Do pseudogenes pose a problem for metabarcoding marine animal communities?

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658-bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 ± 200 bp. Among this total, 75 (24.3%) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (<313 bp) amplicons are used, such as in environmental DNA studies, dietary analyses or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the operational taxonomic unit (OTU) count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defence involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.

Shifting headlines? Size trends of newsworthy fishes.

The shifting baseline syndrome describes a gradual lowering of human cognitive baselines, as each generation accepts a lower standard of resource abundance or size as the new norm. There is strong empirical evidence of declining trends of abundance and body sizes of marine fish species reported from docks and markets. We asked whether these widespread trends in shrinking marine fish are detectable in popular English-language media, or whether news writers, like many marine stakeholders, are captive to shifting baselines. We collected 266 English-language news articles, printed between 1869 and 2015, which featured headlines that used a superlative adjective, such as 'giant', 'huge', or 'monster', to describe an individual fish caught. We combined the reported sizes of the captured fish with information on maximum species-specific recorded sizes to reconstruct trends of relative size (reported size divided by maximum size) of newsworthy fishes over time. We found some evidence of a shifting baseline syndrome in news media over the last 140 years: overall, the relative length of the largest fish worthy of a headline has declined over time. This pattern held for charismatic fish species (e.g. basking sharks, whale sharks, giant mantas), which are now reported in the media at smaller relative lengths than they were near the turn of the 20th century, and for the largest species under high risk of extinction. In contrast, there was no similar trend for pelagic gamefish and oceanic sharks, or for species under lower risk of extinction. While landing any individual of the large-bodied 'megafish' may be newsworthy in part because of their large size relative to other fish species, the 'megafish' covered in our dataset were small relative to their own species-on average only 56% of the species-specific maximum length. The continued use in the English-language media of superlatives to describe fish that are now a fraction of the maximum size they could reach, or a fraction of the size they used to be, does reflect a shifting baseline for some species. Given that media outlets are a powerful tool for shaping public perception and awareness of environmental issues, there is a real concern that such stories might be interpreted as meaning that superlatively large fish still abound.

The risk of midgut volvulus in patients with abdominal wall defects: A multi-institutional study.

BACKGROUND: The management of malrotation in patients with congenital abdominal wall defects has varied among surgeons. We were interested in investigating the risk of midgut volvulus in patients with gastroschisis and omphalocele to help determine if these patients may benefit from undergoing a Ladd procedure. METHODS: A retrospective chart review was performed for all patients managed at three institutions born between 1/1/2000 and 12/31/2008 with a diagnosis of gastroschisis or omphalocele. Patient charts were reviewed through 12/31/2012 for occurrence of midgut volvulus or need for second laparotomy. RESULTS: Of the 414 patients identified with abdominal wall defects, 299 patients (72%) had gastroschisis, and 115 patients (28%) had omphalocele. The mean gestational age at birth was 36.1±2.3weeks, and the mean birth weight was 2.57±0.7kg. There were a total of 8 (1.9%) cases of midgut volvulus: 3 (1.0%) patients with gastroschisis compared to 5 patients (4.4%) with omphalocele (p=0.04). CONCLUSIONS: Patients with omphalocele have a greater risk of developing midgut volvulus, and a Ladd procedure should be considered during definitive repair to mitigate these risks. LEVEL OF EVIDENCE: III; retrospective comparative study.

Evidence for a trophic cascade on rocky reefs following sea star mass mortality in British Columbia.

Echinoderm population collapses, driven by disease outbreaks and climatic events, may be important drivers of population dynamics, ecological shifts and biodiversity. The northeast Pacific recently experienced a mass mortality of sea stars. In Howe Sound, British Columbia, the sunflower star Pycnopodia helianthoides-a previously abundant predator of bottom-dwelling invertebrates-began to show signs of a wasting syndrome in early September 2013, and dense aggregations disappeared from many sites in a matter of weeks. Here, we assess changes in subtidal community composition by comparing the abundance of fish, invertebrates and macroalgae at 20 sites in Howe Sound before and after the 2013 sea star mortality to evaluate evidence for a trophic cascade. We observed changes in the abundance of several species after the sea star mortality, most notably a four-fold increase in the number of green sea urchins, Strongylocentrotus droebachiensis, and a significant decline in kelp cover, which are together consistent with a trophic cascade. Qualitative data on the abundance of sunflower stars and green urchins from a citizen science database show that the patterns of echinoderm abundance detected at our study sites reflected wider local trends. The trophic cascade evident at the scale of Howe Sound was observed at half of the study sites. It remains unclear whether the urchin response was triggered directly, via a reduction in urchin mortality, or indirectly, via a shift in urchin distribution into areas previously occupied by the predatory sea stars. Understanding the ecological implications of sudden and extreme population declines may further elucidate the role of echinoderms in temperate seas, and provide insight into the resilience of marine ecosystems to biological disturbances.

Does the American College of Surgeons NSQIP-Pediatric Accurately Represent Overall Patient Outcomes?

BACKGROUND: The National Surgical Quality Improvement Program-Pediatrics (NSQIP-P) collects data for institutional quality benchmarking of surgery performed on children using a sampling algorithm. The Pediatric and Infant Case Log and Outcomes (PICaLO) is a database of all general and thoracic pediatric surgery (GTPS) procedures performed at our institution with the attendant complications. This study compared postsurgical occurrences in a NSQIP-P sample with all postoperative occurrences at a single institution to test the hypothesis that a sample of higher risk procedures represents the actual event rate for all higher risk procedures. STUDY DESIGN: The definitions of postoperative occurrences used in PICaLO are derived from NSQIP-P but tracked past 30 days postoperatively and include additional occurrences (ie, anastomotic leak). The number and types of occurrences and number of deaths from PICaLO and NSQIP-P databases were compared for procedures specific to pediatric GTPS procedures during 2012 to 2013. A chi-square test evaluated the proportion of occurrences and deaths in PICaLO to NSQIP-P. RESULTS: The NSQIP-P sampled 37.7% of eligible GTS procedures recorded in PICaLO during the study period. The proportion of cases with 1 or more occurrences was significantly higher in the NSQIP-P dataset when compared with all cases in PICaLO (p < 0.0001). When NSQIP-P and PICaLO were compared based on specific CPT codes, NSQIP-P still had a higher event rate (p = 0.004). CONCLUSIONS: In focused comparisons, the data demonstrate that the NSQIP-P sampling algorithm successfully identifies CPT codes with higher postoperative event rates than the overall cohort of pediatric GTPS patients, but may not be reflective of the total experience for procedures with those CPT codes.

The risk of volvulus in abdominal wall defects.

BACKGROUND: Congenital abdominal wall defects are associated with abnormal intestinal rotation and fixation. A Ladd's procedure is not routinely performed in these patients; it is believed intestinal fixation is provided by adhesions that develop post-repair of the defects. However, patients with omphalocele may not have adequately protective postoperative adhesions because of difference in the inflammatory state of the bowel wall and in repair strategy. The aim of this study is to describe the occurrence of midgut volvulus in patients with gastroschisis or omphalocele. METHODS: A retrospective chart review was performed for all patients managed in a single institution born between 1/1/2000 and 12/31/2008 with a diagnosis of gastroschisis or omphalocele. Patient charts were reviewed through 12/31/2012 for occurrence of midgut volvulus or need for second laparotomy. RESULTS: Of the 206 patients identified with abdominal wall defects, 142 patients (69%) had gastroschisis and 64 patients (31%) had omphalocele. Patients' follow up ranged from 4 years to 13 years. The median gestational age was 36 weeks (26-41 weeks) and the median birth weight was 2.42 kg (0.8-4.87 kg). None of the patients with gastroschisis developed midgut volvulus, however two patients (3%) with omphalocele developed midgut volvulus. CONCLUSIONS: No patients with gastroschisis developed midgut volvulus. Therefore, the current practice of not routinely performing a Ladd's procedure is a safe approach during surgical repair of gastroschisis. The two cases of volvulus in patients with omphalocele may be related to less bowel fixation. It is necessary to examine current practice in regards to the need for assessing the risk of volvulus during omphalocele closure and counseling of these patients. This assessment may be achieved via routine examination of the width of the small bowel mesenteric base, whenever feasible; however, the sample size is relatively small to draw any definitive conclusions.