Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2^m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2^m chromosomes in this species. We found that features of ZAL2^m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2^m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2^m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.

Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

Much of our knowledge on regulatory impacts of DNA methylation has come from laboratory‐bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally‐occurring variation in DNA methylation in a wild avian species, the white‐throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a nonrecombining chromosome pair linked to both plumage and behavioural phenotypes. Using novel single‐nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was concentrated in the nonrecombining chromosome pair. Interestingly, a large number of CpGs on the nonrecombining chromosome, localized to transposable elements, have undergone dramatic loss of DNA methylation since the split of the ZAL2 and ZAL2^m chromosomes. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome‐wide DNA methylation that are associated with development and with specific functional categories of genes in white‐throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

see also the Perspective by Jordan A. Anderson and Jenny Tung.

Regional epigenetic differentiation of the Z Chromosome between sexes in a female heterogametic system

In male heterogametic systems, the X Chromosome is epigenetically differentiated between males and females, to facilitate dosage compensation. For example, the X Chromosome in female mammals is largely inactivated. Relative to well-studied male heterogametic systems, the extent of epigenetic differentiation between male and female Z Chromosomes in female heterogametic species, which often lack complete dosage compensation, is poorly understood. Here, we examined the chromosomal DNA methylation landscapes of male and female Z Chromosomes in two distantly related avian species, namely chicken and white-throated sparrow. We show that, in contrast to the pattern in mammals, male and female Z Chromosomes in these species exhibit highly similar patterns of DNA methylation, which is consistent with weak or absent dosage compensation. We further demonstrate that the epigenetic differences between male and female chicken Z Chromosomes are localized to a few regions, including a previously identified male hypermethylated region 1 (MHM1; CGNC: 80601). We discovered a novel region with elevated male-to-female methylation ratios on the chicken Z Chromosome (male hypermethylated region 2 [MHM2]; CGNC: 80602). The MHM1 and MHM2, despite little sequence similarity between them, bear similar molecular features that are likely associated with their functions. We present evidence consistent with female hypomethylation of MHMs and up-regulation of nearby genes. Therefore, despite little methylation differentiation between sexes, extremely localized DNA methylation differences between male and female chicken Z Chromosomes have evolved and affect expression of nearby regions. Our findings offer new insights into epigenetic regulation of gene expression between sexes in female heterogametic systems.

Infection of Ferrets with Influenza Virus Elicits a Light Chain-Biased Antibody Response against Hemagglutinin

The domestic ferret (Mustela putorius furo) is a commonly used animal model for the study of influenza virus infection and vaccination. Recently, our group has developed murine mAbs with specificity for the κ (Igκ) and λ (Igλ) L chains of ferret Ig. These mAbs were used to quantify the abundance of Igκ and Igλ in serum and to evaluate L chain usage of the Ab response against the hemagglutinin (HA) protein elicited by influenza infection. After influenza A infection of immunologically naive ferrets with various H1N1 or H3N2 strains, the acute Ab response against HA exhibited an inherent bias toward λ L chain usage. In contrast, secondary infection of H1N1 preimmune ferrets with an antigenically distinct H1N1 virus elicited a recall response against the original HA that was no longer biased toward Igλ and possessed differential specificity. Moreover, sequential infection of ferrets with H1N1 influenza viruses elicited an Igκ-biased Ab response directed against the HA globular head and stem regions. Furthermore, sequential infection of ferrets with viral vectors expressing chimeric HA, aimed at boosting Ab reactivity against the HA stem region, also elicited an Igκ-biased response. Collectively, these findings suggest that ferret B cells expressing an Igκ or Igλ BCR possess differential specificities, and highlight the utility of our recently developed mAbs for studying the immune response to influenza virus infection and vaccination in the ferret model.

Traumatic abdominal aortic pseudoaneurysm causing biliary obstruction: a case report and review of the literature

A traumatic pseudoaneurysm of the suprarenal abdominal aorta was diagnosed in a 58-year-old man 32 years after he received a gunshot wound to the abdomen. Epigastric pain and obstructive jaundice were the presenting symptoms. Repair was performed by intraluminal polytetrafluoroethylene patch aortoplasty with resolution of the biliary obstruction. The literature on traumatic abdominal aortic pseudoaneurysm is reviewed and reveals that this report is the first to describe biliary obstruction caused by such a lesion.

Laparoscopic hernia repair: a preliminary report

Advances in laparoscopic technique have provided the opportunity to perform preperitoneal herniorrhaphy and potentially avoid the morbidity associated with open techniques. From January 1991 to May 1992, two primary surgeons repaired 63 inguinal hernias (42 indirect, 20 direct, 1 femoral) on 48 patients using a standardized laparoscopic technique. The hernia defect was visualized laparoscopically, and the peritoneum anterior to the defect was incised. The hernia sac was dissected from the inguinal canal. The hernia defect was then loosely packed with rolled 1 x 6-inch polypropylene mesh (average number of rolls used was 3.4). A sheet of polypropylene mesh (average 5 x 8 cm) was then placed over the mesh rolls and the hernia defect and anchored with an endostapler. The peritoneum was closed over the mesh sheet with standard laparoscopic clips. There were 44 males and 4 females in the study group. The mean age was 55 years (range, 17-89 years). The mean follow-up was 5.8 months (range, 1-12 months). Thirty-three patients underwent unilateral hernia repair, and 15 patients underwent bilateral hernia repair. Clinically unsuspected contralateral hernias were identified at the time of laparoscopy in seven patients. The mean duration of surgery was 118 minutes (range, 80-165 minutes) for bilateral hernia repair, and 70 minutes (range, 45-100 minutes) for unilateral hernia repair. All patients with laparoscopic hernia repairs were treated on a same-day or less-than-24-hour in-hospital stay. Complications were designated as minor, moderate, or severe. There were 14 minor complications, which included subcutaneous hematomas at the trocar site, scrotal ecchymosis, groin swelling emphysema, and testicular asymmetry.(ABSTRACT TRUNCATED AT 250 WORDS)

Laparoscopic inguinal herniorrhaphy in a swine model. Third place winner of the Conrad Jobst Award in the Gold Medal paper competition

A simplified method of laparoscopic inguinal herniorrhaphy using prosthetic materials was evaluated in a swine hernia model. The goals of this study were to determine 1) effectiveness of repair in a rapidly growing animal, 2) effectiveness and extent of adhesion formation of different prosthetic materials, 3) the effect of repair on testicular growth, and 4) histologic effects on the hernia site and surrounding structures. In a prospective randomized study, 30 juvenile male swine (average, 23 kg) with 35 congenital indirect inguinal hernias underwent laparoscopic herniorrhaphy using one of three prosthetic materials: Group 1 (polytetrafluoroethylene/Gore-Tex), N = 10; Group 2 (polypropylene mesh/Marlex), N = 10; Group 3 (polypropylene mesh/Prolene), N = 10. A standardized laparoscopic herniorrhaphy technique consisting of stapling prosthetic material over the hernia defect without peritoneal dissection was employed. During the 3-month postoperative period, animals were sequentially examined for normal growth and development, normal testicular development, and signs of hernia recurrence. Clinically apparent complications related to herniorrhaphy occurred in five animals (17%) during the observation period (one with repair failure, one with testicular torsion, two with repair failure and bowel obstruction, and one with intestinal obstruction secondary to adhesions). All three animals with bowel obstruction died. At 90 days after surgery all remaining animals (N = 27) were euthanized (Group 1 = 9, Group 2 = 8, Group 3 = 10). Average weight was 84 kg. Necropsy findings included no additional hernia recurrences, and one mesh erosion into the urinary bladder.(ABSTRACT TRUNCATED AT 250 WORDS)