Use of Occupancy Models to Estimate the Influence of Previous Live Captures on DNA-Based Detection Probabilities of Grizzly Bears

Abstract: Large carnivores potentially change their behavior following physical capture, becoming less responsive to the attractants that resulted in their capture, which can bias population estimates where the change in behavior is not appropriately modeled. We applied occupancy models to efficiently estimate and compare detection probabilities of previously collared grizzly bears (Ursus arctos) with bears captured at DNA hair-snag sites that were not previously collared. We found that previously captured bears had lower detection probabilities, although their detection probabilities were still >0, implying that they were still visible to be sampled via the DNA hair-snag grid, which was able to detect finer differences in capture probabilities of previously collared bears compared with Huggins closed-captures population models. To obtain relatively unbiased population estimates for DNA surveys, heterogeneity caused by previous live capture should be accounted for in the population estimator. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):589–595; 2008)     

Analysis of Covariance Models for Data From Observational Field Studies

Abstract We outline the features of a general class of statistical models (i.e., analysis of covariance [ANCOVA] models) that has proven to be effective for the analysis of data from observational studies. In observational studies, treatments are assigned by Nature in a decidedly nonrandom manner; consequently, many of the crucial assumptions and safeguards of the classic experimental design either fail or are absent. Hence, inferences (causal or associative) are more difficult to justify. Typically, investigators can expect the primary factors of interest, which are usually called environmental exposures rather than treatments, to be involved in complex interactions with each other and with other factors, and these factors will be confounded with still other factors. We provide examples illustrating the application of ANCOVA models to adjust for confounding factors and complex interactions, thereby providing relatively clean estimates of association between exposure and response. We summarize information on available software and supporting literature for implementing ANCOVA models for the analysis of cross-sectional and longitudinal observational field data. We conclude with a brief discussion of critical model fitting issues, including proper specification of the functional form of continuous covariates and problems associated with overfitted models and misspecified models that lack important covariates.     

Phylogenetic analysis of non-stereotyped behavioural sequences with a successive event-pairing method

A new method is proposed which uses transitions among acts in non-stereotyped behavioural sequences as phylogenetic characters. This method is derived from the event-pairing method designed for the phylogenetic study of developmental sequences and from ethological analyses of transition matrices. It is applied to study the phylogenetic relationships within a well-known group, the presocial Zetoborinae cockroaches. The analysis is carried out with three data sets: a behavioural data set with transitions among acts in behavioural dyadic sequences, together with morphological and molecular data sets. Non-stereotyped behaviour proved to be phylogenetically informative and to display low homoplasy. This new method opens an avenue for studying the evolution of behaviour in the framework of phylogenetic analysis, which was restricted until now to the study of stereotyped sequences and/or isolated features involved in courting or building activities.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 853–867.     

A species complex within the isopod genus Haploniscus (Crustacea: Malacostraca: Peracarida) from the Southern Ocean deep sea: a morphological and molecular approach

Seven new species of the genus Haploniscus from the deep Scotia and Weddell Seas are presented, combining morphological and molecular data (mitochondrial 16S rDNA and nuclear 18S rDNA). Haploniscus cassilatus sp. nov. , H. cucullus sp. nov. , H. weddellensis sp. nov. , H. procerus sp. nov. and H. kyrbasia sp. nov. are characterized by a prominent rostral process, the size and shape of which vary among species. The rostrum of H. microkorys sp. nov. is distinctly smaller than that of the former species, while H. nudifrons sp. nov. does not possess a rostrum. The status of the latter as separate species is obvious, owing to the stronger morphological differences. DNA was sequenced from three of the other five species. Genetic distances together with the more subtle morphological variation justify the erection of separate species. Overall morphological variations between these species are small yet noticeable and include, among others, the rostrum, the shape of the pleotelson and setation of pereopods. Our molecular data sets reveal detailed phylogenetic insights within the Haploniscus cucullus complex, supporting the monophyly of all species. We found p -distances of at least 0.0732 (16S rDNA) and 0.0140 (complete 18S rDNA) between pairs of species and show that both genes can be used as a marker for DNA taxonomy.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 655–706.     

A Multilocus Genotypic Analysis of Cryptosporidium meleagridis

ABSTRACT. Cryptosporidium meleagridis is a common cause of cryptosporidiosis in birds. In addition, recent reports have described the parasite as an etiologic agent of cryptosporidiosis in both immunocompetent and immunocompromised humans. Therefore, it is important to genetically characterize isolates of C. meleagridis from different hosts and geographic areas, and to develop molecular tools to differentiate isolates from various hosts or areas. In this study, a total of 11 isolates of Cryptosporidium meleagridis from both human and avian hosts were examined at three genetic loci: the small-subunit rRNA, 60-kDa glycoprotein precursor, and 70-kDa heat shock protein genes. Two genotypes of C. meleagridis were seen at the small-subunit rRNA locus. These differed from each other by the presence or lack of a heterogeneous copy of the gene and an ATT repeat. The 60-kDa glycoprotein precursor gene divided these eleven isolates of C. meleagridis into six genotypes with high sequence diversity between groups. The highest genetic heterogeneity, however, was seen at the 70-kDa heat shock protein locus, and was primarily present at the 3'end of the gene. This heterogeneity separated eight isolates of C. meleagridis into six genotypes. These data could be useful in the development of molecular tools to promote understanding of the transmission of C. meleagridisi in humans.     

Development and Experimental Validation of a Fluid/Structure-Interaction Finite Element Model of a Vacuum-Driven Cell Culture Mechanostimulus System

A new fluid/structure-interaction finite element formulation is reported, by means of which reactive fluid stresses can be determined for what is currently the most widely used laboratory apparatus (the Flexercell Strain Unit) for delivering controlled in vitro mechanical stimuli to cultured cells. The apparatus functions by means of cyclic vacuum application to the undersurface of a membrane-like circular rubber substrate. When operated in its original embodiment (i.e., without axial constraint to substrate motion), the pulsatile vacuum causes appreciable pulsatile excursions (often several millimeters) of the substrate. The mechanical stimuli experienced by cells attached atop the substrate include not only substrate distention, but also potentially confounding reactive fluid stresses due to coupled motions of the overlying liquid culture nutrient medium. Since it is impractical to directly measure reactive fluid stress in such environments, a corresponding mathematical model has been developed. The formulation involves transient continuum finite element solutions for the nutrient medium flow field and for the deformation of the substrate, coupled at their mutual interface (the substrate culture surface). Besides the nonlinearities inherent in the flow field and substrate treatments per se, the numerical problem is complicated by the presence of moving boundaries at the nutrient free surface and at the nutrient/substrate interface, as well as by the need to enforce fluid/structure interaction throughout the duty cycle. Algorithmic considerations appropriate to achieving physically realistic numerical performance are reported, and a confirmatory laboratory validation experiment is described.     

Use of Stable Isotope Methodology to Determine Natal Origins of Mallards at a Fine Scale Within the Upper Midwest

Abstract: Waterfowl managers often attempt to protect local breeding stocks of mallards (Anas platyrhynchos) from hunting pressure, but presently they cannot identify natal origins of birds shot during fall hunting seasons with certainty, unless recovered birds are banded before fledging. Accordingly, we examined whether stable isotope methodology could accurately delineate natal origins of mallards at a fine scale within the upper Midwest (USA). We determined δ¹³C, δD, and δ¹⁵N values from feather samples of 102 flightless mallard ducklings collected in Minnesota, North Dakota, South Dakota, and Wisconsin, USA, from 7 July to 9 September 2002. We detected inverse relationships between latitude and δ¹³C(R² = 0.223) and δD(R² = 0.210). We also detected a weak positive relationship between easterly shifts in longitude and δ¹³C(R² = 0.067) and a weak negative relationship between easterly shifts in longitude and δ¹⁵N(R² = 0.076). The ¹³C and deuterium values differed (P < 0.02) among states: North Dakota was most depleted in ¹³C, and South Dakota was least depleted in deuterium. Discriminant function analysis delineated natal origins of mallard ducklings in Minnesota, North Dakota, South Dakota, and Wisconsin with low-to-moderate accuracy (47%), whereas we predicted natal origins of ducklings among subregions (Prairie [ND, SD] vs. Great Lakes [MN, WI] states) with moderate accuracy (72%). We conclude that stable isotope methodology has a limited ability to determine natal origins of migratory birds along a longitudinal corridor at fine scales but that it improves across ecoregions. However, the ability of deuterium to determine natal origins of migratory birds may vary as hydrological conditions, within and among areas, change throughout time. Researchers should account for annual variation in deuterium found in surface waters when investigating natal origins of migratory birds that use food derived primarily from these waters.     

Other faces in the mirror: a perspective on schizophrenia

A patient with schizophrenia may generate an action (whether manual or verbal), but not attribute the generation of that action to himself. We distinguish self-monitoring and attribution of agency, relating only the former to forward models and the mirror system. We suggest that alien hand experiences occur when an action progresses through hand control pathways with no record of disinhibition having been kept and is then seen but dismissed as external. Analogously, auditory pathways are active during verbal hallucinations and produce a subvocal verbal process, but since no record is kept of the words being created, they are treated as external. The subject then proceeds to confabulate, to provide an account for the agency.     

Development of 22 new microsatellite loci for fishers (Martes pennanti) with variability results from across their range

We developed 22 new microsatellite loci for the fisher (Martes pennanti), a North American mesocarnivore. The loci were developed with samples from the southern Sierra Nevada Mountains in California, and were screened with samples from this population and four other populations. We observed a range of six to 21 polymorphic loci per population, with the Sierra Nevada population exhibiting markedly lower levels of variation compared to the other four.