Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

BACKGROUND The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. FINDINGS We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. CONCLUSIONS These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Capital city and subject province: financial and military relations between Venice and Padua in the later fifteenth century

Between the conquest of Padua in 14O5 and its temporary rebellion in 1509, Venice built the strongest territorial state in Italy, expanding its apparatus of government to incorporate originally heterogeneous lands into an administrative whole. Military defeat in 1509 allowed Padua's secession, an anachronistic return to separate identity motivated by its political class's resentment at subjection to Venice: denied representation in mainstream public life, they enjoyed illusory local administrative autonomy. In military terms Padua's passage under Venetian rule was marked by the adaptation of the terraferma provinces' systems of defence to their new territorial configuration, achieved firatly by the creation of a permanent, professional army. Its units had no particular territorial affiliation; their recruitment, conditions of service and dislocation were decided by central authority. The province of Padua, strategically placed in the terraferma, served to accomodate companies in transit and long-term billetting, and to supply conscript auxiliary forces. Local fortifications were of secondary importance, and in consequence poorly maintained. The army was the main recipient of terraferma taxation, which was dogged by organizational difficulties, in the assignment of income to spending, and in co-ordination between capital and provinces, with a frequent excess of expenditure over effective revenue. Gross imbalance in the distribution of taxation, with delay and abuse in its collection, characterized Padua's fiscal system. Growing intervention by central government, and the diminution of Paduans' residual fiscal competence, were the constant elements in Venice's largely unsuccessful remedial action. Tax therefore became a point of conflict; Venice grew impatient with Paduan inefficiency and illwill, the Paduan political class showed anger at encroachment by Venetian authority, and fear for the loss of the city's fiscal privilege