Individual Quality Explains Association between Plumage Colouration, Arrival Dates and Mate Acquisition in Yellow Warblers (Setophaga petechia)

Background In many bird species colour traits influence social dominance and breeding success. In our study we first evaluated whether the colour of the basic plumage (tail feathers grown at the end of the breeding season), that provides an index of individual quality, influenced winter habitat use by yellow warblers. We then evaluated whether winter habitat use (inferred using δ13C and δ15N signatures of winter grown greater-coverts) influenced alternate plumage colouration, after controlling for individual quality using basic plumage colouration. Finally, we investigated whether basic and alternate plumage colouration influenced arrival dates, mate acquisition, breeding phenology and reproductive success of yellow warblers breeding in southern (Revelstoke, B.C.) and arctic (Inuvik, N.W.T.) Canada. Results The colour (chroma and hue) of tail feathers, grown on the breeding grounds, was not related to subsequent winter habitat use. Greater covert and tail feather colour (chroma and hue) were correlated, suggesting genetics and/or individual quality played a role in pigment deposition. After controlling for individual difference in tail colour, δ13C values did not explain any variation in greater covert colour, but birds with high δ15N signatures had greater coverts with higher chroma. Male arrival dates varied with tail chroma in Revelstoke and tail hue in Inuvik. Males that arrived early paired with older and/or more colourful mates that initiated clutches earlier, and at one site (Revelstoke) were more likely to fledge young. In addition, in Revelstoke (but not Inuvik) males with high tail hue also acquired more colourful mates. In contrast, after controlling for individual differences in tail colour, greater covert colour did not affect male arrival date, the quality of the mate obtained or reproductive success in either population. Conclusions Our results suggest that plumage colour effects on breeding phenology and mate acquisition result from differences in the intrinsic quality of individuals rather than a carry-over effect of winter habitat use

Identification of familial networks reveals sex-specific density dependence in the dispersal and reproductive success of an endangered ungulate

Density is an important demographic parameter that is commonly overlooked in studies of wild populations. Here, we examined the effects of variable spatially explicit density on a range of demographic parameters in a wild population of a cryptic ungulate, boreal woodland caribou (Rangifer tarandus caribou). Using non-invasive genetic sampling, we applied spatial capture–recapture methods with landscape covariates to estimate the density of boreal woodland caribou across a 108,806 km2 study area. We then created a familial network from the reconstructed parent–offspring relationships to determine whether spatial density influenced sex-specific individual reproductive success, female pregnancy status, and dispersal distance. We found that animal density varied greatly in response to land cover types and disturbance; animal density was most influenced by landscape composition and distance to roads varying from 0 in areas with >20% deciduous cover to 270 caribou per 1,000 km2 in areas presenting contiguous older coniferous cover. We found that both male and female reproductive success varied with density, with males showing a higher probability of having offspring in higher-density areas, and the opposite for females. No differences were found in female pregnancy rates occurring in high- and low-density areas. Dispersal distances varied with density, with offspring moving shorter distances when parents were found in higher-density areas. Familial networks showed lower-closeness centrality and lower-degree centrality for females in higher-density areas, indicating that females found in higher-density areas tend to be less broadly associated with animals across the range. Although high-density areas do reflect good-quality caribou habitat, the observed decreased closeness and degree centrality measures, dispersal rates, and lower female recruitment rates suggest that remnant habitat patches across the landscape may create population sinks

Rapid Progressing Allele HLA-B35 Px Restricted Anti-HIV-1 CD8+ T Cells Recognize Vestigial CTL Epitopes

BACKGROUND: The HLA-B*35-Px allele has been associated with rapid disease progression in HIV-1 infection, in contrast to the HLA-B*35-Py allele. METHODOLOGY/PRINCIPAL FINDINGS: Immune responses to two HLA-B*35 restricted HIV-1 specific CTL epitopes and their variants were followed longitudinally during early HIV-1 infection in 16 HLA-B*35+ individuals. Subjects expressing HLA-B*35-Px alleles showed no difference in response to the consensus epitopes compared to individuals with HLA-B*35-Py alleles. Surprisingly, all the HLA-B*35-Px+ individuals responded to epitope-variants even in the absence of a consensus response. Sequencing of the viral population revealed no evidence of variant virus in any of the individuals. CONCLUSIONS/SIGNIFICANCE: This demonstrates a novel phenomenon that distinguishes individuals with the HLA-B*35-Px rapid progressing allele and those with the HLA-B*35-Py slower progressing allele

The “Soluble” Adenylyl Cyclase in Sperm Mediates Multiple Signaling Events Required for Fertilization

SummaryMammalian fertilization is dependent upon a series of bicarbonate-induced, cAMP-dependent processes sperm undergo as they “capacitate,” i.e., acquire the ability to fertilize eggs. Male mice lacking the bicarbonate- and calcium-responsive soluble adenylyl cyclase (sAC), the predominant source of cAMP in male germ cells, are infertile, as the sperm are immotile. Membrane-permeable cAMP analogs are reported to rescue the motility defect, but we now show that these “rescued” null sperm were not hyperactive, displayed flagellar angulation, and remained unable to fertilize eggs in vitro. These deficits uncover a requirement for sAC during spermatogenesis and/or epididymal maturation and reveal limitations inherent in studying sAC function using knockout mice. To circumvent this restriction, we identified a specific sAC inhibitor that allowed temporal control over sAC activity. This inhibitor revealed that capacitation is defined by separable events: induction of protein tyrosine phosphorylation and motility are sAC dependent while acrosomal exocytosis is not dependent on sAC

Consistent sociality but flexible social associations across temporal and spatial foraging contexts in a colonial breeder.

When the consequences of sociality differ depending on the state of individual animals and the experienced environment, individuals may benefit from altering their social behaviours in a context-dependent manner. Thus, to fully address the hypotheses about the role of social associations it is imperative to consider the multidimensional nature of sociality by explicitly examining social associations across multiple scales and contexts. We simultaneously recorded > 8000 associations from 85% of breeding individuals from a colony of Australasian gannets (Morus serrator) over a 2-week period, and examined gregariousness across four foraging states using multilayer social network analysis. We found that social associations varied in a context-dependent manner, highlighting that social associations are most prevalent during foraging (local enhancement) and in regions expected to provide clustered resources. We also provide evidence of individual consistency in gregariousness, but flexibility in social associates, demonstrating that individuals can adjust their social behaviours to match experienced conditions

Werewolf, there wolf : Variants in hairless associated with hypotrichia and roaning in the lykoi cat breed

Publisher Copyright: © 2020 by the authors. Licensee MDPI, Basel, Switzerland.A variety of cat breeds have been developed via novelty selection on aesthetic, dermatological traits, such as coat colors and fur types. A recently developed breed, the lykoi (a.k.a. werewolf cat), was bred from cats with a sparse hair coat with roaning, implying full color and all white hairs. The lykoi phenotype is a form of hypotrichia, presenting as a significant reduction in the average numbers of follicles per hair follicle group as compared to domestic shorthair cats, a mild to severe perifollicular to mural lymphocytic infiltration in 77% of observed hair follicle groups, and the follicles are often miniaturized, dilated, and dysplastic. Whole genome sequencing was conducted on a single lykoi cat that was a cross between two independently ascertained lineages. Comparison to the 99 Lives dataset of 194 non‐lykoi cats suggested two variants in the cat homolog for Hairless (HR) (HR lysine demethylase and nuclear receptor corepressor) as candidate causal gene variants. The lykoi cat was a compound heterozygote for two loss of function variants in HR, an exon 3 c.1255_1256dupGT (chrB1:36040783), which should produce a stop codon at amino acid 420 (p.Gln420Serfs*100) and, an exon 18 c.3389insGACA (chrB1:36051555), which should produce a stop codon at amino acid position 1130 (p.Ser1130Argfs*29). Ascertainment of 14 additional cats from founder lineages from Canada, France and different areas of the USA identified four additional loss of function HR variants likely causing the highly similar phenotypic hair coat across the diverse cats. The novel variants in HR for cat hypotrichia can now be established between minor differences in the phenotypic presentations.Peer reviewe

A deletion in GDF7 is associated with a heritable forebrain commissural malformation concurrent with ventriculomegaly and interhemispheric cysts in cats

Publisher Copyright: © 2020 by the authors.An inherited neurologic syndrome in a family of mixed-breed Oriental cats has been characterized as forebrain commissural malformation, concurrent with ventriculomegaly and interhemispheric cysts. However, the genetic basis for this autosomal recessive syndrome in cats is unknown. Forty-three cats were genotyped on the Illumina Infinium Feline 63K iSelect DNA Array and used for analyses. Genome-wide association studies, including a sib-transmission disequilibrium test and a case-control association analysis, and homozygosity mapping, identified a critical region on cat chromosome A3. Short-read whole genome sequencing was completed for a cat trio segregating with the syndrome. A homozygous 7 bp deletion in growth differentiation factor 7 (GDF7) (c.221_227delGCCGCGC [p.Arg74Profs]) was identified in affected cats, by comparison to the 99 Lives Cat variant dataset, validated using Sanger sequencing and genotyped by fragment analyses. This variant was not identified in 192 unaffected cats in the 99 Lives dataset. The variant segregated concordantly in an extended pedigree. In mice, GDF7 mRNA is expressed within the roof plate when commissural axons initiate ventrally-directed growth. This finding emphasized the importance of GDF7 in the neurodevelopmental process in the mammalian brain. A genetic test can be developed for use by cat breeders to eradicate this variant.Peer reviewe

p53 and ovarian carcinoma survival: an Ovarian Tumor Tissue Analysis consortium study

Our objective was to test whether p53 expression status is associated with survival for women diagnosed with the most common ovarian carcinoma histotypes (high-grade serous carcinoma [HGSC], endometrioid carcinoma [EC], and clear cell carcinoma [CCC]) using a large multi-institutional cohort from the Ovarian Tumor Tissue Analysis (OTTA) consortium. p53 expression was assessed on 6,678 cases represented on tissue microarrays from 25 participating OTTA study sites using a previously validated immunohistochemical (IHC) assay as a surrogate for the presence and functional effect of TP53 mutations. Three abnormal expression patterns (overexpression, complete absence, and cytoplasmic) and the normal (wild type) pattern were recorded. Survival analyses were performed by histotype. The frequency of abnormal p53 expression was 93.4% (4,630/4,957) in HGSC compared to 11.9% (116/973) in EC and 11.5% (86/748) in CCC. In HGSC, there were no differences in overall survival across the abnormal p53 expression patterns. However, in EC and CCC, abnormal p53 expression was associated with an increased risk of death for women diagnosed with EC in multivariate analysis compared to normal p53 as the reference (hazard ratio [HR] = 2.18, 95% confidence interval [CI] 1.36-3.47, p = 0.0011) and with CCC (HR = 1.57, 95% CI 1.11-2.22, p = 0.012). Abnormal p53 was also associated with shorter overall survival in The International Federation of Gynecology and Obstetrics stage I/II EC and CCC. Our study provides further evidence that functional groups of TP53 mutations assessed by abnormal surrogate p53 IHC patterns are not associated with survival in HGSC. In contrast, we validate that abnormal p53 IHC is a strong independent prognostic marker for EC and demonstrate for the first time an independent prognostic association of abnormal p53 IHC with overall survival in patients with CCC

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Urbanization and the temporal patterns of social networks and group foraging behaviors

Urbanization causes dramatic and rapid changes to natural environments, which can lead the animals inhabiting these habitats to adjust their behavioral responses. For social animals, urbanized environments may alter group social dynamics through modification of the external environment (e.g., resource distribution). This might lead to changes in how individuals associate or engage in group behaviors, which could alter the stability and characteristics of social groups. However, the potential impacts of urban habitat use, and of habitat characteristics in general, on the nature and stability of social associations remain poorly understood. Here, we quantify social networks and dynamics of group foraging behaviors of black‐capped chickadees (N = 82, Poecile atricapillus), at four urban and four rural sites weekly throughout the nonbreeding season using feeders with radio frequency identification of individual birds. Because anthropogenic food sources in urban habitats (e.g., bird feeders) provide abundant and reliable resources, we predicted that social foraging associations may be of less value in urban groups, and thus would be less consistent than in rural groups. Additionally, decreased variability of food resources in urban habitats could lead to more predictable foraging patterns (group size, foraging duration, and the distribution of foraging events) in contrast to rural habitats. Networks were found to be highly consistent through time in both urban and rural habitats. No significant difference was found in the temporal clumping of foraging events between habitats. However, as predicted, the repeatability of the clumping of foraging events in time was significantly higher in urban than rural habitats. Our results suggest that individuals living in urban areas have more consistent foraging behaviors throughout the nonbreeding season, whereas rural individuals adjust their tactics due to less predictable foraging conditions. This first examination of habitat‐related differences in the characteristics and consistency of social networks along an urbanization gradient suggests that anthropic habitat use results in subtle modifications in social foraging patterns. Future studies should examine potential implications of these differences for variation in predation risk, energy intake, and information flow