Initial Sequence and Comparative Analysis of the Cat Genome

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence

Geothermal Brine Reinjection from SaltPower Generation: A Microcalorimetry Study

This data set contains: 1) Isothermal titration calorimety (ITC) heat flow for Thisted brine (TB) titrated into Berea sandstone aged with TB and 2*DTB titrated into Berea sandstone aged with TB 2) Pressure measurements from coreflooding experiments 3) Effluent analysis: Ionic composition, alkalinity and iron concentratio

Data from: Female Soay sheep do not adjust their maternal care behaviour to the quality of their home range

Resource availability, through its impact on the costs and benefits of parental care, is expected to influence parental care behaviour. There has, to our knowledge, been no attempt to understand how variation in the resource use of wild individuals influences individual parental care behaviour. To understand how natural resource variability affects maternal care in female St. Kilda Soay sheep, we selected 69 females whose home ranges varied in quality (measured as the mean percentage cover of Holcus lanatus), and recorded the behaviour of each individual and her lamb over the period of maternal care. Home range quality did not influence suckling or non-suckling behaviours of the female or her lamb, suggesting that maternal care did not vary with a female’s access to resources. Growth rate analyses confirmed the behavioural results, with no association between home range quality and the weight gain of lambs between birth and weaning. This work suggests that female Soay sheep faced with poorer resources do not favour their own future success over that of their lamb, and thereby do not exhibit a conservative reproductive strategy. This may be because when resource levels are high during the summer, females are able to offset the costs of lactation by consuming additional resources, regardless of the location of their home range. Our results suggest that more studies characterizing the environment experienced by individual animals will be necessary to fully understand how individuals alter their behaviour in response to temporal and spatial variation in the environment.Regan, Charlotte E.; Pilkington, Jill G.; Smiseth, Per T. (2017), Data from: Female Soay sheep do not adjust their maternal care behaviour to the quality of their home range, Dryad, Dataset, https://doi.org/10.5061/dryad.6nk1

Genetic investigation of Italian domestic pigeons increases knowledge about the long-bred history of Columba livia (Aves: Columbidae)

In this study, we aimed to characterise the genetic diversity of Italian pigeon breeds and describe the relationships among them and other European lineages, conjecturing which processes have led to actual breeds. We analysed the eight most diffused Italian pigeon breeds in addition to 11 foreign lineages that could have shared common ancestors or have been used in the creation of the Italian breeds. We analysed 12 autosomal microsatellite loci in 427 samples collected from 19 breeds belonging to six main groups of domestic pigeons (tumblers and highflyers, structure, owls, wattle, utility and hen). Genetic variability did not differ considerably among breeds, with an average observed heterozygosity (HO) of 0.550 ± 0.072 (max = 0.661 in breed Sottobanca; min = 0.411 in breed Frillback). The 21.34% of total genetic variation found was partitioned among breeds. Italian pigeon breeds were assigned coherently to their respective groups of origin. The analysis supports the origin of homing pigeons from English Carrier and the existence of a close relationship between Old Dutch Capuchine and Italian Owl. Despite the differences in body size, pigeons of the breeds belonging to the hen group are genetically very similar. The sub-populations recognised by breeders inside Italian Owl and Triganino are not genetically supported and their identification as new breeds ought not to be yet proposed, although they are morphologically distinguishable. Consequently, it could also be discussed how the genetic characterisation of domestic lineages could give useful information in breeding and selection processes

Additional file 1: of Automated image analysis for quantification of filamentous bacteria

Piperacillin-induced filamentation in E. coli . The time-lapse movies show E. coli treated with piperacillin (PIP, 64 mg/L) and without (Positive control), respectively; as well as graphs showing growth and average length of the bacteria. (MOV 4671 kb

Genetic investigation of Italian domestic pigeons increases knowledge about the long-bred history of Columba livia (Aves: Columbidae)

In this study, we aimed to characterise the genetic diversity of Italian pigeon breeds and describe the relationships among them and other European lineages, conjecturing which processes have led to actual breeds. We analysed the eight most diffused Italian pigeon breeds in addition to 11 foreign lineages that could have shared common ancestors or have been used in the creation of the Italian breeds. We analysed 12 autosomal microsatellite loci in 427 samples collected from 19 breeds belonging to six main groups of domestic pigeons (tumblers and highflyers, structure, owls, wattle, utility and hen). Genetic variability did not differ considerably among breeds, with an average observed heterozygosity (HO) of 0.550 ± 0.072 (max = 0.661 in breed Sottobanca; min = 0.411 in breed Frillback). The 21.34% of total genetic variation found was partitioned among breeds. Italian pigeon breeds were assigned coherently to their respective groups of origin. The analysis supports the origin of homing pigeons from English Carrier and the existence of a close relationship between Old Dutch Capuchine and Italian Owl. Despite the differences in body size, pigeons of the breeds belonging to the hen group are genetically very similar. The sub-populations recognised by breeders inside Italian Owl and Triganino are not genetically supported and their identification as new breeds ought not to be yet proposed, although they are morphologically distinguishable. Consequently, it could also be discussed how the genetic characterisation of domestic lineages could give useful information in breeding and selection processes

Supplementary material 1 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776

Text S1. Parameters used for parentage analysis

Supplementary material 3 from: Davoli F, Cozzo M, Angeli F, Groff C, Randi E (2018) Infanticide in brown bear: a case-study in the Italian Alps – Genetic identification of perpetrator and implications in small populations. Nature Conservation 25: 55-75. https://doi.org/10.3897/natureconservation.25.23776

Text S3. Detailed results of LRmix STUDIO for each suspected male: Global Composite (ADO 0.55)