The association of bacteriuria with survival and disease progression in cats with azotemic chronic kidney disease

Background Cats with chronic kidney disease (CKD) have an increased prevalence of positive urine cultures (PUC). Limited information is available regarding the prognosis of cats with CKD and concurrent PUC. Objective To determine the association of PUC with survival time and disease progression in cats with CKD. Animals Medical records of 509 cats diagnosed with azotemic CKD between 1997 and 2018. Methods Cats were classified as having “no‐PUC” or “PUC.” The PUC cats were further classified as having 1 or multiple PUC, and also were classified based on the presence or absence of clinical signs of urinary tract infection (UTI). Progression of CKD was defined as a plasma creatinine concentration increase of ≥25% within 365 days of CKD diagnosis; PUC also must have occurred within this time frame. Survival time and frequency of CKD progression were compared between groups. Results No significant difference in survival time was found between cats with no‐PUC and cats with any number of PUC (P = .91), or between cats with no‐PUC, 1 PUC or multiple PUC (P = .37). Also, no significant difference was found in the frequency of CKD progression between PUC and no‐PUC cats (P = .5), or among no‐PUC, 1 PUC and multiple PUC cats (P = .22). When assessing cats with clinical signs of lower UTI, no significant difference was found in the frequency of CKD progression between cats with true UTI, subclinical bacteriuria or no‐PUC (P = .8). Conclusions and Clinical Importance When treated with antibiotics, PUC in cats with CKD do not affect disease progression or survival time

The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.Peer reviewe

The Nature Index: A General Framework for Synthesizing Knowledge on the State of Biodiversity

The magnitude and urgency of the biodiversity crisis is widely recognized within scientific and political organizations. However, a lack of integrated measures for biodiversity has greatly constrained the national and international response to the biodiversity crisis. Thus, integrated biodiversity indexes will greatly facilitate information transfer from science toward other areas of human society. The Nature Index framework samples scientific information on biodiversity from a variety of sources, synthesizes this information, and then transmits it in a simplified form to environmental managers, policymakers, and the public. The Nature Index optimizes information use by incorporating expert judgment, monitoring-based estimates, and model-based estimates. The index relies on a network of scientific experts, each of whom is responsible for one or more biodiversity indicators. The resulting set of indicators is supposed to represent the best available knowledge on the state of biodiversity and ecosystems in any given area. The value of each indicator is scaled relative to a reference state, i.e., a predicted value assessed by each expert for a hypothetical undisturbed or sustainably managed ecosystem. Scaled indicator values can be aggregated or disaggregated over different axes representing spatiotemporal dimensions or thematic groups. A range of scaling models can be applied to allow for different ways of interpreting the reference states, e.g., optimal situations or minimum sustainable levels. Statistical testing for differences in space or time can be implemented using Monte-Carlo simulations. This study presents the Nature Index framework and details its implementation in Norway. The results suggest that the framework is a functional, efficient, and pragmatic approach for gathering and synthesizing scientific knowledge on the state of biodiversity in any marine or terrestrial ecosystem and has general applicability worldwide

Data from: Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation

The river-resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (FST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important

Salmo_salar_for_DRYAD

Microsatellite genotype data for 312 specimens of Atlantic salmon at eight microsatellite loc

Timing is everything: Fishing-season placement may represent the most important angling-induced evolutionary pressure on Atlantic salmon populations

Fisheries-induced evolution can change the trajectory of wild fish populations by selectively targeting certain phenotypes. For important fish species like Atlantic salmon, this could have large implications for their conservation and management. Most salmon rivers are managed by specifying an angling season of predetermined length based on population demography, which is typically established from catch statistics. Given the circularity of using catch statistics to estimate demographic parameters, it may be difficult to quantify the selective nature of angling and its evolutionary impact. In the River Etne in Norway, a recently installed trap permits daily sampling of fish entering the river, some of which are subsequently captured by anglers upstream. Here, we used 31 microsatellites to establish an individual DNA profile for salmon entering the trap, and for many of those subsequently captured by anglers. These data permitted us to investigate time of rod capture relative to river entry, potential body size-selective harvest, and environmental variables associated with river entry. Larger, older fish entered the river earlier than smaller, younger fish of both sexes, and larger, older females were more abundant than males and vice versa. There was good agreement between the sizes of fish harvested by angling, and the size distribution of the population sampled on the trap. These results demonstrate that at least in this river, and with the current timing of the season, the angling catch reflects the population's demographics and there is no evidence of size-selective harvest. We also demonstrated that the probability of being caught by angling declines quickly after river entry. Collectively, these data indicate that that the timing of the fishing season, in relation to the upstream migration patterns of the different demographics of the population, likely represents the most significant directional evolutionary force imposed by angling