Evaluation of Disturbance Factors and Their Effect on Breeding Common Loons at Lake Umbagog National Wildlife Refuge, New Hampshire and Maine

Virtually any person exposed to American movies or television has likely heard the call of a common loon (Gavia immer). Its use as a sound prop has become ubiquitous in any scene related to the outdoors or the wilderness, even if the area filmed is in no way related to true loon habitat. The reason behind this is that the common loon and its haunting cries have come to symbolize the great outdoors. The sound of their call is meant to make the audience feel like the scene they are watching is in a remote area, far from the trappings of civilization, and, in our experience, it works. Hollywood has picked up on a sentiment held by many outdoor enthusiasts and is using it successfully. Unfortunately the southern range of the common loon is contracting and concern has been expressed over disturbance to breeding pairs by human activities, such as shoreline development, boating, and water-skiing, as well as possible contamination with lead, mercury, and other pollutants. If this alarming trend continues it may be that Hollywood movies will be the last place where a loon call can be heard in the United States. In the following chapters I will explore various threats to common loon populations. I will start in Chapter 1 with an evaluation of the potential effects of global warming on common loons within the North American breeding range. In Chapter 2 I review the available literature on wildlife disturbance and discuss some of the shortcomings and future research needs. I then go to a finer scale of study in Chapter 3 with a spatial analysis of disturbance factors and the effects on breeding common loons at Lake Umbagog National Wildlife Refuge. From there, in Chapter 4, I proceed to an analysis of specific behavioral responses exhibited by common loons in response to observed and experimentally imposed disturbance events. Finally, in Chapters 5 and 6, I briefly describe two natural disturbance events observed during our research, an immature bald eagle (Haliaeetus leucocephalus) predating a loon nest, and a loon nest defense of an aggressive American mink (Nevison vison)

Historical and contemporary perspectives on the sediments of Lake Rotorua

Lake Rotorua is probably the oldest continuously inundated lake in New Zealand, occupying a caldera formed by or closely associated with the eruption of the Mamaku ignimbrite and the collapse of the Rotorua caldera (Healy, 1975; Lowe and Green, 1991). The lake has undergone drastic changes in size and depth as a result of tectonics, volcanic activity and erosion. Since the Rotoehu eruption, (~60 kyr), the lake level has fluctuated between 120 m above present (280 m asl) and 10 m below present level. The modern lake covers an area of 79 km2 and has a mean depth of 10 m. Despite its long history of sedimentation, Lake Rotorua has an irregular bathymetry with features including faulted blocks, slumps, hydrothermal explosion craters, springs and large methane discharge pock marks

Assessing estimators of snow leopard abundance

ABSTRACT The secretive nature of snow leopards (Uncia uncia) makes them difficult to monitor, yet conservation efforts require accurate and precise methods to estimate abundance. We assessed accuracy of Snow Leopard Information Management System (SLIMS) sign surveys by comparing them with 4 methods for estimating snow leopard abundance: predator:prey biomass ratios, capture-recapture density estimation, photo-capture rate, and individual identification through genetic analysis. We recorded snow leopard sign during standardized surveys in the SaryChat Zapovednik, the Jangart hunting reserve, and the Tomur Strictly Protected Area, in the Tien Shan Mountains of Kyrgyzstan and China. During June-December 2005, adjusted sign averaged 46.3 (SaryChat), 94.6 (Jangart), and 150.8 (Tomur) occurrences/km. We used counts of ibex (Capra ibex) and argali (Ovis ammon) to estimate available prey biomass and subsequent potential snow leopard densities of 8.7 (SaryChat), 1.0 (Jangart), and 1.1 (Tomur) snow leopards/100 km 2 . Photo capture-recapture density estimates were 0.15 (n ¼ 1 identified individual/1 photo), 0.87 (n ¼ 4/13), and 0.74 (n ¼ 5/6) individuals/100 km 2 in SaryChat, Jangart, and Tomur, respectively. Photo-capture rates (photos/100 trap-nights) were 0.09 (SaryChat), 0.93 (Jangart), and 2.37 (Tomur). Genetic analysis of snow leopard fecal samples provided minimum population sizes of 3 (SaryChat), 5 (Jangart), and 9 (Tomur) snow leopards. These results suggest SLIMS sign surveys may be affected by observer bias and environmental variance. However, when such bias and variation are accounted for, sign surveys indicate relative abundances similar to photo rates and genetic individual identification results. Density or abundance estimates based on capture-recapture or ungulate biomass did not agree with other indices of abundance. Confidence in estimated densities, or even detection of significant changes in abundance of snow leopard, will require more effort and better documentation

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci

We performed fine-mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in/near KCNQ1. “Credible sets” of variants most likely to drive each distinct signal mapped predominantly to non-coding sequence, implying that T2D association is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine-mapping implicated rs10830963 as driving T2D association. We confirmed that this T2D-risk allele increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D-risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease

Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes.

Initial results from sequencing studies suggest that there are relatively few low-frequency (<5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency-large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant-common phenotype associations-11 132 cis-gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (<5%), respectively, low frequency-large effect associations comprised 7% of detectable cis-gene expression traits [89 of 1314 cis-eQTLs at P < 1 × 10(-06) (false discovery rate ∼5%)] and one of eight biomarker associations at P < 8 × 10(-10). Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect

Bloodlines: mammals, leeches, and conservation in southern Asia

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to find mammals in a given area. While these invertebrate-parasite-derived DNA (iDNA) methods are promising, most of the leech species utilized for this type of survey remain unevaluated, notwithstanding that their diversity varies substantially. Here we examine approximately 750 individual leech specimens in the genus Haemadipsa across a large range in southern Asia (Bangladesh, Cambodia, and China), specifically reviewing the diversity of mammals they feed on and their own genetic structuring. Leeches were found to feed on a considerable variety of mammals, corroborating prior studies. Additionally, leeches were found to have fed both on bats and on birds, neither of which has previously been recorded with this method. The genetic structuring of the leeches themselves revealed 15 distinct clades of which only two precisely corresponded to previously characterized species, indicating that much work is needed to finalize classifications in this genus. Most importantly, with regards to mammal conservation, leeches in these clades appear to feed on a broad range of mammals

The SDSS-III Baryon Oscillation Spectroscopic Survey: Quasar Target Selection for Data Release Nine

The SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), a five-year spectroscopic survey of 10,000 deg^2, achieved first light in late 2009. One of the key goals of BOSS is to measure the signature of baryon acoustic oscillations in the distribution of Ly-alpha absorption from the spectra of a sample of ~150,000 z>2.2 quasars. Along with measuring the angular diameter distance at z\approx2.5, BOSS will provide the first direct measurement of the expansion rate of the Universe at z > 2. One of the biggest challenges in achieving this goal is an efficient target selection algorithm for quasars over 2.2 < z < 3.5, where their colors overlap those of stars. During the first year of the BOSS survey, quasar target selection methods were developed and tested to meet the requirement of delivering at least 15 quasars deg^-2 in this redshift range, out of 40 targets deg^-2. To achieve these surface densities, the magnitude limit of the quasar targets was set at g <= 22.0 or r<=21.85. While detection of the BAO signature in the Ly-alpha absorption in quasar spectra does not require a uniform target selection, many other astrophysical studies do. We therefore defined a uniformly-selected subsample of 20 targets deg^-2, for which the selection efficiency is just over 50%. This "CORE" subsample will be fixed for Years Two through Five of the survey. In this paper we describe the evolution and implementation of the BOSS quasar target selection algorithms during the first two years of BOSS operations. We analyze the spectra obtained during the first year. 11,263 new z>2.2 quasars were spectroscopically confirmed by BOSS. Our current algorithms select an average of 15 z > 2.2 quasars deg^-2 from 40 targets deg^-2 using single-epoch SDSS imaging. Multi-epoch optical data and data at other wavelengths can further improve the efficiency and completeness of BOSS quasar target selection. [Abridged]Comment: 33 pages, 26 figures, 12 tables and a whole bunch of quasars. Submitted to Ap

Reference values for body composition and associations with blood pressure in Kenyan adults aged ≥50 years old

Objectives: To develop age and sex-specific centile reference curves for fat free mass (FFM) and fat mass (FM) adjusted for height in an adult Kenyan population and to investigate the association between FM, FFM and blood pressure (BP). Methods: Measures of body composition from bioimpedance analyses and BP were collected in 1,995 participants aged ≥50y in Nakuru County, Kenya. Reference curves were produced using the LMS method. Multivariable linear regression models were used to test the cross-sectional association between body composition indexes and BP. Results: The age and sex-specific reference curves for body composition (FMI and FFMI) confirm that FFMI is lower in both men and women with increasing age. FMI declines with age in women while among men the decline starts after 70 years. FFM was higher in men (47.4 ± 7.2 kg) than in women (38.8 ± 5.5 kg), while FM was lower in men (17.3 ± 8.1 kg) than in women (24.4 ± 10.2 kg). FMI, FFMI and BMI were all positively associated with systolic and diastolic BP, and after adjusting for body weight, FFMI remained positively associated with systolic BP and the FMI remained positively associated with diastolic BP. There was no evidence to suggest that FMI and FFMI were superior to measurement of BMI alone. Conclusion: These body composition reference curves provide normative data on body composition for older adults in Kenya. Further research should consider the prospective associations with health, including frailty-related outcomes