Genomic variation at the tips of the adaptive radiation of Darwin's finches

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site‐associated DNA (RAD‐seq), we characterized 32 569 single‐nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta‐like 1 homologue (DLK1) and high‐mobility group AT‐hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro‐ and macro‐evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.     

How Pronghorn Females Avoid Inbreeding Depression

After a bottleneck in a closed population of pronghorn (Antilocapra americana), some inbred matings occurred, and we detected significant inbreeding depression. But inbred matings occurred less frequently than would be expected by chance. Pronghorn females chose mates after a sampling period and had complete control of the mating decision. Therefore, to discover the behavioral mechanism by which females avoided mating with close kin, we studied female movements and courtship sequences. When females moved from one harem to another in the sampling process, they did not shift to harem males of lower coancestry as they approached estrus. Rather, females progressed more slowly through the later courtship stages when the harem male was related vs. unrelated. Also, the rates of male courtship acts were higher within unrelated vs. related pairs. Some females appeared to use multiple mating as an inbreeding avoidance strategy. Our results suggested that inbreeding avoidance by female pronghorn occurred primarily by reactions to the late stages of male courtship, rather than by spatial avoidance of related males.     

Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles

Membrane‐less organelles in cells are large, dynamic protein/protein or protein/RNA assemblies that have been reported in some cases to have liquid droplet properties. However, the molecular interactions underlying the recruitment of components are not well understood. Herein, we study how the ability to form higher‐order assemblies influences the recruitment of the speckle‐type POZ protein (SPOP) to nuclear speckles. SPOP, a cullin‐3‐RING ubiquitin ligase (CRL3) substrate adaptor, self‐associates into higher‐order oligomers; that is, the number of monomers in an oligomer is broadly distributed and can be large. While wild‐type SPOP localizes to liquid nuclear speckles, self‐association‐deficient SPOP mutants have a diffuse distribution in the nucleus. SPOP oligomerizes through its BTB and BACK domains. We show that BTB‐mediated SPOP dimers form linear oligomers via BACK domain dimerization, and we determine the concentration‐dependent populations of the resulting oligomeric species. Higher‐order oligomerization of SPOP stimulates CRL3^SPOP ubiquitination efficiency for its physiological substrate Gli3, suggesting that nuclear speckles are hotspots of ubiquitination. Dynamic, higher‐order protein self‐association may be a general mechanism to concentrate functional components in membrane‐less cellular bodies.     

From Static to Interactive: Transforming Data Visualization to Improve Transparency

Data presentation for scientific publications in small sample size studies has not changed substantially in decades. It relies on static figures and tables that may not provide sufficient information for critical evaluation, particularly of the results from small sample size studies. Interactive graphics have the potential to transform scientific publications from static reports of experiments into interactive datasets. We designed an interactive line graph that demonstrates how dynamic alternatives to static graphics for small sample size studies allow for additional exploration of empirical datasets. This simple, free, web-based tool (http://statistika.mfub.bg.ac.rs/interactive-graph/) demonstrates the overall concept and may promote widespread use of interactive graphics.     

Eddy covariance captures four‐phase crassulacean acid metabolism (CAM) gas exchange signature in Agave

Mass and energy fluxes were measured over a field of Agave tequilana in Mexico using eddy covariance (EC) methodology. Data were gathered over 252 d, including the transition from wet to dry periods. Net ecosystem exchanges (F_N,EC) displayed a crassulacean acid metabolism (CAM) rhythm that alternated from CO₂ sink at night to CO₂ source during the day, and partitioned canopy fluxes (F_A,EC) showed a characteristic four‐phase CO₂ exchange pattern. Results were cross‐validated against diel changes in titratable acidity, leaf‐unfurling rates, energy exchange fluxes and reported biomass yields. Projected carbon balance (g C m^?2 year^?1, mean ± 95% confidence interval) indicated the site was a net sink of ?333 ± 24, of which contributions from soil respiration were +692 ± 7, and F_A,EC was ?1025 ± 25. EC estimated biomass yield was 20.1 Mg (dry) ha^?1 year^?1. Average integrated daily F_A,EC was ?234 ± 5 mmol CO₂ m^?2 d^?1 and persisted almost unchanged after 70 d of drought conditions. Regression analyses were performed on the EC data to identify the best environmental predictors of F_A. Results suggest that the carbon acquisition strategy of Agave offers productivity and drought resilience advantages over conventional semi‐arid C3 and C4 bioenergy candidates.