysis for the development of a model of hunting quality certificate in Spain

Con esta tesis doctoral se pretende elaborar un modelo de Certificado de Calidad Cinegética independiente, de adhesión voluntaria y aplicable a todo tipo de espacios cinegéticos, de forma que posteriormente pueda convertirse en una metodología que sea empleada como instrumento válido de medición de la Calidad Cinegética y normalizada a través de una familia de Normas aprobadas por un organismo de normalización reconocido a nivel nacional o internacional. En primer lugar, se procedió a la realización de un riguroso y exhaustivo estudio de justificación siguiendo la metodología propuesta por la Norma UNE 66172:2003 IN, Directrices para la justificación y desarrollo de sistemas de gestión (equivalente a la Norma Internacional GUIA ISO/IEC 72:2001). A continuación, se procedió a la identificación y desarrollo de los parámetros de Ordenación Cinegética comunes a cualquier espacio cinegético en España y a la conceptualización de la Calidad Cinegética. Finalmente, se desarrolló un modelo estructurado en nueve Criterios y treinta y cuatro Indicadores de Calidad Cinegética, y un proyecto de familia de Normas para la Certificación de la Calidad Cinegética. ABSTRACT This doctoral thesis aims to produce a model of Hunting Quality Certificate independent, of voluntary adherence and applicable to all types of hunting areas, so that later it can become a methodology to be used as a valid instrument for measuring Hunting Quality and standardized through a family of standards approved by an organization of standardization recognized at a national or an international level. First, we proceeded to carry out a rigorous and comprehensive justification study following the methodology proposed by the UNE 66172: 2003 IN, Guidelines for the justification and development of management systems standards (equivalent to the International Standard GUIA ISO / IEC 72: 2001). Then, we proceeded to the identification and development of Hunting Management parameters common to any hunting area in Spain and the conceptualization of Hunting Quality. Finally, a model structured into nine Criteria and thirty-four Indicators of Hunting Quality and a draft of a family of standards for Hunting Quality Certification were developed.

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.

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.