Spatial Models to Account for Variation in Observer Effort in Bird Atlases

To assess the importance of variation in observer effort between and within bird atlas projects and demonstrate the use of relatively simple conditional autoregressive (CAR) models for analyzing grid-based atlas data with varying effort. Pennsylvania and West Virginia, United States of America. We used varying proportions of randomly selected training data to assess whether variations in observer effort can be accounted for using CAR models and whether such models would still be useful for atlases with incomplete data. We then evaluated whether the application of these models influenced our assessment of distribution change between two atlas projects separated by twenty years (Pennsylvania), and tested our modeling methodology on a state bird atlas with incomplete coverage (West Virginia). Conditional Autoregressive models which included observer effort and landscape covariates were able to make robust predictions of species distributions in cases of sparse data coverage. Further, we found that CAR models without landscape covariates performed favorably. These models also account for variation in observer effort between atlas projects and can have a profound effect on the overall assessment of distribution change. Accounting for variation in observer effort in atlas projects is critically important. CAR models provide a useful modeling framework for accounting for variation in observer effort in bird atlas data because they are relatively simple to apply, and quick to run

Interbank Lending Relationships, Financial Crises, and Monetary Policy

Lucas, A. [Promotor]Koopman, S.J. [Promotor

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, F-ST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program

Carbon sequestration, biomass and soil carbon pool estimation in Oak-dominated forests of Hindu-Kush Range Mountains of Pakistan

The present study aimed to determine the vegetation biomass, soil carbon stocks and carbon sequestration potential of Oak-dominated forests. Thirty forest stands having 10 quadrats of 20×20 were randomly sampled. Out of eighteen tree species, twelve species were associated with Group II followed by Groups I and III, with eight species each. Quercus dilatata was the only Oak species recorded in all three groups having maximum density in Group II (56.14). Quercus semecarpifolia accounted the highest proportion of carbon (235 MgC/ha) in Group II. Quercus baloot, being the dominant species of Group I, is found to accommodate the highest quantities of BMC (335±43 Mg/ha) for all size classes. The highest nitrogen content, total nitrogen and carbon-nitrogen ratio were 0.185%, 8.23 and 59.64, respectively, in Group II. The mean bulk density was 1.519 g/cm3 in Group III. The highest soil organic carbon (SOC) was recorded in Group II (2.69%, 119.82 tons/ha). Because of their large aerial scale and high carbon density, Oak-dominated forests in Group II store most of the carbon. These results suggest that organic carbon is a major source of forest carbon with significant climate change mitigation potential that must be conserved and improved by sustainable forest management

Locus-specific introgression in young hybrid swarms:Drift may dominate selection

Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection

Studies of braided non-Abelian anyons using anyonic tensor networks

The content of this thesis can be broadly summarised into two categories: first, I constructed modified numerical algorithms based on tensor networks to simulate systems of anyons in low dimensions, and second, I used those methods to study the topological phases the anyons form when they braid around one another. In the first phase of my thesis, I extended the anyonic tensor network algorithms, by incorporating U(1) symmetry to give a modified ansatz, Anyon-U(1) tensor networks, which are capable of simulating anyonic systems at any rational filling fraction. In the second phase, I used the numerical methods to study some models of non-Abelian anyons that naturally allows for exchange of anyons. I proposed a lattice model of anyons, which I dubbed anyonic Hubbard model, which is a pair of coupled chains of anyons (or simply called anyonic ladder). Each site of the ladder can either host a single anyonic charge, or it can be empty. The anyons are able to move around, interact with one another, and exchange positions with other anyons, when vacancies exist. Exchange of anyons is a non-trivial process which may influence the formation of different kinds of new phases of matter. I studied this model using the two prominent species of anyons: Fibonacci and Ising anyons, and made a number of interesting discoveries about their phase diagrams. I identified new phases of matter arising from both the interaction between these anyons and their exchange braid statistics.Comment: 150 pages, PhD thesis, Macquarie University, Sydney. Chapter 6 of this thesis titled "Phase transitions in braided non-Abelian anyonic system" contains results which are yet to be finalised and publishe

Genome wide association study for growth in Pakistani dromedary camels using genotyping-by-sequencing

Objective Growth performance and growth-related traits have a crucial role in livestock due to their influence on productivity. This genome-wide association study (GWAS) in Pakistani dromedary camels was conducted to identify single nucleotide polymorphisms (SNPs) associated with growth at specific camel ages, and for selected SNPs, to investigate in detail how their effects change with increasing camel age. This is the first GWAS conducted on dromedary camels in this region. Methods Two Pakistani breeds, Marecha and Lassi, were selected for this study. A genotyping-by-sequencing method was used, and a total of 65,644 SNPs were identified. For GWAS, weight records data with several body weight traits, namely, birthweight, weaning weight, and weights of camels at 1, 2, 4, and 6 years of age were analysed by using model-based growth curve analysis. Age-specific weight data were analysed with a linear mixed model that included fixed effects of SNP genotype as well as sex. Results Based on the q-value method for false discovery control, for Marecha camels, five SNPs at q<0.01 and 96 at q<0.05 were significantly associated with the weight traits considered, while three (q<0.01) and seven (q<0.05) SNP associations were identified for Lassi camels. Several candidate genes harbouring these SNP were discovered. Conclusion These results will help to better understand the genetic architecture of growth including how these genes are expressed at different phases of their life. This will serve to lay the foundations for applied breeding programs of camels by allowing the genetic selection of superior animals

学会抄録

A description of the results of the cross platform (385 K CGH and SNP50 chip) verification of CNV regions [72, 73]. (PDF 8 kb

Mixed-species allometric equations and estimation of aboveground biomass and carbon stocks in restoring degraded landscape in northern Ethiopia

Accurate biomass estimation is critical to quantify the changes in biomass and carbon stocks following the restoration of degraded landscapes. However, there is lack of site-specific allometric equations for the estimation of aboveground biomass (AGB), which consequently limits our understanding of the contributions of restoration efforts in mitigating climate change. This study was conducted in northwestern Ethiopia to develop a multi-species allometric equation and investigate the spatial and temporal variation of C-stocks following the restoration of degraded landscapes. We harvested and weighed 84 trees from eleven dominant species from six grazing exclosures and adjacent communal grazing land. We observed that AGB correlates significantly with diameter at stump height D 30 (R 2 = 0.78; P < 0.01), and tree height H (R 2 = 0.41, P < 0.05). Our best model, which includes D 30 and H as predictors explained 82% of the variations in AGB. This model produced the lowest bias with narrow ranges of errors across different diameter classes. Estimated C-stock showed a significant positive correlation with stem density (R 2 = 0.80, P < 0.01) and basal area (R 2 = 0.84, P < 0.01). At the watershed level, the mean C-stock was 3.8 (±0.5) Mg C ha−1. Plot-level C-stocks varied between 0.1 and 13.7 Mg C ha−1. Estimated C-stocks in three- and seven-year-old exclosures exceeded estimated C-stock in the communal grazing land by 50%. The species that contribute most to C-stocks were Leucaena sp. (28%), Calpurnia aurea (21%), Euclea racemosa (20.9%), and Dodonaea angustifolia (15.8%). The equations developed in this study allow monitoring changes in C-stocks and C-sequestration following the implementation of restoration practices in northern Ethiopia over space and time. The estimated C-stocks can be used as a reference against which future changes in C-stocks can be compared