DNA sequence data reveal a subfamily-level divergence within Thamnophilidae (Aves: Passeriformes)

The Thamnophilidae is a diverse radiation of insectivorous passerine birds that comprises nearly 220 species and is mostly restricted to the lowlands and lower montane forests of the Neotropics. Current classification within Thamnophilidae relies primarily on morphological variation, but recent incorporation of molecular and vocal data has promoted changes at various taxonomic levels. Here we demonstrate that the genus Terenura is polyphyletic because Terenura callinota, T. humeralis, T. spodioptila, and T. sharpei are phylogenetically distant from the type species of the genus, Terenura maculata. More importantly, the former four species are not particularly closely related to any other thamnophilids and represent a clade that is sister to all other members of the family. Because no genus name is available for this previously undetected lineage in the Thamnophilidae, we describe the genus Euchrepomis for callinota, humeralis, spodioptila, and sharpei, and erect the subfamily Euchrepomidinae. We discuss the taxonomic and evolutionary significance of this divergent lineage. This study highlights the importance of taxonomic coverage and the inclusion of type taxa to redefine classifications to reflect accurately evolutionary relationships.     

Subterranean Sympatry: An Investigation into Diet Using Stable Isotope Analysis

In the Western Cape three species of mole-rat occur in sympatry, however, little is known about differences in their dietary preferences. Dietary composition of the three species; the common mole-rat (Cryptomys hottentotus hottentotus), the Cape mole-rat (Georychus capensis) and the Cape dune mole-rat (Bathyergus suillus) were examined using stable isotope analysis. Blood, fur and claw samples were collected from 70 mole-rats, in addition to several potential food items, to assess food selection of the three species under natural conditions. Overall there was a significant difference in the isotopic composition (δ¹³C and δ¹⁵N) between all three species and significant differences in their diet composition. There were also significant differences between tissues in all three species suggesting temporal variation in diet. The small size and colonial lifestyle of C. h. hottentotus allows it to feed almost 100% on bulbs, while the solitary and larger species G. capensis and B. suillus fed to a greater extent on other resources such as grasses and clover. B. suillus, the largest of the species, had the most generalized diet. However, overall all species relied most heavily upon geophytes and consumed the same species suggesting competition for resources could exist. We also showed a high level of individual variation in diet choices. This was most pronounced in B. suillus and G. capensis and less so in C. h. hottentotus. We demonstrate that stable isotope analysis can successfully be applied to examine dietary patterns in subterranean mammals and provide insights into foraging patterns and dietary variation at both the inter and intra population level.     

Reciprocity on the Hardwood: Passing Patterns among Professional Basketball Players

Past theory and research view reciprocal resource sharing as a fundamental building block of human societies. Most studies of reciprocity dynamics have focused on trading among individuals in laboratory settings. But if motivations to engage in these patterns of resource sharing are powerful, then we should observe forms of reciprocity even in highly structured group environments in which reciprocity does not clearly serve individual or group interests. To this end, we investigated whether patterns of reciprocity might emerge among teammates in professional basketball games. Using data from logs of National Basketball Association (NBA) games of the 2008–9 season, we estimated a series of conditional logistic regression models to test the impact of different factors on the probability that a given player would assist another player in scoring a basket. Our analysis found evidence for a direct reciprocity effect in which players who had “received” assists in the past tended to subsequently reciprocate their benefactors. Further, this tendency was time-dependent, with the probability of repayment highest soon after receiving an assist and declining as game time passed. We found no evidence for generalized reciprocity – a tendency to “pay forward” assists – and only very limited evidence for indirect reciprocity – a tendency to reward players who had sent others many assists. These findings highlight the power of reciprocity to shape human behavior, even in a setting characterized by extensive planning, division of labor, quick decision-making, and a focus on inter-group competition.     

The expression of preaxial polydactyly is influenced by modifying genetic elements and is not maintained by chromosomal inversion in an avian biomedical model

Polydactyly (Po) is a common mutation found in many vertebrates. The UCD-Po.003 congenic chicken line was previously characterized for Po inheritance (autosomal dominant) and the mutation was mapped to chromosome 2p. Here, we describe for the first time the range and variability of the phenotype in this congenic line. Further, we studied the hypothesis that a chromosomal inversion was responsible for the maintenance of a large (6.3 Mb) candidate gene region. Fluorescence in situ hybridization employing BACs encompassing a 10.7-Mb region of GGA2p showed that the Po chromosome was normal, i.e. exhibits the wild-type BAC order. Continued fine-mapping along with a change in breeding strategy reduced the size of the causative region to 1.43 Mb. Recent research indicates that the cause of preaxial Po resides within a 794-bp highly conserved zone of polarizing activity regulatory sequence (ZRS) element located in intron 5 of the LMBR1 gene; however, the ZRS polymorphism of interest is found in some but not all breeds of polydactylous chicken. Therefore, we sequenced the ZRS in 101 heterozygous and 30 unaffected (wild-type) individuals to establish the relevance of this region to the Po condition in the UCD-Po.003 congenic line. A single point mutation (C/A at coordinate GGA2p: 8,414,121) within the ZRS segregated with carrier status. The polydactylous UCD-Silkie line also maintains this SNP in addition to a single base deletion. An inheritance analysis of the phenotypic variation in UCD-Po.003 suggests recessive epistasis as the mode of inheritance for the additional modifying genetic elements, residing outside the ZRS, to impact the preaxial polydactyl phenotype. These results contribute to our understanding of the cause of Po in an important vertebrate model.     

Near absence of hybridization between sauger and introduced walleye despite massive releases

We analyzed 11 microsatellite loci to determine the genetic population structure of saugers and to describe the amount and pattern of hybridization with widely introduced walleyes in the upper Missouri River drainage. We detected significant genetic differentiation among saugers spawning upstream and downstream of the confluence of the Bighorn and Yellowstone Rivers. Samples from upstream of the confluence had significantly lower heterozygosity and allelic richness. We suspect this reflects isolation at the periphery of the species’ range and possibly genetic drift resulting from recent population contractions due to dams, diversions, and water development. We detected only eighteen hybrids out of 925 individuals analyzed. Hybridization appeared recent, as nearly 50% of the hybrids showed significant evidence for having a non-hybrid ancestor within two generations. All but one hybrid were detected in the Yellowstone River drainage, despite a substantially higher rate of walleye stocking in the Missouri River drainage, suggesting conditions in the Yellowstone may be more conducive to hybridization. Rarity of hybridization is unexpected, given both massive walleye releases and previous findings of more frequent hybridization in the study area. Introgression of walleye genes into native saugers does not appear to be an immediate threat.     

Conformational stability of PrP amyloid fibrils controls their smallest possible fragment size

Fibril fragmentation is considered to be an essential step in prion replication. Recent studies have revealed a strong correlation between the incubation period to prion disease and conformational stability of synthetic prions. To gain insight into the molecular mechanism that accounts for this correlation, we proposed that the conformational stability of prion fibrils controls their intrinsic fragility or the size of the smallest possible fibrillar fragments. Using amyloid fibrils produced from full-length mammalian prion protein under three growth conditions, we found a correlation between conformational stability and the smallest possible fragment sizes. Specifically, the fibrils that were conformationally less stable were found to produce shorter pieces upon fragmentation. Site-specific denaturation experiments revealed that the fibril conformational stability was controlled by the region that acquires a cross-β-sheet structure. Using atomic force microscopy imaging, we found that fibril fragmentation occurred in both directions—perpendicular to and along the fibrillar axis. Two mechanisms of fibril fragmentation were identified: (i) fragmentation caused by small heat shock proteins, including αB-crystallin, and (ii) fragmentation due to mechanical stress arising from adhesion of the fibril to a surface. This study provides new mechanistic insight into the prion replication mechanism and offers a plausible explanation for the correlation between conformational stability of synthetic prions and incubation time to prion disease.     

Temperature until the 'eyed stage' of embryogenesis programmes the growth trajectory and muscle phenotype of adult Atlantic salmon

We investigated how adult growth in Atlantic salmon (Salmo salar L.) was affected by changing embryonic temperature from fertilization until the completion of eye pigmentation. Fertilized eggs from several hundred families were divided between four temperature treatments (2, 5, 8 or 10 degrees C) and subsequently reared in identical conditions in replicated tanks. Fish exposed to 2 and 5 degrees C treatments were significantly smaller at smoltification than groups at higher temperatures, but showed substantial compensatory catch-up growth. Remarkably, temperature during this short window of embryogenesis dictated adult myogenic phenotype three years later with significant treatment effects on the muscle fibre final number (FFN), maximum diameter, nuclear density and size distribution. FFN was highest for the 5 degrees C treatment and was reduced at higher and lower treatment temperatures. Our results require direct temperature effects on embryonic tissues, such as the stem cell-containing external cell layer, in order to produce persistent effects on juvenile and adult growth.     

Winter feeding of birds increases productivity in the subsequent breeding season

Supplementary food given to birds can have contemporary effects by reducing the risk of starvation, increasing survival and altering movements and reproductive performance. There is, however, a widely held perception that birds benefit from extra food over winter, but that it is better that they 'look after themselves' during breeding. Here we describe a landscape-scale experiment showing for the first time that the effects of increasing food availability only during the winter can be carried over to the subsequent breeding season. Even though food supplementation stopped six weeks prior to breeding, birds living on sites provisioned over winter had advanced laying dates and increased fledging success compared with birds living on unprovisioned sites. Thus, supplemental feeding of wild birds during winter, in a manner mimicking householders provisioning in gardens and backyards, has the potential to alter bird population dynamics by altering future reproductive performance. With levels of bird feeding by the public continuing to increase, the impacts of this additional food supply on wild bird populations may be considerable.     

Role for DNA polymerase kappa in the processing of N2-N2-guanine interstrand cross-links

Although there exists compelling genetic evidence for a homologous recombination-independent pathway for repair of interstrand cross-links (ICLs) involving translesion synthesis (TLS), biochemical support for this model is lacking. To identify DNA polymerases that may function in TLS past ICLs, oligodeoxynucleotides were synthesized containing site-specific ICLs in which the linkage was between N(2)-guanines, similar to cross-links formed by mitomycin C and enals. Here, data are presented that mammalian cell replication of DNAs containing these lesions was approximately 97% accurate. Using a series of oligodeoxynucleotides that mimic potential intermediates in ICL repair, we demonstrate that human polymerase (pol) kappa not only catalyzed accurate incorporation opposite the cross-linked guanine but also replicated beyond the lesion, thus providing the first biochemical evidence for TLS past an ICL. The efficiency of TLS was greatly enhanced by truncation of both the 5 ' and 3 ' ends of the nontemplating strand. Further analyses showed that although yeast Rev1 could incorporate a dCTP opposite the cross-linked guanine, no evidence was found for TLS by pol zeta or a pol zeta/Rev1 combination. Because pol kappa was able to bypass these ICLs, biological evidence for a role for pol kappa in tolerating the N(2)-N(2)-guanine ICLs was sought; both cell survival and chromosomal stability were adversely affected in pol kappa-depleted cells following mitomycin C exposure. Thus, biochemical data and cellular studies both suggest a role for pol kappa in the processing of N(2)-N(2)-guanine ICLs.