Recommendations for optimising pilot and feasibility work in surgery

BACKGROUND

Surgical trials are recognised as inherently challenging. Pilot and feasibility studies (PAFS) are increasingly acknowledged as a key method to optimise the design and conduct of randomised trials but remain limited in surgery. We used a mixed methods approach to develop recommendations for how surgical PAFS could be optimised.

METHODS

The findings from a quantitative analysis of funded surgical PAFS over a 10-year period and in-depth qualitative interviews with surgeons, methodologists and funders were triangulated and synthesised with available methodological guidance on PAFS.

RESULTS

The synthesis informed the development of an explanatory model describing root causes and compounding challenges that contribute to how and why surgical PAFS is not currently optimised. The four root causes identified include issues relating to (i) understanding the full scope of PAFS; (ii) design and conduct of PAFS; (iii) reporting of PAFS; and (iv) lack of appreciation of the value of PAFS by all stakeholder groups. Compounding challenges relate to both cultural issues and access to and interpretation of available methodological PAFS guidance. The study findings and explanatory model were used to inform the development of a practical guidance tool for surgeons and study teams to improve research practice.

CONCLUSIONS

Optimisation of PAFS in surgery requires a cultural shift in research practice amongst funders, academic institutions, regulatory bodies and journal editors, as well as amongst surgeons. Our 'Top Tips' guidance tool offers an accessible framework for surgeons designing PAFS. Adoption and utilisation of these recommendations will optimise surgical PAFS, facilitating successful and efficient future surgical trials.

Museum skins enable identification of introgression associated with cytonuclear discordance

Increased sampling of genomes and populations across closely related species has revealed that levels of genetic exchange during and after speciation are higher than previously thought. One obvious manifestation of such exchange is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from that for nuclear genes more (or less) than expected from differences between mtDNA and nuclear DNA (nDNA) in population size and mutation rate. Given genome-scale datasets and coalescent modelling, we can now confidently identify cases of strong discordance and test specifically for historical or recent introgression as the cause. Using population sampling, combining exon capture data from historical museum specimens and recently collected tissues we showcase how genomic tools can resolve complex evolutionary histories in the brachyotis group of rock-wallabies (Petrogale). In particular, applying population and phylogenomic approaches we can assess the role of demographic processes in driving complex evolutionary patterns and assess a role of ancient introgression and hybridisation. We find that described species are well supported as monophyletic taxa for nDNA genes, but not for mtDNA, with cytonuclear discordance involving at least four operational taxonomic units (OTUs) across four species which diverged 183-278 kya. ABC modelling of nDNA gene trees supports introgression during or after speciation for some taxon pairs with cytonuclear discordance. Given substantial differences in body size between the species involved, this evidence for gene flow is surprising. Heterogenous patterns of introgression were identified but do not appear to be associated with chromosome differences between species. These and previous results suggest that dynamic past climates across the monsoonal tropics could have promoted reticulation among related species.

Functionally mediated cranial allometry evidenced in a genus of rock-wallabies

In assessments of skeletal variation, allometry (disproportionate change of shape with size) is often corrected to examine size-independent variation for hypotheses relating to function. However, size-related trade-offs in functional demands may themselves be an underestimated driver of mammalian cranial diversity. Here, we use geometric morphometrics alongside dental measurements to assess craniodental allometry in the rock-wallaby genus Petrogale (all 17 species, 370 individuals). We identified functional aspects of evolutionary allometry that can be both extensions of, and correlated negatively with, static or ontogenetic allometric patterns. Regarding constraints, larger species tended to have relatively smaller braincases and more posterior orbits, the former of which might represent a constraint on jaw muscle anatomy. However, they also tended to have more anterior dentition and smaller posterior zygomatic arches, both of which support the hypothesis of relaxed bite force demands and accommodation of different selective pressures that favour facial elongation. By contrast, two dwarf species had stouter crania with divergent dental adaptations that together suggest increased relative bite force capacity. This likely allows them to feed on forage that is mechanically similar to that consumed by larger relatives. Our results highlight a need for nuanced considerations of allometric patterns in future research of mammalian cranial diversity.

Current use of drains and management of seroma following mastectomy and axillary surgery: results of a United Kingdom national practice survey

PURPOSE

Up to 40% of the 56,000 women diagnosed with breast cancer each year in the UK undergo mastectomy. Seroma formation following surgery is common, may delay wound healing, and be uncomfortable or delay the start of adjuvant treatment. Multiple strategies to reduce seroma formation include surgical drains, flap fixation and external compression exist but evidence to support best practice is lacking. We aimed to survey UK breast surgeons to determine current practice to inform the feasibility of undertaking a future trial.

METHODS

An online survey was developed and circulated to UK breast surgeons via professional and trainee associations and social media to explore current attitudes to drain use and management of post-operative seroma. Simple descriptive statistics were used to summarise the results.

RESULTS

The majority of surgeons (82/97, 85%) reported using drains either routinely (38, 39%) or in certain circumstances (44, 45%). Other methods for reducing seroma such as flap fixation were less commonly used. Wide variation was reported in the assessment and management of post-operative seromas. Over half (47/91, 52%) of respondents felt there was some uncertainty about drain use after mastectomy and axillary surgery and two-thirds (59/91, 65%) felt that a trial evaluating the use of drains vs no drains after simple breast cancer surgery was needed.

CONCLUSIONS

There is a need for a large-scale UK-based RCT to determine if, when and in whom drains are necessary following mastectomy and axillary surgery. This work will inform the design and conduct of a future trial.

Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Future-proofing the koala: synergising genomic and environmental data for effective species management

Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species' capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high-throughput next-generation sequencing to investigate the mechanisms underlying population structure and adaptive genetic variation in the koala (Phascolarctos cinereus), an iconic Australian marsupial that represents a unique conservation challenge because it is not uniformly threatened across its range. An examination of 250 specimens representing 91 wild source locations revealed that five major genetic clusters currently exist on a continental scale. The initial divergence of these clusters appears to have been concordant with the Mid-Brunhes Transition (∼ 430-300 kya), a major climatic reorganization that increased the amplitude of Pleistocene glacial-interglacial cycles. While signatures of polygenic selection and environmental adaptation were detected, strong evidence for repeated, climate-associated range contractions and demographic bottleneck events suggests that geographically isolated refugia may have played a more significant role in the survival of the koala through the Pleistocene glaciation than in situ adaptation. Consequently, the conservation of genome-wide genetic variation must be aligned with the protection of core koala habitat to increase the resilience of threatened populations to accelerating anthropogenic threats. Finally, we propose that the five major genetic clusters identified in this study should be accounted for in future koala conservation efforts (e.g. guiding translocations), as existing management divisions in the states of Queensland and New South Wales do not reflect historic or contemporary population structure.

303 Mapping the Landscape of Surgical Registries in the United Kingdom

Introduction

Well-designed surgical registries are essential for high-quality patient-centred evaluation of implantable devices and surgical procedures. The importance of registries was highlighted in the recent Cumberlege report that detailed important innovation failures such as the use of vaginal mesh. Many surgical registries exist, but it is currently unclear how different registries are funded; designed; what data are collected; how databases are hosted and if the data can be linked to other datasets. There is therefore a need to understand the characteristics of and variation in existing surgical registries to make recommendations for how these could be improved. The aim of this work is to identify existing surgical registries in the UK and describe and summarise their key characteristics to inform recommendations for how surgical registries may be improved.

Method

Existing surgical registries will be identified using multiple different sources, including society websites; search engine review; a targeted search of Medline and Embase databases and expert knowledge. Details of each registry will be extracted using a standardised data extraction proforma developed by the study team. Characteristics of identified registries will be summarised into a narrative review.

Results

Identification of registries is ongoing. Preliminary data extraction has highlighted marked heterogeneity in the design, content, and structure of existing surgical registries. Data extraction is ongoing, but results will be available for presentation at the ASIT meeting.

Conclusions

There is considerable heterogeneity in existing surgical registries. Further work is needed to establish the extent of this variation and identify areas that can be improved.

Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks

Temperature differences over time and space have been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs from the Eugongylinae subfamily using regression analyses. Temperature is the strongest, positively correlated predictor of variation in substitution rate across the Australian Eugongylinae. It explains 45% of variation in synonymous substitution rate, and 11% after controlling for all the other factors. Synonymous substitution rate is also negatively associated with body size, with a 6% variation explained by body size after controlling for the effects of temperature. Other factors are not associated with synonymous substitution rate after controlling for temperature. Overall, this study points to temperature as a strong predictor of the molecular evolution rate in the Eugongylinae subfamily, and demonstrates the power of large-scale exonic data to identify correlates of the rate of molecular evolution.

Limited introgression between rock-wallabies with extensive chromosomal rearrangements

Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.

510 Transitioning to an In-House In-Situ Hybridisation Assay Accelerates Indeterminate HER-2 Lesion Results

Introduction

NICE guidelines 1.6.5 recommend that: ‘HER2 status [should be] available and recorded at the pre-operative multidisciplinary team (MDT) meeting when systemic treatment is discussed,’ to aid decision-making regarding neoadjuvant therapy. However, indeterminate HER2 lesions require additional testing by in-situ hybridisation (ISH). This may lead to delays in treatment decision-making, particularly if the testing is outsourced. Our institution has recently switched to using an in-house ISH assay. We compared time between biopsy and ISH results over two periods before and after the introduction of in-house testing, to assess if this improved the availability of HER-2 results, in line with NICE guidelines.

Method

This audit gained local approval. All breast cancer patients discussed at MDT over a two-month time period before (1/11/18-31/12/18) and after (1/9/20-30/10/20) the introduction of in-house ISH testing were identified retrospectively. The numbers of patients requiring ISH and the median time from biopsy to ISH report were compared in the two groups using the Mann-Whitney U test.

Results

106 cases were analysed before the intervention, 39 (37%) of which required ISH with a median wait time of 30 days (13-87). 90 cases were analysed after the intervention, 13 (14%) of which required ISH with a median wait time of 7 days (5-16) (p < 0.01).

Conclusions

By setting up an in-house ISH assay, we significantly reduced the delay between biopsy and HER2 status result for patients with borderline HER2 results. HER2 status is now available at the pre-operative MDT meeting to optimise treatment decision making, as recommended by NICE.

Breast Angiosarcoma Surveillance Study: UK national audit of management and outcomes of angiosarcoma of the breast and chest wall

BACKGROUND

Breast angiosarcomas are rare tumours of vascular origin. Secondary angiosarcoma occurs following radiotherapy for breast cancer. Angiosarcomas have high recurrence and poor survival rates. This is concerning owing to the increasing use of adjuvant radiotherapy for the treatment of invasive breast cancer and ductal cancer in situ (DCIS), which could explain the rising incidence of angiosarcoma. Outcome data are limited and provide a poor evidence base for treatment. This paper presents a national, trainee-led, retrospective, multicentre study of a large angiosarcoma cohort.

METHODS

Data for patients with a diagnosis of breast/chest wall angiosarcoma between 2000 and 2015 were collected retrospectively from 15 centres.

RESULTS

The cohort included 183 patients with 34 primary and 149 secondary angiosarcomas. Median latency from breast cancer to secondary angiosarcoma was 6 years. Only 78.9 per cent of patients were discussed at a sarcoma multidisciplinary team meeting. Rates of recurrence were high with 14 of 28 (50 per cent ) recurrences in patients with primary and 80 of 124 (64.5 per cent ) in those with secondary angiosarcoma at 5 years. Many patients had multiple recurrences: total of 94 recurrences in 162 patients (58.0 per cent). Median survival was 5 (range 0-16) years for patients with primary and 5 (0-15) years for those with secondary angiosarcoma. Development of secondary angiosarcoma had a negative impact on predicted breast cancer survival, with a median 10-year PREDICT prognostic rate of 69.6 per cent, compared with 54.0 per cent in the observed cohort.

CONCLUSION

A detrimental impact of secondary angiosarcoma on breast cancer survival has been demonstrated. Although not statistically significant, almost all excess deaths were attributable to angiosarcoma. The increased use of adjuvant radiotherapy to treat low-risk breast cancer and DCIS is a cause for concern and warrants further study.

Innovations for the future of breast surgery

BACKGROUND

Future innovations in science and technology with an impact on multimodal breast cancer management from a surgical perspective are discussed in this narrative review. The work was undertaken in response to the Commission on the Future of Surgery project initiated by the Royal College of Surgeons of England.

METHODS

Expert opinion was sought around themes of surgical de-escalation, reduction in treatment morbidities, and improving the accuracy of breast-conserving surgery in terms of margin status. There was emphasis on how the primacy of surgical excision in an era of oncoplastic and reconstructive surgery is increasingly being challenged, with more effective systemic therapies that target residual disease burden, and permit response-adapted approaches to both breast and axillary surgery.

RESULTS

Technologies for intraoperative margin assessment can potentially half re-excision rates after breast-conserving surgery, and sentinel lymph node biopsy will become a therapeutic procedure for many patients with node-positive disease treated either with surgery or chemotherapy as the primary modality. Genomic profiling of tumours can aid in the selection of patients for neoadjuvant and adjuvant therapies as well as prevention strategies. Molecular subtypes are predictive of response to induction therapies and reductive approaches to surgery in the breast or axilla.

CONCLUSION

Treatments are increasingly being tailored and based on improved understanding of tumour biology and relevant biomarkers to determine absolute benefit and permit delivery of cost-effective healthcare. Patient involvement is crucial for breast cancer studies to ensure relevance and outcome measures that are objective, meaningful, and patient-centred.

O77: DOES MESH IMPROVE PATIENT SATISFACTION AND HEALTH-RELATED QUALITY OF LIFE AFTER IMPLANT-BASED BREAST RECONSTRUCTION? A MULTICENTRE PROSPECTIVE COHORT STUDY

Introduction

Biological and synthetic meshes may improve outcomes of immediate IBBR by facilitating single-stage direct-to-implant procedures. However, high-quality supporting evidence is limited, particularly regarding PROs.

Method

2108 consecutive women undergoing IBBR at 81 centres were prospectively recruited between 2014-2016. Demographic, operative, oncological and 3-month complication data were collected. An 18-month questionnaire assessed PROs using the validated BREAST-Q and a five-point Likert scale rating of overall reconstructive outcome.

The impacts of different IBBR techniques on PROs were explored using mixed-effects regression models adjusted for clinically-relevant confounders and including a random effect to account for clustering by centre. The reference group was two- stage submuscular reconstruction without mesh.

Result

1470 participants consented to receive the questionnaire and 891 completed it. 67 patients underwent two-stage submuscular reconstruction; 764 patients received subpectoral reconstructions with biological mesh (n=495) synthetic mesh (n=95) or dermal sling (n=174). 14 patients underwent prepectoral reconstructions (introduced late in the study).

Compared with two-stage reconstructions, no differences in PROs were seen in biological or synthetic mesh-assisted or dermal sling procedures (p>0.05). However, prepectoral IBBR patients reported better satisfaction with breasts (difference=6.63, 95% confidence interval[1.65–11.61], p=0.009). Outcomes were similar to those in the NMBRA 2008/9 cohort, which included submuscular procedures only.

Conclusion

This study does not suggest that mesh improves PROs of IBBR. It provides early data supporting improved satisfaction with breasts following prepectoral reconstructions. Future trials are needed to robustly evaluate prepectoral techniques.

Abbrev

IBBR: implant-based breast reconstruction, PRO: patient-reported outcome, NMBRA: National Mastectomy and Breast Reconstruction Audit

Take-home message

Although mesh-assisted techniques have become widely adopted, this large, prospective, multicentre cohort study does not suggest that mesh improves patient-reported outcomes of implant-based breast reconstruction compared with standard submuscular techniques. However, it provides early data to support improved satisfaction with breasts in the prepectoral setting, which now requires robust evaluation.

O58: THE IMPACT OF RADIOTHERAPY ON PATIENT-REPORTED OUTCOMES OF IMMEDIATE IMPLANT-BASED BREAST RECONSTRUCTION: RESULTS OF A PROSPECTIVE MULTICENTRE COHORT STUDY

Introduction

Post-mastectomy radiotherapy (PMRT) is increasing given to improve breast cancer outcomes but can increase complication rates following implant-based breast reconstruction (IBBR). Little, however, is known about the impact of PMRT on patient-reported outcomes (PROs) of IBBR, especially in the context of mesh-assisted techniques.

Method

2108 consecutive women undergoing IBBR at 81 UK centres were prospectively recruited between 2014 and 2016. Demographic, operative, oncological and 3-month complication data were collected, and patients who consented received post-operative questionnaires. An 18-month questionnaire assessed PROs using the validated BREAST-Q. The effect of IBBR on PROs was investigated using mixed-effects regression models adjusted for clinically relevant confounders and including a random effect to account for potential clustering by centre.

Result

1693 iBRA participants underwent mastectomy for malignancy, of whom 1187 (70%) consented to receive the 18-month questionnaire and 732 (43%) completed it. Patients undergoing PMRT (n=214) reported significantly worse scores across 3 BREAST-Q domains: satisfaction with breasts (-6.27 points, p=0.008, 95% confidence interval (CI)[-10.91,-1.63]), satisfaction with outcome (-7.53 points, p=0.002, CI[-12.20,-2.85]) and physical well-being (-6.55 points, p<0.001, CI[-9.43,-3.67]). Overall satisfaction was worse in the PMRT group (OR 0.497, p=0.002, CI[0.32,0.77]). Use of biological mesh did not ameliorate the impact of PMRT on patient satisfaction (interaction term p-values [0.173 - 0.826]).

Conclusion:

PMRT adversely affects PROs of IBBR. This should be discussed with patients considering IBBR, especially if PMRT is anticipated or indications are borderline, to enable informed decisions regarding oncological and reconstructive options.

Abbrev

PMRT: post-mastectomy radiotherapy, PRO: patient-reported outcome

Take-home message

This multicentre, prospective cohort study of 732 patients undergoing implant-based breast reconstruction demonstrates worse 18-month patient-reported outcomes in women who received post-mastectomy radiotherapy than those who did not. These data should be discussed with patients to help them make informed decisions about reconstructive surgery.

Patient-reported outcomes of immediate implant-based breast reconstruction with and without biological or synthetic mesh

BACKGROUND

Biological and synthetic meshes may improve the outcomes of immediate implant-based breast reconstruction (IBBR) by facilitating single-stage procedures and improving cosmesis. Supporting evidence is, however, limited. The aim of this study was to explore the impact of biological and synthetic mesh on patient-reported outcomes (PROs) of IBBR 18 months after surgery.

METHODS

Consecutive women undergoing immediate IBBR between February 2014 and June 2016 were recruited to the study. Demographic, operative, oncological and 3-month complication data were collected, and patients received validated BREAST-Q questionnaires at 18 months. The impact of different IBBR techniques on PROs were explored using mixed-effects regression models adjusted for clinically relevant confounders, and including a random effect to account for clustering by centre.

RESULTS

A total of 1470 participants consented to receive the questionnaire and 891 completed it. Of these, 67 women underwent two-stage submuscular reconstructions. Some 764 patients had a submuscular reconstruction with biological mesh (495 women), synthetic mesh (95) or dermal sling (174). Fourteen patients had a prepectoral reconstruction. Compared with two-stage submuscular reconstructions, no significant differences in PROs were seen in biological or synthetic mesh-assisted or dermal sling procedures. However, patients undergoing prepectoral IBBR reported better satisfaction with breasts (adjusted mean difference +6.63, 95 per cent c.i. 1.65 to11.61; P = 0.009). PROs were similar to those in the National Mastectomy and Breast Reconstruction Audit 2008-2009 cohort, which included two-stage submuscular procedures only.

CONCLUSION

This study found no difference in PROs of subpectoral IBBR with or without biological or synthetic mesh, but provides early data to suggest improved satisfaction with breasts following prepectoral reconstruction. Robust evaluation is required before this approach can be adopted as standard practice.

The NeST (Neoadjuvant systemic therapy in breast cancer) study: National Practice Questionnaire of United Kingdom multi-disciplinary decision making

BACKGROUND

Neoadjuvant systemic therapy (NST) is increasingly used in the treatment of breast cancer, yet it is clear that there is significant geographical variation in its use in the UK. This study aimed to examine stated practice across UK breast units, in terms of indications for use, radiological monitoring, pathological reporting of treatment response, and post-treatment surgical management.

METHODS

Multidisciplinary teams (MDTs) from all UK breast units were invited to participate in the NeST study. A detailed questionnaire assessing current stated practice was distributed to all participating units in December 2017 and data collated securely usingREDCap. Descriptive statistics were calculated for each questionnaire item.

RESULTS

Thirty-nine MDTs from a diverse range of hospitals responded. All MDTs routinely offered neoadjuvant chemotherapy (NACT) to a median of 10% (range 5-60%) of patients. Neoadjuvant endocrine therapy (NET) was offered to a median of 4% (range 0-25%) of patients by 66% of MDTs. The principal indication given for use of neoadjuvant therapy was for surgical downstaging. There was no consensus on methods of radiological monitoring of response, and a wide variety of pathological reporting systems were used to assess tumour response. Twenty-five percent of centres reported resecting the original tumour footprint, irrespective of clinical/radiological response. Radiologically negative axillae at diagnosis routinely had post-NACT or post-NET sentinel lymph node biopsy (SLNB) in 73.0 and 84% of centres respectively, whereas 16% performed SLNB pre-NACT. Positive axillae at diagnosis would receive axillary node clearance at 60% of centres, regardless of response to NACT.

DISCUSSION

There is wide variation in the stated use of neoadjuvant systemic therapy across the UK, with general low usage of NET. Surgical downstaging remains the most common indication of the use of NAC, although not all centres leverage the benefits of NAC for de-escalating surgery to the breast and/or axilla. There is a need for agreed multidisciplinary guidance for optimising selection and management of patients for NST. These findings will be corroborated in phase II of the NeST study which is a national collaborative prospective audit of NST utilisation and clinical outcomes.

Patient-Reported Outcome Measures for Post-mastectomy Breast Reconstruction: A Systematic Review of Development and Measurement Properties

BACKGROUND

Breast reconstruction (BR) is performed to improve outcomes for patients undergoing mastectomy. A recently developed core outcome set for BR includes six patient-reported outcomes that should be measured and reported in all future studies. It is vital that any instrument used to measure these outcomes as part of a core measurement set be robustly developed and validated so data are reliable and accurate. The aim of this systematic review is to evaluate the development and measurement properties of existing BR patient-reported outcome measures (PROMs) to inform instrument selection for future studies.

METHODS

A PRISMA-compliant systematic review of development and validation studies of BR PROMs was conducted to assess their measurement properties. PROMs with adequate content validity were assessed using three steps: (1) the methodological quality of each identified study was assessed using the COSMIN Risk of Bias checklist; (2) criteria were applied for assessing good measurement properties; and (3) evidence was summarized and the quality of evidence assessed using a modified GRADE approach.

RESULTS

Fourteen articles reported the development and measurement properties of six PROMs. Of these, only three (BREAST-Q, BRECON-31, and EORTC QLQ-BRECON-23) were considered to have adequate content validity and proceeded to full evaluation. This showed that all three PROMs had been robustly developed and validated and demonstrated adequate quality.

CONCLUSIONS

BREAST-Q, BRECON-31, and EORTC QLQ-BRECON-23 have been well-developed and demonstrate adequate measurement properties. Work with key stakeholders is now needed to generate consensus regarding which PROM should be recommended for inclusion in a core measurement set.

A systematic review and in-depth analysis of outcome reporting in early phase studies of colorectal cancer surgical innovation

AIM

Early phase studies are essential to evaluate new technologies prior to randomized evaluation. Evaluation is limited, however, by inconsistent measurement and reporting of outcomes. This study examines outcome reporting in studies of innovative colorectal cancer surgery.

METHODS

Systematic searches identified studies of invasive procedures treating primary colorectal adenocarcinoma. Included were a random sample of studies which authors reported as 'new' or 'modified'. Outcomes were extracted verbatim and categorized using an existing framework of 32 domains relevant to early phase studies. Outcomes were classified as 'measured' (where there was an explicit statement to that effect or evidence that data collection had occurred) or 'mentioned but not measured' (where outcomes were discussed but data collection was not evident). Patterns of identified outcomes are described.

RESULTS

Of 8373 records, 816 were potentially eligible. Full-text review of a random sample of 218 studies identified 51 for inclusion of which 34 (66%) were 'new' and 17 (33%) were 'modified'. Some 2073 outcomes were identified, and all mapped to domains. 'Anticipated disadvantages' were most frequently identified [660 (32%) outcomes identified across 50 (98%) studies]. No domain was represented in all studies. Under half (944, 46%) of outcomes were 'measured'. 'Surgeon's/operator's experience of the innovation' was more frequently 'mentioned but not measured' [207 (18%) outcomes across 46 (90%) studies] than 'measured' [17 (2%) outcomes, 11 (22%) studies].

CONCLUSION

There is outcome reporting heterogeneity in studies of early phase colorectal cancer surgery. The adoption of core outcome sets may help to resolve these inconsistencies and enable efficient evaluation of surgical innovations.

Marsupial chromosomics: bridging the gap between genomes and chromosomes

Marsupials have unique features that make them particularly interesting to study, and sequencing of marsupial genomes is helping to understand their evolution. A decade ago, it was a huge feat to sequence the first marsupial genome. Now, the advances in sequencing technology have made the sequencing of many more marsupial genomes possible. However, the DNA sequence is only one component of the structures it is packaged into: chromosomes. Knowing the arrangement of the DNA sequence on each chromosome is essential for a genome assembly to be used to its full potential. The importance of combining sequence information with cytogenetics has previously been demonstrated for rapidly evolving regions of the genome, such as the sex chromosomes, as well as for reconstructing the ancestral marsupial karyotype and understanding the chromosome rearrangements involved in the Tasmanian devil facial tumour disease. Despite the recent advances in sequencing technology assisting in genome assembly, physical anchoring of the sequence to chromosomes is required to achieve a chromosome-level assembly. Once chromosome-level assemblies are achieved for more marsupials, we will be able to investigate changes in the packaging and interactions between chromosomes to gain an understanding of the role genome architecture has played during marsupial evolution.

Outcome selection, measurement and reporting for new surgical procedures and devices: a systematic review of IDEAL/IDEAL-D studies to inform development of a core outcome set

BACKGROUND

Outcome selection, measurement and reporting for the evaluation of new surgical procedures and devices is inconsistent and lacks standardization. A core outcome set may promote the safe and transparent evaluation of surgical innovations. This systematic review examined outcome selection, measurement and reporting in studies conducted within the IDEAL (Idea, Development, Exploration, Assessment and Long-term monitoring) framework to examine current practice and inform the development of a core outcome set for early-phase studies of surgical procedures/devices.

METHODS

Web of Science and Scopus citation searches were performed to identify author-reported IDEAL/IDEAL-D studies for any surgical procedure/device. Outcomes were extracted verbatim, including contextual information regarding outcome selection and measurement. Outcomes were categorized to inform a conceptual framework of outcome domains relevant to evaluating innovation.

RESULTS

Some 48 studies were identified. Outcome selection, measurement and reporting varied widely across studies in different IDEAL stages. From 1737 outcomes extracted, 22 domains specific to evaluating innovation were conceptualized under seven broad categories: procedure completion success/failure; modifications; unanticipated events; surgeons' experiences; patients' experiences; resource use specific to the innovative procedure/device; and other innovation-specific outcomes. Most innovation-specific outcomes were measured and reported in only a small number of studies.

CONCLUSION

This review highlighted the need for guidance and standardization in outcome selection and reporting in the evaluation of new surgical procedures/devices. Novel outcome domains specific to innovation have been identified to establish a core outcome set for future evaluations of surgical innovations.

Experiences of implant loss after immediate implant-based breast reconstruction: qualitative study

BACKGROUND

Immediate implant-based breast reconstruction (IBBR) is the most commonly performed reconstructive procedure in the UK, but almost one in ten women experience implant loss and reconstructive failure after this technique. Little is known about how implant loss impacts on patients' quality of life. The first phase of the Loss of implant Breast Reconstruction (LiBRA) study aimed to use qualitative methods to explore women's experiences of implant loss and develop recommendations to improve care.

METHODS

Semistructured interviews were conducted with a purposive sample of women who experienced implant loss after immediate IBBR, performed for malignancy or risk reduction across six centres. Interviews explored decision-making regarding IBBR, and experiences of implant loss and support received. Thematic analysis was used to explore the qualitative interview data. Sampling, data collection and analysis were undertaken concurrently and iteratively until data saturation was achieved.

RESULTS

Twenty-four women were interviewed; 19 had surgery for malignancy and five for risk reduction. The median time between implant loss and interview was 42 (range 22-74) months. Ten women had undergone secondary reconstruction, two were awaiting surgery, and 12 had declined further reconstruction. Three key themes were identified: the need for accurate information about the risks and benefits of IBBR; the need for more information about 'early-warning' signs of postoperative problems, to empower women to seek help; and better support following implant loss.

CONCLUSION

Implant loss is a devastating event for many women. Better preoperative information and support, along with holistic patient-centred care when complications occur, may significantly improve the experience and outcome of care.

Therapeutic mammaplasty is a safe and effective alternative to mastectomy with or without immediate breast reconstruction

BACKGROUND

Therapeutic mammaplasty (TM) may be an alternative to mastectomy, but few well designed studies have evaluated the success of this approach or compared the short-term outcomes of TM with mastectomy with or without immediate breast reconstruction (IBR). Data from the national iBRA-2 and TeaM studies were combined to compare the safety and short-term outcomes of TM and mastectomy with or without IBR.

METHODS

The subgroup of patients in the TeaM study who underwent TM to avoid mastectomy were identified, and data on demographics, complications, oncology and adjuvant treatment were compared with those of patients undergoing mastectomy with or without IBR in the iBRA-2 study. The primary outcome was the percentage of successful breast-conserving procedures in the TM group. Secondary outcomes included postoperative complications and time to adjuvant therapy.

RESULTS

A total of 2916 patients (TM 376; mastectomy 1532; mastectomy and IBR 1008) were included in the analysis. Patients undergoing TM were more likely to be obese and to have undergone bilateral surgery than those having IBR. However, patients undergoing mastectomy with or without IBR were more likely to experience complications than the TM group (TM: 79, 21·0 per cent; mastectomy: 570, 37·2 per cent; mastectomy and IBR: 359, 35·6 per cent; P < 0·001). Breast conservation was possible in 87·0 per cent of patients who had TM, and TM did not delay adjuvant treatment.

CONCLUSION

TM may allow high-risk patients who would not be candidates for IBR to avoid mastectomy safely. Further work is needed to explore the comparative patient-reported and cosmetic outcomes of the different approaches, and to establish long-term oncological safety.

Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogalexanthopusxanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x.xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

Identification of a novel hybrid zone within the black-footed rock-wallaby (Petrogale lateralis) in Western Australia

It is increasingly recognised that intertaxon hybridisation is more common in vertebrates than previously thought. However, recent hybridisation has rarely been reported from wild marsupials, with only three instances of first generation (F1) hybrids reported, all in macropodids. In the 1990s a chromosomally anomalous population of black-footed rock-wallaby (Petrogale lateralis) was identified in the Townsend Ridges in central eastern Western Australia. Individuals from this population had chromosomes characteristic of two P. lateralis subspecies (P. l. centralis and P. l. kimberleyensis). This unusual mixture is suggestive of a novel hybrid zone between subspecies, but it could also represent a P. l. centralis population in which a 9–10 chromosome fusion has independently arisen. To test between these hypotheses, we compared mitochondrial DNA Control Region (CR) sequence data from Townsend Ridges individuals to published data for all P. lateralis subspecies. Two divergent lineages of CR haplotypes were identified at Townsend Ridges, suggesting that it represents a novel rock-wallaby hybrid zone, the third reported in the genus. While one CR haplotype clustered with those typical of P. l. centralis, the other Townsend Ridges haplotypes clustered with those from three different P. lateralis subspecies but not with P. l. kimberleyensis. Additional studies with multiple nuclear genes will be necessary to fully understand the nature of this novel hybrid zone.

The NeST (neoadjuvant systemic therapy in breast cancer) study - Protocol for a prospective multi-centre cohort study to assess the current utilization and short-term outcomes of neoadjuvant systemic therapies in breast cancer

INTRODUCTION

Neoadjuvant systemic therapy (NST) has several potential advantages in the treatment of breast cancer. However, there is currently considerable variation in NST use across the UK. The NeST study is a national, prospective, multicentre cohort study that will investigate current patterns of care with respect to NST in the UK.

METHODS AND ANALYSIS

Phase 1 - a national practice questionnaire (NPQ) to survey current practice.Phase 2 - a multi-centre prospective cohort study of breast cancer patients, undergoing NST.Women undergoing NST as their MDT recommended primary breast cancer treatment between December 2017 and May 2018 will be included. The breast surgery and oncological professional associations and the trainee research collaborative networks will encourage participation by all breast cancer centres.Patient demographics, radiological, oncological, surgical and pathological data will be collected, including complications and the need for further intervention/treatment. Data will be collated to establish current practice in the UK, regarding NST usage and variability of access and provision of these therapies. Prospective data on 600 patients from ~50 centres are anticipated.Trial registration: ISRCTN11160072.

ETHICS AND DISSEMINATION

Research ethics approval is not required for this study, as per the online Health Research Authority decision tool. The information obtained will provide valuable insights to help patients make informed decisions about their treatment. These data should establish current practice in the UK concerning NST, inform future service delivery as well as identifying further research questions.This protocol will be disseminated through the Mammary Fold Academic Research Collaborative (MFAC), the Reconstructive Surgery Trials Network and the Association of Breast Surgery. Participating units will have access to their own data and collective results will be presented at relevant conferences and published in appropriate peer-reviewed journals, as well as being made accessible to relevant patient groups.

Chromosomics: Bridging the Gap between Genomes and Chromosomes

The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.

Value of surgical pilot and feasibility study protocols

BACKGROUND

RCTs in surgery are challenging owing to well established methodological issues. Well designed pilot and feasibility studies (PFS) may help overcome such issues to inform successful main trial design and conduct. This study aimed to analyse protocols of UK-funded studies to explore current use of PFS in surgery and identify areas for practice improvement.

METHODS

PFS of surgical interventions funded by UK National Institute for Health Research programmes from 2005 to 2015 were identified, and original study protocols and associated publications sourced. Data extracted included study design characteristics, reasons for performing the work including perceived uncertainties around conducting a definitive main trial, and whether the studies had been published.

RESULTS

Thirty-five surgical studies were identified, of which 29 were randomized, and over half (15 of 29) included additional methodological components (such as qualitative work examining recruitment, and participant surveys studying current interventions). Most studies focused on uncertainties around recruitment (32 of 35), with far fewer tackling uncertainties specific to surgery, such as intervention stability, implementation or delivery (10 of 35). Only half (19 of 35) had made their results available publicly, to date.

CONCLUSION

The full potential of pretrial work to inform and optimize definitive surgical studies is not being realized.

Is the current training pathway for oncoplastic breast surgeons fit for purpose?

We take a look at the results of a Mammary Fold members' survey to find out.

Taxonomy of rock-wallabies, Petrogale (Marsupialia : Macropodidae). V. A description of two new subspecies of the black-footed rock-wallaby (Petrogale lateralis)

The black-footed rock-wallaby (Petrogale lateralis) is the most widespread member of the endemic Australian macropodid genus Petrogale. Considerable morphological and genetic diversity within this species has long been recognised and P. lateralis is currently divided into three described subspecies (P. lateralis lateralis, P. l. pearsoni, P. l. hacketti) and two undescribed forms (MacDonnell Ranges race, West Kimberley race). Chromosomal, morphological, genic and genomic studies have demonstrated that these five taxa are closely related but distinguishable. Here, we formally name the MacDonnell Ranges race and the West Kimberley race as subspecies of P. lateralis. Taxonomic registration: (LSID publication) http://zoobank.org/urn:lsid:zoobank.org:pub:71C3B7CE-CE3D-4A78-83A6-5EB50FBBA810

Current practice and short-term outcomes of therapeutic mammaplasty in the international TeaM multicentre prospective cohort study

BACKGROUND

Therapeutic mammaplasty, which combines breast reduction and mastopexy techniques with tumour excision, may extend the boundaries of breast-conserving surgery and improve outcomes for patients, but current practice is unknown and high-quality outcome data are lacking. This prospective multicentre cohort study aimed to explore the practice and short-term outcomes of the technique.

METHODS

Consecutive patients undergoing therapeutic mammaplasty at participating centres between 1 September 2016 and 30 June 2017 were recruited to the study. Demographic, preoperative, operative, oncological and complication data were collected. The primary outcome was unplanned reoperation for complications within 30 days of surgery. Secondary outcomes included re-excision rates and time to adjuvant therapy.

RESULTS

Overall, 880 patients underwent 899 therapeutic mammaplasty procedures at 50 centres. The most common indications were avoidance of poor cosmetic outcomes associated with standard breast-conserving surgery (702 procedures, 78·1 per cent) or avoidance of mastectomy (379, 42·2 per cent). Wise-pattern skin incisions were the most common (429 of 899, 47·7 per cent), but a range of incisions and nipple-areola pedicles were used. Immediate contralateral symmetrization was performed in one-third of cases (284 of 880, 32·3 per cent). In total, 205 patients (23·3 per cent) developed a complication, but only 25 (2·8 per cent) required reoperation. Median postoperative lesion size was 24·5 (i.q.r. 16-38) mm. Incomplete excision was seen in 132 procedures (14·7 per cent), but completion mastectomy was required for only 51 lesions (5·7 per cent). Median time to adjuvant therapy was 54 (i.q.r. 42-66) days.

CONCLUSION

Therapeutic mammaplasty is a safe and effective alternative to mastectomy or standard breast-conserving surgery. Further work is required to explore the impact of the technique on quality of life, and to establish cost-effectiveness.

Phylogenetic analysis of the tree-kangaroos (Dendrolagus) reveals multiple divergent lineages within New Guinea

Amongst the Australasian kangaroos and wallabies (Macropodidae) one anomalous genus, the tree-kangaroos, Dendrolagus, has secondarily returned to arboreality. Modern tree-kangaroos are confined to the wet tropical forests of north Queensland, Australia (2 species) and New Guinea (8 species). Due to their behavior, distribution and habitat most species are poorly known and our understanding of the evolutionary history and systematics of the genus is limited and controversial. We obtained tissue samples from 36 individual Dendrolagus including representatives from 14 of the 17 currently recognised or proposed subspecies and generated DNA sequence data from three mitochondrial (3116 bp) and five nuclear (4097 bp) loci. Phylogenetic analysis of these multi-locus data resolved long-standing questions regarding inter-relationships within Dendrolagus. The presence of a paraphyletic ancestral long-footed and derived monophyletic short-footed group was confirmed. Six major lineages were identified: one in Australia (D. lumholtzi, D. bennettianus) and five in New Guinea (D. inustus, D. ursinus, a Goodfellow's group, D. mbaiso and a Doria's group). Two major episodes of diversification within Dendrolagus were identified: the first during the late Miocene/early Pliocene associated with orogenic processes in New Guinea and the second mostly during the early Pleistocene associated with the intensification of climatic cycling. All sampled subspecies showed high levels of genetic divergence and currently recognized species within both the Doria's and Goodfellow's groups were paraphyletic indicating that adjustments to current taxonomy are warranted.

Prevalence and longitudinal trends of food allergy during childhood and adolescence: Results of the Isle of Wight Birth Cohort study

BACKGROUND

The prevalence and time trends of food allergy change during childhood depending on the age of the child and the type of food.

OBJECTIVE

To study prevalence and longitudinal trends in food allergy from birth to 18 years in an unselected birth cohort in the Isle of Wight.

METHOD

Information on food allergy was collected at ages 1, 2, 4, 10 and 18 years from the Isle of Wight Birth Cohort (n = 1456). Skin prick testing (SPT) was performed at the age of 1 and 2 years in symptomatic children. At 4, 10 and 18 years of age, participants were tested to a panel of food and aeroallergens. Food allergy was diagnosed based on the criteria: symptoms suggestive of a typical IgE-mediated reaction and reaction <4 hours following exposure to a known food allergen. McNemar's test was used to determine significance of changes in prevalence over time.

RESULTS

The prevalence of food allergy remained relatively constant in early childhood (5.3%, 4.4% and 5.0% at 1, 2 and 4 years, respectively), with significant decline at 10 years (2.3%, P < .001 vs 4 years) followed by significant rise at 18 years (4%, P = .02 vs 10 years). Cow's milk (1.6%-3.5%) and egg (1.1%-1.4%) were the most common allergens in the first 10 years with peanut (1%) and tree nuts (0.5%) becoming more prevalent beyond 10 years. Fruit and wheat allergy were less common at 10 years, and shellfish and kiwi emerged during adolescence. The prevalence of food allergy plus positive SPT was 1.3%, 0.8%, 0.8%, 0.9% and 2.2% at 1, 2, 4, 10 and 18 years, respectively.

CONCLUSION

Food allergy is highly prevalent in infancy with partial resolution during late childhood. However, a number of children acquire new food allergy during adolescence resulting in a relatively higher prevalence at 18 years.

Phylogenomics of a rapid radiation: the Australian rainbow skinks

Background

The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations. We explore these issues through analyses of an extensive (> 1000 loci) dataset for the Australian rainbow skinks. This group consists of 3 genera and 41 described species, which likely diversified rapidly in Australia during the mid-late Miocene to occupy rainforest, woodland, and rocky habitats with corresponding diversity of morphology and breeding colouration. Previous phylogenetic analyses of this group have revealed short inter-nodes and high discordance among loci, limiting the resolution of inferred trees. A further complication is that many species have deep phylogeographic structure – this poses the question of how to sample individuals within species for analyses using the MSC.

Results

Phylogenies obtained using concatenation and summary coalescent species tree approaches to the full dataset are well resolved with generally consistent topology, including for previously intractable relationships near the base of the clade. As expected, branch lengths at the tips are substantially overestimated using concatenation. Comparisons of different strategies for sampling haplotypes for full Bayesian MSC analyses (for one clade and using smaller sets of loci) revealed, unexpectedly, that combining haplotypes across divergent phylogeographic lineages yielded consistent species trees.

Conclusions

This study of more than 1000 loci provides a strongly-supported estimate of the phylogeny of the Australian rainbow skinks, which will inform future research on the evolution and taxonomy of this group. Our analyses suggest that species tree estimation with the MSC can be quite robust to violation of the assumption that the individuals representing a taxon are sampled from a panmictic population.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1130-4) contains supplementary material, which is available to authorized users.

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary-coalescent methods and enable us to exploit genomic data for phylogenetic inference. [Coalescence; concatenation; Cryptoblepharus; exon capture; gene tree; phylogenomics; species tree.].

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.