Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)?

Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.

Use of DNA profiles for investigation using a simulated national DNA database: Part II. Statistical and ethical considerations on familial searching.

Familial searching consists of searching for a full profile left at a crime scene in a National DNA Database (NDNAD). In this paper we are interested in the circumstance where no full match is returned, but a partial match is found between a database member's profile and the crime stain. Because close relatives share more of their DNA than unrelated persons, this partial match may indicate that the crime stain was left by a close relative of the person with whom the partial match was found. This approach has successfully solved important crimes in the UK and the USA. In a previous paper, a model, which takes into account substructure and siblings, was used to simulate a NDNAD. In this paper, we have used this model to test the usefulness of familial searching and offer guidelines for pre-assessment of the cases based on the likelihood ratio. Siblings of "persons" present in the simulated Swiss NDNAD were created. These profiles (N=10,000) were used as traces and were then compared to the whole database (N=100,000). The statistical results obtained show that the technique has great potential confirming the findings of previous studies. However, effectiveness of the technique is only one part of the story. Familial searching has juridical and ethical aspects that should not be ignored. In Switzerland for example, there are no specific guidelines to the legality or otherwise of familial searching. This article both presents statistical results, and addresses criminological and civil liberties aspects to take into account risks and benefits of familial searching.

Development of Abutment Design Standards for Local Bridge Designs, Volume 1 of 3, Development of Design Methodology, August 2004

Several superstructure design methodologies have been developed for low volume road bridges by the Iowa State University Bridge Engineering Center. However, to date no standard abutment designs have been developed. Thus, there was a need to establish an easy to use design methodology in addition to generating generic abutment standards and other design aids for the more common substructure systems used in Iowa. The final report for this project consists of three volumes. The first volume (this volume) summarizes the research completed in this project. A survey of the Iowa County Engineers was conducted from which it was determined that while most counties use similar types of abutments, only 17 percent use some type of standard abutment designs or plans. A literature review revealed several possible alternative abutment systems for future use on low volume road bridges in addition to two separate substructure lateral load analysis methods. These consisted of a linear and a non-linear method. The linear analysis method was used for this project due to its relative simplicity and the relative accuracy of the maximum pile moment when compared to values obtained from the more complex non-linear analysis method. The resulting design methodology was developed for single span stub abutments supported on steel or timber piles with a bridge span length ranging from 20 to 90 ft and roadway widths of 24 and 30 ft. However, other roadway widths can be designed using the foundation design template provided. The backwall height is limited to a range of 6 to 12 ft, and the soil type is classified as cohesive or cohesionless. The design methodology was developed using the guidelines specified by the American Association of State Highway Transportation Officials Standard Specifications, the Iowa Department of Transportation Bridge Design Manual, and the National Design Specifications for Wood Construction. The second volume introduces and outlines the use of the various design aids developed for this project. Charts for determining dead and live gravity loads based on the roadway width, span length, and superstructure type are provided. A foundation design template was developed in which the engineer can check a substructure design by inputting basic bridge site information. Tables published by the Iowa Department of Transportation that provide values for estimating pile friction and end bearing for different combinations of soils and pile types are also included. Generic standard abutment plans were developed for which the engineer can provide necessary bridge site information in the spaces provided. These tools enable engineers to design and detail county bridge substructures more efficiently. The third volume provides two sets of calculations that demonstrate the application of the substructure design methodology developed in this project. These calculations also verify the accuracy of the foundation design template. The printouts from the foundation design template are provided at the end of each example. Also several tables provide various foundation details for a pre-cast double tee superstructure with different combinations of soil type, backwall height, and pile type.

Development of Abutment Design Standards for Local Bridge Designs, Volume 3 of 3, Verification of Design Methodology, August 2004

Several superstructure design methodologies have been developed for low volume road bridges by the Iowa State University Bridge Engineering Center. However, to date no standard abutment designs have been developed. Thus, there was a need to establish an easy to use design methodology in addition to generating generic abutment standards and other design aids for the more common substructure systems used in Iowa. The final report for this project consists of three volumes. The first volume summarizes the research completed in this project. A survey of the Iowa County Engineers was conducted from which it was determined that while most counties use similar types of abutments, only 17 percent use some type of standard abutment designs or plans. A literature review revealed several possible alternative abutment systems for future use on low volume road bridges in addition to two separate substructure lateral load analysis methods. These consisted of a linear and a non-linear method. The linear analysis method was used for this project due to its relative simplicity and the relative accuracy of the maximum pile moment when compared to values obtained from the more complex non-linear analysis method. The resulting design methodology was developed for single span stub abutments supported on steel or timber piles with a bridge span length ranging from 20 to 90 ft and roadway widths of 24 and 30 ft. However, other roadway widths can be designed using the foundation design template provided. The backwall height is limited to a range of 6 to 12 ft, and the soil type is classified as cohesive or cohesionless. The design methodology was developed using the guidelines specified by the American Association of State Highway Transportation Officials Standard Specifications, the Iowa Department of Transportation Bridge Design Manual, and the National Design Specifications for Wood Construction. The second volume introduces and outlines the use of the various design aids developed for this project. Charts for determining dead and live gravity loads based on the roadway width, span length, and superstructure type are provided. A foundation design template was developed in which the engineer can check a substructure design by inputting basic bridge site information. Tables published by the Iowa Department of Transportation that provide values for estimating pile friction and end bearing for different combinations of soils and pile types are also included. Generic standard abutment plans were developed for which the engineer can provide necessary bridge site information in the spaces provided. These tools enable engineers to design and detail county bridge substructures more efficiently. The third volume (this volume) provides two sets of calculations that demonstrate the application of the substructure design methodology developed in this project. These calculations also verify the accuracy of the foundation design template. The printouts from the foundation design template are provided at the end of each example. Also several tables provide various foundation details for a pre-cast double tee superstructure with different combinations of soil type, backwall height, and pile type.

Development of Abutment Design Standards for Local Bridge Designs, Volume 2 of 3, Design Manual, August 2004

Several superstructure design methodologies have been developed for low volume road bridges by the Iowa State University Bridge Engineering Center. However, to date no standard abutment designs have been developed. Thus, there was a need to establish an easy to use design methodology in addition to generating generic abutment standards and other design aids for the more common substructure systems used in Iowa. The final report for this project consists of three volumes. The first volume summarizes the research completed in this project. A survey of the Iowa County Engineers was conducted from which it was determined that while most counties use similar types of abutments, only 17 percent use some type of standard abutment designs or plans. A literature review revealed several possible alternative abutment systems for future use on low volume road bridges in addition to two separate substructure lateral load analysis methods. These consisted of a linear and a non-linear method. The linear analysis method was used for this project due to its relative simplicity and the relative accuracy of the maximum pile moment when compared to values obtained from the more complex non-linear analysis method. The resulting design methodology was developed for single span stub abutments supported on steel or timber piles with a bridge span length ranging from 20 to 90 ft and roadway widths of 24 and 30 ft. However, other roadway widths can be designed using the foundation design template provided. The backwall height is limited to a range of 6 to 12 ft, and the soil type is classified as cohesive or cohesionless. The design methodology was developed using the guidelines specified by the American Association of State Highway Transportation Officials Standard Specifications, the Iowa Department of Transportation Bridge Design Manual, and the National Design Specifications for Wood Construction. The second volume (this volume) introduces and outlines the use of the various design aids developed for this project. Charts for determining dead and live gravity loads based on the roadway width, span length, and superstructure type are provided. A foundation design template was developed in which the engineer can check a substructure design by inputting basic bridge site information. Tables published by the Iowa Department of Transportation that provide values for estimating pile friction and end bearing for different combinations of soils and pile types are also included. Generic standard abutment plans were developed for which the engineer can provide necessary bridge site information in the spaces provided. These tools enable engineers to design and detail county bridge substructures more efficiently. The third volume provides two sets of calculations that demonstrate the application of the substructure design methodology developed in this project. These calculations also verify the accuracy of the foundation design template. The printouts from the foundation design template are provided at the end of each example. Also several tables provide various foundation details for a pre-cast double tee superstructure with different combinations of soil type, backwall height, and pile type.

On the origin of the MR image phase contrast: an in vivo MR microscopy study of the rat brain at 14.1 T.

Recent studies at high magnetic fields using the phase of gradient-echo MR images have shown the ability to unveil cortical substructure in the human brain. To investigate the contrast mechanisms in phase imaging, this study extends, for the first time, phase imaging to the rodent brain. Using a 14.1 T horizontal bore animal MRI scanner for in vivo micro-imaging, images with an in-plane resolution of 33 microm were acquired. Phase images revealed, often more clearly than the corresponding magnitude images, hippocampal fields, cortical layers (e.g. layer 4), cerebellar layers (molecular and granule cell layers) and small white matter structures present in the striatum and septal nucleus. The contrast of the phase images depended in part on the orientation of anatomical structures relative to the magnetic field, consistent with bulk susceptibility variations between tissues. This was found not only for vessels, but also for white matter structures, such as the anterior commissure, and cortical layers in the cerebellum. Such susceptibility changes could result from variable blood volume. However, when the deoxyhemoglobin content was reduced by increasing cerebral blood flow (CBF) with a carbogen breathing challenge, contrast between white and gray matter and cortical layers was not affected, suggesting that tissue cerebral blood volume (and therefore deoxyhemoglobin) is not a major source of the tissue phase contrast. We conclude that phase variations in gradient-echo images are likely due to susceptibility shifts of non-vascular origin.

Monitoring of the Launched Girder Bridge over the Iowa River on US 20, March 2004

The objective of the study presented in this report was to document the launch of the Iowa River Bridge and to monitor and evaluate the structural performance of the bridge superstructure and substructure during the launch. The Iowa Department of Transportation used an incremental launching method, which is relatively unique for steel I-girder bridges, to construct the Iowa River Bridge over an environmentally sensitive river valley in central Iowa. The bridge was designed as two separate roadways consisting of four steel plate girders each that are approximately 11 ft deep and span approximately 301 ft each over five spans. The concrete bridge deck was not placed until after both roadways had been launched. One of the most significant monitoring and evaluation observations related to the superstructure was that the bottom flange (and associated web region) was subjected to extremely large stresses during the crossing of launch rollers. Regarding the substructure performance, the column stresses did not exceed reasonable design limits during the daylong launches. The scope of the study did not allow adequate quantification of the measured applied launch forces at the piers. Future proposed esearch should provide an opportunity to address this. The overall experimental performance of the bridge during the launch was compared with the predicted design performance. In general, the substructure design, girder contact stress, and total launching force assumptions correlated well with the experimental results. The design assumptions for total axial force in crossframe members, on the other hand, differed from the experimental results by as much as 300%.

Testing demographic models of effective population size.

Due to practical difficulties in obtaining direct genetic estimates of effective sizes, conservation biologists have to rely on so-called 'demographic models' which combine life-history and mating-system parameters with F-statistics in order to produce indirect estimates of effective sizes. However, for the same practical reasons that prevent direct genetic estimates, the accuracy of demographic models is difficult to evaluate. Here we use individual-based, genetically explicit computer simulations in order to investigate the accuracy of two such demographic models aimed at investigating the hierarchical structure of populations. We show that, by and large, these models provide good estimates under a wide range of mating systems and dispersal patterns. However, one of the models should be avoided whenever the focal species' breeding system approaches monogamy with no sex bias in dispersal or when a substructure within social groups is suspected because effective sizes may then be strongly overestimated. The timing during the life cycle at which F-statistics are evaluated is also of crucial importance and attention should be paid to it when designing field sampling since different demographic models assume different timings. Our study shows that individual-based, genetically explicit models provide a promising way of evaluating the accuracy of demographic models of effective size and delineate their field of applicability.

Growth, optical characterization, and laser operation of a stoichiometric crystal KYb(WO4)(2)

We present our recent achievements in the growing and optical characterization of KYb(WO4)2 (hereafter KYbW) crystals and demonstrate laser operation in this stoichiometric material. Single crystals of KYbW with optimal crystalline quality have been grown by the top-seeded-solution growth slow-cooling method. The optical anisotropy of this monoclinic crystal has been characterized, locating the tensor of the optical indicatrix and measuring the dispersion of the principal values of the refractive indices as well as the thermo-optic coefficients. Sellmeier equations have been constructed valid in the visible and near-IR spectral range. Raman scattering has been used to determine the phonon energies of KYbW and a simple physical model is applied for classification of the lattice vibration modes. Spectroscopic studies (absorption and emission measurements at room and low temperature) have been carried out in the spectral region near 1 µm characteristic for the ytterbium transition. Energy positions of the Stark sublevels of the ground and the excited state manifolds have been determined and the vibronic substructure has been identified. The intrinsic lifetime of the upper laser level has been measured taking care to suppress the effect of reabsorption and the intrinsic quantum efficiency has been estimated. Lasing has been demonstrated near 1074 nm with 41% slope efficiency at room temperature using a 0.5 mm thin plate of KYbW. This laser material holds great promise for diode pumped high-power lasers, thin disk and waveguide designs as well as for ultrashort (ps/fs) pulse laser systems.

Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?

The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.

Performance of Strip Seals in Iowa Bridges, Project TR-437, January 2001

A pilot study was conducted on the premature failures of neoprene strip seals in expansion joints in Iowa bridges. In a relatively large number of bridges, strip seals have pulled out of the steel extrusions or otherwise failed well before the expected life span of the seal. The most serious consequence of a strip-seal failure is damage to the bridge substructure due to salt, water, and debris interacting with the substructure. A literature review was performed. Manufacturers’ specifications and recommendations, practices in the states bordering Iowa, and Iowa DOT design and installation guidelines were reviewed. Discussions were held with bridge contractors and the installation of a strip seal system was observed. Iowa DOT bridge databases were analyzed. A national survey was conducted on the use and performance of strip seals. With guidance from the Iowa DOT, twelve in-service bridges with strip-seal expansion joints were selected for detailed investigation. Effective bridge temperatures and corresponding expansion-joint openings were measured, DOT inspection reports were reviewed, and likely cause(s) of premature failures of strip seals were proposed. All of the seals used in the twelve bridges that had the most serious failures were in concrete girder bridges. Experimental results show that for a majority of these serious failures, the joint opening at 0° F predicted by the Iowa DOT design equations, the joint opening at 0° F extrapolated from the experimental data, or both, are larger than the movement rating of the strip seal specified on the bridge plans. Other likely causes of premature failures of seals in the twelve bridges include debris and ice in the seal cavity, a large skew and the corresponding decrease in the movement rating of the seal, improper installation, and improper setting of the initial gap.

Evaluation of the Buena Vista IBRD Bridge: A Furthering of Accelerated Bridge Construction in Iowa, February 2012

The need to construct bridges that last longer, are less expensive, and take less time to build has increased. The importance of accelerated bridge construction (ABC) technologies has been realized by the Federal Highway Administration (FHWA) and the Iowa Department of Transportation (DOT) Office of Bridges and Structures. This project is another in a series of ABC bridge projects undertaken by the Iowa DOT. Buena Vista County, Iowa, with the assistance of the Iowa Department of Transportation (DOT) and the Bridge Engineering Center (BEC) at Iowa State University, constructed a two-lane single-span precast box girder bridge, using rapid construction techniques. The design involved the use of precast, pretensioned components for the bridge superstructure, substructure, and backwalls. This application and demonstration represents an important step in the development and advancement of these techniques in Iowa as well as nationwide. Prior funding for the design and construction of this bridge (including materials) was obtained through the FHWA Innovative Bridge Research and Deployment (IBRD) Program. The Iowa Highway Research Board (IHRB) provided additional funding to test and evaluate the bridge. This project directly addresses the IBRD goal of demonstrating (and documenting) the effectiveness of innovative materials and construction techniques for the construction of new bridge structures. Evaluation of performance was formulated through comparisons with design assumptions and recognized codes and standards including American Association of State Highway and Transportation Officials (AASHTO) specifications.

Development of a Database for Drilled Shaft Foundation Testing (DSHAFT), June 2012

Drilled shafts have been used in the US for more than 100 years in bridges and buildings as a deep foundation alternative. For many of these applications, the drilled shafts were designed using the Working Stress Design (WSD) approach. Even though WSD has been used successfully in the past, a move toward Load Resistance Factor Design (LRFD) for foundation applications began when the Federal Highway Administration (FHWA) issued a policy memorandum on June 28, 2000.The policy memorandum requires all new bridges initiated after October 1, 2007, to be designed according to the LRFD approach. This ensures compatibility between the superstructure and substructure designs, and provides a means of consistently incorporating sources of uncertainty into each load and resistance component. Regionally-calibrated LRFD resistance factors are permitted by the American Association of State Highway and Transportation Officials (AASHTO) to improve the economy and competitiveness of drilled shafts. To achieve this goal, a database for Drilled SHAft Foundation Testing (DSHAFT) has been developed. DSHAFT is aimed at assimilating high quality drilled shaft test data from Iowa and the surrounding regions, and identifying the need for further tests in suitable soil profiles. This report introduces DSHAFT and demonstrates its features and capabilities, such as an easy-to-use storage and sharing tool for providing access to key information (e.g., soil classification details and cross-hole sonic logging reports). DSHAFT embodies a model for effective, regional LRFD calibration procedures consistent with PIle LOad Test (PILOT) database, which contains driven pile load tests accumulated from the state of Iowa. PILOT is now available for broader use at the project website: http://srg.cce.iastate.edu/lrfd/. DSHAFT, available in electronic form at http://srg.cce.iastate.edu/dshaft/, is currently comprised of 32 separate load tests provided by Illinois, Iowa, Minnesota, Missouri and Nebraska state departments of transportation and/or department of roads. In addition to serving as a manual for DSHAFT and providing a summary of the available data, this report provides a preliminary analysis of the load test data from Iowa, and will open up opportunities for others to share their data through this quality–assured process, thereby providing a platform to improve LRFD approach to drilled shafts, especially in the Midwest region.

Modified Sheet Pile Abutments for Low-Volume Road Bridges: Tech Transfer Summary, January 2012

Iowa has about 22,936 bridges on low-volume roads (LVRs). Based on the National Bridge Inventory data, 22 percent of the LVR bridges in Iowa are structurally deficient, while 5 percent of them are functionally obsolete. The substructure components (abutment and foundation elements) are known to be contributing factors for some of these poor ratings. Steel sheet piling was identified as a possible long-term option for LVR bridge substructures; but, due to lack of experience, Iowa needed investigation with regard to vertical and lateral load resistance, construction methods, design methodology, and load test performance. This project was initiated in January 2007 to investigate use of sheet pile abutments. *************Tech Transfer Summary. For full report see: http://publications.iowa.gov/id/eprint/14832*************

Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data.

In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.