Differential RNA Expression Between Metastatic and Primary Neuroblastoma Cells.

INTRODUCTION: Neuroblastoma (NB) is the most common extra-cranial malignancy in children. Poor survival in high-risk NB is attributed to recurrent metastatic disease. To better study metastatic disease, we used a novel mouse model to investigate differential gene expression between primary tumor cells and metastatic cells. We hypothesized that metastatic NB cells have a different gene expression profile from primary tumor cells and cultured cells. METHODS: Using three human NB cell lines (NGP, CHLA255, and SH-SY5Y), orthotopic xenografts were established in immunodeficient nod/scid gamma mice via subcapsular renal injection. Mice were sacrificed and NB cells were isolated from the primary tumor and from sites of metastasis (bone marrow, liver). RNA sequencing, gene set analysis, and pathway analysis were performed to identify differentially expressed genes and molecular pathways in the metastatic cells compared to primary tumor cells. RESULTS: There were 266 differentially expressed genes in metastatic tumor cells (bone marrow and liver combined) compared to primary tumor cells. The top upregulated gene was KCNK1 and the top downregulated genes were PDE7B and NEBL. Top upregulated pathways in the metastatic cells were involved in ion transport, cell signaling, and cell proliferation. Top downregulated pathways were involved in DNA synthesis, transcription, and cellular metabolism. CONCLUSIONS: In metastatic NB cells, our study identified the upregulation of biologic processes involved in cell cycle regulation, cell proliferation, migration, and invasion. Ongoing studies aim to validate downstream translation of these genomic alterations, as well as target these pathways to more effectively suppress and inhibit recurrent metastatic disease in NB.

Evaluation of Postoperative Outcomes After Enterostomy Closure in Low Body Weight Infants: A Multi-Center Retrospective Analysis.

BACKGROUND: The minimum weight for enterostomy closure (EC) in infants remains debated with the current acceptable cut-off of >2 kg. As enterostomy-related complications or high enterostomy output (>30cc/kg/d) may prohibit a premature infant from reaching 2 kg, additional data is needed to evaluate the safety of EC in infants <2 kg. The objective of this study was to evaluate postoperative outcomes in low body weight (<2 kg) infants undergoing EC compared to larger infants. METHODS: We performed a multi-center retrospective analysis from 1/1/2012-12/31/2022 of all infants (age <1 year) who were <4 kg at time of EC. Primary outcomes included postoperative complications and 30-day mortality. Non-parametric analysis was performed using the Kruskal-Wallis one-way analysis of variance and chi-square tests. Univariable logistic regression was performed to identify factors associated with postoperative complications. RESULTS: Of 92 infants, 15 infants (16.3%) underwent EC at <2 kg, 16 (17.4%) at 2-2.49 kg, 31 (33.7%) at 2.5-2.99 kg, and 30 (32.6%) at ≥3 kg. Infants <2 kg at time of EC exhibited higher rates of hyperbilirubinemia (P = .030), neurologic comorbidities (P = .030), and high enterostomy output (P = .041). There was no difference in postoperative complications (P = .460) or 30-day mortality (P = .460) between the <2 kg group and larger weight groups. Low body weight was not associated with an increased risk for developing a postoperative complication (OR: 1.001, 95% CI: 1.001-1.001; P = .032). CONCLUSION: Our findings suggest that EC in infants <2 kg may be safe with comparable postoperative outcomes to larger weight infants. Thus, the timing of EC should be based on the infant's physiologic status, in contrast to a predetermined minimum weight cut-off.

Sex-based Disparities in the Management of Pediatric Gonadal Torsion.

INTRODUCTION: In 2015, the U.S. News and World Report (USNWR) implemented a quality metric to expedite surgery for testicular torsion (TT), but not ovarian torsion (OT). This study examined OR timing among children with suspected TT and OT before and after this metric. METHODS: A single-center retrospective cohort study of children (1-18yr) who underwent surgery for suspected gonadal torsion was performed. Time to OR (TTOR) from hospital presentation to surgery start was calculated. An interrupted time series analysis identified changes in TTOR for suspected TT versus OT after the 2015 USNWR quality metric. RESULTS: Overall, 216 patients presented with TT and 120 with OT. Median TTOR for TT was 147 min (IQR:99-198) versus 462 min (IQR:308-606) for OT. Post-quality metric, children with TT experienced a 27.8 min decrease (95% CI:-51.7,-3.9, p = 0.05) in annual median TTOR. No significant decrease was observed for children with OT (p = 0.22). Children with history of a known ovarian mass (N = 62) experienced a shorter TTOR compared to those without (422 vs 499min; p = 0.04). CONCLUSION: Implementation of a national quality metric for TT expedited surgical care for children with TT, but not children with OT. These findings highlight the need for equitable quality metrics for children presenting with suspected gonadal torsion. LEVEL OF EVIDENCE: III. TYPE OF STUDY: Retrospective Comparative Study, Observational Cohort Study.

A Standardized Post-gastrostomy Feeding Protocol for Pediatric Patients Reduces Time to Postoperative Goal Feeding Volume.

BACKGROUND: Gastrostomy creation is a common pediatric surgical procedure, but the time to initiation of feeds and to goal feeding volumes postoperatively varies greatly. Delays in reaching goal feeding volumes promote malnutrition and may prolong hospital length of stay. We hypothesized that implementing an accelerated, standardized post-gastrostomy feeding protocol would allow patients to reach goal feeding volumes sooner, without increasing postoperative complications. METHODS: We conducted a retrospective cohort study of children who underwent gastrostomy tube placement between 1/1/2022 and 11/30/2023. The feeding protocol was implemented on 11/16/2022, with patients separated into pre- and post-protocol cohorts. Abstracted data included comorbidities, time to initiation of enteral feeds, time to goal feeding volume, and postoperative complications. RESULTS: 322 patients were included: 166 pre-protocol and 156 post-protocol. The post-protocol cohort had a greater proportion of patients with gastrointestinal and/or cardiac comorbidities (P < .001). Through the protocol, postoperative enteral feeds were initiated significantly faster (5.4 hrs [IQR 43-7.7] vs 7.0 hrs [IQR 5.6-14.3]; P < .001). The post-protocol cohort also achieved goal feeding volumes sooner (12.8 hrs [IQR 9.1-25.3] vs 26.3 hrs [IQR 21.6-38.9]; P < .001). Postoperative complication rates did not differ between cohorts. Sub-analysis of children with complex cardiac conditions also demonstrated faster time to goal nutrition without an associated increase in postoperative events. DISCUSSION: These findings demonstrate that our accelerated post-gastrostomy feeding protocol was effective in achieving goal enteral nutrition earlier without increasing postoperative adverse outcomes. This protocol may be used by other centers to safely expedite time to goal enteral feeds in children postoperatively.

Precision Oncology in Pediatric Cancer Surgery.

Pediatric precision oncology has provided a greater understanding of the wide range of molecular alterations in difficult-to-treat or rare tumors with the aims of increasing survival as well as decreasing toxicity and morbidity from current cytotoxic therapies. In this article, the authors discuss the current state of pediatric precision oncology which has increased access to novel targeted therapies while also providing a framework for clinical implementation in this unique population. The authors evaluate the targetable mutations currently under investigation-with a focus on pediatric solid tumors-and discuss the key surgical implications associated with novel targeted therapies.

Optimizing the Postoperative Management of Children Undergoing Resection of High-Risk Abdominal Neuroblastoma.

BACKGROUND: Surgical resection is a mainstay of treatment in high-risk neuroblastoma (HR-NB), but there exists wide variability in perioperative management practices. The aim of this study was to evaluate two standardized adult perioperative enhanced recovery practices (ERPs) in pediatric patients undergoing open resection of abdominal HR-NB. METHODS: All patients with abdominal HR-NB surgically resected at a free-standing children's hospital between 12/2010 and 7/2020 were retrospectively reviewed. Perioperative ERPs of interest included avoidance of routine nasogastric tube (NGT) use and the use of neuraxial anesthesia. Primary outcomes included time to enteral intake, urinary catheter use, opioid utilization, and length of stay (LOS). RESULTS: Overall, 37 children, median age 33 months (IQR: 20-48 months), were identified. Avoidance of an NGT allowed for earlier feeding after surgery (P = .03). Neuraxial anesthesia use more frequently required an indwelling urinary catheter (P < .01) for a longer duration (P = .02), with no difference in total opioid utilization (P = .77) compared to patients without neuraxial anesthesia. Postoperative LOS was unaffected by avoidance of routine NGT use (P = .68) or use of neuraxial anesthesia (P = .89). CONCLUSION: Children undergoing open resection of abdominal HR-NB initiated diet sooner when an NGT was not left postoperatively, and the need for a urinary catheter was significantly higher in patients who received neuraxial anesthesia. However, these two ERP components did not decrease postoperative LOS. To optimize the postoperative management of NB patients, postoperative NGTs should be avoided, while the benefit of neuraxial anesthesia is less clear as it necessitates the placement of a urinary catheter without decreasing opioid utilization.

Outcomes of pediatric pilonidal disease treatment: excision with off-midline flap reconstruction versus endoscopic pilonidal sinus treatment.

PURPOSE: Pilonidal disease (PD) is marked by chronic inflammation and frequent recurrence which can decrease quality of life. However, debate remains regarding the optimal treatment for PD in the pediatric population. This study compares two recommended treatment approaches-excision with off-midline flap reconstruction (OMF: Bascom cleft lift flap, modified Limberg flap) and minimally invasive endoscopic pilonidal sinus treatment (EPSiT). METHODS: Single-center retrospective evaluation of patients 1-21 years of age with PD who underwent either excision with OMF reconstruction or EPSiT between 10/1/2011 and 10/31/2021. Outcomes included were disease recurrence, reoperation, and wound complication rates. Comparisons were performed using Chi-square and Mann-Whitney U tests. RESULTS: 18 patients underwent excision/OMF reconstruction and 45 patients underwent EPSiT. The excision/OMF reconstruction cohort was predominantly male (44.4% vs 17.8% p = 0.028), with history of prior pilonidal infection (33.3% vs 6.7%; p = 0.006), and longer median operative time (60 min vs 17 min; p < 0.001). The excision/OMF reconstruction cohort had a higher rate of wound complications (22.2% vs 0%; p = 0.001), but lower rates of disease recurrence (5.6% vs 33.3%; p = 0.022) and reoperation (5.6% vs 31.1%; p = 0.031). CONCLUSION: In pediatric patients with PD, excision with OMF reconstruction may decrease recurrence and reoperation rates with increased operative times and wound complication rates, compared to EPSiT.

Lessons Learned From the First-In-Human Compassionate Use of Connect-EA™ in Ten Patients With Esophageal Atresia.

INTRODUCTION: Delayed primary repair of esophageal atresia in patients with high-risk physiologic and anatomic comorbidities remains a daunting challenge with an increased risk for peri-operative morbidity and mortality via conventional repair. The Connect-EA device facilitates the endoscopic creation of a secure esophageal anastomosis. This follow-up study reports our long-term outcomes with the novel esophageal magnetic compression anastomosis (EMCA) Connect-EA device for EA repair, as well as lessons learned from the ten first-in-human cases. We propose an algorithm to maximize the advantages of the device for EA repair. METHODS: Under compassionate use approval, from June 2019 to December 2022, ten patients with prohibitive surgical or medical risk factors underwent attempted EMCA with this device. All patients underwent prior gastrostomy, tracheoesophageal fistula ligation (if necessary), and demonstrated pouch apposition prior to EMCA. RESULTS: Successful device deployment and EMCA formation were achieved in nine patients (90%). Mean time to anastomosis formation was 8 days (range 5-14) and the device was retrieved endoscopically in five (56%) cases. At median follow-up of 22 months (range 4-45), seven patients (78%) are tolerating oral nutrition. Balloon dilations (median 4, range 1-11) were performed either prophylactically for radiographic asymptomatic anastomotic narrowing (n = 7, 78%) or to treat clinically-significant anastomotic narrowing (n = 2, 22%) with no ongoing dilations at 3-month follow up post-repair. CONCLUSION: EMCA with the Connect-EA device is a safe and feasible minimally-invasive alterative for EA repair in high-risk surgical patients. Promising post-operative outcomes warrant further Phase I investigation. LEVEL OF EVIDENCE: IV, Case series of novel operative technique without comparison group.

Evaluation of a Magnetic Compression Anastomosis for Jejunoileal Partial Diversion in Rhesus Macaques.

PURPOSE: Metabolic surgery remains underutilized for treating type 2 diabetes, as less invasive alternative interventions with improved risk profiles are needed. We conducted a pilot study to evaluate the feasibility of a novel magnetic compression device to create a patent limited caliber side-to-side jejunoileal partial diversion in a nonhuman primate model. MATERIALS AND METHODS: Using an established nonhuman primate model of diet-induced insulin resistance, a magnetic compression device was used to create a side-to-side jejunoileal anastomosis. Primary outcomes evaluated feasibility (e.g., device mating and anastomosis patency) and safety (e.g., device-related complications). Secondary outcomes evaluated the device's ability to produce metabolic changes associated with jejunoileal partial diversion (e.g., homeostatic model assessment of insulin resistance [HOMA-IR] and body weight). RESULTS: Device mating, spontaneous detachment, and excretion occurred in all animals (n = 5). There were no device-related adverse events. Upon completion of the study, ex vivo anastomoses were widely patent with healthy mucosa and no evidence of stricture. At 6 weeks post-device placement, HOMA-IR improved to below baseline values (p < 0.05). Total weight also decreased in a linear fashion (R2 = 0.97) with total weight loss at 6 weeks post-device placement of 14.4% (p < 0.05). CONCLUSION: The use of this novel magnetic compression device to create a limited caliber side-to-side jejunoileal anastomosis is safe and likely feasible in a nonhuman primate model. The observed glucoregulatory and metabolic effects of a partial jejunoileal bypass with this device warrant further investigation to validate the long-term glucometabolic impact of this approach.

Beyond the gut: spectrum of magnetic surgery devices.

Since the 1970s, magnetic force has been used to augment modern surgical techniques with the aims of minimizing surgical trauma and optimizing minimally-invasive systems. The majority of current clinical applications for magnetic surgery are largely centered around gastrointestinal uses-such as gastrointestinal or bilioenteric anastomosis creation, stricturoplasty, sphincter augmentation, and the guidance of nasoenteric feeding tubes. However, as the field of magnetic surgery continues to advance, the development and clinical implementation of magnetic devices has expanded to treat a variety of non-gastrointestinal disorders including musculoskeletal (pectus excavatum, scoliosis), respiratory (obstructive sleep apnea), cardiovascular (coronary artery stenosis, end-stage renal disease), and genitourinary (stricture, nephrolithiasis) conditions. The purpose of this review is to discuss the current state of innovative magnetic surgical devices under clinical investigation or commercially available for the treatment of non-gastrointestinal disorders.

Anti-CCL2 antibody combined with etoposide prolongs survival in a minimal residual disease mouse model of neuroblastoma.

C-C motif chemokine ligand 2 (CCL2) is a monocyte chemoattractant that promotes metastatic disease and portends a poor prognosis in many cancers. To determine the potential of anti-CCL2 inhibition as a therapy for recurrent metastatic disease in neuroblastoma, a mouse model of minimal residual disease was utilized in which residual disease was treated with anti-CCL2 monoclonal antibody with etoposide. The effect of anti-CCL2 antibody on neuroblastoma cells was determined in vitro with cell proliferation, transwell migration, and 2-dimensional chemotaxis migration assays. The in vivo efficacy of anti-CCL2 antibody and etoposide against neuroblastoma was assessed following resection of primary tumors formed by two cell lines or a patient-derived xenograft (PDX) in immunodeficient NOD-scid gamma mice. In vitro, anti-CCL2 antibody did not affect cell proliferation but significantly inhibited neuroblastoma cell and monocyte migration towards an increasing CCL2 concentration gradient. Treatment of mice with anti-CCL2 antibody combined with etoposide significantly increased survival of mice after resection of primary tumors, compared to untreated mice.

Chaenothecopsis (Mycocaliciales, Ascomycota) from exudates of endemic New Zealand Podocarpaceae.

The order Mycocaliciales (Ascomycota) comprises fungal species with diverse, often highly specialized substrate ecologies. Particularly within the genus Chaenothecopsis, many species exclusively occur on fresh and solidified resins or other exudates of vascular plants. In New Zealand, the only previously known species growing on plant exudate is Chaenothecopsisschefflerae, found on several endemic angiosperms in the family Araliaceae. Here we describe three new species; Chaenothecopsismatai Rikkinen, Beimforde, Tuovila & A.R. Schmidt, C.nodosa Beimforde, Tuovila, Rikkinen & A.R. Schmidt, and C.novae-zelandiae Rikkinen, Beimforde, Tuovila & A.R. Schmidt, all growing on exudates of endemic New Zealand conifers of the Podocarpaceae family, particularly on Prumnopitystaxifolia. Phylogenetic analyses based on ribosomal DNA regions (ITS and LSU) grouped them into a distinct, monophyletic clade. This, as well as the restricted host range, suggests that all three taxa are endemic to New Zealand. Copious insect frass between the ascomata contain ascospores or show an early stage of ascomata development, indicating that the fungi are spread by insects. The three new species represent the first evidence of Chaenothecopsis from any Podocarpaceae species and the first from any gymnosperm exudates in New Zealand.

A Single Center Experience With Bilateral Wilms Tumor.

BACKGROUND: Wilms tumor (WT) is the most common pediatric renal malignancy and bilateral disease (BWT) occurs in 5% of cases and is associated with poor outcomes. Management of BWT includes chemotherapy and oncologic resection while preserving renal function. Previous literature has demonstrated variable approaches in BWT treatment. The aim of this study was to examine a single institution experience and outcomes with BWT. METHODS: A retrospective chart review was performed for all patients with WT treated at a free-standing tertiary children's hospital between 1998 and 2018. Patients with BWT were identified and treatment courses were compared. Outcomes of interest included need for dialysis post-operatively, need for renal transplantation post-operatively, disease recurrence, and overall survival. RESULTS: Of 120 children with WT, 9 children (6F:3M) of median age 32 months (IQR: 24-50 months) and median weight 13.7 kg (IQR: 10.9-16.2 kg) were diagnosed with and treated for BWT. Pre-operative biopsies were obtained in 4/9 patients, 3 of whom received neoadjuvant chemotherapy and 1 who underwent radical nephrectomy. Of the 5 patients who did not undergo biopsy, 4/5 were treated with neoadjuvant chemotherapy, and 1/5 underwent upfront nephrectomy. Post-operatively, 4/9 children required dialysis, of whom 2 subsequently underwent renal transplantation. Two patients were lost to follow-up, and of the remaining 7 patients, disease recurrence occurred in 5/7 children and overall survival was 71% (n=5). CONCLUSION: Management of BWT varies regarding the use of pre-operative biopsy, neoadjuvant chemotherapy, and extent of disease resection. Further guidelines on treatment protocols may optimize outcomes in children with BWT.

The Evolving Use of Magnets in Surgery: Biomedical Considerations and a Review of Their Current Applications.

The novel use of magnetic force to optimize modern surgical techniques originated in the 1970s. Since then, magnets have been utilized as an adjunct or alternative to a wide array of existing surgical procedures, ranging from gastrointestinal to vascular surgery. As the use of magnets in surgery continues to grow, the body of knowledge on magnetic surgical devices from preclinical development to clinical implementation has expanded significantly; however, the current magnetic surgical devices can be organized based on their core function: serving as a guidance system, creating a new connection, recreating a physiologic function, or utilization of an internal-external paired magnet system. The purpose of this article is to discuss the biomedical considerations during magnetic device development and review the current surgical applications of magnetic devices.

Recovery After Thyroid and Parathyroid Surgery: How Do Our Patients Really Feel?

INTRODUCTION: Counseling on the immediate postoperative experience for outpatient procedures is largely based on anecdotal experience. We devised a short messaging service (SMS) survey using mobile phone text messages to evaluate real-time patient recovery following outpatient thyroid or parathyroid surgery. MATERIALS AND METHODS: Daily automated SMS surveys were sent the evening of the operation until postoperative day 10. Pain, opioid use, voice quality, and energy levels were assessed. Impaired voice and energy was defined as a score < 2/3 of normal. RESULTS: One hundred fifty five patients were enrolled with an overall response rate of 81.6%. One hundred thirty three patients had an individual response rate > 50% and were included in the final analysis. Median patient age was 60 y with 102 females (76.7%). Seventy patients (52.6%) underwent parathyroidectomy and 66 (49.6%) thyroidectomy and 10 (7.5%) neck dissection. Forty eight patients (36.1%) did not use any opioids postoperatively. Independent risk factors for higher total pain scores included thyroidectomy and patients with preoperative opioid or tobacco use, while increased opioid use was associated with age < 60 y, body mass index > 30 kg/m2, preoperative opioid or tobacco use, and history of anxiety or depression. Patients with loss of intraoperative recurrent laryngeal nerve signaling had a significantly worse overall voice score (54.65 versus 92.67, P < 0.001). Up to 10% of patients were still using opioids and/or reported impaired voice and energy levels beyond 1 wk postoperatively. CONCLUSIONS: Real-time SMS survey is an effective and potentially valuable way to monitor patient recovery following surgery. A subset of patients reported impaired voice and energy and was still using opioids beyond 1 wk after thyroid and parathyroid surgery and these patients may benefit from closer follow-up and earlier intervention.

Overtransfusion of packed red blood cells during massive transfusion activation: a potential quality metric for trauma resuscitation.

Objectives: The goal of this study was to explore the incidence of overtransfusion in trauma patients requiring massive transfusion protocol (MTP) activation and identify modifiable risk factors. We hypothesized that overtransfusion is common after MTP activation. Methods: Patients admitted to a level I trauma center from July 2016 to December 2019 and who required MTP activation were selected. The primary outcome was overtransfusion, defined as a hemoglobin (Hg) ≥11 g/dL at 24 hours (±2 hours). A Cox regression model was used to identify independent risk factors for overtransfusion. Results: 140 patients met inclusion criteria. The median age was 39.0 years, with the majority (74.3%) being male. The median (IQR) Injury Severity Score (ISS) was 24.0 (58.0) and 38.4% had a penetrating mechanism. The median (IQR) admission Hg was 12.6 (11.7) g/dL. Overall, 71.4% of patients were overtransfused by the conclusion of MTP, 43.6% 24 hours later, and 29.5% at discharge. Overtransfusion did not correlate with the number of units of blood transfused nor with the duration of MTP. Overtransfused patients at 24 hours after the conclusion of MTP were significantly more likely to present with a penetrating injury (52.5% vs. 27.3%, p=0.003) and have a significantly lower ISS (median (IQR) 18.5 (44.0) vs. 26.0 (58.0), p=0.035.) In a Cox regression model, penetrating mechanism (adjusted HR (AHR): 2.93; adjusted p=0.004) and admission base excess (BE) (AHR: 1.15; adjusted p=0.001) were the only variables independently associated with overtransfusion. Conclusions: Overtransfusion of trauma patients requiring MTP activation is highly common, leading to overutilization of a limited resource. Penetrating trauma and BE may be modifiable risk factors that can help limit overtransfusion. Overtransfusion should be tracked as a data point by blood banks and trauma centers and be further studied as a potential quality metric for the resuscitation of massively transfused trauma patients. Level of evidence: III.

Predictions of biodiversity are improved by integrating trait-based competition with abiotic filtering.

All organisms must simultaneously tolerate the environment and access limiting resources if they are to persist. Approaches to understanding abiotic filtering and competitive interactions have generally been developed independently. Consequently, integrating those factors to predict species abundances and community structure remains an unresolved challenge. We introduce a new synthetic framework that models both abiotic filtering and competition by using functional traits. First, our framework estimates species carrying capacities along abiotic gradients. Second, it estimates pairwise competitive interactions as a function of species trait differences. Applied to the study of a complex wetland community, our combined approach more than doubles the explained variance of species abundances compared to a model of abiotic tolerances alone. Trait-based integration of competitive interactions and abiotic filtering improves our ability to predict species abundances, bringing us closer to more accurate predictions of biodiversity structure in a changing world.

Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae).

The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy (Coprosma: 2x, Veronica: 6x) versus high-ploidy (Coprosma: 4-10x, Veronica: 12-18x) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.

Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica.

PREMISE: Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations. METHODS: Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species. RESULTS: We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation. CONCLUSIONS: Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.

The effect of single biome occupancy on the estimation of biome shifts and the detection of biome conservatism.

Biome conservatism is often regarded as common in diversifying lineages, based on the detection of low biome shift rates or high phylogenetic signal. However, many studies testing biome conservatism utilise a single-biome-per-species approach, which may influence the detection of biome conservatism. Meta-analyses show that biome shift rates are significantly lower (less than a tenth), when single biome occupancy approaches are adopted. Using New Zealand plant lineages, estimated biome shifts were also significantly lower (14-67% fewer biome shifts) when analysed under the assumption of a single biome per species. Although a single biome approach consistently resulted in lower biome shifts, it detected fewer instances of biome conservatism. A third of clades (3 out of 9) changed status in biome conservatism tests between single and multiple biome occupancy approaches, with more instances of significant biome conservatism when using a multiple biome occupancy approach. A single biome approach may change the likelihood of finding biome conservatism because it assumes biome specialisation within species, falsely recognises some biome shift types and fails to include other biome shift types. Our results indicate that the degree of biome fidelity assumed has a strong influence on analyses assessing biome shift rates, and biome conservatism testing. We advocate analyses that allow species to occupy multiple biomes.